Macroscopic and microscopic magnetism of metal-metalloid amorphous alloys

International Nuclear Information System (INIS)

Vasconcellos, M.A.Z.; Fichtner, P.F.P.; Livi, F.P.; Costa, M.I. da; Baibich, M.N.

1984-01-01

In this paper is investigated the interrelation between macroscopic and microscopic magnetic phenomena using experimetnal data from Moessbauer effect and the magnetization of layers of amorphous (Fe 1-x Ni x ) 80 B 20 . The Moessbauer effect measurement show a distribution of hyperfine fields in Fe site as well as a likely distribution of isomeric shifts (M.W.O.) [pt

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

Science.gov (United States)

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

2017-07-07

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.

Distribution of protein and RNA in the 30S ribosomal subunit

International Nuclear Information System (INIS)

Ramakrishnan, V.

1986-01-01

In Escherichia coli, the small ribosomal subunit has a sedimentation coefficient of 30S, and consists of a 16S RNA molecule of 1541 nucleotides complexed with 21 proteins. Over the last few years, a controversy has emerged regarding the spatial distribution of RNA and protein in the 30S subunit. Contrast variation with neutron scattering was used to suggest that the RNA was located in a central core of the subunit and the proteins mainly in the periphery, with virtually no separation between the centers of mass of protein and RNA. However, these findings are incompatible with the results of efforts to locate individual ribosomal proteins by immune electron microscopy and triangulation with interprotein distance measurements. The conflict between these two views is resolved in this report of small-angle neutron scattering measurements on 30S subunits with and without protein S1, and on subunits reconstituted from deuterated 16S RNA and unlabeled proteins. The results show that (i) the proteins and RNA are intermingled, with neither component dominating at the core or the periphery, and (ii) the spatial distribution of protein and RNA is asymmetrical, with a separation between their centers of mass of about 25 angstroms

Microscopic Simulation and Macroscopic Modeling for Thermal and Chemical Non-Equilibrium

Science.gov (United States)

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

2013-01-01

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.

Hybrid methods for witnessing entanglement in a microscopic-macroscopic system

International Nuclear Information System (INIS)

Spagnolo, Nicolo; Vitelli, Chiara; Paternostro, Mauro; De Martini, Francesco; Sciarrino, Fabio

2011-01-01

We propose a hybrid approach to the experimental assessment of the genuine quantum features of a general system consisting of microscopic and macroscopic parts. We infer entanglement by combining dichotomic measurements on a bidimensional system and phase-space inference through the Wigner distribution associated with the macroscopic component of the state. As a benchmark, we investigate the feasibility of our proposal in a bipartite-entangled state composed of a single-photon and a multiphoton field. Our analysis shows that, under ideal conditions, maximal violation of a Clauser-Horne-Shimony-Holt-based inequality is achievable regardless of the number of photons in the macroscopic part of the state. The difficulty in observing entanglement when losses and detection inefficiency are included can be overcome by using a hybrid entanglement witness that allows efficient correction for losses in the few-photon regime.

Hybrid methods for witnessing entanglement in a microscopic-macroscopic system

Energy Technology Data Exchange (ETDEWEB)

Spagnolo, Nicolo [Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale Aldo Moro 5, I-00185 Roma (Italy); Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Piazzale Aldo Moro 5, I-00185 Roma (Italy); Vitelli, Chiara [Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale Aldo Moro 5, I-00185 Roma (Italy); Paternostro, Mauro [School of Mathematics and Physics, Queen' s University, BT 7 1NN Belfast (United Kingdom); De Martini, Francesco [Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale Aldo Moro 5, I-00185 Roma (Italy); Accademia Nazionale dei Lincei, via della Lungara 10, I-00165 Roma (Italy); Sciarrino, Fabio [Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale Aldo Moro 5, I-00185 Roma (Italy); Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche (INO-CNR), largo E. Fermi 6, I-50125 Firenze (Italy)

2011-09-15

We propose a hybrid approach to the experimental assessment of the genuine quantum features of a general system consisting of microscopic and macroscopic parts. We infer entanglement by combining dichotomic measurements on a bidimensional system and phase-space inference through the Wigner distribution associated with the macroscopic component of the state. As a benchmark, we investigate the feasibility of our proposal in a bipartite-entangled state composed of a single-photon and a multiphoton field. Our analysis shows that, under ideal conditions, maximal violation of a Clauser-Horne-Shimony-Holt-based inequality is achievable regardless of the number of photons in the macroscopic part of the state. The difficulty in observing entanglement when losses and detection inefficiency are included can be overcome by using a hybrid entanglement witness that allows efficient correction for losses in the few-photon regime.

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

Science.gov (United States)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

Generating macroscopic chaos in a network of globally coupled phase oscillators

Science.gov (United States)

So, Paul; Barreto, Ernest

2011-01-01

We consider an infinite network of globally coupled phase oscillators in which the natural frequencies of the oscillators are drawn from a symmetric bimodal distribution. We demonstrate that macroscopic chaos can occur in this system when the coupling strength varies periodically in time. We identify period-doubling cascades to chaos, attractor crises, and horseshoe dynamics for the macroscopic mean field. Based on recent work that clarified the bifurcation structure of the static bimodal Kuramoto system, we qualitatively describe the mechanism for the generation of such complicated behavior in the time varying case. PMID:21974662

Stochastic space interval as a link between quantum randomness and macroscopic randomness?

Science.gov (United States)

Haug, Espen Gaarder; Hoff, Harald

2018-03-01

For many stochastic phenomena, we observe statistical distributions that have fat-tails and high-peaks compared to the Gaussian distribution. In this paper, we will explain how observable statistical distributions in the macroscopic world could be related to the randomness in the subatomic world. We show that fat-tailed (leptokurtic) phenomena in our everyday macroscopic world are ultimately rooted in Gaussian - or very close to Gaussian-distributed subatomic particle randomness, but they are not, in a strict sense, Gaussian distributions. By running a truly random experiment over a three and a half-year period, we observed a type of random behavior in trillions of photons. Combining our results with simple logic, we find that fat-tailed and high-peaked statistical distributions are exactly what we would expect to observe if the subatomic world is quantized and not continuously divisible. We extend our analysis to the fact that one typically observes fat-tails and high-peaks relative to the Gaussian distribution in stocks and commodity prices and many aspects of the natural world; these instances are all observable and documentable macro phenomena that strongly suggest that the ultimate building blocks of nature are discrete (e.g. they appear in quanta).

The mirrors model: macroscopic diffusion without noise or chaos

International Nuclear Information System (INIS)

Chiffaudel, Yann; Lefevere, Raphaël

2016-01-01

Before stating our main result, we first clarify through classical examples the status of the laws of macroscopic physics as laws of large numbers. We next consider the mirrors model in a finite d-dimensional domain and connected to particles reservoirs at fixed chemical potentials. The dynamics is purely deterministic and non-ergodic but takes place in a random environment. We study the macroscopic current of particles in the stationary regime. We show first that when the size of the system goes to infinity, the behaviour of the stationary current of particles is governed by the proportion of orbits crossing the system. This allows us to formulate a necessary and sufficient condition on the distribution of the set of orbits that ensures the validity of Fick’s law. Using this approach, we show that Fick’s law relating the stationary macroscopic current of particles to the concentration difference holds in three dimensions and above. The negative correlations between crossing orbits play a key role in the argument. (letter)

Macroscopic description of the limb muscles of Tupinambis merianae

Directory of Open Access Journals (Sweden)

Juliana Barbosa Casals

2012-03-01

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.

Determination of Particle Size and Distribution through Image-Based Macroscopic Analysis of the Structure of Biomass Briquettes

Directory of Open Access Journals (Sweden)

Veronika Chaloupková

2018-02-01

Full Text Available Via image-based macroscopic, analysis of a briquettes’ surface structure, particle size, and distribution was determined to better understand the behavioural pattern of input material during agglomeration in the pressing chamber of a briquetting machine. The briquettes, made of miscanthus, industrial hemp and pine sawdust were produced by a hydraulic piston press. Their structure was visualized by a stereomicroscope equipped with a digital camera and software for image analysis and data measurements. In total, 90 images of surface structure were obtained and quantitatively analysed. Using Nikon Instruments Software (NIS-Elements software, the length and area of 900 particles were measured and statistically tested to compare the size of the particles at different surface locations. Results showed statistically significant differences in particles’ size distribution: larger particles were generally on the front side of briquettes and vice versa, smaller particles were on the rear side. As well, larger particles were centred in the middle of cross sections and the smaller particles were centred on the bottom of the briquette.

Macroscopic behaviour of a charged Boltzmann gas

International Nuclear Information System (INIS)

Banyai, L.; Gartner, P.; Protopopescu, V.

1980-08-01

We consider a classical charged gas (with self-consistent Coulomb interaction) described by a solvable linearized Boltzman equation with thermaljzation on unifopmly distributed scatterers. It is shown that jf one scales the time t, the reciprocal space coordinate k vector and the Debye length l as lambda 2 t, k vector/lambda, lambda l respectively, in the lambda→infinity limit the charge density is equal to the solution of the corresponding diffusion-conduction (macroscopic) equation. (author)

Quantum equilibria for macroscopic systems

International Nuclear Information System (INIS)

Grib, A; Khrennikov, A; Parfionov, G; Starkov, K

2006-01-01

Nash equilibria are found for some quantum games with particles with spin-1/2 for which two spin projections on different directions in space are measured. Examples of macroscopic games with the same equilibria are given. Mixed strategies for participants of these games are calculated using probability amplitudes according to the rules of quantum mechanics in spite of the macroscopic nature of the game and absence of Planck's constant. A possible role of quantum logical lattices for the existence of macroscopic quantum equilibria is discussed. Some examples for spin-1 cases are also considered

Microscopic and macroscopic bell inequalities

International Nuclear Information System (INIS)

Santos, E.

1984-01-01

The Bell inequalities, being derived for micro-systems, cannot be tested by (macroscopic) experiments without additional assumptions. A macroscopic definition of local realism is proposed which might be the starting point for deriving Bell inequalities testable without auxiliary assumptions. (orig.)

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

International Nuclear Information System (INIS)

Elgart, Vlad; Jia, Tao; Fenley, Andrew T; Kulkarni, Rahul

2011-01-01

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 distribution. Additionally, if gene expression is repressed such that observed protein bursts arise only from single mRNAs, we show how observations of protein burst distributions (repressed and unrepressed) can be used to completely determine the mRNA burst distribution. Assuming independent contributions from individual bursts, we derive analytical expressions connecting means and variances for burst and steady-state protein distributions. Finally, we validate our general analytical results by considering a specific reaction scheme involving regulation of protein bursts by small RNAs. For a range of parameters, we derive analytical expressions for regulated protein distributions that are validated using stochastic simulations. The analytical results obtained in this work can thus serve as useful inputs for a broad range of studies focusing on stochasticity in gene expression

Quantum equilibria for macroscopic systems

Energy Technology Data Exchange (ETDEWEB)

Grib, A [Department of Theoretical Physics and Astronomy, Russian State Pedagogical University, St. Petersburg (Russian Federation); Khrennikov, A [Centre for Mathematical Modelling in Physics and Cognitive Sciences Vaexjoe University (Sweden); Parfionov, G [Department of Mathematics, St. Petersburg State University of Economics and Finances (Russian Federation); Starkov, K [Department of Mathematics, St. Petersburg State University of Economics and Finances (Russian Federation)

2006-06-30

Nash equilibria are found for some quantum games with particles with spin-1/2 for which two spin projections on different directions in space are measured. Examples of macroscopic games with the same equilibria are given. Mixed strategies for participants of these games are calculated using probability amplitudes according to the rules of quantum mechanics in spite of the macroscopic nature of the game and absence of Planck's constant. A possible role of quantum logical lattices for the existence of macroscopic quantum equilibria is discussed. Some examples for spin-1 cases are also considered.

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.

2009-10-28

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.

Phylogenetic distribution of plant snoRNA families.

Science.gov (United States)

Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie; Hertel, Jana; Grosse, Ivo; Stadler, Peter F

2016-11-24

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 snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. 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 snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.

The origins of macroscopic quantum coherence in high temperature superconductivity

International Nuclear Information System (INIS)

Turner, Philip; Nottale, Laurent

2015-01-01

Highlights: • We propose a new theoretical approach to superconductivity in p-type cuprates. • Electron pairing mechanisms in the superconducting and pseudogap phases are proposed. • A scale free network of dopants is key to macroscopic quantum coherence. - Abstract: A new, theoretical approach to macroscopic quantum coherence and superconductivity in the p-type (hole doped) cuprates is proposed. The theory includes mechanisms to account for e-pair coupling in the superconducting and pseudogap phases and their inter relations observed in these materials. Electron pair coupling in the superconducting phase is facilitated by local quantum potentials created by static dopants in a mechanism which explains experimentally observed optimal doping levels and the associated peak in critical temperature. By contrast, evidence suggests that electrons contributing to the pseudogap are predominantly coupled by fractal spin waves (fractons) induced by the fractal arrangement of dopants. On another level, the theory offers new insights into the emergence of a macroscopic quantum potential generated by a fractal distribution of dopants. This, in turn, leads to the emergence of coherent, macroscopic spin waves and a second associated macroscopic quantum potential, possibly supported by charge order. These quantum potentials play two key roles. The first involves the transition of an expected diffusive process (normally associated with Anderson localization) in fractal networks, into e-pair coherence. The second involves the facilitation of tunnelling between localized e-pairs. These combined effects lead to the merger of the super conducting and pseudo gap phases into a single coherent condensate at optimal doping. The underlying theory relating to the diffusion to quantum transition is supported by Coherent Random Lasing, which can be explained using an analogous approach. As a final step, an experimental program is outlined to validate the theory and suggests a new

Macroscopic constraints on string unification

International Nuclear Information System (INIS)

Taylor, T.R.

1989-03-01

The comparison of sting theory with experiment requires a huge extrapolation from the microscopic distances, of order of the Planck length, up to the macroscopic laboratory distances. The quantum effects give rise to large corrections to the macroscopic predictions of sting unification. I discus the model-independent constraints on the gravitational sector of string theory due to the inevitable existence of universal Fradkin-Tseytlin dilatons. 9 refs

Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex.

Science.gov (United States)

Xie, Ping

2015-10-09

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.

Models for universal reduction of macroscopic quantum fluctuations

International Nuclear Information System (INIS)

Diosi, L.

1988-10-01

If quantum mechanics is universal, then macroscopic bodies would, in principle, possess macroscopic quantum fluctuations (MQF) in their positions, orientations, densities etc. Such MQF, however, are not observed in nature. The hypothesis is adopted that the absence of MQF is due to a certain universal mechanism. Gravitational measures were applied for reducing MQF of the mass density. This model leads to classical trajectories in the macroscopic limit of translational motion. For massive objects, unwanted macroscopic superpositions of quantum states will be destroyed within short times. (R.P.) 34 refs

Interpretation of macroscopic quantum phenomena

International Nuclear Information System (INIS)

Baumann, K.

1986-01-01

It is argued that a quantum theory without observer is required for the interpretation of macroscopic quantum tunnelling. Such a theory is obtained by augmenting QED by the actual electric field in the rest system of the universe. An equation of the motion of this field is formulated form which the correct macroscopic behavior of the universe and the validity of the Born interpretation is derived. Care is taken to use mathematically sound concepts only. (Author)

The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

Science.gov (United States)

Jay, Zackary J; Inskeep, William P

2015-07-09

Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

Macroscopic theory of superconductors

International Nuclear Information System (INIS)

Carr, W.J. Jr.

1981-01-01

A macroscopic theory for bulk superconductors is developed in the framework of the theory for other magnetic materials, where ''magnetization'' current is separated from ''free'' current on the basis of scale. This contrasts with the usual separation into equilibrium and nonequilibrium currents. In the present approach magnetization, on a large macroscopic scale, results from the vortex current, while the Meissner current and other surface currents are surface contributions to the Maxwell j. The results are important for the development of thermodynamics in type-II superconductors. The advantage of the description developed here is that magnetization becomes a local concept and its associated magnetic field can be given physical meaning

Differential distribution of calcineurin Aα isoenzyme mRNA's in rat brain

NARCIS (Netherlands)

Buttini, M.; Limonta, S.; Luyten, M.; Boddeke, H.

1993-01-01

Specific antisense oligonucleotide probes for the α isoforms of the catalytic subunit (A-subunit) of calcineurin were prepared and the distribution of Aα1 and Aα2 mRNA's has been studied in rat brain using in situ hybridization histochemistry. Clear regional differences have been observed for the

Experimental demonstration of macroscopic quantum coherence in Gaussian states

DEFF Research Database (Denmark)

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

2007-01-01

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...

Macroscopic optical response and photonic bands

International Nuclear Information System (INIS)

Pérez-Huerta, J S; Luis Mochán, W; Ortiz, Guillermo P; Mendoza, Bernardo S

2013-01-01

We develop a formalism for the calculation of the macroscopic dielectric response of composite systems made of particles of one material embedded periodically within a matrix of another material, each of which is characterized by a well-defined dielectric function. The nature of these dielectric functions is arbitrary, and could correspond to dielectric or conducting, transparent or opaque, absorptive and dispersive materials. The geometry of the particles and the Bravais lattice of the composite are also arbitrary. Our formalism goes beyond the long-wavelength approximation as it fully incorporates retardation effects. We test our formalism through the study of the propagation of electromagnetic waves in two-dimensional photonic crystals made of periodic arrays of cylindrical holes in a dispersionless dielectric host. Our macroscopic theory yields a spatially dispersive macroscopic response which allows the calculation of the full photonic band structure of the system, as well as the characterization of its normal modes, upon substitution into the macroscopic field equations. We can also account approximately for the spatial dispersion through a local magnetic permeability and analyze the resulting dispersion relation, obtaining a region of left handedness. (paper)

Random generation of RNA secondary structures according to native distributions

Directory of Open Access Journals (Sweden)

Nebel Markus E

2011-10-01

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

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

OpenAIRE

León M., Eric; Sato S., Alberto; Navarrete Z., Miluska; Cisneros S., Jannet

2011-01-01

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...

Maximum Entropy Methods as the Bridge Between Microscopic and Macroscopic Theory

Science.gov (United States)

Taylor, Jamie M.

