Sample records for rna macroscopic distribution

  1. In situ hybridization of oxytocin messenger RNA: macroscopic distribution and quantitation in rat hypothalamic cell groups

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    Burbach, J.P.; Voorhuis, T.A.; van Tol, H.H.; Ivell, R.


    Oxytocin mRNA was detected in the rat hypothalamus by in situ hybridization to a single stranded /sup 35/S-labelled DNA probe and the distribution of oxytocin mRNA-containing cell groups was studied at the macroscopic level. Specificity of hybridization was confirmed by comparison to vasopressin mRNA hybridization in parallel tissue sections. Cell groups containing oxytocin mRNA were confined to a set of hypothalamic cell groups, i.c. the supraoptic, paraventricular, anterior commissural nuclei, nucleus circularis and scattered hypothalamic islets. These cell groups displayed similar densities of autoradiographic signals indicating that the oxytocin gene is expressed at approximately the same average level at these various sites.

  2. Rank distributions: A panoramic macroscopic outlook (United States)

    Eliazar, Iddo I.; Cohen, Morrel H.


    This paper presents a panoramic macroscopic outlook of rank distributions. We establish a general framework for the analysis of rank distributions, which classifies them into five macroscopic "socioeconomic" states: monarchy, oligarchy-feudalism, criticality, socialism-capitalism, and communism. Oligarchy-feudalism is shown to be characterized by discrete macroscopic rank distributions, and socialism-capitalism is shown to be characterized by continuous macroscopic size distributions. Criticality is a transition state between oligarchy-feudalism and socialism-capitalism, which can manifest allometric scaling with multifractal spectra. Monarchy and communism are extreme forms of oligarchy-feudalism and socialism-capitalism, respectively, in which the intrinsic randomness vanishes. The general framework is applied to three different models of rank distributions—top-down, bottom-up, and global—and unveils each model's macroscopic universality and versatility. The global model yields a macroscopic classification of the generalized Zipf law, an omnipresent form of rank distributions observed across the sciences. An amalgamation of the three models establishes a universal rank-distribution explanation for the macroscopic emergence of a prevalent class of continuous size distributions, ones governed by unimodal densities with both Pareto and inverse-Pareto power-law tails.

  3. Macroscopic definition of distributed swarm morphogenesis (United States)

    Aznar, Fidel; Pujol, Mar; Rizo, Ramón


    In this paper, we present a system that will be able to obtain microscopic assembly behaviours for a robotic swarm to achieve an assembly target (macroscopic model). It will be designed taking into consideration the essential features of a self-assembling system needed to be implemented in a real robotic swarm. This system is composed of a typology of generative languages PD0L, and an algorithm for generating individual rules to be processed by the robots. The assembly process will be performed in a distributed manner, and will be also designed to require minimal communication capabilities between robots. Both the expressive capacities of language and the rule generation algorithm will be demonstrated by evaluating their performance with a core set of test morphologies widely used in self-assembly tasks. Furthermore, we compare the assembly time and the number of messages required between a classic controller (centralised) and our distributed approach.

  4. Inverted rank distributions: Macroscopic statistics, universality classes, and critical exponents (United States)

    Eliazar, Iddo; Cohen, Morrel H.


    An inverted rank distribution is an infinite sequence of positive sizes ordered in a monotone increasing fashion. Interlacing together Lorenzian and oligarchic asymptotic analyses, we establish a macroscopic classification of inverted rank distributions into five “socioeconomic” universality classes: communism, socialism, criticality, feudalism, and absolute monarchy. We further establish that: (i) communism and socialism are analogous to a “disordered phase”, feudalism and absolute monarchy are analogous to an “ordered phase”, and criticality is the “phase transition” between order and disorder; (ii) the universality classes are characterized by two critical exponents, one governing the ordered phase, and the other governing the disordered phase; (iii) communism, criticality, and absolute monarchy are characterized by sharp exponent values, and are inherently deterministic; (iv) socialism is characterized by a continuous exponent range, is inherently stochastic, and is universally governed by continuous power-law statistics; (v) feudalism is characterized by a continuous exponent range, is inherently stochastic, and is universally governed by discrete exponential statistics. The results presented in this paper yield a universal macroscopic socioeconophysical perspective of inverted rank distributions.

  5. Enzyme distribution derived from macroscopic particle behavior of an industrial immobilized penicillin-G acylase

    NARCIS (Netherlands)

    Roon, van J.L.; Tramper, J.; Joerink, M.; Schroën, C.G.P.H.; Beeftink, H.H.


    The macroscopic kinetic behavior of an industrially employed immobilized penicillin-G acylase, called Assemblase, formed the basis for a discussion on some simple intraparticle biocatalytic model distributions. Assemblase catalyzes the synthesis of the widely used semisynthetic antibiotic

  6. Macroscopic Differential Phase Shift Quantum Key Distribution Using an Optically Pre-Amplified Receiver (United States)

    Kukita, Tatsuya; Takada, Hiroshi; Inoue, Kyo


    Since it was noted that quantum computers could break public key cryptosystems based on number theory, extensive studies have been undertaken on quantum cryptography, which offers unconditionally secure communication based on quantum mechanics. We investigate a quantum key distribution (QKD) scheme using macroscopic coherent light with optically pre-amplified direct differential detection. A transmitter “Alice” sends a series of two macroscopic nonorthogonal coherent states that partially overlap due to quantum noise. A receiver “Bob” amplifies and receives it with direct differential detection followed by a thresholding process. To avoid difficulties in detection, our scheme uses conventional direct differential photodetection, not single-photon detection or homodyne detection as in previous QKD protocols. System performance assuming some eavesdropping is evaluated, the results of which suggest that our scheme is usable for short or medium distance.

  7. Macroscopic time and altitude distribution of plasma turbulence induced in ionospheric modification experiments

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    Rose, H.; Dubois, D.; Russell, D. [Lodestar Research Corp., Boulder, CO (United States); Hanssen, A. [Univ. of Tromsoe (Norway)


    This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This research concentrated on the time dependence of the heater, induced-turbulence, and electron-density profiles excited in the ionosphere by a powerful radio-frequency heater wave. The macroscopic density is driven by the ponderomotive pressure and the density self-consistently determines the heater propagation. For typical parameters of the current Arecibo heater, a dramatic quasi-periodic behavior was found. For about 50 ms after turn-on of the heater wave, the turbulence is concentrated at the first standing-wave maximum of the heater near reflection altitude. From 50--100 ms the standing-wave pattern drops by about 1--2 km in altitude and the quasi-periodicity reappears at the higher altitudes with a period of roughly 50 ms. This behavior is due to the half-wavelength density depletion grating that is set up by the ponderomotive pressure at the maxima of the heater standing-wave pattern. Once the grating is established the heater can no longer propagate to higher altitudes. The grating is then unsupported by the heater at these altitudes and decays, allowing the heater to propagate again and initiate another cycle. For stronger heater powers, corresponding to the Arecibo upgrade and the HAARP heater now under construction, the effects are much more dramatic.

  8. Tissue distribution of human acetylcholinesterase and butyrylcholinesterase messenger RNA

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    Jbilo, O.; Barteles, C.F.; Chatonnet, A.; Toutant, J.P.; Lockridge, O.


    Tissue distribution of human acetyicholinesterase and butyryicholinesterase messenger RNA. 1 Cholinesterase inhibitors occur naturally in the calabar bean (eserine), green potatoes (solanine), insect-resistant crab apples, the coca plant (cocaine) and snake venom (fasciculin). There are also synthetic cholinesterase inhibitors, for example man-made insecticides. These inhibitors inactivate acetyicholinesterase and butyrylcholinesterase as well as other targets. From a study of the tissue distribution of acetylcholinesterase and butyrylcholinesterase mRNA by Northern blot analysis, we have found the highest levels of butyrylcholinesterase mRNA in the liver and lungs, tissues known as the principal detoxication sites of the human body. These results indicate that butyrylcholinesterase may be a first line of defense against poisons that are eaten or inhaled.

  9. Distribution of miRNA genes in the pig genome. (United States)

    Paczynska, Paulina; Grzemski, Adrian; Szydlowski, Maciej


    Recent completion of swine genome may simplify the production of swine as a large biomedical model. Here we studied sequence and location of known swine miRNA genes, key regulators of protein-coding genes at the level of RNA, and compared them to human and mouse data to prioritize future molecular studies. Distribution of miRNA genes in pig genome shows no particular relation to different genomic features including protein coding genes - proportions of miRNA genes in intergenic regions, introns and exons roughly agree with the size of these regions in the pig genome. Our analyses indicate that host genes harbouring intragenic miRNAs are longer from other protein-coding genes, however, no important GO enrichment was found. Swine mature miRNAs show high sequence similarity to their human and mouse orthologues. Location of miRNA genes relative to protein-coding genes is also similar among studied species, however, there are differences in the precise position in particular intergenic regions and within particular hosts. The most prominent difference between pig and human miRNAs is a large group of pig-specific sequences (53% of swine miRNAs). We found no evidence that this group of evolutionary new pig miRNAs is different from old miRNAs genes with respect to genomic location except that they are less likely to be clustered. There are differences in precise location of orthologues miRNA genes in particular intergenic regions and within particular hosts, and their meaning for coexpression with protein-coding genes deserves experimental studies. Functional studies of a large group of pig-specific sequences in future may reveal limits of the pig as a model organism to study human gene expression.

  10. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

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    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)


    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  11. Random generation of RNA secondary structures according to native distributions

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    Nebel Markus E


    Full Text Available Abstract Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure. Compared to well-known sampling approaches used in several structure prediction tools (such as SFold ours has two major advantages: Firstly, after a preprocessing step in time O(n2 for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om⋅n⋅ log(n while other algorithms typically have a runtime in O(m⋅n2. Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with

  12. CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells. (United States)

    Benoit Bouvrette, Louis Philip; Cody, Neal A L; Bergalet, Julie; Lefebvre, Fabio Alexis; Diot, Cédric; Wang, Xiaofeng; Blanchette, Mathieu; Lécuyer, Eric


    Cells are highly asymmetrical, a feature that relies on the sorting of molecular constituents, including proteins, lipids, and nucleic acids, to distinct subcellular locales. The localization of RNA molecules is an important layer of gene regulation required to modulate localized cellular activities, although its global prevalence remains unclear. We combine biochemical cell fractionation with RNA-sequencing (CeFra-seq) analysis to assess the prevalence and conservation of RNA asymmetric distribution on a transcriptome-wide scale in Drosophila and human cells. This approach reveals that the majority (∼80%) of cellular RNA species are asymmetrically distributed, whether considering coding or noncoding transcript populations, in patterns that are broadly conserved evolutionarily. Notably, a large number of Drosophila and human long noncoding RNAs and circular RNAs display enriched levels within specific cytoplasmic compartments, suggesting that these RNAs fulfill extra-nuclear functions. Moreover, fraction-specific mRNA populations exhibit distinctive sequence characteristics. Comparative analysis of mRNA fractionation profiles with that of their encoded proteins reveals a general lack of correlation in subcellular distribution, marked by strong cases of asymmetry. However, coincident distribution profiles are observed for mRNA/protein pairs related to a variety of functional protein modules, suggesting complex regulatory inputs of RNA localization to cellular organization. © 2018 Benoit Bouvrette et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  13. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation. (United States)

    Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming


    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

  14. Polysome Fractionation to Analyze mRNA Distribution Profiles. (United States)

    Panda, Amaresh C; Martindale, Jennifer L; Gorospe, Myriam


    Eukaryotic cells adapt to changes in external or internal signals by precisely modulating the expression of specific gene products. The expression of protein-coding genes is controlled at the transcriptional and post-transcriptional levels. Among the latter steps, the regulation of translation is particularly important in cellular processes that require rapid changes in protein expression patterns. The translational efficiency of mRNAs is altered by RNA-binding proteins (RBPs) and noncoding (nc)RNAs such as microRNAs (Panda et al., 2014a and 2014b; Abdelmohsen et al., 2014). The impact of factors that regulate selective mRNA translation is a critical question in RNA biology. Polyribosome (polysome) fractionation analysis is a powerful method to assess the association of ribosomes with a given mRNA. It provides valuable information about the translational status of that mRNA, depending on the number of ribosomes with which they are associated, and identifies mRNAs that are not translated (Panda et al., 2016). mRNAs associated with many ribosomes form large polysomes that are predicted to be actively translated, while mRNAs associated with few or no ribosomes are expected to be translated poorly if at all. In sum, polysome fractionation analysis allows the direct determination of translation efficiencies at the level of the whole transcriptome as well as individual mRNAs.

  15. Macroscopic magnetic frustration


    Mellado, Paula; Concha, Andres; Mahadevan, L,


    Although geometrical frustration transcends scale, it has primarily been evoked in the micro and mesoscopic realm to characterize such phases as spin-ice liquids and glasses and to explain the behavior of such materials as multiferroics, high temperature superconductors, colloids and copolymers. Here we introduce a system of macroscopic ferromagnetic rotors arranged in a planar lattice capable of out-of-plane movement that exhibit the characteristic honeycomb spin ice rules studied and seen s...

  16. Phylogenetic distribution of plant snoRNA families

    DEFF Research Database (Denmark)

    Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie


    BACKGROUND: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D sno...... snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. CONCLUSIONS: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant...

  17. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. (United States)

    Strobel, Eric J; Watters, Kyle E; Nedialkov, Yuri; Artsimovitch, Irina; Lucks, Julius B


    RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements

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    Brahmachari Samir K


    Full Text Available Abstract Background The primate-specific Alu elements, which originated 65 million years ago, exist in over a million copies in the human genome. These elements have been involved in genome shuffling and various diseases not only through retrotransposition but also through large scale Alu-Alu mediated recombination. Only a few subfamilies of Alus are currently retropositionally active and show insertion/deletion polymorphisms with associated phenotypes. Retroposition occurs by means of RNA intermediates synthesised by a RNA polymerase III promoter residing in the A-Box and B-Box in these elements. Alus have also been shown to harbour a number of transcription factor binding sites, as well as hormone responsive elements. The distribution of Alus has been shown to be non-random in the human genome and these elements are increasingly being implicated in diverse functions such as transcription, translation, response to stress, nucleosome positioning and imprinting. Results We conducted a retrospective analysis of putative functional sites, such as the RNA pol III promoter elements, pol II regulatory elements like hormone responsive elements and ligand-activated receptor binding sites, in Alus of various evolutionary ages. We observe a progressive loss of the RNA pol III transcriptional potential with concomitant accumulation of RNA pol II regulatory sites. We also observe a significant over-representation of Alus harboring these sites in promoter regions of signaling and metabolism genes of chromosome 22, when compared to genes of information pathway components, structural and transport proteins. This difference is not so significant between functional categories in the intronic regions of the same genes. Conclusions Our study clearly suggests that Alu elements, through retrotransposition, could distribute functional and regulatable promoter elements, which in the course of subsequent selection might be stabilized in the genome. Exaptation of

  19. Subcellular distribution of mitochondrial ribosomal RNA in the mouse oocyte and zygote.

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    Youichirou Ninomiya

    Full Text Available Mitochondrial ribosomal RNAs (mtrRNAs have been reported to translocate extra-mitochondrially and localize to the germ cell determinant of oocytes and zygotes in some metazoa except mammals. To address whether the mtrRNAs also localize in the mammals, expression and distribution of mitochondrion-encoded RNAs in the mouse oocytes and zygotes was examined by whole-mount in situ hybridization (ISH. Both 12S and 16S rRNAs were predominantly distributed in the animal hemisphere of the mature oocyte. This distribution pattern was rearranged toward the second polar body in zygotes after fertilization. The amount of mtrRNAs decreased around first cleavage, remained low during second cleavage and increased after third cleavage. Staining intensity of the 12S rRNA was weaker than that of the 16S rRNA throughout the examined stages. Similar distribution dynamics of the 16S rRNA was observed in strontium-activated haploid parthenotes, suggesting the distribution rearrangement does not require a component from sperm. The distribution of 16S rRNAs did not coincide with that of mitochondrion-specific heat shock protein 70, suggesting that the mtrRNA is translocated from mitochondria. The ISH-scanning electron microscopy confirms the extra-mitochondrial mtrRNA in the mouse oocyte. Chloramphenicol (CP treatment of late pronuclear stage zygotes perturbed first cleavage as judged by the greater than normal disparity in size of blastomeres of 2-cell conceptuses. Two-third of the CP-treated zygotes arrested at either 2-cell or 3-cell stage even after the CP was washed out. These findings indicate that the extra-mitochondrial mtrRNAs are localized in the mouse oocyte and implicated in correct cytoplasmic segregation into blastomeres through cleavages of the zygote.

  20. Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding. (United States)

    Poznanović, Svetlana; Heitsch, Christine E


    We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. Our main theorem gives relations between the expected number of these motifs--independent of the grammar probabilities. These relations are a consequence of proving that the distribution of base pairs, of helices, and of different types of loops is asymptotically Gaussian in this model of RNA folding. Proof techniques use singularity analysis of probability generating functions. We also demonstrate that these asymptotic results capture well the expected number of RNA base pairs in native ribosomal structures, and certain other aspects of their predicted secondary structures. In particular, we find that the predicted structures largely satisfy the expected relations, although the native structures do not.

  1. Connecting protein and mRNA burst distributions for stochastic models of gene expression

    CERN Document Server

    Elgart, Vlad; Fenley, Andrew T; Kulkarni, Rahul V


    The intrinsic stochasticity of gene expression can lead to large variability in protein levels for genetically identical cells. Such variability in protein levels can arise from infrequent synthesis of mRNAs which in turn give rise to bursts of protein expression. Protein expression occurring in bursts has indeed been observed experimentally and recent studies have also found evidence for transcriptional bursting, i.e. production of mRNAs in bursts. Given that there are distinct experimental techniques for quantifying the noise at different stages of gene expression, it is of interest to derive analytical results connecting experimental observations at different levels. In this work, we consider stochastic models of gene expression for which mRNA and protein production occurs in independent bursts. For such models, we derive analytical expressions connecting protein and mRNA burst distributions which show how the functional form of the mRNA burst distribution can be inferred from the protein burst distributio...

  2. Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids. (United States)

    Larsson, Daniel S D; van der Spoel, David


    The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the 5-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of

  3. Distribution of viral RNA in mouse tissues during acute phase of coxsackievirus B5 infection. (United States)

    Moon, Mi Sun; Joo, Chul Hyun; Hwang, In Seok; Ye, Jeong Sook; Jun, Eun Jung; Lee, Hui Sun; Kim, Donghou; Lee, Min-Jae; Lee, Heuiran; Kim, Yoo Kyum


    To investigate histopathological changes and distribution of coxsackievirus B5 (CVB5) RNA in mouse heart, liver, and pancreas during the acute phase of infection. C3H/HeJ male mice, aged 3-4 weeks, were inoculated intraperitoneally with 5 x 10(5) plaque-forming units of CVB5 and sacrificed at 1, 2, 3, 4, 7 and 10 days postinfection (p.i.). Inflammation of the heart, liver, and pancreatic tissue sections was evaluated by hematoxylin and eosin staining, and virus was detected using antibody to viral coat protein VP1. A quantitative real-time RT-PCR method, using primers and probe targeted to the highly conserved sequences in the 5'-untranslated region of the virus, was used to evaluate the kinetics of CVB5 RNA during the development of myocarditis or pancreatitis. Marginal inflammatory changes were observed in the heart tissues although viral RNA was constantly present between 1 and 10 days p.i., peaking at 4 days p.i. The pancreatic tissues displayed massive lymphocyte infiltration and loss of acinar cells at day 4 p.i. and viral RNA was detected between 1 and 10 days p.i., peaking at 2-3 days p.i. In the liver, viral RNA was detected between 1 and 7 days. No mortality was observed. CVB5 induced acute pancreatitis without subsequent development of myocarditis. Clearance of CVB5 RNA from the pancreas and heart was slower than clearance from the liver. Our real-time RT-PCR method, which is more sensitive than conventional plaque assay, may provide valuable insight into viral RNA kinetics during CVB5 infection. Copyright (c) 2005 S. Karger AG, Basel.

  4. Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. (United States)

    Li, Chung-I; Su, Pei-Fang; Guo, Yan; Shyr, Yu


    Sample size determination is an important issue in the experimental design of biomedical research. Because of the complexity of RNA-seq experiments, however, the field currently lacks a sample size method widely applicable to differential expression studies utilising RNA-seq technology. In this report, we propose several methods for sample size calculation for single-gene differential expression analysis of RNA-seq data under Poisson distribution. These methods are then extended to multiple genes, with consideration for addressing the multiple testing problem by controlling false discovery rate. Moreover, most of the proposed methods allow for closed-form sample size formulas with specification of the desired minimum fold change and minimum average read count, and thus are not computationally intensive. Simulation studies to evaluate the performance of the proposed sample size formulas are presented; the results indicate that our methods work well, with achievement of desired power. Finally, our sample size calculation methods are applied to three real RNA-seq data sets.

  5. Asymmetric RNA Distribution among Cells and Their Secreted Exosomes: Biomedical Meaning and Considerations on Diagnostic Applications

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    Marco Ragusa


    Full Text Available Over the past few years, exosomes and their RNA cargo have been extensively studied because of the fascinating biological roles they play in cell-to-cell communication, including the signal exchange among cancer, stromal, and immune cells, leading to modifications of tumor microenvironment. RNAs, especially miRNAs, stored within exosomes, seem to be among the main determinants of such signaling: their sorting into exosomes appears to be cell-specific and related to cellular physiopathology. Accordingly, the identification of exosomal miRNAs in body fluids from pathological patients has become one of the most promising activity in the field of biomarker discovery. Several analyses on the qualitative and quantitative distribution of RNAs between cells and their secreted exosomes have given rise to questions on whether and how accurately exosomal RNAs would represent the transcriptomic snapshot of the physiological and pathological status of secreting cells. Although the exact molecular mechanisms of sorting remain quite elusive, many papers have reported an evident asymmetric quantitative distribution of RNAs between source cells and their exosomes. This phenomenon could depend both on passive and active sorting mechanisms related to: (a RNA turnover; (b maintaining the cytoplasmic miRNA:target equilibrium; (c removal of RNAs not critical or even detrimental for normal or diseased cells. These observations represent very critical issues in the exploitation of exosomal miRNAs as cancer biomarkers. In this review, we will discuss how much the exosomal and corresponding donor cell transcriptomes match each other, to better understand the actual reliability of exosomal RNA molecules as pathological biomarkers reflecting a diseased status of the cells.

  6. Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing. (United States)

    Xu, Chenxi; Sun, Xuepeng; Taylor, Angela; Jiao, Chen; Xu, Yimin; Cai, Xiaofeng; Wang, Xiaoli; Ge, Chenhui; Pan, Guanghui; Wang, Quanxi; Fei, Zhangjun; Wang, Quanhua


    Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases. IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in

  7. Prevalence and Distribution of Leishmania RNA Virus 1 in Leishmania Parasites from French Guiana. (United States)

    Ginouvès, Marine; Simon, Stéphane; Bourreau, Eliane; Lacoste, Vincent; Ronet, Catherine; Couppié, Pierre; Nacher, Mathieu; Demar, Magalie; Prévot, Ghislaine


    In South America, the presence of the Leishmania RNA virus type 1 (LRV1) was described in Leishmania guyanensis and Leishmania braziliensis strains. The aim of this study was to determine the prevalence distribution of LRV1 in Leishmania isolates in French Guiana given that, in this French overseas department, most Leishmania infections are due to these parasite species. The presence of the virus was observed in 74% of Leishmania spp. isolates, with a highest presence in the internal areas of the country. © The American Society of Tropical Medicine and Hygiene.

  8. Statistical thermodynamics understanding the properties of macroscopic systems

    CERN Document Server

    Fai, Lukong Cornelius


    Basic Principles of Statistical PhysicsMicroscopic and Macroscopic Description of StatesBasic PostulatesGibbs Ergodic AssumptionGibbsian EnsemblesExperimental Basis of Statistical MechanicsDefinition of Expectation ValuesErgodic Principle and Expectation ValuesProperties of Distribution FunctionRelative Fluctuation of an Additive Macroscopic ParameterLiouville TheoremGibbs Microcanonical EnsembleMicrocanonical Distribution in Quantum MechanicsDensity MatrixDensity Matrix in Energy RepresentationEntropyThermodynamic FunctionsTemperatureAdiabatic ProcessesPressureThermodynamic IdentityLaws of Th

  9. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus (United States)

    Sanjuán, Rafael; Moya, Andrés; Elena, Santiago F.


    Little is known about the mutational fitness effects associated with single-nucleotide substitutions on RNA viral genomes. Here, we used site-directed mutagenesis to create 91 single mutant clones of vesicular stomatitis virus derived from a common ancestral cDNA and performed competition experiments to measure the relative fitness of each mutant. The distribution of nonlethal deleterious effects was highly skewed and had a long, flat tail. As expected, fitness effects depended on whether mutations were chosen at random or reproduced previously described ones. The effect of random deleterious mutations was well described by a log-normal distribution, with -19% reduction of average fitness; the effects distribution of preobserved deleterious mutations was better explained by a β model. The fit of both models was improved when combined with a uniform distribution. Up to 40% of random mutations were lethal. The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a γ distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations. PMID:15159545

  10. Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution (United States)

    Kaur, Jaskiran; Raj, Monika; Cooperman, Barry S.


    Dihydrouridine (DHU) positions within tRNAs have long been used as sites to covalently attach fluorophores, by virtue of their unique chemical reactivity toward reduction by NaBH4, their abundance within prokaryotic and eukaryotic tRNAs, and the biochemical functionality of the labeled tRNAs so produced. Interpretation of experiments employing labeled tRNAs can depend on knowing the distribution of dye among the DHU positions present in a labeled tRNA. Here we combine matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) analysis of oligonucleotide fragments and thin layer chromatography to resolve and quantify sites of DHU labeling by the fluorophores Cy3, Cy5, and proflavin in Escherichia coli tRNAPhe and E. coli tRNAArg. The MALDI-MS results led us to re-examine the precise chemistry of the reactions that result in fluorophore introduction into tRNA. We demonstrate that, in contrast to an earlier suggestion that has long been unchallenged in the literature, such introduction proceeds via a substitution reaction on tetrahydrouridine, the product of NaBH4 reduction of DHU, resulting in formation of substituted tetrahydrocytidines within tRNA. PMID:21628433

  11. Regional distribution of glycine receptor messenger RNA in the central nervous system of zebrafish. (United States)

    Imboden, M; Devignot, V; Korn, H; Goblet, C


    We report the cloning of the zebrafish beta subunit of the glycine receptor and compare the anatomical distribution of three glycine receptor subunit constituents in adult zebrafish brain (alphaZ1, alphaZ2 and betaZ) to the expression pattern of homologous receptor subunits (alpha1, alpha2 and beta) in the mammalian adult CNS. Non-radioactive hybridization was used to map the distribution of the alphaZ1, alphaZ2 and betaZ glycine receptor subunit messenger RNAs in the adult zebrafish brain. The anterior-posterior expression gradient found in adult zebrafish brain was similar to that reported in mammalian CNS. However, the glycine receptor transcripts, notably the alphaZ1 subunit, were more widely distributed in the anterior regions of the zebrafish than in the adult mammalian brain. The isoform-specific distribution pattern was less regionalized in zebrafish than in the rat mammalian CNS. Nevertheless, there was some regionalization of alphaZ1, alphaZ2 and betaZ transcripts in the diencephalic and mesencephalic nuclei where different sensory and motor centers express either alphaZ1/betaZ or alphaZ2 subunits. In contrast to the widespread distribution of the beta subunit in adult mammalian brain, alphaZ2 messenger RNA presented the widest expression territory of all three glycine receptor subunits tested. alphaZ2 messenger RNA was expressed in the absence of alphaZ1 and betaZ messenger RNA in the outer nuclear layer of the retina, the inferior olive and the raphe of the medulla oblongata, as well as in the nucleus of Cajal of the medulla spinalis. In contrast, an identified central neuron of the reticular formation, the Mauthner cell, expresses all three glycine receptor subunits (alphaZ1, alphaZ2 and betaZ). This report extends the already described glycine receptor expression in the vertebrate CNS and confirms the importance of glycine-mediated inhibition in spinal cord and brainstem.

  12. Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex. (United States)

    Xie, Ping


    Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by "hungry" codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.

  13. Macroscopic Manifestation of Microscopic Entropy Production: Space-Dependent Intermittence


    Grigolini, Paolo; Mannella, Riccardo; Palatella, Luigi


    We study a spatial diffusion process generated by velocity fluctuations of intermittent nature. We note that intermittence reduces the entropy production rate while enhancing the diffusion strength. We study a case of space-dependent intermittence and prove it to result in a deviation from uniform distribution. This macroscopic effect can be used to measure the relative value of the trajectory entropy.

  14. Quantum statistical derivation of the macroscopic Maxwell equations

    NARCIS (Netherlands)

    Schram, K.


    The macroscopic Maxwell equations in matter are derived on a quantum statistical basis from the microscopic equations for the field operators. Both the density operator formalism and the Wigner distribution function method are discussed. By both methods it can be proved that the quantum statistical

  15. Macroscopic Theory of Dark Sector

    Directory of Open Access Journals (Sweden)

    Boris E. Meierovich


    Full Text Available A simple Lagrangian with squared covariant divergence of a vector field as a kinetic term turned out to be an adequate tool for macroscopic description of the dark sector. The zero-mass field acts as the dark energy. Its energy-momentum tensor is a simple additive to the cosmological constant. Massive fields describe two different forms of dark matter. The space-like massive vector field is attractive. It is responsible for the observed plateau in galaxy rotation curves. The time-like massive field displays repulsive elasticity. In balance with dark energy and ordinary matter it provides a four-parametric diversity of regular solutions of the Einstein equations describing different possible cosmological and oscillating nonsingular scenarios of evolution of the Universe. In particular, the singular big bang turns into a regular inflation-like transition from contraction to expansion with the accelerated expansion at late times. The fine-tuned Friedman-Robertson-Walker singular solution is a particular limiting case at the lower boundary of existence of regular oscillating solutions in the absence of vector fields. The simplicity of the general covariant expression for the energy-momentum tensor allows displaying the main properties of the dark sector analytically. Although the physical nature of dark sector is still unknown, the macroscopic theory can help analyze the role of dark matter in astrophysical phenomena without resorting to artificial model assumptions.

  16. 8-Methoxypsoralen DNA interstrand cross-linking of the ribosomal RNA genes in Tetrahymena thermophila. Distribution, repair and effect on rRNA synthesis

    DEFF Research Database (Denmark)

    Fengquin, X; Nielsen, Henrik; Zhen, W


    The distribution and repair of 8-methoxypsoralen-DNA interstrand cross-links in the ribosomal RNA genes (rDNA) in Tetrahymena thermophila have been studied in vivo by Southern blot analysis. It is found that the cross-links at a density of ... between three domains (terminal spacer, transcribed region and central spacer) as defined by restriction enzyme analysis (BamHI and ClaI). It is furthermore shown that a dosage resulting in approximately one cross-link per rDNA molecule (21 kbp, two genes) is sufficient to block RNA synthesis. Finally......, it is shown that the cross-links in the rDNA molecules are repaired at equal rate in all three domains within 24 h and that RNA synthesis is partly restored during this repair period. The majority of the cells also go through one to two cell divisions in this period but do not survive....

  17. Spatial Distribution of Escherichia coli in the Mouse Large Intestine Inferred from rRNA In Situ Hybridization

    DEFF Research Database (Denmark)

    Poulsen, Lars Kærgaard; Lan, Fusheng; Sternberg, Claus


    Fluorescent oligonucleotide probes targeting rRNA were used to develop an in situ hybridization technique by which the spatial distribution of Escherichia coli in the large intestines of streptomycin-treated mice was determined. Single E. coli cells were identified in thin frozen sections from...... the large intestines by the use of a probe specific for E. coli 23S rRNA. Furthermore, the total bacterial population was visualized with an rRNA probe targeting the domain Bacteria. By this technique, all E. coli cells were seen embedded in the mucosal material overlying the epithelial cells of the large...... intestine, and no direct attachment to the epithelium was observed....

  18. Seismic scanning tunneling macroscope - Theory

    KAUST Repository

    Schuster, Gerard T.


    We propose a seismic scanning tunneling macroscope (SSTM) that can detect the presence of sub-wavelength scatterers in the near-field of either the source or the receivers. Analytic formulas for the time reverse mirror (TRM) profile associated with a single scatterer model show that the spatial resolution limit to be, unlike the Abbe limit of λ/2, independent of wavelength and linearly proportional to the source-scatterer separation as long as the point scatterer is in the near-field region; if the sub-wavelength scatterer is a spherical impedance discontinuity then the resolution will also be limited by the radius of the sphere. Therefore, superresolution imaging can be achieved as the scatterer approaches the source. This is analogous to an optical scanning tunneling microscope that has sub-wavelength resolution. Scaled to seismic frequencies, it is theoretically possible to extract 100 Hz information from 20 Hz data by imaging of near-field seismic energy.

  19. Local administration of siRNA through Microneedle: Optimization, Bio-distribution, Tumor Suppression and Toxicity (United States)

    Tang, Tao; Deng, Yan; Chen, Jiao; Zhao, Yi; Yue, Ruifeng; Choy, Kwong Wai; Wang, Chi Chiu; Du, Quan; Xu, Yan; Han, Linxiao; Chung, Tony Kwok Hung


    Although RNA interference may become a novel therapeutic approach for cancer treatment, target-site accumulation of siRNA to achieve therapeutic dosage will be a major problem. Microneedle represents a better way to deliver siRNAs and we have evaluated for the first time the capability of a silicon microneedle array for delivery of Gapdh siRNA to the skin in vivo and the results showed that the microneedle arrays could effectively deliver siRNA to relevant regions of the skin noninvasively. For the further study in this field, we evaluated the efficacy of the injectable microneedle device for local delivery of siRNA to the mouse xenograft. The results presented here indicate that local administration of siRNA through injectable microneedle could effectively deliver siRNA into the tumor region, and inhibit tumor progression without major adverse effects.

  20. A quantitative link between microplastic instability and macroscopic deformation behaviors in metallic glasses (United States)

    Wu, Y.; Chen, G. L.; Hui, X. D.; Liu, C. T.; Lin, Y.; Shang, X. C.; Lu, Z. P.


    Based on mechanical instability of individual shear transformation zones (STZs), a quantitative link between the microplastic instability and macroscopic deformation behavior of metallic glasses was proposed. Our analysis confirms that macroscopic metallic glasses comprise a statistical distribution of STZ embryos with distributed values of activation energy, and the microplastic instability of all the individual STZs dictates the macroscopic deformation behavior of amorphous solids. The statistical model presented in this paper can successfully reproduce the macroscopic stress-strain curves determined experimentally and readily be used to predict strain-rate effects on the macroscopic responses with the availability of the material parameters at a certain strain rate, which offer new insights into understanding the actual deformation mechanism in amorphous solids.

  1. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues | Center for Cancer Research (United States)

    Despite extensive genetic, biochemical and structural studies on Escherichia coli RNA polymerase (RNAP), little is known about its location and distribution in response to environmental changes. To visualize the RNAP by fluorescence microscopy in E. coli under different physiological conditions, we constructed a functional rpoC-gfp gene fusion on the chromosome.

  2. Macroscopic characterisations of Web accessibility (United States)

    Lopes, Rui; Carriço, Luis


    The Web Science framework poses fundamental questions on the analysis of the Web, by focusing on how microscopic properties (e.g. at the level of a Web page or Web site) emerge into macroscopic properties and phenomena. One research topic on the analysis of the Web is Web accessibility evaluation, which centres on understanding how accessible a Web page is for people with disabilities. However, when framing Web accessibility evaluation on Web Science, we have found that existing research stays at the microscopic level. This article presents an experimental study on framing Web accessibility evaluation into Web Science's goals. This study resulted in novel accessibility properties of the Web not found at microscopic levels, as well as of Web accessibility evaluation processes themselves. We observed at large scale some of the empirical knowledge on how accessibility is perceived by designers and developers, such as the disparity of interpretations of accessibility evaluation tools warnings. We also found a direct relation between accessibility quality and Web page complexity. We provide a set of guidelines for designing Web pages, education on Web accessibility, as well as on the computational limits of large-scale Web accessibility evaluations.

  3. Cloud Macroscopic Organization: Order Emerging from Randomness (United States)

    Yuan, Tianle


    Clouds play a central role in many aspects of the climate system and their forms and shapes are remarkably diverse. Appropriate representation of clouds in climate models is a major challenge because cloud processes span at least eight orders of magnitude in spatial scales. Here we show that there exists order in cloud size distribution of low-level clouds, and that it follows a power-law distribution with exponent gamma close to 2. gamma is insensitive to yearly variations in environmental conditions, but has regional variations and land-ocean contrasts. More importantly, we demonstrate this self-organizing behavior of clouds emerges naturally from a complex network model with simple, physical organizing principles: random clumping and merging. We also demonstrate symmetry between clear and cloudy skies in terms of macroscopic organization because of similar fundamental underlying organizing principles. The order in the apparently complex cloud-clear field thus has its root in random local interactions. Studying cloud organization with complex network models is an attractive new approach that has wide applications in climate science. We also propose a concept of cloud statistic mechanics approach. This approach is fully complementary to deterministic models, and the two approaches provide a powerful framework to meet the challenge of representing clouds in our climate models when working in tandem.

  4. Distribution of Repetitive and Nonrepetitive Sequence Transcripts in HeLa mRNA (United States)

    Klein, William H.; Murphy, William; Attardi, Giuseppe; Britten, Roy J.; Davidson, Eric H.


    Polyadenylated messenger RNA extracted from HeLa cells was hybridized with a mass excess of HeLa DNA. The kinetics of the hybridization reaction demonstrated that most of the messenger RNA is transcribed from nonrepetitive DNA. The amount of messenger RNA hybridized to DNA was measured both with and without prior RNase treatment. Comparison of the results indicates that within the limits of detection, HeLa messenger RNA does not contain repetitive sequence elements covalently linked to nonrepetitive sequence transcripts. However, a small fraction of the HeLa messenger RNA preparation is transcribed entirely from repetitive DNA sequences. This fraction represents about 6% of the total polyadenylated messenger RNA preparation. PMID:4525461

  5. What in the (quantum) world is macroscopic? (United States)

    Jaeger, Gregg


    The notion of the macroscopic in fundamental quantum theory is analyzed. After a brief summary of use of the term macroscopic, its use in quantum theory is compared with its previous use elsewhere. Next, the connections specifically to the Copenhagen interpretation of quantum mechanics and quantum measurement theory more generally, where this term first began to deviate from previous uses, are explained and exhibited through a number of examples. Then, recent attempts to define accurately and quantitatively the extent of being macroscopic, that is, macroscopicity are discussed and their implications considered. This is done most particularly in the realm of quantum optics, where it differs most from previous uses and has recently been of considerable interest. Finally, with the benefit of this analysis, recommendations are made regarding future use of the notion of the macroscopic in fundamental physics.

  6. Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy. (United States)

    Gran-Stadniczeñko, Sandra; Šupraha, Luka; Egge, Elianne D; Edvardsen, Bente


    Haptophyta encompasses more than 300 species of mostly marine pico- and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte-specific primers targeting the V4 region of the 18S, and the D1-D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data set also contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology. © 2016 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

  7. Promoting Vaginal Distribution of E7 and MCL-1 siRNA-Silencing Nanoparticles for Cervical Cancer Treatment. (United States)

    Lechanteur, Anna; Furst, Tania; Evrard, Brigitte; Delvenne, Philippe; Piel, Géraldine; Hubert, Pascale


    There is an urgent need to develop a less aggressive and more effective treatment against cervical lesions induced by different high-risk human papillomavirus (HR-HPV). We investigated the potential of a cocktail of small interfering RNA (siRNA) directed against the oncoprotein E6 (E6), the oncoprotein E7 (E7), or the antiapoptotic protein MCL-1 (MCL-1). The combination of siRNA anti-E7 and anti-MCL-1 demonstrated high efficacy on multiple HPV16 and HPV18 cell lines and no effects on healthy keratinocytes. This gene therapy has been considered for a vaginal administration since this route of application holds high potential for the treatment of diseases in the female reproductive tracts. Therefore, PEGylated lipoplexes have been designed and characterized to protect siRNA and to diffuse in the mucosal environment before they reach the cervico/vaginal epithelium. This new nanovector complexed to the combination of active siRNA induced an efficient mRNA knockdown since biological effects were obtained in vitro. This work also provided evidence that the PEGylated lipoplexes had appropriate physicochemical properties to diffuse into a mucin network according to size measurement experiments in artificial mucus. After demonstrating the distribution and the efficacy of siRNA into a 3D-cervical model lesion and through porcine vaginal mucosa, in vivo experiments in mouse have been performed under physiological conditions. This study revealed a complete and sustained coverage of the mucosal epithelium following an unique vaginal administration of fluorescent PEGylated lipoplexes. Overall, our results showed the potential of the PEGylated lipoplexes for the prolonged delivery of active siRNA to treat HPV-induced lesions.

  8. Macroscopic transport by synthetic molecular machines

    NARCIS (Netherlands)

    Berna, J; Leigh, DA; Lubomska, M; Mendoza, SM; Perez, EM; Rudolf, P; Teobaldi, G; Zerbetto, F

    Nature uses molecular motors and machines in virtually every significant biological process, but demonstrating that simpler artificial structures operating through the same gross mechanisms can be interfaced with - and perform physical tasks in - the macroscopic world represents a significant hurdle

  9. Assessments of macroscopicity for quantum optical states

    DEFF Research Database (Denmark)

    Laghaout, Amine; Neergaard-Nielsen, Jonas Schou; Andersen, Ulrik Lund


    With the slow but constant progress in the coherent control of quantum systems, it is now possible to create large quantum superpositions. There has therefore been an increased interest in quantifying any claims of macroscopicity. We attempt here to motivate three criteria which we believe should...... enter in the assessment of macroscopic quantumness: The number of quantum fluctuation photons, the purity of the states, and the ease with which the branches making up the state can be distinguished. © 2014....

  10. Characterization of zebrafish primordial germ cells: morphology and early distribution of vasa RNA. (United States)

    Braat, A K; Zandbergen, T; van de Water, S; Goos, H J; Zivkovic, D


    Research into germ line development is of conceptual and biotechnologic importance. In this study, we used morphology at the level of light and electron microscope to characterize the primordial germ cells (PGCs) of the zebrafish throughout embryonic and larval development. The study was complemented by the detailed analysis of mRNA expression of a putative germ line marker vasa. By morphology alone PGCs were identified at the earliest at the 5-somite stage in the peripheral endoderm in contact with the yolk syncytial layer. Subsequently, they move from lateral to medial positions into the median mesoderm and from there by means of the dorsal mesentery into the gonadal anlage at day 5 postfertilization (pf), to establish gonads with mesenchymal cells by day 9 pf. Ultrastructural analysis of the 4-day-old zebrafish larvae demonstrates the presence of the germ line-specific structures, nuage, and annulate lamellae. vasa RNA-positive cells can be followed during zebrafish embryogenesis from the 32-cell stage onward (Yoon et al., 1997). Upon completion of gastrulation, the RNA is exclusively present in the cells of the hypoblast, which as a consequence of convergence and extension movements first arrange themselves in a V-shaped string-like conformation to end up, by late somitogenesis, as a string of cells on each side of the midline. We show that the localization of maternal vasa RNA in the ovary changes from cytoplasmic, in the previtellogenic oocytes, to cortical in the vitellogenic oocytes, to concentrate at the boundary of the yolk and cytoplasm in the one cell stage zygote. These results demonstrate that the cortical vasa RNA localization precedes its cleavage furrow-associated localization in the embryos and is presumably cytoskeleton dependent. vasa RNA localization changes from asymmetric subcellular at the sphere stage, to become entirely cytoplasmic at the dome stage. These data suggest a close resemblance in modes of segregation of the germ plasma in the

  11. RNA genetics

    Energy Technology Data Exchange (ETDEWEB)

    Domingo, E. (Instituto de Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Madrid, Canto Blanco, Madrid (ES)); Holland, J.J. (California Univ., San Diego, La Jolla, CA (USA). Dept. of Biology); Ahlquist, P. (Wisconsin Univ., Madison, WI (USA). Dept. of Plant Pathology)


    This book contains the proceedings on RNA gentics: Variability of RNA genomes, Volume III. Topics covered include: High error rate, population equilibrium, and evolution of RNA replication systems; Influenza viruses; High rate of nutation and evolution; and Sequence space and quasi species distribution.

  12. PPARg mRNA in the adult mouse hypothalamus: distribution and regulation in response to dietary challenges

    Directory of Open Access Journals (Sweden)

    Yang eLiu


    Full Text Available Peroxisome proliferator-activated receptor gamma (PPARg is a ligand-activated transcription factor that was originally identified as a regulator of peroxisome proliferation and adipocyte differentiation. Emerging evidence suggests that functional PPARg signaling also occurs within the hypothalamus. However, the exact distribution and identities of PPARg-expressing hypothalamic cells remains under debate. The present study systematically mapped PPARg mRNA expression in the adult mouse brain using in situ hybridization histochemistry. PPARg mRNA was found to be expressed at high levels outside the hypothalamus including the neocortex, the olfactory bulb, the organ of the vasculosum of the lamina terminalis, and the subfornical organ. Within the hypothalamus, PPARg was present at moderate levels in the suprachiasmatic nucleus and the ependymal of the 3rd ventricle. In all examined feeding-related hypothalamic nuclei, PPARg was expressed at very low levels that were close to the limit of detection. Using qPCR techniques, we demonstrated that PPARg mRNA expression was upregulated in the suprachiasmatic nucleus in response to fasting. Double in situ hybridization further demonstrated that PPARg was primarily expressed in neurons. Collectively, our observations provide a comprehensive map of PPARg distribution and regulation in the intact adult mouse hypothalamus.

  13. Varieties of charge distributions in coat proteins of ssRNA+  viruses (United States)

    Lošdorfer Božič, Anže; Podgornik, Rudolf


    A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+  viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that—in contrast to the charge on the CPs—the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.

  14. Macroscopic Description for Networks of Spiking Neurons (United States)

    Montbrió, Ernest; Pazó, Diego; Roxin, Alex


    A major goal of neuroscience, statistical physics, and nonlinear dynamics is to understand how brain function arises from the collective dynamics of networks of spiking neurons. This challenge has been chiefly addressed through large-scale numerical simulations. Alternatively, researchers have formulated mean-field theories to gain insight into macroscopic states of large neuronal networks in terms of the collective firing activity of the neurons, or the firing rate. However, these theories have not succeeded in establishing an exact correspondence between the firing rate of the network and the underlying microscopic state of the spiking neurons. This has largely constrained the range of applicability of such macroscopic descriptions, particularly when trying to describe neuronal synchronization. Here, we provide the derivation of a set of exact macroscopic equations for a network of spiking neurons. Our results reveal that the spike generation mechanism of individual neurons introduces an effective coupling between two biophysically relevant macroscopic quantities, the firing rate and the mean membrane potential, which together govern the evolution of the neuronal network. The resulting equations exactly describe all possible macroscopic dynamical states of the network, including states of synchronous spiking activity. Finally, we show that the firing-rate description is related, via a conformal map, to a low-dimensional description in terms of the Kuramoto order parameter, called Ott-Antonsen theory. We anticipate that our results will be an important tool in investigating how large networks of spiking neurons self-organize in time to process and encode information in the brain.

  15. Monitoring the RNA distribution in human embryonic stem cells using Raman micro-spectroscopy and fluorescence imaging (United States)

    Falamas, A.; Kalra, S.; Chis, V.; Notingher, I.


    The aim of this study was to monitor the intracellular distribution of nucleic acids in human embryonic stem cells. Raman micro-spectroscopy and fluorescence imaging investigations were employed to obtain high-spatial resolution maps of nucleic acids. The DNA Raman signal was identified based on the 782 cm-1 band, while the RNA characteristic signal was detected based on the 813 cm-1 fingerprint band assigned to O-P-O symmetric stretching vibrations. Additionally, principal components analysis was performed and nucleic acids characteristic Raman signals were identified in the data set, which were plotted at each position in the cells. In this manner, high intensity RNA signal was identified in the cells nucleolus and cytoplasm, while the nucleus presented a much lower signal.

  16. Macroscopic description of the limb muscles of Tupinambis merianae

    Directory of Open Access Journals (Sweden)

    Juliana Barbosa Casals


    Full Text Available Tegu lizard (Tupinambis merianae belongs to the Teiidae family. It is distributed throughout the Americas, with many species, including Brazilian ones. They are from the Tupinambis genus, the largest representatives of the Teiidae family. For this study three animals (run over coming from donation were used. The dissected lizards were fixed in 10%, formaldehyde, and the macroscopic analysis was carried out in a detailed and photo documented way, keeping the selected structures “in situ”. This paper had as its main aim contributing to the macroscopic description of the chest myology, as well as the thoracic and pelvic limbs of the lizard T. merianae. The results obtained from this research were compared to authors who have studied animals from the same Reptilia class. Thus, we conclude that our macroscopic results are similar to those already described by the researchers Hildebrand (1995, Moro and Abdala (2004 and Abdala and Diogo (2010. We should highlight that the knowledge on anatomy has importance and applications to various areas within Biology, contributing in a substantial way to the areas of human health and technology.

  17. Macroscopic superpositions require tremendous measurement devices

    Directory of Open Access Journals (Sweden)

    Michalis Skotiniotis


    Full Text Available We consider fundamental limits on the detectable size of macroscopic quantum superpositions. We argue that a full quantum mechanical treatment of system plus measurement device is required, and that a (classical reference frame for phase or direction needs to be established to certify the quantum state. When taking the size of such a classical reference frame into account, we show that to reliably distinguish a quantum superposition state from an incoherent mixture requires a measurement device that is quadratically bigger than the superposition state. Whereas for moderate system sizes such as generated in previous experiments this is not a stringent restriction, for macroscopic superpositions of the size of a cat the required effort quickly becomes intractable, requiring measurement devices of the size of the Earth. We illustrate our results using macroscopic superposition states of photons, spins, and position. Finally, we also show how this limitation can be circumvented by dealing with superpositions in relative degrees of freedom.

  18. Macroscopic effects in attosecond pulse generation

    Energy Technology Data Exchange (ETDEWEB)

    Ruchon, T; Varju, K; Mansten, E; Swoboda, M; L' Huillier, A [Department of Physics, Lund University, PO Box 118, SE-221 00 Lund (Sweden); Hauri, C P; Lopez-Martens, R [Laboratoire d' Optique Appliquee, Ecole Nationale Superieure des Techniques Avancees (ENSTA)-Ecole Polytechnique CNRS UMR 7639, 91761 Palaiseau (France)], E-mail:


    We examine how the generation and propagation of high-order harmonics in a partly ionized gas medium affect their strength and synchronization. The temporal properties of the resulting attosecond pulses generated in long gas targets can be significantly influenced by macroscopic effects, in particular by the intensity in the medium and the degree of ionization which control the dispersion. Under some conditions, the use of gas targets longer than the absorption length can lead to the generation of compressed attosecond pulses. We show these macroscopic effects experimentally, using a 6 mm-long argon-filled gas cell as the generating medium.

  19. Nonlocal correlations in a macroscopic measurement scenario (United States)

    Kunkri, Samir; Banik, Manik; Ghosh, Sibasish


    Nonlocality is one of the main characteristic features of quantum systems involving more than one spatially separated subsystem. It is manifested theoretically as well as experimentally through violation of some local realistic inequality. On the other hand, classical behavior of all physical phenomena in the macroscopic limit gives a general intuition that any physical theory for describing microscopic phenomena should resemble classical physics in the macroscopic regime, the so-called macrorealism. In the 2-2-2 scenario (two parties, with each performing two measurements and each measurement having two outcomes), contemplating all the no-signaling correlations, we characterize which of them would exhibit classical (local realistic) behavior in the macroscopic limit. Interestingly, we find correlations which at the single-copy level violate the Bell-Clauser-Horne-Shimony-Holt inequality by an amount less than the optimal quantum violation (i.e., Cirel'son bound 2 √{2 } ), but in the macroscopic limit gives rise to a value which is higher than 2 √{2 } . Such correlations are therefore not considered physical. Our study thus provides a sufficient criterion to identify some of unphysical correlations.

  20. Macroscopic Modeling of Polymer-Electrolyte Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Weber, A.Z.; Newman, J.


    In this chapter, the various approaches for the macroscopic modeling of transport phenomena in polymer-electrolyte membranes are discussed. This includes general background and modeling methodologies, as well as exploration of the governing equations and some membrane-related topic of interest.

  1. Is ergodicity a reasonable hypothesis for macroscopic systems? (United States)

    Gaveau, B.; Schulman, L. S.


    In the physics literature "ergodicity" is sometimes taken to mean that a system, including a macroscopic one, visits all microscopic states in a relatively short time. However, many authors have realized that this is impossible and we provide a rigorous bound demonstrating this fact. A related concept is the "thermal distribution." This enters in an understanding of dissipation, comparing the thermal state (the Boltzmann or Gibbs distribution) to its time evolute using relative entropy. The thermal distribution is based on the microcanonical ensemble, whose equal probability assumption is another phrasing of ergodicity in a macroscopic physical context. The puzzle then is why the results of these assumptions are in agreement with experience. We suggest (as others also have) reasons for this limited agreement, but note that the foundations of statistical mechanics make much stronger assumptions, assumptions that do not have the support of either reason or experience. This article is supplemented with comments by P. Gaspard, Y. Pomeau and H. Qian and a final reply by the authors.

  2. Rat fetuin: distribution of protein and mRNA in embryonic and neonatal rat tissues

    DEFF Research Database (Denmark)

    Terkelsen, O B; Jahnen-Dechent, W; Nielsen, Henrik


    Fetuin is a serum protein widely distributed in the animal kingdom and found in all mammalian species so far investigated. It is mainly a fetal protein, in the sense that the highest concentrations are found in serum and body fluids of embryos and fetuses. In order to elucidate possible biologica...

  3. Distribution of PTPN22 polymorphisms in SLE from western Mexico: correlation with mRNA expression and disease activity. (United States)

    Machado-Contreras, Jesús René; Muñoz-Valle, José Francisco; Cruz, Alvaro; Salazar-Camarena, Diana Celeste; Marín-Rosales, Miguel; Palafox-Sánchez, Claudia Azucena


    Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune inflammatory disease characterized by loss of self-tolerance with hyperactivation of autoreactive T and B cells. Protein tyrosine phosphatase non-receptor type 22 (PTPN22) encodes for lymphoid-specific phosphatase (Lyp), which is a key negative regulator of T lymphocyte activation. The aim of this study was to evaluate the genetic contribution of PTPN22 -1123G>C and +1858C>T polymorphisms and their haplotypes in SLE patients, as well as mRNA expression according to -1123G>C promoter polymorphism and disease activity. One hundred and fifty SLE patients and 150 unrelated healthy controls (HC), both Mexican mestizos, were genotyped by PCR-RFLP technique for the PTPN22 -1123G>C and +1858C>T polymorphisms. PTPN22 mRNA expression levels were determined by real-time PCR from PBMCs of thirty patients with SLE and fifteen HC carrying different genotypes. Distributions of genotype and allelic frequencies were similar between SLE and HC. The most frequent alleles were -1123 G and +1858 C in both groups (69 vs. 66 % and 97 vs. 98 %, in SLE and HC, respectively). However, the recessive model of inheritance analysis showed a lower frequency of -1123 CC genotype in SLE patients (7 vs. 15 %), suggesting a protection effect to develop SLE (OR 0.41, CI 1.10-5.28, p = 0.02). Haplotype analysis showed strong linkage disequilibrium D' = 0.98 for PTPN22 -1123G>C and +1858C>T polymorphisms, but haplotypes were not associated with SLE. The PTPN22 mRNA expression did not show differences among -1123G>C genotypes; nevertheless, a significant negative correlation with disease activity was found (r = -0.64, p SLE inactive patients showed similar PTPN22 mRNA expression levels to healthy controls, whereas in patients with severe flare, the expression was nearly depleted. In conclusion, we found a lack of association of PTPN22 -1123G>C and +1858C>T polymorphisms with the risk of developing SLE in a Mexican population

  4. Distribution and mRNA expression of insulin-like growth factor system in pulmonary lymphangioleiomyomatosis. (United States)

    Valencia, J C; Matsui, K; Bondy, C; Zhou, J; Rasmussen, A; Cullen, K; Yu, Z X; Moss, J; Ferrans, V J


    Insulin-like growth factors (IGF-1 and IGF-2), the IGF-1 receptor (IGF-1R), and IGF-binding proteins (IGFBPs) are involved in normal pulmonary development and in the pathogenesis of smooth muscle cell tumors. To evaluate the role of the IGF system in lymphangioleiomyomatosis (LAM), we used immunohistochemical and in situ hybridization techniques to characterize the expression of IGF-1, IGF-2, IGF-1R, and IGFBP-2, -4, -5, and -6 in lung tissue from 18 LAM patients. IGF-1, ICGF-2, IGF-1R, IGFBP-1, IGFBP-2, IGFBP-4, IGFBP-5, and IGFBP-6 were expressed by LAM cells. Reactivity and mRNA expression for IGF-2 were observed in LAM cells and resembled that found in normal smooth muscle cells during pulmonary development as well as in smooth muscle cell tumors. IGFBP-2, IGFBP-4, and IGFBP-6 were associated with spindle-shaped LAM cells, whereas IGFBP-5 was associated mainly with epithelioid LAM cells. These findings suggest that the IGFBPs modulate the effects of the IGFs on LAM cells. Thus, the patterns of localization and expression of components of the IGF system in LAM strongly suggest that these agents are involved in the proliferation of LAM cells.

  5. Macroscopic Quantum Resonators (MAQRO): 2015 update

    Energy Technology Data Exchange (ETDEWEB)

    Kaltenbaek, Rainer [University of Vienna, Vienna Center for Quantum Science and Technology, Vienna (Austria); Aspelmeyer, Markus; Kiesel, Nikolai [University of Vienna, Vienna Center for Quantum Science and Technology, Vienna (Austria); Barker, Peter F.; Bose, Sougato [University College London, Department of Physics and Astronomy, London (United Kingdom); Bassi, Angelo [University of Trieste, Department of Physics, Trieste (Italy); INFN - Trieste Section, Trieste (Italy); Bateman, James [University of Swansea, Department of Physics, College of Science, Swansea (United Kingdom); Bongs, Kai; Cruise, Adrian Michael [University of Birmingham, School of Physics and Astronomy, Birmingham (United Kingdom); Braxmaier, Claus [University of Bremen, Center of Applied Space Technology and Micro Gravity (ZARM), Bremen (Germany); Institute of Space Systems, German Aerospace Center (DLR), Bremen (Germany); Brukner, Caslav [University of Vienna, Vienna Center for Quantum Science and Technology, Vienna (Austria); Austrian Academy of Sciences, Institute of Quantum Optics and Quantum Information (IQOQI), Vienna (Austria); Christophe, Bruno; Rodrigues, Manuel [The French Aerospace Lab, ONERA, Chatillon (France); Chwalla, Michael; Johann, Ulrich [Airbus Defence and Space GmbH, Immenstaad (Germany); Cohadon, Pierre-Francois; Heidmann, Antoine; Lambrecht, Astrid; Reynaud, Serge [ENS-PSL Research University, Laboratoire Kastler Brossel, UPMC-Sorbonne Universites, CNRS, College de France, Paris (France); Curceanu, Catalina [Laboratori Nazionali di Frascati dell' INFN, Frascati (Italy); Dholakia, Kishan; Mazilu, Michael [University of St. Andrews, School of Physics and Astronomy, St. Andrews (United Kingdom); Diosi, Lajos [Wigner Research Center for Physics, P.O. Box 49, Budapest (Hungary); Doeringshoff, Klaus; Peters, Achim [Humboldt-Universitaet zu Berlin, Institut fuer Physik, Berlin (Germany); Ertmer, Wolfgang; Rasel, Ernst M. [Leibniz Universitaet Hannover, Institut fuer Quantenoptik, Hannover (Germany); Gieseler, Jan; Novotny, Lukas; Rondin, Loic [ETH Zuerich, Photonics Laboratory, Zuerich (Switzerland); Guerlebeck, Norman; Herrmann, Sven; Laemmerzahl, Claus [University of Bremen, Center of Applied Space Technology and Micro Gravity (ZARM), Bremen (Germany); Hechenblaikner, Gerald [Airbus Defence and Space GmbH, Immenstaad (Germany); European Southern Observatory (ESO), Garching bei Muenchen (Germany); Hossenfelder, Sabine [KTH Royal Institute of Technology and Stockholm University, Nordita, Stockholm (Sweden); Kim, Myungshik [Imperial College London, QOLS, Blackett Laboratory, London (United Kingdom); Milburn, Gerard J. [University of Queensland, ARC Centre for Engineered Quantum Systems, Brisbane (Australia); Mueller, Holger [University of California, Department of Physics, Berkeley, CA (United States); Paternostro, Mauro [Queen' s University, Centre for Theoretical Atomic, Molecular and Optical Physics, School of Mathematics and Physics, Belfast (United Kingdom); Pikovski, Igor [Harvard-Smithsonian Center for Astrophysics, ITAMP, Cambridge, MA (United States); Pilan Zanoni, Andre [Airbus Defence and Space GmbH, Immenstaad (Germany); CERN - European Organization for Nuclear Research, EN-STI-TCD, Geneva (Switzerland); Riedel, Charles Jess [Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Roura, Albert [Universitaet Ulm, Institut fuer Quantenphysik, Ulm (Germany); Schleich, Wolfgang P. [Universitaet Ulm, Institut fuer Quantenphysik, Ulm (Germany); Texas A and M University Institute for Advanced Study (TIAS), Institute for Quantum Science and Engineering (IQSE), and Department of Physics and Astronomy, College Station, TX (United States); Schmiedmayer, Joerg [Vienna University of Technology, Vienna Center for Quantum Science and Technology, Institute of Atomic and Subatomic Physics, Vienna (Austria); Schuldt, Thilo [Institute of Space Systems, German Aerospace Center (DLR), Bremen (Germany); Schwab, Keith C. [California Institute of Technology, Applied Physics, Pasadena, CA (United States); Tajmar, Martin [Technische Universitaet Dresden, Institut fuer Luft- und Raumfahrttechnik, Dresden (Germany); Tino, Guglielmo M. [Universita di Firenze, Dipartimento di Fisica e Astronomia and LENS, INFN, Sesto Fiorentino, Firenze (Italy); Ulbricht, Hendrik [University of Southampton, Physics and Astronomy, Southampton (United Kingdom); Ursin, Rupert [Austrian Academy of Sciences, Institute of Quantum Optics and Quantum Information (IQOQI), Vienna (Austria); Vedral, Vlatko [University of Oxford, Atomic and Laser Physics, Clarendon Laboratory, Oxford (United Kingdom); National University of Singapore, Center for Quantum Technologies, Singapore (SG)


    Do the laws of quantum physics still hold for macroscopic objects - this is at the heart of Schroedinger's cat paradox - or do gravitation or yet unknown effects set a limit for massive particles? What is the fundamental relation between quantum physics and gravity? Ground-based experiments addressing these questions may soon face limitations due to limited free-fall times and the quality of vacuum and microgravity. The proposed mission Macroscopic Quantum Resonators (MAQRO) may overcome these limitations and allow addressing such fundamental questions. MAQRO harnesses recent developments in quantum optomechanics, high-mass matter-wave interferometry as well as state-of-the-art space technology to push macroscopic quantum experiments towards their ultimate performance limits and to open new horizons for applying quantum technology in space. The main scientific goal is to probe the vastly unexplored 'quantum-classical' transition for increasingly massive objects, testing the predictions of quantum theory for objects in a size and mass regime unachievable in ground-based experiments. The hardware will largely be based on available space technology. Here, we present the MAQRO proposal submitted in response to the 4th Cosmic Vision call for a medium-sized mission (M4) in 2014 of the European Space Agency (ESA) with a possible launch in 2025, and we review the progress with respect to the original MAQRO proposal for the 3rd Cosmic Vision call for a medium-sized mission (M3) in 2010. In particular, the updated proposal overcomes several critical issues of the original proposal by relying on established experimental techniques from high-mass matter-wave interferometry and by introducing novel ideas for particle loading and manipulation. Moreover, the mission design was improved to better fulfill the stringent environmental requirements for macroscopic quantum experiments. (orig.)