2016-09-01

This paper is concerned with an investigation into a function of macroscopic variables known as the singular potential, building on previous work by Ball and Majumdar. The singular potential is a function of the admissible statistical averages of probability distributions on a state space, defined so that it corresponds to the maximum possible entropy given known observed statistical averages, although non-classical entropy-like objective functions will also be considered. First the set of admissible moments must be established, and under the conditions presented in this work the set is open, bounded and convex allowing a description in terms of supporting hyperplanes, which provides estimates on the development of singularities for related probability distributions. Under appropriate conditions it is shown that the singular potential is strictly convex, as differentiable as the microscopic entropy, and blows up uniformly as the macroscopic variable tends to the boundary of the set of admissible moments. Applications of the singular potential are then discussed, and particular consideration will be given to certain free-energy functionals typical in mean-field theory, demonstrating an equivalence between certain microscopic and macroscopic free-energy functionals. This allows statements about L^1-local minimisers of Onsager's free energy to be obtained which cannot be given by two-sided variations, and overcomes the need to ensure local minimisers are bounded away from zero and +∞ before taking L^∞ variations. The analysis also permits the definition of a dual order parameter for which Onsager's free energy allows an explicit representation. Also, the difficulties in approximating the singular potential by everywhere defined functions, in particular by polynomial functions, are addressed, with examples demonstrating the failure of the Taylor approximation to preserve relevant shape properties of the singular potential.

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

2016-01-01

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...

Influence of microscopic inhomogeneity on macroscopic transport current of Ag/Bi2223 tapes

International Nuclear Information System (INIS)

Ogawa, Kazuhiro; Osamura, Kozo

2004-01-01

In Ag/Bi2223 tapes, inhomogeneities such as spatially distributed weak links or non-superconducting oxides are inevitably introduced because of the complicated manufacturing process and thermodynamic instability. In order to clarify the effect of the difference in such microscopic inhomogeneites on the macroscopic current transport properties, we carried out a numerical analysis. By changing volume fraction (V f ) of the Bi2223 phase and the shape of local distribution of critical current at each weak link, it is revealed that I-V characteristics are largely affected by the breadth of local distributions with different dependence on V f of Bi2223 and calculated results can be analyzed by Weibull distribution function with some parameters including the information of two-dimensional distribution

Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression.

Science.gov (United States)

Stinchcombe, Adam R; Peskin, Charles S; Tranchina, Daniel

2012-06-01

We present a generalization of a population density approach for modeling and analysis of stochastic gene expression. In the model, the gene of interest fluctuates stochastically between an inactive state, in which transcription cannot occur, and an active state, in which discrete transcription events occur; and the individual mRNA molecules are degraded stochastically in an independent manner. This sort of model in simplest form with exponential dwell times has been used to explain experimental estimates of the discrete distribution of random mRNA copy number. In our generalization, the random dwell times in the inactive and active states, T_{0} and T_{1}, respectively, are independent random variables drawn from any specified distributions. Consequently, the probability per unit time of switching out of a state depends on the time since entering that state. Our method exploits a connection between the fully discrete random process and a related continuous process. We present numerical methods for computing steady-state mRNA distributions and an analytical derivation of the mRNA autocovariance function. We find that empirical estimates of the steady-state mRNA probability mass function from Monte Carlo simulations of laboratory data do not allow one to distinguish between underlying models with exponential and nonexponential dwell times in some relevant parameter regimes. However, in these parameter regimes and where the autocovariance function has negative lobes, the autocovariance function disambiguates the two types of models. Our results strongly suggest that temporal data beyond the autocovariance function is required in general to characterize gene switching.

RNA Microarray Analysis of Macroscopically Normal Articular Cartilage from Knees Undergoing Partial Medial Meniscectomy: Potential Prediction of the Risk for Developing Osteoarthritis.

Directory of Open Access Journals (Sweden)

Muhammad Farooq Rai

Full Text Available (i To provide baseline knowledge of gene expression in macroscopically normal articular cartilage, (ii to test the hypothesis that age, body-mass-index (BMI, and sex are associated with cartilage RNA transcriptome, and (iii to predict individuals at potential risk for developing "pre-osteoarthritis" (OA based on screening of genetic risk-alleles associated with OA and gene transcripts differentially expressed between normal and OA cartilage.Healthy-appearing cartilage was obtained from the medial femoral notch of 12 knees with a meniscus tear undergoing arthroscopic partial meniscectomy. Cartilage had no radiographic, magnetic-resonance-imaging or arthroscopic evidence for degeneration. RNA was subjected to Affymetrix microarrays followed by validation of selected transcripts by microfluidic digital polymerase-chain-reaction. The underlying biological processes were explored computationally. Transcriptome-wide gene expression was probed for association with known OA genetic risk-alleles assembled from published literature and for comparison with gene transcripts differentially expressed between healthy and OA cartilage from other studies.We generated a list of 27,641 gene transcripts in healthy cartilage. Several gene transcripts representing numerous biological processes were correlated with age and BMI and differentially expressed by sex. Based on disease-specific Ingenuity Pathways Analysis, gene transcripts associated with aging were enriched for bone/cartilage disease while the gene expression profile associated with BMI was enriched for growth-plate calcification and OA. When segregated by genetic risk-alleles, two clusters of study patients emerged, one cluster containing transcripts predicted by risk studies. When segregated by OA-associated gene transcripts, three clusters of study patients emerged, one of which is remarkably similar to gene expression pattern in OA.Our study provides a list of gene transcripts in healthy

Macroscopic Optomechanically Induced Transparency

Science.gov (United States)

Pate, Jacob; Castelli, Alessandro; Martinez, Luis; Thompson, Johnathon; Chiao, Ray; Sharping, Jay

Optomechanically induced transparency (OMIT) is an effect wherein the spectrum of a cavity resonance is modified through interference between coupled excitation pathways. In this work we investigate a macroscopic, 3D microwave, superconducting radio frequency (SRF) cavity incorporating a niobium-coated, silicon-nitride membrane as the flexible boundary. The boundary supports acoustic vibrational resonances, which lead to coupling with the microwave resonances of the SRF cavity. The theoretical development and physical understanding of OMIT for our macroscopic SRF cavity is the same as that for other recently-reported OMIT systems despite vastly different optomechanical coupling factors and device sizes. Our mechanical oscillator has a coupling factor of g0 = 2 π . 1 ×10-5 Hz and is roughly 38 mm in diameter. The Q = 5 ×107 for the SRF cavity allows probing of optomechanical effects in the resolved sideband regime.

Macroscopic averages in Qed in material media

International Nuclear Information System (INIS)

Dutra, S.M.; Furuya, K.

1997-01-01

The starting point of macroscopic theories of quantum electrodynamics in material media is usually the classical macroscopic Maxwell equations that are then quantized. Such approach however, is based on the assumption that a macroscopic description is attainable, i.e., it assumes that we can describe the effect of the atoms of material on the field only in terms of a dielectric constant in the regime where the field has to be treated quantum mechanically. The problem we address is whether this assumption is valid at all and if so, under what conditions. We have chosen a simple model, which allows us to start from first principles and determine the validity of these approximations, without simply taking them for granted as in previous papers

Dynamical fusion thresholds in macroscopic and microscopic theories

International Nuclear Information System (INIS)

Davies, K.T.R.; Sierk, A.J.; Nix, J.R.

1983-01-01

Macroscopic and microscopic results demonstrating the existence of dynamical fusion thresholds are presented. For macroscopic theories, it is shown that the extra-push dynamics is sensitive to some details of the models used, e.g. the shape parametrization and the type of viscosity. The dependence of the effect upon the charge and angular momentum of the system is also studied. Calculated macroscopic results for mass-symmetric systems are compared to experimental mass-asymmetric results by use of a tentative scaling procedure, which takes into account both the entrance-channel and the saddle-point regions of configuration space. Two types of dynamical fusion thresholds occur in TDHF studies: (1) the microscopic analogue of the macroscopic extra push threshold, and (2) the relatively high energy at which the TDHF angular momentum window opens. Both of these microscopic thresholds are found to be very sensitive to the choice of the effective two-body interaction

Macroscopic quantum tunneling in Mn12-acetat

International Nuclear Information System (INIS)

Beiter, J.; Reissner, M.; Hilscher, G.; Steiner, W.; Pajic, D.; Zadro, K.; Bartel, M.; Linert, W.

2004-01-01

Molecules provide the exciting opportunity to study magnetism on the passage from atomic to macroscopic level. One of the most interesting effects in such mesoscopic systems is the appearance of quantum tunnelling of magnetization (MQT) at low temperatures. In the last decade molecular chemistry has had a large impact in this field by providing new single molecule magnets. They consist of small clusters exhibiting superparamagnetic behavior, similar to that of conventional nanomagnetic particles. The advantage of these new materials is that they form macroscopic samples consisting of regularly arranged small identical high-spin clusters which are widely separated by organic molecules. The lack of distributions in size and shape of the magnetic clusters and the very weak intercluster interaction lead in principle to only one barrier for the spin reversal. We present detailed magnetic investigations on a Mn 12 -ac single crystal. In this compound the tetragonal ordered clusters consist of a central tetrahedron of four Mn 4+ (S = 3/2) atoms surrounded by eight Mn 3+ (S = 2) atoms with antiparallel oriented spins, leading to an overall spin moment of S = 10. In the hysteresis loops nine different jumps at regularly spaced fields are identified in the investigated temperature range (1.5 < T < 3 K). At these fields the relaxation of moment due to thermal activation is superimposed by strong quantum tunnelling. In lowering the temperature the time dependence changes from thermally activated to thermally assisted tunnelling. (author)

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

Directory of Open Access Journals (Sweden)

Rui Soares Barbosa

2014-12-01

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.

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)

2016-05-15

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.

Macroscopic relationship in primal-dual portfolio optimization problem

Science.gov (United States)

Shinzato, Takashi

2018-02-01

In the present paper, using a replica analysis, we examine the portfolio optimization problem handled in previous work and discuss the minimization of investment risk under constraints of budget and expected return for the case that the distribution of the hyperparameters of the mean and variance of the return rate of each asset are not limited to a specific probability family. Findings derived using our proposed method are compared with those in previous work to verify the effectiveness of our proposed method. Further, we derive a Pythagorean theorem of the Sharpe ratio and macroscopic relations of opportunity loss. Using numerical experiments, the effectiveness of our proposed method is demonstrated for a specific situation.

Phylogenetic distribution of plant snoRNA families

DEFF Research Database (Denmark)

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

2016-01-01

RNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied...... in much detail. In plants, however, their evolution has attracted comparably little attention. RESULTS: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom....... In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant...

Macroscopic magnetic Self assembly

NARCIS (Netherlands)

Löthman, Per Arvid

2018-01-01

Exploring the macroscopic scale's similarities to the microscale is part and parcel of this thesis as reflected in the research question: what can we learn about the microscopic scale by studying the macroscale? Investigations of the environment in which the self-assembly takes place, and the

Macroscopic effects in attosecond pulse generation

International Nuclear Information System (INIS)

Ruchon, T; Varju, K; Mansten, E; Swoboda, M; L'Huillier, A; Hauri, C P; Lopez-Martens, R

2008-01-01

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

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: anne.lhuillier@fysik.lth.se

2008-02-15

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.

Decoherence bypass of macroscopic superpositions in quantum measurement

International Nuclear Information System (INIS)

Spehner, Dominique; Haake, Fritz

2008-01-01

We study a class of quantum measurement models. A microscopic object is entangled with a macroscopic pointer such that a distinct pointer position is tied to each eigenvalue of the measured object observable. Those different pointer positions mutually decohere under the influence of an environment. Overcoming limitations of previous approaches we (i) cope with initial correlations between pointer and environment by considering them initially in a metastable local thermal equilibrium, (ii) allow for object-pointer entanglement and environment-induced decoherence of distinct pointer readouts to proceed simultaneously, such that mixtures of macroscopically distinct object-pointer product states arise without intervening macroscopic superpositions, and (iii) go beyond the Markovian treatment of decoherence. (fast track communication)

Quantum laws of the microworld and the wealth of macroscopic structures

International Nuclear Information System (INIS)

Noga, M.

2000-01-01

The reasons are highlighted why classical physics was unable to explain the formation of any collective self-organized arrangement such as magnetism and how the wealth of macroscopic self-organized structures emerges spontaneously from quantum theory applied to the given physical system. This is demonstrated on the simplest multi-electron system, viz. the model of a metal as electron gas with Coulomb interaction with a background of homogeneously distributed positive charge possessing a constant density so as to ensure charge neutrality of the system

Nonequilibrium work relation in a macroscopic system

International Nuclear Information System (INIS)

Sughiyama, Yuki; Ohzeki, Masayuki

2013-01-01

We reconsider a well-known relationship between the fluctuation theorem and the second law of thermodynamics by evaluating stochastic evolution of the density field (probability measure valued process). In order to establish a bridge between microscopic and macroscopic behaviors, we must take the thermodynamic limit of a stochastic dynamical system following the standard procedure in statistical mechanics. The thermodynamic path characterizing a dynamical behavior in the macroscopic scale can be formulated as an infimum of the action functional for the stochastic evolution of the density field. In our formulation, the second law of thermodynamics can be derived only by symmetry of the action functional without recourse to the Jarzynski equality. Our formulation leads to a nontrivial nonequilibrium work relation for metastable (quasi-stationary) states, which are peculiar in the macroscopic system. We propose a prescription for computing the free energy for metastable states based on the resultant work relation. (paper)

Pathways toward understanding Macroscopic Quantum Phenomena

International Nuclear Information System (INIS)

Hu, B L; Subaşi, Y

2013-01-01

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

Macroscopic nonclassical-state preparation via postselection

Science.gov (United States)

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

2017-11-01

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.

Classical behaviour of macroscopic bodies and quantum measurements

International Nuclear Information System (INIS)

Ghirardi, G.; Rimini, A.; Weber, T.

1986-01-01

This report describes a recent attempt of giving a consistent and unified description of microscopic and macroscopic phenomena. The model presented in this paper exhibits the nice features of leaving unaltered the quantum description of microsystems and of accounting for the classical behaviour of the macroscopic objects when their dynamical evolution is consistently deduced from the dynamics of their elementary constituents

Assessments of macroscopicity for quantum optical states

DEFF Research Database (Denmark)

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

2015-01-01

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....

Nuclear fission as a macroscopic quantum tunneling

International Nuclear Information System (INIS)

Takigawa, N.

1995-01-01

We discuss nuclear fission from the point of view of a macroscopic quantum tunneling, one of whose major interests is to study the effects of environments on the tunneling rate of a macroscopic variable. We show that a vibrational excitation of the fissioning nucleus significantly enhances the fission rate. We show this effect by two different methods. The one is to treat the vibrational excitation as an environmental degree of freedom, the other treats the fission as a two dimensional quantum tunneling. (author)

Conversion of light into macroscopic helical motion

Science.gov (United States)

Iamsaard, Supitchaya; Aßhoff, Sarah J.; Matt, Benjamin; Kudernac, Tibor; Cornelissen, Jeroen J. L. M.; Fletcher, Stephen P.; Katsonis, Nathalie

2014-03-01

A key goal of nanotechnology is the development of artificial machines capable of converting molecular movement into macroscopic work. Although conversion of light into shape changes has been reported and compared to artificial muscles, real applications require work against an external load. Here, we describe the design, synthesis and operation of spring-like materials capable of converting light energy into mechanical work at the macroscopic scale. These versatile materials consist of molecular switches embedded in liquid-crystalline polymer springs. In these springs, molecular movement is converted and amplified into controlled and reversible twisting motions. The springs display complex motion, which includes winding, unwinding and helix inversion, as dictated by their initial shape. Importantly, they can produce work by moving a macroscopic object and mimicking mechanical movements, such as those used by plant tendrils to help the plant access sunlight. These functional materials have potential applications in micromechanical systems, soft robotics and artificial muscles.

Structured pathology reporting improves the macroscopic assessment of rectal tumour resection specimens.

Science.gov (United States)

King, Simon; Dimech, Margaret; Johnstone, Susan

2016-06-01

We examined whether introduction of a structured macroscopic reporting template for rectal tumour resection specimens improved the completeness and efficiency in collecting key macroscopic data elements. Fifty free text (narrative) macroscopic reports retrieved from 2012 to 2014 were compared with 50 structured macroscopic reports from 2013 to 2015, all of which were generated at John Hunter Hospital, Newcastle, NSW. The six standard macroscopic data elements examined in this study were reported in all 50 anatomical pathology reports using a structured macroscopic reporting dictation template. Free text reports demonstrated significantly impaired data collection when recording intactness of mesorectum (p<0.001), relationship to anterior peritoneal reflection (p=0.028) and distance of tumour to the non-peritonealised circumferential margin (p<0.001). The number of words used was also significantly (p<0.001) reduced using pre-formatted structured reports compared to free text reports. The introduction of a structured reporting dictation template improves data collection and may reduce the subsequent administrative burden when macroscopically evaluating rectal resections. Copyright © 2016 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.

Superconductivity and macroscopic quantum phenomena

International Nuclear Information System (INIS)

Rogovin, D.; Scully, M.

1976-01-01

It is often asserted that superconducting systems are manifestations of quantum mechanics on a macroscopic scale. In this review article it is demonstrated that this quantum assertion is true within the framework of the microscopic theory of superconductivity. (Auth.)

Macroscopic quantum tunnelling in a current biased Josephson junction

International Nuclear Information System (INIS)

Martinis, J.M.; Devoret, M.H.; Clarke, J.; Urbina, C.

1984-11-01

We discuss in this work an attempt to answer experimentally the question: do macroscopic variables obey quantum mechanics. More precisely, this experiment deals with the question of quantum-mechanical tunnelling of a macroscopic variable, a subject related to the famous Schrodinger's cat problem in the theory of measurement

Physically-based modeling of the cyclic macroscopic behaviour of metals

International Nuclear Information System (INIS)

Sauzay, M.; Evrard, P.; Steckmeyer, A.; Ferrie, E.

2010-01-01

Grain size seems to have only a minor influence on the cyclic strain strain curves (CSSCs) of metallic polycrystals of medium to high stacking fault energy (SFE). That is why many authors tried to deduce the macroscopic CSSCs curves from the single crystals ones. Either crystals oriented for single slip or crystals oriented for multiple slip could be considered. In addition, a scale transition law should be used (from the grain scale to the macroscopic scale). Authors generally used either the Sachs rule (homogeneous single slip) or the Taylor one (homogeneous plastic strain, multiple slip). But the predicted macroscopic CSSCs do not generally agree with the experimental data for metals and alloys, presenting various SFE values. In order to avoid the choice of a particular scale transition rule, many finite element (FE) computations have been carried out using meshes of polycrystals including more than one hundred grains without texture. This allows the study of the influence of the crystalline constitutive laws on the macroscopic CSSCs. Activation of a secondary slip system in grains oriented for single slip is either allowed or hindered (slip planarity), which affects strongly the macroscopic CSSCs. The more planar the slip, the higher the predicted macroscopic stress amplitudes. If grains oriented for single slip obey slip planarity and two crystalline CSSCs are used (one for single slip grains and one for multiple slip grains), then the predicted macroscopic CSSCs agree well with experimental data provided the SFE is not too low (316L, copper, nickel, aluminium). Finally, the incremental self-consistent Hill-Hutchinson homogenization model is used for predicting CSS curves and partially validated with respect to the curves computed by the FE method. (authors)

Macroscopic Quantum Resonators (MAQRO): 2015 update

International Nuclear Information System (INIS)

Kaltenbaek, Rainer; Aspelmeyer, Markus; Kiesel, Nikolai; Barker, Peter F.; Bose, Sougato; Bassi, Angelo; Bateman, James; Bongs, Kai; Cruise, Adrian Michael; Braxmaier, Claus; Brukner, Caslav; Christophe, Bruno; Rodrigues, Manuel; Chwalla, Michael; Johann, Ulrich; Cohadon, Pierre-Francois; Heidmann, Antoine; Lambrecht, Astrid; Reynaud, Serge; Curceanu, Catalina; Dholakia, Kishan; Mazilu, Michael; Diosi, Lajos; Doeringshoff, Klaus; Peters, Achim; Ertmer, Wolfgang; Rasel, Ernst M.; Gieseler, Jan; Novotny, Lukas; Rondin, Loic; Guerlebeck, Norman; Herrmann, Sven; Laemmerzahl, Claus; Hechenblaikner, Gerald; Hossenfelder, Sabine; Kim, Myungshik; Milburn, Gerard J.; Mueller, Holger; Paternostro, Mauro; Pikovski, Igor; Pilan Zanoni, Andre; Riedel, Charles Jess; Roura, Albert; Schleich, Wolfgang P.; Schmiedmayer, Joerg; Schuldt, Thilo; Schwab, Keith C.; Tajmar, Martin; Tino, Guglielmo M.; Ulbricht, Hendrik; Ursin, Rupert; Vedral, Vlatko

2016-01-01

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.)

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)

2016-12-15

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.)

A Review on Macroscopic Pedestrian Flow Modelling

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Anna Kormanová

2013-12-01

Full Text Available This paper reviews several various approaches to macroscopic pedestrian modelling. It describes hydrodynamic models based on similarity of pedestrian flow with fluids and gases; first-order flow models that use fundamental diagrams and conservation equation; and a model similar to LWR vehicular traffic model, which allows non-classical shocks. At the end of the paper there is stated a comparison of described models, intended to find appropriate macroscopic model to eventually be a part of a hybrid model. The future work of the author is outlined.

How the macroscopic current correlates with the microscopic flux-line distribution in a type-II superconductor: an experimental study

International Nuclear Information System (INIS)

Hecher, Johannes; Zehetmayer, Martin; Weber, Harald W

2014-01-01

We present a study of the real-space flux-line lattice (FLL) of pristine and neutron irradiated conventional type-II superconductors using scanning tunnelling microscopy. Our work is focused on the magnetic field range, where the critical current density shows a second peak as a result of neutron irradiation. Scanning tunnelling microscopy images, including more than 2000 flux lines, are used to evaluate various microscopic parameters describing the disorder of the FLL, such as the defect density, the nearest neighbour distances and correlation functions. These parameters are compared with the macroscopic critical current density of the samples. The results show a direct correlation of the micro- and macroscopic properties. We observe a clear transition from an ordered to a disordered lattice at the onset of the second peak. Moreover, we discuss the defects of the FLL and their accumulation to large clusters in the second peak region. (papers)

Microscopic to macroscopic depletion model development for FORMOSA-P

International Nuclear Information System (INIS)

Noh, J.M.; Turinsky, P.J.; Sarsour, H.N.

1996-01-01

Microscopic depletion has been gaining popularity with regard to employment in reactor core nodal calculations, mainly attributed to the superiority of microscopic depletion in treating spectral history effects during depletion. Another trend is the employment of loading pattern optimization computer codes in support of reload core design. Use of such optimization codes has significantly reduced design efforts to optimize reload core loading patterns associated with increasingly complicated lattice designs. A microscopic depletion model has been developed for the FORMOSA-P pressurized water reactor (PWR) loading pattern optimization code. This was done for both fidelity improvements and to make FORMOSA-P compatible with microscopic-based nuclear design methods. Needless to say, microscopic depletion requires more computational effort compared with macroscopic depletion. This implies that microscopic depletion may be computationally restrictive if employed during the loading pattern optimization calculation because many loading patterns are examined during the course of an optimization search. Therefore, the microscopic depletion model developed here uses combined models of microscopic and macroscopic depletion. This is done by first performing microscopic depletions for a subset of possible loading patterns from which 'collapsed' macroscopic cross sections are obtained. The collapsed macroscopic cross sections inherently incorporate spectral history effects. Subsequently, the optimization calculations are done using the collapsed macroscopic cross sections. Using this approach allows maintenance of microscopic depletion level accuracy without substantial additional computing resources

Active Polar Two-Fluid Macroscopic Dynamics

Science.gov (United States)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

On Macroscopic Quantum Phenomena in Biomolecules and Cells: From Levinthal to Hopfield

Directory of Open Access Journals (Sweden)

Dejan Raković

2014-01-01

Full Text Available 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 (semiclassically 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.

Automatic macroscopic characterization of diesel sprays by means of a new image processing algorithm

Science.gov (United States)

Rubio-Gómez, Guillermo; Martínez-Martínez, S.; Rua-Mojica, Luis F.; Gómez-Gordo, Pablo; de la Garza, Oscar A.

2018-05-01

A novel algorithm is proposed for the automatic segmentation of diesel spray images and the calculation of their macroscopic parameters. The algorithm automatically detects each spray present in an image, and therefore it is able to work with diesel injectors with a different number of nozzle holes without any modification. The main characteristic of the algorithm is that it splits each spray into three different regions and then segments each one with an individually calculated binarization threshold. Each threshold level is calculated from the analysis of a representative luminosity profile of each region. This approach makes it robust to irregular light distribution along a single spray and between different sprays of an image. Once the sprays are segmented, the macroscopic parameters of each one are calculated. The algorithm is tested with two sets of diesel spray images taken under normal and irregular illumination setups.

Macroscopic erosion of divertor and first wall armour in future tokamaks

Science.gov (United States)

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

2002-12-01

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.

Macroscopic erosion of divertor and first wall armour in future tokamaks

International Nuclear Information System (INIS)

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

2002-01-01

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

Macroscopic and non-linear quantum games

International Nuclear Information System (INIS)

Aerts, D.; D'Hooghe, A.; Posiewnik, A.; Pykacz, J.

2005-01-01

Full text: We consider two models of quantum games. The first one is Marinatto and Weber's 'restricted' quantum game in which only the identity and the spin-flip operators are used. We show that this quantum game allows macroscopic mechanistic realization with the use of a version of the 'macroscopic quantum machine' described by Aerts already in 1980s. In the second model we use non-linear quantum state transformations which operate on points of spin-1/2 on the Bloch sphere and which can be used to distinguish optimally between two non-orthogonal states. We show that efficiency of these non-linear strategies out-perform any linear ones. Some hints on the possible theory of non-linear quantum games are given. (author)

Macroscopic quantum phenomena from the large N perspective

International Nuclear Information System (INIS)

Chou, C H; Hu, B L; Subasi, Y

2011-01-01

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 there is no a priori

Cloud Macroscopic Organization: Order Emerging from Randomness

Science.gov (United States)

Yuan, Tianle

2011-01-01

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.

Macroscopic models for traffic safety.

NARCIS (Netherlands)

Oppe, S.

1988-01-01

Recently there has been an increased interest in the application of macroscopic models for the description of developments in traffic safety. A discussion was started on the causes of the sudden decrease in the number of fatal and injury accidents after 1974. Before that time these numbers had

antaRNA: ant colony-based RNA sequence design.

Science.gov (United States)

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

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

2000-07-01

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.)

Docosahexaenoic Acid Conjugation Enhances Distribution and Safety of siRNA upon Local Administration in Mouse Brain

Directory of Open Access Journals (Sweden)

Mehran Nikan

2016-01-01

Full Text Available The use of siRNA-based therapies for the treatment of neurodegenerative disease requires efficient, nontoxic distribution to the affected brain parenchyma, notably the striatum and cortex. Here, we describe the synthesis and activity of a fully chemically modified siRNA that is directly conjugated to docosahexaenoic acid (DHA, the most abundant polyunsaturated fatty acid in the mammalian brain. DHA conjugation enables enhanced siRNA retention throughout both the ipsilateral striatum and cortex following a single, intrastriatal injection (ranging from 6–60 μg. Within these tissues, DHA conjugation promotes internalization by both neurons and astrocytes. We demonstrate efficient and specific silencing of Huntingtin mRNA expression in both the ipsilateral striatum (up to 73% and cortex (up to 51% after 1 week. Moreover, following a bilateral intrastriatal injection (60 μg, we achieve up to 80% silencing of a secondary target, Cyclophilin B, at both the mRNA and protein level. Importantly, DHA-hsiRNAs do not induce neural cell death or measurable innate immune activation following administration of concentrations over 20 times above the efficacious dose. Thus, DHA conjugation is a novel strategy for improving siRNA activity in mouse brain, with potential to act as a new therapeutic platform for the treatment of neurodegenerative disorders.

Thermal activation and macroscopic quantum tunneling in a DC SQUID

International Nuclear Information System (INIS)

Sharifi, F.; Gavilano, J.L.; VanHarlingen, D.J.

1989-01-01

The authors report measurements of the transition rate from metastable minima in the two-dimensional 1 of a dc SQUID as a function of applied flux temperature. The authors observe a crossover from energy-activated escape to macroscopic quantum tunneling at a critical temperature. The macroscopic quantum tunneling rate is substantially reduced by damping, and also broadens the crossover region. Most interestingly, the authors observe thermal rates that are suppressed from those predicted by the two-dimensional thermal activation model. The authors discuss possible explanations for this based on the interaction of the macroscopic degree of freedom in the device and energy level effects

Averaging problem in general relativity, macroscopic gravity and using Einstein's equations in cosmology.

Science.gov (United States)

Zalaletdinov, R. M.

1998-04-01

The averaging problem in general relativity is briefly discussed. A new setting of the problem as that of macroscopic description of gravitation is proposed. A covariant space-time averaging procedure is described. The structure of the geometry of macroscopic space-time, which follows from averaging Cartan's structure equations, is described and the correlation tensors present in the theory are discussed. The macroscopic field equations (averaged Einstein's equations) derived in the framework of the approach are presented and their structure is analysed. The correspondence principle for macroscopic gravity is formulated and a definition of the stress-energy tensor for the macroscopic gravitational field is proposed. It is shown that the physical meaning of using Einstein's equations with a hydrodynamic stress-energy tensor in looking for cosmological models means neglecting all gravitational field correlations. The system of macroscopic gravity equations to be solved when the correlations are taken into consideration is given and described.

Prediction of macroscopic and local stress-strain behaviors of perforated plates under primary and secondary creep conditions

International Nuclear Information System (INIS)

Igari, Toshihide; Tokiyoshi, Takumi; Mizokami, Yorikata

2000-01-01

Prediction methods of macroscopic and local creep behaviors of perforated plates are examined in order to apply these methods to the structural design of perforated structures such as heat exchangers used in elevated temperatures. Both primary and secondary creeps are considered for predicting macroscopic and local creep behaviors of perorated plates which are made of actual structural materials. Both uniaxial and multiaxial loading of perforated plates are taken into consideration. The concept of effective stress is applied to the prediction of macroscopic creep behaviors of perforated plates, and the predicted results are compared with the numerical results by FEM for the unit section of perorated plated under creep, in order to confirm the propriety of the proposed method. Based on the idea that stress exponents in creep equations govern the stress distribution of perforated plates, a modified Neuber's rule is used for predicting local stress and strain concentrations. The propriety of this prediction method is shown through a comparison of the prediction with the numerical results by FEM for the unit section of perforated plates under creep, and experimental results by the Moire method. (author)

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

DEFF Research Database (Denmark)

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

2014-01-01

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...

Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.

Science.gov (United States)

Awazu, Akinori; Tanabe, Takahiro; Kamitani, Mari; Tezuka, Ayumi; Nagano, Atsushi J

2018-05-29

Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a feedback loop. The fitting function suggested that gene expression levels with long-tailed ePDFs would be strongly influenced by feedback regulation. Furthermore, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian-like ePDF while those of genes encoding nucleic acid-binding proteins and transcription factors exhibit long-tailed ePDF.

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

Directory of Open Access Journals (Sweden)

Yang eLiu

2015-09-01

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.

Effect of texture on grain boundary misorientation distributions in polycrystalline high temperature superconductors

International Nuclear Information System (INIS)

Goyal, A.; Specht, E.D.; Kroeger, D.M.; Mason, T.A.

1996-01-01

Computer simulations were performed to determine the most probable grain boundary misorientation distribution (GBMD) in model polycrystalline superconductors. GBMDs in polycrystalline superconductors can be expected to dictate the macroscopic transport critical current density, J c . Calculations were performed by simulating model polycrystals and then determining the GBMD. Such distributions were calculated for random materials having cubic, tetragonal, and orthorhombic crystal symmetry. In addition, since most high temperature superconductors are tetragonal or pseudotetragonal, the effect of macroscopic uniaxial and biaxial grain orientation texture on the GBMD was determined for tetragonal materials. It is found that macroscopic texture drastically alters the grain boundary misorientation distribution. The fraction of low angle boundaries increases significantly with uniaxial and biaxial texture. The results of this study are important in correlating the macroscopic transport J c with the measured grain orientation texture as determined by x-ray diffraction copyright 1996 American Institute of Physics

Bimodality in macroscopic dynamics of nuclear fission

International Nuclear Information System (INIS)

Bastrukov, S.I.; Salamatin, V.S.; Strteltsova, O.I.; Molodtsova, I.V.; Podgainy, D.V.; )

2000-01-01

The elastodynamic collective model of nuclear fission is outlined whose underlying idea is that the stiff structure of nuclear shells imparts to nucleus properties typical of a small piece of an elastic solid. Emphasis is placed on the macroscopic dynamics of nuclear deformations resulting in fission by two energetically different modes. The low-energy S-mode is the fission due to disruption of elongated quadrupole spheroidal shape. The characteristic features of the high-energy T-mode of division by means of torsional shear deformations is the compact scission configuration. Analytic and numerical estimates for the macroscopic fission-barrier heights are presented, followed by discussion of fingerprints of the above dynamical bimodality in the available data [ru

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

Regularized κ-distributions with non-diverging moments

Science.gov (United States)

Scherer, K.; Fichtner, H.; Lazar, M.

2017-12-01

For various plasma applications the so-called (non-relativistic) κ-distribution is widely used to reproduce and interpret the suprathermal particle populations exhibiting a power-law distribution in velocity or energy. Despite its reputation the standard κ-distribution as a concept is still disputable, mainly due to the velocity moments M l which make a macroscopic characterization possible, but whose existence is restricted only to low orders l definition of the κ-distribution itself is conditioned by the existence of the moment of order l = 2 (i.e., kinetic temperature) satisfied only for κ > 3/2 . In order to resolve these critical limitations we introduce the regularized κ-distribution with non-diverging moments. For the evaluation of all velocity moments a general analytical expression is provided enabling a significant step towards a macroscopic (fluid-like) description of space plasmas, and, in general, any system of κ-distributed particles.

Stochastic and Macroscopic Thermodynamics of Strongly Coupled Systems

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Christopher Jarzynski

2017-01-01

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.

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.

Science.gov (United States)

Mann, Martin; Wright, Patrick R; Backofen, Rolf

2017-07-03

The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

From microscopic taxation and redistribution models to macroscopic income distributions

Science.gov (United States)

Bertotti, Maria Letizia; Modanese, Giovanni

2011-10-01

We present here a general framework, expressed by a system of nonlinear differential equations, suitable for the modeling of taxation and redistribution in a closed society. This framework allows one to describe the evolution of income distribution over the population and to explain the emergence of collective features based on knowledge of the individual interactions. By making different choices of the framework parameters, we construct different models, whose long-time behavior is then investigated. Asymptotic stationary distributions are found, which enjoy similar properties as those observed in empirical distributions. In particular, they exhibit power law tails of Pareto type and their Lorenz curves and Gini indices are consistent with some real world ones.

Microscopic and macroscopic models for the onset and progression of Alzheimer's disease

Science.gov (United States)

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

2017-10-01

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

Macroscopic realism and quantum measurement: measurers as a natural kind

International Nuclear Information System (INIS)

Jaeger, Gregg

2014-01-01

The notion of macroscopic realism has been used in attempts to achieve consistency between physics and everyday experience and to locate some boundary between the realms of classical mechanics and quantum meachanics. Its ostensibly underlying conceptual components, realism and macroscopicity, have most often appeared in the foundations of physics in relation to quantum measurement: reality became a prominent topic of discussion in quantum physics after the notion of element of reality was defined and used by Einstein, Podolsky and Rosen in that context, and macroscopicity is often explicitly assumed to be an essential property of any measuring apparatus. However, macroscopicity turns out to be a rather vaguer and less consistently understood notion than typically assumed by physicists who have not explicitly explored the notion themselves. For this reason, it behooves those investigating the foundations of quantum mechanics from a realist perspective to look for alternative notions for grounding quantum measurement. Here, the merits of treating the measuring instrument as a ‘natural kind’ as a means of avoiding anthropocentrism in the foundations of quantum measurement are pointed out as a means of advancing quantum measurement theory. (paper)

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales.

Science.gov (United States)

Huang, Shiping

2017-11-13

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.