  6. Macroscopic approach to the Casimir friction force


    Nesterenko, V. V.; Nesterenko, A. V.


    The general formula is derived for the vacuum friction force between two parallel perfectly flat planes bounding two material media separated by a vacuum gap and moving relative to each other with a constant velocity $\\mathbf{v}$. The material media are described in the framework of macroscopic electrodynamics whereas the nonzero temperature and dissipation are taken into account by making use of the Kubo formulae from non-equilibrium statistical thermodynamics. The formula obtained provides ...

  7. Macroscopic Interpretability of Quantum Component Systems (United States)

    Ascoli, R.


    Preliminary accounts on three subjects are produced in Secs. 1, 2, 3. The guiding idea is Universality of Physics, by which we mean that the boundary between the system {S} that is selected, and which is described by Quantum Theory, and the macroscopic environment {A} where the single physical events as well as the events of ordinary life occur, which is described within a Boolean structure, may always be shifted by constructing a Quantum Model also of the environment {A} (to be selected from the "further environment"), as it is set forth in Sec. 1. This introduces the subject of Sec. 2, which examines what should be understood when saying that the quantum component system {A} may be macroscopically or at least "semimacroscopically" interpreted. In its turn this introduces Sec. 3, reporting two still unpublished theorems produced at Camerino 1988, which very closely connect the above requirements on the Quantum Model of {A} with some properties of the operations that the "instrument" {A} performs on {S}, with the result that the macroscopicity conditions of Sec. 2 turn out to be widely model-independent ("environmental").

  8. Macroscopic nonclassical-state preparation via postselection (United States)

    Montenegro, Víctor; Coto, Raúl; Eremeev, Vitalie; Orszag, Miguel


    Macroscopic quantum superposition states are fundamental to test the classical-quantum boundary and present suitable candidates for quantum technologies. Although the preparation of such states has already been realized, the existing setups commonly consider external driving and resonant interactions, predominantly by considering Jaynes-Cummings-like and beam-splitter-like interactions, as well as the nonlinear radiation pressure interaction in cavity optomechanics. In contrast to previous works on the matter, we propose a feasible probabilistic scheme to generate a macroscopic mechanical qubit, as well as phononic Schrödinger's cat states with no need of any energy exchange with the macroscopic mechanical oscillator. Essentially, we investigate an open dispersive spin-mechanical system in the absence of any external driving under nonideal conditions, such as the detrimental effects due to the oscillator and spin energy losses in a thermal bath at nonzero temperature. In our work, we show that the procedure to generate the mechanical qubit state is solely based on spin postselection in the weak to moderate coupling regime. Finally, we demonstrate that the mechanical superposition is related to the amplification of the mean values of the mechanical quadratures as they maximize the quantum coherence.

  9. Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy. (United States)

    Jordanova, Albena; Irobi, Joy; Thomas, Florian P; Van Dijck, Patrick; Meerschaert, Kris; Dewil, Maarten; Dierick, Ines; Jacobs, An; De Vriendt, Els; Guergueltcheva, Velina; Rao, Chitharanjan V; Tournev, Ivailo; Gondim, Francisco A A; D'Hooghe, Marc; Van Gerwen, Veerle; Callaerts, Patrick; Van Den Bosch, Ludo; Timmermans, Jean-Pièrre; Robberecht, Wim; Gettemans, Jan; Thevelein, Johan M; De Jonghe, Peter; Kremensky, Ivo; Timmerman, Vincent


    Charcot-Marie-Tooth (CMT) neuropathies are common disorders of the peripheral nervous system caused by demyelination or axonal degeneration, or a combination of both features. We previously assigned the locus for autosomal dominant intermediate CMT neuropathy type C (DI-CMTC) to chromosome 1p34-p35. Here we identify two heterozygous missense mutations (G41R and E196K) and one de novo deletion (153-156delVKQV) in tyrosyl-tRNA synthetase (YARS) in three unrelated families affected with DI-CMTC. Biochemical experiments and genetic complementation in yeast show partial loss of aminoacylation activity of the mutant proteins, and mutations in YARS, or in its yeast ortholog TYS1, reduce yeast growth. YARS localizes to axonal termini in differentiating primary motor neuron and neuroblastoma cultures. This specific distribution is significantly reduced in cells expressing mutant YARS proteins. YARS is the second aminoacyl-tRNA synthetase found to be involved in CMT, thereby linking protein-synthesizing complexes with neurodegeneration.

  10. JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure. (United States)

    Troshin, Peter V; Procter, James B; Sherstnev, Alexander; Barton, Daniel L; Madeira, Fábio; Barton, Geoffrey J


    JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800,000 analyses for users worldwide. JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from:

  11. Characterization of the 3' end of the mouse SERCA 3 gene and tissue distribution of mRNA spliced variants. (United States)

    Ozog, A; Pouzet, B; Bobe, R; Lompré, A M


    The sarco(endo)plasmic reticulum Ca2+ ATPase (SERCA) type 1 and 2 genes are alternatively spliced at their 3' end. We hypothesized that similar mechanism may occur for SERCA 3. Two spliced variants were identified by RNase protection analysis. We then isolated and sequenced the 3' end portion of the mouse SERCA 3 gene, and confirmed the presence of an alternative mRNA transcript by sequencing a cDNA fragment obtained by RT-PCR. Tissue distribution of the alternatively spliced mRNAs was studied by RT-PCR: SERCA 3b was the only isoform expressed in endothelial cells from aorta and heart and also was the major isoform in lung and kidney whereas SERCA 3a and 3b were coexpressed in trachea, intestine, thymus, spleen, and fetal liver.

  12. Understanding the Pulsar High Energy Emission: Macroscopic and Kinetic Models (United States)

    Kalapotharakos, Constantinos; Brambilla, Gabriele; Timokhin, Andrey; Kust Harding, Alice; Kazanas, Demos


    Pulsars are extraordinary objects powered by the rotation of magnetic fields of order 10^8, 10^12G anchored onto neutron stars and rotating with periods 10^(-3)-10s. These fields mediate the conversion of their rotational energy into MHD winds and at the same time accelerate particles to energies sufficiently high to produce GeV photons. Fermi, since its launch in 2008, has established several trends among the observed gamma-ray pulsar properties playing a catalytic role in the current modeling of the high energy emission in pulsar magnetospheres. We judiciously use the guidance provided by the Fermi data to yield meaningful constraints on the macroscopic parameters of our global dissipative pulsar magnetosphere models. Our FIDO (Force-Free Inside, Dissipative Outside) models indicate that the dissipative regions lie outside the light cylinder near the equatorial current sheet. Our models reproduce the light-curve phenomenology while a detailed comparison of the model spectral properties with those observed by Fermi reveals the dependence of the macroscopic conductivity parameter on the spin-down rate providing a unique insight into the understanding of the physical mechanisms behind the high-energy emission in pulsar magnetospheres. Finally, we further exploit these important results by building self-consistent 3D global kinetic particle-in-cell (PIC) models which, eventually, provide the dependence of the macroscopic parameter behavior (e.g. conductivity) on the microphysical properties (e.g. particle multiplicities, particle injection rates). Our PIC models provide field structures and particle distributions that are not only consistent with each other but also able to reproduce a broad range of the observed gamma-ray phenomenology (light curves and spectral properties) of both young and millisecond pulsars.

  13. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Field, K.G.; Gordon, D.; Wright, T. [Oregon State Univ., Corvallis, OR (United States)] [and others


    Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result form artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the {alpha} subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m im the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes. 48 refs., 7 figs., 3 tabs.

  14. Pathways toward understanding Macroscopic Quantum Phenomena (United States)

    Hu, B. L.; Subaşi, Y.


    Macroscopic quantum phenomena refer to quantum features in objects of 'large' sizes, systems with many components or degrees of freedom, organized in some ways where they can be identified as macroscopic objects. This emerging field is ushered in by several categories of definitive experiments in superconductivity, electromechanical systems, Bose-Einstein condensates and others. Yet this new field which is rich in open issues at the foundation of quantum and statistical physics remains little explored theoretically (with the important exception of the work of A J Leggett [1], while touched upon or implied by several groups of authors represented in this conference. Our attitude differs in that we believe in the full validity of quantum mechanics stretching from the testable micro to meso scales, with no need for the introduction of new laws of physics.) This talk summarizes our thoughts in attempting a systematic investigation into some key foundational issues of quantum macroscopic phenomena, with the goal of ultimately revealing or building a viable theoretical framework. Three major themes discussed in three intended essays are the large N expansion [2], the correlation hierarchy [3] and quantum entanglement [4]. We give a sketch of the first two themes and then discuss several key issues in the consideration of macro and quantum, namely, a) recognition that there exist many levels of structure in a composite body and only by judicious choice of an appropriate set of collective variables can one give the best description of the dynamics of a specific level of structure. Capturing the quantum features of a macroscopic object is greatly facilitated by the existence and functioning of these collective variables; b) quantum entanglement, an exclusively quantum feature [5], is known to persist to high temperatures [6] and large scales [7] under certain conditions, and may actually decrease with increased connectivity in a quantum network [8]. We use entanglement as a

  15. Macroscopic Subdivision of Silica Aerogel Collectors for Sample Return Missions

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, H A; Bradley, J P


    Silica aerogel collector tiles have been employed for the collection of particles in low Earth orbit and, more recently, for the capture of cometary particles by NASA's Stardust mission. Reliable, reproducible methods for cutting these and future collector tiles from sample return missions are necessary to maximize the science output from the extremely valuable embedded particles. We present a means of macroscopic subdivision of collector tiles by generating large-scale cuts over several centimeters in silica aerogel with almost no material loss. The cut surfaces are smooth and optically clear allowing visual location of particles for analysis and extraction. This capability is complementary to the smaller-scale cutting capabilities previously described [Westphal (2004), Ishii (2005a, 2005b)] for removing individual impacts and particulate debris in tiny aerogel extractions. Macroscopic cuts enable division and storage or distribution of portions of aerogel tiles for immediate analysis of samples by certain techniques in situ or further extraction of samples suited for other methods of analysis.

  16. Macroscopic modeling of plant water uptake: soil and root resistances (United States)

    Vogel, Tomas; Votrubova, Jana; Dohnal, Michal; Dusek, Jaromir


    The macroscopic physically-based plant root water uptake (RWU) model, based on water-potential-gradient formulation (Vogel et al., 2013), was used to simulate the observed soil-plant-atmosphere interactions at a forest site located in a temperate humid climate of central Europe and to gain an improved insight into the mutual interplay of RWU parameters that affects the soil water distribution in the root zone. In the applied RWU model, the uptake rates are directly proportional to the potential gradient and indirectly proportional to the local soil and root resistances to water flow. The RWU algorithm is implemented in a one-dimensional dual-continuum model of soil water flow based on Richards' equation. The RWU model is defined by four parameters (root length density distribution, average active root radius, radial root resistance, and the threshold value of the root xylem potential). In addition, soil resistance to water extraction by roots is related to soil hydraulic conductivity function and actual soil water content. The RWU model is capable of simulating both the compensatory root water uptake, in situations when reduced uptake from dry layers is compensated by increased uptake from wetter layers, and the root-mediated hydraulic redistribution of soil water, contributing to more natural soil moisture distribution throughout the root zone. The present study focusses on the sensitivity analysis of the combined soil water flow and RWU model responses in respect to variations of RWU model parameters. Vogel T., M. Dohnal, J. Dusek, J. Votrubova, and M. Tesar. 2013. Macroscopic modeling of plant water uptake in a forest stand involving root-mediated soil-water redistribution. Vadose Zone Journal, 12, 10.2136/vzj2012.0154.

  17. Macroscopic properties of fractured porous media (United States)

    Sangare, D.; Thovert, J.-F.; Adler, P. M.


    The macroscopic properties of fractured porous media locally governed by a Laplace equation are determined by several methods. The first one consists in discretizing the porous medium and the fractures and in solving the Laplace equation in the discretized structure. The other methods consist in successive upscalings. The first upscaling replaces the porous medium by a continuum with a given transport property. The second upscaling replaces the fractures by surfaces with equivalent properties. The results of the various methods give very close results. They suggest a simple approximation which is successful when the properties of the fluid and of the continuous porous medium are not too different.

  18. Macroscopic invisibility cloaking of visible light

    DEFF Research Database (Denmark)

    Chen, Xianzhong; Luo, Y.; Zhang, Jingjing


    invisibility cloaks has been reported at various electromagnetic frequencies. All the invisibility cloaks demonstrated thus far, however, have relied on nano- or micro-fabricated artificial composite materials with spatially varying electromagnetic properties, which limit the size of the cloaked region...... to a few wavelengths. Here, we report the first realization of a macroscopic volumetric invisibility cloak constructed from natural birefringent crystals. The cloak operates at visible frequencies and is capable of hiding, for a specific light polarization, three-dimensional objects of the scale...

  19. Rainbow correlation imaging with macroscopic twin beam (United States)

    Allevi, Alessia; Bondani, Maria


    We present the implementation of a correlation-imaging protocol that exploits both the spatial and spectral correlations of macroscopic twin-beam states generated by parametric downconversion. In particular, the spectral resolution of an imaging spectrometer coupled to an EMCCD camera is used in a proof-of-principle experiment to encrypt and decrypt a simple code to be transmitted between two parties. In order to optimize the trade-off between visibility and resolution, we provide the characterization of the correlation images as a function of the spatio-spectral properties of twin beams generated at different pump power values.

  20. Self-assembly of free-standing RNA membranes (United States)

    Han, Daehoon; Park, Yongkuk; Kim, Hyejin; Lee, Jong Bum


    RNA has emerged as a promising material for nanostructure and microstructure engineering. Although rare, some macroscopic RNA structures have also been constructed using lipid or polymer materials. Here, we report the first example of an enzymatically generated RNA membrane. This robust and free-standing RNA membrane has a macroscopic structure and is generated without any polymer support or complexation. Our RNA membrane is fabricated following two sequential processes, complementary rolling circle transcription and evaporation-induced self-assembly, and its structural and functional properties are rationally controlled by adjusting RNA base pairing. In this study, three types of RNA membranes are fabricated and are used to demonstrate potential applications.

  1. Wet-chemical preparation of copper foam monoliths with tunable densities and complex macroscopic shapes. (United States)

    Kränzlin, Niklaus; Niederberger, Markus


    Macroscopic monoliths of copper foams have been prepared by a template-assisted wet-chemical process. The method offers subtle control over the pore size and size distribution, density and macroscopic size and shape of the metal foam. Uniaxial compression tests revealed different deformation behavior depending on the relative density. Non-vacuum-based and low-temperature routes are attractive for the cost-effective production of metal foams. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system

    Directory of Open Access Journals (Sweden)

    Sigurdsson Martin I


    Full Text Available Abstract Background A defense system against transposon activity in the human germline based on PIWI proteins and piRNA has recently been discovered. It represses the activity of LINE-1 elements via DNA methylation by a largely unknown mechanism. Based on the dispersed distribution of clusters of piRNA genes in a strand-specific manner on all human chromosomes, we hypothesized that this system might work preferentially on local and proximal sequences. We tested this hypothesis with a methylation-associated SNP (mSNP marker which is based on the density of C-T transitions in CpG dinucleotides as a surrogate marker for germline methylation. Results We found significantly higher density of mSNPs flanking piRNA clusters in the human genome for flank sizes of 1-16 Mb. A dose-response relationship between number of piRNA genes and mSNP density was found for up to 16 Mb of flanking sequences. The chromosomal density of hypermethylated LINE-1 elements had a significant positive correlation with the chromosomal density of piRNA genes (r = 0.41, P = 0.05. Genome windows of 1-16 Mb containing piRNA clusters had significantly more hypermethylated LINE-1 elements than windows not containing piRNA clusters. Finally, the minimum distance to the next piRNA cluster was significantly shorter for hypermethylated LINE-1 compared to normally methylated elements (14.4 Mb vs 16.1 Mb. Conclusions Our observations support our hypothesis that the piRNA-PIWI system preferentially methylates sequences in close proximity to the piRNA clusters and perhaps physically adjacent sequences on other chromosomes. Furthermore they suggest that this proximity effect extends up to 16 Mb. This could be due to an unknown localization signal, transcription of piRNA genes near the nuclear membrane or the presence of an unknown RNA molecule that spreads across the chromosome and targets the methylation directed by the piRNA-PIWI complex. Our data suggest a region specific molecular

  3. Making Macroscopic Assemblies of Aligned Carbon Nanotubes (United States)

    Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting; hide


    A method of aligning and assembling single-wall carbon nanotubes (SWNTs) to fabricate macroscopic structures has been invented. The method entails suspending SWNTs in a fluid, orienting the SWNTs by use of a magnetic and/or electric field, and then removing the aligned SWNTs from suspension in such a way as to assemble them while maintaining the alignment. SWNTs are essentially tubular extensions of fullerene molecules. It is desirable to assemble aligned SWNTs into macroscopic structures because the common alignment of the SWNTs in such a structure makes it possible to exploit, on a macroscopic scale, the unique mechanical, chemical, and electrical properties that individual oriented SWNTs exhibit at the molecular level. Because of their small size and high electrical conductivity, carbon nanotubes, and especially SWNTs, are useful for making electrical connectors in integrated circuits. Carbon nanotubes can be used as antennas at optical frequencies, and as probes in scanning tunneling microscopes, atomic-force microscopes, and the like. Carbon nanotubes can be used with or instead of carbon black in tires. Carbon nanotubes are useful as supports for catalysts. Ropes of SWNTs are metallic and, as such, are potentially useful in some applications in which electrical conductors are needed - for example, they could be used as additives in formulating electrically conductive paints. Finally, macroscopic assemblies of aligned SWNTs can serve as templates for the growth of more and larger structures of the same type. The great variety of tubular fullerene molecules and of the structures that could be formed by assembling them in various ways precludes a complete description of the present method within the limits of this article. It must suffice to present a typical example of the use of one of many possible variants of the method to form a membrane comprising SWNTs aligned substantially parallel to each other in the membrane plane. The apparatus used in this variant

  4. Quantum teleportation between stationary macroscopic objects

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Xiao-Hui; Yuan, Zhen-Sheng; Pan, Jian-Wei [Physikalisches Institut, Universitaet Heidelberg (Germany); Hefei National Laboratory for Physical Sciences at Microscale, Department of Modern Physics, University of Science and Technology of China, Hefei (China); Xu, Xiao-Fan [Physikalisches Institut, Universitaet Heidelberg (Germany); Li, Che-Ming [Physikalisches Institut, Universitaet Heidelberg (Germany); Department of Physics, National Center for Theoretical Sciences, National Cheng Kung University, Tainan (China)


    Quantum teleportation is a process to transfer a quantum state of an object without transferring the state carrier itself. So far, most of the teleportation experiments realized are within the photonic regime. For the teleportation of stationary states, the largest system reported is a single ion. We are now performing an experiment to teleport the state of an macroscopic atomic cloud which consists about 10{sup 6} single atoms. In our experiment two atomic ensembles are utilized. In the first ensemble A we prepare the collective atomic state to be teleported using the quantum feedback technique. The second ensemble B is utilized to generate entanglement between it collective state with a scattered single-photon. Teleportation is realized by converting the atomic state of A to a single-photon and making a Bell state measurement with the scattered single-photon from ensemble B.

  5. Macroscopic anatomy, irrigation and venous drainage of female reproductive apparatus of llama (Lama glama)


    León M., Eric; Laboratorio de Anatomía Animal y Fauna Silvestre, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima; Sato S., Alberto; Laboratorio de Anatomía Animal y Fauna Silvestre, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima; Navarrete Z., Miluska; Laboratorio de Anatomía Animal y Fauna Silvestre, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima; Cisneros S., Jannet; Laboratorio de Anatomía Animal y Fauna Silvestre, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima


    The anatomical description of the reproductive tract of the female llama was studied in four animals. Macroscopically, the reproductive system is morphologically similar to the cow. However, the difference is the absence of intercornual ligament and cotyledons, and the presence of an intercornual septum, as in the alpaca. The distribution of the arteries and veins that irrigated and drained the blood to and from the pelvic cavity and reproductive system presented a vascular distribution almos...

  6. Cloning and tissue distribution of rat hear fatty acid binding protein mRNA: identical forms in heart and skeletal muscle

    Energy Technology Data Exchange (ETDEWEB)

    Claffey, K.P.; Herrera, V.L.; Brecher, P.; Ruiz-Opazo, N.


    A fatty acid binding protein (FABP) as been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a lambda gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14,776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source.

  7. Macroscopic resonant tunnelling through Andreev interferometers. (United States)

    Goorden, M C; Jacquod, Ph; Weiss, J


    We investigate the conductance through and the spectrum of ballistic chaotic quantum dots attached to two s-wave superconductors, as a function of the phase difference phi between the two order parameters. A combination of analytical techniques-random matrix theory, Nazarov's circuit theory and the trajectory-based semiclassical theory-allows us to explore the quantum-to-classical crossover in detail. When the superconductors are not phase-biased, phi = 0, we recover known results that the spectrum of the quantum dot exhibits an excitation gap, while the conductance across two normal leads carrying N(N) channels and connected to the dot via tunnel contacts of transparency Gamma(N) is [Formula: see text]. In contrast, when phi = pi, the excitation gap closes and the conductance becomes [Formula: see text] in the universal regime. For [Formula: see text], we observe an order-of-magnitude enhancement of the conductance towards [Formula: see text] in the short-wavelength limit. We relate this enhancement to resonant tunnelling through a macroscopic number of levels close to the Fermi energy. Our predictions are corroborated by numerical simulations.

  8. Macroscopic liquid-state molecular hydrodynamics. (United States)

    Keanini, R G; Tkacik, Peter T; Fleischhauer, Eric; Shahinian, Hossein; Sholar, Jodie; Azimi, Farzad; Mullany, Brid


    Experimental evidence and theoretical modeling suggest that piles of confined, high-restitution grains, subject to low-amplitude vibration, can serve as experimentally-accessible analogs for studying a range of liquid-state molecular hydrodynamic processes. Experiments expose single-grain and multiple-grain, collective dynamic features that mimic those either observed or predicted in molecular-scale, liquid state systems, including: (i) near-collision-time-scale hydrodynamic organization of single-molecule dynamics, (ii) nonequilibrium, long-time-scale excitation of collective/hydrodynamic modes, and (iii) long-time-scale emergence of continuum, viscous flow. In order to connect directly observable macroscale granular dynamics to inaccessible and/or indirectly measured molecular hydrodynamic processes, we recast traditional microscale equilibrium and nonequilibrium statistical mechanics for dense, interacting microscale systems into self-consistent, macroscale form. The proposed macroscopic models, which appear to be new with respect to granular physics, and which differ significantly from traditional kinetic-theory-based, macroscale statistical mechanics models, are used to rigorously derive the continuum equations governing viscous, liquid-like granular flow. The models allow physically-consistent interpretation and prediction of observed equilibrium and non-equilibrium, single-grain, and collective, multiple-grain dynamics.

  9. Searching for the nanoscopic–macroscopic boundary

    Energy Technology Data Exchange (ETDEWEB)

    Velásquez, E.A. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Grupo de Investigación en Modelamiento y Simulación Computacional, Universidad de San Buenaventura Sec. Medellín, A.A. 5222, Medellín (Colombia); Altbir, D. [Departamento de Física, Universidad de Santiago de Chile (USACH), CEDENNA, Santiago (Chile); Mazo-Zuluaga, J. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Duque, L.F. [GICM and GES Groups, Instituto de Física-FCEN, Universidad de Antioquia UdeA, Calle 70 No. 52-21 Medellín (Colombia); Grupo de Física Teórica, Aplicada y Didáctica, Facultad de Ciencias Exactas y Aplicadas Instituto Tecnológico Metropolitano, Medellín (Colombia); Mejía-López, J., E-mail: [Facultad de Física, Pontificia Universidad Católica de Chile, CEDENNA, Santiago (Chile)


    Several studies have focused on the size-dependent properties of elements, looking for a unique definition of the nanoscopic–macroscopic boundary. By using a novel approach consisting of an energy variational method combined with a quantum Heisenberg model, here we address the size at which the ordering temperature of a magnetic nanoparticle reaches its bulk value. We consider samples with sizes in the range 1–500 nm, as well as several geometries and crystalline lattices and observe that, contrarily to what is commonly argued, the nanoscopic-microscopic boundary depends on both factors: shape and crystalline structure. This suggests that the surface-to-volume ratio is not the unique parameter that defines the behavior of a nanometric sample whenever its size increases reaching the bulk dimension. Comparisons reveal very good agreement with experimental evidence with differences less than 2%. Our results have broad implications for practical issues in measurements on systems at the nanometric scale. - Highlights: • A novel quantum-Heisenberg variational energy method is implemented. • The asymptotic behavior toward the thermodynamic limit is explored. • An important dependence of the nano-bulk boundary on the geometry is found. • And also an important dependence on the crystalline lattice. • We obtain a very good agreement with experimental evidence with differences <2%.

  10. Investigation of dissipative forces near macroscopic media

    Energy Technology Data Exchange (ETDEWEB)

    Becker, R.S.


    The interaction of classical charged particles with the fields they induce in macroscopic dielectric media is investigated. For 10- to 1000-eV electrons, the angular perturbation of the trajectory by the image potential for surface impact parameters of 50 to 100 A is shown to be of the order of 0.001 rads over a distance of 100 A. The energy loss incurred by low-energy particles due to collective excitations such as surface plasmons is shown to be observable with a transition probability of 0.01 to 0.001 (Becker, et al., 1981b). The dispersion of real surface plasmon modes in planar and cylindrical geometries is discussed and is derived for pinhole geometry described in terms of a single-sheeted hyperboloid of revolution. An experimental apparatus for the measurement of collective losses for medium-energy electrons translating close to a dielectric surface is described and discussed. Data showing such losses at electron energies of 500 to 900 eV in silver foils containing many small apertures are presented and shown to be in good agreement with classical stopping power calculations and quantum mechanical calculations carried out in the low-velocity limit. The data and calculations are compared and contrasted with earlier transmission and reflection measurements, and the course of further investigation is discussed.

  11. Macroscopic liquid-state molecular hydrodynamics (United States)

    Keanini, R. G.; Tkacik, Peter T.; Fleischhauer, Eric; Shahinian, Hossein; Sholar, Jodie; Azimi, Farzad; Mullany, Brid


    Experimental evidence and theoretical modeling suggest that piles of confined, high-restitution grains, subject to low-amplitude vibration, can serve as experimentally-accessible analogs for studying a range of liquid-state molecular hydrodynamic processes. Experiments expose single-grain and multiple-grain, collective dynamic features that mimic those either observed or predicted in molecular-scale, liquid state systems, including: (i) near-collision-time-scale hydrodynamic organization of single-molecule dynamics, (ii) nonequilibrium, long-time-scale excitation of collective/hydrodynamic modes, and (iii) long-time-scale emergence of continuum, viscous flow. In order to connect directly observable macroscale granular dynamics to inaccessible and/or indirectly measured molecular hydrodynamic processes, we recast traditional microscale equilibrium and nonequilibrium statistical mechanics for dense, interacting microscale systems into self-consistent, macroscale form. The proposed macroscopic models, which appear to be new with respect to granular physics, and which differ significantly from traditional kinetic-theory-based, macroscale statistical mechanics models, are used to rigorously derive the continuum equations governing viscous, liquid-like granular flow. The models allow physically-consistent interpretation and prediction of observed equilibrium and non-equilibrium, single-grain, and collective, multiple-grain dynamics.

  12. PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. (United States)

    Hu, Yu; Liu, Yichuan; Mao, Xianyun; Jia, Cheng; Ferguson, Jane F; Xue, Chenyi; Reilly, Muredach P; Li, Hongzhe; Li, Mingyao


    Correctly estimating isoform-specific gene expression is important for understanding complicated biological mechanisms and for mapping disease susceptibility genes. However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not appropriately corrected, can affect isoform expression estimation and downstream analysis. In this article, we present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution. Instead of making parametric assumptions, we give adequate weight to the underlying data by the use of a non-parametric approach. Our rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. We evaluate the performance of PennSeq using both simulated data with known ground truth, and using two real Illumina RNA-Seq data sets including one with quantitative real time polymerase chain reaction measurements. Our results indicate superior performance of PennSeq over existing methods, particularly for isoforms demonstrating severe non-uniformity. PennSeq is freely available for download at

  13. Correlation between genotypes of tRNA-linked short tandem repeats in Entamoeba nuttalli isolates and the geographical distribution of host rhesus macaques. (United States)

    Feng, Meng; Komiyama, Tomoyoshi; Yanagi, Tetsuo; Cheng, Xunjia; Sherchand, Jeevan B; Tachibana, Hiroshi


    Several polymorphic markers, including serine-rich protein genes, have been used for the genotyping of isolates from the morphologically indistinguishable protozoan parasites Entamoeba histolytica, Entamoeba dispar, and Entamoeba nuttalli. Genotypes of tRNA-linked short tandem repeats (STRs) are highly polymorphic, but the correlation with geographical distribution is unknown. We have recently isolated 15 E. nuttalli strains from wild rhesus macaques in four locations in Kathmandu Valley, Nepal. The sequences of the serine-rich protein genes of the E. nuttalli strains differed among the four locations. In this study, we analyzed tRNA-linked STRs in six loci of the 15 strains. Two genotypes were found in loci N-K2, R-R, and S(TGA)-D, three in locus S-Q, and five in locus D-A. In locus A-L, one major genotype and ten minor genotypes were found, resulting in mixtures of two to six genotypes in eight strains. By combination of the main genotypes in the six loci, the 15 strains were divided into nine genotypes. The genotypes observed in E. nuttalli strains were quite different from those in E. histolytica and E. dispar. A phylogenetic tree constructed from tRNA-linked STRs in the six loci reflected the different places of isolation. These results suggest that sequence diversity of tRNA-linked STRs in E. nuttalli occurs with relatively high frequency and might be a marker of geographical distribution of host rhesus macaques, even in limited areas.

  14. The Connection between Macroscopic and Microscopic Properties in Chemical Transformations


    Bolysbek Utelbaev; Esen Suleimenov; Akmaral Utelbaeva


    This article examines the chemical interaction of substances and their polymorphic transformations inclusive of their microscopic and macroscopic properties. This process involves the rearrangement of the elementary particles and electronic structures of “chemical individuums” at microscopic level and the release (absorption) of heat and formation of massive aggregates at macroscopic level, which form this work’s subject of discussion.

  15. Experimental test of macroscopic realism in a superconducting flux qubit (United States)

    Kakuyanagi, Kosuke; Knee, George; Yeh, Mao-Chuang; Matsuzaki, Yuichiro; Toida, Hiraku; Yamaguchi, Hiroshi; Saito, Shiro; Leggett, Anthony; Munro, William

    A superconducting flux qubit has been considered a macroscopic quantum system because its energy eigenstates correspond to clockwise and anti-clockwise macroscopic current. In order to test macroscopic realism in a superconducting flux qubit, we can measure the violation of the traditional Leggett-Garg inequality (LGI). The LGI is always satisfied if realism is correct, however it can be violated in systems that do not obey realism, for example microscopic systems (atoms, photons) described by quantum mechanics. To show violation of realism in a quantum system, we used a Josephson bifurcation amplifier (JBA) to read out the quantum state of our system in a fast, but low back-action fashion. We tested macroscopic realism with a simplified (but equivalent) LGI and obtained strong and significant evidence for the superposition of states of nontrivial macroscopic objects.

  16. Chaotic advection at the pore scale: Mechanisms, upscaling and implications for macroscopic transport (United States)

    Lester, D. R.; Trefry, M. G.; Metcalfe, G.


    The macroscopic spreading and mixing of solute plumes in saturated porous media is ultimately controlled by processes operating at the pore scale. Whilst the conventional picture of pore-scale mechanical dispersion and molecular diffusion leading to persistent hydrodynamic dispersion is well accepted, this paradigm is inherently two-dimensional (2D) in nature and neglects important three-dimensional (3D) phenomena. We discuss how the kinematics of steady 3D flow at the pore scale generate chaotic advection-involving exponential stretching and folding of fluid elements-the mechanisms by which it arises and implications of microscopic chaos for macroscopic dispersion and mixing. Prohibited in steady 2D flow due to topological constraints, these phenomena are ubiquitous due to the topological complexity inherent to all 3D porous media. Consequently 3D porous media flows generate profoundly different fluid deformation and mixing processes to those of 2D flow. The interplay of chaotic advection and broad transit time distributions can be incorporated into a continuous-time random walk (CTRW) framework to predict macroscopic solute mixing and spreading. We show how these results may be generalised to real porous architectures via a CTRW model of fluid deformation, leading to stochastic models of macroscopic dispersion and mixing which both honour the pore-scale kinematics and are directly conditioned on the pore-scale architecture.

  17. A novel method for room temperature distribution and conservation of RNA and DNA reference materials for guaranteeing performance of molecular diagnostics in onco-hematology: A GBMHM study. (United States)

    Cayuela, Jean-Michel; Mauté, Carole; Fabre, Anne-Lise; Nibourel, Olivier; Dulucq, Stéphanie; Delabesse, Eric; Villarèse, Patrick; Hayette, Sandrine; Mozziconacci, Marie-Joelle; Macintyre, Elizabeth


    Performance of methods used for molecular diagnostics must be closely controlled by regular analysis of internal quality controls. However, conditioning, shipping and long lasting storage of nucleic acid controls remain problematic. Therefore, we evaluated the minicapsule-based innovative process developed by Imagene (Evry, France) for implementing DNA and RNA controls designed for clonality assessment of lymphoproliferations and BCR-ABL1 mRNA quantification, respectively. DNA samples were extracted from 12 cell lines selected for giving specific amplifications with most BIOMED-2 PCR tubes. RNA samples were extracted from 8 cell line mixtures expressing various BCR-ABL1 transcript levels. DNA and RNA were encapsulated by Imagene and shipped at room temperature to participating laboratories. Biologists were asked to report quality data of recovered nucleic acids as well as PCR results. Encapsulated nucleic acids samples were easily and efficiently recovered from minicapsules. The expected rearrangements at immunoglobulin, T-cell receptor and BCL2 loci were detected in DNA samples by all laboratories. Quality of RNA was consistent between laboratories and met the criteria requested for quantification of BCR-ABL1 transcripts. Expression levels measured by the 5 laboratories were within ±2 fold interval from the corresponding pre-encapsulation reference value. Moreover aging studies of encapsulated RNA simulating up to 100 years storage at room temperature show no bias in quantitative outcome. Therefore, Imagene minicapsules are suitable for storage and distribution at room temperature of genetic material designed for proficiency control of molecular diagnostic methods based on end point or real-time quantitative PCR. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  18. Evolvement law of a macroscopic traffic model accounting for density-dependent relaxation time (United States)

    Wang, Yu-Qing; Chu, Xing-Jian; Zhou, Chao-Fan; Jia, Bin; Lin, Sen; Wu, Zi-Han; Zhu, Hua-Bing; Gao, Zi-You


    In this paper, a modified macroscopic traffic flow model is presented. The term of the density-dependent relaxation time is introduced here. The relation between the relaxation time and the density in traffic flow is presented quantitatively. Besides, a factor R depicting varied properties of traffic flow in different traffic states is also introduced in the formulation of the model. Furthermore, the evolvement law of traffic flow with distinctly initial density distribution and boundary perturbations is emphasized.

  19. Study on Tensile Properties of Nanoreinforced Epoxy Polymer: Macroscopic Experiments and Nanoscale FEM Simulation Prediction


    Zhenqing Wang; Fang Liu; Wenyan Liang; Limin Zhou


    The effect of nanosilica contents on mechanical properties of the epoxy matrix with some nanoparticle aggregations was studied in macroscopic experiments and nanoscale simulation, particularly with regard to the effective modulus and ultimate stress. Three analytical models were used to obtain the effective elastic modulus of nanoparticle-reinforced composites. Based on Monte-Carlo method, the special program for the automatic generation of 2D random distribution particles without overlapping...

  20. Distribution of glutamic acid decarboxylase mRNA in the forebrain of the rainbow trout as studied by in situ hybridization. (United States)

    Anglade, I; Mazurais, D; Douard, V; Le Jossic-Corcos, C; Mañanos, E L; Michel, D; Kah, O


    By using degenerate primers designed from glutamate decarboxylase (GAD) sequences of mammals, Xenopus and Drosophila, a 270-bp cDNA fragment was cloned by reverse transcriptase-polymerase chain reaction (RT-PCR) from cerebellum total RNA of rainbow trout. This partial cDNA shows 90% identity with mammalian GAD 65 and presents the Asn-Pro-His-Lys (NPHK) sequence corresponding to the pyridoxal-binding region of porcine DOPA decarboxylase or mammalian GAD. The distribution of GAD 65 mRNA-expressing neurons in the forebrain of the trout was studied by in situ hybridization using either digoxigenin- or 35S-labeled probes. The results demonstrate that gamma-amino butyric acid (GABA) neurons are widely distributed throughout the forebrain, with a high density in the periventricular regions. In this study, we report their precise distribution in the telencephalon and diencephalon. GAD mRNA-expressing cells were particularly abundant in the preoptic region and the mediobasal hypothalamus, two major neuroendocrine and estrogen-sensitive regions in fish. The presence of GAD mRNA-expressing neurons was observed in visually related structures such as the suprachiasmatic nucleus, the pretectal region, and the thalamus. Immunohistochemistry with antibodies directed against mouse GAD failed to demonstrate the presence of immunoreactive cell bodies, but showed a very high concentration of GAD-immunoreactive fibers in many brain regions, notably in the preoptic area, hypothalamus, and neurohypophyseal digitations of the pituitary, in particular in the proximal pars distalis. These results indicate that GABA neurons are ideally placed to modulate neuroendocrine activities at the hypothalamic and pituitary levels and to participate in the processing of sensorial information.

  1. Experimental demonstration of macroscopic quantum coherence in Gaussian states

    DEFF Research Database (Denmark)

    Marquardt, C.; Andersen, Ulrik Lund; Leuchs, G.


    We witness experimentally the presence of macroscopic coherence in Gaussian quantum states using a recently proposed criterion [E. G. Cavalcanti and M. D. Reid, Phys. Rev. Lett. 97 170405 (2006)]. The macroscopic coherence stems from interference between macroscopically distinct states in phase...... space, and we prove experimentally that a coherent state contains these features with a distance in phase space of 0.51 +/- 0.02 shot noise units. This is surprising because coherent states are generally considered being at the border between classical and quantum states, not yet displaying any...

  2. Exploratory numerical experiments with a macroscopic theory of interfacial interactions (United States)

    Giordano, D.; Solano-López, P.; Donoso, J. M.


    Phenomenological theories of interfacial interactions are founded on the core idea to model macroscopically the thin layer that forms between media in contact as a two-dimensional continuum (surface phase or interface) characterised by physical properties per unit area; the temporal evolution of the latter is governed by surface balance equations whose set acts as bridging channel in between the governing equations of the volume phases. These theories have targeted terrestrial applications since long time and their exploitation has inspired our research programme to build up, on the same core idea, a macroscopic theory of gas-surface interactions targeting the complex phenomenology of hypersonic reentry flows as alternative to standard methods in aerothermodynamics based on accommodation coefficients. The objective of this paper is the description of methods employed and results achieved in the exploratory study that kicked off our research programme, that is, the unsteady heat transfer between two solids in contact in planar and cylindrical configurations with and without interface. It is a simple numerical-demonstrator test case designed to facilitate quick numerical calculations but, at the same time, to bring forth already sufficiently meaningful aspects relevant to thermal protection due to the formation of the interface. The paper begins with a brief introduction on the subject matter and a review of relevant literature within an aerothermodynamics perspective. Then the case is considered in which the interface is absent. The importance of tension (force per unit area) continuity as boundary condition on the same footing of heat-flux continuity is recognised and the role of the former in governing the establishment of the temperature-difference distribution over the separation surface is explicitly shown. Evidence is given that the standard temperature-continuity boundary condition is just a particular case. Subsequently the case in which the interface is

  3. Microscopic Simulation and Macroscopic Modeling for Thermal and Chemical Non-Equilibrium (United States)

    Liu, Yen; Panesi, Marco; Vinokur, Marcel; Clarke, Peter


    This paper deals with the accurate microscopic simulation and macroscopic modeling of extreme non-equilibrium phenomena, such as encountered during hypersonic entry into a planetary atmosphere. The state-to-state microscopic equations involving internal excitation, de-excitation, dissociation, and recombination of nitrogen molecules due to collisions with nitrogen atoms are solved time-accurately. Strategies to increase the numerical efficiency are discussed. The problem is then modeled using a few macroscopic variables. The model is based on reconstructions of the state distribution function using the maximum entropy principle. The internal energy space is subdivided into multiple groups in order to better describe the non-equilibrium gases. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients. The modeling is completely physics-based, and its accuracy depends only on the assumed expression of the state distribution function and the number of groups used. The model makes no assumption at the microscopic level, and all possible collisional and radiative processes are allowed. The model is applicable to both atoms and molecules and their ions. Several limiting cases are presented to show that the model recovers the classical twotemperature models if all states are in one group and the model reduces to the microscopic equations if each group contains only one state. Numerical examples and model validations are carried out for both the uniform and linear distributions. Results show that the original over nine thousand microscopic equations can be reduced to 2 macroscopic equations using 1 to 5 groups with excellent agreement. The computer time is decreased from 18 hours to less than 1 second.

  4. Comparison of GLUT1, GLUT3, and GLUT4 mRNA and the subcellular distribution of their proteins in normal human muscle (United States)

    Stuart, C. A.; Wen, G.; Gustafson, W. C.; Thompson, E. A.


    Basal, "insulin-independent" glucose uptake into skeletal muscle is provided by glucose transporters positioned at the plasma membrane. The relative amount of the three glucose transporters expressed in muscle has not been previously quantified. Using a combination of qualitative and quantitative ribonuclease protection assay (RPA) methods, we found in normal human muscle that GLUT1, GLUT3, and GLUT4 mRNA were expressed at 90 +/- 10, 46 +/- 4, and 156 +/- 12 copies/ng RNA, respectively. Muscle was fractionated by DNase digestion and differential sedimentation into membrane fractions enriched in plasma membranes (PM) or low-density microsomes (LDM). GLUT1 and GLUT4 proteins were distributed 57% to 67% in LDM, whereas GLUT3 protein was at least 88% in the PM-enriched fractions. These data suggest that basal glucose uptake into resting human muscle could be provided in part by each of these three isoforms.

  5. Single-Phase Bundle Flows Including Macroscopic Turbulence Model

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Jun; Yoon, Han Young [KAERI, Daejeon (Korea, Republic of); Yoon, Seok Jong; Cho, Hyoung Kyu [Seoul National University, Seoul (Korea, Republic of)


    To deal with various thermal hydraulic phenomena due to rapid change of fluid properties when an accident happens, securing mechanistic approaches as much as possible may reduce the uncertainty arising from improper applications of the experimental models. In this study, the turbulence mixing model, which is well defined in the subchannel analysis code such as VIPRE, COBRA, and MATRA by experiments, is replaced by a macroscopic k-e turbulence model, which represents the aspect of mathematical derivation. The performance of CUPID with macroscopic turbulence model is validated against several bundle experiments: CNEN 4x4 and PNL 7x7 rod bundle tests. In this study, the macroscopic k-e model has been validated for the application to subchannel analysis. It has been implemented in the CUPID code and validated against CNEN 4x4 and PNL 7x7 rod bundle tests. The results showed that the macroscopic k-e turbulence model can estimate the experiments properly.

  6. An introduction to macroscopic quantum phenomena and quantum dissipation

    CERN Document Server

    Caldeira, Amir O


    Reviewing macroscopic quantum phenomena and quantum dissipation, from the phenomenology of magnetism and superconductivity to the presentation of alternative models for quantum dissipation, this book develops the basic material necessary to understand the quantum dynamics of macroscopic variables. Macroscopic quantum phenomena are presented through several examples in magnetism and superconductivity, developed from general phenomenological approaches to each area. Dissipation naturally plays an important role in these phenomena, and therefore semi-empirical models for quantum dissipation are introduced and applied to the study of a few important quantum mechanical effects. The book also discusses the relevance of macroscopic quantum phenomena to the control of meso- or nanoscopic devices, particularly those with potential applications in quantum computation or quantum information. It is ideal for graduate students and researchers.

  7. Chaotic macroscopic phases in one-dimensional oscillators (United States)

    Politi, Antonio; Pikovsky, Arkady; Ullner, Ekkehard


    The connection between the macroscopic description of collective chaos and the underlying microscopic dynamics is thoroughly analysed in mean-field models of one-dimensional oscillators. We investigate to what extent infinitesimal perturbations of the microscopic configurations can provide information also on the stability of the corresponding macroscopic phase. In ensembles of identical one-dimensional dynamical units, it is possible to represent the microscopic configurations so as to make transparent their connection with the macroscopic world. As a result, we find evidence of an intermediate, mesoscopic, range of distances, over which the instability is neither controlled by the microscopic equations nor by the macroscopic ones. We examine a whole series of indicators, ranging from the usual microscopic Lyapunov exponents, to the collective ones, including finite-amplitude exponents. A system of pulse-coupled oscillators is also briefly reviewed as an example of non-identical phase oscillators where collective chaos spontaneously emerges.

  8. Micro- and macroscopic photonic control of matter (United States)

    Ryabtsev, Anton

    parameters. In order for measurements not to be skewed, these interactions need to be taken into account and mitigated at the time of the experiment or handled later in data analysis and simulations. Experimental results are presented in four chapters. Chapter 2 describes two topics: (1) single-shot real-time monitoring and correction of spectral phase drifts, which commonly originate from temperature and pointing fluctuations inside the laser cavity when the pulses are generated; (2) an all-optical method for controlling the dispersion of femtosecond pulses using other pulses. Chapter 3 focuses on the effects of the propagation media--how intense laser pulses modify media and how, in turn, the media modifies them back--and how these effects can be counteracted. Self-action effects in fused silica are discussed, along with some interesting and unexpected results. A method is then proposed for mitigating self-action processes using binary modulation of the spectral phases of laser pulses. Chapter 4 outlines the design of two laser systems, which are specifically tailored for particular spectroscopic applications and incorporate the comprehensive pulse control described in previous chapters. Chapter 5 shows how control of spatial beam characteristics can be applied to measurements of the mechanical motion of microscale particles and how it can potentially be applied to molecular motion. It also describes an experiment on laser-induced flow in air in which attempts were made to control the macroscopic molecular rotation of gases. My research, with a pulse shaper as the enabling tool, provides important insights into ultrafast scientific studies by making femtosecond laser research more predictable, reliable and practical for measurement and control. In the long term, some of the research methods in this thesis may help the transition of femtosecond lasers from the laboratory environment into clinics, factories, airports, and other everyday settings.

  9. The Connection between Macroscopic and Microscopic Properties in Chemical Transformations

    Directory of Open Access Journals (Sweden)

    Bolysbek Utelbaev


    Full Text Available This article examines the chemical interaction of substances and their polymorphic transformations inclusive of their microscopic and macroscopic properties. This process involves the rearrangement of the elementary particles and electronic structures of “chemical individuums” at microscopic level and the release (absorption of heat and formation of massive aggregates at macroscopic level, which form this work’s subject of discussion.

  10. Quantum Communication Using Macroscopic Phase Entangled States (United States)


    realistic requirement. vi. List of patents • Patent application # 14/508,741, “Quantum key distribution over large distances using amplifiers...and unitary transformations”, James Franson, Todd Pittman, Brian Kirby, and Garrett Hickman 8 vii. List of publications • G. Jaeger, D. S

  11. From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

    KAUST Repository

    Baker, Ruth E.


    Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is an almost ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environmental cues. In the last 20 years, a lot of attention has been devoted to connecting macroscopic PDEs with more detailed microscopic models of cellular motility, including models of directional sensing and signal transduction pathways. However, domain growth is largely omitted in the literature. In this paper, individual-based models describing cell movement and domain growth are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge by making the lattice size variable over time. A reaction-diffusion master equation formalism is generalised to the case of growing lattices and used in the derivation of the macroscopic PDEs. © 2009 Society for Mathematical Biology.

  12. Transport processes in macroscopically disordered media from mean field theory to percolation

    CERN Document Server

    Snarskii, Andrei A; Sevryukov, Vladimir A; Morozovskiy, Alexander; Malinsky, Joseph


    This book reflects on recent advances in the understanding of percolation systems to present a wide range of transport phenomena in inhomogeneous disordered systems. Further developments in the theory of macroscopically inhomogeneous media are also addressed. These developments include galvano-electric, thermoelectric, elastic properties, 1/f noise and higher current momenta, Anderson localization, and harmonic generation in composites in the vicinity of the percolation threshold. The book describes how one can find effective characteristics, such as conductivity, dielectric permittivity, magnetic permeability, with knowledge of the distribution of different components constituting an inhomogeneous medium. Considered are a wide range of recent studies dedicated to the elucidation of physical properties of macroscopically disordered systems. Aimed at researchers and advanced students, it contains a straightforward set of useful tools which will allow the reader to derive the basic physical properties of compli...

  13. Some work and some play: microscopic and macroscopic approaches to labor and leisure.

    Directory of Open Access Journals (Sweden)

    Ritwik K Niyogi


    Full Text Available Given the option, humans and other animals elect to distribute their time between work and leisure, rather than choosing all of one and none of the other. Traditional accounts of partial allocation have characterised behavior on a macroscopic timescale, reporting and studying the mean times spent in work or leisure. However, averaging over the more microscopic processes that govern choices is known to pose tricky theoretical problems, and also eschews any possibility of direct contact with the neural computations involved. We develop a microscopic framework, formalized as a semi-Markov decision process with possibly stochastic choices, in which subjects approximately maximise their expected returns by making momentary commitments to one or other activity. We show macroscopic utilities that arise from microscopic ones, and demonstrate how facets such as imperfect substitutability can arise in a more straightforward microscopic manner.

  14. A screen in mice uncovers repression of lipoprotein lipase by microRNA-29a as a mechanism for lipid distribution away from the liver. (United States)

    Mattis, Aras N; Song, Guisheng; Hitchner, Kelly; Kim, Roy Y; Lee, Andrew Y; Sharma, Amar D; Malato, Yann; McManus, Michael T; Esau, Christine C; Koller, Erich; Koliwad, Suneil; Lim, Lee P; Maher, Jacquelyn J; Raffai, Robert L; Willenbring, Holger


    Identification of microRNAs (miRNAs) that regulate lipid metabolism is important to advance the understanding and treatment of some of the most common human diseases. In the liver, a few key miRNAs have been reported that regulate lipid metabolism, but since many genes contribute to hepatic lipid metabolism, we hypothesized that other such miRNAs exist. To identify genes repressed by miRNAs in mature hepatocytes in vivo, we injected adult mice carrying floxed Dicer1 alleles with an adenoassociated viral vector expressing Cre recombinase specifically in hepatocytes. By inactivating Dicer in adult quiescent hepatocytes we avoided the hepatocyte injury and regeneration observed in previous mouse models of global miRNA deficiency in hepatocytes. Next, we combined gene and miRNA expression profiling to identify candidate gene/miRNA interactions involved in hepatic lipid metabolism and validated their function in vivo using antisense oligonucleotides. A candidate gene that emerged from our screen was lipoprotein lipase (Lpl), which encodes an enzyme that facilitates cellular uptake of lipids from the circulation. Unlike in energy-dependent cells like myocytes, LPL is normally repressed in adult hepatocytes. We identified miR-29a as the miRNA responsible for repressing LPL in hepatocytes, and found that decreasing hepatic miR-29a levels causes lipids to accumulate in mouse livers. Our screen suggests several new miRNAs are regulators of hepatic lipid metabolism. We show that one of these, miR-29a, contributes to physiological lipid distribution away from the liver and protects hepatocytes from steatosis. Our results, together with miR-29a's known antifibrotic effect, suggest miR-29a is a therapeutic target in fatty liver disease. © 2014 by the American Association for the Study of Liver Diseases.

  15. Macroscopic domain formation during cooling in the platelet plasma membrane: an issue of low cholesterol content. (United States)

    Bali, Rachna; Savino, Laura; Ramirez, Diego A; Tsvetkova, Nelly M; Bagatolli, Luis; Tablin, Fern; Crowe, John H; Leidy, Chad


    There has been ample debate on whether cell membranes can present macroscopic lipid domains as predicted by three-component phase diagrams obtained by fluorescence microscopy. Several groups have argued that membrane proteins and interactions with the cytoskeleton inhibit the formation of large domains. In contrast, some polarizable cells do show large regions with qualitative differences in lipid fluidity. It is important to ask more precisely, based on the current phase diagrams, under what conditions would large domains be expected to form in cells. In this work we study the thermotropic phase behavior of the platelet plasma membrane by FTIR, and compare it to a POPC/Sphingomyelin/Cholesterol model representing the outer leaflet composition. We find that this model closely reflects the platelet phase behavior. Previous work has shown that the platelet plasma membrane presents inhomogeneous distribution of DiI18:0 at 24 degrees C, but not at 37 degrees C, which suggests the formation of macroscopic lipid domains at low temperatures. We show by fluorescence microscopy, and by comparison with published phase diagrams, that the outer leaflet model system enters the macroscopic domain region only at the lower temperature. In addition, the low cholesterol content in platelets ( approximately 15 mol%), appears to be crucial for the formation of large domains during cooling.

  16. [Macroscopic and microscopic identification of Chinese herb belonging to genus Senecio]. (United States)

    Yang, Xue-Jing; Yang, Li; Xu, Hong; Zhang, Mian; Wang, Zheng-Tao


    The medicinal herbs derived from genus Senecio have been commonly used in Chinese medicine and triggered attention in recent decades for that they contain the hepatotoxic pyrrolizidine alkaloids. Therefore the botanical pharmacognostic study to authenticate those herbs based on their macroscopic and microscopic characteristics is important for the assurance of safety when they are applied as raw material for extracts or for finished products. In this paper, 13 taxa (11 species and 2 varieties) of Senecio plants were collected and their macroscopic and microscopic characteristics were observed and described by digital microscopic illustration. The results showed that the distribution of collenchyma in the cortex, the level of development for pericycle, the location of the phloem, and the ratio of pith in transverse sections of the stems, and the morphology of the leaf epidermal cells, the stomatal types and the non-glandular hairs in leaf surface view were found to be the main microscopic characteristics for authentication of different Senecio species. The herbs derived from genus Senecio can be distinguished from each other on the basis of their macroscopic and microscopic characteristics, and those observation can be used for the identification of commercial crude drugs from Senecio plants.

  17. Correlation of Structural and Macroscopic Properties of Starches with Their Tabletability Using the SM(2) Approach. (United States)

    Dave, Vivek S; Chanda, Monica; Sayles, Matt; Popielarczyk, Michael; Boyce, Heather; Bompelliwar, Sai Krishna; Bates, Simon; Morris, Ken R; Haware, Rahul V


    The effects of PURE-DENT® and SPRESS® starch properties on their compression behavior was characterized using "SM(2) " approach (structural properties, macroscopic properties, and multivariate analysis). Moisture sorption rate constants, moisture content, amylose and amylopectin degradation enthalpy, percent crystallinity, amylose-amylopectin ratio, and cross-linking degree were used to profile starch structural properties. Particle density, particle size distribution, and Heckel compression descriptors [yield pressure (YP) of plastic deformation, and elastic recovery] were used as macroscopic descriptors. The structural and macroscopic properties were correlated qualitatively [principal component analysis (PCA)] and quantitatively [standard least square regression (SLSR)] with the tablet mechanical strength (TMS). These analyses revealed that the differences correlated with amylose-amylopectin content, particle density, compression mechanisms, and TMS between the starch grades. Univariate analysis proved lacking; however, PCA identified the particle size, moisture content, percent crystallinity, amylose-amylopectin ratio, and YP of plastic deformation and elastic recovery as the main factors influencing the starch TMS. SLSR quantified the positive influence of Fourier transform infrared spectra absorbance ratio at 1022-1003 and YP of the immediate elastic recovery, and the negative contribution of amylopectin content on the TMS. Therefore, starch amylose and amylopectin content, crystallinity, and lower elastic recovery are mainly responsible for better TMS. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

  18. Fibrous random materials: From microstructure to macroscopic properties (United States)

    Yazdchi, K.; Luding, S.


    Fibrous porous materials are involved in a wide range of applications including composite materials, fuel cells, heat exchangers and (biological)filters. Fluid flow through these materials plays an important role in many engineering applications and processes, such as textiles and paper manufacturing or transport of (under)ground water and pollutants. While most porous materials have complex geometry, some can be seen as two-dimensional particulate/fibrous systems, in which we introduce several microscopic quantities, based on Voronoi and Delaunay tessellations, to characterize their microstructure. In particular, by analyzing the topological properties of Voronoi polygons, we observe a smooth transition from disorder to order, for increasing packing fraction. Using fully resolved finite element (FE) simulations of Newtonian, incompressible fluid flow perpendicular to the fibres, the macroscopic permeability is calculated in creeping flow regimes. The effect of fibre arrangement and local crystalline regions on the macroscopic permeability is discussed and the macroscopic property is linked to the microscopic structural quantities.

  19. Graphene chiral liquid crystals and macroscopic assembled fibres (United States)

    Xu, Zhen; Gao, Chao


    Chirality and liquid crystals are both widely expressed in nature and biology. Helical assembly of mesophasic molecules and colloids may produce intriguing chiral liquid crystals. To date, chiral liquid crystals of 2D colloids have not been explored. As a typical 2D colloid, graphene is now receiving unprecedented attention. However, making macroscopic graphene fibres is hindered by the poor dispersibility of graphene and by the lack of an assembly method. Here we report that soluble, chemically oxidized graphene or graphene oxide sheets can form chiral liquid crystals in a twist-grain-boundary phase-like model with simultaneous lamellar ordering and long-range helical frustrations. Aqueous graphene oxide liquid crystals were continuously spun into metres of macroscopic graphene oxide fibres; subsequent chemical reduction gave the first macroscopic neat graphene fibres with high conductivity and good mechanical performance. The flexible, strong graphene fibres were knitted into designed patterns and into directionally conductive textiles.

  20. [Studies on macroscopic and microscopic characteristics of Ophiocordyceps xuefengensis]. (United States)

    Liu, Hao; Zhen, Lan-ping; Zhu, Ru-cai; Zhang, Shui-han; Huang, Hui-yong


    The macroscopic characteristics, tissue, caterpillar body wall and powder of Ophiocordyceps xuefengensis in different batch numbers were observed and researched by the macroscopic and microscopic identification methods. The result shows that the morphology, size, abdominal annulations of caterpillar, etc. of 0. xuefengensis are the macroscopic identification characteristics, the caterpillar body surface mycelium, body wall sculpture and crochets on abdominal legs are the microscopic identification characteristics. These characters are stable and regular discriminant features, which are proved to be the identification basis of O. xuefengensis. In addition, The characters such as crochets on abdominal legs arrange in two parallel ellipse rings, the inner crochets are long strip, and the external toes are unciform, are specific.

  1. Microscopic-Macroscopic Mass Calculations with Wigner-Kirkwood expansion

    Energy Technology Data Exchange (ETDEWEB)

    Bhagwat, A [UM-DAE Centre for Excellence in Basic Sciences, Mumbai 400 098 (India); Vinas, X; Centelles, M [Departament d' Estructura i Constituents de la Materia and Institut de Ciencies del Cosmos, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Wyss, R [KTH (Royal Institute of Technology), Alba Nova University Center, Department of Nuclear Physics, S-10691 Stockholm (Sweden); Schuck, P, E-mail: [Institut de Physique Nucleaire, IN2P3-CNRS, Universite Paris-Sud, F-91406 Orsay Cedex (France)


    The systematic study and calculation of ground state nuclear masses continues to be one of the active and important areas of research in nuclear physics. The present work is an attempt to determine the ground state masses of nuclei spanning the entire periodic table, using the Microscopic-Macroscopic approach. The semi-classical Wigner-Kirkwood (WK) h expansion method is used to calculate shell corrections for spherical and deformed nuclei. The expansion is achieved upto the fourth order in h. The shell corrections, along with the pairing energies obtained by using the Lipkin-Nogami scheme, constitute the microscopic part of the nuclear masses. The macroscopic part is obtained from a liquid drop formula with six adjustable parameters. It is shown that the Microscopic-Macroscopic mass calculation thus achieved, yields reliable description of ground state masses of nuclei across the periodic table. The present status of the WK mass calculations and the possible future perspectives are discussed.