Role of stochastic fluctuations in the charge on macroscopic particles in dusty plasmas

International Nuclear Information System (INIS)

Vaulina, O.S.; Nefedov, A.P.; Petrov, O.F.; Khrapak, S.A.

1999-01-01

The currents which charge a macroscopic particle placed in a plasma consist of discrete charges; hence, the charge can undergo random fluctuations about its equilibrium value. These random fluctuations can be described by a simple model which, if the mechanisms for charging of macroscopic particles are known, makes it possible to determine the dependence of the temporal and amplitude characteristics of the fluctuations on the plasma parameters. This model can be used to study the effect of charge fluctuations on the dynamics of the macroscopic particles. The case of so-called plasma-dust crystals (i.e., highly ordered structures which develop because of strong interactions among macroscopic particles) in laboratory gaseous discharge plasmas is considered as an example. The molecular dynamics method shows that, under certain conditions, random fluctuations in the charge can effectively heat a system of macroscopic particles, thereby impeding the ordering process

Macroscopic fluorescence imaging: a novel technique to monitor retention and distribution of injected microspheres in an experimental model of ischemic heart failure.

Science.gov (United States)

Martens, Andreas; Rojas, Sebastian V; Baraki, Hassina; Rathert, Christian; Schecker, Natalie; Hernandez, Sara Rojas; Schwanke, Kristin; Zweigerdt, Robert; Martin, Ulrich; Saito, Shunsuke; Haverich, Axel; Kutschka, Ingo

2014-01-01

The limited effectiveness of cardiac cell therapy has generated concern regarding its clinical relevance. Experimental studies show that cell retention and engraftment are low after injection into ischemic myocardium, which may restrict therapy effectiveness significantly. Surgical aspects and mechanical loss are suspected to be the main culprits behind this phenomenon. As current techniques of monitoring intramyocardial injections are complex and time-consuming, the aim of the study was to develop a fast and simple model to study cardiac retention and distribution following intramyocardial injections. For this purpose, our main hypothesis was that macroscopic fluorescence imaging could adequately serve as a detection method for intramyocardial injections. A total of 20 mice underwent ligation of the left anterior descending artery (LAD) for myocardial infarction. Fluorescent microspheres with cellular dimensions were used as cell surrogates. Particles (5 × 10(5)) were injected into the infarcted area of explanted resting hearts (Ex vivo myocardial injetions EVMI, n = 10) and in vivo into beating hearts (In vivo myocardial injections IVMI, n = 10). Microsphere quantification was performed by fluorescence imaging of explanted organs. Measurements were repeated after a reduction to homogenate dilutions. Cardiac microsphere retention was 2.78 × 10(5) ± 0.31 × 10(5) in the EVMI group. In the IVMI group, cardiac retention of microspheres was significantly lower (0.74 × 10(5) ± 0.18 × 10(5); pfluorescence imaging revealed venous drainage through the coronary sinus, resulting in a microsphere accumulation in the left (0.90 × 10(5) ± 0.20 × 10(5)) and the right (1.07 × 10(5) ± 0.17 × 10(5)) lung. Processing to homogenates involved further particle loss (pfluorescence imaging method for biodistribution analysis which enabled the quantification of fluorescent microspheres after intramyocardial delivery using macroscopic fluorescence imaging. This new technique

Bell-inequality tests with macroscopic entangled states of light

Energy Technology Data Exchange (ETDEWEB)

Stobinska, M. [Max Planck Institute for the Science of Light, Erlangen (Germany); Institute for Theoretical Physics II, Erlangen-Nuernberg University, Erlangen (Germany); Sekatski, P.; Gisin, N. [Group of Applied Physics, University of Geneva, Geneva (Switzerland); Buraczewski, A. [Faculty of Electronics and Information Technology, Warsaw University of Technology, Warsaw (Poland); Leuchs, G. [Max Planck Institute for the Science of Light, Erlangen (Germany); Institute for Optics, Information and Photonics, Erlangen-Nuernberg University, Erlangen (Germany)

2011-09-15

Quantum correlations may violate the Bell inequalities. Most experimental schemes confirming this prediction have been realized in all-optical Bell tests suffering from the detection loophole. Experiments which simultaneously close this loophole and the locality loophole are highly desirable and remain challenging. An approach to loophole-free Bell tests is based on amplification of the entangled photons (i.e., on macroscopic entanglement), for which an optical signal should be easy to detect. However, the macroscopic states are partially indistinguishable by classical detectors. An interesting idea to overcome these limitations is to replace the postselection by an appropriate preselection immediately after the amplification. This is in the spirit of state preprocessing revealing hidden nonlocality. Here, we examine one of the possible preselections, but the presented tools can be used for analysis of other schemes. Filtering methods making the macroscopic entanglement useful for Bell tests and quantum protocols are the subject of an intensive study in the field nowadays.

Macroscopic quantum electrodynamics of high-Q cavities

International Nuclear Information System (INIS)

Khanbekyan, Mikayel

2009-01-01

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 possible

Microfluidic Synthesis of Highly Potent Limit-size Lipid Nanoparticles for In Vivo Delivery of siRNA

Directory of Open Access Journals (Sweden)

Nathan M Belliveau

2012-01-01

Full Text Available Lipid nanoparticles (LNP are the leading systems for in vivo delivery of small interfering RNA (siRNA for therapeutic applications. Formulation of LNP siRNA systems requires rapid mixing of solutions containing cationic lipid with solutions containing siRNA. Current formulation procedures employ macroscopic mixing processes to produce systems 70-nm diameter or larger that have variable siRNA encapsulation efficiency, homogeneity, and reproducibility. Here, we show that microfluidic mixing techniques, which permit millisecond mixing at the nanoliter scale, can reproducibly generate limit size LNP siRNA systems 20 nm and larger with essentially complete encapsulation of siRNA over a wide range of conditions with polydispersity indexes as low as 0.02. Optimized LNP siRNA systems produced by microfluidic mixing achieved 50% target gene silencing in hepatocytes at a dose level of 10 µg/kg siRNA in mice. We anticipate that microfluidic mixing, a precisely controlled and readily scalable technique, will become the preferred method for formulation of LNP siRNA delivery systems.

Macroscopic quantum waves in non local theories

International Nuclear Information System (INIS)

Ventura, I.

1979-01-01

By means of an expansion in the density, it is shown that Macroscopic Quantum Waves also appear in non local theories. This result reinforces the conjecture that these waves should exist in liquid 4 He [pt

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

Directory of Open Access Journals (Sweden)

O. V. Sokolova

2014-01-01

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.

Macroscopic and radiographic examination of proximal root surface caries

International Nuclear Information System (INIS)

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

1988-01-01

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

Macroscopic quantum waves in non local theories

International Nuclear Information System (INIS)

Ventura, I.

1979-01-01

By means of an expansion in the density, it is shown that Macroscopic Quantum Waves also apear in non local theories. This result reinforces the conjecture that these waves should exist in liquid 4 He. (Author) [pt

Extended Macroscopic Study of Dilute Gas Flow within a Microcavity

Directory of Open Access Journals (Sweden)

Mohamed Hssikou

2016-01-01

Full Text Available The behaviour of monatomic and dilute gas is studied in the slip and early transition regimes using the extended macroscopic theory. The gas is confined within a two-dimensional microcavity where the longitudinal sides are in the opposite motion with constant velocity ±Uw. The microcavity walls are kept at the uniform and reference temperature T0. Thus, the gas flow is transported only by the shear stress induced by the motion of upper and lower walls. From the macroscopic point of view, the regularized 13-moment equations of Grad, R13, are solved numerically. The macroscopic gas proprieties are studied for different values of the so-called Knudsen number (Kn, which gives the gas-rarefaction degree. The results are compared with those obtained using the classical continuum theory of Navier-Stokes and Fourier (NSF.

Macroscopically constrained Wang-Landau method for systems with multiple order parameters and its application to drawing complex phase diagrams

Science.gov (United States)

Chan, C. H.; Brown, G.; Rikvold, P. A.

2017-05-01

A generalized approach to Wang-Landau simulations, macroscopically constrained Wang-Landau, is proposed to simulate the density of states of a system with multiple macroscopic order parameters. The method breaks a multidimensional random-walk process in phase space into many separate, one-dimensional random-walk processes in well-defined subspaces. Each of these random walks is constrained to a different set of values of the macroscopic order parameters. When the multivariable density of states is obtained for one set of values of fieldlike model parameters, the density of states for any other values of these parameters can be obtained by a simple transformation of the total system energy. All thermodynamic quantities of the system can then be rapidly calculated at any point in the phase diagram. We demonstrate how to use the multivariable density of states to draw the phase diagram, as well as order-parameter probability distributions at specific phase points, for a model spin-crossover material: an antiferromagnetic Ising model with ferromagnetic long-range interactions. The fieldlike parameters in this model are an effective magnetic field and the strength of the long-range interaction.

Macroscopic balance equations for two-phase flow models

International Nuclear Information System (INIS)

Hughes, E.D.

1979-01-01

The macroscopic, or overall, balance equations of mass, momentum, and energy are derived for a two-fluid model of two-phase flows in complex geometries. These equations provide a base for investigating methods of incorporating improved analysis methods into computer programs, such as RETRAN, which are used for transient and steady-state thermal-hydraulic analyses of nuclear steam supply systems. The equations are derived in a very general manner so that three-dimensional, compressible flows can be analysed. The equations obtained supplement the various partial differential equation two-fluid models of two-phase flow which have recently appeared in the literature. The primary objective of the investigation is the macroscopic balance equations. (Auth.)

Macroscopic phase-resetting curves for spiking neural networks

Science.gov (United States)

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

2017-10-01

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.

Macroscopic phase-resetting curves for spiking neural networks.

Science.gov (United States)

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

2017-10-01

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.

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

International Nuclear Information System (INIS)

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

1987-01-01

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 λ 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

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.

1987-12-01

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.

A macroscopic cross-section model for BWR pin-by-pin core analysis

International Nuclear Information System (INIS)

Fujita, Tatsuya; Endo, Tomohiro; Yamamoto, Akio

2014-01-01

A macroscopic cross-section model used in boiling water reactor (BWR) pin-by-pin core analysis is studied. In the pin-by-pin core calculation method, pin-cell averaged cross sections are calculated for many combinations of core state and depletion history variables and are tabulated prior to core calculations. Variations of cross sections in a core simulator are caused by two different phenomena (i.e. instantaneous and history effects). We treat them through the core state variables and the exposure-averaged core state variables, respectively. Furthermore, the cross-term effect among the core state and the depletion history variables is considered. In order to confirm the calculation accuracy and discuss the treatment of the cross-term effect, the k-infinity and the pin-by-pin fission rate distributions in a single fuel assembly geometry are compared. Some cross-term effects could be negligible since the impacts of them are sufficiently small. However, the cross-term effects among the control rod history (or the void history) and other variables have large impacts; thus, the consideration of them is crucial. The present macroscopic cross-section model, which considers such dominant cross-term effects, well reproduces the reference results and can be a candidate in practical applications for BWR pin-by-pin core analysis on the normal operations. (author)

Solvable Quantum Macroscopic Motions and Decoherence Mechanisms in Quantum Mechanics on Nonstandard Space

Science.gov (United States)

Kobayashi, Tsunehiro

1996-01-01

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.

Information and self-organization a macroscopic approach to complex systems

CERN Document Server

Haken, Hermann

1988-01-01

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...

Macroscopic quantum tunneling in 1 μm Nb junctions below 100mK

International Nuclear Information System (INIS)

Voss, R.F.; Webb, R.A.

1981-01-01

The transition probabilities out of the superconducting state of low current density 1 μm Nb Josephson junctions with capacitance < 0.15 pF have been measured as a function of temperature T down to 3 mK. Below 100 mK the distribution widths become independent of T. Junctions with critical currents that differ by an order of magnitude have the same dependence of relative width on T. The low T results are interpreted in terms of quantum tunneling of the (macroscopic) junction phase. The observed low temperature widths are smaller than expected indicating the necessity of corrections to the simple WKB tunneling rates. (orig.)

On quantum mechanics for macroscopic systems

International Nuclear Information System (INIS)

Primas, H.

1992-01-01

The parable of Schroedinger's cat may lead to several up-to date questions: how to treat open systems in quantum theory, how to treat thermodynamically irreversible processes in the quantum mechanics framework, how to explain, following the quantum theory, the existence, phenomenologically evident, of classical observables, what implies the predicted existence by the quantum theory of non localized macroscopic material object ?

Macroscopic quantum mechanics: theory and experimental concepts of optomechanics

International Nuclear Information System (INIS)

Chen Yanbei

2013-01-01

Rapid experimental progress has recently allowed the use of light to prepare macroscopic mechanical objects into nearly pure quantum states. This research field of quantum optomechanics opens new doors towards testing quantum mechanics, and possibly other laws of physics, in new regimes. In the first part of this article, I will review a set of techniques of quantum measurement theory that are often used to analyse quantum optomechanical systems. Some of these techniques were originally designed to analyse how a classical driving force passes through a quantum system, and can eventually be detected with an optimal signal-to-noise ratio—while others focus more on the quantum-state evolution of a mechanical object under continuous monitoring. In the second part of this article, I will review a set of experimental concepts that will demonstrate quantum mechanical behaviour of macroscopic objects—quantum entanglement, quantum teleportation and the quantum Zeno effect. Taking the interplay between gravity and quantum mechanics as an example, I will review a set of speculations on how quantum mechanics can be modified for macroscopic objects, and how these speculations—and their generalizations—might be tested by optomechanics. (invited review)

Plasmonic direct writing lithography with a macroscopical contact probe

Science.gov (United States)

Huang, Yuerong; Liu, Ling; Wang, Changtao; Chen, Weidong; Liu, Yunyue; Li, Ling

2018-05-01

In this work, we design a plasmonic direct writing lithography system with a macroscopical contact probe to achieve nanometer scale spots. The probe with bowtie-shaped aperture array adopts spring hinge and beam deflection method (BDM) to realize near-field lithography. Lithography results show that a macroscopical plasmonic contact probe can achieve a patterning resolution of around 75 nm at 365 nm wavelength, and demonstrate that the lithography system is promising for practical applications due to beyond the diffraction limit, low cost, and simplification of system configuration. CST calculations provide a guide for the design of recording structure and the arrangement of placing polarizer.

Macroscopic description of isoscalar giant multipole resonances

International Nuclear Information System (INIS)

Nix, J.R.; Sierk, A.J.

1980-01-01

On the basis of a simple macroscopic model, we calculate the isoscalar giant-resonance energy as a function of mass number and multipole degree. The restoring force is determined from the distortion of the Fermi surface, and the inertia is determined for the incompressible, irrotational flow of nucleons with unit effective mass. With no adjustable parameters, the resulting closed expression reproduces correctly the available experimental data, namely the magnitude and dependence upon mass number of the giant quadrupole energy and the magnitude of the giant octupole energy for 208 Pb. We also calculate the isoscalar giant-resonance width as a function of mass number and multipole degree for various macroscopic damping mechanisms, including two-body viscosity, one-body dissipation, and modified one-body dissipation. None of these damping mechanisms reproduces correctly all features of the available experimental data, namely the magnitude and dependence upon mass number of the giant quadrupole width and the magnitude of the giant octupole width for 208 Pb

Microscopic and macroscopic models for the onset and progression of Alzheimer's disease

International Nuclear Information System (INIS)

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

2017-01-01

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 (A β from now on), a protein fragment that healthy brains regularly produce and eliminate. In case of dementia A β 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

Quantum mechanics versus macroscopic realism: Is the flux there when nobody looks

International Nuclear Information System (INIS)

Leggett, A.J.; Garg, A.

1985-01-01

It is shown that, in the contect of an idealized ''macroscopic quantum coherence'' experiment, the prediction of quantum mechanics are incompattible with the conjunction of two general assimptions which are designated ''macroscopic realism'' and ''noninvasive measurability at the macroscopiclevel.'' The conditions under which quantum mechanics can be tested against these assumptions in a realistic experiment are discussed

Macroscopic charge quantization in single-electron devices

NARCIS (Netherlands)

Burmistrov, I.S.; Pruisken, A.M.M.

2010-01-01

In a recent paper by the authors [I. S. Burmistrov and A. M. M. Pruisken, Phys. Rev. Lett. 101, 056801 (2008)] it was shown that single-electron devices (single-electron transistor or SET) display "macroscopic charge quantization" which is completely analogous to the quantum Hall effect observed on

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

International Nuclear Information System (INIS)

Rose, H.; Dubois, D.; Russell, D.; Hanssen, A.

1996-01-01

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

Prevalence and Distribution of Leishmania RNA Virus 1 in Leishmania Parasites from French Guiana.

Science.gov (United States)

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

2016-01-01

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.

Testing quantum mechanics against macroscopic realism using the output of χ(2) nonlinearity

International Nuclear Information System (INIS)

Podoshvedov, Sergey A.; Kim, Jaewan

2006-01-01

We suggest an all-optical scheme to generate entangled superposition of a single photon with macroscopic entangled states for testing macroscopic realism. The scheme consists of source of single photons, a Mach-Zehnder interferometer in routes of which a system of coupled-down converters with type-I phase matching is inserted, and a beam splitter for the other auxiliary modes of the scheme. We use quantization of the pumping modes, depletion of the coherent states passing through the system, and interference effect in the pumping modes in the process of erasing which-path information of the single-photon on exit from the Mach-Zehnder interferometer. We show the macroscopic fields of the output superposition are distinguishable states. This scheme generates macroscopic entangled state that violates Bell's inequality. Moreover, the detailed analysis concerning change of amplitudes of entangled superposition by means of repeating this process many times is accomplished. We show our scheme works without photon number resolving detection and it is robust to detector inefficiency

Measurement-Induced Macroscopic Superposition States in Cavity Optomechanics

DEFF Research Database (Denmark)

Hoff, Ulrich Busk; Kollath-Bönig, Johann; Neergaard-Nielsen, Jonas Schou

2016-01-01

A novel protocol for generating quantum superpositions of macroscopically distinct states of a bulk mechanical oscillator is proposed, compatible with existing optomechanical devices operating in the bad-cavity limit. By combining a pulsed optomechanical quantum nondemolition (QND) interaction...

[Satellite RNA (RNA3) of tomato black ring virus is found with one of the 2 major RNAs (RNA2) in a new capsid nucleoprotein].

Science.gov (United States)

Doz, B; Dunez, J; Bove, J M

1977-12-19

Tomato Black Ring Virus (TBRV) like other NEPOviruses posseses two nucleoproteins M and B and two major RNAs, RNA1 and RNA2 respectively distributed in B and M. A new nucleoprotein has just been discovered and comprises one molecule of RNA2 associated with one molecule of RNA3. RNA3 is a small RNA of molecular weight 500,000 d considered to be a satellite RNA. Its level appears to depend on the infection stage, local or systemic. RNA3 is able to modify the relative proportions of nucleoproteins M and B and their respective RNAs. The satellite RNA, might be part of the genome and represent a monocistronic mRNA for protein capsid synthesis. However it seems perhaps more tempting to correlate TBRV-RNA3 with satellite RNA5 of certain strains of Cucumber mosaic virus.

Macroscopic sizes of field of superrelativistic charges

International Nuclear Information System (INIS)

Strel'tsov, V.N.

1995-01-01

Based on the equation of Lienard-Wiechert equipotentials, it is shown that the field of superrelativistic charges reaches macroscopic sizes (e.g., R || = 2 m at E e = 50 GeV). This phenomenon serves an initial cause of the known considerable growth of formation length at high energies. 3 refs., 1 tab

Macroscopic Quantum Tunneling in Superconducting Junctions of β-Ag2Se Topological Insulator Nanowire.

Science.gov (United States)

Kim, Jihwan; Kim, Bum-Kyu; Kim, Hong-Seok; Hwang, Ahreum; Kim, Bongsoo; Doh, Yong-Joo

2017-11-08

We report on the fabrication and electrical transport properties of superconducting junctions made of β-Ag 2 Se topological insulator (TI) nanowires in contact with Al superconducting electrodes. The temperature dependence of the critical current indicates that the superconducting junction belongs to a short and diffusive junction regime. As a characteristic feature of the narrow junction, the critical current decreases monotonously with increasing magnetic field. The stochastic distribution of the switching current exhibits the macroscopic quantum tunneling behavior, which is robust up to T = 0.8 K. Our observations indicate that the TI nanowire-based Josephson junctions can be a promising building block for the development of nanohybrid superconducting quantum bits.

Emergence of an urban traffic macroscopic fundamental diagram

DEFF Research Database (Denmark)

Ranjan, Abhishek; Fosgerau, Mogens; Jenelius, Erik

2016-01-01

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...

Macroscopic behavior of fast reactor fuel subjected to simulated thermal transients

International Nuclear Information System (INIS)

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

1983-06-01

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 μmoles/gm 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

Macroscopic effects of the quantum trace anomaly

International Nuclear Information System (INIS)

Mottola, Emil; Vaulin, Ruslan

2006-01-01

The low energy effective action of gravity in any even dimension generally acquires nonlocal terms associated with the trace anomaly, generated by the quantum fluctuations of massless fields. The local auxiliary field description of this effective action in four dimensions requires two additional scalar fields, not contained in classical general relativity, which remain relevant at macroscopic distance scales. The auxiliary scalar fields depend upon boundary conditions for their complete specification, and therefore carry global information about the geometry and macroscopic quantum state of the gravitational field. The scalar potentials also provide coordinate invariant order parameters describing the conformal behavior and divergences of the stress tensor on event horizons. We compute the stress tensor due to the anomaly in terms of its auxiliary scalar potentials in a number of concrete examples, including the Rindler wedge, the Schwarzschild geometry, and de Sitter spacetime. In all of these cases, a small number of classical order parameters completely determine the divergent behaviors allowed on the horizon, and yield qualitatively correct global approximations to the renormalized expectation value of the quantum stress tensor

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

CERN Document Server

François, Dominique; Zaoui, André

2012-01-01

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...

Fission observables from 4D Langevin calculations with macroscopic transport coefficients

Directory of Open Access Journals (Sweden)

Usang Mark D.

2018-01-01

Full Text Available We have extended the Langevin equations to 4 dimensions (4D by allowing the independent deformation for the left (δ1 and right fragments (δ2 of the fissioning nucleus. At the moment we are only able to use them in conjunction with the macroscopic transport coefficients. Nevertheless, we can see a considerable improvement in the preliminary results for the fission observables, especially those related to the total kinetic energy (TKE of fission fragments. By plotting the TKE distributions we have revealed the super-long fission modes in 236U and super-short fission modes in 257Fm. By plotting the distribution of δ against the fragment’s TKE we have noted a correlation between the values of δ and Brosa’s fission modes. We have found that the standard fission modes correspond to prolate tips of the light fragments while the complementary heavy fragments have oblate fission tips. On the other hand, if both fragments were prolate at the tips, we get super-long fission modes. If both fragments were oblate at the tips, we get super-short fission modes.

Macroscopic domain formation in the platelet plasma membrane

DEFF Research Database (Denmark)

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

2009-01-01

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 d...

Berkeley Experiments on Superfluid Macroscopic Quantum Effects

International Nuclear Information System (INIS)

Packard, Richard

2006-01-01

This paper provides a brief history of the evolution of the Berkeley experiments on macroscopic quantum effects in superfluid helium. The narrative follows the evolution of the experiments proceeding from the detection of single vortex lines to vortex photography to quantized circulation in 3He to Josephson effects and superfluid gyroscopes in both 4He and 3He

Nuclear distribution of the Trypanosoma cruzi RNA Pol I subunit RPA31 during growth and metacyclogenesis, and characterization of its nuclear localization signal.

Science.gov (United States)

Canela-Pérez, Israel; López-Villaseñor, Imelda; Cevallos, Ana María; Hernández, Roberto

2018-03-01

Trypanosoma cruzi is the aetiologic agent of Chagas disease. Our research group studies ribosomal RNA (rRNA) gene transcription and nucleolus dynamics in this species of trypanosomes. RPA31 is an essential subunit of RNA polymerase I (Pol I) whose presence is apparently restricted to trypanosomes. Using fluorescent-tagged versions of this protein (TcRPA31-EGFP), we describe its nuclear distribution during growth and metacyclogenesis. Our findings indicate that TcRPA31-EGFP alters its nuclear presence from concentrated nucleolar localization in exponentially growing epimastigotes to a dispersed granular distribution in the nucleoplasm of stationary epimastigotes and metacyclic trypomastigotes. These changes likely reflect a structural redistribution of the Pol I transcription machinery in quiescent cellular stages where downregulation of rRNA synthesis is known to occur. In addition, and related to the nuclear internalization of this protein, the presence of a classical bipartite-type nuclear localization signal was identified towards its C-terminal end. The functionality of this motif was demonstrated by its partial or total deletion in recombinant versions of the tagged fluorescent protein. Moreover, ivermectin inhibited the nuclear localization of the labelled chimaera, suggesting the involvement of the importin α/β transport system.

Therapeutic miRNA and siRNA: Moving from Bench to Clinic as Next Generation Medicine

Directory of Open Access Journals (Sweden)

Chiranjib Chakraborty

2017-09-01

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. Keywords: miRNA, siRNA, drug development

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

Directory of Open Access Journals (Sweden)

A. E. Greijer

2012-01-01

Full Text Available 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 blood compartments of stem cell transplant (SCT; n=5, solid organ transplant recipients (SOT; n=15, and SOT having chronic elevated EBV-DNA load (n=12. In SCT, EBV DNA was heterogeneously distributed, either in plasma or leukocytes or both. In SOT, EBV DNA load was always cell associated, predominantly in B cells, but occasionally in T cells (CD4 and CD8 or monocytes. All SCT with cell-associated EBV DNA showed BARTs and EBNA1 expression, while LMP1 and LMP2 mRNA was found in 1 and 3 cases, respectively. In SOT, expression of BARTs was detected in all leukocyte samples. LMP2 and EBNA1 mRNA was found in 5/15 and 2/15, respectively, but LMP1 mRNA in only 1, coinciding with severe PTLD and high EBV DNA. Conclusion: EBV DNA is differently distributed between white cells and plasma in SOT versus SCT. EBV RNA profiling in blood is feasible and may have added value for understanding pathogenic virus activity in patients with elevated EBV-DNA.

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

DEFF Research Database (Denmark)

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

1999-01-01

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...... in chondrocytes of osteoarthritic cartilage mainly in the superficial and middle zone of the cartilage rather than the deep zone. There was a tendency for high number of YKL-40 positive chondrocytes in areas of the femoral head with a considerable biomechanical load. The number of chondrocytes with a positive...

Scaling from single molecule to macroscopic adhesion at polymer/metal interfaces.

Science.gov (United States)

Utzig, Thomas; Raman, Sangeetha; Valtiner, Markus

2015-03-10

Understanding the evolution of macroscopic adhesion based on fundamental molecular interactions is crucial to designing strong and smart polymer/metal interfaces that play an important role in many industrial and biomedical applications. Here we show how macroscopic adhesion can be predicted on the basis of single molecular interactions. In particular, we carry out dynamic single molecule-force spectroscopy (SM-AFM) in the framework of Bell-Evans' theory to gain information about the energy barrier between the bound and unbound states of an amine/gold junction. Furthermore, we use Jarzynski's equality to obtain the equilibrium ground-state energy difference of the amine/gold bond from these nonequilibrium force measurements. In addition, we perform surface forces apparatus (SFA) experiments to measure macroscopic adhesion forces at contacts where approximately 10(7) amine/gold bonds are formed simultaneously. The SFA approach provides an amine/gold interaction energy (normalized by the number of interacting molecules) of (36 ± 1)k(B)T, which is in excellent agreement with the interaction free energy of (35 ± 3)k(B)T calculated using Jarzynski's equality and single-molecule AFM experiments. Our results validate Jarzynski's equality for the field of polymer/metal interactions by measuring both sides of the equation. Furthermore, the comparison of SFA and AFM shows how macroscopic interaction energies can be predicted on the basis of single molecular interactions, providing a new strategy to potentially predict adhesive properties of novel glues or coatings as well as bio- and wet adhesion.

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

Science.gov (United States)

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding. PMID:26327359

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism.

Science.gov (United States)

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding.

Departure of microscopic friction from macroscopic drag in molecular fluid dynamics

Energy Technology Data Exchange (ETDEWEB)

Hanasaki, Itsuo [Institute of Engineering, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588 (Japan); Fujiwara, Daiki; Kawano, Satoyuki, E-mail: kawano@me.es.osaka-u.ac.jp [Graduate School of Engineering Science, Osaka University, Machikaneyama-cho 1-3, Toyonaka, Osaka 560-8531 (Japan)

2016-03-07

Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.

Macroscopic acoustoelectric charge transport in graphene

Science.gov (United States)

Bandhu, L.; Lawton, L. M.; Nash, G. R.

2013-09-01

We demonstrate macroscopic acoustoelectric transport in graphene, transferred onto piezoelectric lithium niobate substrates, between electrodes up to 500 μm apart. Using double finger interdigital transducers we have characterised the acoustoelectric current as a function of both surface acoustic wave intensity and frequency. The results are consistent with a relatively simple classical relaxation model, in which the acoustoelectric current is proportional to both the surface acoustic wave intensity and the attenuation of the wave caused by the charge transport.

Nuclear physics: Macroscopic aspects

International Nuclear Information System (INIS)

Swiatecki, W.J.

1993-12-01

A systematic macroscopic, leptodermous approach to nuclear statics and dynamics is described, based formally on the assumptions ℎ → 0 and b/R << 1, where b is the surface diffuseness and R the nuclear radius. The resulting static model of shell-corrected nuclear binding energies and deformabilities is accurate to better than 1 part in a thousand and yields a firm determination of the principal properties of the nuclear fluid. As regards dynamics, the above approach suggests that nuclear shape evolutions will often be dominated by dissipation, but quantitative comparisons with experimental data are more difficult than in the case of statics. In its simplest liquid drop version the model exhibits interesting formal connections to the classic astronomical problem of rotating gravitating masses

Investigation of representing hysteresis in macroscopic models of two-phase flow in porous media using intermediate scale experimental data

Science.gov (United States)

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

2017-01-01

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.

cDNA cloning, mRNA distribution and heterogeneity, chromosomal location, and RFLP analysis of human osteopontin (OPN)

DEFF Research Database (Denmark)

Young, M F; Kerr, J M; Termine, J D

1990-01-01

A human osteopontin (OP) cDNA was isolated from a library made from primary cultures of human bone cells. The distribution of osteopontin mRNA in human tissues was investigated by Northern analysis and showed that the human message was predominant in cultures of bone cells and in decidua cells...... osteopontin cDNA indicated that the gene is a single copy with an approximate length of 5.4-8.2 kb....

Experimental observation of the quantum behavior of a macroscopic degree of freedom

International Nuclear Information System (INIS)

Devoret, M.H.; Martinis, J.M.; Esteve, D.

1986-08-01

At Berkeley a series of experiments have been performed, that demonstrates the quantum behavior of one macroscopic degree of freedom, namely the phase difference across a current biased Josephson junction. Here we will focus on the praticalities involved in such a demonstration. The emphasis is put on the particular procedures used to solve the two problems of noise shielding and parameter determination. To begin, a short description of the macroscopic system investigated, the current biased Josephson junction is given

Thermodynamical properties and thermoelastic coupling of complex macroscopic structure

International Nuclear Information System (INIS)

Fabbri, M.; Sacripanti, A.

1996-11-01

Gross qualitative/quantitative analysis about thermodynamical properties and thermoelastic coupling (or elastocaloric effect) of complex macroscopic structure (running shoes) is performed by infrared camera. The experimental results showed the achievability of a n industrial research project

The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues | Center for Cancer Research

Science.gov (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.

Macroscopic reality and the dynamical reduction program

International Nuclear Information System (INIS)

Ghirardi, G.C.

1995-10-01

With reference to recently proposed theoretical models accounting for reduction in terms of a unified dynamics governing all physical processes, we analyze the problem of working out a worldview accommodating our knowledge about natural phenomena. We stress the relevant conceptual differences between the considered models and standard quantum mechanics. In spite of the fact that both theories describe individual physical systems within a genuine Hilbert space framework, the nice features of spontaneous reduction theories drastically limit the class of states which are dynamically stable. This allows one to work out a description of the world in terms of a mass density function in ordinary configuration space. A topology based on this function and differing radically from the one characterizing the Hilbert space is introduced and in terms of it the idea of similarity of macroscopic situations is made precise. Finally it is shown how the formalism and the proposed interpretation yield a natural criterion for establishing the psychophysical parallelism. The conclusion is that, within the considered theoretical models and at the nonrelativistic level, one can satisfy all sensible requirements for a consistent, unified, and objective description of reality at the macroscopic level. (author). 16 refs

Macroscopic reality and the dynamical reduction program

Energy Technology Data Exchange (ETDEWEB)

Ghirardi, G C

1995-10-01

With reference to recently proposed theoretical models accounting for reduction in terms of a unified dynamics governing all physical processes, we analyze the problem of working out a worldview accommodating our knowledge about natural phenomena. We stress the relevant conceptual differences between the considered models and standard quantum mechanics. In spite of the fact that both theories describe individual physical systems within a genuine Hilbert space framework, the nice features of spontaneous reduction theories drastically limit the class of states which are dynamically stable. This allows one to work out a description of the world in terms of a mass density function in ordinary configuration space. A topology based on this function and differing radically from the one characterizing the Hilbert space is introduced and in terms of it the idea of similarity of macroscopic situations is made precise. Finally it is shown how the formalism and the proposed interpretation yield a natural criterion for establishing the psychophysical parallelism. The conclusion is that, within the considered theoretical models and at the nonrelativistic level, one can satisfy all sensible requirements for a consistent, unified, and objective description of reality at the macroscopic level. (author). 16 refs.

Experimental Entanglement Distribution by Separable States

Science.gov (United States)

Vollmer, Christina E.; Schulze, Daniela; Eberle, Tobias; Händchen, Vitus; Fiurášek, Jaromír; Schnabel, Roman

2013-12-01

Distribution of entanglement between macroscopically separated parties is crucial for future quantum information networks. Surprisingly, it has been theoretically shown that two distant systems can be entangled by sending a third system that is not entangled with either of them. Here, we experimentally distribute entanglement and successfully prove that our transmitted light beam is indeed not entangled with the parties’ local systems. Our work demonstrates an unexpected variant of entanglement distribution and improves the understanding necessary to engineer multipartite quantum networks.

Wave speeds in the macroscopic extended model for ultrarelativistic gases

Energy Technology Data Exchange (ETDEWEB)

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

2013-11-15

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.

Macroscopic phase separation in high-temperature superconductors

Science.gov (United States)

Wen, Hai-Hu

2000-01-01

High-temperature superconductivity is recovered by introducing extra holes to the Cu-O planes, which initially are insulating with antiferromagnetism. In this paper I present data to show the macroscopic electronic phase separation that is caused by either mobile doping or electronic instability in the overdoped region. My results clearly demonstrate that the electronic inhomogeneity is probably a general feature of high-temperature superconductors. PMID:11027323

Species-independent MicroRNA Gene Discovery

KAUST Repository

Kamanu, Timothy K.

2012-12-01

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

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)

2015-12-31

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.

Estimation of macroscopic elastic characteristics for hierarchical anisotropic solids based on probabilistic approach

Science.gov (United States)

Smolina, Irina Yu.

2015-10-01

Mechanical properties of a cable are of great importance in design and strength calculation of flexible cables. The problem of determination of elastic properties and rigidity characteristics of a cable modeled by anisotropic helical elastic rod is considered. These characteristics are calculated indirectly by means of the parameters received from statistical processing of experimental data. These parameters are considered as random quantities. With taking into account probable nature of these parameters the formulas for estimation of the macroscopic elastic moduli of a cable are obtained. The calculating expressions for macroscopic flexural rigidity, shear rigidity and torsion rigidity using the macroscopic elastic characteristics obtained before are presented. Statistical estimations of the rigidity characteristics of some cable grades are adduced. A comparison with those characteristics received on the basis of deterministic approach is given.

Hedgehog signaling pathway is active in GBM with GLI1 mRNA expression showing a single continuous distribution rather than discrete high/low clusters.