  2. A microfluidics approach to the problem of creating separate solution environments accessible from macroscopic volumes. (United States)

    Olofsson, Jessica; Pihl, Johan; Sinclair, Jon; Sahlin, Eskil; Karlsson, Mattias; Orwar, Owe


    We report on a microfluidic device that generates separate solution environments in macroscopic volumes. Spatially distinct patterns are created by emitting fluids from 16 different sources (closely spaced microchannels) into a solution-filled macroscopic chamber. The fluid in neighboring microchannels couples viscously in the macroscopic container, generating one single interdigitated stream. Scanning nanoelectrode amperometry was used for characterizing the concentration landscape and the diffusion zones between solutions running in parallel at different coordinates in the stream. These experiments were complemented by finite element simulations of the Navier-Stokes and mass transport equations to describe the velocity distributions and the diffusion behavior. For in channel flow velocities of 50 mm.s(-1), patterns could persist on the order of millimeters to centimeters in the open volume. The most narrow diffusion zones with widths less than 10 microm (5-95% concentration change) were found some tens of micrometers out in the macroscopic container. We demonstrate that a 14-microm-diameter nearly spherical object (biological cell) attached to a micropipet can be moved from one solution environment to another by a lateral displacement of only 8 microm. The device is suitable for applications where the solution environment around a microscopic or nanoscopic sensor needs to be changed multiple times, i.e., in order to build layered structures, for obtaining binding isotherms, and kinetic information, for example, on ion channels, enzymes, and receptors as well as in applications where different loci on an object need to be exposed to different environments or where complex solution environments need to be created for studies of interfacial chemistry between two streaming layers. Copyright 2004 American Chemical Society

  3. Macroscopic violation of the law of heat conduction (United States)

    Cândido, Michael M.; Morgado, Welles A. M.; Duarte Queirós, Sílvio M.


    We analyze a model describing an anharmonic macroscopic chain in contact with general reservoirs that follow the Lévy-Itô theorem on the Gaussian-Poissonian decomposition of the measure. We do so by considering a perturbative approach to compute the heat flux and the (canonical) temperature profile when the system reaches the steady state. This approach allows observing a macroscopic violation of the law of the heat conduction equivalent to that found for small (N =2 ) systems in contact with general reservoirs, which conveys the ascendency of the nature of the reservoirs over the size of the system.

  4. Macroscopic and radiographic examination of proximal root surface caries

    Energy Technology Data Exchange (ETDEWEB)

    Nordenram, G.; Bergvist, A.; Johnson, G.; Henriksen, C.O.; Anneroth, G.


    The purpose of the study was to compare macroscopic and radiographic examination of proximal root surface caries of extracted teeth from patients aged 65-95 years. Although the study conditions for macroscopic and radiographic diagnosis favored more sensitive evaluations than routine clinical conditions, there was a 24% disagreement in diagnosis. This finding indicates that under routine clinical conditions it is difficult to register with certainty all superficial root carious lesions. Even in the absence of clinically detectable root surface caries, preventive measures should be considered for elderly people with exposed root surfaces.

  5. Relaxin family peptide receptors Rxfp1 and Rxfp2: mapping of the mRNA and protein distribution in the reproductive tract of the male rat

    Directory of Open Access Journals (Sweden)

    Porto Catarina S


    Full Text Available Abstract Background Relaxin is the endogenous ligand of the G-protein coupled receptor RXFP1, previously known as LGR7. In humans relaxin can also activate, but with lower affinity, the closely related receptor for the insulin-like peptide from Leydig cells, RXFP2, previously known as LGR8. The lack of relaxin impairs male fertility but the precise distribution and the function of relaxin receptors in the male reproductive tract is not known. We investigated the distribution of Rxfp1 and Rxfp2 in the reproductive tract of the male rat and the function of relaxin in the vas deferens, a tissue with high expression of both receptors. Methods The presence of mRNA for Rxfp1 and Rxfp2 was investigated in testes, cultured Sertoli cells, epididymis, vas deferens, seminal vesicle, prostate, and spermatozoa by RT-PCR and Southern blot. Protein expression in the testis, vas deferens, primary culture of Sertoli cells, and spermatozoa was assessed by immunohistochemistry and immunofluorescence. The role of relaxin in the vas deferens was evaluated by contractility studies and radioimmunoassay of cAMP production. The effect of relaxin on mRNA levels for metalloproteinase-7 was measured by Northern blot. Results Transcripts for Rxfp1 and Rxfp2 were present in almost all parts of the male reproductive tract, with high levels in testis and vas deferens. Both receptors were immunolocalized in late stage germ cells but not in mature spermatozoa, although mRNAs for both receptors were also present in mature spermatozoa. Rxfp1 but not Rxfp2 was detected in cultured Sertoli cells. Strong immunostaining for Rxfp1 and Rxfp2 was seen in muscular and epithelial layers of the vas deferens and in arteriolar walls. Relaxin did not affect contractility and cyclic AMP production of the vas deferens, but increased the levels of mRNA for metalloproteinase-7. Conclusion Rxfp1 and Rxfp2 are widely and similarly distributed throughout the male reproductive tract. Our results

  6. Restricted distribution of mrg-1 mRNA in C. elegans primordial germ cells through germ granule-independent regulation. (United States)

    Miwa, Takashi; Takasaki, Teruaki; Inoue, Kunio; Sakamoto, Hiroshi


    The chromodomain protein MRG-1 is an essential maternal factor for proper germline development that protects germ cells from cell death in C. elegans. Unlike germ granules, which are exclusively segregated to the germline blastomeres at each cell division from the first cleavage of the embryo, MRG-1 is abundant in all cells in early embryos and is then gradually restricted to the primordial germ cells (PGCs) by the morphogenesis stage. Here, we show that this characteristic spatiotemporal expression pattern is dictated by the mrg-1 3'UTR and is differentially regulated at the RNA level between germline and somatic cells. Asymmetric segregation of germ granules is not necessary to localize MRG-1 to the PGCs. We found that MES-4, an essential chromatin regulator in germ cells, also accumulates in the PGCs in a germ granule-independent manner. We propose that C.elegans PGCs have a novel mechanism to accumulate at least some chromatin-associated proteins that are essential for germline immortality. © 2015 The Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  7. Macroscopic and microscopic changes in the fallopian tube after ...

    African Journals Online (AJOL)

    A total of 43 patients who had undergone laparoscopic tubal occl usion by means of bipolar cauterization underwent bilateral salpingectomy 6- 30 months later. The macroscopic and microscopic changes in the fallopian tubes are described. Although 35 patients appeared to have occluded tubes on macro-scopic ...

  8. Vascular flora and macroscopic fauna on the Fernow Experimental Forest (United States)

    Darlene M. Madarish; Jane L. Rodrigue; Mary Beth Adams


    This report is the first comprehensive inventory of the vascular flora and macroscopic fauna known to occur within the Fernow Experimental Forest in north-central West Virignia. The compendium is based on information obtained from previous surveys, current research, and the personal observations of USDA Forest Service personnel and independent scientists. More than 750...

  9. Charge of a macroscopic particle in a plasma sheath. (United States)

    Samarian, A A; Vladimirov, S V


    Charging of a macroscopic body levitating in a rf plasma sheath is studied experimentally and theoretically. The nonlinear charge vs size dependence is obtained. The observed nonlinearity is explained on the basis of an approach taking into account different plasma conditions for the levitation positions of different particles. The importance of suprathermal electrons' contribution to the charging process is demonstrated.

  10. Macroscopic model of geomagnetic-radiation from air showers

    NARCIS (Netherlands)

    Scholten, Olaf; Werner, Klaus


    We have developed a macroscopic description of coherent electro-magnetic radiation from air showers initiated by ultra-high energy cosmic rays in the presence of the geomagnetic field. This description offers a simple and direct insight in the relation between the properties of the air shower and

  11. Prevalence of characteristic macroscopic lung pathologies in pigs at ...

    African Journals Online (AJOL)

    Considering the importance of pork in daily nutrition and livelihood of the people, the relatively large pig population in Benue State, coupled with others from neighbouring states, this cross-sectional study was aimed at estimating the prevalence of definable macroscopic lung lesions in pigs slaughtered in Makurdi. Lesions ...

  12. Microscopic derivation of macroscopic Van der Waals forces

    NARCIS (Netherlands)

    Renne, M.J.; Nijboer, B.R.A.


    For a general system of isotropic harmonic oscillators with non-retarded dipole interaction a formula for the interatomic forces is derived. It is used to give an atomistic derivation of macroscopic Van der Waals forces in terms of the dielectric constant.

  13. Stereodynamics: From elementary processes to macroscopic chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Kasai, Toshio [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Graduate School of Science, Department of Chemistry, Osaka University, Toyonaka, 560-0043 Osaka (Japan); Che, Dock-Chil [Graduate School of Science, Department of Chemistry, Osaka University, Toyonaka, 560-0043 Osaka (Japan); Tsai, Po-Yu [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Lin, King-Chuen [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Palazzetti, Federico [Scuola Normale Superiore, Pisa (Italy); Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Aquilanti, Vincenzo [Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Roma (Italy); Instituto de Fisica, Universidade Federal da Bahia, Salvador (Brazil)


    This paper aims at discussing new facets on stereodynamical behaviors in chemical reactions, i.e. the effects of molecular orientation and alignment on reactive processes. Further topics on macroscopic processes involving deviations from Arrhenius behavior in the temperature dependence of chemical reactions and chirality effects in collisions are also discussed.

  14. Macroscopic quantum dynamics of pi-junction with ferromagnetic insulators

    NARCIS (Netherlands)

    Kawabata, S.; Kawabata, Shiro; Kashiwaya, Satoshi; Asano, Yasuhiro; Tanaka, Yukio; Golubov, Alexandre Avraamovitch


    We theoretically investigate the macroscopic quantum dynamics of a π junction with a superconductor (S) and a multiferroic material or a ferromagnetic insulator (FI). By deriving the effective action from a microscopic Hamiltonian, a π-junction qubit (a S-FI-S superconducting quantum interference

  15. Microcracking and macroscopic failure in intermetallic titanium aluminides; Mikrorissbildung und makroskopisches Versagen in intermetallischen Titanaluminiden

    Energy Technology Data Exchange (ETDEWEB)

    Wiesand-Valk, B. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Werkstofforschung


    This paper deals with the correlations between microstructural disorder, that means statistical distribution of phases and local material properties, and macroscopic failure of disordered multiphase materials. On a microscopic level the microstructural disorder leads to randomly distributed local damage before failure (in brittle materials to microcracks) and eventually to localisation of damage. On a macroscopic level the value and scatter of fracture strength and its dependence on specimen size are essentially determined by the microstructural disorder. The failure behaviour is treated by using the discrete chain-of-bundles-model, which treats the details of the microstructure not explicitly but as locally distributed fluctuations of characteristical material parameters. The model has been verified by comparing with experimental results for four intermetallic titanium aluminides and its validity has been demonstrated. (orig.) [German] Die Arbeit behandelt die Zusammenhaenge zwischen der Stochastizitaet des Gefueges, das heisst, einer statistischen Verteilung von Phasen und lokalen Materialeigenschaften und dem makroskopischen Versagen von ungeordneten mehrphasigen Werkstoffen. Auf mikroskopischer Ebene fuehrt die Stochastizitaet des Gefueges vor dem Versagen zu lokalen Schaedigungen (in sproeden Werkstoffen zu Mikrorissen) und schliesslich (abhaengig vom Grad der Unordnung) zur Lokalisierung des Bruchgeschehens. Makroskopisch werden die Groesse und Streuung von Bruchfestigkeitswerten und ihre Probengroessenabhaengigkeit durch die mikrostrukturelle Unordnung wesentlich bestimmt. Dieses Versagensverhalten wird in dem diskreten Chain-of-Bundles-Modell beschrieben, das die Details der Mikrostruktur nicht explizit sondern als lokale statistische Schwankungen von charakteristischen Werkstoffparametern erfasst. Am Beispiel von vier ausgewaehlten Titan-Aluminiden wird das Modell validiert und verifiziert. (orig.)

  16. RNA topology


    Frank-Kamenetskii, Maxim D.


    A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.

  17. Macroscopic quantum phenomena from the large N perspective

    Energy Technology Data Exchange (ETDEWEB)

    Chou, C H [department of Physics, National Cheng Kung University, Tainan, Taiwan 701 (China) and National Center for Theoretical Sciences (South), Tainan, Taiwan 701 (China); Hu, B L; Subasi, Y, E-mail: [Joint Quantum Institute and Maryland Center for Fundamental Physics, University of Maryland, College Park, Maryland 20742 (United States)


    Macroscopic quantum phenomena (MQP) is a relatively new research venue, with exciting ongoing experiments and bright prospects, yet with surprisingly little theoretical activity. What makes MQP intellectually stimulating is because it is counterpoised against the traditional view that macroscopic means classical. This simplistic and hitherto rarely challenged view need be scrutinized anew, perhaps with much of the conventional wisdoms repealed. In this series of papers we report on a systematic investigation into some key foundational issues of MQP, with the hope of constructing a viable theoretical framework for this new endeavour. The three major themes discussed in these three essays are the large N expansion, the correlation hierarchy and quantum entanglement for systems of 'large' sizes, with many components or degrees of freedom. In this paper we use different theories in a variety of contexts to examine the conditions or criteria whereby a macroscopic quantum system may take on classical attributes, and, more interestingly, that it keeps some of its quantum features. The theories we consider here are, the O(N) quantum mechanical model, semiclassical stochastic gravity and gauge / string theories; the contexts include that of a 'quantum roll' in inflationary cosmology, entropy generation in quantum Vlasov equation for plasmas, the leading order and next-to-leading order large N behaviour, and hydrodynamic / thermodynamic limits. The criteria for classicality in our consideration include the use of uncertainty relations, the correlation between classical canonical variables, randomization of quantum phase, environment-induced decoherence, decoherent history of hydrodynamic variables, etc. All this exercise is to ask only one simple question: Is it really so surprising that quantum features can appear in macroscopic objects? By examining different representative systems where detailed theoretical analysis has been carried out, we find that

  18. On monogamy of non-locality and macroscopic averages: examples and preliminary results

    Directory of Open Access Journals (Sweden)

    Rui Soares Barbosa


    Full Text Available We explore a connection between monogamy of non-locality and a weak macroscopic locality condition: the locality of the average behaviour. These are revealed by our analysis as being two sides of the same coin. Moreover, we exhibit a structural reason for both in the case of Bell-type multipartite scenarios, shedding light on but also generalising the results in the literature [Ramanathan et al., Phys. Rev. Lett. 107, 060405 (2001; Pawlowski & Brukner, Phys. Rev. Lett. 102, 030403 (2009]. More specifically, we show that, provided the number of particles in each site is large enough compared to the number of allowed measurement settings, and whatever the microscopic state of the system, the macroscopic average behaviour is local realistic, or equivalently, general multipartite monogamy relations hold. This result relies on a classical mathematical theorem by Vorob'ev [Theory Probab. Appl. 7(2, 147-163 (1962] about extending compatible families of probability distributions defined on the faces of a simplicial complex – in the language of the sheaf-theoretic framework of Abramsky & Brandenburger [New J. Phys. 13, 113036 (2011], such families correspond to no-signalling empirical models, and the existence of an extension corresponds to locality or non-contextuality. Since Vorob'ev's theorem depends solely on the structure of the simplicial complex, which encodes the compatibility of the measurements, and not on the specific probability distributions (i.e. the empirical models, our result about monogamy relations and locality of macroscopic averages holds not just for quantum theory, but for any empirical model satisfying the no-signalling condition. In this extended abstract, we illustrate our approach by working out a couple of examples, which convey the intuition behind our analysis while keeping the discussion at an elementary level.

  19. Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales (United States)

    Huang, Shiping


    The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

  20. A novel pathway of TEF regulation mediated by microRNA-125b contributes to the control of actin distribution and cell shape in fibroblasts.

    Directory of Open Access Journals (Sweden)

    Olga Gutierrez

    Full Text Available BACKGROUND: Thyrotroph embryonic factor (TEF, a member of the PAR bZIP family of transcriptional regulators, has been involved in neurotransmitter homeostasis, amino acid metabolism, and regulation of apoptotic proteins. In spite of its relevance, nothing is known about the regulation of TEF. PRINCIPAL FINDINGS: p53-dependent genotoxic agents have been shown to be much more harmful for PAR bZIP-deficient mice as compared to wild type animals. Here we demonstrate that TEF expression is controlled by p53 through upregulation of microRNA-125b, as determined by both regulating the activity of p53 and transfecting cells with microRNA-125b precursors. We also describe a novel role for TEF in controlling actin distribution and cell shape in mouse fibroblasts. Lack of TEF is accompanied by dramatic increase of cell area and decrease of elongation (bipolarity and dispersion (multipolarity. Staining of actin cytoskeleton also showed that TEF (-/- cells are characterized by appearance of circumferential actin bundles and disappearance of straight fibers. Interestingly, transfection of TEF (-/- fibroblasts with TEF induced a wild type-like phenotype. Consistent with our previous findings, transfection of wild type fibroblasts with miR-125b promoted a TEF (-/--like phenotype, and a similar but weaker effect was observed following exogenous expression of p53. CONCLUSIONS/SIGNIFICANCE: These findings provide the first evidence of TEF regulation, through a miR-125b-mediated pathway, and describes a novel role of TEF in the maintenance of cell shape in fibroblasts.

  1. Diagnosis of bladder tumours in patients with macroscopic haematuria

    DEFF Research Database (Denmark)

    Gandrup, Karen L; Løgager, Vibeke B; Bretlau, Thomas


    OBJECTIVE: The aim of this study was to compare split-bolus computed tomography urography (CTU), magnetic resonance urography (MRU) and flexible cystoscopy in patients with macroscopic haematuria regarding the diagnosis of bladder tumours. MATERIALS AND METHODS: In this prospective study, 150...... patients underwent CTU, MRU and flexible cystoscopy. Two uroradiologists individually reviewed the images without any clinical information, using a questionnaire. Patient records and pathology reports were also reviewed. RESULTS: At flexible cystoscopy, MRU and CTU, 32, 19 and 15 bladder lesions were...... of bladder tumours, compared with histopathology, was reported in seven CTUs and nine MRUs, whereas the number of false-negative findings was five for CTUs and three for MRUs. CONCLUSIONS: Split-bolus CTU or MRU cannot replace cystoscopy in cases of macroscopic haematuria. MRU has a higher sensitivity than...

  2. Macroscopic quantum coherence and mechanical squeezing of a graphene sheet (United States)

    Li, Xiyun; Nie, Wenjie; Chen, Aixi; Lan, Yueheng


    We theoretically investigate the macroscopic quantum coherence and the mechanical squeezing of a mechanical oscillator in a hybrid optomechanical system consisting of a suspended graphene sheet and an ultracold atomic ensemble trapped inside a Fabry-Pérot cavity. In the study the vacuum is used to mediate an effective optomechanical coupling between the graphene oscillator and the cavity field driven by an external laser beam. We find that in the presence of this coupling, the macroscopic quantum coherence and the mechanical squeezing of the graphene sheet can be attained in a certain range of driving power. In particular, the quantum coherence in the optomechanical system can be transferred from the optical field to the mechanical oscillator. We also investigate in detail the spectrum and the squeezing of the output field and the attained results may be used to study the mechanical squeezing of a graphene sheet.

  3. Wave speeds in the macroscopic extended model for ultrarelativistic gases

    Energy Technology Data Exchange (ETDEWEB)

    Borghero, F., E-mail: [Dip. Matematica e Informatica, Università di Cagliari, Via Ospedale 72, 09124 Cagliari (Italy); Demontis, F., E-mail: [Dip. Matematica, Università di Cagliari, Viale Merello 92, 09123 Cagliari (Italy); Pennisi, S., E-mail: [Dip. Matematica, Università di Cagliari, Via Ospedale 72, 09124 Cagliari (Italy)


    Equations determining wave speeds for a model of ultrarelativistic gases are investigated. This model is already present in literature; it deals with an arbitrary number of moments and it was proposed in the context of exact macroscopic approaches in Extended Thermodynamics. We find these results: the whole system for the determination of the wave speeds can be divided into independent subsystems which are expressed by linear combinations, through scalar coefficients, of tensors all of the same order; some wave speeds, but not all of them, are expressed by square roots of rational numbers; finally, we prove that these wave speeds for the macroscopic model are the same of those furnished by the kinetic model.

  4. Hydrodynamic dispersion in porous media with macroscopic disorder of parameters (United States)

    Goldobin, D. S.; Maryshev, B. S.


    We present an analytical derivation of the macroscopic hydrodynamic dispersion for flows in porous media with frozen disorder of macroscopic parameters: porosity and permeability. The parameter inhomogeneities generate inhomogeneities of filtration flow which perform fluid mixing and, on the large spacial scale, act as an additional effective diffusion (eddy diffusivity or hydrodynamic dispersion). The derivation is performed for the general case, where the only restrictions are (i) the spatial autocorrelation functions of parameter inhomogeneities decay with the distance r not slower than 1/rn with n > 1, and (ii) the amplitudes of inhomogeneities are small compared to the mean value of parameters. Our analytical findings are confirmed with the results of direct numerical simulation for the transport of a passive scalar in inhomogeneous filtration flow.

  5. Extension of Seismic Scanning Tunneling Macroscope to Elastic Waves

    KAUST Repository

    Tarhini, Ahmad


    The theory for the seismic scanning tunneling macroscope is extended from acoustic body waves to elastic body-wave propagation. We show that, similar to the acoustic case, near-field superresolution imaging from elastic body waves results from the O(1/R) term, where R is the distance between the source and near-field scatterer. The higher-order contributions R−n for n>1 are cancelled in the near-field region for a point source with normal stress.

  6. Some critical remarks to Landau's (macroscopic) phase transitions theory

    CERN Document Server

    Iurato, A G


    Let put to the general attentions, the existence of a particular formal model (drew from Theoretical Astronomy) the thermodynamical phenomenology of which, shows a possible second order phase transition (in the sense of macroscopic Thermodynamical Theory of Landau) that seems do not check the (Birman-Goldrich-Jaric) ''chain subduction criterion'' and the (Ascher's) ''maximality criterion'' of the Landau's Phenomenological Theory. Afterwards, in particular, it follows that Landau's Phenomenological Theory is much restrictive than the Landau's Thermodynamical Theory.

  7. Toward a superconducting quantum computer. Harnessing macroscopic quantum coherence. (United States)

    Tsai, Jaw-Shen


    Intensive research on the construction of superconducting quantum computers has produced numerous important achievements. The quantum bit (qubit), based on the Josephson junction, is at the heart of this research. This macroscopic system has the ability to control quantum coherence. This article reviews the current state of quantum computing as well as its history, and discusses its future. Although progress has been rapid, the field remains beset with unsolved issues, and there are still many new research opportunities open to physicists and engineers.

  8. Macroscopic travel time reliability diagrams for freeway networks


    Tu, H.; Li, H.; Van Lint, J.W.C.; Knoop, V.L.; Sun, L.


    Travel time reliability is considered to be one of the key indicators of transport system performance. Knowledge of the mechanisms of travel time unreliability enables the derivation of explanatory models with which travel time reliability can be predicted and utilized in traffic management. Inspired by the macroscopic fundamental diagram (MFD), describing the relationship between production (average flow completing the trips) and vehicle accumulation (average density) in a traffic network, t...

  9. Extension of Seismic Scanning Tunneling Macroscope to Elastic Waves (United States)

    Tarhini, Ahmad; Guo, Bowen; Dutta, Gaurav; Schuster, Gerard T.


    The theory for the seismic scanning tunneling macroscope is extended from acoustic body waves to elastic body-wave propagation. We show that, similar to the acoustic case, near-field superresolution imaging from elastic body waves results from the O(1/R) term, where R is the distance between the source and near-field scatterer. The higher-order contributions R^{-n} for n>1 are cancelled in the near-field region for a point source with normal stress.

  10. Probing High Frequency Noise with Macroscopic Resonant Tunneling


    Lanting, T.; Amin, M. H. S.; Johnson, M. W.; Altomare, F.; Berkley, A. J.; Gildert, S.; Harris, R; Johansson, J; Bunyk, P.; Ladizinsky, E.; Tolkacheva, E.; Averin, D. V.


    We have developed a method for extracting the high-frequency noise spectral density of an rf-SQUID flux qubit from macroscopic resonant tunneling (MRT) rate measurements. The extracted noise spectral density is consistent with that of an ohmic environment up to frequencies ~ 4 GHz. We have also derived an expression for the MRT lineshape expected for a noise spectral density consisting of such a broadband ohmic component and an additional strongly peaked low-frequency component. This hybrid m...

  11. Stochastic and Macroscopic Thermodynamics of Strongly Coupled Systems

    Directory of Open Access Journals (Sweden)

    Christopher Jarzynski


    Full Text Available We develop a thermodynamic framework that describes a classical system of interest S that is strongly coupled to its thermal environment E. Within this framework, seven key thermodynamic quantities—internal energy, entropy, volume, enthalpy, Gibbs free energy, heat, and work—are defined microscopically. These quantities obey thermodynamic relations including both the first and second law, and they satisfy nonequilibrium fluctuation theorems. We additionally impose a macroscopic consistency condition: When S is large, the quantities defined within our framework scale up to their macroscopic counterparts. By satisfying this condition, we demonstrate that a unifying framework can be developed, which encompasses both stochastic thermodynamics at one end, and macroscopic thermodynamics at the other. A central element in our approach is a thermodynamic definition of the volume of the system of interest, which converges to the usual geometric definition when S is large. We also sketch an alternative framework that satisfies the same consistency conditions. The dynamics of the system and environment are modeled using Hamilton’s equations in the full phase space.

  12. Macroscopic phase-resetting curves for spiking neural networks (United States)

    Dumont, Grégory; Ermentrout, G. Bard; Gutkin, Boris


    The study of brain rhythms is an open-ended, and challenging, subject of interest in neuroscience. One of the best tools for the understanding of oscillations at the single neuron level is the phase-resetting curve (PRC). Synchronization in networks of neurons, effects of noise on the rhythms, effects of transient stimuli on the ongoing rhythmic activity, and many other features can be understood by the PRC. However, most macroscopic brain rhythms are generated by large populations of neurons, and so far it has been unclear how the PRC formulation can be extended to these more common rhythms. In this paper, we describe a framework to determine a macroscopic PRC (mPRC) for a network of spiking excitatory and inhibitory neurons that generate a macroscopic rhythm. We take advantage of a thermodynamic approach combined with a reduction method to simplify the network description to a small number of ordinary differential equations. From this simplified but exact reduction, we can compute the mPRC via the standard adjoint method. Our theoretical findings are illustrated with and supported by numerical simulations of the full spiking network. Notably our mPRC framework allows us to predict the difference between effects of transient inputs to the excitatory versus the inhibitory neurons in the network.

  13. Mesoscopic Kinetic Basis of Macroscopic Chemical Thermodynamics: A Mathematical Theory

    CERN Document Server

    Ge, Hao


    From a mathematical model that describes a complex chemical kinetic system of $N$ species and $M$ elementrary reactions in a rapidly stirred vessel of size $V$ as a Markov process, we show that a macroscopic chemical thermodynamics emerges as $V\\rightarrow\\infty$. The theory is applicable to linear and nonlinear reactions, closed systems reaching chemical equilibrium, or open, driven systems approaching to nonequilibrium steady states. A generalized mesoscopic free energy gives rise to a macroscopic chemical energy function $\\varphi^{ss}(\\vx)$ where $\\vx=(x_1,\\cdots,x_N)$ are the concentrations of the $N$ chemical species. The macroscopic chemical dynamics $\\vx(t)$ satisfies two emergent laws: (1) $(\\rd/\\rd t)\\varphi^{ss}[\\vx(t)]\\le 0$, and (2)$(\\rd/\\rd t)\\varphi^{ss}[\\vx(t)]=\\text{cmf}(\\vx)-\\sigma(\\vx)$ where entropy production rate $\\sigma\\ge 0$ represents the sink for the chemical energy, and chemical motive force $\\text{cmf}\\ge 0$ is non-zero if the system is driven under a sustained nonequilibrium chemos...

  14. Solvable Quantum Macroscopic Motions and Decoherence Mechanisms in Quantum Mechanics on Nonstandard Space (United States)

    Kobayashi, Tsunehiro


    Quantum macroscopic motions are investigated in the scheme consisting of N-number of harmonic oscillators in terms of ultra-power representations of nonstandard analysis. Decoherence is derived from the large internal degrees of freedom of macroscopic matters.

  15. Micromechanical study of macroscopic friction and dissipation in idealised granular materials: the effect of interparticle friction

    NARCIS (Netherlands)

    Kruyt, Nicolaas P.; Gutkowski, Witold; Rothenburg, L.; Kowalewski, Tomasz A.


    Using Discrete Element Method (DEM) simulations with varying interparticle friction coefficient, the relation between interparticle friction coefficient and macroscopic continuum friction and dissipation is investigated. As expected, macroscopic friction and dilatancy increase with interparticle

  16. Granule structure and distribution of allomorphs in C-type high-amylose rice starch granule modified by antisense RNA inhibition of starch branching enzyme. (United States)

    Wei, Cunxu; Qin, Fengling; Zhou, Weidong; Yu, Huaguang; Xu, Bin; Chen, Chong; Zhu, Lijia; Wang, Youping; Gu, Minghong; Liu, Qiaoquan


    C-type starch, which is a combination of both A-type and B-type crystal starch, is usually found in legumes and rhizomes. We have developed a high-amylose transgenic line of rice (TRS) by antisense RNA inhibition of starch branching enzymes. The starch in the endosperm of this TRS was identified as typical C-type crystalline starch, but its fine granular structure and allomorph distribution remained unclear. In this study, we conducted morphological and spectroscopic studies on this TRS starch during acid hydrolysis to determine the distribution of A- and B-type allomorphs. The morphology of starch granules after various durations of acid hydrolysis was compared by optical microscopy, scanning electron microscopy, and transmission electron microscopy. The results showed that amorphous regions were located at the center part of TRS starch subgranules. During acid hydrolysis, starch was degraded from the interior of the subgranule to the outer surface, while the peripheral part of the subgranules and the surrounding band of the starch granule were highly resistant to acid hydrolysis. The spectroscopic changes detected by X-ray powder diffraction, 13C cross-polarization magic-angle spinning NMR, and attenuated total reflectance Fourier transform infrared showed that the A-type allomorph was hydrolyzed more rapidly than the B-type, and that the X-ray diffraction profile gradually changed from a native C-type to a CB-type with increasing hydrolysis time. Our results showed that, in TRS starch, the A-type allomorph was located around the amorphous region, and was surrounded by the B-type allomorph located in the peripheral region of the subgranules and the surrounding band of the starch granule. Thus, the positions of A- and B-type allomorphs in the TRS C-type starch granule differ markedly from those in C-type legume and rhizome starch.

  17. Novel genes participating in the formation of prismatic and nacreous layers in the pearl oyster as revealed by their tissue distribution and RNA interference knockdown.

    Directory of Open Access Journals (Sweden)

    Daisuke Funabara

    Full Text Available In our previous publication, we identified novel gene candidates involved in shell formation by EST analyses of the nacreous and prismatic layer-forming tissues in the pearl oyster Pinctada fucata. In the present study, 14 of those genes, including two known genes, were selected and further examined for their involvement in shell formation using the RNA interference. Molecular characterization based on the deduced amino acid sequences showed that seven of the novel genes encode secretory proteins. The tissue distribution of the transcripts of the genes, as analyzed by RT-PCR and in situ hybridization, was mostly consistent with those obtained by the EST analysis reported previously. Shells in the pearl oysters injected with dsRNAs targeting genes 000027, 000058, 000081, 000096, 000113 (nacrein, 000118, 000133 and 000411 (MSI60, which showed expression specific to the nacreous layer forming tissues, showed abnormal surface appearance in this layer. Individuals injected with dsRNAs targeting genes 000027, 000113 and 000133 also exhibited abnormal prismatic layers. Individuals injected with dsRNAs targeting genes 000031, 000066, 000098, 000145, 000194 and 000200, which showed expression specific to prismatic layer forming tissues, displayed an abnormal surface appearance in both the nacreous and prismatic layers. Taken together, the results suggest that the genes involved in prismatic layer formation might also be involved in the formation of the nacreous layers.

  18. In regard to the question of macroscopic differential diagnosis of alcoholic and dilated cardiomyopathy

    Directory of Open Access Journals (Sweden)

    O. V. Sokolova


    Full Text Available The differential diagnosis of alcoholic and dilated cardiomyopathy according to the macroscopic data is represented in the article. The identity of macroscopic changes of heart, related to alcoholic and dilated cardiomyopathy, cannot diagnose these diseases based on the macroscopic characteristics; especially if there are no other visceral manifestations typical for chronic alcoholism.

  19. Microscopic and macroscopic models for the onset and progression of Alzheimer's disease (United States)

    Bertsch, Michiel; Franchi, Bruno; Carla Tesi, Maria; Tosin, Andrea


    In the first part of this paper we review a mathematical model for the onset and progression of Alzheimer’s disease (AD) that was developed in subsequent steps over several years. The model is meant to describe the evolution of AD in vivo. In Achdou et al (2013 J. Math. Biol. 67 1369-92) we treated the problem at a microscopic scale, where the typical length scale is a multiple of the size of the soma of a single neuron. Subsequently, in Bertsch et al (2017 Math. Med. Biol. 34 193-214) we concentrated on the macroscopic scale, where brain neurons are regarded as a continuous medium, structured by their degree of malfunctioning. In the second part of the paper we consider the relation between the microscopic and the macroscopic models. In particular we show under which assumptions the kinetic transport equation, which in the macroscopic model governs the evolution of the probability measure for the degree of malfunctioning of neurons, can be derived from a particle-based setting. The models are based on aggregation and diffusion equations for β-Amyloid (Aβ from now on), a protein fragment that healthy brains regularly produce and eliminate. In case of dementia Aβ monomers are no longer properly washed out and begin to coalesce forming eventually plaques. Two different mechanisms are assumed to be relevant for the temporal evolution of the disease: (i) diffusion and agglomeration of soluble polymers of amyloid, produced by damaged neurons; (ii) neuron-to-neuron prion-like transmission. In the microscopic model we consider mechanism (i), modelling it by a system of Smoluchowski equations for the amyloid concentration (describing the agglomeration phenomenon), with the addition of a diffusion term as well as of a source term on the neuronal membrane. At the macroscopic level instead we model processes (i) and (ii) by a system of Smoluchowski equations for the amyloid concentration, coupled to a kinetic-type transport equation for the distribution function of the

  20. Macroscopic nanoporous graphene membranes for molecular-sieving-based gas separation (United States)

    Boutilier, Michael; Karnik, Rohit; Hadjiconstantinou, Nicolas


    Nanoporous graphene membranes have the potential to exceed permeance and selectivity limits of existing gas separation membranes. This is made possible by the atomic thickness of the material, which can support sub-nanometer pores that enable molecular sieving while presenting low resistance to permeate flow. The feasibility of gas separation by graphene nanopores has been demonstrated experimentally on micron-scale areas of graphene. However, scaling up to macroscopic membrane areas presents significant challenges, including graphene imperfections and control of the selective nanopore size distribution across large areas. Towards this goal, gas permeance experiments are conducted on single and few layer graphene membranes to understand leakage pathways and a model is developed to predict conditions under which molecular sieving can occur in macroscopic membranes. Approaches to seal or mitigate the effects of micron and nanometer scale defects in graphene are investigated and methods of creating a high density of selectively permeable nanopores are explored. Experimental results demonstrating separation ratios exceeding the Knudsen effusion limit, indicating molecular sieving in agreement with the model predictions, are presented and discussed.

  1. On macroscopic quantum phenomena in biomolecules and cells: from Levinthal to Hopfield. (United States)

    Raković, Dejan; Dugić, Miroljub; Jeknić-Dugić, Jasmina; Plavšić, Milenko; Jaćimovski, Stevo; Setrajčić, Jovan


    In the context of the macroscopic quantum phenomena of the second kind, we hereby seek for a solution-in-principle of the long standing problem of the polymer folding, which was considered by Levinthal as (semi)classically intractable. To illuminate it, we applied quantum-chemical and quantum decoherence approaches to conformational transitions. Our analyses imply the existence of novel macroscopic quantum biomolecular phenomena, with biomolecular chain folding in an open environment considered as a subtle interplay between energy and conformation eigenstates of this biomolecule, governed by quantum-chemical and quantum decoherence laws. On the other hand, within an open biological cell, a system of all identical (noninteracting and dynamically noncoupled) biomolecular proteins might be considered as corresponding spatial quantum ensemble of these identical biomolecular processors, providing spatially distributed quantum solution to a single corresponding biomolecular chain folding, whose density of conformational states might be represented as Hopfield-like quantum-holographic associative neural network too (providing an equivalent global quantum-informational alternative to standard molecular-biology local biochemical approach in biomolecules and cells and higher hierarchical levels of organism, as well).

  2. Macroscopic domain formation in the platelet plasma membrane

    DEFF Research Database (Denmark)

    Bali, Rachna; Savino, Laura; Ramirez, Diego A.


    phase behavior of the platelet plasma membrane by FTIR, and compare it to a POPC/Sphingomyelin/Cholesterol model representing the outer leaflet composition. We find that this model closely reflects the platelet phase behavior. Previous work has shown that the platelet plasma membrane presents......There has been ample debate on whether cell membranes can present macroscopic lipid domains as predicted by three-component phase diagrams obtained by fluorescence microscopy. Several groups have argued that membrane proteins and interactions with the cytoskeleton inhibit the formation of large...

  3. Seismic scanning tunneling macroscope - Elastic simulations and Arizona mine test

    KAUST Repository

    Hanafy, Sherif M.


    Elastic seismic simulations and field data tests are used to validate the theory of a seismic scanning tunneling macroscope (SSTM). For nearfield elastic simulation, the SSTM results show superresolution to be better than λ/8 if the only scattered data are used as input data. If the direct P and S waves are muted then the resolution of the scatterer locations are within about λ/5. Seismic data collected in an Arizona tunnel showed a superresolution limit of at least λ/19. These test results are consistent with the theory of the SSTM and suggest that the SSTM can be a tool used by geophysicists as a probe for near-field scatterers.

  4. Probing high-frequency noise with macroscopic resonant tunneling (United States)

    Lanting, T.; Amin, M. H. S.; Johnson, M. W.; Altomare, F.; Berkley, A. J.; Gildert, S.; Harris, R.; Johansson, J.; Bunyk, P.; Ladizinsky, E.; Tolkacheva, E.; Averin, D. V.


    We have developed a method for extracting the high-frequency noise spectral density of an rf-SQUID flux qubit from macroscopic resonant tunneling (MRT) rate measurements. The extracted noise spectral density is consistent with that of an ohmic environment up to frequencies ~4 GHz. We have also derived an expression for the MRT line shape expected for a noise spectral density consisting of such a broadband ohmic component and an additional strongly peaked low-frequency component. This hybrid model provides an excellent fit to experimental data across a range of tunneling amplitudes and temperatures.

  5. Entropy and the Time Evolution of Macroscopic Systems

    CERN Document Server

    Grandy, Walter T


    This book is based on the premise that the entropy concept, a fundamental element of probability theory as logic, governs all of thermal physics, both equilibrium and nonequilibrium. The variational algorithm of J. Willard Gibbs, dating from the 19th Century and extended considerably over the following 100 years, is shown to be the governing feature over the entire range of thermal phenomena, such that only the nature of the macroscopic constraints changes. Beginning with a shorthistory of the development of the entropy concept by Rudolph Clausius and his predecessors, along with the formaliza

  6. Violation of smooth observable macroscopic realism in a harmonic oscillator. (United States)

    Leshem, Amir; Gat, Omri


    We study the emergence of macrorealism in a harmonic oscillator subject to consecutive measurements of a squeezed action. We demonstrate a breakdown of dynamical realism in a wide parameter range that is maximized in a scaling limit of extreme squeezing, where it is based on measurements of smooth observables, implying that macroscopic realism is not valid in the harmonic oscillator. We propose an indirect experimental test of these predictions with entangled photons by demonstrating that local realism in a composite system implies dynamical realism in a subsystem.

  7. PHD TUTORIAL: Quantum memory and teleportation using macroscopic gas samples (United States)

    Sherson, J.; Krauter, H.; Olsson, R. K.; Julsgaard, B.; Polzik, E. S.


    A long-standing goal in the quantum information community has been to realize quantum networks between distant sites. In this tutorial we describe the experimental demonstration of three crucial components in such a network using the off-resonant Faraday interaction between macroscopic atomic ensembles and coherent light. These are the realization of (a) deterministic entanglement between atomic samples in separate environments, (b) quantum mapping of an unknown light state into an atomic memory and (c) disembodied transport of states between quantum nodes via light-atom teleportation.

  8. Macroscopic quantum properties of spin polarized 3He (United States)

    Lhuillier, C.


    At low temperature the polarization of the nuclear spins of an assembly of 3He atoms is a very sensitive probe of their quantum collective behaviour. Via the Pauli principle nuclear polarization strongly affects collision processes and macroscopic transport properties. Theoretical predictions relative to these transport properties (heat conduction, spin diffusion, spin waves) are confronted to recent experimental results. At low temperature the phase diagramm of 3He may be strongly altered by nuclear polarization. A brief overview of the experimental efforts directed towards this problem is given. Optical pumping by I.R. lasers appears to be a good candidate for obtaining spin polarized liquid at saturated vapour pressure.

  9. Interdisciplinary applications of network dynamics: From microscopic to Macroscopic (United States)

    Jeong, Hawoong

    ``Everything touches everything.'' We are living in a connected world, which has been modeled successfully by complex networks. Ever since, network science becomes new paradigm for understanding our connected yet complex world. After investigating network structure itself, our focus naturally moved to dynamics of/on the network because our connected world is not static but dynamic. In this presentation, we will briefly review the historical development of network science and show some applications of network dynamics ranging from microscopic (metabolic engineering, PNAS, 104 13638) to macroscopic scale (price of anarchy in transportation network, Phys.Rev.Lett. 101 128701). Supported by National Research Foundation of Korea through Grant No. 2011-0028908.

  10. Emergence of an urban traffic macroscopic fundamental diagram

    DEFF Research Database (Denmark)

    Ranjan, Abhishek; Fosgerau, Mogens; Jenelius, Erik


    This paper examines mild conditions under which a macroscopic fundamental diagram (MFD) emerges, relating space-averaged speed to occupancy in some area. These conditions are validated against empirical data. We allow local speedoccupancy relationships and, in particular, require no equilibrating...... process to be in operation. This means that merely observing the stable relationship between the space-averages of speed, flow and occupancy are not sufficient to infer a robust relationship and the emerging MFD cannot be guaranteed to be stable if traffic interventions are implemented....

  11. Flagella bending affects macroscopic properties of bacterial suspensions

    Energy Technology Data Exchange (ETDEWEB)

    Potomkin, M.; Tournus, M.; Berlyand, L. V.; Aranson, I. S.


    To survive in harsh conditions, motile bacteria swim in complex environments and respond to the surrounding flow. Here, we develop a mathematical model describing how flagella bending affects macroscopic properties of bacterial suspensions. First, we show how the flagella bending contributes to the decrease in the effective viscosity observed in dilute suspension. Our results do not impose tumbling (random reorientation) as was previously done to explain the viscosity reduction. Second, we demonstrate how a bacterium escapes from wall entrapment due to the self-induced buckling of flagella. Our results shed light on the role of flexible bacterial flagella in interactions of bacteria with shear flow and walls or obstacles.

  12. The distribution of YKL-40 in osteoarthritic and normal human articular cartilage

    DEFF Research Database (Denmark)

    Volck, B; Ostergaard, K; Johansen, J S


    YKL-40, also called human cartilage glycoprotein-39, is a major secretory protein of human chondrocytes in cell culture. YKL-40 mRNA is expressed by cartilage from patients with rheumatoid arthritis, but is not detectable in normal human cartilage. The aim was to investigate the distribution of YKL......-40 in osteoarthritic (n=9) and macroscopically normal (n=5) human articular cartilage, collected from 12 pre-selected areas of the femoral head, to discover a potential role for YKL-40 in cartilage remodelling in osteoarthritis. Immunohistochemical analysis showed that YKL-40 staining was found...

  13. Molecular testing of adult Pacific salmon and trout (Oncorhynchus spp.) for several RNA viruses demonstrates widespread distribution of piscine orthoreovirus in Alaska and Washington (United States)

    Purcell, Maureen; Thompson, Rachel L.; Evered, Joy; Kerwin, John; Meyers, Ted R.; Stewart, Bruce; Winton, James


    This research was initiated in conjunction with a systematic, multiagency surveillance effort in the United States (U.S.) in response to reported findings of infectious salmon anaemia virus (ISAV) RNA in British Columbia, Canada. In the systematic surveillance study reported in a companion paper, tissues from various salmonids taken from Washington and Alaska were surveyed for ISAV RNA using the U.S.-approved diagnostic method, and samples were released for use in this present study only after testing negative. Here, we tested a subset of these samples for ISAV RNA with three additional published molecular assays, as well as for RNA from salmonid alphavirus (SAV), piscine myocarditis virus (PMCV) and piscine orthoreovirus (PRV). All samples (n = 2,252; 121 stock cohorts) tested negative for RNA from ISAV, PMCV, and SAV. In contrast, there were 25 stock cohorts from Washington and Alaska that had one or more individuals test positive for PRV RNA; prevalence within stocks varied and ranged from 2% to 73%. The overall prevalence of PRV RNA-positive individuals across the study was 3.4% (77 of 2,252 fish tested). Findings of PRV RNA were most common in coho (Oncorhynchus kisutch Walbaum) and Chinook (O. tshawytscha Walbaum) salmon.

  14. The fetlock tunnel syndrome: a macroscopic and microscopic study. (United States)

    van den Berg, M J; Rijkenhuizen, A B; Németh, F; Gruys, E


    Chronic changes of several structures in around the fetlock tunnel can be a cause of the so-called fetlock tunnel syndrome (FTS) in the horse. Forty-nine annular ligaments (AL) from dead horses without a known history or clinical evidence of lameness and/or digital tendon sheath problems in these legs and 30 AL biopsies from horses suffering from FTS were studied macroscopically and microscopically. Macroscopically, the normal AL had a shiny white appearance, whereas the affected AL were often thicker and less white. Microscopically, the normal AL were about +/- 1 mm thick and were composed of undulating, parallel bundles of collagen. Small blood vessels with a diameter of 0.03-0.12 mm were found. The affected AL showed an increased thickness of collagen bundles, a changed direction of longitudinal axis of collagen bundles, and irregularly dispersed fibroblast nuclei. The number of blood vessels had increased, the external diameter of arteriolae could be up to 0.3 mm and arterial wall changes were observed. Possible relationships between the histological findings and the aetiology of the FTS are discussed.

  15. Macroscopic Biological Characteristics of Individualized Therapy in Chinese Mongolian Osteopathy (United States)

    Namula, Zhao; Mei, Wang; Li, Xue-en

    Objective: Chinese Mongolian osteopathy has been passed down from ancient times and includes unique practices and favorable efficacy. In this study, we investigate the macroscopic biological characteristics of individualized Chinese Mongolian osteopathy, in order to provide new principle and methods for the treatment of bone fracture. Method: With a view to provide a vital link between nature and humans, the four stages of Chinese Mongolian osteopathy focus on the unity of the mind and body, the limbs and body organs, the body and its functions, and humans and nature. Results: We discuss the merits of individualized osteopathy in terms of the underlying concepts, and evaluate the approaches and principles of traditional medicine, as well as biomechanics. Conclusions: Individualized Mongolian osteopathy targets macroscopic biological components including dynamic reduction, natural fixation, and functional healing. Chinese Mongolian osteopathy is a natural, ecological and non-invasive osteopathy that values the link between nature and humans, including the unity of mind and body. The biological components not only serve as a foundation for Chinese Mongolian osteopathy but are also important for the future development of modern osteopathy, focusing on individualization, actualization and integration.

  16. Friction in macroscopic thermodynamics: A kinetic point of view (United States)

    Bizarro, João P. S.


    To provide a solid support to a macroscopic framework developed to explicitly account for friction in thermodynamics, a kinetic description of frictional dissipation is developed. Using either a dissipative Fokker-Planck equation for Brownian motion or a Boltzmann equation with a friction-force term added, it is shown that both approaches lead to the emergence of the macroscopic thermodynamic relations that state the first and second laws with friction. The analysis is directly applied to the problem of determining the minimum amount of heating generated by memory erasure, known in computer science as Landauer's bound, and leads to a better understanding of the energetics behind the latter. A generalisation of Boltzmann's H theorem to include friction explicitly is also recovered, and the thermodynamics of granular rotators acted by a frictional torque and of radio-frequency (RF) current drive of fusion plasmas, in which collisional drag is present, are addressed as well. Various physics results are revisited employing the first and second laws with friction that have been derived from the appropriate dissipative kinetic equations, lower bounds for entropy production rates being derived both for granular rotators and for RF current drive.

  17. Macroscopic superposition states and decoherence by quantum telegraph noise

    Energy Technology Data Exchange (ETDEWEB)

    Abel, Benjamin Simon


    In the first part of the present thesis we address the question about the size of superpositions of macroscopically distinct quantum states. We propose a measure for the ''size'' of a Schroedinger cat state, i.e. a quantum superposition of two many-body states with (supposedly) macroscopically distinct properties, by counting how many single-particle operations are needed to map one state onto the other. We apply our measure to a superconducting three-junction flux qubit put into a superposition of clockwise and counterclockwise circulating supercurrent states and find this Schroedinger cat to be surprisingly small. The unavoidable coupling of any quantum system to many environmental degrees of freedom leads to an irreversible loss of information about an initially prepared superposition of quantum states. This phenomenon, commonly referred to as decoherence or dephasing, is the subject of the second part of the thesis. We have studied the time evolution of the reduced density matrix of a two-level system (qubit) subject to quantum telegraph noise which is the major source of decoherence in Josephson charge qubits. We are able to derive an exact expression for the time evolution of the reduced density matrix. (orig.)

  18. How does Planck’s constant influence the macroscopic world? (United States)

    Yang, Pao-Keng


    In physics, Planck’s constant is a fundamental physical constant accounting for the energy-quantization phenomenon in the microscopic world. The value of Planck’s constant also determines in which length scale the quantum phenomenon will become conspicuous. Some students think that if Planck’s constant were to have a larger value than it has now, the quantum effect would only become observable in a world with a larger size, whereas the macroscopic world might remain almost unchanged. After reasoning from some basic physical principles and theories, we found that doubling Planck’s constant might result in a radical change on the geometric sizes and apparent colors of macroscopic objects, the solar spectrum and luminosity, the climate and gravity on Earth, as well as energy conversion between light and materials such as the efficiency of solar cells and light-emitting diodes. From the discussions in this paper, students can appreciate how Planck’s constant affects various aspects of the world in which we are living now.

  19. Influence of Carbon Nanotube Characteristics on Macroscopic Fiber Properties. (United States)

    Tsentalovich, Dmitri E; Headrick, Robert J; Mirri, Francesca; Hao, Junli; Behabtu, Natnael; Young, Colin C; Pasquali, Matteo


    We study how intrinsic parameters of carbon nanotube (CNT) samples affect the properties of macroscopic CNT fibers with optimized structure. We measure CNT diameter, number of walls, aspect ratio, graphitic character, and purity (residual catalyst and non-CNT carbon) in samples from 19 suppliers; we process the highest quality CNT samples into aligned, densely packed fibers, by using an established wet-spinning solution process. We find that fiber properties are mainly controlled by CNT aspect ratio and that sample purity is important for effective spinning. Properties appear largely unaffected by CNT diameter, number of walls, and graphitic character (determined by Raman G/D ratio) as long as the fibers comprise thin few-walled CNTs with high G/D ratio (above ∼20). We show that both strength and conductivity can be improved simultaneously by assembling high aspect ratio CNTs, producing continuous CNT fibers with an average tensile strength of 2.4 GPa and a room temperature electrical conductivity of 8.5 MS/m, ∼2 times higher than the highest reported literature value (∼15% of copper's value), obtained without postspinning doping. This understanding of the relationship of intrinsic CNT parameters to macroscopic fiber properties is key to guiding CNT synthesis and continued improvement of fiber properties, paving the way for CNT fiber introduction in large-scale aerospace, consumer electronics, and textile applications.

  20. Macroscopic electrical propagation in the guinea pig urinary bladder. (United States)

    Hammad, F T; Stephen, B; Lubbad, L; Morrison, J F B; Lammers, W J


    There is little knowledge about macroscopic electrical propagation in the wall of the urinary bladder. Recording simultaneously from a large number of extracellular electrodes is one technology that could be used to study the patterns of macroscopic electrical propagations. The urinary bladders from 14 guinea pigs were isolated and placed in an organ bath. A 16 × 4-electrode array was positioned at various sites on the serosal bladder surface, and recordings were performed at different intravesical volumes. In four experiments, carbachol (CCH; 10(-6) M), nifedipine (10 mM), or tetrodotoxin (TTX; 10(-6) M) was added to the superfusing fluid. After the experiments, the extracellular signals were analyzed and propagation maps were constructed. Electrical waves were detected at all sites on the bladder surface and propagated for a limited distance before terminating spontaneously. The majority of waves (>90%) propagated in the axial direction (i.e., from dome to base or vice versa). An increase in vesicle volume significantly decreased the conduction velocity (from 4.9 ± 1.5 to 2.7 ± 0.7 cm/s; P bladder surface. Two types of electrical activities were detected on the bladder surface: 1) electrical waves propagating preferentially in the axial direction and 2) electrical patches. The propagating electrical waves could form the basis for local spontaneous contractions in the bladder during the filling phase. Copyright © 2014 the American Physiological Society.

  1. Study on Tensile Properties of Nanoreinforced Epoxy Polymer: Macroscopic Experiments and Nanoscale FEM Simulation Prediction

    Directory of Open Access Journals (Sweden)

    Zhenqing Wang


    Full Text Available The effect of nanosilica contents on mechanical properties of the epoxy matrix with some nanoparticle aggregations was studied in macroscopic experiments and nanoscale simulation, particularly with regard to the effective modulus and ultimate stress. Three analytical models were used to obtain the effective elastic modulus of nanoparticle-reinforced composites. Based on Monte-Carlo method, the special program for the automatic generation of 2D random distribution particles without overlapping was developed for nanocomposite modeling. Weight fractions of nanoparticles were converted to volume fractions, in order to coordinate the content unit in the simulation. In numerical analysis, the weak interface strengthening and toughening mechanism was adopted. Virtual crack closure technique (VCCT and extended finite element method (XFEM were used to simulate phenomena of nanoparticle debonding and matrix crack growth. Experimental and simulation results show a good agreement with each other. By way of simulation, the weak interface toughening and strengthening mechanism of nanocomposites is confirmed.

  2. Crowd Flow Modeling of Athletes in Mass Sports Events -- a Macroscopic Approach

    CERN Document Server

    Treiber, Martin


    We propose a macroscopic model in form of a dispersion-transport equation for non-congested flow of the athletes which is coupled to a kinematic-wave model for congested flow. The model takes into account the performance (i.e., free-flow speed distributions) of the athletes in the different starting groups. The model is calibrated and validated on data of the German $\\textit{Rennsteig Half Marathon 2012}$ and the Swedish $\\textit{Vasaloppet 2012}$ cross-country ski race. Simulations of the model allow the event managers to improve the organization by determining the optimum number of starting groups, the maximum size of each group, whether a wave start with a certain starting delay between the groups is necessary, or what will be the effects of changing the course. We apply the model to simulate a planned course change for the Rennsteig Half Marathon 2013, and determine whether critical congestions are likely to occur.

  3. Macroscopic surface tension in a lattice Bhatnagar-Gross-Krook model of two immiscible fluids (United States)

    Halliday, I.; Thompson, S. P.; Care, C. M.


    We present a method by which an interface generating algorithm, similar to that of earlier lattice Boltzmann models of immiscible fluids, may be extended to a two component, two-speed two-dimensional (D2), nine-link (Q9) lattice Bhatnagar-Gross-Krook fluid. For two-dimensional, microcurrent-free planar interfaces between the two immiscible fluids we derive expressions for static interfacial tensions and interfacial distributions of the two fluids. Extending our analysis to curved interfaces, we propose a scheme for incorporating the influence of interfacial microcurrents that is based upon general symmetry arguments and is correct to second order in lattice velocity. The analysis demonstrates that the interfacial microcurrents have only second-order influence upon the macroscopic behavior of the model. We find good agreement between our calculations and simulation results based on the microcurrent stream function and surface tension results from the pressure tensor or Laplace law.

  4. Macroscopic Surface Tension in a Lattice Boltzmann BGK Model of Two Immiscible Fluids. (United States)

    Thompson, S. P.; Halliday, I.; Care, C. M.


    We present a method by which an interface generating algorithm, similar to that of earlier lattice Boltzmann models of immisible fluids, may be extended to a two component, two-speed D2Q9 lattice Bhatnagar Gross Krook fluid. For two-dimensional, microcurrent-free planar interfaces between the two immiscible fluids we derive expressions for static interfacial tensions and interfacial distributions of the two fluids. Extending our analysis to curved interfaces we propose a scheme for incorporating the influence of interfacial microcurrents which is based upon general symmetry arguments and is correct to second order in lattice velocity. The analysis demonstrates that the interfacial microcurrents have only second order influence upon the macroscopic behaviour of the model. We find good agreement between our calculations and simulation results based on the microcurrent stream function and surface tension results from the pressure tensor or Laplace law.

  5. Strongly coupled plasmonic modes on macroscopic areas via template-assisted colloidal self-assembly. (United States)

    Hanske, Christoph; Tebbe, Moritz; Kuttner, Christian; Bieber, Vera; Tsukruk, Vladimir V; Chanana, Munish; König, Tobias A F; Fery, Andreas


    We present ensembles of surface-ordered nanoparticle arrangements, which are formed by template-assisted self-assembly of monodisperse, protein-coated gold nanoparticles in wrinkle templates. Centimeter-squared areas of highly regular, linear assemblies with tunable line width are fabricated and their extinction cross sections can be characterized by conventional UV/vis/NIR spectroscopy. Modeling based on electrodynamic simulations shows a clear signature of strong plasmonic coupling with an interparticle spacing of 1-2 nm. We find evidence for well-defined plasmonic modes of quasi-infinite chains, such as resonance splitting and multiple radiant modes. Beyond elementary simulations on the individual chain level, we introduce an advanced model, which considers the chain length distribution as well as disorder. The step toward macroscopic sample areas not only opens perspectives for a range of applications in sensing, plasmonic light harvesting, surface enhanced spectroscopy, and information technology but also eases the investigation of hybridization and metamaterial effects fundamentally.

  6. Connecting macroscopic dynamics with microscopic properties in active microtubule network contraction (United States)

    Foster, Peter J.; Yan, Wen; Fürthauer, Sebastian; Shelley, Michael J.; Needleman, Daniel J.


    The cellular cytoskeleton is an active material, driven out of equilibrium by molecular motor proteins. It is not understood how the collective behaviors of cytoskeletal networks emerge from the properties of the network’s constituent motor proteins and filaments. Here we present experimental results on networks of stabilized microtubules in Xenopus oocyte extracts, which undergo spontaneous bulk contraction driven by the motor protein dynein, and investigate the effects of varying the initial microtubule density and length distribution. We find that networks contract to a similar final density, irrespective of the length of microtubules or their initial density, but that the contraction timescale varies with the average microtubule length. To gain insight into why this microscopic property influences the macroscopic network contraction time, we developed simulations where microtubules and motors are explicitly represented. The simulations qualitatively recapitulate the variation of contraction timescale with microtubule length, and allowed stress contributions from different sources to be estimated and decoupled.

  7. mRNA distribution of CGRP and its receptor components in the trigeminovascular system and other pain related structures in rat brain, and effect of intracerebroventricular administration of CGRP on Fos expression in the TNC

    DEFF Research Database (Denmark)

    Bhatt, Deepak Kumar; Gupta, Saurabh; Ploug, Kenneth B


    . The level of Fos protein expression in TNC was analysed by immunohistochemistry (IHC). mRNA expression of CGRP and its receptor components in trigeminovascular and other pain processing structures in the brain was also studied. CGRP i.c.v. infusion did not induce Fos activation in the TNC. mRNA expression...... profile showed that CGRP and its receptor components were widely distributed in trigeminovascular and other pain processing structures. The widespread presence of CGRP receptor mRNA in the various central pain pathways suggests that CGRP might play a role in migraine pathogenesis.......Calcitonin gene-related peptide (CGRP) infusion in humans provokes headache resembling spontaneous migraine, and CGRP receptor antagonists are effective against acute migraine. We hypothesized that CGRP infusion in the lateral ventricle (LV) will induce neuronal activation reflected by increase...

  8. Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties. (United States)

    Zhang, Z; Fenter, P; Cheng, L; Sturchio, N C; Bedzyk, M J; Predota, M; Bandura, A; Kubicki, J D; Lvov, S N; Cummings, P T; Chialvo, A A; Ridley, M K; Bénézeth, P; Anovitz, L; Palmer, D A; Machesky, M L; Wesolowski, D J


    A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and

  9. Micro and macroscopic investigation to quantify tillage impact on soil hydrodynamic behaviour (United States)

    Beckers, E.; Roisin, C.; Plougonven, E.; Deraedt, D.; Léonard, A.; Degré, A.


    H1 and H2 for both management practices: 100cm3 samples were used to establish pF curves with the Richards procedure, and 35cm3 samples were used for X-ray microtomography investigation. Samples for microtomography were air-dried at 40°C in order to empty meso- and macroporosity and then scanned using a Skyscan-1172 high-resolution desktop micro-CT system (Skyscan, Kontich, Belgium). Macroscopic measurements show consistent results: penetrometry profiles confirm the presence of two different horizons for RT, with a permeable superficial horizon between 0 and 10cm and a compacted subjacent horizon. Despite the long-term experiment, the old plough pan is still observed. The superficial horizon is equivalent in terms of pF curves to CT. The second horizon in RT shows significant differences with CT: porosity and especially effective porosity are greater for CT than RT. Infiltration tests confirm these reports with a higher conductivity for CT than RT. In fact, the first permeable horizon for RT is thin and the second horizon impacts vertical infiltration. These observations will be completed with microtomograms analysis. Pore size distribution, but particularly morphological parameters like eccentricity, orientation, connectivity and anisotropy of the pore network will be quantified and connected with macroscopic measurements.