Science.gov (United States)

Chandra, Vikas; Das, Tapojyoti; Gulati, Puneet; Biswas, Nidhan K; Rote, Sarang; Chatterjee, Uttara; Ghosh, Samarendra N; Deb, Sumit; Saha, Suniti K; Chowdhury, Anup K; Ghosh, Subhashish; Rudin, Charles M; Mukherjee, Ankur; Basu, Analabha; Dhara, Surajit

2015-01-01

Hedgehog (Hh) signaling pathway is a valid therapeutic target in a wide range of malignancies. We focus here on glioblastoma multiforme (GBM), a lethal malignancy of the central nervous system (CNS). By analyzing RNA-sequencing based transcriptomics data on 149 clinical cases of TCGA-GBM database we show here a strong correlation (r = 0.7) between GLI1 and PTCH1 mRNA expression--as a hallmark of the canonical Hh-pathway activity in this malignancy. GLI1 mRNA expression varied in 3 orders of magnitude among the GBM patients of the same cohort showing a single continuous distribution-unlike the discrete high/low-GLI1 mRNA expressing clusters of medulloblastoma (MB). When compared with MB as a reference, the median GLI1 mRNA expression in GBM appeared 14.8 fold lower than that of the "high-Hh" cluster of MB but 5.6 fold higher than that of the "low-Hh" cluster of MB. Next, we demonstrated statistically significant up- and down-regulation of GLI1 mRNA expressions in GBM patient-derived low-passage neurospheres in vitro by sonic hedgehog ligand-enriched conditioned media (shh-CM) and by Hh-inhibitor drug vismodegib respectively. We also showed clinically achievable dose (50 μM) of vismodegib alone to be sufficient to induce apoptosis and cell cycle arrest in these low-passage GBM neurospheres in vitro. Vismodegib showed an effect on the neurospheres, both by down-regulating GLI1 mRNA expression and by inducing apoptosis/cell cycle arrest, irrespective of their relative endogenous levels of GLI1 mRNA expression. We conclude from our study that this single continuous distribution pattern of GLI1 mRNA expression technically puts almost all GBM patients in a single group rather than discrete high- or low-clusters in terms of Hh-pathway activity. That is suggestive of therapies with Hh-pathway inhibitor drugs in this malignancy without a need for further stratification of patients on the basis of relative levels of Hh-pathway activity among them.

A constitutive model and numerical simulation of sintering processes at macroscopic level

Science.gov (United States)

Wawrzyk, Krzysztof; Kowalczyk, Piotr; Nosewicz, Szymon; Rojek, Jerzy

2018-01-01

This paper presents modelling of both single and double-phase powder sintering processes at the macroscopic level. In particular, its constitutive formulation, numerical implementation and numerical tests are described. The macroscopic constitutive model is based on the assumption that the sintered material is a continuous medium. The parameters of the constitutive model for material under sintering are determined by simulation of sintering at the microscopic level using a micro-scale model. Numerical tests were carried out for a cylindrical specimen under hydrostatic and uniaxial pressure. Results of macroscopic analysis are compared against the microscopic model results. Moreover, numerical simulations are validated by comparison with experimental results. The simulations and preparation of the model are carried out by Abaqus FEA - a software for finite element analysis and computer-aided engineering. A mechanical model is defined by the user procedure "Vumat" which is developed by the first author in Fortran programming language. Modelling presented in the paper can be used to optimize and to better understand the process.

A strict experimental test of macroscopic realism in a superconducting flux qubit.

Science.gov (United States)

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

2016-11-04

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.

Dipolar-induced interplay between inter-level physics and macroscopic phase transitions in triple-well potentials

International Nuclear Information System (INIS)

Zhang Aixia; Xue Jukui

2012-01-01

We propose a scheme to reveal the interplay between dipole–dipole interaction (DDI), inter-level coupling and macroscopic phase transitions in dipolar condensates. By considering a macroscopic sample of dipolar bosons in triple-well potentials, DDI-induced coupling between the inter-level physics and the macroscopic phase transitions is presented. When the DDI exceeds certain thresholds, the degeneracy of the two lowest energy levels and the excitation of new eigenstates occur, respectively. Interestingly, these thresholds give the boundaries of various quantum phase transitions. That is, the quantum phase transitions are the consequence of the levels' degeneracy and the new eigenstates' excitation. Furthermore, DDI-induced long-range macroscopic Josephson oscillations are observed and long-range coherent quantum transportation is achieved. Our results give clear proof of the interplay between the multi-level physics and quantum phase transitions, and also provide a way for designing the long-range coherent quantum transportation. (paper)

Macroscopic sessile tumor architecture is a pathologic feature of biologically aggressive upper tract urothelial carcinoma.

Science.gov (United States)

Fritsche, Hans-Martin; Novara, Giacomo; Burger, Maximilian; Gupta, Amit; Matsumoto, Kazumasa; Kassouf, Wassim; Sircar, Kanishka; Zattoni, Filiberto; Walton, Tom; Tritschler, Stefan; Baba, Shiro; Bastian, Patrick J; Martínez-Salamanca, Juan I; Seitz, Christian; Otto, Wolfgang; Wieland, Wolf Ferdinand; Karakiewicz, Pierre I; Ficarra, Vincenzo; Hartmann, Arndt; Shariat, Shahrokh F

2012-09-01

Macroscopic sessile tumor architecture was associated with adverse outcomes after radical nephroureterectomy (RNU) for upper tract urothelial carcinoma (UTUC). Before inclusion in daily clinical decision-making, the prognostic value of tumor architecture needs to be validated in an independent, external dataset. We tested whether macroscopic tumor architecture improves outcome prediction in an international cohort of patients. We retrospectively studied 754 patients treated with RNU for UTUC without neoadjuvant chemotherapy at 9 centers located in Asia, Canada, and Europe. Tumor architecture was macroscopically categorized as either papillary or sessile. Univariable and multivariable Cox regression analyses were used to address recurrence-free (RFS) and cancer-specific survival (CSS) estimates. Macroscopic sessile architecture was present in 20% of the patients. Its prevalence increased with advancing pathologic stage and it was significantly associated with established features of biologically aggressive UTUC, such as tumor grade, lymph node metastasis, lymphovascular invasion, and concomitant CIS (all P values architecture were 85% and 90%, compared with 58% and 66% for those with macroscopic sessile architecture, respectively (P values architecture was an independent predictor of both RFS (hazard ratio {HR}: 1.5; P = 0.036) and CSS (HR: 1.5; P = 0.03). We confirmed the independent prognostic value of macroscopic tumor architecture in a large, independent, multicenter UTUC cohort. It should be reported in every pathology report and included in post-RNU predictive models in order to refine current clinical decision making regarding follow-up protocol and adjuvant therapy. Copyright © 2012 Elsevier Inc. All rights reserved.

Special relativity - the foundation of macroscopic physics

International Nuclear Information System (INIS)

Dixon, W.G.

1978-01-01

This book aims to show that an understanding of the basic laws of macroscopic systems can be gained more easily within relativistic physics than within Newtonian physics. The unity of dynamics, thermodynamics and electromagnetism under the umbrella of special relativity is examined under chapter headings entitled: the physics of space and time, affine spaces in mathematics and physics, foundations of dynamics, relativistic simple fluids, and, electrodynamics of polarizable fluids. (U.K.)

Thermomechanical macroscopic model of shape memory alloys

International Nuclear Information System (INIS)

Volkov, A.E.; Sakharov, V.Yu.

2003-01-01

The phenomenological macroscopic model of the mechanical behaviour of the titanium nickelide-type shape memory alloys is proposed. The model contains as a parameter the average phase shear deformation accompanying the martensite formation. It makes i possible to describe correctly a number of functional properties of the shape memory alloys, in particular, the pseudoelasticity ferroplasticity, plasticity transformation and shape memory effects in the stressed and unstressed samples [ru

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.

2004-01-01

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

Macroscopic modeling for heat and water vapor transfer in dry snow by homogenization.

Science.gov (United States)

Calonne, Neige; Geindreau, Christian; Flin, Frédéric

2014-11-26

Dry snow metamorphism, involved in several topics related to cryospheric sciences, is mainly linked to heat and water vapor transfers through snow including sublimation and deposition at the ice-pore interface. In this paper, the macroscopic equivalent modeling of heat and water vapor transfers through a snow layer was derived from the physics at the pore scale using the homogenization of multiple scale expansions. The microscopic phenomena under consideration are heat conduction, vapor diffusion, sublimation, and deposition. The obtained macroscopic equivalent model is described by two coupled transient diffusion equations including a source term arising from phase change at the pore scale. By dimensional analysis, it was shown that the influence of such source terms on the overall transfers can generally not be neglected, except typically under small temperature gradients. The precision and the robustness of the proposed macroscopic modeling were illustrated through 2D numerical simulations. Finally, the effective vapor diffusion tensor arising in the macroscopic modeling was computed on 3D images of snow. The self-consistent formula offers a good estimate of the effective diffusion coefficient with respect to the snow density, within an average relative error of 10%. Our results confirm recent work that the effective vapor diffusion is not enhanced in snow.

Parametric equations for calculation of macroscopic cross sections

International Nuclear Information System (INIS)

Botelho, Mario Hugo; Carvalho, Fernando

2015-01-01

Neutronic calculations of the core of a nuclear reactor is one thing necessary and important for the design and management of a nuclear reactor in order to prevent accidents and control the reactor efficiently as possible. To perform these calculations a library of nuclear data, including cross sections is required. Currently, to obtain a cross section computer codes are used, which require a large amount of processing time and computer memory. This paper proposes the calculation of macroscopic cross section through the development of parametric equations. The paper illustrates the proposal for the case of macroscopic cross sections of absorption (Σa), which was chosen due to its greater complexity among other cross sections. Parametric equations created enable, quick and dynamic way, the determination of absorption cross sections, enabling the use of them in calculations of reactors. The results show efficient when compared with the absorption cross sections obtained by the ALPHA 8.8.1 code. The differences between the cross sections are less than 2% for group 2 and less than 0.60% for group 1. (author)

The polarized distribution of poly(A+)-mRNA-induced functional ion channels in the Xenopus oocyte plasma membrane is prevented by anticytoskeletal drugs.

Science.gov (United States)

Peter, A B; Schittny, J C; Niggli, V; Reuter, H; Sigel, E

1991-08-01

Foreign mRNA was expressed in Xenopus laevis oocytes. Newly expressed ion currents localized in defined plasma membrane areas were measured using the two-electrode voltage clamp technique in combination with a specially designed chamber, that exposed only part of the surface on the oocytes to channel agonists or inhibitors. Newly expressed currents were found to be unequally distributed in the surface membrane of the oocyte. This asymmetry was most pronounced during the early phase of expression, when channels could almost exclusively be detected in the animal hemisphere of the oocyte. 4 d after injection of the mRNA, or later, channels could be found at a threefold higher density at the animal than at the vegetal pole area. The pattern of distribution was observed to be similar with various ion channels expressed from crude tissue mRNA and from cRNAs coding for rat GABAA receptor channel subunits. Electron microscopical analysis revealed very similar microvilli patterns at both oocyte pole areas. Thus, the asymmetric current distribution is not due to asymmetric surface structure. Upon incubation during the expression period in either colchicine or cytochalasin D, the current density was found to be equal in both pole areas. The inactive control substance beta-lumicolchicine had no effect on the asymmetry of distribution. Colchicine was without effect on the amplitude of the expressed whole cell current. Our measurements reveal a pathway for plasma membrane protein expression endogenous to the Xenopus oocyte, that may contribute to the formation and maintenance of polarity of this highly organized cell.

Magnetic properties and macroscopic heterogeneity of FeCoNbB Hitperms

Science.gov (United States)

Butvin, Pavol; Butvinová, Beata; Sitek, Jozef; Degmová, Jarmila; Vlasák, Gabriel; Švec, Peter; Janičkovič, Dušan

Nanocrystalline ribbons of Fe 81-xCo xNb 7B 12 (where x ranges from 0 to 40.5 at%) Hitperm alloys have been investigated as to their basic magnetic properties and the influence of the macroscopic heterogeneity. Different crystalline share at surfaces compared with the volume average is observed by conversion electron Mössbauer spectroscopy (CEMS) and Mössbauer spectroscopy (MS), respectively. This marks the presence of macroscopic heterogeneity in these Hitperms. The heterogeneity is generally more significant in Ar-annealed samples than in the vacuum-annealed ones. The characteristic slant hysteresis loops (hard-ribbon-axis) are seen as a rule with few exceptions. An inspection of hysteresis loop response of resin potted samples shows that the surfaces bi-axially squeeze the ribbon interior in heterogeneous Hitperms when the ribbons cool down after annealing. Certain compositions show macroscopic viscous flow prior to crystallization so the heterogeneity gets another chance to induce anisotropy during annealing. The induction attains 1.5 T but saturates poorly due to the heterogeneity and the ensuing anisotropy. Moreover the heterogeneity appears to hamper the crystallization within the ribbon interior. Unlike Finemets, the density of these Hitperms show no pronounced trend with annealing.

Compressor Has No Moving Macroscopic Parts

Science.gov (United States)

Gasser, Max

1995-01-01

Compressor containing no moving macroscopic parts functions by alternating piston and valve actions of successive beds of magnetic particles. Fabricated easily because no need for precisely fitting parts rotating or sliding on each other. Also no need for lubricant fluid contaminating fluid to be compressed. Compressor operates continuously, eliminating troublesome on/off cycling of other compressors, and decreasing consumption of energy. Phased cells push fluid from bottom to top, adding increments of pressure. Each cell contains magnetic powder particles loose when electromagnet coil deenergized, but tightly packed when coil energized.

Macroscopic polarization in crystalline dielectrics: the geometric phase approach

International Nuclear Information System (INIS)

Resta, R.

1994-01-01

The macroscopic electric polarization of a crystal is often defined as the dipole of a unit cell. In fact, such a dipole moment is ill defined, and the above definition is incorrect. Looking more closely, the quantity generally measured is differential polarization, defined with respect to a ''reference state'' of the same material. Such differential polarizations include either derivatives of the polarization (dielectric permittivity, Born effective charges, piezoelectricity, pyroelectricity) or finite differences (ferroelectricity). On the theoretical side, the differential concept is basic as well. Owing to continuity, a polarization difference is equivalent to a macroscopic current, which is directly accessible to the theory as a bulk property. Polarization is a quantum phenomenon and cannot be treated with a classical model, particularly whenever delocalized valence electrons are present in the dielectric. In a quantum picture, the current is basically a property of the phase of the wave functions, as opposed to the charge, which is a property of their modulus. An elegant and complete theory has recently been developed by King-Smith and Vanderbilt, in which the polarization difference between any two crystal states--in a null electric field--takes the form of a geometric quantum phase. This gives a comprehensive account of this theory, which is relevant for dealing with transverse-optic phonons, piezoelectricity, and ferroelectricity. Its relation to the established concepts of linear-response theory is also discussed. Within the geometric phase approach, the relevant polarization difference occurs as the circuit integral of a Berry connection (or ''vector potential''), while the corresponding curvature (or ''magnetic field'') provides the macroscopic linear response

Macroscopic Fundamental Diagram for pedestrian networks : Theory and applications

NARCIS (Netherlands)

Hoogendoorn, S.P.; Daamen, W.; Knoop, V.L.; Steenbakkers, Jeroen; Sarvi, Majid

2017-01-01

The Macroscopic Fundamental diagram (MFD) has proven to be a powerful concept in understanding and managing vehicular network dynamics, both from a theoretical angle and from a more application-oriented perspective. In this contribution, we explore the existence and the characteristics of the

Intratumoral Macroscopic Fat and Hemorrhage Combination Useful in the Differentiation of Benign and Malignant Solid Renal Masses.

Science.gov (United States)

Sun, Jun; Xing, Zhaoyu; Xing, Wei; Zheng, Linfeng; Chen, Jie; Fan, Min; Chen, Tongbing; Zhang, Zhuoli

2016-03-01

To evaluate the value of combining the detection of intratumoral macroscopic fat and hemorrhage in the differentiation of the benign from malignant solid renal masses.Conventional magnetic resonance imaging (MRI), chemical shift (CS)-MRI, and susceptibility-weighted imaging were performed in 152 patients with 152 solid renal masses, including 48 benign and 104 malignant masses all pathologically confirmed. The presence of macroscopic fat detected by CS-MRI and hemorrhage detected by susceptibility-weighted imaging were evaluated in all masses. The rates of macroscopic fat and hemorrhage observed between benign and malignant masses were compared by a χ test. All masses found to contain macroscopic fat with or without hemorrhage were considered to be benign. The remaining masses (without macroscopic fat) found not to contain hemorrhage were considered to be benign. Only those found to contain hemorrhage alone were considered to be malignant. The evaluation indexes for differentiating and forecasting the benign and malignant masses were calculated.Significant differences in the rate of macroscopic fat (observed in 85.42% of benign masses vs. 0% of malignant masses) and hemorrhage (observed in 4.17% of benign masses vs. 95.19% of malignant masses) were measured in the benign and malignant groups (P benign and malignant masses were 96.05%, 95.19%, and 97.92%, respectively, and the accuracy and error rate of forecasting the benign and malignant masses were 95.39% and 4.61%, respectively.Combining the detection intratumoral macroscopic fat and hemorrhage can be used to differentiate the benign from malignant solid renal masses.

Microscopic and macroscopic models for pedestrian crowds

OpenAIRE

Makmul, Juntima

2016-01-01

This thesis is concerned with microscopic and macroscopic models for pedes- trian crowds. In the first chapter, we consider pedestrians exit choices and model human behaviour in an evacuation process. Two microscopic models, discrete and continuous, are studied in this chapter. The former is a cellular automaton model and the latter is a social force model. Different numerical test cases are investigated and their results are compared. In chapter 2, a hierarchy of models for...

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

Directory of Open Access Journals (Sweden)

Xingtuan Yang

2015-05-01

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.

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

Science.gov (United States)

Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

2013-07-01

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

Guiding effect of bent macroscopic quartz tube for high current electron beam

International Nuclear Information System (INIS)

Zhang Mingwu; Chen Jing; Wu Yehong; Yang Bian; Wang Wei; Xue Yingli; Yu Deyang; Cai Xiaohong

2012-01-01

By using an incident electron beam with the high current and high energy, the guiding effect of the bent macroscopic quartz tube for the electron beam has been investigated. The angular distributions of outgoing electrons depending on the current and energy of incident electrons were measured. The dependences of electron transmitted fraction on energy and current of incident electrons are also shown. As the incident electron energy increasing, the electron transmitted fraction increases, but it decreases while the incident electron current increasing. The results have been compared with the present data. This work presents, the process of guiding electrons is essentially different from that of guiding highly charged ions, the guiding electron beam was caused by both elastic and inelastic collisions between electrons and inner walls of quartz tube, rather than self-organized charging effect on the surface of inner wall of quartz tube. (authors)

Problems related to macroscopic electric fields in the magnetosphere

International Nuclear Information System (INIS)

Faelthammar, C.