  10. Symmetry properties of macroscopic transport coefficients in porous media (United States)

    Lasseux, D.; Valdés-Parada, F. J.


    We report on symmetry properties of tensorial effective transport coefficients characteristic of many transport phenomena in porous systems at the macroscopic scale. The effective coefficients in the macroscopic models (derived by upscaling (volume averaging) the governing equations at the underlying scale) are obtained from the solution of closure problems that allow passing the information from the lower to the upper scale. The symmetry properties of the macroscopic coefficients are identified from a formal analysis of the closure problems and this is illustrated for several different physical mechanisms, namely, one-phase flow in homogeneous porous media involving inertial effects, slip flow in the creeping regime, momentum transport in a fracture relying on the Reynolds model including slip effects, single-phase flow in heterogeneous porous media embedding a porous matrix and a clear fluid region, two-phase momentum transport in homogeneous porous media, as well as dispersive heat and mass transport. The results from the analysis of these study cases are summarized as follows. For inertial single-phase flow, the apparent permeability tensor is irreducibly decomposed into its symmetric (viscous) and skew-symmetric (inertial) parts; for creeping slip-flow, the apparent permeability tensor is not symmetric; for one-phase slightly compressible gas flow in the slip regime within a fracture, the effective transmissivity tensor is symmetric, a result that remains valid in the absence of slip; for creeping one-phase flow in heterogeneous media, the permeability tensor is symmetric; for two-phase flow, we found the dominant permeability tensors to be symmetric, whereas the coupling tensors do not exhibit any special symmetry property; finally for dispersive heat transfer, the thermal conductivity tensors include a symmetric and a skew-symmetric part, the latter being a consequence of convective transport only. A similar result is achieved for mass dispersion. Beyond the

  11. Distinct Molecular Features of Different Macroscopic Subtypes of Colorectal Neoplasms (United States)

    Konda, Kenichi; Konishi, Kazuo; Yamochi, Toshiko; Ito, Yoichi M.; Nozawa, Hisako; Tojo, Masayuki; Shinmura, Kensuke; Kogo, Mari; Katagiri, Atsushi; Kubota, Yutaro; Muramoto, Takashi; Yano, Yuichiro; Kobayashi, Yoshiya; Kihara, Toshihiro; Tagawa, Teppei; Makino, Reiko; Takimoto, Masafumi; Imawari, Michio; Yoshida, Hitoshi


    Background Colorectal adenoma develops into cancer with the accumulation of genetic and epigenetic changes. We studied the underlying molecular and clinicopathological features to better understand the heterogeneity of colorectal neoplasms (CRNs). Methods We evaluated both genetic (mutations of KRAS, BRAF, TP53, and PIK3CA, and microsatellite instability [MSI]) and epigenetic (methylation status of nine genes or sequences, including the CpG island methylator phenotype [CIMP] markers) alterations in 158 CRNs including 56 polypoid neoplasms (PNs), 25 granular type laterally spreading tumors (LST-Gs), 48 non-granular type LSTs (LST-NGs), 19 depressed neoplasms (DNs) and 10 small flat-elevated neoplasms (S-FNs) on the basis of macroscopic appearance. Results S-FNs showed few molecular changes except SFRP1 methylation. Significant differences in the frequency of KRAS mutations were observed among subtypes (68% for LST-Gs, 36% for PNs, 16% for DNs and 6% for LST-NGs) (P<0.001). By contrast, the frequency of TP53 mutation was higher in DNs than PNs or LST-Gs (32% vs. 5% or 0%, respectively) (P<0.007). We also observed significant differences in the frequency of CIMP between LST-Gs and LST-NGs or PNs (32% vs. 6% or 5%, respectively) (P<0.005). Moreover, the methylation level of LINE-1 was significantly lower in DNs or LST-Gs than in PNs (58.3% or 60.5% vs. 63.2%, P<0.05). PIK3CA mutations were detected only in LSTs. Finally, multivariate analyses showed that macroscopic morphologies were significantly associated with an increased risk of molecular changes (PN or LST-G for KRAS mutation, odds ratio [OR] 9.11; LST-NG or DN for TP53 mutation, OR 5.30; LST-G for PIK3CA mutation, OR 26.53; LST-G or DN for LINE-1 hypomethylation, OR 3.41). Conclusion We demonstrated that CRNs could be classified into five macroscopic subtypes according to clinicopathological and molecular differences, suggesting that different mechanisms are involved in the pathogenesis of colorectal

  12. Distinct molecular features of different macroscopic subtypes of colorectal neoplasms.

    Directory of Open Access Journals (Sweden)

    Kenichi Konda

    Full Text Available Colorectal adenoma develops into cancer with the accumulation of genetic and epigenetic changes. We studied the underlying molecular and clinicopathological features to better understand the heterogeneity of colorectal neoplasms (CRNs.We evaluated both genetic (mutations of KRAS, BRAF, TP53, and PIK3CA, and microsatellite instability [MSI] and epigenetic (methylation status of nine genes or sequences, including the CpG island methylator phenotype [CIMP] markers alterations in 158 CRNs including 56 polypoid neoplasms (PNs, 25 granular type laterally spreading tumors (LST-Gs, 48 non-granular type LSTs (LST-NGs, 19 depressed neoplasms (DNs and 10 small flat-elevated neoplasms (S-FNs on the basis of macroscopic appearance.S-FNs showed few molecular changes except SFRP1 methylation. Significant differences in the frequency of KRAS mutations were observed among subtypes (68% for LST-Gs, 36% for PNs, 16% for DNs and 6% for LST-NGs (P<0.001. By contrast, the frequency of TP53 mutation was higher in DNs than PNs or LST-Gs (32% vs. 5% or 0%, respectively (P<0.007. We also observed significant differences in the frequency of CIMP between LST-Gs and LST-NGs or PNs (32% vs. 6% or 5%, respectively (P<0.005. Moreover, the methylation level of LINE-1 was significantly lower in DNs or LST-Gs than in PNs (58.3% or 60.5% vs. 63.2%, P<0.05. PIK3CA mutations were detected only in LSTs. Finally, multivariate analyses showed that macroscopic morphologies were significantly associated with an increased risk of molecular changes (PN or LST-G for KRAS mutation, odds ratio [OR] 9.11; LST-NG or DN for TP53 mutation, OR 5.30; LST-G for PIK3CA mutation, OR 26.53; LST-G or DN for LINE-1 hypomethylation, OR 3.41.We demonstrated that CRNs could be classified into five macroscopic subtypes according to clinicopathological and molecular differences, suggesting that different mechanisms are involved in the pathogenesis of colorectal tumorigenesis.

  13. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment

    DEFF Research Database (Denmark)

    Sahm, K.; MacGregor, BJ; Jørgensen, BB


    In the past, enumeration of sulphate-reducing bacteria (SRB) by cultivation-based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot-blot hybridization...... between 18% and 25% to the prokaryotic rRNA pool. The dominant SRB were related to complete oxidizing genera (Desulphococcus, Desulphosarcina and Desulphobacterium), while Desulpho-bacter could not be detected. The vertical profile and quantity of rRNA from SRB was compared with sulphate reduction rates......, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI-stained cells indicated a population size for SRB of 2.4-6.1 x 10(8) cells cm(-3) wet sediment. Cellular sulphate reduction rates calculated on the basis...

  14. Macroscopic Modeling of Transport Phenomena in Direct Methanol Fuel Cells

    DEFF Research Database (Denmark)

    Olesen, Anders Christian

    An increasing need for energy efficiency and high energy density has sparked a growing interest in direct methanol fuel cells for portable power applications. This type of fuel cell directly generates electricity from a fuel mixture consisting of methanol and water. Although this technology...... for studying their transport. In this PhD dissertation the macroscopic transport phenomena governing direct methanol fuel cell operation are analyzed, discussed and modeled using the two-fluid approach in the computational fluid dynamics framework of CFX 14. The overall objective of this work is to extend...... the present fundamental understanding of direct methanol fuel cell operation by developing a three-dimensional, two-phase, multi-component, non-isotherm mathematical model including detailed non-ideal thermodynamics, non-equilibrium phase change and non-equilibrium sorption-desorption of methanol and water...

  15. Fault detection by surface seismic scanning tunneling macroscope: Field test

    KAUST Repository

    Hanafy, Sherif M.


    The seismic scanning tunneling macroscope (SSTM) is proposed for detecting the presence of near-surface impedance anomalies and faults. Results with synthetic data are consistent with theory in that scatterers closer to the surface provide brighter SSTM profiles than those that are deeper. The SSTM profiles show superresolution detection if the scatterers are in the near-field region of the recording line. The field data tests near Gulf of Aqaba, Haql, KSA clearly show the presence of the observable fault scarp, and identify the subsurface presence of the hidden faults indicated in the tomograms. Superresolution detection of the fault is achieved, even when the 35 Hz data are lowpass filtered to the 5-10 Hz band.

  16. Approach to thermal equilibrium of macroscopic quantum systems. (United States)

    Goldstein, Sheldon; Lebowitz, Joel L; Mastrodonato, Christian; Tumulka, Roderich; Zanghi, Nino


    We consider an isolated macroscopic quantum system. Let H be a microcanonical "energy shell," i.e., a subspace of the system's Hilbert space spanned by the (finitely) many energy eigenstates with energies between E and E+deltaE . The thermal equilibrium macrostate at energy E corresponds to a subspace H(eq) of H such that dim H(eq)/dim H is close to 1. We say that a system with state vector psi is the element of H is in thermal equilibrium if psi is "close" to H(eq). We show that for "typical" Hamiltonians with given eigenvalues, all initial state vectors psi(0) evolve in such a way that psi(t) is in thermal equilibrium for most times t. This result is closely related to von Neumann's quantum ergodic theorem of 1929.

  17. Anisotropic magnetothermopower in ferromagnetic thin films grown on macroscopic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Jayathilaka, P.B. [Department of Physical Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale (Sri Lanka); Belyea, D.D. [Department of Physics, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620 (United States); Fawcett, T.J. [College of Engineering, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620 (United States); Miller, Casey W. [School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623 (United States)


    We report observing the anisotropic magnetothermopower in a variety of ferromagnetic thin films grown on macroscopic substrates. These measurements were enabled by eliminating spurious signals related to the Anomalous Nernst Effect by butt-mounting the sample to the heat source and sink, and appropriate positioning of electrical contacts to avoid unwanted thermal gradients. This protocol enabled detailed measurements of the magnetothermopower in the transverse and longitudinal configurations. This may enable Spin Seebeck Effect studies in the in-plane geometry. - Highlights: • Unintentional thermal gradients along surface normal mitigated via butt-mounting. • Longitudinal/transverse magnetothermopower measured on many systems. • Anomalous Nernst Effect reduced. • Importance of magnetic anisotropy identified with angle-dependent measurements.

  18. Innovating e-waste management: From macroscopic to microscopic scales. (United States)

    Zeng, Xianlai; Yang, Congren; Chiang, Joseph F; Li, Jinhui


    Waste electrical and electronic equipment (WEEE or e-waste) has become a global problem, due to its potential environmental pollution and human health risk, and its containing valuable resources (e.g., metals, plastics). Recycling for e-waste will be a necessity, not only to address the shortage of mineral resources for electronics industry, but also to decline environmental pollution and human health risk. To systematically solve the e-waste problem, more attention of e-waste management should transfer from macroscopic to microscopic scales. E-waste processing technology should be significantly improved to diminish and even avoid toxic substance entering into downstream of material. The regulation or policy related to new production of hazardous substances in recycled materials should also be carried out on the agenda. All the findings can hopefully improve WEEE legislation for regulated countries and non-regulated countries. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Probing Noise in Flux Qubits via Macroscopic Resonant Tunneling (United States)

    Harris, R.; Johnson, M. W.; Han, S.; Berkley, A. J.; Johansson, J.; Bunyk, P.; Ladizinsky, E.; Govorkov, S.; Thom, M. C.; Uchaikin, S.; Bumble, B.; Fung, A.; Kaul, A.; Kleinsasser, A.; Amin, M. H. S.; Averin, D. V.


    Macroscopic resonant tunneling between the two lowest lying states of a bistable rf SQUID is used to characterize noise in a flux qubit. Measurements of the incoherent decay rate as a function of flux bias revealed a Gaussian-shaped profile that is not peaked at the resonance point but is shifted to a bias at which the initial well is higher than the target well. The rms amplitude of the noise, which is proportional to the dephasing rate 1/τφ, was observed to be weakly dependent on temperature below 70 mK. Analysis of these results indicates that the dominant source of low energy flux noise in this device is a quantum mechanical environment in thermal equilibrium.

  20. Micromechanical model for protein materials: From macromolecules to macroscopic fibers (United States)

    Puglisi, G.; De Tommasi, D.; Pantano, M. F.; Pugno, N. M.; Saccomandi, G.


    We propose a model for the mechanical behavior of protein materials. Based on a limited number of experimental macromolecular parameters (persistence and contour length) we obtain the macroscopic behavior of keratin fibers (human, cow, and rabbit hair), taking into account the damage and residual stretches effects that are fundamental in many functions of life. We also show the capability of our approach to describe the main dissipation and permanent strain effects observed in the more complex spider silk fibers. The comparison between our results and the data obtained experimentally from cyclic tests demonstrates that our model is robust and is able to reproduce with a remarkable accuracy the experimental behavior of all protein materials we tested.

  1. Macroscopic quantum electrodynamics of high-Q cavities

    Energy Technology Data Exchange (ETDEWEB)

    Khanbekyan, Mikayel


    In this thesis macroscopic quantum electrodynamics in linear media was applied in order to develop an universally valid quantum theory for the description of the interaction of the electromagnetic field with atomic sources in high-Q cavities. In this theory a complete description of the characteristics of the emitted radiation is given. The theory allows to show the limits of the applicability of the usually applied theory. In order to establish an as possible generally valid theory first the atom-field interaction was studied in the framework of macroscopic quantum electrodynamics in dispersive and absorptive media. In order to describe the electromagnetic field from Maxwell's equations was started, whereby the noise-current densities, which are connected with the absorption of the medium, were included. The solution of these equations expresses the electromagnetic field variables by the noise-current densities by means of Green's tensor of the macroscopic Maxwell equations. The explicit quantization is performed by means of the noise-current densities, whereby a diagonal Hamiltonian is introduced, which then guarantees the time development according to Maxwell's equation and the fulfillment of the fundamental simultaneous commutation relations of the field variables. In the case of the interaction of the medium-supported field with atoms the Hamiltonian must be extended by atom-field interactions energies, whereby the canonical coupling schemes of the minimal or multipolar coupling can be used. The dieelectric properties of the material bodies as well as their shape are coded in the Green tensor of the macroscopic Maxwell equations. As preparing step first the Green tensor was specified in order to derive three-dimensional input-output relations for the electromagnetic field operators on a plane multilayer structure. Such a general dewscription of the electromagnetic field allows the inclusion both of dispersion and absorption of the media and the

  2. Non-Poissonian photon statistics from macroscopic photon cutting materials. (United States)

    de Jong, Mathijs; Meijerink, Andries; Rabouw, Freddy T


    In optical materials energy is usually extracted only from the lowest excited state, resulting in fundamental energy-efficiency limits such as the Shockley-Queisser limit for single-junction solar cells. Photon-cutting materials provide a way around such limits by absorbing high-energy photons and 'cutting' them into multiple low-energy excitations that can subsequently be extracted. The occurrence of photon cutting or quantum cutting has been demonstrated in a variety of materials, including semiconductor quantum dots, lanthanides and organic dyes. Here we show that photon cutting results in bunched photon emission on the timescale of the excited-state lifetime, even when observing a macroscopic number of optical centres. Our theoretical derivation matches well with experimental data on NaLaF 4 :Pr 3+ , a material that can cut deep-ultraviolet photons into two visible photons. This signature of photon cutting can be used to identify and characterize new photon-cutting materials unambiguously.

  3. Macroscopic self-reorientation of interacting two-dimensional crystals (United States)

    Woods, C. R.; Withers, F.; Zhu, M. J.; Cao, Y.; Yu, G.; Kozikov, A.; Ben Shalom, M.; Morozov, S. V.; van Wijk, M. M.; Fasolino, A.; Katsnelson, M. I.; Watanabe, K.; Taniguchi, T.; Geim, A. K.; Mishchenko, A.; Novoselov, K. S.


    Microelectromechanical systems, which can be moved or rotated with nanometre precision, already find applications in such fields as radio-frequency electronics, micro-attenuators, sensors and many others. Especially interesting are those which allow fine control over the motion on the atomic scale because of self-alignment mechanisms and forces acting on the atomic level. Such machines can produce well-controlled movements as a reaction to small changes of the external parameters. Here we demonstrate that, for the system of graphene on hexagonal boron nitride, the interplay between the van der Waals and elastic energies results in graphene mechanically self-rotating towards the hexagonal boron nitride crystallographic directions. Such rotation is macroscopic (for graphene flakes of tens of micrometres the tangential movement can be on hundreds of nanometres) and can be used for reproducible manufacturing of aligned van der Waals heterostructures.

  4. Macroscopic Quantum Self-Trapping in Dynamical Tunneling (United States)

    Wüster, Sebastian; Dabrowska, Beata J.; Davis, Matthew J.


    It is well known that increasing the nonlinearity due to repulsive atomic interactions in a double-well Bose-Einstein condensate suppresses quantum tunneling between the two sites. Here we find analogous behavior in the dynamical tunneling of a Bose-Einstein condensate between period-one resonances in a single driven potential well. For small nonlinearities we find unhindered tunneling between the resonances, but with an increasing period as compared to the noninteracting system. For nonlinearities above a critical value we generally observe that the tunneling shuts down. However, for certain regimes of modulation parameters we find that dynamical tunneling reemerges for large enough nonlinearities, an effect not present in spatial double-well tunneling. We develop a two-mode model in good agreement with full numerical simulations over a wide range of parameters, which allows the suppression of tunneling to be attributed to macroscopic quantum self-trapping.


    Directory of Open Access Journals (Sweden)



    Full Text Available It is only the eutherian mammals that have evolved a complex organ - “ The Placenta ” which not only protect but also gives nutrition to the embryo till its birth. We should see that the placenta is more than just some messy after birth to be discarded and ignored in the excitement and joy over the birth of a beautiful new child. So, this study aims to evaluate the macroscopic study of placenta and to explore the morphological variation of placenta with respect to preterm, term and post term pregnancy. MATERIALS AND METHOD: It’s a hospital based Prospective Nonrandomized Observational stud y of 90 placentae, conducted in the Department of Anatomy and the Department of Obstetrics and Gynaecology, FAAMCH, Barpeta. RESULTS: The macroscopic study of placenta revealed that most of the placentae were discoidal in shape, only a few oval. The weight of the term and post term placentae were more than preterm placentae. Comparison of weight between preterm and term categories were found to be significant (p<0.01 whereas comparison of weight between term and post - term were found to be just significant (p<0.05. A difference in diameter between preterm and term cases were seen whereas the difference was less in respect to term and post - term cases, statistically just significant (p<0.05. Thickness showed no major difference, the number of cotyledons foun d were 15 – 20 and the arrangement of chorionic vessels were similar in all the three categories of placentae. O ut of 90 placentae two placentae had marginal attachment and seven had velamentous insertion of cord, rest of them were eccentric in position. CON CLUSION: Therefore, it is obvious that the various parameters of placenta are subjected to slight variations in preterm, term and post - term placentae. Direct examination and assessment of placental parameters contribute to the assessment of the neonate; he lp to explain certain antenatal events and aid in the management of the puerpera.

  6. Pre- and post- scission particle emission in 3D Langevin calculations with various macroscopic potentials

    Directory of Open Access Journals (Sweden)

    Mazurek K.


    Full Text Available The fission dynamics described by solving differential equations of the Langevin type in three dimensional space of the deformation parameters is very sensitive on the choice of the macroscopic components such as potential energy models. The mass or charge distribution or total kinetic energy has been already shown to be different when one uses the Finite Range Liquid Drop Model or Lublin - Strasbourg Drop model. Also the shape-dependent congruence or shape-dependent Wigner energy and A0 terms are important especially for the fission of medium mass nuclei. We would like to make step forward and answer the question about the varying of the post-scission multiplicity by including different PES. Up to now there are only few experimental data for the medium mass nuclei where the pre- and post- scission emission has been estimated and isotopic distributions have been shown. The isotopic distributions of the fission products for light compound nucleus such as 111 In with two beam energies (Ebeam = 10.6 AMeV and 5.9 AMeV and two heavy systems: 229Np with Ebeam = 7.4 AMeV and 260 No (Ebeam = 6 AMeV and 7.5 AMeV have been studied theoretically. The agreement with the experimental data is discussed.

  7. A simple three-dimensional macroscopic root water uptake model based on the hydraulic architecture approach

    Directory of Open Access Journals (Sweden)

    V. Couvreur


    Full Text Available Many hydrological models including root water uptake (RWU do not consider the dimension of root system hydraulic architecture (HA because explicitly solving water flow in such a complex system is too time consuming. However, they might lack process understanding when basing RWU and plant water stress predictions on functions of variables such as the root length density distribution. On the basis of analytical solutions of water flow in a simple HA, we developed an "implicit" model of the root system HA for simulation of RWU distribution (sink term of Richards' equation and plant water stress in three-dimensional soil water flow models. The new model has three macroscopic parameters defined at the soil element scale, or at the plant scale, rather than for each segment of the root system architecture: the standard sink fraction distribution SSF, the root system equivalent conductance Krs and the compensatory RWU conductance Kcomp. It clearly decouples the process of water stress from compensatory RWU, and its structure is appropriate for hydraulic lift simulation. As compared to a model explicitly solving water flow in a realistic maize root system HA, the implicit model showed to be accurate for predicting RWU distribution and plant collar water potential, with one single set of parameters, in dissimilar water dynamics scenarios. For these scenarios, the computing time of the implicit model was a factor 28 to 214 shorter than that of the explicit one. We also provide a new expression for the effective soil water potential sensed by plants in soils with a heterogeneous water potential distribution, which emerged from the implicit model equations. With the proposed implicit model of the root system HA, new concepts are brought which open avenues towards simple and mechanistic RWU models and water stress functions operational for field scale water dynamics simulation.

  8. Excavating abiotic stress-related gene resources of terrestrial macroscopic cyanobacteria for crop genetic engineering: dawn and challenge. (United States)

    Ye, Shuifeng; Gao, Xiang


    Genetically engineered (GE) crops with resistance to environmental stresses are one of the most important solutions for future food security. Numerous genes associated to plant stress resistance have been identified and characterized. However, the current reality is that only a few transgenic crops expressing prokaryotic genes are successfully applied in field conditions. These few prokaryotic genes include Agrobacterium strain CP4 EPSPS gene, Bacillus thuringiensis Cry1Ab gene and a bacterial chaperonin gene. Thus, the excavation of potentially critical genes still remains an arduous task for crop engineering. Terrestrial macroscopic cyanobacteria, Nostoc commune and Nostoc flagelliforme, which exhibit extreme resistance to desiccation stress, may serve as new prokaryotic bioresources for excavating critical genes. Recently, their marker gene wspA was heterologously expressed in Arabidopsis plant and the transgenics exhibited more flourishing root systems than wild-type plants under osmotic stress condition. In addition, some new genes associated with drought response and adaptation in N. flagelliforme are being uncovered by our ongoing RNA-seq analysis. Although the relevant work about the terrestrial macroscopic cyanobacteria is still underway, we believe that the prospect of excavating their critical genes for application in GE crops is quite optimistic.

  9. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria

    NARCIS (Netherlands)

    Zwart, G.; Hiorns, W.D.; Methe, B.A.; Agterveld, M.P. van; Huismans, R.; Nold, S.C.; Zehr, J.P.; Laanbroek, H.J.


    We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related

  10. Variable EBV DNA Load Distributions and Heterogeneous EBV mRNA Expression Patterns in the Circulation of Solid Organ versus Stem Cell Transplant Recipients

    NARCIS (Netherlands)

    Greijer, A. E.; Stevens, S. J.; Verkuijlen, S. A.; Juwana, H.; Fleig, S. C.; Verschuuren, E. A.; Hepkema, B. G.; Cornelissen, J. J.; Brooimans, R. A.; Verdonck, L. F.; Middeldorp, J. M.


    Epstein-Barr virus (EBV) driven post-transplant lymphoproliferative disease (PTLD) is a heterogeneous and potentially life-threatening condition. Early identification of aberrant EBV activity may prevent progression to B-cell lymphoma. We measured EBV DNA load and RNA profiles in plasma and cellular

  11. Variable EBV DNA load distributions and heterogeneous EBV mRNA expression patterns in the circulation of solid organ versus stem cell transplant recipients

    NARCIS (Netherlands)

    A.E. Greijer; S.J. Stevens; S.A. Verkuijlen; H. Juwana; S.C. Fleig; E.A. Verschuuren; B.G. Hepkema (Bouke); J.J. Cornelissen (Jan); R.A. Brooimans (Rik); L.F. Verdonck (Leo); J.M. Middeldorp (Jaap)


    textabstractEpstein-Barr virus (EBV) driven post-transplant lymphoproliferative disease (PTLD) is a heterogeneous and potentially life-threatening condition. Early identification of aberrant EBV activity may prevent progression to B-cell lymphoma. We measured EBV DNA load and RNA profiles in plasma

  12. Theory and feasibility tests for a seismic scanning tunnelling macroscope

    KAUST Repository

    Schuster, Gerard T.


    We propose a seismic scanning tunnelling macroscope (SSTM) that can detect subwavelength scatterers in the near-field of either the source or the receivers. Analytic formulas for the time reverse mirror (TRM) profile associated with a single scatterer model show that the spatial resolution limit to be, unlike the Abbe limit of λ/2, independent of wavelength and linearly proportional to the source-scatterer separation as long as the scatterer is in the near-field region. This means that, as the scatterer approaches the source, imaging of the scatterer with super-resolution can be achieved. Acoustic and elastic simulations support this concept, and a seismic experiment in an Arizona tunnel shows a TRM profile with super-resolution adjacent to the fault location. The SSTM is analogous to the optical scanning tunnelling microscopes having subwavelength resolution. Scaled to seismic frequencies, it is theoretically possible to extract 100 Hz information from 20 Hz data by the imaging of near-field seismic energy.

  13. The macroscopic delamination of thin films from elastic substrates (United States)

    Vella, Dominic; Bico, José; Boudaoud, Arezki; Roman, Benoit; Reis, Pedro M.


    The wrinkling and delamination of stiff thin films adhered to a polymer substrate have important applications in “flexible electronics.” The resulting periodic structures, when used for circuitry, have remarkable mechanical properties because stretching or twisting of the substrate is mostly accommodated through bending of the film, which minimizes fatigue or fracture. To date, applications in this context have used substrate patterning to create an anisotropic substrate-film adhesion energy, thereby producing a controlled array of delamination “blisters.” However, even in the absence of such patterning, blisters appear spontaneously, with a characteristic size. Here, we perform well-controlled experiments at macroscopic scales to study what sets the dimensions of these blisters in terms of the material properties and explain our results by using a combination of scaling and analytical methods. Besides pointing to a method for determining the interfacial toughness, our analysis suggests a number of design guidelines for the thin films used in flexible electronic applications. Crucially, we show that, to avoid the possibility that delamination may cause fatigue damage, the thin film thickness must be greater than a critical value, which we determine. PMID:19556551

  14. From power law intermittence to macroscopic coherent regime. (United States)

    Bologna, Mauro; Budini, Adrián A; Giraldi, Filippo; Grigolini, Paolo


    We address the problem of establishing which is the proper form of quantum master equation generating a survival probability identical to that corresponding to the nonergodic sequence of "light on" and "light off" fluorescence fluctuations in blinking quantum dots. We adopt a theoretical perspective based on the assumption that the abrupt transitions from the light on to light off state are the results of many collisions between system and environment, properly described by the Lindblad equation, and that between two consecutive collisions the system dynamics are frozen. This generates a quantum master equation belonging to the recently proposed class of generalized Lindblad equations, with a time convoluted structure, involving in the specific case of this paper both the unitary and the nonunitary contribution of the Lindblad equation. This is the property that under the low-frequency condition makes the new class of generalized Lindblad equation generates the required survival probability. We make the conjecture that this equation corresponds to the cooperative dynamics of many units that, in isolation, are described by the ordinary Lindblad equation. When the time scale of the unitary term of the Lindblad equation is shorter than the dephasing time, the cooperation generates a surprisingly extended macroscopic coherence.

  15. Macroscopic study of testicular descent in caprine fetus

    Directory of Open Access Journals (Sweden)

    S Hejazi


    Full Text Available In this study, fetus samples were collected randomly from 200 pregnant goats which were slaughtered at Tabriz  abattoir during autumn. The age of collected fetuses was calculated by the formula X=2.74 Y+30.15 proposed by Gull et al. After opening the abdominal cavity of the fetuses at different ages, the location of the testicles in the abdominal cavity and the time of their descent into the scrotum were investigated. Macroscopic studies indicated that the first testicular migration coincides with mesonephrous degeneration in 45 days old fetuses. At the age of 59 days, the mesonephrous is completely diminished and the remains of the mesonephric duct changed to epididymis. At this age, the gubernacular tissue is inflated and expanded. In days 89, testis is seen in the middle of the inguinal canal and until day 106 of pregnancy it descents from final  of the inguinal canal into the opening of the scrotum. At the age of 153 days (birth time complete descent of the testis into the scrotum takes place. On the basis of the results of the present study it can be concluded that the location of testis in the goat is similar to cattle, sheep, horse and humans at birth and its descent into scrotum follows retraction and degeneration of the gubernacular tissue.

  16. Macroscopic singlet oxygen model incorporating photobleaching as an input parameter (United States)

    Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.


    A macroscopic singlet oxygen model for photodynamic therapy (PDT) has been used extensively to calculate the reacted singlet oxygen concentration for various photosensitizers. The four photophysical parameters (ξ, σ, β, δ) and threshold singlet oxygen dose ([1O2]r,sh) can be found for various drugs and drug-light intervals using a fitting algorithm. The input parameters for this model include the fluence, photosensitizer concentration, optical properties, and necrosis radius. An additional input variable of photobleaching was implemented in this study to optimize the results. Photobleaching was measured by using the pre-PDT and post-PDT sensitizer concentrations. Using the RIF model of murine fibrosarcoma, mice were treated with a linear source with fluence rates from 12 - 150 mW/cm and total fluences from 24 - 135 J/cm. The two main drugs investigated were benzoporphyrin derivative monoacid ring A (BPD) and 2-[1-hexyloxyethyl]-2-devinyl pyropheophorbide-a (HPPH). Previously published photophysical parameters were fine-tuned and verified using photobleaching as the additional fitting parameter. Furthermore, photobleaching can be used as an indicator of the robustness of the model for the particular mouse experiment by comparing the experimental and model-calculated photobleaching ratio.

  17. Tunable Broadband Transparency of Macroscopic Quantum Superconducting Metamaterials

    Directory of Open Access Journals (Sweden)

    Daimeng Zhang


    Full Text Available Narrow-band invisibility in an otherwise opaque medium has been achieved by electromagnetically induced transparency (EIT in atomic systems. The quantum EIT behavior can be classically mimicked by specially engineered metamaterials via carefully controlled interference with a “dark mode.” However, the narrow transparency window limits the potential applications that require a tunable wideband transparent performance. Here, we present a macroscopic quantum superconducting metamaterial with manipulative self-induced broadband transparency due to a qualitatively novel nonlinear mechanism that is different from conventional EIT or its classical analogs. A near-complete disappearance of resonant absorption under a range of applied rf flux is observed experimentally and explained theoretically. The transparency comes from the intrinsic bistability of the meta-atoms and can be tuned on and off easily by altering rf and dc magnetic fields, temperature, and history. Hysteretic in situ 100% tunability of transparency paves the way for autocloaking metamaterials, intensity-dependent filters, and fast-tunable power limiters.

  18. Connecting local active forces to macroscopic stress in elastic media. (United States)

    Ronceray, Pierre; Lenz, Martin


    In contrast with ordinary materials, living matter drives its own motion by generating active, out-of-equilibrium internal stresses. These stresses typically originate from localized active elements embedded in an elastic medium, such as molecular motors inside the cell or contractile cells in a tissue. While many large-scale phenomenological theories of such active media have been developed, a systematic understanding of the emergence of stress from the local force-generating elements is lacking. In this paper, we present a rigorous theoretical framework to study this relationship. We show that the medium's macroscopic active stress tensor is equal to the active elements' force dipole tensor per unit volume in both continuum and discrete linear homogeneous media of arbitrary geometries. This relationship is conserved on average in the presence of disorder, but can be violated in nonlinear elastic media. Such effects can lead to either a reinforcement or an attenuation of the active stresses, giving us a glimpse of the ways in which nature might harness microscopic forces to create active materials.

  19. Properties of nuclear matter from macroscopic-microscopic mass formulas (United States)

    Wang, Ning; Liu, Min; Ou, Li; Zhang, Yingxun


    Based on the standard Skyrme energy density functionals together with the extended Thomas-Fermi approach, the properties of symmetric and asymmetric nuclear matter represented in two macroscopic-microscopic mass formulas: Lublin-Strasbourg nuclear drop energy (LSD) formula and Weizsäcker-Skyrme (WS*) formula, are extracted through matching the energy per particle of finite nuclei. For LSD and WS*, the obtained incompressibility coefficients of symmetric nuclear matter are K∞ = 230 ± 11 MeV and 235 ± 11 MeV, respectively. The slope parameter of symmetry energy at saturation density is L = 41.6 ± 7.6 MeV for LSD and 51.5 ± 9.6 MeV for WS*, respectively, which is compatible with the liquid-drop analysis of Lattimer and Lim [4]. The density dependence of the mean-field isoscalar and isovector effective mass, and the neutron-proton effective masses splitting for neutron matter are simultaneously investigated. The results are generally consistent with those from the Skyrme Hartree-Fock-Bogoliubov calculations and nucleon optical potentials, and the standard deviations are large and increase rapidly with density. A better constraint for the effective mass is helpful to reduce uncertainties of the depth of the mean-field potential.

  20. Quantum-limited heat conduction over macroscopic distances (United States)

    Partanen, Matti; Tan, Kuan Yen; Govenius, Joonas; Lake, Russell E.; Mäkelä, Miika K.; Tanttu, Tuomo; Möttönen, Mikko


    The emerging quantum technological apparatuses, such as the quantum computer, call for extreme performance in thermal engineering. Cold distant heat sinks are needed for the quantized electric degrees of freedom owing to the increasing packaging density and heat dissipation. Importantly, quantum mechanics sets a fundamental upper limit for the flow of information and heat, which is quantified by the quantum of thermal conductance. However, the short distance between the heat-exchanging bodies in the previous experiments hinders their applicability in quantum technology. Here, we present experimental observations of quantum-limited heat conduction over macroscopic distances extending to a metre. We achieved this improvement of four orders of magnitude in the distance by utilizing microwave photons travelling in superconducting transmission lines. Thus, it seems that quantum-limited heat conduction has no fundamental distance cutoff. This work establishes the integration of normal-metal components into the framework of circuit quantum electrodynamics, which provides a basis for the superconducting quantum computer. Especially, our results facilitate remote cooling of nanoelectronic devices using faraway in situ-tunable heat sinks. Furthermore, quantum-limited heat conduction is important in contemporary thermodynamics. Here, the long distance may lead to ultimately efficient mesoscopic heat engines with promising practical applications.

  1. Zero time tunneling: macroscopic experiments with virtual particles

    Directory of Open Access Journals (Sweden)

    Nimtz Günter


    Full Text Available Feynman introduced virtual particles in his diagrams as intermediate states of an interaction process. They represent necessary intermediate states between observable real states. Such virtual particles were introduced to describe the interaction process between an electron and a positron and for much more complicated interaction processes. Other candidates for virtual particles are evanescent modes in optics and in elastic fields. Evanescent modes have a purely imaginary wave number, they represent the mathematical analogy of the tunneling solutions of the Schrödinger equation. Evanescent modes exist in the forbidden frequency bands of a photonic lattice and in undersized wave guides, for instance. The most prominent example for the occurrence of evanescent modes is the frustrated total internal reflection (FTIR at double prisms. Evanescent modes and tunneling lie outside the bounds of the special theory of relativity. They can cause faster than light (FTL signal velocities. We present examples of the quantum mechanical behavior of evanescent photons and phonons at a macroscopic scale. The evanescent modes of photons are described by virtual particles as predicted by former QED calculations.

  2. Macroscopic Strain-Induced Transition from Quasi-infinite Gold Nanoparticle Chains to Defined Plasmonic Oligomers. (United States)

    Steiner, Anja Maria; Mayer, Martin; Seuss, Maximilian; Nikolov, Svetoslav; Harris, Kenneth D; Alexeev, Alexander; Kuttner, Christian; König, Tobias A F; Fery, Andreas


    We investigate the formation of chains of few plasmonic nanoparticles-so-called plasmonic oligomers-by strain-induced fragmentation of linear particle assemblies. Detailed investigations of the fragmentation process are conducted by in situ atomic force microscopy and UV-vis-NIR spectroscopy. Based on these experimental results and mechanical simulations computed by the lattice spring model, we propose a formation mechanism that explains the observed decrease of chain polydispersity upon increasing strain and provides experimental guidelines for tailoring chain length distribution. By evaluation of the strain-dependent optical properties, we find a reversible, nonlinear shift of the dominant plasmonic resonance. We could quantitatively explain this feature based on simulations using generalized multiparticle Mie theory (GMMT). Both optical and morphological characterization show that the unstrained sample is dominated by chains with a length above the so-called infinite chain limit-above which optical properties show no dependency on chain length-while during deformation, the average chain length decrease below this limit and chain length distribution becomes more narrow. Since the formation mechanism results in a well-defined, parallel orientation of the oligomers on macroscopic areas, the effect of finite chain length can be studied even using conventional UV-vis-NIR spectroscopy. The scalable fabrication of oriented, linear plasmonic oligomers opens up additional opportunities for strain-dependent optical devices and mechanoplasmonic sensing.

  3. Sine-Gordon modulation solutions: application to macroscopic friction, regular and slow earthquakes and fault dynamics (United States)

    Gershenzon, Naum; Bambakidis, Gust


    The Frenkel-Kontorova (FK) model and its continuum approximation, the sine-Gordon (SG) equation, are widely used for modeling various phenomena. In many practical applications the wave-train solution, which includes many solitons, is required. In such cases the system of Whitham's modulation equations, superimposed on the SG equation, provides such a solution. Here we consider several applications which use the SG modulation solutions [1-3]. Fault dynamics in the earth's crust, i.e. the nucleation and development of regular and slow earthquakes, is a complicated multidisciplinary problem which has been investigated using diverse approaches. Our approach, inspired by dislocation dynamics in crystals, is based on the FK model introduced to describe plasticity. In the model we propose, sliding occurs due to the movement of defects of a certain type (i.e. areas on the frictional surface with locally stressed material, known as a macroscopic dislocation or slip pulse) nucleated by shear stress in the presence of asperities. The spatial translation of a dislocation requires only a small fraction of the stress necessary for the uniform relative displacement of frictional surfaces. This is a fundamental distinction between our approach to macroscopic dry friction and those of others such as the Burridge-Knopoff and rate-and-state types of models. We show how this model can be applied to the qualitative and quantitative description of fault dynamics in general, and slow and regular earthquakes in particular. The three fundamental speeds of plate movement, earthquake migration, and seismic waves are shown to be connected in the FK model. The velocity of nonelastic stress propagation along faults is a function of accumulated stress. It changes from a few km/s during earthquakes to a few dozen km per day, month, or year during afterslip and inter-earthquake periods. The distribution of aftershocks in this model is consistent with both the Omori law for temporal distribution

  4. Distribution of serotonin 2A and 2C receptor mRNA expression in the cervical ventral horn and phrenic motoneurons following spinal cord hemisection. (United States)

    Basura, G J; Zhou, S Y; Walker, P D; Goshgarian, H G


    Cervical spinal cord injury leads to a disruption of bulbospinal innervation from medullary respiratory centers to phrenic motoneurons. Animal models utilizing cervical hemisection result in inhibition of ipsilateral phrenic nerve activity, leading to paralysis of the hemidiaphragm. We have previously demonstrated a role for serotonin (5-HT) as one potential modulator of respiratory recovery following cervical hemisection, a mechanism that likely occurs via 5-HT2A and/or 5-HT2C receptors. The present study was designed to specifically examine if 5-HT2A and/or 5-HT2C receptors are colocalized with phrenic motoneurons in both intact and spinal-hemisected rats. Adult female rats (250-350 g; n = 6 per group) received a left cervical (C2) hemisection and were injected with the fluorescent retrograde neuronal tracer Fluorogold into the left hemidiaphragm. Twenty-four hours later, animals were killed and spinal cords processed for in situ hybridization and immunohistochemistry. Using (35)S-labeled cRNA probes, cervical spinal cords were probed for 5-HT2A and 5-HT2C receptor mRNA expression and double-labeled using an antibody to Fluorogold to detect phrenic motoneurons. Expression of both 5-HT2A and 5-HT2C receptor mRNA was detected in motoneurons of the cervical ventral horn. Despite positive expression of both 5-HT2A and 5-HT2C receptor mRNA-hybridization signal over phrenic motoneurons, only 5-HT2A silver grains achieved a signal-to-noise ratio representative of colocalization. 5-HT2A mRNA levels in identified phrenic motoneurons were not significantly altered following cervical hemisection compared to sham-operated controls. Selective colocalization of 5-HT2A receptor mRNA with phrenic motoneurons may have implications for recently observed 5-HT2A receptor-mediated regulation of respiratory activity and/or recovery in both intact and injury-compromised states. Copyright 2001 Academic Press.

  5. Macroscopic erosion of divertor and first wall armour in future tokamaks (United States)

    Würz, H.; Bazylev, B.; Landman, I.; Pestchanyi, S.; Safronov, V.


    Sputtering, evaporation and macroscopic erosion determine the lifetime of the 'in vessel' armour materials CFC, tungsten and beryllium presently under discussion for future tokamaks. For CFC armour macroscopic erosion means brittle destruction and dust formation whereas for metallic armour melt layer erosion by melt motion and droplet splashing. Available results on macroscopic erosion from hot plasma and e-beam simulation experiments and from tokamaks are critically evaluated and a comprehensive discussion of experimental and numerical macroscopic erosion and its extrapolation to future tokamaks is given. Shielding of divertor armour materials by their own vapor exists during plasma disruptions. The evolving plasma shield protects the armour from high heat loads, absorbs the incoming energy and reradiates it volumetrically thus reducing drastically the deposited energy. As a result, vertical target erosion by vaporization turns out to be of the order of a few microns per disruption event and macroscopic erosion becomes the dominant erosion source.

  6. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.


    RNA modification has attracted increasing interest as it is realized that epitranscriptomics is important in disease development. In type 2 diabetes we have suggested that high urinary excretion of 8-oxo-2'-Guanosine (8oxoGuo), as a measure of global RNA oxidation, is associated with poor survival.......9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...... diabetes. In agreement with our previous finding, DNA oxidation did not show any prognostic value. RNA oxidation represents oxidative stress intracellularly, presumably predominantly in the cytosol. The mechanism of RNA oxidation is not clear, but hypothesized to result from mitochondrial dysfunction...

  7. aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments. (United States)

    Alonso, Arnald; Lasseigne, Brittany N; Williams, Kelly; Nielsen, Josh; Ramaker, Ryne C; Hardigan, Andrew A; Johnston, Bobbi; Roberts, Brian S; Cooper, Sara J; Marsal, Sara; Myers, Richard M


    The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis. ; DOI: 10.5281/zenodo.202950. Supplementary data are available at Bioinformatics online.

  8. Automatic Detection of Malignant Melanoma using Macroscopic Images. (United States)

    Ramezani, Maryam; Karimian, Alireza; Moallem, Payman


    In order to distinguish between benign and malignant types of pigmented skin lesions, computerized procedures have been developed for images taken by different equipment that the most available one of them is conventional digital cameras. In this research, a new procedure to detect malignant melanoma from benign pigmented lesions using macroscopic images is presented. The images are taken by conventional digital cameras with spatial resolution higher than one megapixel and by considering no constraints and special conditions during imaging. In the proposed procedure, new methods to weaken the effect of nonuniform illumination, correction of the effect of thick hairs and large glows on the lesion and also, a new threshold-based segmentation algorithm are presented. 187 features representing asymmetry, border irregularity, color variation, diameter and texture are extracted from the lesion area and after reducing the number of features using principal component analysis (PCA), lesions are determined as malignant or benign using support vector machine classifier. According to the dermatologist diagnosis, the proposed processing methods have the ability to detect lesions area with high accuracy. The evaluation measures of classification have indicated that 13 features extracted by PCA method lead to better results than all of the extracted features. These results led to an accuracy of 82.2%, sensitivity of 77% and specificity of 86.93%. The proposed method may help dermatologists to detect the malignant lesions in the primary stages due to the minimum constraints during imaging, the ease of usage by the public and nonexperts, and high accuracy in detection of the lesion type.

  9. Nuclear magnetic resonance studies of macroscopic morphology and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Barrall, Geoffrey Alden [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry


    Nuclear magnetic resonance techniques are traditionally used to study molecular level structure and dynamics with a noted exception in medically applied NMR imaging (MRI). In this work, new experimental methods and theory are presented relevant to the study of macroscopic morphology and dynamics using NMR field gradient techniques and solid state two-dimensional exchange NMR. The goal in this work is not to take some particular system and study it in great detail, rather it is to show the utility of a number of new and novel techniques using ideal systems primarily as a proof of principle. By taking advantage of the analogy between NMR imaging and diffraction, one may simplify the experiments necessary for characterizing the statistical properties of the sample morphology. For a sample composed of many small features, e.g. a porous medium, the NMR diffraction techniques take advantage of both the narrow spatial range and spatial isotropy of the sample`s density autocorrelation function to obtain high resolution structural information in considerably less time than that required by conventional NMR imaging approaches. The time savings of the technique indicates that NMR diffraction is capable of finer spatial resolution than conventional NMR imaging techniques. Radio frequency NMR imaging with a coaxial resonator represents the first use of cylindrically symmetric field gradients in imaging. The apparatus as built has achieved resolution at the micron level for water samples, and has the potential to be very useful in the imaging of circularly symmetric systems. The study of displacement probability densities in flow through a random porous medium has revealed the presence of features related to the interconnectedness of the void volumes. The pulsed gradient techniques used have proven successful at measuring flow properties for time and length scales considerably shorter than those studied by more conventional techniques.

  10. Emergence of macroscopic directed motion in populations of motile colloids (United States)

    Bricard, Antoine; Caussin, Jean-Baptiste; Desreumaux, Nicolas; Dauchot, Olivier; Bartolo, Denis


    From the formation of animal flocks to the emergence of coordinated motion in bacterial swarms, populations of motile organisms at all scales display coherent collective motion. This consistent behaviour strongly contrasts with the difference in communication abilities between the individuals. On the basis of this universal feature, it has been proposed that alignment rules at the individual level could solely account for the emergence of unidirectional motion at the group level. This hypothesis has been supported by agent-based simulations. However, more complex collective behaviours have been systematically found in experiments, including the formation of vortices, fluctuating swarms, clustering and swirling. All these (living and man-made) model systems (bacteria, biofilaments and molecular motors, shaken grains and reactive colloids) predominantly rely on actual collisions to generate collective motion. As a result, the potential local alignment rules are entangled with more complex, and often unknown, interactions. The large-scale behaviour of the populations therefore strongly depends on these uncontrolled microscopic couplings, which are extremely challenging to measure and describe theoretically. Here we report that dilute populations of millions of colloidal rolling particles self-organize to achieve coherent motion in a unique direction, with very few density and velocity fluctuations. Quantitatively identifying the microscopic interactions between the rollers allows a theoretical description of this polar-liquid state. Comparison of the theory with experiment suggests that hydrodynamic interactions promote the emergence of collective motion either in the form of a single macroscopic `flock', at low densities, or in that of a homogenous polar phase, at higher densities. Furthermore, hydrodynamics protects the polar-liquid state from the giant density fluctuations that were hitherto considered the hallmark of populations of self-propelled particles. Our

  11. Macroscopic and Microscopic Analysis of the Thumb Carpometacarpal Ligaments (United States)

    Ladd, Amy L.; Lee, Julia; Hagert, Elisabet


    Background: Stability and mobility represent the paradoxical demands of the human thumb carpometacarpal joint, yet the structural origin of each functional demand is poorly defined. As many as sixteen and as few as four ligaments have been described as primary stabilizers, but controversy exists as to which ligaments are most important. We hypothesized that a comparative macroscopic and microscopic analysis of the ligaments of the thumb carpometacarpal joint would further define their role in joint stability. Methods: Thirty cadaveric hands (ten fresh-frozen and twenty embalmed) from nineteen cadavers (eight female and eleven male; average age at the time of death, seventy-six years) were dissected, and the supporting ligaments of the thumb carpometacarpal joint were identified. Ligament width, length, and thickness were recorded for morphometric analysis and were compared with use of the Student t test. The dorsal and volar ligaments were excised from the fresh-frozen specimens and were stained with use of a triple-staining immunofluorescent technique and underwent semiquantitative analysis of sensory innervation; half of these specimens were additionally analyzed for histomorphometric data. Mixed-effects linear regression was used to estimate differences between ligaments. Results: Seven principal ligaments of the thumb carpometacarpal joint were identified: three dorsal deltoid-shaped ligaments (dorsal radial, dorsal central, posterior oblique), two volar ligaments (anterior oblique and ulnar collateral), and two ulnar ligaments (dorsal trapeziometacarpal and intermetacarpal). The dorsal ligaments were significantly thicker (p thumb carpometacarpal joint provides further evidence regarding the stability and mobility of this joint that is often affected by osteoarthritis. PMID:22992815

  12. Innovations in macroscopic evaluation of pancreatic specimens and radiologic correlation

    Directory of Open Access Journals (Sweden)

    Charikleia Triantopoulou


    Full Text Available The purpose of this study was to evaluate the feasibility of a novel dissection technique of surgical specimens in different cases of pancreatic tumors and provide a radiologic pathologic correlation. In our hospital, that is a referral center for pancreatic diseases, the macroscopic evaluation of the pancreatectomy specimens is performed by the pathologists using the axial slicing technique (instead of the traditional procedure with longitudinal opening of the main pancreatic and/or common bile duct and slicing along the plane defined by both ducts. The specimen is sliced in an axial plane that is perpendicular to the longitudinal axis of the descending duodenum. The procedure results in a large number of thin slices (3–4 mm. This plane is identical to that of CT or MRI and correlation between pathology and imaging is straightforward. We studied 70 cases of suspected different solid and cystic pancreatic tumors and we correlated the tumor size and location, the structure—consistency (areas of necrosis—hemorrhage—fibrosis—inflammation, the degree of vessels’ infiltration, the size of pancreatic and common bile duct and the distance from resection margins. Missed findings by imaging or pitfalls were recorded and we tried to explain all discrepancies between radiology evaluation and the histopathological findings. Radiologic-pathologic correlation is extremely important, adding crucial information on imaging limitations and enabling quality assessment of surgical specimens. The deep knowledge of different pancreatic tumors’ consistency and way of extension helps to improve radiologists’ diagnostic accuracy and minimize the radiological-surgical mismatching, preventing patients from unnecessary surgery.

  13. Proton irradiation effects on beryllium – A macroscopic assessment

    Energy Technology Data Exchange (ETDEWEB)

    Simos, Nikolaos, E-mail: [Nuclear Sciences & Technology Department, Brookhaven National Laboratory, Upton, NY, 11973 (United States); Elbakhshwan, Mohamed [Nuclear Sciences & Technology Department, Brookhaven National Laboratory, Upton, NY, 11973 (United States); Zhong, Zhong [Photon Sciences, NSLS II, Brookhaven National Laboratory, Upton, NY, 11973 (United States); Camino, Fernando [Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973 (United States)


    Beryllium, due to its excellent neutron multiplication and moderation properties, in conjunction with its good thermal properties, is under consideration for use as plasma facing material in fusion reactors and as a very effective neutron reflector in fission reactors. While it is characterized by unique combination of structural, chemical, atomic number, and neutron absorption cross section it suffers, however, from irradiation generated transmutation gases such as helium and tritium which exhibit low solubility leading to supersaturation of the Be matrix and tend to precipitate into bubbles that coalesce and induce swelling and embrittlement thus degrading the metal and limiting its lifetime. Utilization of beryllium as a pion production low-Z target in high power proton accelerators has been sought both for its low Z and good thermal properties in an effort to mitigate thermos-mechanical shock that is expected to be induced under the multi-MW power demand. To assess irradiation-induced changes in the thermal and mechanical properties of Beryllium, a study focusing on proton irradiation damage effects has been undertaken using 200 MeV protons from the Brookhaven National Laboratory Linac and followed by a multi-faceted post-irradiation analysis that included the thermal and volumetric stability of irradiated beryllium, the stress-strain behavior and its ductility loss as a function of proton fluence and the effects of proton irradiation on the microstructure using synchrotron X-ray diffraction. The mimicking of high temperature irradiation of Beryllium via high temperature annealing schemes has been conducted as part of the post-irradiation study. This paper focuses on the thermal stability and mechanical property changes of the proton irradiated beryllium and presents results of the macroscopic property changes of Beryllium deduced from thermal and mechanical tests.

  14. Macroscopic behavior and microscopic magnetic properties of nanocarbon

    Energy Technology Data Exchange (ETDEWEB)

    Lähderanta, E., E-mail: [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); Ryzhov, V.A. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, Orlova Coppice, Gatchina, Leningrad province 188300 (Russian Federation); Lashkul, A.V. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); Galimov, D.M. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); South Ural State University, 454080 Chelyabinsk (Russian Federation); Titkov, A.N. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); A. F. Ioffe Physico-Technical Institute, 194021 St. Petersburg (Russian Federation); Matveev, V.V. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); Saint-Petersburg State University, Saint-Petersburg 198504 (Russian Federation); Mokeev, M.V. [Institute of Macromolecular Compounds, Russian Academy of Sciences, St. Petersburg (Russian Federation); Kurbakov, A.I. [Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, Orlova Coppice, Gatchina, Leningrad province 188300 (Russian Federation); Lisunov, K.G. [Lappeenranta University of Technology, PO Box 20, FIN-53851 Lappeenranta (Finland); Institute of Applied Physics ASM, Academiei Str., 5, MD 2028 Kishinev (Moldova, Republic of)


    Here are presented investigations of powder and glass-like samples containing carbon nanoparticles, not intentionally doped and doped with Ag, Au and Co. The neutron diffraction study reveals an amorphous structure of the samples doped with Au and Co, as well as the magnetic scattering due to a long-range FM order in the Co-doped sample. The composition and molecular structure of the sample doped with Au is clarified with the NMR investigations. The temperature dependence of the magnetization, M (T), exhibits large irreversibility in low fields of B=1–7 mT. M (B) saturates already above 2 T at high temperatures, but deviates from the saturation behavior below ~50 (150 K). Magnetic hysteresis is observed already at 300 K and exhibits a power-law temperature decay of the coercive field, B{sub c} (T). The macroscopic behavior above is typical of an assembly of partially blocked magnetic nanoparticles. The values of the saturation magnetization, M{sub s}, and the blocking temperature, T{sub b}, are obtained as well. However, the hysteresis loop in the Co-doped sample differs from that in other samples, and the values of B{sub c} and M{sub s} are noticeably increased. - Highlights: • We have investigated powder and glassy samples with carbon nanoparticles. • They include an undoped sample and those doped with Ag, Au and Co. • Neutron diffraction study reveals amorphous structure of Au- and Co-doped samples. • Composition and molecular structure of Au-doped sample was investigated with NMR. • Magnetic behavior is typical of an assembly of partially blocked magnetic nanoparticles.

  15. Emergence of macroscopic directed motion in populations of motile colloids. (United States)

    Bricard, Antoine; Caussin, Jean-Baptiste; Desreumaux, Nicolas; Dauchot, Olivier; Bartolo, Denis


    From the formation of animal flocks to the emergence of coordinated motion in bacterial swarms, populations of motile organisms at all scales display coherent collective motion. This consistent behaviour strongly contrasts with the difference in communication abilities between the individuals. On the basis of this universal feature, it has been proposed that alignment rules at the individual level could solely account for the emergence of unidirectional motion at the group level. This hypothesis has been supported by agent-based simulations. However, more complex collective behaviours have been systematically found in experiments, including the formation of vortices, fluctuating swarms, clustering and swirling. All these (living and man-made) model systems (bacteria, biofilaments and molecular motors, shaken grains and reactive colloids) predominantly rely on actual collisions to generate collective motion. As a result, the potential local alignment rules are entangled with more complex, and often unknown, interactions. The large-scale behaviour of the populations therefore strongly depends on these uncontrolled microscopic couplings, which are extremely challenging to measure and describe theoretically. Here we report that dilute populations of millions of colloidal rolling particles self-organize to achieve coherent motion in a unique direction, with very few density and velocity fluctuations. Quantitatively identifying the microscopic interactions between the rollers allows a theoretical description of this polar-liquid state. Comparison of the theory with experiment suggests that hydrodynamic interactions promote the emergence of collective motion either in the form of a single macroscopic 'flock', at low densities, or in that of a homogenous polar phase, at higher densities. Furthermore, hydrodynamics protects the polar-liquid state from the giant density fluctuations that were hitherto considered the hallmark of populations of self-propelled particles. Our

  16. Human type 2 17beta-hydroxysteroid dehydrogenase mRNA and protein distribution in placental villi at mid and term pregnancy

    Directory of Open Access Journals (Sweden)

    Plante Julie


    Full Text Available Abstract Background During human pregnancy, the placental villi produces high amounts of estradiol. This steroid is secreted by the syncytium, which is directly in contact with maternal blood. Estradiol has to cross placental foetal vessels to reach foetal circulation. The enzyme 17beta-hydroxysteroid dehydrogenase type 2 (17beta-HSD2 was detected in placental endothelial cells of foetal vessels inside the villi. This enzyme catalyzes the conversion of estradiol to estrone, and of testosterone to androstenedione. It was proposed that estradiol level into foetal circulation could be regulated by 17beta-HSD2. Methods We obtained placentas from 10 to 26 6/7 weeks of pregnancy from women undergoing voluntary termination of pregnancy, term placentas were collected after normal spontaneous vaginal deliveries. We quantified 17beta-HSD2 mRNA levels in mid-gestation and term human placenta by RT-QPCR. We produced a new anti-17beta-HSD2 antibody to study its spatio-temporal expression by immunohistochemistry. We also compared steroid levels (testosterone, estrone and estradiol and 17beta-HSD2 mRNA and protein levels between term placenta and endometrium. Results High 17beta-HSD2 mRNA and protein levels were found in both mid-gestation and term placentas. However, we showed that 17beta-HSD2 mRNA levels increase by 2.27 fold between mid-gestation and term. This period coincides with a transitional phase in the development of the villous vasculature. In mid-gestation placenta, high levels of 17beta-HSD2 were found in mesenchymal villi and immature intermediate villi, more precisely in endothelial cells of the stromal channel. At term, high levels of 17beta-HSD2 were found in the numerous sinusoidal capillaries of terminal villi. 17beta-HSD2 mRNA and protein levels in term placentas were respectively 25.4 fold and 30 to 60 fold higher than in the endometrium. Steroid levels were also significantly higher in term placenta than in the endometrium. Conclusion

  17. Combined thermotherapy and cryotherapy for efficient virus eradication: relation of virus distribution, subcellular changes, cell survival and viral RNA degradation in shoot tips. (United States)

    Wang, Qiaochun; Cuellar, Wilmer J; Rajamäki, Minna-Liisa; Hirata, Yukimasa; Valkonen, Jari P T


    Accumulation of viruses in vegetatively propagated plants causes heavy yield losses. Therefore, supply of virus-free planting materials is pivotal to sustainable crop production. In previous studies, Raspberry bushy dwarf virus (RBDV) was difficult to eradicate from raspberry (Rubus idaeus) using the conventional means of meristem tip culture. As shown in the present study, it was probably because this pollen-transmitted virus efficiently invades leaf primordia and all meristematic tissues except the least differentiated cells of the apical dome. Subjecting plants to thermotherapy prior to meristem tip culture heavily reduced viral RNA2, RNA3 and the coat protein in the shoot tips, but no virus-free plants were obtained. Therefore, a novel method including thermotherapy followed by cryotherapy was developed for efficient virus eradication. Heat treatment caused subcellular alterations such as enlargement of vacuoles in the more developed, virus-infected cells, which were largely eliminated following subsequent cryotherapy. Using this protocol, 20-36% of the treated shoot tips survived, 30-40% regenerated and up to 35% of the regenerated plants were virus-free, as tested by ELISA and reverse transcription loop-mediated isothermal amplification. Novel cellular and molecular insights into RBDV-host interactions and the factors influencing virus eradication were obtained, including invasion of shoot tips and meristematic tissues by RBDV, enhanced viral RNA degradation and increased sensitivity to freezing caused by thermotherapy, and subcellular changes and subsequent death of cells caused by cryotherapy. This novel procedure should be helpful with many virus-host combinations in which virus eradication by conventional means has proven difficult.

  18. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane (United States)

    Briggs, B.R.; Pohlman, J.W.; Torres, M.; Riedel, M.; Brodie, E.L.; Colwell, F.S.


    Methane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 10 7 to 10 8 cells cm -3. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated by Deltaproteobacteria, candidate division WS3, and Chloroflexi, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade, Thermoplasmatales, and Desulfurococcales, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla of Methanosarcinales and Desulfurococcales. The stable carbon isotope composition of the biofilm from the SMT (-35 to-43%) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments. ?? 2011, American Society for Microbiology.