1977-01-01

The macroscopic electric fields in the magnetosphere originate from internal as well as external sources. The fields are intimately coupled with the dynamics of magnetospheric plasma convection. They also depend on the complicated electrical properties of the hot collisionless plasma. Macroscopic electric fields are responsible for some important kinds of energization of charged particles that take place in the magnetosphere and affect not only particles of auroral energy but also, by multistep processes, trapped high-energy particles. A particularly interesting feature of magnetospheric electric fields is that they can have substantial components along the geomagnetic field, as has recently been confirmed by observations. Several physical mechanisms have been identified by which such electric fields can be supported even when collisions between particles are negligible. Comments are made on the magnetic mirror effect, anomalous resistivity, the collisionless thermoelectric effect, and electric double layers, emphasizing key features and differences and their significance in the light of recent observational data

Estimating minimum polycrystalline aggregate size for macroscopic material homogeneity

International Nuclear Information System (INIS)

Kovac, M.; Simonovski, I.; Cizelj, L.

2002-01-01

During severe accidents the pressure boundary of reactor coolant system can be subjected to extreme loadings, which might cause failure. Reliable estimation of the extreme deformations can be crucial to determine the consequences of severe accidents. Important drawback of classical continuum mechanics is idealization of inhomogenous microstructure of materials. Classical continuum mechanics therefore cannot predict accurately the differences between measured responses of specimens, which are different in size but geometrical similar (size effect). A numerical approach, which models elastic-plastic behavior on mesoscopic level, is proposed to estimate minimum size of polycrystalline aggregate above which it can be considered macroscopically homogeneous. The main idea is to divide continuum into a set of sub-continua. Analysis of macroscopic element is divided into modeling the random grain structure (using Voronoi tessellation and random orientation of crystal lattice) and calculation of strain/stress field. Finite element method is used to obtain numerical solutions of strain and stress fields. The analysis is limited to 2D models.(author)

Preparation of rock samples for measurement of the thermal neutron macroscopic absorption cross-section

International Nuclear Information System (INIS)

Czubek, J.A.; Burda, J.; Drozdowicz, K.; Igielski, A.; Kowalik, W.; Krynicka-Drozdowicz, E.; Woznicka, U.

1986-03-01

Preparation of rock samples for the measurement of the thermal neutron macroscopic absorption cross-section in small cylindrical two-region systems by a pulsed technique is presented. Requirements which should be fulfilled during the preparation of the samples due to physical assumptions of the method are given. A cylindrical vessel is filled with crushed rock and saturated with a medium strongly absorbing thermal neutrons. Water solutions of boric acid of well-known macroscopic absorption cross-section are used. Mass contributions of the components in the sample are specified. This is necessary for the calculation of the thermal neutron macroscopic absorption cross-section of the rock matrix. The conditions necessary for assuring the required accuracy of the measurement are given and the detailed procedure of preparation of the rock sample is described. (author)

Using small RNA (sRNA) deep sequencing to understand global virus distribution in plants

Science.gov (United States)

Small RNAs (sRNAs), a class of regulatory RNAs, have been used to serve as the specificity determinants of suppressing gene expression in plants and animals. Next generation sequencing (NGS) uncovered the sRNA landscape in most organisms including their associated microbes. In the current study, w...

Grasping the Second Law of Thermodynamics at University: The Consistency of Macroscopic and Microscopic Explanations

Science.gov (United States)

Leinonen, Risto; Asikainen, Mervi A.; Hirvonen, Pekka E.

2015-01-01

This study concentrates on evaluating the consistency of upper-division students' use of the second law of thermodynamics at macroscopic and microscopic levels. Data were collected by means of a paper and pencil test (N = 48) focusing on the macroscopic and microscopic features of the second law concerned with heat transfer processes. The data…

Magnetic properties and macroscopic heterogeneity of FeCoNbB Hitperms

Energy Technology Data Exchange (ETDEWEB)

Butvin, Pavol [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia)], E-mail: fyzipbut@savba.sk; Butvinova, Beata [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia); Sitek, Jozef; Degmova, Jarmila [Department of Nuclear Physics and Technology, FEI, Slovak University of Technology, Ilkovicova 3, 812 19 Bratislava (Slovakia); Vlasak, Gabriel; Svec, Peter; Janickovic, Dusan [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia)

2008-03-15

Nanocrystalline ribbons of Fe{sub 81-x}Co{sub x}Nb{sub 7}B{sub 12} (where x ranges from 0 to 40.5 at%) Hitperm alloys have been investigated as to their basic magnetic properties and the influence of the macroscopic heterogeneity. Different crystalline share at surfaces compared with the volume average is observed by conversion electron Moessbauer spectroscopy (CEMS) and Moessbauer spectroscopy (MS), respectively. This marks the presence of macroscopic heterogeneity in these Hitperms. The heterogeneity is generally more significant in Ar-annealed samples than in the vacuum-annealed ones. The characteristic slant hysteresis loops (hard-ribbon-axis) are seen as a rule with few exceptions. An inspection of hysteresis loop response of resin potted samples shows that the surfaces bi-axially squeeze the ribbon interior in heterogeneous Hitperms when the ribbons cool down after annealing. Certain compositions show macroscopic viscous flow prior to crystallization so the heterogeneity gets another chance to induce anisotropy during annealing. The induction attains 1.5 T but saturates poorly due to the heterogeneity and the ensuing anisotropy. Moreover the heterogeneity appears to hamper the crystallization within the ribbon interior. Unlike Finemets, the density of these Hitperms show no pronounced trend with annealing.

mRNA localization mechanisms in Trypanosoma cruzi.

Directory of Open Access Journals (Sweden)

Lysangela R Alves

Full Text Available Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3'UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.

A Macroscopic Multifractal Analysis of Parabolic Stochastic PDEs

Science.gov (United States)

Khoshnevisan, Davar; Kim, Kunwoo; Xiao, Yimin

2018-05-01

It is generally argued that the solution to a stochastic PDE with multiplicative noise—such as \\dot{u}= 1/2 u''+uξ, where {ξ} denotes space-time white noise—routinely produces exceptionally-large peaks that are "macroscopically multifractal." See, for example, Gibbon and Doering (Arch Ration Mech Anal 177:115-150, 2005), Gibbon and Titi (Proc R Soc A 461:3089-3097, 2005), and Zimmermann et al. (Phys Rev Lett 85(17):3612-3615, 2000). A few years ago, we proved that the spatial peaks of the solution to the mentioned stochastic PDE indeed form a random multifractal in the macroscopic sense of Barlow and Taylor (J Phys A 22(13):2621-2626, 1989; Proc Lond Math Soc (3) 64:125-152, 1992). The main result of the present paper is a proof of a rigorous formulation of the assertion that the spatio-temporal peaks of the solution form infinitely-many different multifractals on infinitely-many different scales, which we sometimes refer to as "stretch factors." A simpler, though still complex, such structure is shown to also exist for the constant-coefficient version of the said stochastic PDE.

Reversible optical control of macroscopic polarization in ferroelectrics

Science.gov (United States)

Rubio-Marcos, Fernando; Ochoa, Diego A.; Del Campo, Adolfo; García, Miguel A.; Castro, Germán R.; Fernández, José F.; García, José E.

2018-01-01

The optical control of ferroic properties is a subject of fascination for the scientific community, because it involves the establishment of new paradigms for technology1-9. Domains and domain walls are known to have a great impact on the properties of ferroic materials1-24. Progress is currently being made in understanding the behaviour of the ferroelectric domain wall, especially regarding its dynamic control10-12,17,19. New research is being conducted to find effective methodologies capable of modulating ferroelectric domain motion for future electronics. However, the practical use of ferroelectric domain wall motion should be both stable and reversible (rewritable) and, in particular, be able to produce a macroscopic response that can be monitored easily12,17. Here, we show that it is possible to achieve a reversible optical change of ferroelectric domains configuration. This effect leads to the tuning of macroscopic polarization and its related properties by means of polarized light, a non-contact external control. Although this is only the first step, it nevertheless constitutes the most crucial one in the long and complex process of developing the next generation of photo-stimulated ferroelectric devices.

A Macroscopic Multifractal Analysis of Parabolic Stochastic PDEs

Science.gov (United States)

Khoshnevisan, Davar; Kim, Kunwoo; Xiao, Yimin

2018-04-01

It is generally argued that the solution to a stochastic PDE with multiplicative noise—such as \\dot{u}= 1/2 u''+uξ, where {ξ} denotes space-time white noise—routinely produces exceptionally-large peaks that are "macroscopically multifractal." See, for example, Gibbon and Doering (Arch Ration Mech Anal 177:115-150, 2005), Gibbon and Titi (Proc R Soc A 461:3089-3097, 2005), and Zimmermann et al. (Phys Rev Lett 85(17):3612-3615, 2000). A few years ago, we proved that the spatial peaks of the solution to the mentioned stochastic PDE indeed form a random multifractal in the macroscopic sense of Barlow and Taylor (J Phys A 22(13):2621-2626, 1989; Proc Lond Math Soc (3) 64:125-152, 1992). The main result of the present paper is a proof of a rigorous formulation of the assertion that the spatio-temporal peaks of the solution form infinitely-many different multifractals on infinitely-many different scales, which we sometimes refer to as "stretch factors." A simpler, though still complex, such structure is shown to also exist for the constant-coefficient version of the said stochastic PDE.

Measurement contextuality is implied by macroscopic realism

International Nuclear Information System (INIS)

Chen Zeqian; Montina, A.

2011-01-01

Ontological theories of quantum mechanics provide a realistic description of single systems by means of well-defined quantities conditioning the measurement outcomes. In order to be complete, they should also fulfill the minimal condition of macroscopic realism. Under the assumption of outcome determinism and for Hilbert space dimension greater than 2, they were all proved to be contextual for projective measurements. In recent years a generalized concept of noncontextuality was introduced that applies also to the case of outcome indeterminism and unsharp measurements. It was pointed out that the Beltrametti-Bugajski model is an example of measurement noncontextual indeterminist theory. Here we provide a simple proof that this model is the only one with such a feature for projective measurements and Hilbert space dimension greater than 2. In other words, there is no extension of quantum theory providing more accurate predictions of outcomes and simultaneously preserving the minimal labeling of events through projective operators. As a corollary, noncontextuality for projective measurements implies noncontextuality for unsharp measurements. By noting that the condition of macroscopic realism requires an extension of quantum theory, unless a breaking of unitarity is invoked, we arrive at the conclusion that the only way to solve the measurement problem in the framework of an ontological theory is by relaxing the hypothesis of measurement noncontextuality in its generalized sense.

Dynamical and quasi-static multi-physical models of a diesel internal combustion engine using Energetic Macroscopic Representation

International Nuclear Information System (INIS)

Horrein, L.; Bouscayrol, A.; Cheng, Y.; El Fassi, M.

2015-01-01

Highlights: • Internal Combustion Engine (ICE) dynamical and static models. • Organization of ICE model using Energetic Macroscopic Representation. • Description of the distribution of the chemical, thermal and mechanical power. • Implementation of the ICE model in a global vehicle model. - Abstract: In the simulation of new vehicles, the Internal Combustion Engine (ICE) is generally modeled by a static map. This model yields the mechanical power and the fuel consumption. But some studies require the heat energy from the ICE to be considered (i.e. waste heat recovery, thermal regulation of the cabin). A dynamical multi-physical model of a diesel engine is developed to consider its heat energy. This model is organized using Energetic Macroscopic Representation (EMR) in order to be interconnected to other various models of vehicle subsystems. An experimental validation is provided. Moreover a multi-physical quasi-static model is also derived. According to different modeling aims, a comparison of the dynamical and the quasi-static model is discussed in the case of the simulation of a thermal vehicle. These multi-physical models with different simulation time consumption provide good basis for studying the effects of the thermal energy on the vehicle behaviors, including the possibilities of waste heat recovery

The use of multi representative learning materials: definitive, macroscopic, microscopic, symbolic, and practice in analyzing students’ concept understanding

Science.gov (United States)

Susilaningsih, E.; Wulandari, C.; Supartono; Kasmui; Alighiri, D.

2018-03-01

This research aims to compose learning material which contains definitive macroscopic, microscopic and symbolic to analyze students’ conceptual understanding in acid-base learning materials. This research was conducted in eleven grade, natural science class, senior high school 1 (SMAN 1) Karangtengah, Demak province, Indonesia as the low level of students’ conceptual understanding and the high level of students’ misconception. The data collecting technique is by test to assess the cognitive aspect, questionnaire to assess students’ responses to multi representative learning materials (definitive, macroscopic, microscopic, symbolic), and observation to assess students’ macroscopic aspects. Three validators validate the multi-representative learning materials (definitive, macroscopic, microscopic, symbolic). The results of the research show that the multi-representative learning materials (definitive, macroscopic, microscopes, symbolic) being used is valid in the average score 62 of 75. The data is analyzed using the descriptive qualitative method. The results of the research show that 72.934 % students understand, 7.977 % less understand, 8.831 % do not understand, and 10.256 % misconception. In comparison, the second experiment class shows 54.970 % students understand, 5.263% less understand, 11.988 % do not understand, 27.777 % misconception. In conclusion, the application of multi representative learning materials (definitive, macroscopic, microscopic, symbolic) can be used to analyze the students’ understanding of acid-base materials.

Mass distribution of fission fragments within the Born-Oppenheimer approximation

Energy Technology Data Exchange (ETDEWEB)

Pomorski, K.; Nerlo-Pomorska, B. [M.C.S. University, Department of Theoretical Physics, Lublin (Poland); Ivanyuk, F.A. [Institute for Nuclear Research, Kiev (Ukraine)

2017-03-15

The fission fragments mass-yield of {sup 236} U is obtained by an approximate solution of the eigenvalue problem of the collective Hamiltonian that describes the dynamics of the fission process whose degrees of freedom are: the fission (elongation), the neck and mass-asymmetry modes. The macroscopic-microscopic method is used to evaluate the potential energy surface. The macroscopic energy part is calculated using the liquid drop model and the microscopic corrections are obtained using a Woods-Saxon single-particle levels. The four-dimensional modified Cassini ovals shape parametrization is used to describe the shape of the fissioning nucleus. The mass tensor is taken within a cranking-type approximation. The final fragment mass distribution is obtained by weighting the adiabatic density distribution in the collective space with the neck-dependent fission probability. The neck degree of freedom is found to play a significant role in determining the final fragment mass distribution. (orig.)

Testing quantum behaviour at the macroscopic level

International Nuclear Information System (INIS)

Ghirardi, G.C.

1994-07-01

We reconsider recent proposals to test macro realism versus quantum mechanics in experiments involving noninvasive measurement processes on a Squid. In spite of the fact that we are able to prove that the proposed experiments do not represent a test of macro realism but simply of macroscopic quantum coherence we call attention to their extreme conceptual relevance. We also discuss some recent criticisms which have been raised against the considered proposal and we show that they are not relevant. (author). 12 refs

Pseudo-Goldstone bosons and new macroscopic forces

International Nuclear Information System (INIS)

Hill, C.T.; Ross, G.G.

1988-01-01

Pseudoscalar Goldstone bosons may readily be associated with weakly, explicitly broken symmetries giving them mixed CP quantum numbers. In general this leads to scalar couplings to nucleons and leptons, which produces coherent long range forces. This can naturally accommodate detectable long range macroscopic forces mediated by bosons completely consistent with conventional cosmological limits, e.g., new interactions with the range of present 'fifth force' searches which probe a scale of new physics of f ≅ 10 14 GeV. (orig.)

Local administration of siRNA through Microneedle: Optimization, Bio-distribution, Tumor Suppression and Toxicity

Science.gov (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

2016-07-01

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.

Comparison of collisionless macroscopic models and application to the ion-electron instability

International Nuclear Information System (INIS)

Ahedo, E.; Lapuerta, V.

2001-01-01

In a first part, different macroscopic models of linear Landau damping are compared using a concise one-dimensional (1-D) collisionless formulation. The three-moment model of Chang and Callen (CC) [Phys. Fluids B 4, 1167 (1992)] with two closure relations (complex in the Fourier space) for the viscous stress and the heat conduction is found to be equivalent to the two-moment model of Stubbe-Sukhorukov (SS) [Phys. Plasmas 6, 2976 (1999)], which uses a single (complex) closure relation for the pressure. The comparison of the respective closure relations favors clearly the SS pressure law, which associates an anomalous resistivity to the Landau damping. In a second part, a macroscopic interpretation, with the SS model, of the ion-electron instability shows its resistive character for low and intermediate drift velocities, and the transition to the reactive Buneman limit. The pressure law for the electrons is found to verify a simple law, whereas approximate laws are discussed for the ion pressure. These laws are used to close a macroscopic model for stability analyses of nonhomogeneous plasma structures, where SS and CC models are not applicable easily

Photoinduced macroscopic chiral structures in a series of azobenzene copolyesters

DEFF Research Database (Denmark)

Nedelchev, L.; Nikolova, L.; Matharu, A.

2002-01-01

A study of the propagation of elliptically polarized light and the resulting formation of macroscopic chiral structures in a series of azobenzene side-chain copolyesters, in which the morphology is varied from liquid crystalline to amorphous, is reported. Real-time measurements are presented...

Microstructure and macroscopic properties of polydisperse systems of hard spheres

NARCIS (Netherlands)

Ogarko, V.

2014-01-01

This dissertation describes an investigation of systems of polydisperse smooth hard spheres. This includes the development of a fast contact detection algorithm for computer modelling, the development of macroscopic constitutive laws that are based on microscopic features such as the moments of the

Modification of the Charlesby law. Pt. 2. Macroscopic sensitivity

International Nuclear Information System (INIS)

Schiltz, A.; Weil, A.; Paniez, P.

1984-01-01

In part II, results are presented showing that for doses below macroscopic sensitivity, Qsub(sm), degradation due to fluence of the particles seems to be non-uniform over the entire area. In the light of this, a modification of the Charlesby's law is proposed providing a solution to the problems considered in part I [fr

The macroscopic harmonic oscillator and quantum measurements

International Nuclear Information System (INIS)

Hayward, R.W.