  19. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge

    for biosensorer,  der kan spore enten microRNA’er eller små molekyler, eksemplificeret ved S-adenosylmethionin (SAM). Slutteligt indikerer foreløbige resultater, at apta-FRET SAM sensoren kan udtrykkes i Escherichia coli-celler, hvilket viser, at RNA-origami arkitekturen muliggør cotransskriptionel foldning af...... fra en enkelt RNA-streng, og udfører en lang række komplekse cellulære funktioner. Mange af funktionerne er blevet udnyttet til at skabe funktionelle RNA-baserede nanoapparater, men den nuværende litteratur giver kun få eksempler på cotranskriptionel produktion af RNA-nanostrukturer. I 2014...... introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...

  20. Polymorphic phase transitions: Macroscopic theory and molecular simulation. (United States)

    Anwar, Jamshed; Zahn, Dirk


    Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic

  1. Microscopical, macroscopical and chemical investigations and their uses in chemotaxonomy of Crataegus pontica C. Koch

    Directory of Open Access Journals (Sweden)

    Nasrollah Ghassemi Dehkordi


    Full Text Available The Crataegus genus is widely distributed in Iran. This genus belongs to Rosaceae family and has 17 species in Iran one of which is Crataegus pontica C. Koch. In this paper, we analyzed some microscopic and macroscopic characteristics of this plant, then compared them with other features that were presented previously in previous reports. We analyzed all components in C. pontica, using thin layer chromatography method and then specified the type of flavonoids and hydroxycinnamic acid in C. pontica. Hyproside, rutin and chlorogenic acid were the main flavonoids and hydroxycinnamic occurred acid in this plant. Also, we analyzed its flavonoids quantitatively based on Deutsch Pharmacopoeia method according to hyproside content. Because, to determine the chemosystematic relevancies in some species flavonoids are used, so in this paper we compared C. pontica with 3 other species of its genus such as C. monogyna, C. melanocarpa and C. curvisepala that are found in Iran, and also with the medicinal standard species of Crataegus genus which is called C. oxyacantha. Finally we concluded that hyproside, rutin and chlorogenic acid were the main and common structural components in all species of that genus which were mentioned above.

  2. Theory of Macroscopic Quantum Tunneling in High-T_c c-Axis Josephson Junctions

    CERN Document Server

    Yokoyama, Takehito; Kato, Takeo; Tanaka, Yukio


    We study macroscopic quantum tunneling (MQT) in c-axis twist Josephson junctions made of high-T_c superconductors in order to clarify the influence of the anisotropic order parameter symmetry (OPS) on MQT. The dependence of the MQT rate on the twist angle $\\gamma$ about the c-axis is calculated by using the functional integral and the bounce method. Due to the d-wave OPS, the $\\gamma$ dependence of standard deviation of the switching current distribution and the crossover temperature from thermal activation to MQT are found to be given by $\\cos2\\gamma$ and $\\sqrt{\\cos2\\gamma}$, respectively. We also show that a dissipative effect resulting from the nodal quasiparticle excitation on MQT is negligibly small, which is consistent with recent MQT experiments using Bi${}_2$Sr${}_2$CaCu${}_2$O${}_{8 + \\delta}$ intrinsic junctions. These results indicate that MQT in c-axis twist junctions becomes a useful experimental tool for testing the OPS of high-T_c materials at low temperature, and suggest high potential of suc...

  3. Equation-Free Analysis of Macroscopic Behavior in Traffic and Pedestrian Flow

    DEFF Research Database (Denmark)

    Marschler, Christian; Sieber, Jan; Hjorth, Poul G.


    Equation-free methods make possible an analysis of the evolution of a few coarse-grained or macroscopic quantities for a detailed and realistic model with a large number of fine-grained or microscopic variables, even though no equations are explicitly given on the macroscopic level. This will fac......Equation-free methods make possible an analysis of the evolution of a few coarse-grained or macroscopic quantities for a detailed and realistic model with a large number of fine-grained or microscopic variables, even though no equations are explicitly given on the macroscopic level....... This will facilitate a study of how the model behavior depends on parameter values including an understanding of transitions between different types of qualitative behavior. These methods are introduced and explained for traffic jam formation and emergence of oscillatory pedestrian counter flow in a corridor...

  4. Three-dimensional Fe3O4-graphene macroscopic composites for arsenic and arsenate removal. (United States)

    Guo, Liangqia; Ye, Peirong; Wang, Jing; Fu, Fengfu; Wu, Zujian


    3D graphene macroscopic gel synthesized via self-assembly of GO nanosheets under basic conditions at low temperature is modified with polydopamine and Fe3O4 nanoparticles. The modification of polydopamine can not only strengthen the 3D graphene-based macroscopic architecture but also enhance the loadage and binding ability of Fe3O4 nanoparticles. The synthesized 3D Fe3O4-graphene macroscopic composites are characterized by SEM, XRD, XPS, BET, Raman and magnetic property and used as a versatile adsorbent for sub-ppm concentration of As(III) and As(V) removal from aqueous solutions. The experimental results suggest that the synthesized 3D Fe3O4-graphene macroscopic composites are promising for treating low concentration of arsenic contaminated water. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Macroscopic order and electro-optic response of dipolar chromophore-polymer materials. (United States)

    Pereverzev, Yuriy V; Prezhdo, Oleg V; Dalton, Larry R


    This Minireview considers the key factors that govern the organization of macroscopic polarization in nonlinear optical systems obtained by electric poling of organic dipolar chromophores dissolved in polymer matrices. The macroscopic electric polarization depends on the thermodynamic state of the dipole system. The dependence of the paraelectric and antiferroelectric states of dipolar chromophores on the chromophore concentration and the strength of the poling field is discussed. Phase transitions between the para- and antiferroelectric states are investigated within the limits of the Ising and isotropic models for the chromophore dipoles and are considered for varying chromophore concentration, poling field strength, and macroscopic shape of the sample used for poling. The macroscopic polarization and electro-optic coefficient of the material change drastically upon phase transition. The theories are compared with the experimental data on the electro-optic coefficient dependence on the chromophore concentration. The isotropic dipole model shows excellent agreement with experiment for the chromophore systems most commonly used in nonlinear optics.

  6. Macroscopic Properties of Nuclei within Self-Consistent and Liquid Drop Models (United States)

    Nerlo-Pomorska, B.; Sykut, J.


    A set of parameters of the relativistic-mean-field theory (RMFT) is obtained by adjusting the macroscopic part of the RMFT binding energies of 142 spherical even-even nuclei to the phenomenological Lublin-Strasbourg-Drop (LSD) model.

  7. Magnetic susceptibility anisotropy: cylindrical symmetry from macroscopically ordered anisotropic molecules and accuracy of MRI measurements using few orientations. (United States)

    Wisnieff, Cynthia; Liu, Tian; Spincemaille, Pascal; Wang, Shuai; Zhou, Dong; Wang, Yi


    White matter is an essential component of the central nervous system and is of major concern in neurodegenerative diseases such as multiple sclerosis (MS). Recent MRI studies have explored the unique anisotropic magnetic properties of white matter using susceptibility tensor imaging. However, these measurements are inhibited in practice by the large number of different head orientations needed to accurately reconstruct the susceptibility tensor. Adding reasonable constraints reduces the number of model parameters and can help condition the tensor reconstruction from a small number of orientations. The macroscopic magnetic susceptibility is decomposed as a sum of molecular magnetic polarizabilities, demonstrating that macroscopic order in molecular arrangement is essential to the existence of and symmetry in susceptibility anisotropy and cylindrical symmetry is a natural outcome of an ordered molecular arrangement. Noise propagation in the susceptibility tensor reconstruction is analyzed through its condition number, showing that the tensor reconstruction is highly susceptible to the distribution of acquired subject orientations and to the tensor symmetry properties, with a substantial over- or under-estimation of susceptibility anisotropy in fiber directions not favorably oriented with respect to the acquired orientations. It was found that a careful acquisition of three non-coplanar orientations and the use of cylindrical symmetry guided by diffusion tensor imaging allowed reasonable estimation of magnetic susceptibility anisotropy in certain major white matter tracts in the human brain. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Value of conventional cytology in the presence of macroscopic lesions of the anal canal


    Barcellos,Lêda Pereira de; Russomano, Fábio; Coutinho,José Ricardo Hildebrandt


    OBJECTIVES: To verify the value of conventional cytology for the diagnosis of macroscopic lesions of the anal canal and to describe the limitations of the samples.METHOD: We evaluated 395 conventional cytology samples obtained by brushing the anal canal of patients (predominantly male, HIV-positive) and compared them to the presence of macroscopic lesions of the anal canal observed under anorectal examination.RESULTS: Of the total, 91.6% of samples were classified as adequate. Cellular elemen...

  9. Relaxation to equilibrium of the expectation values in macroscopic quantum systems. (United States)

    Monnai, Takaaki


    A quantum mechanical explanation of the relaxation to equilibrium is shown for macroscopic systems for nonintegrable cases and numerically verified. The macroscopic system is initially in an equilibrium state, subsequently externally perturbed during a finite time, and then isolated for a sufficiently long time. We show a quantitative explanation that the initial microcanonical state typically reaches a state whose expectation values are well approximated by the average over another microcanonical ensemble.

  10. Energetics of macroscopic helical domain in different tube geometries and loading


    Sun Q.P.; Zhou R


    Superelastic NiTi polycrystalline shape memory alloy tubes, when subject to slow quasistatic stretching, transform to a high strain phase by the formation and growth of a macroscopic helix-shaped domain as deformation progresses. This paper performed an experimental study on the effects of the external applied nominal strain and the tube geometry (tube radius R, wall-thickness h and length L) on the helical domains in isothermal stretching of the tubes. The evolution of the macroscopic ...

  11. Approximation of macroscopic conductivity for a multiscale model by using mortar methods (United States)

    Kim, Hyea Hyun; Kim, Ji Eun


    For a model with highly varying and multiscale conductivity, its macroscopic conductivity is approximated by using a mortar method. Macroscopic conductivity is useful in forming macroscopic models for porous media flow applications and in the setting of multiscale fast solvers. Many previous studies are based on the following procedure. Microscale models in each small cell are solved independently with an appropriate boundary condition and the solutions from the localized microscale problems are used to approximate the macroscopic conductivity. The size of the small cell and the boundary conditions affect the accuracy of the approximation. In this work, a mortar method is utilized to form localized microscale problems which are less sensitive to the boundary conditions. In addition, a simple and explicit formula for optimally determined macroscopic conductivity is derived by solving a nonlinear minimization problem. No postprocessing is thus required in our approach to calculate the macroscopic conductivity from the solutions of localized microscopic models. The new approach is numerically studied for various test models and compared to existing methods.

  12. The distribution of circulating microRNA and their relation to coronary disease [v1; ref status: indexed,

    Directory of Open Access Journals (Sweden)

    Jane E Freedman


    Full Text Available Background: MicroRNAs (miRNAs are small RNAs that regulate gene expression by suppressing protein translation and may influence RNA expression. MicroRNAs are detected in extracellular locations such as plasma; however, the extent of miRNA expression in plasma its relation to cardiovascular disease is not clear and many clinical studies have utilized array-based platforms with poor reproducibility. Methods and Results: Initially, to define distribution of miRNA in human blood; whole blood, platelets, mononuclear cells, plasma, and serum from 5 normal individuals were screened for 852 miRNAs using high-throughput micro-fluidic quantitative RT-PCR (qRT-PCR. In total; 609, 448, 658, 147, and 178 miRNAs were found to be expressed in moderate to high levels in whole blood, platelets, mononuclear cells, plasma, and serum, respectively, with some miRNAs uniquely expressed. To determine the cardiovascular relevance of blood miRNA expression, plasma miRNA (n=852 levels were measured in 83 patients presenting for cardiac catheterization. Eight plasma miRNAs were found to have over 2-fold increased expression in patients with significant coronary disease (≥70% stenosis as compared to those with minimal coronary disease (less than 70% stenosis or normal coronary arteries. Expression of miR-494, miR-490-3p, and miR-769-3p were found to have significantly different levels of expression. Using a multivariable regression model including cardiovascular risk factors and medications, hsa-miR-769-3p was found to be significantly correlated with the presence of significant coronary atherosclerosis. Conclusions: This study utilized a superior high-throughput qRT-PCR based method and found that miRNAs are found to be widely expressed in human blood with differences expressed between cellular and extracellular fractions. Importantly, specific miRNAs from circulating plasma are associated with the presence of significant coronary disease.

  13. Investigation of representing hysteresis in macroscopic models of two-phase flow in porous media using intermediate scale experimental data (United States)

    Cihan, Abdullah; Birkholzer, Jens; Trevisan, Luca; Gonzalez-Nicolas, Ana; Illangasekare, Tissa


    Incorporating hysteresis into models is important to accurately capture the two phase flow behavior when porous media systems undergo cycles of drainage and imbibition such as in the cases of injection and post-injection redistribution of CO2 during geological CO2 storage (GCS). In the traditional model of two-phase flow, existing constitutive models that parameterize the hysteresis associated with these processes are generally based on the empirical relationships. This manuscript presents development and testing of mathematical hysteretic capillary pressure—saturation—relative permeability models with the objective of more accurately representing the redistribution of the fluids after injection. The constitutive models are developed by relating macroscopic variables to basic physics of two-phase capillary displacements at pore-scale and void space distribution properties. The modeling approach with the developed constitutive models with and without hysteresis as input is tested against some intermediate-scale flow cell experiments to test the ability of the models to represent movement and capillary trapping of immiscible fluids under macroscopically homogeneous and heterogeneous conditions. The hysteretic two-phase flow model predicted the overall plume migration and distribution during and post injection reasonably well and represented the postinjection behavior of the plume more accurately than the nonhysteretic models. Based on the results in this study, neglecting hysteresis in the constitutive models of the traditional two-phase flow theory can seriously overpredict or underpredict the injected fluid distribution during post-injection under both homogeneous and heterogeneous conditions, depending on the selected value of the residual saturation in the nonhysteretic models.

  14. Aspects of macroscopic phase separation and interstitial oxygen ordering in oxygen doped La{sub 2}CuO{sub 4+{delta}}

    Energy Technology Data Exchange (ETDEWEB)

    Hammel, P.C.; Fisk, Z. [Los Alamos National Lab., NM (United States); Statt, B.W. [Univ. of Toronto, Toronto (Canada). Dept. of Physics; Chou, F.C.; Johnston, D.C. [Ames Lab., IA (United States); Cheong, S.W. [AT& T Bell Labs., Murray Hill, NJ (United States); Schirber, J.E. [Sandia National Labs., Albuquerque, NM (United States)


    NMR and neutron diffraction measurements reveal that macroscopic phase separation and the tetragonal to orthorhombic (TO) structural phase coincide at two distinct points in the temperature-doping phase plot for oxygen doped La{sub 2}CuO{sub 4+{delta}}. Thus the TO phase line coincides with the phase separation line. This is evidence that the macroscopic phase separation is inhibited in the tetragonal phase. We propose that the interstitial oxygen has higher mobility in the orthorhombic phase and that insufficient mobility suppresses macroscopic phase separation in the tetragonal phase. Neutron diffraction measurements also reveal superlattice peaks which indicate ordering of the interstitial oxygen. Our NMR measurements, have demonstrated a distribution of tilts of the CuO{sub 6} octahedra. We propose a sawtooth modulation of the octahedral tilt in which the sign of the tilt changes when the tilt reaches a maximum value can explain this distribution. The large openings in the La-O layer resulting from the abrupt switch of the sign of the tilt provide an attractive location for the interstitial oxygen. This mechanism would lead to stripe ordering of the interstitial oxygen.

  15. Distribution analysis of profilin isoforms at transcript resolution with mRNA-seq and secondary structure in various organs of Rattus norvegicus. (United States)

    Tariq, Naila; Basharat, Zarrin; Butt, Saba; Baig, Deeba Noreen


    Profilin (Pfn) is an actin binding protein, ubiquitously found in mammals and is essential for the actin polymerization in cells. In brain, it plays a pivotal role in neurogenesis and synapse formation by interacting with various proteins. Four Pfn isoforms have been identified in mammals. This study presents the identification and transcriptional expression of various Pfn isoforms (Pfn1, Pfn2, Pfn3 and Pfn4) in brain, heart, kidney, liver, and muscle and testis of Rattus norvegicus. Organs have been classified into groups based on some similarities. Group I includes brain and testis, Group II includes skeletal muscle and heart, while Group III includes kidney and liver. Pfn1 has been identified in all groups, Pfn2 and Pfn3 have been identified in group I, group III and in one organ (skeletal muscle) of group II. To the best of the authors knowledge, no report of Pfn1 and Pfn2 presence in testis, Pfn3 in brain, liver and skeletal muscle, Pfn4 in kidney and skeletal muscle exists to date. Transcriptional expression showed variations among expression level of different Pfn isoforms in various organs with respect to the control gene GADPH. We hypothesize that this could be attributed to profilin isoform specific mRNA structure and corresponding motifs, which generally contribute to similar or varied decay rates, cellular localization, post transcriptional regulation pattern and ligand binding. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Detection of the European epidemic strain of Trichomonas gallinae in finches, but not other non-columbiformes, in the absence of macroscopic disease. (United States)

    Zu Ermgassen, Erasmus K H J; Durrant, Chris; John, Shinto; Gardiner, Roxanne; Alrefaei, Abdulwahed F; Cunningham, Andrew A; Lawson, Becki


    Finch trichomonosis is an emerging infectious disease affecting European passerines caused by a clonal strain of Trichomonas gallinae. Migrating chaffinches (Fringilla coelebs) were proposed as the likely vector of parasite spread from Great Britain to Fennoscandia. To test for such parasite carriage, we screened samples of oesophagus/crop from 275 Apodiform, Passeriform and Piciform birds (40 species) which had no macroscopic evidence of trichomonosis (i.e. necrotic ingluvitis). These birds were found dead following the emergence of trichomonosis in Great Britain, 2009-2012, and were examined post-mortem. Polymerase chain reactions were used to detect (ITS1/5·8S rRNA/ITS2 region and single subunit rRNA gene) and to subtype (Fe-hydrogenase gene) T. gallinae. Trichomonas gallinae was detected in six finches [three chaffinches, two greenfinches (Chloris chloris) and a bullfinch (Pyrrhula pyrrhula)]. Sequence data had 100% identity to the European finch epidemic A1 strain for each species. While these results are consistent with finches being vectors of T. gallinae, alternative explanations include the presence of incubating or resolved T. gallinae infections. The inclusion of histopathological examination would help elucidate the significance of T. gallinae infection in the absence of macroscopic lesions.

  17. Neuropeptide Y (NPY), cocaine- and amphetamine-regulated transcript (CART) and cholecystokinin (CCK) in winter skate (Raja ocellata): cDNA cloning, tissue distribution and mRNA expression responses to fasting. (United States)

    MacDonald, Erin; Volkoff, Hélène


    cDNAs encoding for neuropeptide Y (NPY), cocaine- and amphetamine-regulated transcript (CART) and cholecystokinin (CCK) were cloned in an elasmobranch fish, the winter skate. mRNA tissue distribution was examined for the three peptides as well as the effects of two weeks of fasting on their expression. Skate NPY, CART and CCK sequences display similarities with sequences for teleost fish but in general the degree of identity is relatively low (50%). All three peptides are present in brain and in several peripheral tissues, including gut and gonads. Within the brain, the three peptides are expressed in the hypothalamus, telencephalon, optic tectum and cerebellum. Two weeks of fasting induced an increase in telencephalon NPY and an increase in CCK in the gut but had no effects on hypothalamic NPY, CART and CCK, or on telencephalon CART. Our results provide basis for further investigation into the regulation of feeding in winter skate.

  18. Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis. (United States)

    Meyer, Birte; Kuever, Jan


    Denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA, aprA, and amoA genes demonstrated that a phylogenetically diverse and complex microbial community was associated with the Caribbean deep-water sponge Polymastia cf. corticata Ridley and Dendy, 1887. From the 38 archaeal and bacterial 16S rRNA phylotypes identified, 53% branched into the sponge-specific, monophyletic sequence clusters determined by previous studies (considering predominantly shallow-water sponge species), whereas 26% appeared to be P. cf. corticata specifically associated microorganisms ("specialists"); 21% of the phylotypes were confirmed to represent seawater- and sediment-derived proteobacterial species ("contaminants") acquired by filtration processes from the host environment. Consistently, the aprA and amoA gene-based analyses indicated the presence of environmentally derived sulfur- and ammonia-oxidizers besides putative sponge-specific sulfur-oxidizing Gammaproteobacteria and Alphaproteobacteria and a sulfate-reducing archaeon. A sponge-specific, endosymbiotic sulfur cycle as described for marine oligochaetes is proposed to be also present in P. cf. corticata. Overall, the results of this work support the recent studies that demonstrated the sponge species specificity of the associated microbial community while the biogeography of the host collection site has only a minor influence on the composition. In P. cf. corticata, the specificity of the sponge-microbe associations is even extended to the spatial distribution of the microorganisms within the sponge body; distinct bacterial populations were associated with the different tissue sections, papillae, outer and inner cortex, and choanosome. The local distribution of a phylotype within P. cf. corticata correlated with its (1) phylogenetic affiliation, (2) classification as sponge-specific or nonspecifically associated microorganism, and (3) potential ecological role in the host sponge.

  19. Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria (United States)

    Glöckner, Frank Oliver; Zaichikov, Evgeny; Belkova, Natalia; Denissova, Ludmilla; Pernthaler, Jakob; Pernthaler, Annelie; Amann, Rudolf


    In a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16S ribosomal DNA (rDNA) sequences from three different lakes (Lake Gossenköllesee, Austria; Lake Fuchskuhle, Germany; and Lake Baikal, Russia). The phylogenetic comparison with the currently available rDNA data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rDNA sequences of primarily freshwater and soil, but not marine, origin. Six of the clusters were affiliated with the α, four were affiliated with the β, and one was affiliated with the γ subclass of the Proteobacteria; four were affiliated with the Cytophaga-Flavobacterium-Bacteroides group; and one was affiliated with the class Actinobacteria (formerly known as the high-G+C gram-positive bacteria). The latter cluster (hgcI) is monophyletic and so far includes only sequences directly retrieved from aquatic environments. Fluorescence in situ hybridization (FISH) with probes specific for the hgcI cluster showed abundances of up to 1.7 × 105 cells ml−1 in Lake Gossenköllesee, with strong seasonal fluctuations, and high abundances in the two other lakes investigated. Cell size measurements revealed that Actinobacteria in Lake Gossenköllesee can account for up to 63% of the bacterioplankton biomass. A combination of phylogenetic analysis and FISH was used to reveal 16 globally distributed sequence clusters and to confirm the broad distribution, abundance, and high biomass of members of the class Actinobacteria in freshwater ecosystems. PMID:11055963

  20. Thermal Equilibrium of a Macroscopic Quantum System in a Pure State. (United States)

    Goldstein, Sheldon; Huse, David A; Lebowitz, Joel L; Tumulka, Roderich


    We consider the notion of thermal equilibrium for an individual closed macroscopic quantum system in a pure state, i.e., described by a wave function. The macroscopic properties in thermal equilibrium of such a system, determined by its wave function, must be the same as those obtained from thermodynamics, e.g., spatial uniformity of temperature and chemical potential. When this is true we say that the system is in macroscopic thermal equilibrium (MATE). Such a system may, however, not be in microscopic thermal equilibrium (MITE). The latter requires that the reduced density matrices of small subsystems be close to those obtained from the microcanonical, equivalently the canonical, ensemble for the whole system. The distinction between MITE and MATE is particularly relevant for systems with many-body localization for which the energy eigenfuctions fail to be in MITE while necessarily most of them, but not all, are in MATE. We note, however, that for generic macroscopic systems, including those with MBL, most wave functions in an energy shell are in both MATE and MITE. For a classical macroscopic system, MATE holds for most phase points on the energy surface, but MITE fails to hold for any phase point.

  1. Single-crystal Ih ice surfaces unveil connection between macroscopic and molecular structure. (United States)

    Brumberg, Alexandra; Hammonds, Kevin; Baker, Ian; Backus, Ellen H G; Bisson, Patrick J; Bonn, Mischa; Daghlian, Charles P; Mezger, Markus D; Shultz, Mary Jane


    Physics and chemistry of ice surfaces are not only of fundamental interest but also have important impacts on biological and environmental processes. As ice surfaces-particularly the two prism faces-come under greater scrutiny, it is increasingly important to connect the macroscopic faces with the molecular-level structure. The microscopic structure of the ubiquitous ice Ih crystal is well-known. It consists of stacked layers of chair-form hexagonal rings referred to as molecular hexagons. Crystallographic unit cells can be assembled into a regular right hexagonal prism. The bases are labeled crystallographic hexagons. The two hexagons are rotated 30° with respect to each other. The linkage between the familiar macroscopic shape of hexagonal snowflakes and either hexagon is not obvious per se. This report presents experimental data directly connecting the macroscopic shape of ice crystals and the microscopic hexagons. Large ice single crystals were used to fabricate samples with the basal, primary prism, or secondary prism faces exposed at the surface. In each case, the same sample was used to capture both a macroscopic etch pit image and an electron backscatter diffraction (EBSD) orientation density function (ODF) plot. Direct comparison of the etch pit image and the ODF plot compellingly connects the macroscopic etch pit hexagonal profile to the crystallographic hexagon. The most stable face at the ice-water interface is the smallest area face at the ice-vapor interface. A model based on the molecular structure of the prism faces accounts for this switch.

  2. Distribution of Borna disease virus antigen and RNA in tissues of naturally infected bicolored white-toothed shrews, Crocidura leucodon, supporting their role as reservoir host species. (United States)

    Puorger, M E; Hilbe, M; Müller, J-P; Kolodziejek, J; Nowotny, N; Zlinszky, K; Ehrensperger, F


    Borna disease is a severe viral-induced disorder of the central nervous system of horses, sheep, and a few other animal species, occurring in certain areas of central Europe. Pathogenesis and epidemiology of natural Borna disease virus (BDV) infections are still not fully understood; several unique epidemiologic features, however, point toward the existence of BDV reservoir populations other than the final hosts. In this study, 69 mice and 12 shrews were trapped and examined. The virus distribution was investigated in detail in 2 BDV-positive bicolored white-toothed shrews, Crocidura leucodon, by immunohistochemistry and TaqMan real-time reverse transcription polymerase chain reaction (RT-PCR). RT-PCR amplification products were sequenced, and the sequences were compared. These shrews had been collected in a BDV-endemic geographical region using live traps and did not show obvious clinical or pathological disease signs. BDV antigen and nucleic acid were identified in several organs, including the brain, mainly in nerve tissue and neurons, respectively, but also in parenchymal cells (eg, hepatocytes, Leydig cells) and epithelial cells, particularly of the respiratory and urogenital tract.

  3. Macroscopic extent of gastric mucosal atrophy: increased risk factor for esophageal squamous cell carcinoma in Japan

    Directory of Open Access Journals (Sweden)

    Kobayashi Noritoshi


    Full Text Available Abstract Background We aimed to estimate whether the macroscopic extent of gastric mucosal atrophy is associated with a risk for esophageal squamous cell carcinoma using a case-control study in Japanese subjects, a population known to have a high prevalence of CagA-positive H. pylori infection. Methods Two hundred and fifty-three patients who were diagnosed as having esophageal squamous cell carcinoma, and 253 sex- and age-matched controls were enrolled in the present study. The macroscopic extent of gastric mucosal atrophy was evaluated based on the Kimura and Takemoto Classification. A conditional logistic regression model with adjustment for potential confounding factors was used to assess the associations. Results Body gastritis, defined endoscopically, was independently associated with an increased risk for esophageal squamous cell carcinoma. Conclusion Our findings suggest that macroscopic body gastritis may be a risk factor for esophageal squamous cell carcinoma in Japan. Further studies are needed to confirm these findings.

  4. Macroscopic Polarization Enhancement Promoting Photo- and Piezoelectric-Induced Charge Separation and Molecular Oxygen Activation. (United States)

    Huang, Hongwei; Tu, Shuchen; Zeng, Chao; Zhang, Tierui; Reshak, Ali H; Zhang, Yihe


    Efficient photo- and piezoelectric-induced molecular oxygen activation are both achieved by macroscopic polarization enhancement on a noncentrosymmetric piezoelectric semiconductor BiOIO 3 . The replacement of V 5+ ions for I 5+ in IO 3 polyhedra gives rise to strengthened macroscopic polarization of BiOIO 3 , which facilitates the charge separation in the photocatalytic and piezoelectric catalytic process, and renders largely promoted photo- and piezoelectric induced reactive oxygen species (ROS) evolution, such as superoxide radicals ( . O 2 - ) and hydroxyl radicals ( . OH). This work advances piezoelectricity as a new route to efficient ROS generation, and also discloses macroscopic polarization engineering on improvement of multi-responsive catalysis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Wet-spinning assembly of continuous, neat, and macroscopic graphene fibers. (United States)

    Cong, Huai-Ping; Ren, Xiao-Chen; Wang, Ping; Yu, Shu-Hong


    Graphene is now the most attractive carbon-based material. Integration of 2D graphene sheets into macroscopic architectures such as fibers illuminates the direction to translate the excellent properties of individual graphene into advanced hierarchical ensembles for promising applications in new graphene-based nanodevices. However, the lack of effective, low-cost and convenient assembly strategy has blocked its further development. Herein, we demonstrate that neat and macroscopic graphene fibers with high mechanical strength and electrical conductivity can be fluidly spun from the common graphene oxide (GO) suspensions in large scale followed with chemical reduction. The curliness-fold formation mechanism of GO fiber has been proposed. This wet-spinning technique presented here facilitates the multifunctionalization of macroscopic graphene-based fibers with various organic or inorganic components by an easy-handle in situ or post-synthesis approach, which builds the solid foundation to access a new family of advanced composite materials for the next practical applications.

  6. A strict experimental test of macroscopic realism in a superconducting flux qubit. (United States)

    Knee, George C; Kakuyanagi, Kosuke; Yeh, Mao-Chuang; Matsuzaki, Yuichiro; Toida, Hiraku; Yamaguchi, Hiroshi; Saito, Shiro; Leggett, Anthony J; Munro, William J


    Macroscopic realism is the name for a class of modifications to quantum theory that allow macroscopic objects to be described in a measurement-independent manner, while largely preserving a fully quantum mechanical description of the microscopic world. Objective collapse theories are examples which aim to solve the quantum measurement problem through modified dynamical laws. Whether such theories describe nature, however, is not known. Here we describe and implement an experimental protocol capable of constraining theories of this class, that is more noise tolerant and conceptually transparent than the original Leggett-Garg test. We implement the protocol in a superconducting flux qubit, and rule out (by ∼84 s.d.) those theories which would deny coherent superpositions of 170 nA currents over a ∼10 ns timescale. Further, we address the 'clumsiness loophole' by determining classical disturbance with control experiments. Our results constitute strong evidence for the superposition of states of nontrivial macroscopic distinctness.

  7. In situ carcinoma of the esophagus. Macroscopic study with particular reference to the Lugol test. (United States)

    Mandard, A M; Tourneux, J; Gignoux, M; Blanc, L; Segol, P; Mandard, J C


    The results presented here concern the study of in situ cancer and marked dysplasia revealed during the pathological study of 39 specimens removed during esophagogastrectomy for invasive carcinoma of the esophagus. In 12 cases, macroscopic study made it possible to define precisely the macroscopic features of in situ canccer; in one case, however, the mucous membrane at the site of the in situ cancer was macroscopically normal. The iodine test performed in 37 cases showed that the normal esophageal mucosa is iodine-positive and that in situ and invasive squamous cell carcinoma are always represented by sharply defined iodine-negative zones: in the case in which it was sufficiently extensive, marked dysplasia presented the same iodine-negative character. The possibilities for applying these results to early endoscopic diagnosis of esophageal cancer are presented.

  8. Mechanical Behaviour of Materials Volume 1 Micro- and Macroscopic Constitutive Behaviour

    CERN Document Server

    François, Dominique; Zaoui, André


    Advances in technology are demanding ever-increasing mastery over the materials being used: the challenge is to gain a better understanding of their behaviour, and more particularly of the relations between their microstructure and their macroscopic properties.   This work, of which this is the first volume, aims to provide the means by which this challenge may be met. Starting from the mechanics of deformation, it develops the laws governing macroscopic behaviour – expressed as the constitutive equations – always taking account of the physical phenomena which underlie rheological behaviour. The most recent developments are presented, in particular those concerning heterogeneous materials such as metallic alloys, polymers and composites. Each chapter is devoted to one of the major classes of material behaviour.   As the subtitles indicate, Volume 1 deals with micro- and macroscopic constitutive behaviour and Volume 2 with damage and fracture mechanics. A third volume will be devoted to exercises and the...

  9. Signatures of a macroscopic switching transition for a dynamic microtubule (United States)

    Aparna, J. S.; Padinhateeri, Ranjith; Das, Dibyendu


    Characterising complex kinetics of non-equilibrium self-assembly of bio-filaments is of general interest. Dynamic instability in microtubules, consisting of successive catastrophes and rescues, is observed to occur as a result of the non-equilibrium conversion of GTP-tubulin to GDP-tubulin. We study this phenomenon using a model for microtubule kinetics with GTP/GDP state-dependent polymerisation, depolymerisation and hydrolysis of subunits. Our results reveal a sharp switch-like transition in the mean velocity of the filaments, from a growth phase to a shrinkage phase, with an associated co-existence of the two phases. This transition is reminiscent of the discontinuous phase transition across the liquid-gas boundary. We probe the extent of discontinuity in the transition quantitatively using characteristic signatures such as bimodality in velocity distribution, variance and Binder cumulant, and also hysteresis behaviour of the system. We further investigate ageing behaviour in catastrophes of the filament, and find that the multi-step nature of catastrophes is intensified in the vicinity of the switching transition. This assumes importance in the context of Microtubule Associated Proteins which have the potential of altering kinetic parameter values.

  10. Macroscopic Properties of Hollow Cone Spray Using an Outwardly Opening Piezoelectric Injector in GCI Engine

    KAUST Repository

    Cheng, Penghui


    Fuel mixture formation and spray characteristics are crucial for the advancement of Gasoline Compression Ignition (GCI) engine. For investigations of spray characteristics, a high-pressure high-temperature spray chamber with constant volume has been designed, tested and commissioned at CCRC, KAUST. Back light illumination technique has been applied to investigate the macroscopic spray properties of an outwardly opening piezoelec- tric injector. Three parameters including injection pressure, ambient pressure, and ambient temperature have been involved. A total of 18 combinations of experimental conditions were tested under non-reactive conditions. Through qualitative analysis of spray morphology under different operating conditions, an apparent distinction of spray morphology has been noticed. Spray morphology and propagation have shown strong dependencies on ambient pressure and ambient tempera- ture while injection pressure has a negligible effect on spray shape. Increasingly compact and bushier spray patterns were observed in the cases of high ambient pressure due to in- creasing aerodynamic drag force on spray boundary. It should also be noted that ambient temperature plays a fairly important role in fuel evaporation rate. At 200 °C, oscillating and considerably short spray shape was produced. Also, circumferential ring-like vortices and distinctive string-like structures have been identified for the fuel spray exiting this hollow cone injector. It has been observed that high ambient pressure conditions (Pamb = 4 bar and 10.5 bar) are favorable to the vortices generation, which has also been reported in previous literature. The quantitative description of macroscopic spray properties reveals that ambient pres- sure and ambient temperature are found to be the most influential parameters on liquid penetration length. The rise of ambient pressure results in considerably shorter liquid pen- etration length. Ambient temperature also appears to be a very effective

  11. Thomson's formulation of the second law for macroscopic and finite work sources

    Directory of Open Access Journals (Sweden)

    Theo M. Nieuwenhuizen


    Full Text Available Abstract: Thomson's formulation of the second law states: no work can be extracted from an equilibrium system through a cyclic process. A simple, general proof is presented for the case of macroscopic sources of work. Next the setup is generalized towards situations, where the corresponding work-source is not macroscopic. It is shown that using such a source one can extract energy from an equilibrium system by means of a cyclic process. However, this extraction is accompanied by an entropy increase of the source, in a manner resembling the Clausius inequality.

  12. Macroscopic Einstein Equations for a Cosmological Model with $\\lambda$-term

    CERN Document Server

    Ignat'ev, Yurii


    Through averaging the Einstein equations over transverse gravitational perturbations it is obtained a closed system of two ordinary differential equations describing macroscopic cosmological evolution of the isotropic space-flat Universe filled with gravitational radiation. It is found an asymptotic solution of evolution equation for gravitational perturbation amplitude. Making the substitution of this solution into Einstein equation averaged over gravitational perturbations, the single evolution non-linear ordinary differential second-order equation relative to macroscopic scale factor is obtained. It is also found a solution of evolution equation for scale factor in WKB-approximation which analytically describes the process of transformation from ultrarelativistic regime of cosmological extension to inflationary one.

  13. Macroscopic crack formation and extension in pristine and artificially aged PBX 9501

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Cheng [Los Alamos National Laboratory; Thompson, Darla G [Los Alamos National Laboratory


    A technique has been developed to quantitatively describe macroscopic cracks, both their location and extent, in heterogeneous high explosive and mock materials. By combining such a technique with the deformation field measurement using digital image correlation (DIC), we conduct observation and measurement of the initiation, extension, and coalescence of internal cracks in the compression of Brazilian disk made of pristine and artificially aged PBX 9501 hjgh explosives. Our results conclude quantitatively that aged PBX 9501 is not only weaker but also much more brittle than the pristine one, thus is more susceptible to macroscopic cracking.

  14. Entanglement of Macroscopic Test Masses and the Standard Quantum Limit in Laser Interferometry (United States)

    Müller-Ebhardt, Helge; Rehbein, Henning; Schnabel, Roman; Danzmann, Karsten; Chen, Yanbei


    We show that the generation of entanglement of two heavily macroscopic mirrors is feasible with state of the art techniques of high-precision laser interferometry. The basis of such a demonstration would be a Michelson interferometer with suspended mirrors and simultaneous homodyne detections at both interferometer output ports. We present the connection between the generation of entanglement and the standard quantum limit (SQL) for a free mass. The SQL is a well-known reference limit in operating interferometers for gravitational-wave detection and provides a measure of when macroscopic entanglement can be observed in the presence of realistic decoherence processes.

  15. Surface-Directed Spinodal Decomposition on a Macroscopic Scale in a Nitrogen and Carbon Alloyed Steel (United States)

    Aichmayer, Barbara; Fratzl, Peter; Puri, Sanjay; Saller, Gabriele


    Interactions with the macroscopic specimen surface can profoundly modify phase-separation processes. This has previously been observed in liquids and polymer films and is theoretically described by the theory of surface-directed spinodal decomposition (SDSD). Here we report first observations of SDSD in a metallic alloy on a macroscopic scale. The influence of the surface leads to the development of concentric domains extending over the whole 10mm thick cylindrical steel specimen, due to long-range interactions via elastic stresses and long-range diffusion of the interstitial elements nitrogen and carbon.

  16. Light tries the expert eye: the introduction of photography in nineteenth-century macroscopic neuroanatomy. (United States)

    de Rijcke, Sarah


    It is often argued that photography's scientific inauguration meaningfully coincided with a shift towards the ideal of mechanical objectivity. Values of disinterestedness and precision were readily attributed to photography and were cherished by the emerging field of neurology as well. However, after the publication of the first neuroanatomical atlas to contain photographs, Jules Bernard Luys' Iconographie Photographique des Centres Nerveux (1873), the use of photography in macroscopic neuroanatomy remained rare. The present article sketches this largely overlooked terrain of investigation and will expand on why in macroscopical neuroanatomy photography failed to offer a satisfactory alternative to drawing or engraving.


    Lorian, Victor


    Lorian, Victor (Laboratório Central de Tuberculose, Rio de Janeiro, Brazil). Macroscopic patterns of bacteria after development in drops of liquid medium. J. Bacteriol. 86:582–584. 1963.—Cultures of bacteria in liquid media with 0.06% triphenyltetrazolium hydrochloride showed visible macroscopic development and a characteristic pattern for each strain, when deposited in 0.35-ml drops on the surface of silicone-coated glass or in concavities of slides, after 3 to 4 hr of immobility in an incubator at 37 C. These patterns could be due to sedimentation or autoagglutination occurring as the bacteria developed under these conditions. Images PMID:14066441

  18. Macroscopic behavior of fast reactor fuel subjected to simulated thermal transients

    Energy Technology Data Exchange (ETDEWEB)

    Fenske, G.R.; Emerson, J.E.; Savoie, F.E.


    High-speed cinematography has been used to characterize the macroscopic behavior of irradiated and unirradiated fuel subjected to thermal transients prototypical of fast reactor transients. The results demonstrate that as the cladding melts, the fuel can disperse via spallation if the fuel contains in excess of approx. 16 of fission gas. Once the cladding has melted, the macroscopic behavior (time to failure and dispersive nature) was strongly influenced by the presence of volatile fission products and the heating rate.

  19. Ancient sedimentary structures in the Mars, that resemble macroscopic morphology, spatial associations, and temporal succession in terrestrial microbialites. (United States)

    Noffke, Nora


    Sandstone beds of the Mars have been interpreted as evidence of an ancient playa lake environment. On Earth, such environments have been sites of colonization by microbial mats from the early Archean to the present time. Terrestrial microbial mats in playa lake environments form microbialites known as microbially induced sedimentary structures (MISS). On Mars, three lithofacies of the Gillespie Lake Member sandstone display centimeter- to meter-scale structures similar in macroscopic morphology to terrestrial MISS that include "erosional remnants and pockets," "mat chips," "roll-ups," "desiccation cracks," and "gas domes." The microbially induced sedimentary-like structures identified in Curiosity rover mission images do not have a random distribution. Rather, they were found to be arranged in spatial associations and temporal successions that indicate they changed over time. On Earth, if such MISS occurred with this type of spatial association and temporal succession, they would be interpreted as having recorded the growth of a microbially dominated ecosystem that thrived in pools that later dried completely: erosional pockets, mat chips, and roll-ups resulted from water eroding an ancient microbial mat-covered sedimentary surface; during the course of subsequent water recess, channels would have cut deep into the microbial mats, leaving erosional remnants behind; desiccation cracks and gas domes would have occurred during a final period of subaerial exposure of the microbial mats. In this paper, the similarities of the macroscopic morphologies, spatial associations, and temporal succession of sedimentary structures on Mars to MISS preserved on Earth has led to the following hypothesis: The sedimentary structures in the Mars are ancient MISS produced by interactions between microbial mats and their environment. Proposed here is a strategy for detecting, identifying, confirming, and differentiating possible MISS during current and future Mars missions.

  20. Macroscopic quantum self-trapping of a spin–orbit-coupled Bose–Einstein condensate in a double-well potential (United States)

    Wang, Wen-Yuan; Dou, Fu-Quan; Duan, Wen-Shan


    We investigate the macroscopic quantum self-trapping (MQST) phenomenon of a spin–orbit-coupled Bose–Einstein condensate (BEC) in a double-well potential, emphasizing the critical behavior at the transition to MQST. We show that as the nonlinear parameter characterizing the atomic interaction increases, the spin–orbit-coupled BEC appears as MQST, manifesting an asymmetric distribution of the atom in two wells. Then, the effect of the initial condition on the critical behavior at the transition to MQST is given. Analytic expressions for the dependence of the transition parameters on the system parameters and the initial condition are derived, which are in agreement with our numerical simulations.

  1. Effect of the isovector coupling channel on the macroscopic part of ...

    Indian Academy of Sciences (India)

    The effect of isovector coupling channel on the macroscopic part of the nuclear binding energy is studied using the relativistic density-dependent Thomas–Fermi approach. The dependency of this effect on the number of neutrons and protons is also studied. The isovector coupling channel leads to increased nuclear binding ...

  2. Analysis of macroscopic and microscopic rotating motions in rotating jets: A direct numerical simulation

    Directory of Open Access Journals (Sweden)

    Xingtuan Yang


    Full Text Available A direct numerical simulation study of the characteristics of macroscopic and microscopic rotating motions in swirling jets confined in a rectangular flow domain is carried out. The different structures of vortex cores for different swirl levels are illustrated. It is found that the vortex cores of low swirl flows are of regular cylindrical-helix patterns, whereas those of the high swirl flows are characterized by the formation of the bubble-type vortex breakdown followed by the radiant processing vortex cores. The results of mean velocity fields show the general procedures of vortex origination. Moreover, the effects of macroscopic and microscopic rotating motions with respect to the mean and fluctuation fields of the swirling flows are evaluated. The microscopic rotating effects, especially the effects with respect to the turbulent fluctuation motion, are increasingly intermittent with the increase in the swirl levels. In contrast, the maximum value of the probability density functions with respect to the macroscopic rotating effects of the fluctuation motion occurs at moderate swirl levels since the macroscopic rotating effects are attenuated by the formation of the bubble vortex breakdown with a region of stagnant fluids at supercritical swirl levels.

  3. Effect of the isovector coupling channel on the macroscopic part of ...

    Indian Academy of Sciences (India)

    United States of America, the SPIRAL2 at GANIL/France, and the GSI Facility FAIR in. Germany, which produce new data for neutron-rich nuclei. In this work, the effect of isovector coupling channel of the nucleon–nucleon inter- action on the macroscopic part of the binding energy is studied, and the dependency of this effect ...

  4. Students' Mind Wandering in Macroscopic and Submicroscopic Textual Narrations and Its Relationship with Their Reading Comprehension (United States)

    Al-Balushi, Sulaiman M.; Al-Harthy, Ibrahim S.


    The aim of the current study was to investigate students' mind wandering while reading different types of textual narrations (macroscopic and submicroscopic) in chemistry. Another goal was to determine the relationship between mind wandering and students' reading comprehension. The participants were 65 female ninth grade students in Oman. Using a…

  5. Surface-enhanced Raman spectroscopy for the analysis of smokeless gunpowders and macroscopic gunshot residues. (United States)

    López-López, María; Merk, Virginia; García-Ruiz, Carmen; Kneipp, Janina


    Gunshot residues (GSR) result from the discharge of a firearm being a potential piece of evidence in criminal investigations. The macroscopic GSR particles are basically formed by burned and non-burned gunpowder. Motivated by the demand of trace analysis of these samples, in this paper, the use of surface-enhanced Raman scattering (SERS) was evaluated for the analysis of gunpowders and macroscopic GSR particles. Twenty-one different smokeless gunpowders were extracted with ethanol. SERS spectra were obtained from the diluted extracts using gold nanoaggregates and an excitation wavelength of 633 nm. They show mainly bands that could be assigned to the stabilizers diphenylamine and ethylcentralite present in the gunpowders. Then, macroscopic GSR particles obtained after firing two different ammunition cartridges on clothing were also measured using the same procedure. SERS allowed the detection of the particles collected with an aluminum stub from cloth targets without interferences from the adhesive carbon. The results demonstrate the great potential of SERS for the analysis of macroscopic GSR particles. Furthermore, they indicate that the grain-to-grain inhomogeneity of the gunpowders needs to be considered. Graphical Abstract SERS allows the detection of GSR particles collected with adhesive stubs from cloth targets using gold nanoaggregates and an excitation wavelength of 633 nm.

  6. Quantum Control of Light and Matter: From the Macroscopic to the Nano Scale (United States)


    the coupling (read) beam is a 2.6 µs (120 ns) square pulse. The peak Rabi frequency of the coupling (read) beam is 12.5 MHz (29.5 MHz), and the peak...its atomic thinness and its inherent lattice defects leave it vulnerable to macroscopic tearing and rupturing. Additionally, although Gr is very rigid

  7. Quantum-state preparation and macroscopic entanglement in gravitational-wave detectors (United States)

    Müller-Ebhardt, Helge; Rehbein, Henning; Li, Chao; Mino, Yasushi; Somiya, Kentaro; Schnabel, Roman; Danzmann, Karsten; Chen, Yanbei


    Long-baseline laser-interferometer gravitational-wave (GW) detectors are operating at a factor of ˜10 (in amplitude) above the standard quantum limit (SQL) within a broad frequency band (in the sense that Δf˜f ). Such a low-noise budget has already allowed the creation of a controlled 2.7 kg macroscopic oscillator with an effective eigenfrequency of 150 Hz and an occupation number of ˜200 . This result, along with the prospect for further improvements, heralds the possibility of experimentally probing macroscopic quantum mechanics (MQM)—quantum mechanical behavior of objects in the realm of everyday experience—using GW detectors. In this paper, we provide the mathematical foundation for the first step of a MQM experiment: the preparation of a macroscopic test mass into a nearly minimum-Heisenberg-limited Gaussian quantum state, which is possible if the interferometer’s classical noise beats the SQL in a broad frequency band. Our formalism, based on Wiener filtering, allows a straightforward conversion from the noise budget of a laser interferometer, in terms of noise spectra, into the strategy for quantum-state preparation and the quality of the prepared state. Using this formalism, we consider how Gaussian entanglement can be built among two macroscopic test masses and the performance of the planned Advanced LIGO interferometers in quantum-state preparation.

  8. Bilateral subacromial bursitis with macroscopic rice bodies: Ultrasound, CT and MR appearance

    Energy Technology Data Exchange (ETDEWEB)

    Law, T.C.; Chong, S.F.; Lu, P.P. [Kwong Wah Hospital (Hong Kong). Department of Radiology; Mak, K.H. [Kwong Wah Hospital (Hong Kong). Department of Orthopaedics and Traumatology


    The radiological findings of ultrasound, CT and MR of a case of bilateral subacromial bursitis with macroscopic rice bodies is described. MRI is the investigation of choice and the intravenous gadolinium-enhanced usefulness was noted. The previous literature is also reviewed. Copyright (1998) Blackwell Science Pty Ltd 5 refs., 1 tab., 4 figs.

  9. X-ray-generated heralded macroscopical quantum entanglement of two nuclear ensembles. (United States)

    Liao, Wen-Te; Keitel, Christoph H; Pálffy, Adriana


    Heralded entanglement between macroscopical samples is an important resource for present quantum technology protocols, allowing quantum communication over large distances. In such protocols, optical photons are typically used as information and entanglement carriers between macroscopic quantum memories placed in remote locations. Here we investigate theoretically a new implementation which employs more robust x-ray quanta to generate heralded entanglement between two crystal-hosted macroscopical nuclear ensembles. Mössbauer nuclei in the two crystals interact collectively with an x-ray spontaneous parametric down conversion photon that generates heralded macroscopical entanglement with coherence times of approximately 100 ns at room temperature. The quantum phase between the entangled crystals can be conveniently manipulated by magnetic field rotations at the samples. The inherent long nuclear coherence times allow also for mechanical manipulations of the samples, for instance to check the stability of entanglement in the x-ray setup. Our results pave the way for first quantum communication protocols that use x-ray qubits.

  10. Transition from Casimir to van der Waals force between macroscopic bodies

    NARCIS (Netherlands)

    Palasantzas, G.; van Zwol, P. J.; De Hosson, J. Th. M.


    The transition of van der Waals to Casimir forces between macroscopic gold surfaces is investigated by atomic force microscopy in the plane-sphere geometry. It was found that the transition appears to take place at separations similar to 10% the plasma wavelength lambda(p) for evaporated gold

  11. Energetics of macroscopic helical domain in different tube geometries and loading

    Directory of Open Access Journals (Sweden)

    Sun Q.P.


    Full Text Available Superelastic NiTi polycrystalline shape memory alloy tubes, when subject to slow quasistatic stretching, transform to a high strain phase by the formation and growth of a macroscopic helix-shaped domain as deformation progresses. This paper performed an experimental study on the effects of the external applied nominal strain and the tube geometry (tube radius R, wall-thickness h and length L on the helical domains in isothermal stretching of the tubes. The evolution of the macroscopic domains with the applied strain in different tube geometries are quantified by in-situ optical measurement. We demonstrate that the equilibrium shape of the macroscopic helical domain and its evolution are governed by the competition between the domain front energy and the elastic-misfit bending strain energy of the tube system. The former favors a short helical domain, while the latter favors a long slim helical domain. The experimental results provided basic physical and experimental foundations for further modelling and quantification of the macroscopic domain morphology evolution in tube geometries.

  12. Energetics of macroscopic helical domain in different tube geometries and loading (United States)

    Zhou, R.; Sun, Q. P.


    Superelastic NiTi polycrystalline shape memory alloy tubes, when subject to slow quasistatic stretching, transform to a high strain phase by the formation and growth of a macroscopic helix-shaped domain as deformation progresses. This paper performed an experimental study on the effects of the external applied nominal strain and the tube geometry (tube radius R, wall-thickness h and length L) on the helical domains in isothermal stretching of the tubes. The evolution of the macroscopic domains with the applied strain in different tube geometries are quantified by in-situ optical measurement. We demonstrate that the equilibrium shape of the macroscopic helical domain and its evolution are governed by the competition between the domain front energy and the elastic-misfit bending strain energy of the tube system. The former favors a short helical domain, while the latter favors a long slim helical domain. The experimental results provided basic physical and experimental foundations for further modelling and quantification of the macroscopic domain morphology evolution in tube geometries.

  13. Macroscopic treatment of radio emission from cosmic ray air showers based on shower simulations

    NARCIS (Netherlands)

    Werner, Klaus; Scholten, Olaf

    We present a macroscopic calculation of coherent electro-magnetic radiation from air showers initiated by ultra-high energy cosmic rays, based on currents obtained from Monte Carlo simulations of air showers in a realistic geo-magnetic field. We can clearly relate the time signal to the time

  14. Bouncing droplets : A classroom experiment to visualize wave-particle duality on the macroscopic level

    NARCIS (Netherlands)

    Sleutel, Pascal; Dietrich, Erik; Van Der Veen, Jan T.; Van Joolingen, Wouter R.


    This study brings a recently discovered macroscopic phenomenon with wave-particle characteristics into the classroom. The system consists of a liquid droplet levitating over a vertically shaken liquid pool. The droplets allow visualization of a wave-particle system in a directly observable way. We

  15. Macroscopic and microscopic spectral properties of brain networks during local and global synchronization

    NARCIS (Netherlands)

    Maksimenko, V.A.; Lüttjohann, A.; Makarov, V.V.; Goremyko, M.V.; Koronovskii, A.A.; Nedaivozov, V.; Runnova, A.E.; Luijtelaar, E.L.J.M. van; Hramov, A.E.; Boccaletti, S.


    We introduce a practical and computationally not demanding technique for inferring interactions at various microscopic levels between the units of a network from the measurements and the processing of macroscopic signals. Starting from a network model of Kuramoto phase oscillators which evolve

  16. Simulation of root water uptake. I. Non-uniform transient salinity using different macroscopic reduction functions

    NARCIS (Netherlands)

    Homaee, M.; Dirksen, C.; Feddes, R.A.


    A macroscopic root extraction model was used with four different reduction functions for salinity stress in the numerical simulation model HYSWASOR. Most of the parameter values originally proposed for these functions did not provide good agreement with the experimental data. Therefore, the

  17. Theory of macroscopic quantum tunneling in Nb/Au/YBCO Josephson junctions

    NARCIS (Netherlands)

    Kawabata, S.; Kawabata, S.; Golubov, Alexandre Avraamovitch; Ariando, A.; Verwijs, C.J.M.; Hilgenkamp, Johannes W.M.


    We have theoretically investigated macroscopic quantum tunneling (MQT) in s-wave/d-wave (Nb/Au/YBCO) Josephson junctions, and the influence of the nodal-quasiparticle and the zero energy bound states (ZES) on MQT. In contrast to d-wave/d-wave junctions, low-energy quasiparticle excitations resulting

  18. Theory of macroscopic quantum tunnelling and dissipation in high-Tc Josephson junctions

    NARCIS (Netherlands)

    Kawabata, S.; Kawabata, Shiro; Kashiwaya, Satoshi; Asano, Yasuhiro; Tanaka, Yukio; Kato, Takeo; Kato, T.; Golubov, Alexandre Avraamovitch


    We have investigated macroscopic quantum tunnelling (MQT) in in-plane high-Tc superconductor Josephson junctions and the influence of the nodal-quasiparticle and zero energy bound states (ZES) on MQT. We have shown that the presence of ZES at the interface between the insulator and the

  19. Relations between macroscopic and microscopic adhesion of Streptococcus mitis strains to surfaces

    NARCIS (Netherlands)

    Vadillo-Rodriguez, V.; Busscher, H.J.; Norde, W.; Vries, de J.; Mei, van der H.C.


    Application of physico-chemical models to describe bacterial adhesion to surfaces has hitherto only been partly successful due to the structural and chemical heterogeneities of bacterial surfaces, which remain largely unaccounted for in macroscopic physico-chemical characterizations of the cell

  20. Macroscopic networks in the human brain: mapping connectivity in healthy and damaged brains

    NARCIS (Netherlands)

    Nijhuis, E.H.J.


    The human brain contains a network of interconnected neurons. Recent advances in functional and structural in-vivo magnetic resonance neuroimaging (MRI) techniques have provided opportunities to model the networks of the human brain on a macroscopic scale. This dissertation investigates the

  1. RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. (United States)

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong


    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (, an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  2. Macroscopic Hematuria After Conventional or Hypofractionated Radiation Therapy: Results From a Prospective Phase 3 Study. (United States)

    Sanguineti, Giuseppe; Arcidiacono, Fabio; Landoni, Valeria; Saracino, Bianca Maria; Farneti, Alessia; Arcangeli, Stefano; Petrongari, Maria Grazia; Gomellini, Sara; Strigari, Lidia; Arcangeli, Giorgio


    To assess the macroscopic hematuria rates within a single-institution randomized phase 3 trial comparing dose-escalated, conventionally fractionated radiation therapy (CFRT) and moderately hypofractionated radiation therapy (MHRT) for localized prostate cancer. Patients with intermediate- to high-risk localized prostate cancer were treated with conformal RT and short-course androgen deprivation. Both the prostate and the entire seminal vesicles were treated to 80 Gy in 40 fractions over 8 weeks (CFRT) or 62 Gy in 20 fractions over 5 weeks (MHRT). The endpoint of the present study was the development of any episode or grade of macroscopic hematuria. The median follow-up period was 93 months (range 6-143). Macroscopic hematuria was reported by 25 of 168 patients (14.9%). The actuarial estimate of hematuria at 8 years was 17.0% (95% confidence interval [CI] 10.7%-23.3%). The number of patients with hematuria was 6 and 19 in the CFRT and MHRT arms, respectively, for an actuarial 8-year estimate of 9.7% and 24.3%, respectively (hazard ratio 3.468, 95% CI 1.385-8.684; P=.008). Overall, 8 of 25 patients were found to have biopsy-proven urothelial carcinoma (3 in the CFRT arm and 5 in the MHRT arm; P=.27). Thus, the 8-year actuarial incidence of macroscopic hematuria (after censoring urothelial cancer-related episodes) was 4.1% and 18.2% after CFRT and MHRT, respectively (hazard ratio 4.961, 95% CI 1.426-17.263; P=.012). The results were confirmed by multivariate analysis after accounting for several patient-, treatment-, and tumor-related covariates. MHRT was associated with a statistically significant increased risk of macroscopic hematuria compared with CFRT. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles. (United States)

    Afonin, Kirill A; Viard, Mathias; Kagiampakis, Ioannis; Case, Christopher L; Dobrovolskaia, Marina A; Hofmann, Jen; Vrzak, Ashlee; Kireeva, Maria; Kasprzak, Wojciech K; KewalRamani, Vineet N; Shapiro, Bruce A


    Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.

  4. Advances in imaging RNA in plants

    DEFF Research Database (Denmark)

    Christensen, Nynne Meyn; Oparka, Karl J.; Tilsner, Jens


    Increasing evidence shows that many RNAs are targeted to specific locations within cells, and that RNA-processing pathways occur in association with specific subcellular structures. Compartmentation of mRNA translation and RNA processing helps to assemble large RNA–protein complexes, while RNA...... targeting allows local protein synthesis and the asymmetric distribution of transcripts during cell polarisation. In plants, intercellular RNA trafficking also plays an additional role in plant development and pathogen defence. Methods that allow the visualisation of RNA sequences within a cellular context......, and preferably at subcellular resolution, can help to answer important questions in plant cell and developmental biology. Here, we summarise the approaches currently available for localising RNA in vivo and address the specific limitations inherent with plant systems....

  5. Macroscopic retrocausation (United States)

    Costa de Beauregard, O.


    Referring to Stapp's and Schmidt's recent papers: a Feynman transition amplitude | I>psychokinesis—Jaynes' qualification of the mind-induced-quantum-collapse concept. Time extendedness of matter, final cause, information-negentropy reversibility, are features inherent in relativistic quantum mechanics.

  6. A Novel Derivation of the Time Evolution of the Entropy for Macroscopic Systems in Thermal Non-Equilibrium

    Directory of Open Access Journals (Sweden)

    Enrico Sciubba


    Full Text Available The paper discusses how the two thermodynamic properties, energy (U and exergy (E, can be used to solve the problem of quantifying the entropy of non-equilibrium systems. Both energy and exergy are a priori concepts, and their formal dependence on thermodynamic state variables at equilibrium is known. Exploiting the results of a previous study, we first calculate the non-equilibrium exergy En-eq can be calculated for an arbitrary temperature distributions across a macroscopic body with an accuracy that depends only on the available information about the initial distribution: the analytical results confirm that En-eq exponentially relaxes to its equilibrium value. Using the Gyftopoulos-Beretta formalism, a non-equilibrium entropy Sn-eq(x,t is then derived from En-eq(x,t and U(x,t. It is finally shown that the non-equilibrium entropy generation between two states is always larger than its equilibrium (herein referred to as “classical” counterpart. We conclude that every iso-energetic non-equilibrium state corresponds to an infinite set of non-equivalent states that can be ranked in terms of increasing entropy. Therefore, each point of the Gibbs plane corresponds therefore to a set of possible initial distributions: the non-equilibrium entropy is a multi-valued function that depends on the initial mass and energy distribution within the body. Though the concept cannot be directly extended to microscopic systems, it is argued that the present formulation is compatible with a possible reinterpretation of the existing non-equilibrium formulations, namely those of Tsallis and Grmela, and answers at least in part one of the objections set forth by Lieb and Yngvason. A systematic application of this paradigm is very convenient from a theoretical point of view and may be beneficial for meaningful future applications in the fields of nano-engineering and biological sciences.

  7. Extracellular RNA Communication (ExRNA) (United States)

    Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

  8. A numerical multi-scale model to predict macroscopic material anisotropy of multi-phase steels from crystal plasticity material definitions (United States)

    Ravi, Sathish Kumar; Gawad, Jerzy; Seefeldt, Marc; Van Bael, Albert; Roose, Dirk


    A numerical multi-scale model is being developed to predict the anisotropic macroscopic material response of multi-phase steel. The embedded microstructure is given by a meso-scale Representative Volume Element (RVE), which holds the most relevant features like phase distribution, grain orientation, morphology etc., in sufficient detail to describe the multi-phase behavior of the material. A Finite Element (FE) mesh of the RVE is constructed using statistical information from individual phases such as grain size distribution and ODF. The material response of the RVE is obtained for selected loading/deformation modes through numerical FE simulations in Abaqus. For the elasto-plastic response of the individual grains, single crystal plasticity based plastic potential functions are proposed as Abaqus material definitions. The plastic potential functions are derived using the Facet method for individual phases in the microstructure at the level of single grains. The proposed method is a new modeling framework and the results presented in terms of macroscopic flow curves are based on the building blocks of the approach, while the model would eventually facilitate the construction of an anisotropic yield locus of the underlying multi-phase microstructure derived from a crystal plasticity based framework.

  9. Ring Shuttling Controls Macroscopic Motion in a Three-Dimensional Printed Polyrotaxane Monolith. (United States)

    Lin, Qianming; Hou, Xisen; Ke, Chenfeng


    Amplification of molecular motions into the macroscopic world has great potential in the development of smart materials. Demonstrated here is an approach that integrates mechanically interlocked molecules into complex three-dimensional (3D) architectures by direct-write 3D printing. The design and synthesis of polypseudorotaxane hydrogels, which are composed of α-cyclodextrins and poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers, and their subsequent fabrication into polyrotaxane-based lattice cubes by 3D printing followed by post-printing polymerization are reported. By switching the motion of the α-cyclodextrin rings between random shuttling and stationary states through solvent exchange, the polyrotaxane monolith not only exhibits macroscopic shape-memory properties but is also capable of converting the chemical energy input into mechanical work by lifting objects against gravity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Cavity-Assisted Generation of Sustainable Macroscopic Entanglement of Ultracold Gases

    Directory of Open Access Journals (Sweden)

    Chaitanya Joshi


    Full Text Available Prospects for reaching persistent entanglement between two spatially-separated atomic Bose–Einstein condensates are outlined. The system setup comprises two condensates loaded in an optical lattice, which, in return, is confined within a high-Q optical resonator. The system is driven by an external laser that illuminates the atoms, such that photons can scatter into the cavity. In the superradiant phase, a cavity field is established, and we show that the emerging cavity-mediated interactions between the two condensates is capable of entangling them despite photon losses. This macroscopic atomic entanglement is sustained throughout the time-evolution apart from occasions of sudden deaths/births. Using an auxiliary photon mode and coupling it to a collective quadrature of the two condensates, we demonstrate that the auxiliary mode’s squeezing is proportional to the atomic entanglement, and as such, it can serve as a probe field of the macroscopic entanglement.

  11. Measurements of effective total macroscopic cross sections and effective energy of continuum beam

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Hisao [Rikkyo Univ., Yokosuka, Kanagawa (Japan). Inst. for Atomic Energy


    Two practically useful quantities are introduced in this study to characterize a continuum neutron beam and to describe transmission phenomena of the beam in field of quantitative neutron radiography: an effective energy instead of a peak energy or a mean energy of the spectrum and an effective total macroscopic (ETM) cross section instead of a total macroscopic (TM) cross section defined at the monochromatic energy. The effective energy was evaluated by means of energy dependence of ETM cross section. To realize the method a beam quality indicator (BQI) has been proposed recently. Several effective energies were measured for non-filtered, filtered neutron beams, and outputs of neutron guide tubes in world by the BQI. A thermal neutron beam and three beams modulated by Pb filters with different thicknesses are studied to measure ETM cross sections for various materials and summarized in a table. Validity of the effective energy determined by the BQI is discussed relating with ETM cross sections of materials. (author)

  12. Macroscopic observables experimentally linked to microscopic processes in the explosive fracture and fragmentation of metals

    Energy Technology Data Exchange (ETDEWEB)

    Hull, Lawrence M [Los Alamos National Laboratory


    The response of a metal element to explosive loading depends on a broad spectrum of explosive and metal properties, macroscopic geometry plays a crucial role in defining the localized loading history and the resulting gradients of interest, while microscopic effects and defects are generally believed responsible for damage nucleation. Certain experiments reduce the complexity by producing conditions that are uniform in some sense, allowing dynamic measurement of variables that can be correlated with corresponding microscopic effects observed in recovery experiments. Spherical expansion of thin shells, that eventually fragment, and steady wave loading of flat plates are two such experiments. Proton radiography, x-radiography, laser velocimetry, imaging IR, and visible light photography all have produced dynamic measurements in 4340 steel, copper, uranium alloys, tantalum, and titanium. Correlation of the macroscopic measurements with microscopy on recovered samples has been done with a statistical approach.

  13. Macroscopic degeneracy and order in the 3D plaquette Ising model (United States)

    Johnston, Desmond A.; Mueller, Marco; Janke, Wolfhard


    The purely plaquette 3D Ising Hamiltonian with the spins living at the vertices of a cubic lattice displays several interesting features. The symmetries of the model lead to a macroscopic degeneracy of the low-temperature phase and prevent the definition of a standard magnetic order parameter. Consideration of the strongly anisotropic limit of the model suggests that a layered, “fuki-nuke” order still exists and we confirm this with multi-canonical simulations. The macroscopic degeneracy of the low-temperature phase also changes the finite-size scaling corrections at the first-order transition in the model and we see this must be taken into account when analyzing our measurements.

  14. Macroscopic and large scale phenomena coarse graining, mean field limits and ergodicity

    CERN Document Server

    Rademacher, Jens; Zagaris, Antonios


    This book is the offspring of a summer school school “Macroscopic and large scale phenomena: coarse graining, mean field limits and ergodicity”, which was held in 2012 at the University of Twente, the Netherlands. The focus lies on mathematically rigorous methods for multiscale problems of physical origins. Each of the four book chapters is based on a set of lectures delivered at the school, yet all authors have expanded and refined their contributions. Francois Golse delivers a chapter on the dynamics of large particle systems in the mean field limit and surveys the most significant tools and methods to establish such limits with mathematical rigor. Golse discusses in depth a variety of examples, including Vlasov--Poisson and Vlasov--Maxwell systems. Lucia Scardia focuses on the rigorous derivation of macroscopic models using $\\Gamma$-convergence, a more recent variational method, which has proved very powerful for problems in material science. Scardia illustrates this by various basic examples and a mor...

  15. Determination of crystallographic and macroscopic orientation of planar structures in TEM

    DEFF Research Database (Denmark)

    Huang, X.; Liu, Q.


    With the aid of a double-tilt holder in a transmission electron microscope (TEM), simple methods are described for determination of the crystallographic orientation of a planar structure and for calculation of the macroscopic orientation of the planar structure. The correlation between a planar...... structure and a crystallographic plane can be found by comparing the differences in their trace directions on the projection plane and inclination angles with respect to that plane. The angles between the traces of planar structures and the sample axis measured from the TEM micrographs, which have been...... taken at tilted positions, can be transformed to the real macroscopic orientation of the planar structures with estimated error of about +/- 2 degrees. (C) 1998 Elsevier Science B.V. All rights reserved....

  16. Macroscopic description of complex adaptive networks co-evolving with dynamic node states

    CERN Document Server

    Wiedermann, Marc; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen


    In many real-world complex systems, the time-evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here, we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the co-evolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we show that in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability play a crucial role for the sustainability of the system's equilibrium state. We derive a macroscopic description of the system which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network and is applicable to many fields of study, such as epidemic spreading or social modeling.

  17. Effect of mesoscopic conservative phenomena in the dynamics of chemical reactions at the macroscopic scale (United States)

    Zárate-Navarro, Marco A.; García-Sandoval, J. Paulo; Dochain, Denis; Hudon, Nicolas


    This paper studies the influence of conservative phenomena at the mesoscopic scale that affect the behavior of macroscopic variables in chemical reactions, generally understood as purely dissipative processes and whose mathematical formulation is usually derived using macroscopic variables. It is shown that conservative phenomena at the mesoscopic scale can affect the entropy production by transiently ;pulling away; the system from the thermodynamic equilibrium. Two case studies are presented to illustrate this fact: the first one is an isolated system with a single reaction including two different scenarios, a purely dissipative reaction; and a second one that considers the influence of conservative elements at the mesoscopic scale. The second case generalizes the results to multiple reactions.

  18. A macroscopic relationship for preferential flow in the vadose zone: Theory and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, H.H.; Zhang, R.D.


    Preferential flow commonly observed in unsaturated soils allows rapid movement of solute from the ground surface or vadose zone to the groundwater, bypassing a significant volume of unsaturated soil and increasing the risk of groundwater contamination. A variety of evidence indicates that complex preferential flow patterns observed from fields are fractals. This paper discusses a macroscopic rela-tionship for modeling preferential flow in the vadose zone. Conceptually, the flow domain can be di-vided into active and inactive regions. Flow occurs preferentially in the active region (characterized by fractals), and inactive region is simply bypassed. The portion of the active region was found to be a power function of saturation. The validity of this macroscopic relationship is demonstrated by its consistency with field observations and the related numerical experiments.

  19. Density-Gradient Theory: A Macroscopic Approach to Quantum Confinement and Tunneling in Semiconductor Devices (United States)


    heterostructure lasers; in 2D they are the FINFETs and nanowires currently of considerable research interest; and in 3D they are the semiconductor quantum dots...J Comput Electron (2011) 10:65–97 DOI 10.1007/s10825-011-0356-9 Density-gradient theory: a macroscopic approach to quantum confinement and tunneling ...both quantum confinement and quantum tunneling situations are then reviewed. In doing so, particular emphasis is put on understanding the range of va

  20. Macroscopic and Microscopic Investigation of Densification Behavior for Gadolinium-doped Ceria upon Sintering

    Energy Technology Data Exchange (ETDEWEB)

    Kosaka, T [Department of Chemistry, Tokyo Gakugei University, Nukuikita 4-1-1, Koganei, Tokyo 184-8501 (Japan); Sato, K, E-mail: [Department of Environmental Sciences, Tokyo Gakugei University, Nukuikita 4-1-1, Koganei, Tokyo 184-8501 (Japan)


    The densification behaviour of Gadolinium-doped ceria (GDC) upon sintering is investigated from macroscopic and microscopic points of view. The time-resolved length-change measurement with high-resolution dilatometry and positron lifetime spectroscopy are conducted. Positron lifetime spectroscopy reveals the presence of nanovoids at grain boundaries in GDC. Time-dependent length-change measurement reveals that particle rearrangement occurs at the initial stage of sintering. Densifications at the sintering neck and inside the particle grain are discussed.

  1. Dynamic nuclear polarisation by thermal mixing: quantum theory and macroscopic simulations. (United States)

    Karabanov, Alexander; Kwiatkowski, Grzegorz; Perotto, Carlo U; Wiśniewski, Daniel; McMaster, Jonathan; Lesanovsky, Igor; Köckenberger, Walter


    A theory of dynamic nuclear polarisation (DNP) by thermal mixing is suggested based on purely quantum considerations. A minimal 6-level microscopic model is developed to test the theory and link it to the well-known thermodynamic model. Optimal conditions for the nuclear polarization enhancement and effects of inhomogeneous broadening of the electron resonance are discussed. Macroscopic simulations of nuclear polarization spectra displaying good agreement with experiments, involving BDPA and trityl free radicals, are presented.

  2. Macroscopic domain formation during cooling in the platelet plasma membrane: an issue of low cholesterol content


    Bali, Rachna; Savino, Laura; Ramirez, Diego A.; Tsvetkova, Nelly M.; Bagatolli, Luis; Tablin, Fern; Crowe, John H.; Leidy, Chad


    There has been ample debate on whether cell membranes can present macroscopic lipid domains as predicted by three-component phase diagrams obtained by fluorescence microscopy. Several groups have argued that membrane proteins and interactions with the cytoskeleton inhibit the formation of large domains. In contrast, some polarizable cells do show large regions with qualitative differences in lipid fluidity. It is important to ask more precisely, based on the current phase diagrams, under what...

  3. Macroscopic generation of attosecond-pulse trains in strongly ionized media (United States)

    Tosa, V.; Kim, K. T.; Nam, C. H.


    The characteristics of attosecond-pulse trains (APT) obtained from high-order harmonics are investigated by using a nonadiabatic three-dimensional model. A time-dependent phase matching approach is used in order to analyze the macroscopic formation of the APT. Under high ionization conditions, the process of APT formation is found to be the result of an interlace among the driving laser field, single atom response, phase matching effects in the near field and burst interference in the far field.

  4. State-space based analysis and forecasting of macroscopic road safety trends in Greece. (United States)

    Antoniou, Constantinos; Yannis, George


    In this paper, macroscopic road safety trends in Greece are analyzed using state-space models and data for 52 years (1960-2011). Seemingly unrelated time series equations (SUTSE) models are developed first, followed by richer latent risk time-series (LRT) models. As reliable estimates of vehicle-kilometers are not available for Greece, the number of vehicles in circulation is used as a proxy to the exposure. Alternative considered models are presented and discussed, including diagnostics for the assessment of their model quality and recommendations for further enrichment of this model. Important interventions were incorporated in the models developed (1986 financial crisis, 1991 old-car exchange scheme, 1996 new road fatality definition) and found statistically significant. Furthermore, the forecasting results using data up to 2008 were compared with final actual data (2009-2011) indicating that the models perform properly, even in unusual situations, like the current strong financial crisis in Greece. Forecasting results up to 2020 are also presented and compared with the forecasts of a model that explicitly considers the currently on-going recession. Modeling the recession, and assuming that it will end by 2013, results in more reasonable estimates of risk and vehicle-kilometers for the 2020 horizon. This research demonstrates the benefits of using advanced state-space modeling techniques for modeling macroscopic road safety trends, such as allowing the explicit modeling of interventions. The challenges associated with the application of such state-of-the-art models for macroscopic phenomena, such as traffic fatalities in a region or country, are also highlighted. Furthermore, it is demonstrated that it is possible to apply such complex models using the relatively short time-series that are available in macroscopic road safety analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography (United States)

    Liebi, Marianne; Georgiadis, Marios; Menzel, Andreas; Schneider, Philipp; Kohlbrecher, Joachim; Bunk, Oliver; Guizar-Sicairos, Manuel


    The mechanical properties of many materials are based on the macroscopic arrangement and orientation of their nanostructure. This nanostructure can be ordered over a range of length scales. In biology, the principle of hierarchical ordering is often used to maximize functionality, such as strength and robustness of the material, while minimizing weight and energy cost. Methods for nanoscale imaging provide direct visual access to the ultrastructure (nanoscale structure that is too small to be imaged using light microscopy), but the field of view is limited and does not easily allow a full correlative study of changes in the ultrastructure over a macroscopic sample. Other methods of probing ultrastructure ordering, such as small-angle scattering of X-rays or neutrons, can be applied to macroscopic samples; however, these scattering methods remain constrained to two-dimensional specimens or to isotropically oriented ultrastructures. These constraints limit the use of these methods for studying nanostructures with more complex orientation patterns, which are abundant in nature and materials science. Here, we introduce an imaging method that combines small-angle scattering with tensor tomography to probe nanoscale structures in three-dimensional macroscopic samples in a non-destructive way. We demonstrate the method by measuring the main orientation and the degree of orientation of nanoscale mineralized collagen fibrils in a human trabecula bone sample with a spatial resolution of 25 micrometres. Symmetries within the sample, such as the cylindrical symmetry commonly observed for mineralized collagen fibrils in bone, allow for tractable sampling requirements and numerical efficiency. Small-angle scattering tensor tomography is applicable to both biological and materials science specimens, and may be useful for understanding and characterizing smart or bio-inspired materials. Moreover, because the method is non-destructive, it is appropriate for in situ measurements and

  6. Microbial agents in macroscopically healthy mammary gland tissues of small ruminants


    Liliana Spuria; Elena Biasibetti; Donal Bisanzio; Ilaria Biasato; Daniele De Meneghi; Patrizia Nebbia; Patrizia Robino; Paolo Bianco; Michele Lamberti; Claudio Caruso; Alessia Di Blasio; Simone Peletto; Loretta Masoero; Alessandro Dondo; Maria Teresa Capucchio


    Background Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. Methods This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions...

  7. The 5'-3' Distance of RNA Secondary Structures

    DEFF Research Database (Denmark)

    Han, Hillary S W; Reidys, Christian


    Abstract Recently, Yoffe and colleagues observed that the average distances between 5'-3' ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical arguments maximizing certain entropy functionals....... In this article, we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite n. Furthermore, we compute the limit distribution and show that for n = 30 the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA secondary...... structures are distinctively lower than those of minimum free energy structures of random RNA sequences....

  8. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    Energy Technology Data Exchange (ETDEWEB)

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. [MSKCC


    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  9. Graphene and Other 2D Colloids: Liquid Crystals and Macroscopic Fibers. (United States)

    Liu, Yingjun; Xu, Zhen; Gao, Weiwei; Cheng, Zhengdong; Gao, Chao


    Two-dimensional colloidal nanomaterials are running into renaissance after the enlightening researches of graphene. Macroscopic one-dimensional fiber is an optimal ordered structural form to express the in-plane merits of 2D nanomaterials, and the formation of liquid crystals (LCs) allows the creation of continuous fibers. In the correlated system from LCs to fibers, understanding their macroscopic organizing behavior and transforming them into new solid fibers is greatly significant for applications. Herein, we retrospect the history of 2D colloids and discuss about the concept of 2D nanomaterial fibers in the context of LCs, elaborating the motivation, principle and possible strategies of fabrication. Then we highlight the creation, development and typical applications of graphene fibers. Additionally, the latest advances of other 2D nanomaterial fibers are also summarized. Finally, conclusions, challenges and perspectives are provided to show great expectations of better and more fibrous materials of 2D nanomaterials. This review gives a comprehensive retrospect of the past century-long effort about the whole development of 2D colloids, and plots a clear roadmap - "lamellar solid - LCs - macroscopic fibers - flexible devices", which will certainly open a new era of structural-multifunctional application for the conventional 2D colloids. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Characterization of Mangifera indica cultivars in Thailand based on macroscopic, microscopic, and genetic characters

    Directory of Open Access Journals (Sweden)

    Aunyachulee Ganogpichayagrai


    Full Text Available Thai mango cultivars are classified into six groups plus one miscellaneous group according to germplasm database for mango. Characterization is important for conservation and the development of Thai mango cultivars. This study investigated macroscopic, microscopic leaf characteristics, and genetic relationship among 17 cultivars selected from six groups of mango in Thailand. Selected mango samples were obtained from three different locations in Thailand (n = 57. They were observed for their leaf and fruit macroscopic characteristics. Leaf measurement for the stomatal number, veinlet termination number, and palisade ratio was evaluated under a microscope attached with digital camera. DNA fingerprint was performed using CTAB extraction of DNA and inter-simple sequence repeat (ISSR amplification. Forty-five primers were screened; then, seven primers that amplified the reproducible band patterns were selected to amplified and generate dendrogram by Unweighted Pair-Group Method with Arithmetic Average. These selected 17 Thai mango cultivars had individually macroscopic characteristics based on fruits and leaves. For microscopic characteristics, the stomatal number, veinlet termination number, and palisade ratio were slightly differentiable. For genetic identification, 78 bands of 190-2660 bps were amplified, of which 82.05% were polymorphic. The genetic relationship among these cultivars was demonstrated and categorized into two main clusters. It was shown that ISSR markers could be useful for Thai mango cultivar identification.

  11. Information and self-organization a macroscopic approach to complex systems

    CERN Document Server

    Haken, Hermann


    Complex systems are ubiquitous, and practically all branches of science ranging from physics through chemistry and biology to economics and sociology have to deal with them. In this book we wish to present concepts and methods for dealing with complex systems from a unifying point of view. Therefore it may be of inter­ est to graduate students, professors and research workers who are concerned with theoretical work in the above-mentioned fields. The basic idea for our unified ap­ proach sterns from that of synergetics. In order to find unifying principles we shall focus our attention on those situations where a complex system changes its macroscopic behavior qualitatively, or in other words, where it changes its macroscopic spatial, temporal or functional structure. Until now, the theory of synergetics has usually begun with a microscopic or mesoscopic description of a complex system. In this book we present an approach which starts out from macroscopic data. In particular we shall treat systems that acquir...

  12. Monitoring road traffic congestion using a macroscopic traffic model and a statistical monitoring scheme

    KAUST Repository

    Zeroual, Abdelhafid


    Monitoring vehicle traffic flow plays a central role in enhancing traffic management, transportation safety and cost savings. In this paper, we propose an innovative approach for detection of traffic congestion. Specifically, we combine the flexibility and simplicity of a piecewise switched linear (PWSL) macroscopic traffic model and the greater capacity of the exponentially-weighted moving average (EWMA) monitoring chart. Macroscopic models, which have few, easily calibrated parameters, are employed to describe a free traffic flow at the macroscopic level. Then, we apply the EWMA monitoring chart to the uncorrelated residuals obtained from the constructed PWSL model to detect congested situations. In this strategy, wavelet-based multiscale filtering of data has been used before the application of the EWMA scheme to improve further the robustness of this method to measurement noise and reduce the false alarms due to modeling errors. The performance of the PWSL-EWMA approach is successfully tested on traffic data from the three lane highway portion of the Interstate 210 (I-210) highway of the west of California and the four lane highway portion of the State Route 60 (SR60) highway from the east of California, provided by the Caltrans Performance Measurement System (PeMS). Results show the ability of the PWSL-EWMA approach to monitor vehicle traffic, confirming the promising application of this statistical tool to the supervision of traffic flow congestion.

  13. Sialic Acid-Responsive Polymeric Interface Material: From Molecular Recognition to Macroscopic Property Switching (United States)

    Xiong, Yuting; Jiang, Ge; Li, Minmin; Qing, Guangyan; Li, Xiuling; Liang, Xinmiao; Sun, Taolei


    Biological systems that utilize multiple weak non-covalent interactions and hierarchical assemblies to achieve various bio-functions bring much inspiration for the design of artificial biomaterials. However, it remains a big challenge to correlate underlying biomolecule interactions with macroscopic level of materials, for example, recognizing such weak interaction, further transforming it into regulating material’s macroscopic property and contributing to some new bio-applications. Here we designed a novel smart polymer based on polyacrylamide (PAM) grafted with lactose units (PAM-g-lactose0.11), and reported carbohydrate-carbohydrate interaction (CCI)-promoted macroscopic properties switching on this smart polymer surface. Detailed investigations indicated that the binding of sialic acid molecules with the grafted lactose units via the CCIs induced conformational transformation of the polymer chains, further resulted in remarkable and reversible switching in surface topography, wettability and stiffness. With these excellent recognition and response capacities towards sialic acid, the PAM-g-lactose0.11 further facilitated good selectivity, strong anti-interference and high adsorption capacity in the capture of sialylated glycopeptides (important biomarkers for cancers). This work provides some enlightenment for the development of biointerface materials with tunable property, as well as high-performance glycopeptide enrichment materials.

  14. Macroscopic Graphene Fibers Directly Assembled from CVD-Grown Fiber-Shaped Hollow Graphene Tubes. (United States)

    Chen, Tao; Dai, Liming


    Using a copper wire as the substrate for the CVD growth of a hollow multilayer graphene tube, we prepared a macroscopic porous graphene fiber by removing the copper in an aqueous mixture solution of iron chloride (FeCl3, 1 M) and hydrochloric acid (HCl, 3 M) and continuously drawing the newly released graphene tube out of the liquid. The length of the macroscopic graphene fiber thus produced is determined mainly by the length of the copper wire used. The resultant macroscopic graphene fiber with the integrated graphene structure exhibited a high electrical conductivity (127.3 S cm(-1)) and good flexibility over thousands bending cycles, showing great promise as flexible electrodes for wearable optoelectronics and energy devices-exemplified by its use as a flexible conductive wire for lighting a LED and a cathode in a fiber-shaped dye-sensitized solar cell (DSSC) with one of the highest energy conversion efficiencies (3.25%) among fiber-shaped DSSCs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Macroscopical, Histological, and Characterization of Nonosteoarthritic Versus Osteoarthritic Hip Joint Cartilage

    Directory of Open Access Journals (Sweden)

    Jessica Badendick


    Full Text Available Osteoarthritis (OA might affect chondrocyte culture characteristics and complement expression. Therefore, this study addressed the interrelation between macroscopical and microscopical structure, complement expression, and chondrocyte culture characteristics in non-OA and OA cartilage. Femoral head cartilage samples harvested from patients with femoral neck fractures (FNFs and OA were analyzed for macroscopical alterations using an in-house scoring system, graded histologically (Mankin score, and immunolabeled for complement regulatory proteins (CRPs and receptors. Morphology of monolayer cultured chondrocytes isolated from a subset of samples was assessed. The macroscopical score distinguished the FNF and OA cartilage samples and correlated significantly with the histological results. Chondrocyte phenotype from FNF or OA cartilage differed. Complement receptor C5aR, CRPs CD55 and CD59, and weakly receptor C3AR were detected in the investigated FNF and OA cartilage, except for CD46, which was detected in only two of the five investigated donors. The in-house score also allows inexperienced observers to distinguish non-OA and OA cartilage for experimental purposes.

  16. Macroscopic Profile Modification and Microscopic Displacement Mechanism of Weak Gel Flowing in Porous Media

    Directory of Open Access Journals (Sweden)

    Jian Wang


    Full Text Available In this paper, the flowing mechanism and function on the macroscopic and microscopic scale in the porous media of a widely used weak gel of an acrylamide based polymer crosslinked with chromium(III were studied. Innovative microscopic plane visualization model was designed for microscopic scale experiment and sand pack physical model for macroscopic scale. The microscopic displacing experiments indicate that weak gel mainly intrudes into big pores rather than small ones, which can improve the conformance horizontally and increase the sweep efficiency benefiting from fluid diversion. Additionally, due to good viscoelasticity of weak gel, the negative pressure effect was formed enhancing oil recovery flow from small pore throats. Results of macroscopic physical sand pack flow experiment indicate positive influence of weak gel on vertical conformance control. Although the high permeable layer was not completely blocked, the oil recovery improved as a result of weak gel movement by continuous water flooding. Experiments results lead to conclusion, the primary function of weak gel is oil displacement, profile modification is secondary, and its effect is temporary.

  17. Fission properties of Po isotopes in different macroscopic-microscopic models (United States)

    Bartel, J.; Pomorski, K.; Nerlo-Pomorska, B.; Schmitt, Ch


    Fission-barrier heights of nuclei in the Po isotopic chain are investigated in several macroscopic-microscopic models. Using the Yukawa-folded single-particle potential, the Lublin-Strasbourg drop (LSD) model, the Strutinsky shell-correction method to yield the shell corrections and the BCS theory for the pairing contributions, fission-barrier heights are calculated and found in quite good agreement with the experimental data. This turns out, however, to be only the case when the underlying macroscopic, liquid-drop (LD) type, theory is well chosen. Together with the LSD approach, different LD parametrizations proposed by Moretto et al are tested. Four deformation parameters describing respectively elongation, neck-formation, reflectional-asymmetric, and non-axiality of the nuclear shape thus defining the so called modified Funny Hills shape parametrization are used in the calculation. The present study clearly demonstrates that nuclear fission-barrier heights constitute a challenging and selective tool to discern between such different macroscopic approaches.

  18. Macroscopic Models of Local Field Potentials and the Apparent 1/f Noise in Brain Activity (United States)

    Bédard, Claude; Destexhe, Alain


    The power spectrum of local field potentials (LFPs) has been reported to scale as the inverse of the frequency, but the origin of this 1/f noise is at present unclear. Macroscopic measurements in cortical tissue demonstrated that electric conductivity (as well as permittivity) is frequency-dependent, while other measurements failed to evidence any dependence on frequency. In this article, we propose a model of the genesis of LFPs that accounts for the above data and contradictions. Starting from first principles (Maxwell equations), we introduce a macroscopic formalism in which macroscopic measurements are naturally incorporated, and also examine different physical causes for the frequency dependence. We suggest that ionic diffusion primes over electric field effects, and is responsible for the frequency dependence. This explains the contradictory observations, and also reproduces the 1/f power spectral structure of LFPs, as well as more complex frequency scaling. Finally, we suggest a measurement method to reveal the frequency dependence of current propagation in biological tissue, and which could be used to directly test the predictions of this formalism. PMID:19348744

  19. First-principles based calculation of the macroscopic α/β interface in titanium

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dongdong [School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Key Lab of Nonferrous Materials of Ministry of Education, Central South University, Changsha 410083 (China); Zhu, Lvqi; Shao, Shouqi [School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Jiang, Yong, E-mail: [School of Materials Science and Engineering, Central South University, Changsha 410083 (China); Key Lab of Nonferrous Materials of Ministry of Education, Central South University, Changsha 410083 (China); National Key Lab for Powder Metallurgy, Central South University, Changsha 410083 (China); Shenzhen Research Institute of Central South University, Shenzhen 518057 (China)


    The macroscopic α/β interface in titanium and titanium alloys consists of a ledge interface (112){sub β}/(01-10){sub α} and a side interface (11-1){sub β}/(2-1-10){sub α} in a zig-zag arrangement. Here, we report a first-principles study for predicting the atomic structure and the formation energy of the α/β-Ti interface. Both component interfaces were calculated using supercell models within a restrictive relaxation approach, with various staking sequences and high-symmetry parallel translations being considered. The ledge interface energy was predicted as 0.098 J/m{sup 2} and the side interface energy as 0.811 J/m{sup 2}. By projecting the zig-zag interface area onto the macroscopic broad face, the macroscopic α/β interface energy was estimated to be as low as ∼0.12 J/m{sup 2}, which, however, is almost double the ad hoc value used in previous phase-field simulations.

  20. Sialic acid-triggered macroscopic properties switching on a smart polymer surface (United States)

    Xiong, Yuting; Li, Minmin; Wang, Hongxi; Qing, Guangyan; Sun, Taolei


    Constructing smart surfaces with responsive polymers capable of dynamically and reversibly changing their chemical and physical properties by responding to the recognition of biomolecules remains a challenging task. And, the key to achieving this purpose relies on the design of polymers to precisely interact with the target molecule and successfully transform the interaction signal into tunable macroscopic properties, further achieve special bio-functions. Herein, inspired by carbohydrate-carbohydrate interaction (CCI) in life system, we developed a three-component copolymer poly(NIPAAm-co-PT-co-Glc) bearing a binding unit glucose (Glc) capable of recognizing sialic acid, a type of important molecular targets for cancer diagnosis and therapy, and reported the sialic acid triggered macroscopic properties switching on this smart polymer surface. Detailed mechanism studies indicated that multiple hydrogen bonding interactions between Glc unit and Neu5Ac destroyed the initial hydrogen bond network of the copolymer, leading to a reversible ;contraction-to-swelling; conformational transition of the copolymer chains, accompanied with distinct macroscopic property switching (i.e., surface wettability, morphology, stiffness) of the copolymer film. And these features enabled this copolymer to selectively capture sialic acid-containing glycopeptides from complex protein samples. This work provides an inspiration for the design of novel smart polymeric materials with sensitive responsiveness to sialic acid, which would promote the development of sialic acid-specific bio-devices and drug delivery systems.

  1. RNA Sequencing Analysis of Salivary Extracellular RNA. (United States)

    Majem, Blanca; Li, Feng; Sun, Jie; Wong, David T W


    Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.

  2. Species-independent MicroRNA Gene Discovery

    KAUST Repository

    Kamanu, Timothy K.


    MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA genes are classified into different groups (miRNA families). This study reports about 19,000 unknown miRNA genes in nine species whereby approximately 15,300 predictions were computationally validated to contain at least one experimentally verified functional miRNA product. The predictions are based on a novel computational strategy which relies on miRNA family groupings and exploits the physics and geometry of miRNA genes to unveil the hidden palindromic signals and symmetries in miRNA gene sequences. Unlike conventional computational miRNA gene discovery methods, the algorithm developed here is species-independent: it allows prediction at higher accuracy and resolution from arbitrary RNA/DNA sequences in any species and thus enables examination of repeat-prone genomic regions which are thought to be non-informative or ’junk’ sequences. The information non-redundancy of uni-directional RNA sequences compared to information redundancy of bi-directional DNA is demonstrated, a fact that is overlooked by most pattern discovery algorithms. A novel method for computing upstream and downstream miRNA gene boundaries based on mathematical/statistical functions is suggested, as well as cutoffs for annotation of miRNA genes in different miRNA families. Another tool is proposed to allow hypotheses generation and visualization of data matrices, intra- and inter-species chromosomal distribution of miRNA genes or miRNA families. Our results indicate that: miRNA and miRNA

  3. RNA recognition by a human antibody against brain cytoplasmic 200 RNA. (United States)

    Jung, Euihan; Lee, Jungmin; Hong, Hyo Jeong; Park, Insoo; Lee, Younghoon


    Diverse functional RNAs participate in a wide range of cellular processes. The RNA structure is critical for function, either on its own or as a complex form with proteins and other ligands. Therefore, analysis of the RNA conformation in cells is essential for understanding their functional mechanisms. However, no appropriate methods have been established as yet. Here, we developed an efficient strategy for panning and affinity maturation of anti-RNA human monoclonal antibodies from a naïve antigen binding fragment (Fab) combinatorial phage library. Brain cytoplasmic 200 (BC200) RNA, which is also highly expressed in some tumors, was used as an RNA antigen. We identified MabBC200-A3 as the optimal binding antibody. Mutagenesis and SELEX experiments showed that the antibody recognized a domain of BC200 in a structure- and sequence-dependent manner. Various breast cancer cell lines were further examined for BC200 RNA expression using conventional hybridization and immunoanalysis with MabBC200-A3 to see whether the antibody specifically recognizes BC200 RNA among the total purified RNAs. The amounts of antibody-recognizable BC200 RNA were consistent with hybridization signals among the cell lines. Furthermore, the antibody was able to discriminate BC200 RNA from other RNAs, supporting the utility of this antibody as a specific RNA structure-recognizing probe. Intriguingly, however, when permeabilized cells were subjected to immunoanalysis instead of purified total RNA, the amount of antibody-recognizable RNA was not correlated with the cellular level of BC200 RNA, indicating that BC200 RNA exists as two distinct forms (antibody-recognizable and nonrecognizable) in breast cancer cells and that their distribution depends on the cell type. Our results clearly demonstrate that anti-RNA antibodies provide an effective novel tool for detecting and analyzing RNA conformation. © 2014 Jung et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. A macroscopic model of proton transport through the membrane-ionomer interface of a polymer electrolyte membrane fuel cell (United States)

    Kumar, Milan; Edwards, Brian J.; Paddison, Stephen J.


    The membrane-ionomer interface is the critical interlink of the electrodes and catalyst to the polymer electrolyte membrane (PEM); together forming the membrane electrode assembly in current state-of-the-art PEM fuel cells. In this paper, proton conduction through the interface is investigated to understand its effect on the performance of a PEM fuel cell. The water containing domains at this interface were modeled as cylindrical pores/channels with the anionic groups (i.e., -SO3-) assumed to be fixed on the pore wall. The interactions of each species with all other species and an applied external field were examined. Molecular-based interaction potential energies were computed in a small test element of the pore and were scaled up in terms of macroscopic variables. Evolution equations of the density and momentum of the species (water molecules and hydronium ions) were derived within a framework of nonequilibrium thermodynamics. The resulting evolution equations for the species were solved analytically using an order-of-magnitude analysis to obtain an expression for the proton conductivity. Results show that the conductivity increases with increasing water content and pore radius, and strongly depends on the separation distance between the sulfonate groups and their distribution on the pore wall. It was also determined that the conductivity of two similar pores of different radii in series is limited by the pore with the smaller radius.

  5. Experimental scoring systems for macroscopic articular cartilage repair correlate with the MOCART score assessed by a high-field MRI at 9.4 T--comparative evaluation of five macroscopic scoring systems in a large animal cartilage defect model

    National Research Council Canada - National Science Library

    Goebel, L; Orth, P; Müller, A; Zurakowski, D; Bücker, A; Cucchiarini, M; Pape, D; Madry, H


    To develop a new macroscopic scoring system which allows for an overall judgment of experimental articular cartilage repair and compare it with four existing scoring systems and high-field magnetic resonance imaging (MRI...

  6. Equation of state, universal profiles, scaling and macroscopic quantum effects in warm dark matter galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Vega, H.J. de [Sorbonne Universites, Universite Pierre et Marie Curie UPMC Paris VI, LPTHE CNRS UMR 7589, Paris Cedex 05 (France); Sanchez, N.G. [Observatoire de Paris PSL Research University, Sorbonne Universites UPMC Paris VI, Observatoire de Paris, LERMA CNRS UMR 8112, Paris (France)


    The Thomas-Fermi approach to galaxy structure determines self-consistently and non-linearly the gravitational potential of the fermionic warm dark matter (WDM) particles given their quantum distribution function f(E). This semiclassical framework accounts for the quantum nature and high number of DM particles, properly describing gravitational bounded and quantum macroscopic systems as neutron stars, white dwarfs and WDM galaxies. We express the main galaxy magnitudes as the halo radius r{sub h}, mass M{sub h}, velocity dispersion and phase space density in terms of the surface density which is important to confront to observations. From these expressions we derive the general equation of state for galaxies, i.e., the relation between pressure and density, and provide its analytic expression. Two regimes clearly show up: (1) Large diluted galaxies for M{sub h} >or similar 2.3 x 10{sup 6} M {sub CircleDot} and effective temperatures T{sub 0} > 0.017 K described by the classical self-gravitating WDM Boltzman gas with a space-dependent perfect gas equation of state, and (2) Compact dwarf galaxies for 1.6 x 10{sup 6} M {sub CircleDot} >or similar M{sub h} >or similar M{sub h,min} ≅ 3.10 x 10{sup 4} (2 keV/m){sup (16)/(5)} M {sub CircleDot}, T{sub 0} < 0.011 K described by the quantum fermionic WDM regime with a steeper equation of state close to the degenerate state. In particular, the T{sub 0} = 0 degenerate or extreme quantum limit yields the most compact and smallest galaxy. In the diluted regime, the halo radius r{sub h}, the squared velocity v{sup 2}(r{sub h}) and the temperature T{sub 0} turn to exhibit square-root of M{sub h} scaling laws. The normalized density profiles ρ(r)/ρ(0) and the normalized velocity profiles v{sup 2}(r)/v{sup 2}(0) are universal functions of r/r{sub h} reflecting the WDM perfect gas behavior in this regime. These theoretical results contrasted to robust and independent sets of galaxy data remarkably reproduce the observations. For

  7. Efficient extraction of RNA from various Camellia species rich in ...

    African Journals Online (AJOL)

    Camellia species, an important economic plants widely distributed in Asia, are recalcitrant to RNA extraction. Here, we developed a method for high quality RNA isolation. Based on the RNA isolated from flower buds, deep transcriptome sequencing of Camellia oleifera, Camellia chekiangoleosa and Camellia brevistyla ...

  8. cDNA sequence and tissue distribution of the mRNA for bovine and murine p11, the S100-related light chain of the protein-tyrosine kinase substrate p36 (calpactin I)

    DEFF Research Database (Denmark)

    Saris, Chris J M; Kristensen, Torsten; D’Eustachio, Peter


    RNA and of 68 nucleotides in murine p l l mRNA. The deduced bovine p l l amino acid equence is identical to the previously published partial bovine and complete porcine pl1 protein sequence except for an additional COOH-terminal lysine residue. The bovine and murine pl 1 proteins are 92% homologous, whereas....... They are very low in liver, heart, andt estes, moderate in brain,s pleen, and hymus, and high in kidney, intestine, andlu ng. Analysis of the same RNA samples for p36 mRNA levels showed that expression of p l l and p36 mRNAs is not always coordinated. Brain and the mouse embryonal carcinoma cell line F9 contain...

  9. The method of the spatial locating of macroscopic throats based-on the inversion of dynamic interwell connectivity (United States)

    Lv, Aimin; Li, Xuyan; Yu, Miao; Li, Gangzhu; Wang, Shoulong; Peng, Ruigang; Zheng, Yawen


    This paper presents a practical technique to quantitatively locate macroscopic throats between injector/producer pairs in a reservoir, considering the problems of extensively developed macroscopic throats and the low sweep efficiency of waterflooding on high water cut stage. The method combines dynamic and static data, based on the results of geological research and the inversion of dynamic interwell connectivity. This technique has implemented the spatial locating of macroscopic throats, using the data of injection/production profiles and tracer test over the years, considering the sedimentary facies of each small layer and the permeability of each sand body. The results of this work show that this method is more convenient and less expensive than previous ones. It is able to locate macroscopic throats in a reservoir accurately and quantitatively. Multiple materials ensure the accuracy of results, and this method is convenient to be applied in the oilfield.

  10. Fast-track access to urologic care for patients with macroscopic haematuria is efficient and cost-effective

    DEFF Research Database (Denmark)

    Liedberg, Fredrik; Gerdtham, Ulf; Gralén, Katarina


    : In all 275 patients who called 'the Red Phone' hotline were investigated, and 47 of them (17%) were diagnosed with cancer and 36 of those had bladder cancer. Median time from patient-reported haematuria to diagnosis was 29 (interquartile range (IQR) 14-104) days and 50 (IQR 27-165) days......BACKGROUND: The delay between onset of macroscopic haematuria and diagnosis of bladder cancer is often long. METHODS: We evaluated timely diagnosis and health-care costs for patients with macroscopic haematuria given fast-track access to diagnostics. During a 15-month period, a telephone hotline...... for fast-track diagnostics was provided in nine Swedish municipalities for patients aged ⩾50 years with macroscopic haematuria. The control group comprised 101 patients diagnosed with bladder cancer in the same catchment area with macroscopic haematuria who underwent regular diagnostic process. RESULTS...

  11. RNA recognition by a human antibody against brain cytoplasmic 200 RNA (United States)

    Jung, Euihan; Lee, Jungmin; Hong, Hyo Jeong; Park, Insoo; Lee, Younghoon


    Diverse functional RNAs participate in a wide range of cellular processes. The RNA structure is critical for function, either on its own or as a complex form with proteins and other ligands. Therefore, analysis of the RNA conformation in cells is essential for understanding their functional mechanisms. However, no appropriate methods have been established as yet. Here, we developed an efficient strategy for panning and affinity maturation of anti-RNA human monoclonal antibodies from a naïve antigen binding fragment (Fab) combinatorial phage library. Brain cytoplasmic 200 (BC200) RNA, which is also highly expressed in some tumors, was used as an RNA antigen. We identified MabBC200-A3 as the optimal binding antibody. Mutagenesis and SELEX experiments showed that the antibody recognized a domain of BC200 in a structure- and sequence-dependent manner. Various breast cancer cell lines were further examined for BC200 RNA expression using conventional hybridization and immunoanalysis with MabBC200-A3 to see whether the antibody specifically recognizes BC200 RNA among the total purified RNAs. The amounts of antibody-recognizable BC200 RNA were consistent with hybridization signals among the cell lines. Furthermore, the antibody was able to discriminate BC200 RNA from other RNAs, supporting the utility of this antibody as a specific RNA structure-recognizing probe. Intriguingly, however, when permeabilized cells were subjected to immunoanalysis instead of purified total RNA, the amount of antibody-recognizable RNA was not correlated with the cellular level of BC200 RNA, indicating that BC200 RNA exists as two distinct forms (antibody-recognizable and nonrecognizable) in breast cancer cells and that their distribution depends on the cell type. Our results clearly demonstrate that anti-RNA antibodies provide an effective novel tool for detecting and analyzing RNA conformation. PMID:24759090

  12. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian


    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  13. Statistics of canonical RNA pseudoknot structures. (United States)

    Huang, Fenix W D; Reidys, Christian M


    In this paper we study canonical RNA pseudoknot structures. We prove central limit theorems for the distributions of the arc-numbers of k-noncrossing RNA structures with given minimum stack-size tau over n nucleotides. Furthermore we compare the space of all canonical structures with canonical minimum free energy pseudoknot structures. Our results generalize the analysis of Schuster et al. obtained for RNA secondary structures [Hofacker, I.L., Schuster, P., Stadler, P.F., 1998. Combinatorics of RNA secondary structures. Discrete Appl. Math. 88, 207-237; Jin, E.Y., Reidys, C.M., 2007b. Central and local limit theorems for RNA structures. J. Theor. Biol. 250 (2008), 547-559; 2007a. Asymptotic enumeration of RNA structures with pseudoknots. Bull. Math. Biol., 70 (4), 951-970] to k-noncrossing RNA structures. Here k2 and tau are arbitrary natural numbers. We compare canonical pseudoknot structures to arbitrary structures and show that canonical pseudoknot structures exhibit significantly smaller exponential growth rates. We then compute the asymptotic distribution of their arc-numbers. Finally, we analyze how the minimum stack-size and crossing number factor into the distributions.

  14. Empirical insights into the stochasticity of small RNA sequencing


    Qin, Li-Xuan; Tuschl, Thomas; Singer, Samuel


    The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic na...

  15. Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory? (United States)

    Brezinski, Mark E; Rupnick, Maria


    Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems.

  16. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Directory of Open Access Journals (Sweden)

    Miguel Fribourg


    Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

  17. Experimental evaluation of freezing preparation for the macroscopic inspection in putrefied brain. (United States)

    Hyodoh, Hideki; Matoba, Kotaro; Murakami, Manabu; Matoba, Tomoko; Saito, Atsuko; Feng, Fei; Jin, Shigeki


    To evaluate the usefulness of freezing preparation for macroscopic investigation in advanced putrefied brain. After sealing in individual plastic bags, 10 pig heads were stored at 20°C for 5days allow postmortem change (putrefaction) to progress. After an observation period, they were divided into 2 groups to evaluate the usefulness of the freezing effect in macroscopic investigation. The process over the postmortem period and the freezing process were examined. At day-5, the presence of air density was detected between the inner surface of the cranium and the brain parenchyma. Intra-cranial air accumulation presented on CT in all heads. In the control group, the brain parenchyma leaked out from the hole in the meninges, and the gray-white matter difference was clear in 3/72 (4.2%), moderate in 7/72 (9.7%), ambiguous in 17/72 (23.6%), and poor in 45/72 (62.5%). In the freezing group, the brain parenchyma presented homogeneous low density after more than 14h freezing. On opening the cranium, the entire brains were frozen, and the gray-white matter difference was clear in 33/72 (46.0%), moderate in 17/72 (24.0%), ambiguous in 15/72 (21.0%), and poor in 7/72 (10.0%). The freezing group afforded greater clarity in the gray-white matter inspection (pFreezing preparation was useful for the macroscopic investigation of putrefied brain compared with the ordinary autopsy. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Investigating macroscopic, submicroscopic, and symbolic connections in a college-level general chemistry laboratory (United States)

    Thadison, Felicia Culver

    Explanations of chemical phenomena rely on understanding the behavior of submicroscopic particles. Because this level is "invisible," it is described using symbols such as models, diagrams and equations. For this reason, students often view chemistry as a "difficult" subject. The laboratory offers a unique opportunity for the students to experience chemistry macroscopically as well as symbolically. The purpose of this investigation was to determine how chemistry lab students explained chemical phenomenon on the macroscopic, submicroscopic, and representational/symbolic level. The participants were undergraduate students enrolled in an introductory level general chemistry lab course. Students' background information (gender, the number of previous chemistry courses), scores on final exams, and final average for the course were collected. Johnstone's triangle of representation guided the design and implementation of this study. A semi-structured interview was also conducted to bring out student explanations. The questionnaires required students to draw a molecule of water, complete acid base reaction equations, represent, submicroscopically, the four stages of an acid-base titration, and provide definitions of various terms. Students were able represent the submicroscopic level of water. Students were not able to represent the submicroscopic level of the reaction between an acid and a base. Students were able to represent the macroscopic level of an acid base reaction. Students were able to symbolically represent the reaction of an acid and a base. These findings indicate that students can use all three levels of chemical representation. However, students showed an inability to connect the levels in relation to acid-base chemistry. There was no relationship between a student's ability to use the levels and his or her final score in the course.

  19. The validity of the macroscopic appearance of lymph node biopsy in the diagnosis of tuberculosis. (United States)

    Houlden, Christopher; Woodfield, John


    Tuberculosis (TB) is a common disease with profound morbidity, mortality and effects on global public health. The differential diagnosis of lymphadenopathy is wide, particularly in areas where HIV is prevalent. Most hospitals in sub-Saharan Africa and across the developing world have limited, if any, histology facilities. This study will assess the validity of the assessment of the lymph nodes by their macroscopic appearance for the diagnosis of TB. Its sensitivity and specificity will be compared to full histological examination. This is a single-centre prospective study conducted in a remote rural district hospital in Zambia over a time period of 16 months. All patients with palpable lymphadenopathy where TB was considered in the differential diagnosis were included. The patients underwent an excision lymph node biopsy. The cut surface was judged by the operating surgeon as to the presence of caseation. The excised nodes were then sent for histological examination. In total, 59.8% of patients (64 of 107 patients) in this group had a final histological diagnosis of TB. This is equivalent to the TB disease prevalence in this group of patients that have palpable lymphadenopathy in this population. The diagnostic sensitivity based on macroscopic appearance of the lymph node was 81.25% (95% CI, 69.5-89.9%). The specificity was 97.67% (95% CI, 87.7-99.6%). This study has shown that lymph node appearance is a useful diagnostic test even without laboratory histopathological facilities in the diagnosis of TB. This assessment of the macroscopic appearance is both sensitive and specific. © The Author(s) 2015.

  20. Macroscopic Study of the Isthmus of the Thyroid Gland in Bangladeshi People: A Postmortem Study

    Directory of Open Access Journals (Sweden)

    Fakhrul Amin Mohammad Hasanul Banna


    Full Text Available Background: The position and size of isthmus of thyroid gland varies considerably in human with age, sex, physiologic state, race and geographical location and sometimes the isthmus may be absent. So this study was designed to find out the macroscopic differences in isthmus of thyroid gland of different age and sex groups in Bangladeshi people. Objective: To record the macroscopic characteristics of isthmus of thyroid gland with advancing age in both sexes with a view to help establishing normal standard of Bangladeshi people. Materials and Methods: This descriptive cross-sectional study was carried out on 54 autopsied human thyroid glands aged 5 to 65 years. Thyroid glands were collected from unclaimed dead bodies autopsied in the morgue of Sylhet M. A. G. Osmani Medical College, Sylhet. The collected specimens were divided into groups –– A (20 years and below, B (21 to 50 years and C (50 years and above. All specimens were examined morphologically by careful gross dissection method. Results: The isthmus was absent in 5.56% cases. In most of the cases (35.29% it was against the 1st–4th tracheal rings. There was significant difference in length between Group A and Group C (p<0.05 and in breadth between Group A and Group C and between Group B and Group C (p<0.05. No significant difference was found in length, breadth and thickness of isthmus of the thyroid gland between males and females. Conclusion: The presence or absence, positional change and variation in gross dimension of isthmus of thyroid gland were evident in human. The macroscopic difference was found with increasing age but not with sex.

  1. Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory? (United States)

    Brezinski, Mark E; Rupnick, Maria


    Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems. PMID:29200743

  2. Gecko toe and lamellar shear adhesion on macroscopic, engineered rough surfaces. (United States)

    Gillies, Andrew G; Henry, Amy; Lin, Hauwen; Ren, Angela; Shiuan, Kevin; Fearing, Ronald S; Full, Robert J


    The role in adhesion of the toes and lamellae - intermediate-sized structures - found on the gecko foot remains unclear. Insight into the function of these structures can lead to a more general understanding of the hierarchical nature of the gecko adhesive system, but in particular how environmental topology may relate to gecko foot morphology. We sought to discern the mechanics of the toes and lamellae by examining gecko adhesion on controlled, macroscopically rough surfaces. We used live Tokay geckos, Gekko gecko, to observe the maximum shear force a gecko foot can attain on an engineered substrate constructed with sinusoidal patterns of varying amplitudes and wavelengths in sizes similar to the dimensions of the toes and lamellae structures (0.5 to 6 mm). We found shear adhesion was significantly decreased on surfaces that had amplitudes and wavelengths approaching the lamella length and inter-lamella spacing, losing 95% of shear adhesion over the range tested. We discovered that the toes are capable of adhering to surfaces with amplitudes much larger than their dimensions even without engaging claws, maintaining 60% of shear adhesion on surfaces with amplitudes of 3 mm. Gecko adhesion can be predicted by the ratio of the lamella dimensions to surface feature dimensions. In addition to setae, remarkable macroscopic-scale features of gecko toes and lamellae that include compliance and passive conformation are necessary to maintain contact, and consequently, generate shear adhesion on macroscopically rough surfaces. Findings on the larger scale structures in the hierarchy of gecko foot function could provide the biological inspiration to drive the design of more effective and versatile synthetic fibrillar adhesives.

  3. Quantum dynamics of a macroscopic magnet operating as an environment of a mechanical oscillator (United States)

    Foti, C.; Cuccoli, A.; Verrucchi, P.


    We study the dynamics of a bipartite quantum system in a way such that its formal description keeps holding even if one of its parts becomes macroscopic; the problem is related to the analysis of the quantum-to-classical crossover, but our approach implies that the whole system stays genuinely quantum. The aim of the work is to understand (1) if, (2) to what extent, and possibly (3) how the evolution of a macroscopic environment testifies to the coupling with its microscopic quantum companion. To this purpose we consider a magnetic environment made of a large number of spin-1/2 particles, coupled with a quantum mechanical oscillator, possibly in the presence of an external magnetic field. We take the value of the total environmental spin S constant and large, which allows us to consider the environment as one single macroscopic system, and further deal with the hurdles of the spin-algebra via approximations that are valid in the large-S limit. We find an insightful expression for the propagator of the whole system, where we identify an effective "back-action" term, i.e., an operator acting on the magnetic environment only, and yet missing in the absence of the quantum principal system. This operator emerges as a time-dependent magnetic anisotropy whose character, whether uniaxial or planar, also depends on the detuning between the frequency of the oscillator and the level splitting in the spectrum of the free magnetic system, induced by the possible presence of the external field. The time dependence of the anisotropy is analyzed, and its effects on the dynamics of the magnet, as well as its relation to the entangling evolution of the overall system, are discussed.

  4. Nonminimal Macroscopic Models of a Scalar Field Based on Microscopic Dynamics. II. Transport Equations

    CERN Document Server

    Ignat'ev, Yu G


    The article proposes generalizations of the macroscopic model of plasma of scalar charged particles to the cases of inter-particle interaction with multiple scalar fields and negative effective masses of these particles. The model is based on the microscopic dynamics of a particle at presence of scalar fields. The theory is managed to be generalized naturally having strictly reviewed a series of its key positions depending on a sign of particle masses. Thereby, it is possible to remove the artificial restriction contradicting the more fundamental principle of action functional additivity. Additionally, as a condition of internal consistency of the theory, particle effective mass function is found.

  5. Adhesion of hydrogels under water by hydrogen bonding: from molecular interactions to macroscopic adhesion (United States)

    Creton, Costantino


    Hydrogels are an essential part of living organisms and are widely used in biotechnologies, health care and food science. Although swelling properties, cell adhesion on gel surfaces and gel elasticity have attracted much interest, macroscopic adhesion of hydrogels on solid surfaces in aqueous environment is much less well understood. We studied systematically and in aqueous environment, the reversible adhesion by hydrogen bonding of macroscopic model hydrogels of polydimethylacrylamide (PDMA) or of polyacrylamide (PAAm) on solid surfaces functionalized with polyacrylic acid (PAA) polymer brushes. The hydrogels were synthesized by free radical polymerization and the brushes were prepared by grafting polytertbutyl acrylate chains and converting them by pyrolisis into polyacrylic acid. A new adhesion tester based on the flat punch geometry was designed and used to control the contact area, contact time, contact pressure and debonding velocity of the gels from the surface while the samples were fully immersed in water. The adhesion tests were performed at different pH and temperatures and the modulus of the gel and grafting density and molecular weight of the brushes was varied. Macroscopic adhesion results were compared with phase diagrams in dilute solution to detect molecular interactions. While the PDMA/PAA pair behaved very similarly in solution and in macroscopic adhesion tests, the PAAm/PAA pair showed an unexpectedly high adhesion level relatively to its complexation ability in dilute solution. Surprisingly, time dependent experiments showed that the kinetics of H-bond formation and breakup at interfaces was very slow resulting in adhesion energies which were very dependent on contact time up to one hour of contact. At the molecular level, neutron reflectivity showed that the equilibrium brush conformation when in contact with the gels was more extended at pH2 (H-bonds activated) than at pH9 (H-bonds deactivated) and that a certain applied pressure was

  6. [Membrana interossea antebrachii--a common ligament of the radius-ulna joint. I: Macroscopic structure]. (United States)

    Küsswetter, W


    In 64 cadaveric forearm-specimens of different donorage the membrana interossea antebrachii was investigated macroscopically. The extension of the membrana interossea at the forearm was measured as well as its thickness. The direction of its fibers was also determinated in its different sections and prevalent fibrous structures reinforcing the membrana interossea were investigated. The results characterize the membrana interossea in its middle and proximal section as a taut, strong ligament, which stabilizes the forearm and coordinates pronation and supination in both radioulnar joints.

  7. Quantum teleportation from light beams to vibrational states of a macroscopic diamond (United States)

    Hou, P.-Y.; Huang, Y.-Y.; Yuan, X.-X.; Chang, X.-Y.; Zu, C.; He, L.; Duan, L.-M.


    With the recent development of optomechanics, the vibration in solids, involving collective motion of trillions of atoms, gradually enters into the realm of quantum control. Here, building on the recent remarkable progress in optical control of motional states of diamonds, we report an experimental demonstration of quantum teleportation from light beams to vibrational states of a macroscopic diamond under ambient conditions. Through quantum process tomography, we demonstrate average teleportation fidelity (90.6±1.0)%, clearly exceeding the classical limit of 2/3. The experiment pushes the target of quantum teleportation to the biggest object so far, with interesting implications for optomechanical quantum control and quantum information science. PMID:27240553

  8. First-principles theory of van der Waals forces between macroscopic bodies. (United States)

    Yannopapas, Vassilios; Vitanov, Nikolay V


    We present a first-principles method for the determination of the van der Waals interactions for a collection of finite-sized macroscopic bodies. The method is based on fluctuational electrodynamics and a rigorous multiple-scattering method for the electromagnetic field. As such, the method takes fully into account retardation, many-body, multipolar, and near-fields effects. By application of the method to the case of two metallic nanoparticles, we demonstrate the breakdown of the standard 1/r(2) distance law as the van der Waals force decays exponentially with distance when the nanoparticles are too close or too far apart.

  9. Formation law and criterion of nebulous macroscopic segregation in ZL205A alloy castings

    Directory of Open Access Journals (Sweden)

    Li Yusheng


    Full Text Available The appearance of macroscopic segregation in ZL205A alloy castings bears a super resemblance to the appearance of shrinkage porosity, and the chemical composition of the segregation is Al2Cu whose microstructure is in the form of dentrite or skeleton crystal. According to the characteristic of nebulous segregation, the formation process could be divided into two steps by the eutectic temperature of Al2Cu. Then a criterion for each of the two steps is brought forward on the basis of the shrinkage porosity criterion of low pressure casting.

  10. Tryptophan Substitutions at Lipid-exposed Positions of the Gamma M3 Transmembrane Domain Increase the Macroscopic Ionic Current Response of the Torpedo californica Nicotinic Acetylcholine Receptor (United States)

    Cruz-Martín, A.; Mercado, J.L.; Rojas, L.V.; McNamee, M.G.; Lasalde-Dominicci, J.A.


    Our previous amino-acid substitutions at the postulated lipid-exposed transmembrane segment M4 of the Torpedo californica acetylcholine receptor (AChR) focused on the alpha subunit. In this study we have extended the mutagenesis analysis using single tryptophan replacements in seven positions (I288, M291, F292, S294, L296, M299 and N300) near the center of the third transmembrane domain of the gamma subunit (γM3). All the tryptophan substitution mutants were expressed in Xenopus laevis oocytes following mRNA injections at levels close to wild type. The functional response of these mutants was evaluated using macroscopic current analysis in voltage-clamped oocytes. For all the substitutions the concentration for half-maximal activation, EC50, is similar to wild type using acetylcholine. For F292W, L296W and M299W the normalized macroscopic responses are 2- to 3-fold higher than for wild type. Previous photolabeling studies demonstrated that these three positions were in contact with membrane lipids. Each of these M3 mutations was co-injected with the previously characterized αC418W mutant to examine possible synergistic effects of single lipid-exposed mutations on two different subunits. For the γM3/αM4 double mutants, the EC50s were similar to those measured for the αC418W mutant alone. Tryptophan substitutions at positions that presumably face the interior of the protein (S294 and M291) or neighboring helices (I288) did not cause significant inhibition of channel function or surface expression of AChRs. PMID:11547353

  11. RNA structures regulating nidovirus RNA synthesis

    NARCIS (Netherlands)

    Born, Erwin van den


    Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the

  12. Working with RNA

    DEFF Research Database (Denmark)

    Nielsen, Henrik


    Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when...... possible and ribonucleases kept in check. The chapter outlines the specific precautions recommended for work with RNA and describes some of the modifications to standard protocols in molecular biology that are relevant to RNA work. The methods are applicable to all types of RNA and require a minimum...

  13. From Planck Size to Macroscopical Size:The Dutch Equation Under The Concept Of The Macroscopic Spacetime Shortcuts In The Manyfold Universe

    CERN Document Server

    Loup, F


    According to some authors,the presence of Dark Matter in the Universe can only be explained by the Manyfold Universe Model using Extra Dimensions.Such Dimensions are very small(compactified to the Planck Scale $10^{-35}$ m) allowing only gravity to uses these Extra Dimensions as Spacetime Shortcuts to reach us in minutes from remote parts of the Universe while light remains trapped in our 3+1 Einsteinian spacetime and needs billion years to make the same trip.This is why we cannot "see" Dark Matter and a object will remain Dark in the interval between the arrival of gravity and the arrival of light. If we could enlarge these Extra Dimensions from Planck Size to Macroscopical one we could theoretically reach these remote parts of the Universe responsible for the Dark Matter in short periods of time with a apparent "Superluminal" velocity although as a matter of fact we are "Subluminal" but taking advantages of the Geometry of the Manyfold Universe and with low and positive energy densities. We present here the...

  14. Empirical insights into the stochasticity of small RNA sequencing (United States)

    Qin, Li-Xuan; Tuschl, Thomas; Singer, Samuel


    The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic nature of exponential PCR amplification. We validated our findings with two independent datasets, one for microRNA sequencing and another for RNA sequencing. Motivated by the gamma distributed stochasticity, we provided a simple method for the analysis of RNA sequencing data and showed its superiority to three existing methods for differential expression analysis using three data examples of technical replicate data and biological replicate data.

  15. Detailed Simulation of Complex Hydraulic Problems with Macroscopic and Mesoscopic Mathematical Methods

    Directory of Open Access Journals (Sweden)

    Chiara Biscarini


    Full Text Available The numerical simulation of fast-moving fronts originating from dam or levee breaches is a challenging task for small scale engineering projects. In this work, the use of fully three-dimensional Navier-Stokes (NS equations and lattice Boltzmann method (LBM is proposed for testing the validity of, respectively, macroscopic and mesoscopic mathematical models. Macroscopic simulations are performed employing an open-source computational fluid dynamics (CFD code that solves the NS combined with the volume of fluid (VOF multiphase method to represent free-surface flows. The mesoscopic model is a front-tracking experimental variant of the LBM. In the proposed LBM the air-gas interface is represented as a surface with zero thickness that handles the passage of the density field from the light to the dense phase and vice versa. A single set of LBM equations represents the liquid phase, while the free surface is characterized by an additional variable, the liquid volume fraction. Case studies show advantages and disadvantages of the proposed LBM and NS with specific regard to the computational efficiency and accuracy in dealing with the simulation of flows through complex geometries. In particular, the validation of the model application is developed by simulating the flow propagating through a synthetic urban setting and comparing results with analytical and experimental laboratory measurements.

  16. Macroscopic and microscopic spectral properties of brain networks during local and global synchronization (United States)

    Maksimenko, Vladimir A.; Lüttjohann, Annika; Makarov, Vladimir V.; Goremyko, Mikhail V.; Koronovskii, Alexey A.; Nedaivozov, Vladimir; Runnova, Anastasia E.; van Luijtelaar, Gilles; Hramov, Alexander E.; Boccaletti, Stefano


    We introduce a practical and computationally not demanding technique for inferring interactions at various microscopic levels between the units of a network from the measurements and the processing of macroscopic signals. Starting from a network model of Kuramoto phase oscillators, which evolve adaptively according to homophilic and homeostatic adaptive principles, we give evidence that the increase of synchronization within groups of nodes (and the corresponding formation of synchronous clusters) causes also the defragmentation of the wavelet energy spectrum of the macroscopic signal. Our methodology is then applied to getting a glance into the microscopic interactions occurring in a neurophysiological system, namely, in the thalamocortical neural network of an epileptic brain of a rat, where the group electrical activity is registered by means of multichannel EEG. We demonstrate that it is possible to infer the degree of interaction between the interconnected regions of the brain during different types of brain activities and to estimate the regions' participation in the generation of the different levels of consciousness.

  17. Encapsulation of DNA in macroscopic and nanosized calcium alginate gel particles. (United States)

    Machado, Alexandra H E; Lundberg, Dan; Ribeiro, António J; Veiga, Francisco J; Miguel, Maria G; Lindman, Björn; Olsson, Ulf


    Calcium alginate beads, which are biodegradable and biocompatible, have been widely employed as delivery matrices for biomacromolecules. In the present work, the feasibility of encapsulation of DNA (which is used as a model biomacromolecule) in calcium alginate nanobeads (sub-200 nm size), prepared using a recently developed protocol based on the phase inversion temperature (PIT) emulsification method [Machado et al. Langmuir 2012, 28, 4131-4141], was assessed. The properties of the nanobeads were compared to those of the corresponding macroscopic (millimeter sized) calcium alginate beads. It was found that DNA, representing a relatively stiff and highly charged polyanion (thus like-charged to alginate), could be efficiently encapsulated in both nanosized and macroscopic beads, with encapsulation yields in the range of 77-99%. Complete release of DNA from the beads could be accomplished on dissolution of the gel by addition of a calcium-chelating agent. Importantly, the DNA was not denatured or fragmented during the preparation and collection of the nanobeads, which are good indicators of the mildness of the preparation protocol used. The calcium alginate nanobeads prepared by the herein utilized protocol thus show good potential to be used as carriers of sensitive biomacromolecules.

  18. Development of the Liver in Alpaca (Vicugna pacos): A Microscopic and Macroscopic Description. (United States)

    Castro, A N C; Domínguez, M T; Gómez, S A; Mendoza Torres, G J; Llerena Zavala, C A; Ghezzi, M D; Barbeito, C G


    South American camelids have several biological, morphological and behavioural adaptations that allow them to live in geographical areas dominated by high altitudes. The liver has hematopoietic functions during the prenatal life, which could be modified in response to the unfavorable habitat. However, there are no previous data on the prenatal development of the liver in these species. In the present work, a study on the macroscopic and microscopic morphology of the liver of the alpaca during ontogeny was performed. Forty-one animals ranging in age from 20 days of embryonic development to adults were studied. Macroscopic and microscopic observations were performed on samples subjected to different techniques. Less than 7-g specimens were studied with stereoscopic magnifying glass. The general characteristics of the prenatal liver are similar to those of other mammals, and the structures related to hematopoietic function follow an ontogenic pattern similar to that of previously studied precocial species. However, there are differences in morphology when compared to descriptions for the Old World camelids, including the absence of relation between the caudate lobe and the right kidney and the lack of interlobular connective tissue. © 2015 Blackwell Verlag GmbH.

  19. Radiographic evaluation of feline appendicular degenerative joint disease vs. Macroscopic appearance of articular cartilage. (United States)

    Freire, Mila; Robertson, Ian; Bondell, Howard D; Brown, James; Hash, Jon; Pease, Anthony P; Lascelles, B Duncan X


    Degenerative joint disease (DJD) is common in domesticated cats. Our purpose was to describe how radiographic findings thought to indicate feline DJD relate to macroscopic cartilage degeneration in appendicular joints. Thirty adult cats euthanized for reasons unrelated to this study were evaluated. Orthogonal digital radiographs of the elbow, tarsus, stifle, and coxofemoral joints were evaluated for the presence of DJD. The same joints were dissected for visual inspection of changes indicative of DJD and macroscopic cartilage damage was graded using a Total Cartilage Damage Score. When considering all joints, there was statistically significant fair correlation between cartilage damage and the presence of osteophytes and joint-associated mineralizations, and the subjective radiographic DJD score. Most correlations were statistically significant when looking at the different joints individually, but only the correlation between the presence of osteophytes and the subjective radiographic DJD score with the presence of cartilage damage in the elbow and coxofemoral joints had a value above 0.4 (moderate correlation). The joints most likely to have cartilage damage without radiographic evidence of DJD are the stifle (71% of radiographically normal joints) followed by the coxofemoral joint (57%), elbow (57%), and tarsal joint (46%). Our data support radiographic findings not relating well to cartilage degeneration, and that other modalities should be evaluated to aid in making a diagnosis of feline DJD. © 2011 Veterinary Radiology & Ultrasound.

  20. Prediction of esophageal and gastric histology by macroscopic diagnosis during upper endoscopy in pediatric celiac disease. (United States)

    Boschee, Erin D; Yap, Jason Y K; Turner, Justine M


    To determine the sensitivity of macroscopic appearance for predicting histological diagnosis at sites other than duodenum in pediatric celiac disease (CD). Endoscopic and histologic findings in pediatric patients undergoing upper endoscopy for first-time diagnosis of CD at Stollery Children's Hospital from 2010-2012 were retrospectively reviewed. Clinical charts from 140 patients were reviewed. Esophageal and gastric biopsies were taken in 54.3% and 77.9% of patients, respectively. Endoscopic appearance was normal in the esophagus and stomach in 75% and 86.2%. Endoscopic esophageal diagnoses were eosinophilic esophagitis (EE) (11.8%), esophagitis (7.9%), glycogenic acanthosis (1.3%) and non-specific abnormalities (3.9%). Endoscopic gastric diagnoses were gastritis (8.3%), pancreatic rest (0.9%), and non-specific abnormalities (4.6%). Histology was normal in 76.3% of esophageal and 87.2% of gastric specimens. Abnormal esophageal histology was EE (10.5%), esophagitis (10.5%), glycogenic acanthosis (1.3%) and non-specific (1.3%). Gastritis was reported in 12.8% of specimens. Sensitivity and specificity of normal endoscopy for predicting normal esophageal histology was 86.2% and 61.1%, and for normal gastric histology was 87.4% and 21.4%. In the absence of macroscopic abnormalities, routine esophageal and gastric biopsy during endoscopy for pediatric CD does not identify major pathologies. These findings have cost and time saving implications for clinical practice.

  1. Quantum entanglement at ambient conditions in a macroscopic solid-state spin ensemble. (United States)

    Klimov, Paul V; Falk, Abram L; Christle, David J; Dobrovitski, Viatcheslav V; Awschalom, David D


    Entanglement is a key resource for quantum computers, quantum-communication networks, and high-precision sensors. Macroscopic spin ensembles have been historically important in the development of quantum algorithms for these prospective technologies and remain strong candidates for implementing them today. This strength derives from their long-lived quantum coherence, strong signal, and ability to couple collectively to external degrees of freedom. Nonetheless, preparing ensembles of genuinely entangled spin states has required high magnetic fields and cryogenic temperatures or photochemical reactions. We demonstrate that entanglement can be realized in solid-state spin ensembles at ambient conditions. We use hybrid registers comprising of electron-nuclear spin pairs that are localized at color-center defects in a commercial SiC wafer. We optically initialize 10(3) identical registers in a 40-μm(3) volume (with [Formula: see text] fidelity) and deterministically prepare them into the maximally entangled Bell states (with 0.88 ± 0.07 fidelity). To verify entanglement, we develop a register-specific quantum-state tomography protocol. The entanglement of a macroscopic solid-state spin ensemble at ambient conditions represents an important step toward practical quantum technology.

  2. Macroscopic Rock Texture Image Classification Using a Hierarchical Neuro-Fuzzy Class Method

    Directory of Open Access Journals (Sweden)

    Laercio B. Gonçalves


    Full Text Available We used a Hierarchical Neuro-Fuzzy Class Method based on binary space partitioning (NFHB-Class Method for macroscopic rock texture classification. The relevance of this study is in helping Geologists in the diagnosis and planning of oil reservoir exploration. The proposed method is capable of generating its own decision structure, with automatic extraction of fuzzy rules. These rules are linguistically interpretable, thus explaining the obtained data structure. The presented image classification for macroscopic rocks is based on texture descriptors, such as spatial variation coefficient, Hurst coefficient, entropy, and cooccurrence matrix. Four rock classes have been evaluated by the NFHB-Class Method: gneiss (two subclasses, basalt (four subclasses, diabase (five subclasses, and rhyolite (five subclasses. These four rock classes are of great interest in the evaluation of oil boreholes, which is considered a complex task by geologists. We present a computer method to solve this problem. In order to evaluate system performance, we used 50 RGB images for each rock classes and subclasses, thus producing a total of 800 images. For all rock classes, the NFHB-Class Method achieved a percentage of correct hits over 73%. The proposed method converged for all tests presented in the case study.

  3. Cholesterics of colloidal helices: predicting the macroscopic pitch from the particle shape and thermodynamic state. (United States)

    Dussi, Simone; Belli, Simone; van Roij, René; Dijkstra, Marjolein


    Building a general theoretical framework to describe the microscopic origin of macroscopic chirality in (colloidal) liquid crystals is a long-standing challenge. Here, we combine classical density functional theory with Monte Carlo calculations of virial-type coefficients to obtain the equilibrium cholesteric pitch as a function of thermodynamic state and microscopic details. Applying the theory to hard helices, we observe both right- and left-handed cholesteric phases that depend on a subtle combination of particle geometry and system density. In particular, we find that entropy alone can even lead to a (double) inversion in the cholesteric sense of twist upon changing the packing fraction. We show how the competition between single-particle properties (shape) and thermodynamics (local alignment) dictates the macroscopic chiral behavior. Moreover, by expanding our free-energy functional, we are able to assess, quantitatively, Straley's theory of weak chirality, which is used in several earlier studies. Furthermore, by extending our theory to different lyotropic and thermotropic liquid-crystal models, we analyze the effect of an additional soft interaction on the chiral behavior of the helices. Finally, we provide some guidelines for the description of more complex chiral phases, like twist-bend nematics. Our results provide new insights into the role of entropy in the microscopic origin of this state of matter.

  4. A contribution to the identification of charcoal origin in Brazil II - Macroscopic characterization of Cerrado species. (United States)

    Gonçalves, Thaís A P; Nisgoski, Silvana; Oliveira, Julia S; Marcati, Carmen R; Ballarin, Adriano W; Muñiz, Graciela I B


    The Brazilian Cerrado is the richest savanna in the world. It is also one of the biomes more threatened in the country and a hotspot for conservation priorities. The main causes of deforestation in Cerrado are agricultural practices, livestock and charcoal production. Although charcoal has a minor impact, its consumption represents the deforestation of 16.000 Km² of the Cerrado. To contribute for the biomes's conservation it is very important to improve forestry supervision. Thus, in this work we present the macroscopic characterization of charcoal from 25 Cerrado's species. We simulate the real conditions of forest controllers by using the magnifications of 10x, 25x and 65x. Likewise, the charcoals micrographs are all of transverse sections due to the larger amount of anatomical information. We also analyzed texture, brightness, vitrification, ruptures and some special features. The species present several differences in their anatomical structure. Although some of them are very unique, this work does not intent to identify charcoals only by macroscopic analyses. But it might give directions to future identification of genera or species. It also provides knowledge for government agents to verify the documents of forestry origin by fast analyzing a sample of charcoal itself.

  5. A contribution to the identification of charcoal origin in Brazil II - Macroscopic characterization of Cerrado species

    Directory of Open Access Journals (Sweden)



    Full Text Available The Brazilian Cerrado is the richest savanna in the world. It is also one of the biomes more threatened in the country and a hotspot for conservation priorities. The main causes of deforestation in Cerrado are agricultural practices, livestock and charcoal production. Although charcoal has a minor impact, its consumption represents the deforestation of 16.000 Km² of the Cerrado. To contribute for the biomes's conservation it is very important to improve forestry supervision. Thus, in this work we present the macroscopic characterization of charcoal from 25 Cerrado's species. We simulate the real conditions of forest controllers by using the magnifications of 10x, 25x and 65x. Likewise, the charcoals micrographs are all of transverse sections due to the larger amount of anatomical information. We also analyzed texture, brightness, vitrification, ruptures and some special features. The species present several differences in their anatomical structure. Although some of them are very unique, this work does not intent to identify charcoals only by macroscopic analyses. But it might give directions to future identification of genera or species. It also provides knowledge for government agents to verify the documents of forestry origin by fast analyzing a sample of charcoal itself.

  6. Modeling two-stage bunch compression with wakefields: Macroscopic properties and microbunching instability

    Directory of Open Access Journals (Sweden)

    R. A. Bosch


    Full Text Available In a two-stage compression and acceleration system, where each stage compresses a chirped bunch in a magnetic chicane, wakefields affect high-current bunches. The longitudinal wakes affect the macroscopic energy and current profiles of the compressed bunch and cause microbunching at short wavelengths. For macroscopic wavelengths, impedance formulas and tracking simulations show that the wakefields can be dominated by the resistive impedance of coherent edge radiation. For this case, we calculate the minimum initial bunch length that can be compressed without producing an upright tail in phase space and associated current spike. Formulas are also obtained for the jitter in the bunch arrival time downstream of the compressors that results from the bunch-to-bunch variation of current, energy, and chirp. Microbunching may occur at short wavelengths where the longitudinal space-charge wakes dominate or at longer wavelengths dominated by edge radiation. We model this range of wavelengths with frequency-dependent impedance before and after each stage of compression. The growth of current and energy modulations is described by analytic gain formulas that agree with simulations.

  7. Synchronized Molecular-Dynamics Simulation via Macroscopic Heat and Momentum Transfer: An Application to Polymer Lubrication

    Directory of Open Access Journals (Sweden)

    Shugo Yasuda


    Full Text Available A synchronized molecular-dynamics simulation via macroscopic heat and momentum transfer is proposed to model the nonisothermal flow behaviors of complex fluids. In this method, the molecular-dynamics simulations are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum-transport equations. This method is applied to the lubrication of a polymeric liquid composed of short chains of ten beads between parallel plates. The rheological properties and conformation of the polymer chains coupled with local viscous heating are investigated with a nondimensional parameter, the Nahme-Griffith number, which is defined as the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and a transitional behavior of the conformation of the polymer chains are exhibited with a rapid temperature rise when the Nahme-Griffith number exceeds unity. The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains with heat generation under shear flows.

  8. Macroscopically ordered hexagonal arrays by directed self-assembly of block copolymers with minimal topographic patterns. (United States)

    Choi, Jaewon; Gunkel, Ilja; Li, Yinyong; Sun, Zhiwei; Liu, Feng; Kim, Hyeyoung; Carter, Kenneth R; Russell, Thomas P


    A simple and robust method has been developed for the generation of macroscopically ordered hexagonal arrays from the directed self-assembly (DSA) of cylinder-forming block copolymers (BCPs) based on minimal trench patterns with solvent vapor annealing. The use of minimal trench patterns allows us to probe the guided hexagonal arrays of cylindrical microdomains using grazing incidence small angle X-ray scattering (GISAXS), where the sample stage is rotated on the basis of the six-fold symmetry of a hexagonal system. It is found that the (10) planes of hexagonal arrays of cylindrical microdomains are oriented parallel to the underlying trench direction over macroscopic length scales (∼1 × 1 cm2). However, there are misorientations of the hexagonal arrays with short-range ordering. GISAXS patterns show that the hexagonal arrays on the minimal trench pattern are distorted, deviating from a perfect hexagonal lattice. This distortion has been attributed to the absence of topographic constraints in the unconfined direction on the 1-D minimal trench pattern. Also, the frustration of BCP microdomains, arising from the incommensurability between the trench pitch and natural period of the BCP at the base of the trench, influences the distortion of the hexagonal arrays.

  9. Macroscopic and microscopic study of 1-ethyl-3-methyl-imidazolium acetate-DMSO mixtures. (United States)

    Radhi, Asanah; Le, Kim Anh; Ries, Michael E; Budtova, Tatiana


    Macroscopic (steady-state viscosity, density) and microscopic (NMR chemical shifts, (1)H NMR relaxation times, and diffusion) properties of the 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc])-dimethyl sulfoxide (DMSO) mixture were studied in detail as a function of DMSO molar fraction at various temperatures. Temperature dependencies were used to calculate the activation energies. NMR results indicate that at low molar fraction of DMSO (<0.4), it weakly associates with the cation and in doing so disrupts the strong ion-ion association that exists in the pure ionic liquid. Stokes-Einstein equation, which linearly correlates the diffusion coefficient of a spherical molecule and macroscopic viscosity, was shown to work well for the [EMIM][OAc]-DMSO mixture. The influence of DMSO on the "anomalous" diffusion in [EMIM][OAc] ("quick" cation vs "slow" anion) was investigated; it was demonstrated that DMSO makes the cation diffusion slower. All parameters studied showed relatively small deviations from the ideal mixing rule behavior (from 20% to 50% difference between experimental and theoretically predicted results), confirming weak interactions between the components.

  10. Single Carbon Fibers with a Macroscopic-Thickness, 3D Highly Porous Carbon Nanotube Coating. (United States)

    Zou, Mingchu; Zhao, Wenqi; Wu, Huaisheng; Zhang, Hui; Xu, Wenjing; Yang, Liusi; Wu, Shiting; Wang, Yunsong; Chen, Yijun; Xu, Lu; Cao, Anyuan


    Carbon fiber (CF) grafted with a layer of carbon nanotubes (CNTs) plays an important role in composite materials and other fields; to date, the applications of CNTs@CF multiscale fibers are severely hindered by the limited amount of CNTs grafted on individual CFs and the weak interfacial binding force. Here, monolithic CNTs@CF fibers consisting of a 3D highly porous CNT sponge layer with macroscopic-thickness (up to several millimeters), which is directly grown on a single CF, are fabricated. Mechanical tests reveal high sponge-CF interfacial strength owing to the presence of a thin transitional layer, which completely inhibits the CF slippage from the matrix upon fracture in CNTs@CF fiber-epoxy composites. The porous conductive CNTs@CF hybrid fibers also act as a template for introducing active materials (pseudopolymers and oxides), and a solid-state fiber-shaped supercapacitor and a fiber-type lithium-ion battery with high performances are demonstrated. These CNTs@CF fibers with macroscopic CNT layer thickness have many potential applications in areas such as hierarchically reinforced composites and flexible energy-storage textiles. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Elucidation of enzyme control mechanisms using macroscopic measurements in a mixed substrate fermentation system. (United States)

    Pih, N; De Bernardez, E; Dhurjati, P


    The objective of this work was to relate macroscopically measurable on-line fermentation parameters such as dissolved oxygen, off-gas oxygen and carbon dioxide, and cell mass, to the controlled production of key intracellular enzymes under carbon limited conditions. Both batch and perturbed batch aerobic fermentations were performed using two different strains of Escherichia coli, with glucose and lactose as the sole carbon sources. The two strains differed from each other only in the lac operon region of their genome. The parent strain, E. coli 3000, was inducible for the enzyme beta-galactosidase. The other strain, E. coli 3300, was a constitutive mutant in the production of beta-galactosidase. In all experiments, off-line assays of sugars and beta-galactosidase activity were performed. It was observed that there is a clear relationship between the macroscopic on-line measurements, dissolved oxygen tension, carbon dioxide evolution rate and oxygen uptake rate, and the microscopic control phenomena of catabolite repression, catabolite inhibition, and inducer repression.

  12. Macroscopic inhomogeneous deformation behavior arising in single crystal Ni-Mn-Ga foils under tensile loading (United States)

    Murasawa, Go; Yeduru, Srinivasa R.; Kohl, Manfred


    This study investigated macroscopic inhomogeneous deformation occurring in single-crystal Ni-Mn-Ga foils under uniaxial tensile loading. Two types of single-crystal Ni-Mn-Ga foil samples were examined as-received and after thermo-mechanical training. Local strain and the strain field were measured under tensile loading using laser speckle and digital image correlation. The as-received sample showed a strongly inhomogeneous strain field with intermittence under progressive deformation, but the trained sample result showed strain field homogeneity throughout the specimen surface. The as-received sample is a mainly polycrystalline-like state composed of the domain structure. The sample contains many domain boundaries and large domain structures in the body. Its structure would cause large local strain band nucleation with intermittence. However, the trained one is an ideal single-crystalline state with a transformation preferential orientation of variants after almost all domain boundary and large domain structures vanish during thermo-mechanical training. As a result, macroscopic homogeneous deformation occurs on the trained sample surface during deformation.

  13. RNA modifications by oxidation

    DEFF Research Database (Denmark)

    Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper


    The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found...... to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...

  14. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin


    The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...... procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct plausible conformations by stringing together short fragments obtained from experimental structures. However...... efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D...

  15. Antisense RNA Approach

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Antisense RNA Approach. Antisense RNA approach is already well documented and well established in therapeutic research. Our system can also be subjected to such an approach. Which gene to target? Our objective would be to target the leader RNA as is thought ...

  16. Messenger RNA transcripts (United States)

    Dan Cullen


    In contrast to DNA, messenger RNA (mRNA) in complex substrata is rarely analyzed, in large part because labile RNA molecules are difficult to purify. Nucleic acid extractions from fungi that colonize soil are particularly difficult and plagued by humic substances that interfere with Taq polymerase (Tebbe and Vahjen 1993 and references therein). Magnetic capture...

  17. RNA self-assembly and RNA nanotechnology. (United States)

    Grabow, Wade W; Jaeger, Luc


    CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such

  18. Fast Prediction of RNA-RNA Interaction (United States)

    Salari, Raheleh; Backofen, Rolf; Sahinalp, S. Cenk

    Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.

  19. On the biological basis for competing macroscopic dose descriptors for kilovoltage dosimetry: cellular dosimetry for brachytherapy and diagnostic radiology (United States)

    Thomson, R. M.; Carlsson Tedgren, Å.; Williamson, J. F.


    The purpose of this work is to investigate how alternative macroscopic dose descriptors track absorbed dose to biologically relevant subcellular targets via Monte Carlo (MC) analysis of cellular models for a variety of cancerous and normal soft tissues for kilovoltage radiation. The relative mass distributions of water, light inorganic elements, and protein components of nuclear and cytoplasm compartments for various tissues are determined from a literature review. These data are used to develop representative cell models to demonstrate the range of mass elemental compositions of these subcellular structures encountered in the literature from which radiological quantities (energy absorption and attenuation coefficients; stopping powers) are computed. Using representative models of cell clusters, doses to subcellular targets are computed using MC simulation for photon sources of energies between 20 and 370 keV and are compared to bulk medium dose descriptors. It is found that cells contain significant and varying mass fractions of protein and inorganic elements, leading to variations in mass energy absorption coefficients for cytoplasm and nuclear media as large as 10% compared to water for sub-50 keV photons. Doses to subcellular structures vary by as much as 23% compared to doses to the corresponding average bulk medium or to small water cavities embedded in the bulk medium. Relationships between cellular target doses and doses to the bulk medium or to a small water cavity embedded in the bulk medium are sensitive to source energy and cell morphology, particularly for lower energy sources, e.g., low energy brachytherapy (subcellular targets for the range of cellular morphologies and tissues considered.

  20. Macroscopic versus microscopic photovoltaic response of heterojunctions based on mechanochemically prepared nanopowders of kesterite and n-type semiconductors

    Directory of Open Access Journals (Sweden)

    O.P. Dimitriev


    Full Text Available Mechanochemically prepared nanopowder of selenium-free kesterite Cu2ZnSnS4 (CZTS in combination with n-type semiconductors, i.e., CdS, ZnO and TiO2, was tested in planar and bulk-heterojunction solar cells. The samples have been studied by macroscopic current-voltage (I-V measurements and Kelvin-probe atomic-force microscopy (KPFM. KPFM images taken under light illumination showed the distribution of the potential across the surface, with negative potential on the n-type semiconductor domains and positive potential on the CZTS domains, which indicated charge separation at the interface of the counterparts. The best result was found for the CdS-CZTS composition, which showed a potential difference between the domains up to 250 mV. These results were compared with the planar heterojunctions of CdS/CZTS and TiO2/CZTS, where CZTS nanopowder was pressed/deposited directly onto the surface of films of the corresponding n-type semiconductors. Again, I-V characteristics showed that cells based on CdS/CZTS heterojunctions have the best performance, with a photovoltage up to 200 mV and photocurrent densities up to 0.1 mA/cm2. However, the carrier generation was found to occur mainly in the CdS semiconductor, while CZTS showed no photo-response and served as the hole-transporting layer only. It is concluded that sensitization of the kesterite powder obtained by mechanochemical method is necessary to improve the performance of the corresponding solar cells.

  1. Hydrogel Synthesis Directed Toward Tissue Engineering: Impact of Reaction Condition on Structural Parameters and Macroscopic Properties of Xerogels

    Directory of Open Access Journals (Sweden)

    Borivoj Adnadjević


    Full Text Available The existence of correlation and functional relationships between reaction conditions (concentrations of crosslinker, monomer and initiator, and neutralization degree of monomer, primary structural parameters (crosslinking density of network, average molar mass between crosslinks, and distance between macromolecular chains, and macroscopic properties (equilibrium swelling degree and xerogel density of the synthesized xerogels which are important for application in tissue engineering is investigated. The structurally different xerogels samples of poly(acrylic acid, poly(methacrylic acid, and poly(acrylic acid-g-gelatin were synthesized by applying different methods of polymerization: crosslinking polymerization, crosslinking polymerization in high concentrated aqueous solution, and crosslinking graft polymerization. The values of primary structural parameters and macroscopic properties were determined for the synthesized xerogels samples. For all of the investigated methods of polymerization, an existence of empirical power function of the dependence of primary structural parameters and macroscopic properties on the reaction conditions was established. The scaling laws between primary structural parameters and macroscopic properties on average molar mass between crosslinks were established. It is shown that scaling exponent is independent from the type of monomer and other reaction conditions within the same polymerization method. The physicochemical model that could be used for xerogel synthesis with predetermined macroscopic properties was suggested.

  2. Combinatorics of RNA-RNA interaction. (United States)

    Li, Thomas J X; Reidys, Christian M


    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

  3. Analysis of macroscopic gunshot residues by Raman spectroscopy to assess the weapon memory effect. (United States)

    López-López, María; Delgado, Juan Jose; García-Ruiz, Carmen


    Gunshot residues (GSR) are valuable evidence which provide the forensic analyst with useful information about a crime scene when proper analytical methods are used. Nowadays, the method of choice for analyzing GSR is scanning electron microscopy coupled with energy dispersive X-ray analysis (SEM/EDX). However, SEM/EDX presents limitations when the GSR identification of "non-toxic" ammunition types is performed. To overcome this drawback, Raman spectroscopy has been recently proposed as a complementary technique to SEM/EDX. However, for the time being, it can only be used in a limited number of casework (e.g. examining the macroscopic GSR produced at short distance over victim's clothes) and further research to know when this technique could support SEM-EDX results is required. In the present work, the memory effect of the weapon, which plays an important role to link the GSR found and the ammunition fired, is studied. Twenty shots were fired at close distance (~30 cm) at paper targets using the same weapon with two different types of ammunition. The first, third, ninth, and twentieth shots were fired with the first ammunition and the shots among them using the second ammunition. The macroscopic GSR produced by the first ammunition were analyzed using Raman spectroscopy. First, the spectra obtained were visually differentiated by taking into account the band at about 1342 cm(-1). This first approach shown that in the first shot were no GSR particles from the second ammunition, but 1.5-7.5% of analyzed particles corresponded to the second ammunition in the third, ninth, and twentieth shots. Additionally, the same differentiation was then performed by discriminant analysis using the spectral range from 1800 to 800 cm(-1). Although using this second approach only one GSR was identified as the second ammunition, was remarkable that after the shots with different ammunition the GSR obtained shows greater variability. The results obtained suggest that the memory effect of

  4. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...

  5. The NIH Extracellular RNA Communication Consortium

    Directory of Open Access Journals (Sweden)

    Alexandra M. Ainsztein


    Full Text Available The Extracellular RNA (exRNA Communication Consortium, funded as an initiative of the NIH Common Fund, represents a consortium of investigators assembled to address the critical issues in the exRNA research arena. The overarching goal is to generate a multi-component community resource for sharing fundamental scientific discoveries, protocols, and innovative tools and technologies. The key initiatives include (a generating a reference catalogue of exRNAs present in body fluids of normal healthy individuals that would facilitate disease diagnosis and therapies, (b defining the fundamental principles of exRNA biogenesis, distribution, uptake, and function, as well as development of molecular tools, technologies, and imaging modalities to enable these studies, (c identifying exRNA biomarkers of disease, (d demonstrating clinical utility of exRNAs as therapeutic agents and developing scalable technologies required for these studies, and (e developing a community resource, the exRNA Atlas, to provide the scientific community access to exRNA data, standardized exRNA protocols, and other useful tools and technologies generated by funded investigators.

  6. Therapeutic miRNA and siRNA: Moving from Bench to Clinic as Next Generation Medicine

    Directory of Open Access Journals (Sweden)

    Chiranjib Chakraborty


    Full Text Available In the past few years, therapeutic microRNA (miRNA and small interfering RNA (siRNA are some of the most important biopharmaceuticals that are in commercial space as future medicines. This review summarizes the patents of miRNA- and siRNA-based new drugs, and also provides a snapshot about significant biopharmaceutical companies that are investing for the therapeutic development of miRNA and siRNA molecules. An insightful view about individual siRNA and miRNA drugs has been depicted with their present status, which is gaining attention in the therapeutic landscape. The efforts of the biopharmaceuticals are discussed with the status of their preclinical and/or clinical trials. Here, some of the setbacks have been highlighted during the biopharmaceutical development of miRNA and siRNA as individual therapeutics. Finally, a snapshot is illustrated about pharmacokinetics, pharmacodynamics with absorption, distribution, metabolism, and excretion (ADME, which is the fundamental development process of these therapeutics, as well as the delivery system for miRNA- and siRNA-based drugs.

  7. Multiscale stochastic simulations for tensile testing of nanotube-based macroscopic cables. (United States)

    Pugno, Nicola M; Bosia, Federico; Carpinteri, Alberto


    Thousands of multiscale stochastic simulations are carried out in order to perform the first in-silico tensile tests of carbon nanotube (CNT)-based macroscopic cables with varying length. The longest treated cable is the space-elevator megacable but more realistic shorter cables are also considered in this bottom-up investigation. Different sizes, shapes, and concentrations of defects are simulated, resulting in cable macrostrengths not larger than approximately 10 GPa, which is much smaller than the theoretical nanotube strength (approximately 100 GPa). No best-fit parameters are present in the multiscale simulations: the input at level 1 is directly estimated from nanotensile tests of CNTs, whereas its output is considered as the input for the level 2, and so on up to level 5, corresponding to the megacable. Thus, five hierarchical levels are used to span lengths from that of a single nanotube (approximately 100 nm) to that of the space-elevator megacable (approximately 100 Mm).

  8. A Macroscopic Performance Analysis of NASA’s Northrop Grumman RQ-4A

    Directory of Open Access Journals (Sweden)

    Enric Pastor


    Full Text Available This paper presents the process of identification, from a macroscopic point of view, of the Northrop Grumman RQ-4A Global Hawk Remote-Piloted Aircraft System from real, but limited flight information. Performance parameters and operational schemes will be extracted by analyzing available data from two specific science flights flown by the Global Hawk back in 2010. Each phase of the flight, take-off, climb, cruise climb, descent and landing, is analyzed from various points of view: speed profile, altitude, climb/descent ratios and rate of turn. The key performance parameters derived from individual flights will be confirmed by performing a wider statistical validation with additional flight trajectories. Derived data are exploited to validate a simulated RQ-4A vehicle employed in extensive real-time air traffic management simulated integration exercises and to complement the development of a future RQ-4A trajectory predictor.

  9. Multiple superficial basal cell carcinoma of the skin that appeared macroscopically healthy after radiotherapy. Case report

    Energy Technology Data Exchange (ETDEWEB)

    Handa, Yoshihiro; Takakuwa, Sachiko; Yamada, Motohito; Ono, Hiroki; Tomita, Yasushi [Nagoya Univ. (Japan). School of Medicine


    The patient was a 76-year-old woman with multiple superficial basal cell carcinomas. She had undergone radiotherapy for a 1-year period after hysterectomy for uterine carcinoma 38 years previously, and the basal cell carcinomas coincided with the irradiated parts. No clear symptoms of chronic radioepithelitis could be found macroscopically, but the lesions were thought to represent radiation-induced carcinoma based on the histopathological findings (atrophy of the epidermis, hyalinization and sclerosis of dermal connective tissue, inflammatory cell infiltration, and capillary dilatation). The lesion was removed to the depth of the adipose tissue with a 5 mm margin around the tumor, and primary closure was achieved. No recurrences or new carcinomas have been detected during the 16 months since the operation. (K.H.)

  10. Macroscopic QED in linearly responding media and a Lorentz-Force approach to dispersion forces

    Energy Technology Data Exchange (ETDEWEB)

    Raabe, Christian


    In this thesis, a very general quantization scheme for the macroscopic electromagnetic field in arbitrary linearly responding media is presented. It offers a unified approach to QED in such media. Applying the quantization scheme, a theory of the dispersion forces on the basis of the Lorentz force is developed. By regarding the dispersion force as the (ground-state or thermal-state) expectation value of the Lorentz force that acts on appropriately defined charge and current densities, Casimir, Casimir-Polder, and van der Waals forces are united in a very natural way that makes transparent their common physical basis. Application of the theory to planar structures yields generalizations of well-known Lifschitz and Casimir-type formulas. (orig.)

  11. Macroscopic Ensembles of Aligned Carbon Nanotubes in Bubble Imprints Studied by Polarized Raman Microscopy

    Directory of Open Access Journals (Sweden)

    Shota Ushiba


    Full Text Available We study the alignment of single-wall carbon nanotubes (SWCNTs in bubble imprints through polarized Raman microscopy. A hemispherical bubble containing SWCNTs is pressed against a glass substrate, resulting in an imprint of the bubble membrane with a coffee ring on the substrate. We find that macroscopic ensembles of aligned SWCNTs are obtained in the imprints, in which there are three patterns of orientations: (i azimuthal alignment on the coffee ring, (ii radial alignment at the edge of the membrane, and (iii random orientation at the center of the membrane. We also find that the alignment of SWCNTs in the imprints can be manipulated by spinning bubbles. The orientation of SWCNTs on the coffee ring is directed radially, which is orthogonal to the case of unspun bubbles. This approach enables one to align SWCNTs in large quantities and in a short time, potentially opening up a wide range of CNT-based electronic and optical applications.

  12. Penetration of fast projectiles into resistant media: From macroscopic to subatomic projectiles (United States)

    Gaite, José


    The penetration of a fast projectile into a resistant medium is a complex process that is suitable for simple modeling, in which basic physical principles can be profitably employed. This study connects two different domains: the fast motion of macroscopic bodies in resistant media and the interaction of charged subatomic particles with matter at high energies, which furnish the two limit cases of the problem of penetrating projectiles of different sizes. These limit cases actually have overlapping applications; for example, in space physics and technology. The intermediate or mesoscopic domain finds application in atom cluster implantation technology. Here it is shown that the penetration of fast nano-projectiles is ruled by a slightly modified Newton's inertial quadratic force, namely, F ∼v 2 - β, where β vanishes as the inverse of projectile diameter. Factors essential to penetration depth are ratio of projectile to medium density and projectile shape.

  13. Imaging of whole tumor cut sections using a novel scanning beam confocal fluorescence MACROscope (United States)

    Constantinou, Paul; Vukovic, Vojislav; Haugland, Hans K.; Nicklee, Trudey; Hedley, David W.; Wilson, Brian C.


    Hypoxia caused by inadequate structure and function of the tumor vasculature has been found to negatively determine the prognosis of cancer patients. Hence, understanding the biological basis of tumor hypoxia is of significant clinical interest. To study solid tumor microenvironments in sufficient detail, large areas (several mm in diameter) need to be imaged at micrometers resolutions. We have used a novel confocal scanning laser MACROscopeTM (CSLM) capable of acquiring images over fields of view up to 2 cm X 2 cm. To demonstrate its performance, frozen sections from a cervical carcinoma xenograft were triple labeled for tissue hypoxia, blood vessels and hypoxia-inducible transcription factor 1 alpha (HIF-1(alpha) ), imaged using the CSLM and compared to images obtained using a standard epifluorescence microscope imaging system. The results indicate that the CSLM is a useful instrument for imaging tissue-based fluorescence at resolutions comparable to standard low-power microscope objectives.

  14. Universal correlation between solvent polarity, fluorescence lifetime and macroscopic viscosity of alcohol solutions. (United States)

    Kumar, Pradip; Bohidar, H B


    In this report, we show interesting correlation between solvent polarity of alcohol solutions and fluorescence lifetime (τ(av)), estimated from time-resolved fluorescence spectroscopy (TRFS), and macroscopic viscosity (η). Non-functionalized carbon nanoparticles (NCNP) were successfully used as flurophores in these measurements. The solvent polarity, described through polarizability (Δf) of dielectric continuum theory, could universally describe both τ(av)/τ(max) and η/η(max) through the relation, [Formula: see text] with X = τ(av)/τ(max) or η/η(max), (subscript OH represents corresponding values for alcohols) for alcohol solutions of methanol, ethanol and 1-propanol at room temperature. We show that fluorescence lifetime and solvent viscosity are universal functions of solvent polarity for alcohol solutions.

  15. Predictions for 232U cluster-decays within the macroscopic-microscopic approximation (United States)

    Mirea, Mihail; Sandulescu, Aureliu; Delion, Doru Sabin


    The decay dynamical path is determined within the macroscopic-microscopic model for the emission of 24Ne from 232U. The nuclear shape parametrization is characterized five degrees of freedom. The single particle energies and the nucleon wave functions are obtained within the superasymmetric Woods-Saxon two center shell model. It turns out that the cluster decay follows a potential magic valley, starting from the ground state of the parent and reaching a configuration of two touching nuclei at scission. A small pocket in the potential barrier is evidenced, as a result of large shell effects in the nascent fragments. The half-life is computed by using several approaches for the effective mass. It is shown that the inertia within by the Gaussian overlap approach gives the closest values to the experimental ones. Half-lives for different cluster decays are predicted. The theoretical values are compared to various phenomenological estimates.

  16. Neoclassical theory of electromagnetic interactions a single theory for macroscopic and microscopic scales

    CERN Document Server

    Babin, Anatoli


    In this monograph, the authors present their recently developed theory of electromagnetic interactions. This neoclassical approach extends the classical electromagnetic theory down to atomic scales and allows the explanation of various non-classical phenomena in the same framework. While the classical Maxwell–Lorentz electromagnetism theory succeeds in describing the physical reality at macroscopic scales, it struggles at atomic scales. Here, quantum mechanics traditionally takes over to describe non-classical phenomena such as the hydrogen spectrum and de Broglie waves. By means of modifying the classical theory, the approach presented here is able to consistently explain quantum-mechanical effects, and while similar to quantum mechanics in some respects, this neoclassical theory also differs markedly from it. In particular, the newly developed framework omits probabilistic interpretations of the wave function and features a new fundamental spatial scale which, at the size of the free electron, is much lar...

  17. A Mini Review on Nanocarbon-Based 1D Macroscopic Fibers: Assembly Strategies and Mechanical Properties (United States)

    Kou, Liang; Liu, Yingjun; Zhang, Cheng; Shao, Le; Tian, Zhanyuan; Deng, Zengshe; Gao, Chao


    Nanocarbon-based materials, such as carbon nanotubes (CNTs) and graphene have been attached much attention by scientific and industrial community. As two representative nanocarbon materials, one-dimensional CNTs and two-dimensional graphene both possess remarkable mechanical properties. In the past years, a large amount of work have been done by using CNTs or graphene as building blocks for constructing novel, macroscopic, mechanically strong fibrous materials. In this review, we summarize the assembly approaches of CNT-based fibers and graphene-based fibers in chronological order, respectively. The mechanical performances of these fibrous materials are compared, and the critical influences on the mechanical properties are discussed. Personal perspectives on the fabrication methods of CNT- and graphene-based fibers are further presented.

  18. Probing Temperature Dependent Noise in Flux Qubits via Macroscopic Resonant Tunneling (United States)

    Berkley, A. J.; Harris, R.; Johnson, M. W.; Johansson, J.; Bunyk, P.; Govorkov, S.; Thom, M. C.; Uchaikin, S.; Truncik, C. J. S.; Amin, M. H. S.; Han, S.; Bumble, B.; Fung, A.; Kaul, A.; Kleinsasser, A.; Averin, D. V.


    Macroscopic resonant tunneling between the two lowest lying states of a bistable RF-SQUID is used to characterize flux noise in a potential qubit. Detailed measurements of incoherent decay rates as a function of flux bias revealed that the Gaussian shaped tunneling rate is not peaked at the resonance point, but is shifted to a flux bias at which the initial well is higher than the target well. This observation indicates that the dominant low frequency (1/f) flux noise in this device is quantum mechanical in nature. The r.m.s. amplitude of the noise, which is proportional to decoherence rate 1/T^*2, was observed to be weakly dependent on temperature below 70 mK.

  19. Inter-band phase fluctuations in macroscopic quantum tunneling of multi-gap superconducting Josephson junctions

    Energy Technology Data Exchange (ETDEWEB)

    Asai, Hidehiro, E-mail: [Electronics and Photonics Research Institute (ESPRIT), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Ota, Yukihiro [CCSE, Japan Atomic Energy Agency, Kashiwa, Chiba 277-8587 (Japan); Kawabata, Shiro [Electronics and Photonics Research Institute (ESPRIT), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Nori, Franco [CEMS, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Physics Department, University of Michigan, Ann Arbor, MI 48109-1040 (United States)


    Highlights: • We study MQT in Josephson junctions composed of multi-gap superconductors. • We derive a formula of the MQT escape rate for multiple phase differences. • We investigate the effect of inter-band phase fluctuation on MQT. • The MQT escape rate is significantly enhanced by the inter-band phase fluctuation. - Abstract: We theoretically investigate macroscopic quantum tunneling (MQT) in a hetero Josephson junction formed by a conventional single-gap superconductor and a multi-gap superconductor. In such Josephson junctions, phase differences for each tunneling channel are defined, and the fluctuation of the relative phase differences appear which is referred to as Josephson–Leggett’s mode. We take into account the effect of the fluctuation in the tunneling process and calculate the MQT escape rate for various junction parameters. We show that the fluctuation of relative phase differences drastically enhances the escape rate.

  20. Study of n-Butyl Acrylate Self-Initiation Reaction Experimentally and via Macroscopic Mechanistic Modeling

    Directory of Open Access Journals (Sweden)

    Ahmad Arabi Shamsabadi


    Full Text Available This paper presents an experimental study of the self-initiation reaction of n-butyl acrylate (n-BA in free-radical polymerization. For the first time, the frequency factor and activation energy of the monomer self-initiation reaction are estimated from measurements of n-BA conversion in free-radical homo-polymerization initiated only by the monomer. The estimation was carried out using a macroscopic mechanistic mathematical model of the reactor. In addition to already-known reactions that contribute to the polymerization, the model considers a n-BA self-initiation reaction mechanism that is based on our previous electronic-level first-principles theoretical study of the self-initiation reaction. Reaction rate equations are derived using the method of moments. The reaction-rate parameter estimates obtained from conversion measurements agree well with estimates obtained via our purely-theoretical quantum chemical calculations.

  1. Photovoltaic characterization of graphene/silicon Schottky junctions from local and macroscopic perspectives (United States)

    Hájková, Zdeňka; Ledinský, Martin; Vetushka, Aliaksei; Stuchlík, Jiří; Müller, Martin; Fejfar, Antonín; Bouša, Milan; Kalbáč, Martin; Frank, Otakar


    We present Schottky junction solar cell composed of graphene transferred onto hydrogenated amorphous and microcrystalline silicon, a low-cost alternative to well-explored crystalline silicon. We demonstrated sample with open-circuit voltage of 445 mV, a remarkable value for undoped graphene-based solar cell. Photovoltaic characteristics of this sample remained stable over 11 months and could be further improved by doping. The graphene/silicon junctions were characterized by current-voltage curves obtained locally by conductive atomic force microscopy (C-AFM) and macroscopically by standard solar simulator. Very good correlation between both independent measurements proved C-AFM as highly useful tool for photovoltaic characterization on nano- and micrometer scale.

  2. Desing of a virtual interactive tutorial of the equine encephalon macroscopic anatomy for veterinary students

    Directory of Open Access Journals (Sweden)

    Carlos Alberto Venegas Cortes


    Full Text Available In order to answer the problem of what could be the most appropriate innovative didactic to improve the learning process of equine encephalon anatomy in the School of Veterinary Medicine of La Salle University, this project began to design, apply and evaluate a didactic prototype Computerized Educative Media CEM in macroscopic anatomy of equine encephalon, to improve the «significant learning» in this subject. The project was developed in three phases regarding the Galviz software engineering, as well as the selected environment for learning, within the framework of the conceptual Novak maps, the significant learning of Ausubel, and the test of usability adapted and applied to the anatomy students, as a MEC evaluation.

  3. Photoactuators for Direct Optical-to-Mechanical Energy Conversion: From Nanocomponent Assembly to Macroscopic Deformation. (United States)

    Hu, Ying; Li, Zhe; Lan, Tian; Chen, Wei


    Photoactuators with integrated optical-to-mechanical energy conversion capacity have attracted growing research interest in the last few decades due to their unique features of remote control and their wide applications ranging from bionic robots, biomedical devices, and switches to motors. For the photoactuator design, the energy conversion route and structure assembly are two important parts, which directly affect the performance of the photoactuators. In particular, the architectural designs at the molecular, nano-, micro-, and macro- level, are found to play a significant role in accumulating molecular-scale strain/stress to macroscale strain/stress. Here, recent progress on photoactuators based on photochemical and photothermal effects is summarized, followed by a discussion of the important assembly strategies for the amplification of the photoresponsive components at nanoscale to macroscopic scale motions. The application advancement of current photoactuators is also presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Macroscopic Dynamic Modeling of Sequential Batch Cultures of Hybridoma Cells: An Experimental Validation

    Directory of Open Access Journals (Sweden)

    Laurent Dewasme


    Full Text Available Hybridoma cells are commonly grown for the production of monoclonal antibodies (MAb. For monitoring and control purposes of the bioreactors, dynamic models of the cultures are required. However these models are difficult to infer from the usually limited amount of available experimental data and do not focus on target protein production optimization. This paper explores an experimental case study where hybridoma cells are grown in a sequential batch reactor. The simplest macroscopic reaction scheme translating the data is first derived using a maximum likelihood principal component analysis. Subsequently, nonlinear least-squares estimation is used to determine the kinetic laws. The resulting dynamic model reproduces quite satisfactorily the experimental data, as evidenced in direct and cross-validation tests. Furthermore, model predictions can also be used to predict optimal medium renewal time and composition.

  5. Electric field induced orientation of polymer chains in macroscopically aligned electrospun polymer nanofibers. (United States)

    Kakade, Meghana V; Givens, Steven; Gardner, Kenncorwin; Lee, Keun Hyung; Chase, D Bruce; Rabolt, John F


    The results presented in this work show for the first time that an electric field used to macroscopically align polymer nanofibers can also align polymer chains parallel to the fiber axis. This important result indicates that anisotropic structural properties (mechanical, electrical, etc.) can be induced in polymer nanofibers during the electrospinning process. Such uniaxially oriented nanofibers exhibit a variety of potential applications in biomedicine, microelectronics, and optics. A simple technique of vertical electrospinning with an electric field induced, stationary collection was employed to obtain the molecular orientation in polymer nanofibers. This manuscript describes the orientation process via electrospinning and verifies this molecular orientation in the polymer nanofibers using three independent methods: polarized Fourier transform infrared spectroscopy, polarized Raman scattering, and X-ray diffraction.

  6. Nonlinear brain dynamics as macroscopic manifestation of underlying many-body field dynamics

    CERN Document Server

    Freeman, Walter J


    Neural activity patterns related to behavior occur at many scales in time and space from the atomic and molecular to the whole brain. Here we explore the feasibility of interpreting neurophysiological data in the context of many-body physics by using tools that physicists have devised to analyze comparable hierarchies in other fields of science. We focus on a mesoscopic level that offers a multi-step pathway between the microscopic functions of neurons and the macroscopic functions of brain systems revealed by hemodynamic imaging. We use electroencephalographic (EEG) records collected from high-density electrode arrays fixed on the epidural surfaces of primary sensory and limbic areas in rabbits and cats trained to discriminate conditioned stimuli (CS) in the various modalities. High temporal resolution of EEG signals with the Hilbert transform gives evidence for diverse intermittent spatial patterns of amplitude (AM) and phase modulations (PM) of carrier waves that repeatedly re-synchronize in the beta and g...

  7. Information and Self-Organization A Macroscopic Approach to Complex Systems

    CERN Document Server

    Haken, Hermann


    This book presents the concepts needed to deal with self-organizing complex systems from a unifying point of view that uses macroscopic data. The various meanings of the concept "information" are discussed and a general formulation of the maximum information (entropy) principle is used. With the aid of results from synergetics, adequate objective constraints for a large class of self-organizing systems are formulated and examples are given from physics, life and computer science. The relationship to chaos theory is examined and it is further shown that, based on possibly scarce and noisy data, unbiased guesses about processes of complex systems can be made and the underlying deterministic and random forces determined. This allows for probabilistic predictions of processes, with applications to numerous fields in science, technology, medicine and economics. The extensions of the third edition are essentially devoted to an introduction to the meaning of information in the quantum context. Indeed, quantum inform...

  8. Shock structure and temperature overshoot in macroscopic multi-temperature model of mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Madjarević, Damir, E-mail:; Simić, Srboljub, E-mail: [Department of Mechanics, Faculty of Technical Sciences, University of Novi Sad, Trg Dositeja Obradovića 6, 21000 Novi Sad (Serbia); Ruggeri, Tommaso, E-mail: [Department of Mathematics and Research Center of Applied Mathematics, University of Bologna, Via Saragozza 8, 40123 Bologna (Italy)


    The paper discusses the shock structure in macroscopic multi-temperature model of gaseous mixtures, recently established within the framework of extended thermodynamics. The study is restricted to weak and moderate shocks in a binary mixture of ideal gases with negligible viscosity and heat conductivity. The model predicts the existence of temperature overshoot of heavier constituent, like more sophisticated approaches, but also puts in evidence its non-monotonic behavior not documented in other studies. This phenomenon is explained as a consequence of weak energy exchange between the constituents, either due to large mass difference, or large rarefaction of the mixture. In the range of small Mach number it is also shown that shock thickness (or equivalently, the inverse of Knudsen number) decreases with the increase of Mach number, as well as when the mixture tends to behave like a single-component gas (small mass difference and/or presence of one constituent in traces)

  9. Applicability of Macroscopic Wear and Friction Laws on the Atomic Length Scale. (United States)

    Eder, S J; Feldbauer, G; Bianchi, D; Cihak-Bayr, U; Betz, G; Vernes, A


    Using molecular dynamics, we simulate the abrasion process of an atomically rough Fe surface with multiple hard abrasive particles. By quantifying the nanoscopic wear depth in a time-resolved fashion, we show that Barwell's macroscopic wear law can be applied at the atomic scale. We find that in this multiasperity contact system, the Bowden-Tabor term, which describes the friction force as a function of the real nanoscopic contact area, can predict the kinetic friction even when wear is involved. From this the Derjaguin-Amontons-Coulomb friction law can be recovered, since we observe a linear dependence of the contact area on the applied load in accordance with Greenwood-Williamson contact mechanics.

  10. Agent-based and macroscopic modeling of the complex socio-economic systems

    CERN Document Server

    Kononovicius, Aleksejus


    The current economic crisis has provoked an active response from the interdisciplinary scientific community. As a result many papers suggesting what can be improved in understanding of the complex socio-economics systems were published. Some of the most prominent papers on the topic include (Bouchaud, 2009; Farmer and Foley, 2009; Farmer et al, 2012; Helbing, 2010; Pietronero, 2008). These papers share the idea that agent-based modeling is essential for the better understanding of the complex socio-economic systems and consequently better policy making. Yet in order for an agent-based model to be useful it should also be analytically tractable, possess a macroscopic treatment (Cristelli et al, 2012). In this work we shed a new light on our research group's contributions towards understanding of the correspondence between the inter-individual interactions and collective behavior. We also provide some new insights into the implications of the global and local interactions, the leadership and the predator-prey i...

  11. Macroscopic rates, microscopic observations, and molecular models of the dissolution of carbonate phases.

    Energy Technology Data Exchange (ETDEWEB)

    Duckworth, Owen W. (Harvard University, Cambridge, MA); Cygan, Randall Timothy; Martin, Scot T. (Harvard University, Cambridge, MA)


    Bulk and surface energies are calculated for endmembers of the isostructural rhombohedral carbonate mineral family, including Ca, Cd, Co, Fe, Mg, Mn, Ni, and Zn compositions. The calculations for the bulk agree with the densities, bond distances, bond angles, and lattice enthalpies reported in the literature. The calculated energies also correlate with measured dissolution rates: the lattice energies show a log-linear relationship to the macroscopic dissolution rates at circumneutral pH. Moreover, the energies of ion pairs translated along surface steps are calculated and found to predict experimentally observed microscopic step retreat velocities. Finally, pit formation excess energies decrease with increasing pit size, which is consistent with the nonlinear dissolution kinetics hypothesized for the initial stages of pit formation.

  12. Macroscopic and microscopic study of 1-ethyl-3-methyl-imidazolium acetate-water mixtures. (United States)

    Hall, Craig A; Le, Kim A; Rudaz, Cyrielle; Radhi, Asanah; Lovell, Christopher S; Damion, Robin A; Budtova, Tatiana; Ries, Michael E


    Mixtures of 1-ethyl-3-methyl-imidazolium acetate ([C2mim][OAc]) and water across the entire composition range, from pure [C2mim][OAc] to pure water, have been investigated using density, viscosity, and NMR spectroscopy, relaxometry, and diffusion measurements. These results have been compared to ideal mixing laws for the microscopic data obtained from the NMR results and macroscopic data through the viscosity and density. It was also found that the mixing of the two fluids is exothermal. The proton spectra indicate though that [C2mim][OAc] and water are interacting without the formation of new compounds. The maximal deviations of experimental data from theoretical mixing rules were all found to occur within the range 0.74 ± 0.06 mol fraction of water, corresponding to approximately three water molecules per [C2mim][OAc] molecule.

  13. Macroscopic Model and Simulation Analysis of Air Traffic Flow in Airport Terminal Area

    Directory of Open Access Journals (Sweden)

    Honghai Zhang


    Full Text Available We focus on the spatiotemporal characteristics and their evolvement law of the air traffic flow in airport terminal area to provide scientific basis for optimizing flight control processes and alleviating severe air traffic conditions. Methods in this work combine mathematical derivation and simulation analysis. Based on cell transmission model the macroscopic models of arrival and departure air traffic flow in terminal area are established. Meanwhile, the interrelationship and influential factors of the three characteristic parameters as traffic flux, density, and velocity are presented. Then according to such models, the macro emergence of traffic flow evolution is emulated with the NetLogo simulation platform, and the correlativity of basic traffic flow parameters is deduced and verified by means of sensitivity analysis. The results suggest that there are remarkable relations among the three characteristic parameters of the air traffic flow in terminal area. Moreover, such relationships evolve distinctly with the flight procedures, control separations, and ATC strategies.

  14. Macroscopic modelling of fluid dynamics in large-scale circulating fluidized beds

    Energy Technology Data Exchange (ETDEWEB)

    Pallares, David; Johnsson, Filip [Department of Energy and Environment, Energy Conversion, Chalmers University of Technology, SE 412 96 Goeteborg (Sweden)


    Macroscopic (semi-empirical) models for fluid dynamics of circulating fluidized bed (CFB) units are presented, with emphasize on applications for conditions relevant to industrial units such as fluidized-bed combustors. In order to make a structured analysis of the models, the CFB unit is divided into 6 fluid dynamical zones, which have been shown to exhibit different fluid-dynamical behaviour (bottom bed, freeboard, exit zone, exit duct, cyclone and downcomer and particle seal). The paper summarizes the main basis and assumptions for each model together with major advantages and drawbacks. In addition, a practical example on how a selected set of these local models can be linked to an overall model of the fluid dynamics of the entire CFB loop is presented. It is shown that it is possible to reach good agreement between the overall model and experimental data from industrial units. (author)

  15. Dynamic Chiral Magnetic Effect and Faraday Rotation in Macroscopically Disordered Helical Metals. (United States)

    Ma, J; Pesin, D A


    We develop an effective medium theory for electromagnetic wave propagation through gapless nonuniform systems with a dynamic chiral magnetic effect. The theory allows us to calculate macroscopic-disorder-induced corrections to the values of optical, as well as chiral magnetic conductivities. In particular, we show that spatial fluctuations of the optical conductivity induce corrections to the effective value of the chiral magnetic conductivity. The absolute value of the effect varies strongly depending on the system parameters, but yields the leading frequency dependence of the polarization rotation and circular dichroism signals. Experimentally, these corrections can be observed as features in the Faraday rotation angle near frequencies that correspond to the bulk plasmon resonances of a material. Such features are not expected to be present in single-crystal samples.

  16. Local inhibitory plasticity tunes macroscopic brain dynamics and allows the emergence of functional brain networks. (United States)

    Hellyer, Peter J; Jachs, Barbara; Clopath, Claudia; Leech, Robert


    Rich, spontaneous brain activity has been observed across a range of different temporal and spatial scales. These dynamics are thought to be important for efficient neural functioning. A range of experimental evidence suggests that these neural dynamics are maintained across a variety of different cognitive states, in response to alterations of the environment and to changes in brain configuration (e.g., across individuals, development and in many neurological disorders). This suggests that the brain has evolved mechanisms to maintain rich dynamics across a broad range of situations. Several mechanisms based around homeostatic plasticity have been proposed to explain how these dynamics emerge from networks of neurons at the microscopic scale. Here we explore how a homeostatic mechanism may operate at the macroscopic scale: in particular, focusing on how it interacts with the underlying structural network topology and how it gives rise to well-described functional connectivity networks. We use a simple mean-field model of the brain, constrained by empirical white matter structural connectivity where each region of the brain is simulated using a pool of excitatory and inhibitory neurons. We show, as with the microscopic work, that homeostatic plasticity regulates network activity and allows for the emergence of rich, spontaneous dynamics across a range of brain configurations, which otherwise show a very limited range of dynamic regimes. In addition, the simulated functional connectivity of the homeostatic model better resembles empirical functional connectivity network. To accomplish this, we show how the inhibitory weights adapt over time to capture important graph theoretic properties of the underlying structural network. Therefore, this work presents suggests how inhibitory homeostatic mechanisms facilitate stable macroscopic dynamics to emerge in the brain, aiding the formation of functional connectivity networks. Copyright © 2015 Elsevier Inc. All rights

  17. Diagnostic criteria for selenium toxicosis in aquatic birds: dietary exposure, tissue concentrations, and macroscopic effects (United States)

    Albers, P.H.; Green, D.E.; Sanderson, C.J.


    A feeding study with mallard ducks (Anas platyrhynchos) was conducted during March-July, 1988 in Laurel, Maryland, to identify diagnostic criteria for selenium toxicosis in birds. One-year-old male mallards in groups of 21 were fed diets containing 0, 10, 20, 40, or 80 parts per million (ppm) selenium, as seleno-DL-methionine, for 16 weeks. All ducks receiving 80 ppm died. Ducks receiving 40 or 80 ppm selenium consumed less feed than ducks in the other treatment groups. Body weights of ducks receiving 40 or 80 ppm selenium declined during the study. The post-breeding molt was delayed in ducks receiving 40 ppm; most ducks receiving 80 ppm selenium died prior to the onset of molt. At necropsy, numerous abnormalities were observed in ducks that died but only a small number of abnormalities were observed in ducks surviving to the end of the study in the 40 ppm group. Weights of the heart, spleen, and pancreas were mostly lower and weights of the kidney were higher for ducks dying during the study than for euthanized ducks. Liver weights were unaffected. Selenium accumulated in soft tissues approximately in proportion to dietary concentrations. Selenium concentrations in tissues of all ducks that died were different from those of surviving ducks in the 0, 10, and 20 ppm groups, but were not different from those of surviving ducks in the 40 ppm group. Proposed diagnostic criteria for fatal chronic selenosis were derived from body weight, macroscopic abnormalities, organ weights, and concentrations of selenium in the liver. Proposed diagnostic criteria for non-fatal chronic selenosis were derived from body weight, plumage condition, macroscopic abnormalities, concentrations of selenium in the liver, reproductive failure, and alterations of blood and tissue chemistries. Lead or dioxin poisoning have diagnostic criteria most similar to selenium toxicosis.

  18. Microbial agents in macroscopically healthy mammary gland tissues of small ruminants. (United States)

    Spuria, Liliana; Biasibetti, Elena; Bisanzio, Donal; Biasato, Ilaria; De Meneghi, Daniele; Nebbia, Patrizia; Robino, Patrizia; Bianco, Paolo; Lamberti, Michele; Caruso, Claudio; Di Blasio, Alessia; Peletto, Simone; Masoero, Loretta; Dondo, Alessandro; Capucchio, Maria Teresa


    Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06-0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69-37.77]) of being infected with lentiviruses. The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.

  19. Microbial agents in macroscopically healthy mammary gland tissues of small ruminants

    Directory of Open Access Journals (Sweden)

    Liliana Spuria


    Full Text Available Background Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. Methods This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats, also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Results Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%, followed by environmental opportunists (34.76%, others (10.14% and pathogens (8.68%. Most mammary glands showed coinfections (75%. Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89 and acute suppurative mastitis (4/89. Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06–0.71] of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69–37.77] of being infected with lentiviruses. Discussion The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.

  20. A comparison of macroscopic models describing the collective response of sedimenting rod-like particles in shear flows (United States)

    Helzel, Christiane; Tzavaras, Athanasios E.


    We consider a kinetic model, which describes the sedimentation of rod-like particles in dilute suspensions under the influence of gravity, presented in Helzel and Tzavaras (submitted for publication). Here we restrict our considerations to shear flow and consider a simplified situation, where the particle orientation is restricted to the plane spanned by the direction of shear and the direction of gravity. For this simplified kinetic model we carry out a linear stability analysis and we derive two different nonlinear macroscopic models which describe the formation of clusters of higher particle density. One of these macroscopic models is based on a diffusive scaling, the other one is based on a so-called quasi-dynamic approximation. Numerical computations, which compare the predictions of the macroscopic models with the kinetic model, complete our presentation.

  1. A comparison of macroscopic models describing the collective response of sedimenting rod-like particles in shear flows

    KAUST Repository

    Helzel, Christiane


    We consider a kinetic model, which describes the sedimentation of rod-like particles in dilute suspensions under the influence of gravity, presented in Helzel and Tzavaras (submitted for publication). Here we restrict our considerations to shear flow and consider a simplified situation, where the particle orientation is restricted to the plane spanned by the direction of shear and the direction of gravity. For this simplified kinetic model we carry out a linear stability analysis and we derive two different nonlinear macroscopic models which describe the formation of clusters of higher particle density. One of these macroscopic models is based on a diffusive scaling, the other one is based on a so-called quasi-dynamic approximation. Numerical computations, which compare the predictions of the macroscopic models with the kinetic model, complete our presentation.

  2. Peptidomimetics with beta-peptoid resudies as carriers for intracellular delivery of small interfering RNA (siRNA)

    DEFF Research Database (Denmark)

    Foged, Camilla

    complexes with and transport small interfering RNA (siRNA) into the cell cytoplasm. These new compounds are peptidomimetic dodecamers based on alternating repeats of chiral N-alkylated ß-alanine residues (ß-peptoids) and a-amino acids with a net charge of +6. Complexes of siRNA and peptidomimetics were...... prepared by mixing and characterized with respect to size and surface charge. At ratios of peptide nitrogen to siRNA phosphate (N/P) of 1 and below, particles with narrow size distributions (poly dispersity indexes lower than 0.11) ranging from approximately 100 to 350 nm were formed, and they showed...... cytometry. We conclude that simple complex formation via electrostatic interactions between siRNA and the cationic peptidomimetics is not sufficient for the delivery of siRNA to the RNA interference (RNAi) pathway in the cytoplasm. We are currently testing chemical conjugates of siRNA...


    Basu, Christopher; Stoll, Alexander L; Dixon, Jonathon; Molenaar, Fieke Marije; Flach, Edmund; Smith, Ken C


    An adult male reticulated giraffe (Giraffa camelopardalis reticulata) was presented for postmortem examination. During radiologic examination of the hindlimbs, osseous cyst-like lesions were detected in both medial femoral condyles. These lesions were subsequently examined macroscopically and histologically. The gross appearance suggested a diagnosis of bilateral osteochondrosis that was confirmed with histopathologic examination. This finding has not previously been reported in giraffes. Macroscopic visualization of the major limb joints, including the femorotibial joints, is therefore encouraged in future postmortem examinations of giraffes (Giraffa camelopardalis), and further assessment of clinical significance is required.

  4. Mycoviruses, RNA silencing, and viral RNA recombination. (United States)

    Nuss, Donald L


    In contrast to viruses of plants and animals, viruses of fungi, mycoviruses, uniformly lack an extracellular phase to their replication cycle. The persistent, intracellular nature of the mycovirus life cycle presents technical challenges to experimental design. However, these properties, coupled with the relative simplicity and evolutionary position of the fungal host, also provide opportunities for examining fundamental aspects of virus-host interactions from a perspective that is quite different from that pertaining for most plant and animal virus infections. This chapter presents support for this view by describing recent advances in the understanding of antiviral defense responses against one group of mycoviruses for which many of the technical experimental challenges have been overcome, the hypoviruses responsible for hypovirulence of the chestnut blight fungus Cryphonectria parasitica. The findings reveal new insights into the induction and suppression of RNA silencing as an antiviral defense response and an unexpected role for RNA silencing in viral RNA recombination. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Topology of RNA-RNA interaction structures

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Huang, Fenix Wenda; Penner, Robert


    Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exis...... complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities.......Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist...

  6. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo


    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs....

  7. Exploring the RNA landscape of endothelial exosomes. (United States)

    Perez-Boza, Jennifer; Lion, Michelle; Struman, Ingrid


    Exosomes are small extracellular vesicles of around 100nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes is still not completely elucidated. In this study, by the use of next generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and non-coding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis to study the involvement of RNA-binding proteins capable to recognize RNA sequences and their role in the export of RNAs into exosomes. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. (United States)

    Zamora, Miguel; Méndez-López, Eduardo; Agirrezabala, Xabier; Cuesta, Rebeca; Lavín, José L; Sánchez-Pina, M Amelia; Aranda, Miguel A; Valle, Mikel


    Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.

  9. Agent-Based and Macroscopic Modeling of the Complex Socio-Economic Systems

    Directory of Open Access Journals (Sweden)

    Aleksejus Kononovičius


    Full Text Available Purpose – The focus of this contribution is the correspondence between collective behavior and inter-individual interactions in the complex socio-economic systems. Currently there is a wide selection of papers proposing various models for the both collective behavior and inter-individual interactions in the complex socio-economic systems. Yet the papers directly relating these two concepts are still quite rare. By studying this correspondence we discuss a cutting edge approach to the modeling of complex socio-economic systems. Design/methodology/approach – The collective behavior is often modeled using stochastic and ordinary calculus, while the inter-individual interactions are modeled using agent-based models. In order to obtain the ideal model, one should start from these frameworks and build a bridge to reach another. This is a formidable task, if we consider the top-down approach, namely starting from the collective behavior and moving towards inter-individual interactions. The bottom-up approach also fails, if complex inter-individual interaction models are considered, yet in this case we can start with simple models and increase the complexity as needed. Findings – The bottom-up approach, considering simple agent-based herding model as a model for the inter-individual interactions, allows us to derive certain macroscopic models of the complex socio-economic systems from the agent-based perspective. This provides interesting insights into the collective behavior patterns observed in the complex socio-economic systems. Research limitations/implications –The simplicity of the agent-based herding model might be considered to be somewhat limiting. Yet this simplicity implies that the model is highly universal. It reproduces universal features of social behavior and also can be further extended to fit different socio-economic scenarios. Practical implications – Insights provided in this contribution might be used to modify existing

  10. Nonlocal quantum macroscopic superposition in a high-thermal low-purity state. (United States)

    Brezinski, Mark E; Liu, Bin


    Quantum state exchange between light and matter is an important ingredient for future quantum information networks as well as other applications. Photons are the fastest and simplest carriers of information for transmission but in general, it is difficult to localize and store photons, so usually one prefers choosing matter as quantum memory elements. Macroscopic superposition and nonlocal quantum interactions have received considerable interest for this purpose over recent years in fields ranging from quantum computers to cryptography, in addition to providing major insights into physical laws. However, these experiments are generally performed either with equipment or under conditions that are unrealistic for practical applications. Ideally, the two can be combined using conventional equipment and conditions to generate a "quantum teleportation"-like state, particularly with a very small amount of purity existing in an overall highly mixed thermal state (relatively low decoherence at high temperatures). In this study we used an experimental design to demonstrate these principles. We performed optical coherence tomography (OCT) using a thermal source at room temperatures of a specifically designed target in the sample arm. Here, position uncertainty (i.e., dispersion) was induced in the reference arm. In the sample arm (target) we placed two glass plates separated by a different medium while altering position uncertainty in the reference arm. This resulted in a chirped signal between the glass plate reflective surfaces in the combined interferogram. The chirping frequency, as measured by the fast Fourier transform (FFT), varies with the medium between the plates, which is a nonclassical phenomenon. These results are statistically significant and occur from a superposition between the glass surface and the medium with increasing position uncertainty, a true quantum-mechanical phenomenon produced by photon pressure from two-photon interference. The differences in

  11. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

    NARCIS (Netherlands)

    Méndez-Garcia, C.; Mesa, V.; Sprenger, R.R.; Richter, M.; Suarez Diez, M.; Solano, J.; Bargiela, R.; Golyshina, O.V.; Manteca, A.; Ramos, J.L.; Gallego, J.R.; Llorente, I.; Martins Dos Santos, V.A.P.; Jensen, O.N.; Paláez, A.I.; Sánchez, J.; Ferrer, M.


    Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH

  12. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

    DEFF Research Database (Denmark)

    Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard Remko


    and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.The ISME Journal advance...

  13. Macroscopic quantum tunneling and quasiparticle-tunneling blockade effect in s-wave/d-wave hybrid junctions

    NARCIS (Netherlands)

    Kawabata, S.; Kawabata, S.; Golubov, Alexandre Avraamovitch; Ariando, A.; Verwijs, C.J.M.; Verwijs, C.J.M.; Hilgenkamp, Johannes W.M.; Kirtley, J.R.


    We have theoretically investigated macroscopic quantum tunneling (MQT) and the influence of nodal quasiparticles and zero energy bound states (ZESs) on MQT in s-wave/d-wave hybrid Josephson junctions. In contrast to d-wave/d-wave junctions, the low-energy quasiparticle dissipation resulting from

  14. Macroscopic modelling of environmental influence on growth and form of sponges and corals using the accretive growth model

    NARCIS (Netherlands)

    Kaandorp, J.A.


    We discuss a macroscopical growth model which can be used to simulate growth forms of complex-shaped branching organisms with radiate accretive growth. This type of growth processes can be found in many different marine sessile organisms. We use scleractinian corals and a branching sponge as an

  15. Introducing the Core Probability Framework and Discrete-Element Core Probability Model for efficient stochastic macroscopic modelling

    NARCIS (Netherlands)

    Calvert, S.C.; Taale, H.; Hoogendoorn, S.P.


    In this contribution the Core Probability Framework (CPF) is introduced with the application of the Discrete-Element Core Probability Model (DE-CPM) as a new DNL for dynamic macroscopic modelling of stochastic traffic flow. The model is demonstrated for validation in a test case and for

  16. Macroscopic quantum tunneling in Josephson pi-junctions with insulating ferromagnets and its application to phase qubits

    NARCIS (Netherlands)

    Kawabata, Shiro; Kawabata, S.; Golubov, Alexandre Avraamovitch


    We theoretically investigate macroscopic quantum tunneling (MQT) in a current-biased π junction with a superconductor (S) and an insulating ferromagnet (IF). By using the functional integral method and the instanton approximation, the influence of the quasiparticle dissipation on MQT is found to be

  17. Correction of gradient echo images for first and second order macroscopic signal dephasing using phase derivative mapping. (United States)

    de Leeuw, H; Bakker, C J G


    Gradient echo techniques are often hampered by signal dephasing due to macroscopic phase perturbations because of system imperfections (shimming) or object induced perturbations of the magnetic field (hemorrhagic lesions, calcified tissue, air-tissue interfaces). Many techniques have been proposed to reduce the effects of macroscopic phase variations. Among these techniques are tuned pulse sequences, fitting techniques and reconstruction algorithms. These methods, however, suffer from one or more of the following drawbacks: they require longer acquisition times, require additional acquisitions, compensate only locally, can only be applied to multi-gradient echo data or may result in inaccurate results. In this work a generally applicable post-processing technique is presented to evaluate and compensate signal alterations invoked by first and second order macroscopic phase incoherences. In this technique, the derivatives of the signal phase are determined by applying the Fourier derivative theorem on the complex data. As a result, the phase derivatives are obtained without phase unwrapping and without compromising the resolution. The method is validated for single and multi-echo acquisitions by experiments on a co-axial cylinder phantom with known macroscopic field disturbances. The potential of the method is demonstrated on a multi-gradient echo acquisition on the head of a human volunteer. In general a first order correction is shown to be sufficient, however higher order correction is found to be beneficial near sharp transitions of the magnetic field. Copyright © 2011 Elsevier Inc. All rights reserved.


    Flavio Ruffinatto; Alan Crivellaro; Alex Wiedenhoeft


    With the adoption of a number of anti-illegal logging laws, treaties, memoranda, and international agreements around the world, there is broad and renewed interest in wood identification, especially in the field at the macroscopic level. In response to this interest, and to begin to fill an obvious gap in the corpus of wood anatomical reference material, we review...

  19. Heterogeneous Inhibition in Macroscopic Current Responses of Four Nicotinic Acetylcholine Receptor Subtypes by Cholesterol Enrichment. (United States)

    Báez-Pagán, Carlos A; Del Hoyo-Rivera, Natalie; Quesada, Orestes; Otero-Cruz, José David; Lasalde-Dominicci, José A


    The nicotinic acetylcholine receptor (nAChR), located in the cell membranes of neurons and muscle cells, mediates the transmission of nerve impulses across cholinergic synapses. In addition, the nAChR is also found in the electric organs of electric rays (e.g., the genus Torpedo). Cholesterol, which is a key lipid for maintaining the correct functionality of membrane proteins, has been found to alter the nAChR function. We were thus interested to probe the changes in the functionality of different nAChRs expressed in a model membrane with modified cholesterol to phospholipid ratios (C/P). In this study, we examined the effect of increasing the C/P ratio in Xenopus laevis oocytes expressing the neuronal α7, α4β2, muscle-type, and Torpedo californica nAChRs in their macroscopic current responses. Using the two-electrode voltage clamp technique, it was found that the neuronal α7 and Torpedo nAChRs are significantly more sensitive to small increases in C/P than the muscle-type nAChR. The peak current versus C/P profiles during enrichment display different behaviors; α7 and Torpedo nAChRs display a hyperbolic decay with two clear components, whereas muscle-type and α4β2 nAChRs display simple monophasic decays with different slopes. This study clearly illustrates that a physiologically relevant increase in membrane cholesterol concentration produces a remarkable reduction in the macroscopic current responses of the neuronal α7 and Torpedo nAChRs functionality, whereas the muscle nAChR appears to be the most resistant to cholesterol inhibition among all four nAChR subtypes. Overall, the present study demonstrates differential profiles for cholesterol inhibition among the different types of nAChR to physiological cholesterol increments in the plasmatic membrane. This is the first study to report a cross-correlation analysis of cholesterol sensitivity among different nAChR subtypes in a model membrane.

  20. Improving macroscopic modeling of the effect of water and osmotic stresses on root water uptake. (United States)

    Jorda Guerra, Helena; Vanderborght, Jan


    Accurate modeling of water and salt stresses on root water uptake is critical for predicting impacts of global change and climate variability on crop production and soil water balances. Soil-hydrological models use reduction functions to represent the effect of osmotic stress in transpiration. However, these functions, which were developed empirically, present limitations in relation to the time and spatial scale at which they need to be used, fail to include compensation processes and do not agree on how water and salt stresses interact. This research intends to develop a macroscopic reduction function for water and osmotic stresses based on biophysical knowledge. Simulation experiments are conducted for a range of atmospheric conditions, soil and plant properties, irrigation water quality and scheduling using a 3-D physically-based model that resolves flow and transport to individual root segments and that couples flow in the soil and root system (Schröder et al., 2013). The effect of salt concentrations on water flow in the soil-root system is accounted for by including osmotic water potential gradients between the solution at the soil root interface and the root xylem sap in the hydraulic gradient between the soil and root. In a first step, simulation experiments are carried out in a soil volume around a single root segment. We discuss how the simulation setup can be defined so as to represent: (i) certain characteristics of the root system such as rooting depth and root length density, (ii) plant transpiration rate, (iii) leaching fraction of the irrigation, and (iii) salinity of the irrigation water. The output of these simulation experiments gives a first insight in the effect of salinity on transpiration and on the relation between the bulk salinity in the soil voxel, which is used in macroscopic salt stress functions of models that do not resolve processes at the root segment scale, and the salinity at the soil-root interface, which determines the actual

  1. The alignment of carbon nanotubes: an effective route to extend their excellent properties to macroscopic scale. (United States)

    Sun, Xuemei; Chen, Tao; Yang, Zhibin; Peng, Huisheng


    To improve the practical application of carbon nanotubes, it is critically important to extend their physical properties from the nanoscale to the macroscopic scale. Recently, chemists aligned continuous multiwalled carbon nanotube (MWCNT) sheets and fibers to produce materials with high mechanical strength and electrical conductivity. This provided an important clue to the use of MWCNTs at macroscopic scale. Researchers have made multiple efforts to optimize this aligned structure and improve the properties of MWCNT sheets and fibers. In this Account, we briefly highlight the new synthetic methods and promising applications of aligned MWCNTs for organic optoelectronic materials and devices. We describe several general methods to prepare both horizontally and perpendicularly aligned MWCNT/polymer composite films, through an easy solution or melting process. The composite films exhibit the combined properties of being flexible, transparent, and electrically conductive. These advances may pave the way to new flexible substrates for organic solar cells, sensing devices, and other related applications. Similarly, we discuss the synthesis of aligned MWCNT/polymer composite fibers with interesting mechanical and electrical properties. Through these methods, we can incorporate a wide variety of soluble or fusible polymers for such composite films and fibers. In addition, we can later introduce functional polymers with conjugated backbones or side chains to improve the properties of these composite materials. In particular, cooperative interactions between aligned MWCNTs and polymers can produce novel properties that do not occur individually. Common examples of this are two types of responsive polymers, photodeformable azobenzene-containing liquid crystalline polymer and chromatic polydiacetylene. Aligning the structure of MWCNTs induces the orientation of azobenzene-containing mesogens, and produces photodeformable polymer elastomers. This strategy also solves the long

  2. The integration of macroscopic tumor invasion of adjacent organs into TNM staging system for colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Ji-Wang Liang

    Full Text Available OBJECTIVE: In addition to pathological TNM (pTNM staging, the macroscopic staging (surgical TNM, sTNM is another method used to stage and assess tumors, and it also potentially influences patient treatment guidelines. However, for the same patient, surgeons and pathologists might assess tumor depth differently. We aimed to evaluate the prognosis of patients who exhibit unconformity of intraoperative and postoperative results and propose a revised pT category (r-pT category to predict survival in colorectal cancer. METHODS AND RESULTS: In our study, 948 colorectal cancer patients were reviewed. We proposed a novel r-pT category in which surgical macroscopic T4b (sT4b is incorporated into the pT category, namely, patients in the pT3 category with sT4b cancers are reclassified as being in the r-pT4a category; patients in the pT4a category with sT4b cancers are reclassified as being in the r-pT4b category. Cancer-specific survival according to the r-pT category was analyzed using Kaplan-Meier survival curves. A two-step multivariate analysis was used to determine correlations between the r-pT category and the prognosis. Harrell's C statistic was utilized to test the predictive capacity. There were significant prognostic differences among the r-pT subcategories. We substituted the r-pT category for the pT category in current TNM staging in a 2-step multivariate analysis. The Harrell's C statistical analysis results demonstrated that the r-pT category had superior predictive capacity compared to the pT category (Harrell' C: 0.668 vs. 0.636; P = 0.002. CONCLUSIONS: Patients in the pT3 category with sT4b cancers, and patients in the pT4a category with sT4b cancers, are potentially under-staged, reclassification into higher categories could potentially benefit these patients. The results indicate that the r-pT category we proposed is potentially superior to the pT category in the assessment of prognosis for colorectal cancer.

  3. The integration of macroscopic tumor invasion of adjacent organs into TNM staging system for colorectal cancer. (United States)

    Liang, Ji-Wang; Gao, Peng; Wang, Zhen-Ning; Song, Yong-Xi; Xu, Ying-Ying; Wang, Mei-Xian; Dong, Yu-Lan; Xu, Hui-Mian


    In addition to pathological TNM (pTNM) staging, the macroscopic staging (surgical TNM, sTNM) is another method used to stage and assess tumors, and it also potentially influences patient treatment guidelines. However, for the same patient, surgeons and pathologists might assess tumor depth differently. We aimed to evaluate the prognosis of patients who exhibit unconformity of intraoperative and postoperative results and propose a revised pT category (r-pT category) to predict survival in colorectal cancer. In our study, 948 colorectal cancer patients were reviewed. We proposed a novel r-pT category in which surgical macroscopic T4b (sT4b) is incorporated into the pT category, namely, patients in the pT3 category with sT4b cancers are reclassified as being in the r-pT4a category; patients in the pT4a category with sT4b cancers are reclassified as being in the r-pT4b category. Cancer-specific survival according to the r-pT category was analyzed using Kaplan-Meier survival curves. A two-step multivariate analysis was used to determine correlations between the r-pT category and the prognosis. Harrell's C statistic was utilized to test the predictive capacity. There were significant prognostic differences among the r-pT subcategories. We substituted the r-pT category for the pT category in current TNM staging in a 2-step multivariate analysis. The Harrell's C statistical analysis results demonstrated that the r-pT category had superior predictive capacity compared to the pT category (Harrell' C: 0.668 vs. 0.636; P = 0.002). Patients in the pT3 category with sT4b cancers, and patients in the pT4a category with sT4b cancers, are potentially under-staged, reclassification into higher categories could potentially benefit these patients. The results indicate that the r-pT category we proposed is potentially superior to the pT category in the assessment of prognosis for colorectal cancer.

  4. RNA Localization in Astrocytes

    DEFF Research Database (Denmark)

    Thomsen, Rune


    Messenger RNA (mRNA) localization is a mechanism by which polarized cells can regulate protein synthesis to specific subcellular compartments in a spatial and temporal manner, and plays a pivotal role in multiple physiological processes from embryonic development to cell differentiation......, regulation of the blood brain barrier and glial scar tissue formation. Despite the involvement in various CNS functions only a limited number of studies have addressed mRNA localization in astrocytes. This PhD project was initially focused on developing and implementing methods that could be used to asses mRNA...... localization in astrocyte protrusions, and following look into the subcellular localization pattern of specific mRNA species of both primary astrocytes isolated from cortical hemispheres of newborn mice, and the mouse astrocyte cell line, C8S. The Boyden chamber cell fractionation assay was optimized, in a way...

  5. Practical urinalysis in the cat: 1: Urine macroscopic examination 'tips and traps'. (United States)

    Reppas, George; Foster, Susan F


    This is the first article in a two-part series on urinalysis in the cat. The focus of Part 1 is urine macroscopic examination. Part 2, to appear in the May 2016 issue, discusses urine microscopic examination. Urinalysis is an essential procedure in feline medicine but often little attention is paid to optimising the data yielded or minimising factors that can affect the results. For the best results, appropriately collected urine should be prepared promptly by specialist laboratory personnel for the relevant tests and assessed by a clinical pathologist. This is invariably impractical in clinical settings but careful attention can minimise artefacts and allow maximum useful information to be obtained from this seemingly simple process. Clinical pathologists would be familiar with the information provided in this article, but it is rarely available to general or specialist practitioners, and both can potentially benefit. Most of the required equipment is routinely available to veterinarians. However, instructions have been provided to give practical alternatives for specialist procedures in some instances. Evidence for much of the data on urinalysis in cats is lacking. Validation of the human equipment used routinely, such as dipsticks, is also lacking. As such, the evidence base for feline urinalysis is quite poor and information has largely been extrapolated from the human literature. Information from feline studies has been included where available. In addition, practical clinicopathological and clinical observations are provided. © The Author(s) 2016.

  6. Macroscopic law of conservation revealed in the population dynamics of Toll-like receptor signaling

    Directory of Open Access Journals (Sweden)

    Selvarajoo Kumar


    Full Text Available Abstract Stimulating the receptors of a single cell generates stochastic intracellular signaling. The fluctuating response has been attributed to the low abundance of signaling molecules and the spatio-temporal effects of diffusion and crowding. At population level, however, cells are able to execute well-defined deterministic biological processes such as growth, division, differentiation and immune response. These data reflect biology as a system possessing microscopic and macroscopic dynamics. This commentary discusses the average population response of the Toll-like receptor (TLR 3 and 4 signaling. Without requiring detailed experimental data, linear response equations together with the fundamental law of information conservation have been used to decipher novel network features such as unknown intermediates, processes and cross-talk mechanisms. For single cell response, however, such simplicity seems far from reality. Thus, as observed in any other complex systems, biology can be considered to possess order and disorder, inheriting a mixture of predictable population level and unpredictable single cell outcomes.

  7. Improved determination of macroscopic parasite preparations using S10 modified plastination procedure

    Directory of Open Access Journals (Sweden)

    Elena Atanaskova


    Full Text Available Macroscopic preparations of parasites fixed in formaldehyde or alcohol don’t fulfill in complete the requests for education, as well as their determination, mainly because of the toxic fumes and not enough visible structure of fixed parasite. Using the modified С10 plastination method, parasites from three different phylum were prepared: Plathelminthes: Class Cestoda (Dipilidum caninum, Moniezia spp and larvae from T.Echinococcus granulosus - Echinococcus unilocularis, larvae from T. pisiformis - Cysticercus pisiformis, , larvae from T. hidatigena - Cysticercus tenuicollis, Phylum Nemathelminthes, Class Nematoda, (Ascaris suum, Macracanthorhynchus hirudinaceus, Diro filaria immitis, Phylum Arthropoda, Class Arachnida (tick from the Ixodidae family and Class Insecta (Gasterophilus intestinalis, Hypoderma bovis. The aim of this study was conserving the parasites in native condition with plastination method and improved determination according to their visible morphologic structure. Parasites were previously kept in 10% formaldehyde. Prepared parasites were dry, chemical free, not toxic and safe for the environment, flexible and with detained form and structure. There was a variation in the natural colors in some of the parasites, as a result from long-time formalin fixation. Preparations made with this method are permanent educative material which enables improved study of parasite’s structure.

  8. Micro- and macroscopic hematuria caused by renal vein entrapment: systematic review of the literature. (United States)

    Vianello, Federica A; Mazzoni, Marta B M; Peeters, Gabriëlla G A M; Fossali, Emilio F; Camozzi, Pietro; Bianchetti, Mario G; Milani, Gregorio P


    Hematuria secondary to renal vein entrapment is mentioned only passing in textbooks and reviews. We performed a search of the National Library of Medicine database for peer-reviewed publications using the terms "renal vein" or "nutcracker" and "hematuria". We identified 187 published reports/studies that covered 736 patients, of whom 288 had microscopic hematuria and 448 had macroscopic hematuria. The patient cohort comprised 159 patients aged ≤17 years. Abdominal pain was absent in  approximately 65% of all patients, and a clinically relevant left-sided varicocele was observed in 29% of the male patients. A normal pre-aortic left renal vein and an anomalous anatomy were noted in 680 and 56 patients, respectively. The body mass index (BMI) was lower in patients with renal vein entrapment than in the controls, with a regression of hematuria correlating with an increase in BMI. A surgical procedure was attempted in 34% of the patients, of which the most common were endovascular stenting and transposition of the renal vein distally into the vena cava. In cases of unexplained hematuria with or without abdominal pain, clinicians should consider the diagnosis of renal vein congestion, especially in males with varicocele. Ultrasonic Doppler flow scanning is the recommended initial diagnostic modality in these patients. Expectation management is advised in the great majority of cases.

  9. Macroscopic study of the digestive tract of Gracilinanus microtarsus (Wagner, 1842 (Mammalia: Didelphidae

    Directory of Open Access Journals (Sweden)

    Luis Miguel Lobo


    Full Text Available Gracilinanus microtarsus is a small marsupial species belonging to the Didelphidae family. It has an omnivorous/frugivorous feeding habit and, therefore, it has a great ecological importance, because it is a seed-dispersing species. This article aims to describe the macroscopic morphology of the digestive tract in G. microtarsus. We used 4 animals fixed in 10% formaldehyde. The organs were dissected, measured, and photographed. The animals under study had the dental formula 2x I 5/4 C 1/1 P 3/3 M 4/4. This is the dental formula of the whole Didelphidae family. The dorsum of the tongue had vallate, fungiform, and filiform papillae. Tubular esophagus evidenced the cervical, thoracic, and abdominal portions. The unicavitary stomach consisted of glandular and aglandular region and gastric folds. Small intestine had 3 portions: duodenum, jejunum, and ileum. Large intestine consisted of: cecum, colon, and rectum. Parotid salivary gland was the largest and it had a flattened shape. The sublingual salivary gland, whi h was the smallest, had a flattened and elongated shape. Mandibular salivary gland had an oval shape. Pancreas had a dispersed shape and lobulated aspect. Liver had a dome shape and it consisted of the lobes right medial, square, right side, left medial, left side, and caudate. The digestive tract of the animals under study is similar to the marsupial species described in the literature.

  10. Ghost Cell Suspensions as Blood Analogue Fluid for Macroscopic Particle Image Velocimetry Measurements. (United States)

    Jansen, Sebastian V; Müller, Indra; Nachtsheim, Max; Schmitz-Rode, Thomas; Steinseifer, Ulrich


    Spatially resolved measurement of blood flow is of great interest in the development of artificial blood-carrying devices such as blood pumps, heart valve prostheses, and oxygenators. Particle image velocimetry (PIV) is able to measure instantaneous velocity fields in a plane with high accuracy and is being used more frequently for the development of such devices. However, as this measurement technique is based on optical access, blood flow at physiological hematocrit values is difficult to measure due to its low transparency and multiscattering properties. So far, only very small dimensions (in the range of 400 μm) can be measured using PIV. A suspension of ghost cells (GCs) offers a higher optical transparency than blood while having a similar rheological behavior. In this study, a procedure for the production of GC suspensions containing a very low intracellular hemoglobin concentration is presented. With the help of multiple rounds of controlled cell lysis, the intracellular hemoglobin concentration could be decreased to a point where a standard macroscopic PIV measurement was possible. A velocity profile of a 44% GC suspension in a circular channel with a diameter of 9.5 mm was measured with high spatial resolution. Meanwhile, the rheological behavior was found to be comparable with blood. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

  11. Macroscopic and microscopic (non-)universality of compact support random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Akemann, G.; Vernizzi, G


    A random matrix model with a {sigma}-model like constraint, the restricted trace ensemble (RTE), is solved in the large-n limit. In the macroscopic limit the smooth connected two-point resolvent G(z,w) is found to be non-universal, extending previous results from monomial to arbitrary polynomial potentials. Using loop equation techniques we give a closed though non-universal expression for G(z,w), which extends recursively to all higher k-point resolvents. These findings are in contrast to the usual unconstrained one-matrix model. However, in the microscopic large-n limit, which probes only correlations at distance of the mean level spacing, we are able to show that the constraint does not modify the universal sine-law. In the case of monomial potentials V(M)=M{sup 2p}, we provide a relation valid for finite-n between the k-point correlation function of the RTE and the unconstrained model. In the microscopic large-n limit they coincide which proves the microscopic universality of RTEs.

  12. Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: Formation of macroscopic granules in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Gerngross, T.U.; Martin, D.P. [Metabolix, Inc., Cambridge, MA (United States)


    A combined chemical and enzymatic procedure has been developed to synthesize macroscopic poly[(R)-(-)-3-hydroxybutyrate] (PHB) granules in vitro. The granules form in a matter of minutes when purified polyhydroxyalkanoate (PHA) synthase from Alcaligenes eutrophus is exposed to synthetically prepared (R)-3-hydroxybutyryl coenzyme A, thereby establishing the minimal requirements for PHB granule formation. The artificial granules are spherical with diameters of up to 3 {mu}m and significantly larger than their native counterparts (0.5 {mu}m). The isolated PHB was characterized by {sup 1}H and {sup 13}C NMR, gel-permeation chromatography, and chemical analysis. The in vitro polymerization system yields PHB with a molecular mass > 10 x 10{sup 6} Da, exceeding by an order of magnitude the mass of PHAs typically extracted from microorganisms. We also demonstrate that the molecular mass of the polymer can be controlled by the initial PHA synthase concentration. Preliminary kinetic analysis of de novo granule formation confirms earlier findings of a lag time for the enzyme but suggests the involvement of an additional granule assembly step. Minimal requirements for substrate recognition were investigated. Since substrate analogs lacking the adenosine 3{prime}, 5{prime}-bisphosphate moiety of (R)-3-hydroxybutyryl coenzyme A were not accepted by the PHA synthase, we provide evidence that this structural element of the substrate is essential for catalysis. PHAs provide a range of natural, renewable, biodegradable thermoplastics with a broad range of useful material properties. 33 refs., 6 figs., 1 tab.

  13. Nanocomposites fabrication by self-assembly method to modify macroscopic properties (United States)

    Lopez-Barbosa, N.; Osma, J. F.


    Polymeric nanocomposites have been in the scope of scientists for the last decade due to their multiple applications and simple synthesis. Self-assembly fabrication can be performed through different methods such as layer-by-layer or the controlled growth of nanostructures on a surface. These methods allow fast elaboration of nanocomposites that can be readily integrated in sensors or films. The current work exposes the self-assembly of nanocomposites for the modification of material’s macroscopic properties such as hydrophobicity and temperature’s resistance on textiles. Hydrophobicity properties of cotton textiles were modified by the application of functionalized silica nanoparticles on their surfaces. Thermal resistance of cotton textiles was achieved by incorporating TiO2 nanoparticles into the matrix, increasing the scope of their applications. Functionalization was attained by chloro-trimethyl-silane (CTS) and γ-amino(propyl) triethoxy silane (APTES) in organic and inorganic solvents. Wetting phenomena characteristics appeared to highly depend on the synthesis parameters.

  14. Influence of fractal substructures of the percolating cluster on transferring processes in macroscopically disordered environments (United States)

    Kolesnikov, B. P.


    The presented work belongs to the issue of searching for the effective kinetic properties of macroscopically disordered environments (MDE). These properties characterize MDE in general on the sizes which significantly exceed the sizes of macro inhomogeneity. The structure of MDE is considered as a complex of interpenetrating percolating and finite clusters consolidated from homonymous components, topological characteristics of which influence on the properties of the whole environment. The influence of percolating clusters’ fractal substructures (backbone, skeleton of backbone, red bonds) on the transfer processes during crossover (a structure transition from fractal to homogeneous condition) is investigated based on the offered mathematical approach for finding the effective conductivity of MDEs and on the percolating cluster model. The nature of the change of the critical conductivity index t during crossover from the characteristic value for the area close to percolation threshold to the value corresponded to homogeneous condition is demonstrated. The offered model describes the transfer processes in MDE with the finite conductivity relation of «conductive» and «low conductive» phases above and below percolation threshold and in smearing area (an analogue of a blur area of the second-order phase transfer).

  15. Analysis of the Macroscopic Behavior of Server Systems in the Internet Environment

    Directory of Open Access Journals (Sweden)

    Yusuke Tanimura


    Full Text Available Elasticity is one of the key features of cloud-hosted services built on virtualization technology. To utilize the elasticity of cloud environments, administrators should accurately capture the operational status of server systems, which changes constantly according to service requests incoming irregularly. However, it is difficult to detect and avoid in advance that operating services are falling into an undesirable state. In this paper, we focus on the management of server systems that include cloud systems, and propose a new method for detecting the sign of undesirable scenarios before the system becomes overloaded as a result of various causes. In this method, a measure that utilizes the fluctuation of the macroscopic operational state observed in the server system is introduced. The proposed measure has the property of drastically increasing before the server system is in an undesirable state. Using the proposed measure, we realize a function to detect that the server system is falling into an overload scenario, and we demonstrate its effectiveness through experiments.

  16. Nanoscale patterning, macroscopic reconstruction, and enhanced surface stress by organic adsorption on vicinal surfaces (United States)

    Pollinger, Florian; Schmitt, Stefan; Sander, Dirk; Tian, Zhen; Kirschner, Jürgen; Vrdoljak, Pavo; Stadler, Christoph; Maier, Florian; Marchetto, Helder; Schmidt, Thomas; Schöll, Achim; Umbach, Eberhard


    Self-organization is a promising method within the framework of bottom-up architectures to generate nanostructures in an efficient way. The present work demonstrates that self-organization on the length scale of a few to several tens of nanometers can be achieved by a proper combination of a large (organic) molecule and a vicinal metal surface if the local bonding of the molecule on steps is significantly stronger than that on low-index surfaces. In this case thermal annealing may lead to large mass transport of the subjacent substrate atoms such that nanometer-wide and micrometer-long molecular stripes or other patterns are being formed on high-index planes. The formation of these patterns can be controlled by the initial surface orientation and adsorbate coverage. The patterns arrange self-organized in regular arrays by repulsive mechanical interactions over long distances accompanied by a significant enhancement of surface stress. We demonstrate this effect using the planar organic molecule PTCDA as adsorbate and Ag(10 8 7) and Ag(775) surfaces as substrate. The patterns are directly observed by STM, the formation of vicinal surfaces is monitored by high-resolution electron diffraction, the microscopic surface morphology changes are followed by spectro-microscopy, and the macroscopic changes of surface stress are measured by a cantilever bending method. The in situ combination of these complementary techniques provides compelling evidence for elastic interaction and a significant stress contribution to long-range order and nanopattern formation.

  17. Certified quantum non-demolition measurement of a macroscopic material system (United States)

    Sewell, R. J.; Napolitano, M.; Behbood, N.; Colangelo, G.; Mitchell, M. W.


    Quantum non-demolition (QND) measurements improve sensitivity by evading measurement back-action. The technique was first proposed to detect mechanical oscillations in gravity-wave detectors and demonstrated in the measurement of optical fields, which led to the development of rigorous criteria to distinguish QND from similar non-classical measurements. Recent QND measurements of macroscopic material systems such as atomic ensembles and mechanical oscillators show some QND features, but not full QND character. Here we demonstrate certified QND measurement of the collective spin of an atomic ensemble. We observed quantum-state preparation (QSP) and information-damage trade-off (IDT) beyond their classical limits by seven and 12 standard deviations, respectively. Our techniques complement recent work with microscopic systems and can be used for quantum metrology and memory, the preparation and detection of non-Gaussian states, and proposed quantum simulation and information protocols. They should enable QND measurements of dynamical quantum variables and the realization of QND-based quantum information protocols.

  18. A method for measuring macroscopic cross-sections for thermal neutrons. (United States)

    El Abd, A; Taha, G; Ellithi, A Y


    A method was proposed for measuring macroscopic absorption and scattering cross-sections for thermal neutrons. It is based on a Pu-Be neutron source and He-3 neutron detectors assembly. A beam of neutrons was obtained from the source imbedded in a water tank. The He-3 detectors oriented inside the sample and at 180° and 0° with respect to the incident neutron beam were used to register neutrons after interaction with the samples. Neutron count rates (detectors responses) were obtained for large (5.5l) as well as small (1.3l) volumes of standard samples. Sensitivities of the results obtained for the large and small samples were compared. A semi-empirical model was proposed to fit the results. It describes the relative detector responses in terms of a dimensionless variable which depends on the geometrical parameters and cross section of the standard samples used. The model successfully fits the results obtained. Advantages and limitations of the method were discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Transport properties at fluids interfaces: a molecular study for a macroscopic modelling (United States)

    Russo, Antonio; Morciano, Matteo; Sibley, David N.; Nold, Andreas; Goddard, Benjamin D.; Asinari, Pietro; Kalliadasis, Serafim


    Rapid developments in the field of micro- and nano-fluidics require detailed analysis of the properties of matter at the molecular level. But despite numerous works in the literature, appropriate macroscopic relations able to integrate a microscopic description of fluid and soft matter properties at liquid-vapour and multi-fluid interfaces are missing. As a consequence, studies on interfacial phenomena and micro-device designs often rely on oversimplified assumptions, e.g. that the viscosities can be considered constant across interfaces. In our work, we present non-equilibrium MD simulations to scrutinise efficiently and systematically, through the tools of statistical mechanics, the anisotropic properties of fluids, namely density variations, stress tensor, and shear viscosity, at the fluid interfaces between liquid and vapour and between two partially miscible fluids. Our analysis has led to the formulation of a general relation between shear viscosity and density variations validated for a wide spectrum of interfacial fluid problems. In addition, it provides a rational description of other interfacial quantities of interest, including surface tension and its origins, and more generally, it offers valuable insight of molecular transport phenomena at interfaces.

  20. Demagnetization harmonic effects on the magnetization of granular systems on a macroscopic scale: the superconducting case (United States)

    Mancusi, D.; Galluzzi, A.; Pace, S.; Polichetti, M.


    A model has been developed to determine the effective ac magnetic response of magnetic systems, taking into account the demagnetization effects arising from the sample geometry which determine the out-of-phase components of the applied fundamental frequency and higher harmonic components. Indeed, demagnetization fields and their intermodulation can significantly affect the ac magnetic response. This approach provides a system of self-consistent linear equations relating the magnetic response to the external magnetic field by means of nonlinear magnetic susceptibility. The model is extended to the magnetic response of granular systems in terms of the contributions of the individual grains and of the whole sample in the presence of demagnetization effects of the whole sample and of the grains on a macroscopic scale. In particular, our model is applied to a granular superconducting system. The comparison between the performed numerical simulations and the experimental data shows that the demagnetization fields of the single grains and of the whole sample, and their intermodulation, are relevant if magnetic measurements are used to extract detailed information about the analyzed material.

  1. Incidence of crystal growth conditions on the formation of macroscopic liquid inclusions in ciclopirox crystals (United States)

    Waldschmidt, Audrey; Dupray, Valérie; Berton, Benjamin; Couvrat, Nicolas; Petit, Samuel; Coquerel, Gérard


    Using an accurate and rigorous protocol, the crystal growth behavior in solution of the antifungal drug ciclopirox was investigated with the aim to identify the experimental factors responsible for the appearance of macroscopic inclusions of saturated solution. Counterintuitively, these inclusions are produced only when the relative supersaturation is below a critical threshold; simultaneously the crystals exhibit a hexagonal morphology. An increase in the driving force leads to a rod-shaped morphology without inclusion and without any change of the crystal phase, as confirmed by X-ray diffraction. The correlation between this morphological transition and the occurrence of liquid inclusions could be rationalized by considering the associated change of growth rates of {(1 1 1)} and {(1 1 -1)} faces. However, the nature of the solvent, the presence of impurities and diffusion in solution appeared to have no detectable incidence on the formation of liquid inclusions, inducing that the presumed contribution of a chemical adsorption phenomenon—side products or solvents—could not be established.

  2. Computational investigation of porous media phase field formulations: Microscopic, effective macroscopic, and Langevin equations (United States)

    Ververis, Antonios; Schmuck, Markus


    We consider upscaled/homogenized Cahn-Hilliard/Ginzburg-Landau phase field equations as mesoscopic formulations for interfacial dynamics in strongly heterogeneous domains such as porous media. A recently derived effective macroscopic formulation, which takes systematically the pore geometry into account, is computationally validated. To this end, we compare numerical solutions obtained by fully resolving the microscopic pore-scale with solutions of the upscaled/homogenized porous media formulation. The theoretically derived convergence rate O (ɛ 1 / 4) is confirmed for circular pore-walls. An even better convergence of O (ɛ1) holds for square shaped pore-walls. We also compute the homogenization error over time for different pore geometries. We find that the quality of the time evolution shows a complex interplay between pore geometry and heterogeneity. Finally, we study the coarsening of interfaces in porous media with computations of the homogenized equation and the microscopic formulation fully resolving the pore space. We recover the experimentally validated and theoretically rigorously derived coarsening rate of O (t 1 / 3) in the periodic porous media setting. In the case of critical quenching and after adding thermal noise to the microscopic porous media formulation, we observe that the influence of thermal fluctuations on the coarsening rate shows after a short, expected phase of universal coarsening, a sharp transition towards a different regime.

  3. Observation of a macroscopic topological insulator phase in an assembly of coupled topological insulator nanocrystals (United States)

    Sen, Diptiman; Banerjee, Abhishek; Deb, Oindrila; Majhi, Kunjalata; Ganesan, R.; Kumar, P. S. Anil

    We study an assembly of tunnel coupled topological insulator (TI) nanocrystals. We demonstrate experimentally that a macroscopic topological insulator phase can emerge in this system. Electrical transport measurements on thin films of Bi2Se3 nanocrystals reveal the presence of decoupled top and bottom topological surface states above a certain film thickness. The surface state penetration depth is found to be unusually large, 30nm at 2K, and decreases with increasing temperature. For samples with low film thickness, we observe deviations of the surface state Berry phase from π due to hybridization of opposite surface states. This weakens the effective spin-orbit coupling field to as low as 30T at 2K. Remarkably, the topological insulating behavior becomes more pronounced with increasing temperature. Our work exhibits a model TI that is distinct from bulk/single crystal TIs and also displays phenomena that are expected, but normally not accessible in the latter systems. K.M. thanks CSIR, India for financial support. D.S. thanks DST, India for support under Grant No. SR/S2/JCB-44/2010. P.S.A.K. acknowledges Nanomission, DST, Govt. of India for support.

  4. Application of a single root-scale model to improve macroscopic modeling of root water uptake: focus on osmotic stress (United States)

    Jorda, Helena; Perelman, Adi; Lazarovitch, Naftali; Vanderborght, Jan


    Root water uptake is a fundamental process in the hydrological cycle and it largely regulates the water balance in the soil vadose zone. Macroscopic stress functions are currently used to estimate the effect of salinity on root water uptake. These functions commonly assume stress to be a function of bulk salinity and of the plant sensitivity to osmotic stress expressed as the salinity at which transpiration is reduced by half or so called tolerance value. However, they fail to integrate additional relevant factors such as atmospheric conditions or root architectural traits. We conducted a comprehensive simulation study on a single root using a 3-D physically-based model that resolves flow and transport to individual root segments and that couples flow in the soil and root system. The effect of salt concentrations on root water uptake was accounted for by including osmotic water potential gradients between the solution at the soil root interface and the root xylem sap in the hydraulic gradient between the soil and root. A large set of factors were studied, namely, potential transpiration rate and dynamics, root length density (RLD), irrigation water quality and irrigation frequency, and leaching fraction. Results were fitted to the macroscopic function developed by van Genuchten and Hoffman (1984) and the dependency of osmotic stress and the fitted macroscopic parameters on the studied factors was evaluated. Osmotic stress was found to be highly dependent on RLD. Low RLDs result in a larger stress to the plant due to high evaporative demand per root length unit. In addition, osmotic stress was positively correlated to potential transpiration rate, and sinusoidal potential transpiration lead to larger stress than when imposed as a constant boundary condition. Macroscopic parameters are usually computed as single values for each crop and used for the entire growing season. However, our study shows that both tolerance value and shape parameter p from the van Genuchten

  5. Social Free Energy of a Pareto-Like Resource Distribution

    Directory of Open Access Journals (Sweden)

    Vinko Zlatić


    Full Text Available For an organisation with a Pareto-like distribution of the relevant resources we determine the social free energy and related social quantities using thermodynamical formalism. Macroscopic dynamics of the organisation is linked with the changes in the attributed thermodynamical quantities through changes in resource distribution function. It is argued that quantities of thermodynamical origin form the optimised set of organisation’s state indicators, which is reliable expression of micro-dynamics.

  6. Modeling ancient Egyptian mummification on fresh human tissue: macroscopic and histological aspects. (United States)

    Papageorgopoulou, Christina; Shved, Natallia; Wanek, Johann; Rühli, Frank J


    Many studies have been concerned with the ancient Egyptian mummification method; nevertheless, little effort has been made to explore it experimentally. The goal of this study is to apply evidence-based diagnostic criteria and state-of-the art methodology in order to improve knowledge on soft tissues preservation and postmortem alterations. Two human lower limbs (LL) from a female donor were (1) "naturally" mummified by dry heat and (2) artificially in natron. At specific time intervals a macroscopic and radiological examination of the LL was performed and skin and muscle samples were taken for histological and biomolecular analysis. Temperature, humidity, pH, and weight of the LL were systematically measured. The mummification by dry heat was stopped after 7 days due to unexpected lack of mummification progress. The mummification in natron was completed successfully after 208 days. The humidity, the external temperature, and the pH were proven with Pearson correlation and principal component analysis as important factors for the mummification process. The steady removal of water from the tissues through the natron has prevented the putrefaction. This is also evident in the absence of bacteria or fungi through the microbiological analysis. The histological analysis revealed very good preservation of the skin and the muscle tissues. In the muscular sample certain degree of structural disintegration can be seen, particularly affecting the epimysium whilst in the skin samples the epidermis, especially the stratum corneum, is mostly affected. The samples show better preservation compared with ancient Egyptian sections and other mummified tissues from historic or forensic context. © 2015 Wiley Periodicals, Inc.

  7. Relationship Between Filler-Matrix Interface and Macroscopical Properties of Polymer Nanocomposites

    KAUST Repository

    Aguilar Ventura, Isaac Enrique


    The macroscopic properties of Multiwall Carbon Nanotube (MWCNT) polymer nano-composites and multiscale composites have been studied from a multifunctional standpoint. The objective is to understand and correlate the mechanisms in which the addition of a small content of MWCNTs can affect the mechanical, thermal and electrical properties of thermoplastic and thermoset polymer nanocomposites. While CNTs are well-known to possess extraordinary properties in the nanoscale, it has been shown that, the CNT/polymer matrix and CNT/CNT interactions are mainly responsible for the modification of properties in the nanocomposites. Observation of the mechanical properties revealed that the addition of CNTs can increase the stiffness of the material, but the increment of interfacial regions can accelerate the damage process under cyclic loading conditions. Additionally, CNTs can interact with polymer chains in the matrix affecting thermomechanical properties such as the glass transition temperature and the storage modulus. A low content of well-dispersed CNTs can form percolated networks within the matrix, which, due to the nature of the electrical conduction mechanism, have demonstrated potential in increasing the electrical conductivity of the nanocomposites. In contrast, high phonon scattering at the interconnections along the CNT network are responsible for marginal increases in thermal conductivity. In this study, a special focus was placed in modifying the CNT interconnections with a conductive polymer "bridge" to increase the efficiency of the electrical carrier transport. Additional experimental observations such as piezoresistivity and electrical conductivity/temperature dependency, demonstrated the major role of the interfacial regions with respect to the observed material properties in the macroscale. Controlling the interactions that occur in these regions is key to achieve tailorable, multifunctional nanocomposites.

  8. Cultivation of macroscopic marine algae and freshwater aquatic weeds. Progress report, May 1--December 31, 1976

    Energy Technology Data Exchange (ETDEWEB)

    Ryther, J. H.


    Research was divided between basic physiological studies of the growth and nutrient-uptake kinetics of macroscopic marine algae and the more applied problems involved in the selection of species and the development of inexpensive, non-energy intensive culture methods for growing seaweeds and freshwater plants as a biomass source for conversion to energy. Best growth of the seaweeds occurs at low (0.1 to 1.0 concentration of major nutrients, with ammonia as a nitrogen source, with rapid exchange of the culture medium (residence time of 0.05 days or less). Of 43 species of seaweeds evaluated, representatives of the large red alga genus Gracilaria appear most promising with potential yields, in a highly intensive culture system under optimal conditions, of some 129 metric dry tons per hectare per year (about half of which is organic). Non-intensive culture methods have yielded one-third to one-half that figure. Unexplained periodicity of growth and overgrowth by epiphytes remain the most critical constraint to large-scale seaweed culture. Freshwater weed species in culture include water hyacinth (Eichhornia crassipes), duckweed (Lemna minor), and Hydrilla vertecillata, with yields to date averaging 15, 4, and 8 g dry wt/m/sup 2//day, respectively. However, these plants have not yet been grown through the winter, so average annual yields are expected to be lower. In contrast to the seaweeds, the freshwater plants grow well at high nutrient concentrations and slow culture volume exchange rates (residence time ca. 20 days or more). Experiments were initiated on the recycling of digester residues from the fermentation of the freshwater and marine plants as a possible nutrient source for growth of the same species.

  9. Signatures of granular superconductivity and Josephson effects in macroscopic measurements: the case of new superconductors

    Directory of Open Access Journals (Sweden)

    S Senoussi


    Full Text Available   We report systematic investigations of the magnetic superconducting properties of the new superconducting materials (NS: New high temperature superconductors (HTS, Organic superconductors (OS, fullerenes, carbon nanotubes, MgB2 etc. We show that, contrary to conventional superconductors where the superconducting state can be coherent over several tenths of km, the macroscopic coherence range lc of the NS is often as short as 0.1 to 10 µm typically. As a consequence, the magnetic properties are dominated by granular-like effects as well as Josephson coupling between grains. Here, we concentrate on HTS ceramics and organic superconductors exclusively. In the first case we observe three distinct regimes: (i At very low field (H < 5 Oe to say all the grains are coupled via Josephson effect and lc can be considered as infinite. (2 At intermediate field (5 < H < 50 Oe, typically the grains are gradually decoupled by H and/or T. (iii At higher fields all the grains are decoupled and lc roughly coincides with the diameter of the metallurgical grains. The case of OS is more subtle and is connected with a kind of order-disorder transition that occurs in most of them. For instance, in this study, we exploit quenched disorder (after crossing such a transition in the -(BEDT-TTF2Cu[N(CN2]Br layered organic superconductor to get new insights on both the superconducting state (T £ 11.6 K and the glassy transition at Tg, by studying the superconducting properties as functions of annealing time and annealing temperature around the glassy transition. Our main result is that the data can be described by a percolation molecular cluster model in which the topology and the growth of the molecular clusters obey an Ising spin-glass-like model with Tg ≈ 80 K for the hydrogenated compound and Tg ≈ 55 K for the fully deuterated one.

  10. Plant RNA binding proteins for control of RNA virus infection

    Directory of Open Access Journals (Sweden)

    Sung Un eHuh


    Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.

  11. Generation of siRNA Nanosheets for Efficient RNA Interference (United States)

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum


    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.

  12. RNA gets in phase. (United States)

    Saha, Shambaditya; Hyman, Anthony A


    Several neurological disorders are linked to tandem nucleotide repeat expansion in the mutated gene. Jain and Vale (2017. Nature. show that, above a pathological threshold repeat number, base pairing interactions drive phase separation of RNA into membrane-less gels, suggesting that RNA can scaffold the assembly of phase-separated compartments that sequester proteins/RNAs causing toxicity. © 2017 Saha and Hyman.

  13. Shapes of interacting RNA complexes

    DEFF Research Database (Denmark)

    Fu, Benjamin Mingming; Reidys, Christian


    Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....

  14. Processivity and coupling in messenger RNA transcription.

    Directory of Open Access Journals (Sweden)

    Stuart Aitken


    Full Text Available The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. In this simple on/off model, the many processes involved in active transcription are represented by a single reaction. These processes include elongation, which has a minimum time for completion and processing that is not captured in the model.In this paper, we explore the impact on the mRNA distribution of representing the elongation process in more detail. Consideration of the mechanisms of elongation leads to two alternative models of the coupling between the elongating polymerase and the state of the promoter: Processivity allows polymerases to complete elongation irrespective of the promoter state, whereas coupling requires the promoter to be active to produce a full-length transcript. We demonstrate that these alternatives have a significant impact on the predicted distributions. Models are simulated by the Gillespie algorithm, and the third and fourth moments of the resulting distribution are computed in order to characterise the length of the tail, and sharpness of the peak. By this methodology, we show that the moments provide a concise summary of the distribution, showing statistically-significant differences across much of the feasible parameter range.We conclude that processivity is not fully consistent with the on/off model unless the probability of successfully completing elongation is low--as has been observed. The results also suggest that some form of coupling between the promoter and a rate-limiting step in transcription may explain the cell's inability to maintain high mRNA levels at low noise--a prediction of the on/off model that has no supporting evidence.

  15. RNA catalysis through compartmentalization (United States)

    Strulson, Christopher A.; Molden, Rosalynn C.; Keating, Christine D.; Bevilacqua, Philip C.


    RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.

  16. Microstructure control of macroscopic graphene paper by electrospray deposition and its effect on thermal and electrical conductivities (United States)

    Xin, Guoqing; Zhu, Weiguang; Yao, Tiankai; Scott, Spencer Michael; Lian, Jie


    Macroscopic graphene paper is fabricated by an electrospray deposition approach, and the microstructure can be controlled from highly porous to highly compact geometries by varying deposition parameters including graphene colloid concentration and deposition rate. Free-standing graphene films can be separated from substrates via a simple water exfoliation method in which the surface properties of graphene films and substrates control film exfoliation. Specifically, water exfoliation can be achieved when the contact angle of substrates is 64° or below. Thermal and electrical conductivities of the macroscopic graphene paper upon thermal annealing are measured, enabling the establishment of the process-microstructure-property correlation beneficial for further development and property manipulation of graphene-based materials.

  17. Macroscopic lattice Boltzmann model for heat and moisture transfer process with phase transformation in unsaturated porous media during freezing process (United States)

    Song, Wenyu; Zhang, Yaning; Li, Bingxi; Xu, Fei; Fu, Zhongbin


    In the current study, a macroscopic lattice Boltzmann model for simulating the heat and moisture transport phenomenon in unsaturated porous media during the freezing process was proposed. The proposed model adopted percolation threshold to reproduce the extra resistance in frozen fringe during the freezing process. The freezing process in Kanagawa sandy loam soil was demonstrated by the proposed model. The numerical result showed good agreement with the experimental result. The proposed model also offered higher computational efficiency and better agreement with the experimental result than the existing numerical models. Lattice Boltzmann method is suitable for simulating complex heat and mass transfer process in porous media at macroscopic scale under proper dimensionless criterion, which makes it a potentially powerful tool for engineering application.


    Directory of Open Access Journals (Sweden)

    C. G. Maciel


    Full Text Available The macroscopic fungi performance a important role in the maintenance of forest environments, and studies related with the identification of species are fundamental to the research progress. This study aimed to realize a survey the species diversity of wood decomposing fungi in populations of Pinus elliottii Engelm, Eucalyptus globulus Labill, Acacia mearnsii de Wild and natural forest, in State Foundation for Agricultural Research - FEPAGRO, Forestry Research Center, located in Santa Maria, RS. Were collected 53 samples of macroscopic fungi in four areas, being 16 samples in forest of P. Elliottii; 12 samples in forest of E. globulus, 12 samples in forest of A. mearnsii and 13 samples in of native forest. In the laboratory, five genera were identified to the species level: Fuligo septica (L. F.H. Wigg, Gloeoporus dichrous (Fr. Bress., Lycogala epidendrum (L. Fr. e Trametes villosa (Sw. Kreisel.

  19. Mechanism of Macroscopic Motion of Oleate Helical Assemblies: Cooperative Deprotonation of Carboxyl Groups Triggered by Photoisomerization of Azobenzene Derivatives. (United States)

    Kageyama, Yoshiyuki; Ikegami, Tomonori; Kurokome, Yuta; Takeda, Sadamu


    Macroscopic and spatially ordered motions of self-assemblies composed of oleic acid and a small amount of an azobenzene derivative, induced by azobenzene photoisomerization, was previously reported. However, the mechanism of the generation of submillimeter-scale motions by the nanosized structural transition of azobenzene was not clarified. Herein, an underlying mechanism of the motions is proposed in which deprotonation of carboxyl groups in cooperation with azobenzene photoisomerization causes a morphological transition of the self-assembly, which in turn results in macroscopic forceful dynamics. The photoinduced deprotonation was investigated by potentiometric pH titration and FTIR spectroscopy. The concept of hierarchical molecular interaction generating macroscale function is expected to promote the next stage of supramolecular chemistry. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Complete separation of macroscopic rod-like bimetallic nanoassembly perpendicular and parallel on substrate for simultaneous sensing of microorganisms (United States)

    Jia, HaoWei; Wang, Jin; Qiu, Li; Ge, HongGua


    Although two kinds of macroscopic ordered tridimensional nanoassemblies, i.e., alignment of nanorods, can be yielded by controllable droplet evaporation methods, complete separation of the nanoassembly perpendicular or parallel to substrate is quite challenging. It can, however, be realized by the aid of facet blocking combined with the tuning of ionic strength and colloidal concentration. The as-fabricated rod-like bimetallic nanoassembly has proved to be an excellent SERS active substrate compared to random aggregates. It should be mentioned that macroscopic ordered tridimensional nanoassembly perpendicular to the substrate can be used as a highly active SERS substrate with good uniformity and can be successfully applied for finely discriminating two microorganisms: Escherichia coli bacteria and Saccharomycetes.