1982-01-01

A quantum mechanical description of a one-dimensional macroscopic harmonic oscillator interacting with its environment is given. Quasi-coherent states are introduced to serve as convenient basis states for application of a density matrix formalism to characterize the system. Attention is given to the pertinent quantum limits to the precision of measurement of physical observables that may provide some information on the nature of a weak classical force interacting with the oscillator. A number of ''quantum nondemolition'' schemes proposed by various authors are discussed. (Auth.)

Sialic acid-triggered macroscopic properties switching on a smart polymer surface

Science.gov (United States)

Xiong, Yuting; Li, Minmin; Wang, Hongxi; Qing, Guangyan; Sun, Taolei

2018-01-01

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.

Microscopic and Macroscopic Structures of Carbon Nanotubes Produced by Pyrolysis of Iron Phthalocyanine

International Nuclear Information System (INIS)

Huang Shaoming; Dai Liming

2002-01-01

By pyrolysis of iron phthalocyanine (FePc), either in a patterned or non-patterned fashion, under an Ar/H 2 atmosphere, we have demonstrated the large-scale production of aligned carbon nanotubes perpendicular to the substrate surface useful for building devices with three-dimensional structures. Depending on the particular pyrolytic conditions used, carbon nanotubes with a wide range of microscopic structures having curved, helical, coiled, branched, and tube-within-tube shapes have also been prepared by the pyrolysis of FePc. This, coupled with several microfabrication methods (photolithography, soft-lithography, self-assembling, micro-contact transfer, etc.), has enabled us to produce carbon nanotube arrays of various macroscopic architectures including polyhedral, flower-like, dendritic, circular, multilayered, and micropatterned geometries. In this article, we summarize our work on the preparation of FePc-generated carbon nanotubes with the large variety of microscopic and macroscopic structures and give a brief overview on the perspectives of making carbon nanotubes with tailor-made microscopic/macroscopic structures, and hence well-defined physicochemical properties, for specific applications

Feedback Gating Control for Network Based on Macroscopic Fundamental Diagram

Directory of Open Access Journals (Sweden)

YangBeibei Ji

2016-01-01

Full Text Available Empirical data from Yokohama, Japan, showed that a macroscopic fundamental diagram (MFD of urban traffic provides for different network regions a unimodal low-scatter relationship between network vehicle density and network space-mean flow. This provides new tools for network congestion control. Based on MFD, this paper proposed a feedback gating control policy which can be used to mitigate network congestion by adjusting signal timings of gating intersections. The objective of the feedback gating control model is to maximize the outflow and distribute the allowed inflows properly according to external demand and capacity of each gating intersection. An example network is used to test the performance of proposed feedback gating control model. Two types of background signalization types for the intersections within the test network, fixed-time and actuated control, are considered. The results of extensive simulation validate that the proposed feedback gating control model can get a Pareto improvement since the performance of both gating intersections and the whole network can be improved significantly especially under heavy demand situations. The inflows and outflows can be improved to a higher level, and the delay and queue length at all gating intersections are decreased dramatically.

Single-cell mRNA transfection studies: delivery, kinetics and statistics by numbers.

Science.gov (United States)

Leonhardt, Carolin; Schwake, Gerlinde; Stögbauer, Tobias R; Rappl, Susanne; Kuhr, Jan-Timm; Ligon, Thomas S; Rädler, Joachim O

2014-05-01

In artificial gene delivery, messenger RNA (mRNA) is an attractive alternative to plasmid DNA (pDNA) since it does not require transfer into the cell nucleus. Here we show that, unlike for pDNA transfection, the delivery statistics and dynamics of mRNA-mediated expression are generic and predictable in terms of mathematical modeling. We measured the single-cell expression time-courses and levels of enhanced green fluorescent protein (eGFP) using time-lapse microscopy and flow cytometry (FC). The single-cell analysis provides direct access to the distribution of onset times, life times and expression rates of mRNA and eGFP. We introduce a two-step stochastic delivery model that reproduces the number distribution of successfully delivered and translated mRNA molecules and thereby the dose-response relation. Our results establish a statistical framework for mRNA transfection and as such should advance the development of RNA carriers and small interfering/micro RNA-based drugs. This team of authors established a statistical framework for mRNA transfection by using a two-step stochastic delivery model that reproduces the number distribution of successfully delivered and translated mRNA molecules and thereby their dose-response relation. This study establishes a nice connection between theory and experimental planning and will aid the cellular delivery of mRNA molecules. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

On the problem of contextuality in macroscopic magnetization measurements

International Nuclear Information System (INIS)

Soeda, Akihito; Kurzyński, Paweł; Ramanathan, Ravishankar; Grudka, Andrzej; Thompson, Jayne; Kaszlikowski, Dagomir

2013-01-01

We show that sharp measurements of total magnetization cannot be used to reveal contextuality in macroscopic many-body systems of spins of arbitrary dimension. We decompose each such measurement into set of projectors corresponding to well-defined value of total magnetization. We then show that such sets of projectors are too restricted to construct Kochen–Specker sets.

RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

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Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

2007-02-08

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

Relationship Between Filler-Matrix Interface and Macroscopical Properties of Polymer Nanocomposites

KAUST Repository

Ventura, Isaac Aguilar

2017-01-01

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

Effect of isovector coupling channel on the macroscopic part of the nuclear binding energy

International Nuclear Information System (INIS)

Haddad, S.

2011-04-01

The effect of the isovector coupling channel on the macroscopic part of the nuclear binding energy is determined utilizing the relativistic density dependent Thomas-Fermi approach for the calculation of the macroscopic part of the nuclear binding energy, and the dependency of this effect on the numbers of neutrons and protons is studied. The isovector coupling channel leads to increased nuclear binding energy, and this effect sharpens with growing excess of the number of neutrons on the number of protons. (author)

The effect of interlayer adhesion on the mechanical behaviors of macroscopic graphene oxide papers.

Science.gov (United States)

Gao, Yun; Liu, Lu-Qi; Zu, Sheng-Zhen; Peng, Ke; Zhou, Ding; Han, Bao-Hang; Zhang, Zhong

2011-03-22

High mechanical performances of macroscopic graphene oxide (GO) papers are attracting great interest owing to their merits of lightweight and multiple functionalities. However, the loading role of individual nanosheets and its effect on the mechanical properties of the macroscopic GO papers are not yet well understood. Herein, we effectively tailored the interlayer adhesions of the GO papers by introducing small molecules, that is, glutaraldehyde (GA) and water molecules, into the gallery regions. With the help of in situ Raman spectroscopy, we compared the varied load-reinforcing roles of nanosheets, and further predicted the Young's moduli of the GO papers. Systematic mechanical tests have proven that the enhancement of the tensile modulus and strength of the GA-treated GO paper arose from the improved load-bearing capability of the nanosheets. On the basis of Raman and macroscopic mechanical tests, the influences of interlayer adhesions on the fracture mechanisms of the strained GO papers were inferred.

Time-dependent entropy evolution in microscopic and macroscopic electromagnetic relaxation

International Nuclear Information System (INIS)

Baker-Jarvis, James

2005-01-01

This paper is a study of entropy and its evolution in the time and frequency domains upon application of electromagnetic fields to materials. An understanding of entropy and its evolution in electromagnetic interactions bridges the boundaries between electromagnetism and thermodynamics. The approach used here is a Liouville-based statistical-mechanical theory. I show that the microscopic entropy is reversible and the macroscopic entropy satisfies an H theorem. The spectral entropy development can be very useful for studying the frequency response of materials. Using a projection-operator based nonequilibrium entropy, different equations are derived for the entropy and entropy production and are applied to the polarization, magnetization, and macroscopic fields. I begin by proving an exact H theorem for the entropy, progress to application of time-dependent entropy in electromagnetics, and then apply the theory to relevant applications in electromagnetics. The paper concludes with a discussion of the relationship of the frequency-domain form of the entropy to the permittivity, permeability, and impedance

Analysis and Enhancements of a Prolific Macroscopic Model of Epilepsy

Directory of Open Access Journals (Sweden)

Christopher Fietkiewicz

2016-01-01

Full Text Available Macroscopic models of epilepsy can deliver surprisingly realistic EEG simulations. In the present study, a prolific series of models is evaluated with regard to theoretical and computational concerns, and enhancements are developed. Specifically, we analyze three aspects of the models: (1 Using dynamical systems analysis, we demonstrate and explain the presence of direct current potentials in the simulated EEG that were previously undocumented. (2 We explain how the system was not ideally formulated for numerical integration of stochastic differential equations. A reformulated system is developed to support proper methodology. (3 We explain an unreported contradiction in the published model specification regarding the use of a mathematical reduction method. We then use the method to reduce the number of equations and further improve the computational efficiency. The intent of our critique is to enhance the evolution of macroscopic modeling of epilepsy and assist others who wish to explore this exciting class of models further.

Processivity and coupling in messenger RNA transcription.

Directory of Open Access Journals (Sweden)

Stuart Aitken

2010-01-01

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.

Macroscopic quantum electrodynamics of high-Q cavities

Energy Technology Data Exchange (ETDEWEB)

Khanbekyan, Mikayel

2009-10-27

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

Triboelectricity: macroscopic charge patterns formed by self-arraying ions on polymer surfaces.

Science.gov (United States)

Burgo, Thiago A L; Ducati, Telma R D; Francisco, Kelly R; Clinckspoor, Karl J; Galembeck, Fernando; Galembeck, Sergio E

2012-05-15

Tribocharged polymers display macroscopically patterned positive and negative domains, verifying the fractal geometry of electrostatic mosaics previously detected by electric probe microscopy. Excess charge on contacting polyethylene (PE) and polytetrafluoroethylene (PTFE) follows the triboelectric series but with one caveat: net charge is the arithmetic sum of patterned positive and negative charges, as opposed to the usual assumption of uniform but opposite signal charging on each surface. Extraction with n-hexane preferentially removes positive charges from PTFE, while 1,1-difluoroethane and ethanol largely remove both positive and negative charges. Using suitable analytical techniques (electron energy-loss spectral imaging, infrared microspectrophotometry and carbonization/colorimetry) and theoretical calculations, the positive species were identified as hydrocarbocations and the negative species were identified as fluorocarbanions. A comprehensive model is presented for PTFE tribocharging with PE: mechanochemical chain homolytic rupture is followed by electron transfer from hydrocarbon free radicals to the more electronegative fluorocarbon radicals. Polymer ions self-assemble according to Flory-Huggins theory, thus forming the experimentally observed macroscopic patterns. These results show that tribocharging can only be understood by considering the complex chemical events triggered by mechanical action, coupled to well-established physicochemical concepts. Patterned polymers can be cut and mounted to make macroscopic electrets and multipoles.

In situ DNA-RNA hybridization using in vitro 125I-labeled ribosomal RNA of higher plant

International Nuclear Information System (INIS)

Sato, Seiichi; Kikuchi, Tadatoshi; Ishida, M.R.; Tanaka, Ryuso.

1975-01-01

In situ hybridization using 125 I-labeled ribosomal RNA was applied to plant cells. Cytoplasmic 25 s rRNA, which was eluted from acrylamide gels after electrophoretic separation, was labeled in vitro with carrier-free 125 I and hybridized with the interphase nuclei in root tips of Vicia faba. In most of the preparations, the nucleoli were more heavily labeled than the other regions within nuclei, and several types of grain distribution were observed on the nucleoli. From these results, it was confirmed that in situ hybridization using 125 I-labeled rRNA can be used very effectively to detect the annealing sites of different molecular species of rRNA within the nuclei of plant cells, for which it is not as easy to obtain high specific radioactive rRNA in vivo as it is in the case of cultured animal cells. (auth.)

Charge of a macroscopic particle in a plasma sheath

International Nuclear Information System (INIS)

Samarian, A.A.; Vladimirov, S.V.

2003-01-01

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

Connecting grain-scale physics to macroscopic granular flow behavior using discrete contact-dynamics simulations, centrifuge experiments, and continuum modeling

Science.gov (United States)

Reitz, Meredith; Stark, Colin; Hung, Chi-Yao; Smith, Breannan; Grinspin, Eitan; Capart, Herve; Li, Liming; Crone, Timothy; Hsu, Leslie; Ling, Hoe

2014-05-01

A complete theoretical understanding of geophysical granular flow is essential to the reliable assessment of landslide and debris flow hazard and for the design of mitigation strategies, but several key challenges remain. Perhaps the most basic is a general treatment of the processes of internal energy dissipation, which dictate the runout velocity and the shape and scale of the affected area. Currently, dissipation is best described by macroscopic, empirical friction coefficients only indirectly related to the grain-scale physics. Another challenge is describing the forces exerted at the boundaries of the flow, which dictate the entrainment of further debris and the erosion of cohesive surfaces. While the granular effects on these boundary forces have been shown to be large compared to predictions from continuum approximations, the link between granular effects and erosion or entrainment rates has not been settled. Here we present preliminary results of a multi-disciplinary study aimed at improving our understanding of granular flow energy dissipation and boundary forces, through an effort to connect grain-scale physics to macroscopic behaviors. Insights into grain-scale force distributions and energy dissipation mechanisms are derived from discrete contact-dynamics simulations. Macroscopic erosion and flow behaviors are documented from a series of granular flow experiments, in which a rotating drum half-filled with grains is placed within a centrifuge payload, in order to drive effective gravity levels up to ~100g and approach the forces present in natural systems. A continuum equation is used to characterize the flowing layer depth and velocity resulting from the force balance between the down-slope pull of gravity and the friction at the walls. In this presentation we will focus on the effect of granular-specific physics such as force chain networks and grain-grain collisions, derived from the contact dynamics simulations. We will describe our efforts to

tmRDB (tmRNA database)

DEFF Research Database (Denmark)

Zwieb, Christian; Gorodkin, Jan; Knudsen, Bjarne

2003-01-01

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Bioinforma......Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http......://www.ag.auburn.edu/mirror/tmRDB/) and the Bioinformatics Research Center, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB collects and distributes information relevant to the study of tmRNA. In trans-translation, this molecule combines properties of tRNA and mRNA and binds several proteins to form the tmRNP. Related RNPs are likely...

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.; Yates, Christian A.; Erban, Radek

2009-01-01

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

On creating macroscopically identical granular systems with different numbers of particles

Science.gov (United States)

van der Meer, Devaraj; Rivas, Nicolas

2015-11-01

One of the fundamental differences between granular and molecular hydrodynamics is the enormous difference in the total number of constituents. The small number of particles implies that the role of fluctuations in granular dynamics is of paramount importance. To obtain more insight in these fluctuations, we investigate to what extent it is possible to create identical granular hydrodynamic states with different number of particles. A definition is given of macroscopically equivalent systems, and the dependency of the conservation equations on the particle size is studied. We show that, in certain cases, and by appropriately scaling the microscopic variables, we are able to compare systems with significantly different number of particles that present the same macroscopic phenomenology. We apply these scalings in simulations of a vertically vibrated system, namely the density inverted granular Leidenfrost state and its transition to a buoyancy-driven convective state.

The RNA of turnip yellow mosaic virus exhibits icosahedral order

International Nuclear Information System (INIS)

Larson, Steven B.; Lucas, Robert W.; Greenwood, Aaron; McPherson, Alexander

2005-01-01

Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses

Macroscopic superposition states and decoherence by quantum telegraph noise

Energy Technology Data Exchange (ETDEWEB)

Abel, Benjamin Simon

2008-12-19

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.)

Parameterized representation of macroscopic cross section for PWR reactor

International Nuclear Information System (INIS)

Fiel, João Cláudio Batista; Carvalho da Silva, Fernando; Senra Martinez, Aquilino; Leal, Luiz C.

2015-01-01

Highlights: • This work describes a parameterized representation of the homogenized macroscopic cross section for PWR reactor. • Parameterization enables a quick determination of problem-dependent cross-sections to be used in few group calculations. • This work allows generating group cross-section data to perform PWR core calculations without computer code calculations. - Abstract: The purpose of this work is to describe, by means of Chebyshev polynomials, a parameterized representation of the homogenized macroscopic cross section for PWR fuel element as a function of soluble boron concentration, moderator temperature, fuel temperature, moderator density and 235 92 U enrichment. The cross-section data analyzed are fission, scattering, total, transport, absorption and capture. The parameterization enables a quick and easy determination of problem-dependent cross-sections to be used in few group calculations. The methodology presented in this paper will allow generation of group cross-section data from stored polynomials to perform PWR core calculations without the need to generate them based on computer code calculations using standard steps. The results obtained by the proposed methodology when compared with results from the SCALE code calculations show very good agreement

Macroscopic superposition states and decoherence by quantum telegraph noise

International Nuclear Information System (INIS)

Abel, Benjamin Simon

2008-01-01

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.)

Localization of insulin receptor mRNA in rat brain by in situ hybridization

International Nuclear Information System (INIS)

Marks, J.L.; Porte, D. Jr.; Stahl, W.L.; Baskin, D.G.

1990-01-01

Insulin receptor mRNA was demonstrated in rat brain slices by in situ hybridization with three 35 S-oligonucleotide probes and contact film autoradiography. Specificity was confirmed by showing that (a) excess unlabeled probe abolished the signal, (b) an oligonucleotide probe for rat neuropeptide Y mRNA showed a different distribution of hybridization signal, and (c) the distribution of insulin receptor binding was consistent with the distribution of insulin receptor mRNA. Insulin receptor mRNA was most abundant in the granule cell layers of the olfactory bulb, cerebellum and dentate gyrus, in the pyramidal cell body layers of the pyriform cortex and hippocampus, in the choroid plexus and in the arcuate nucleus of the hypothalamus

IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions

Science.gov (United States)

Mann, Martin; Wright, Patrick R.

2017-01-01

Abstract The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA–RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. PMID:28472523

Macroscopic Hematuria After Conventional or Hypofractionated Radiation Therapy: Results From a Prospective Phase 3 Study

Energy Technology Data Exchange (ETDEWEB)

Sanguineti, Giuseppe, E-mail: sanguineti@ifo.it [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy); Arcidiacono, Fabio [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy); Landoni, Valeria [Department of Physics, Regina Elena National Cancer Institute, Rome (Italy); Saracino, Bianca Maria; Farneti, Alessia; Arcangeli, Stefano; Petrongari, Maria Grazia; Gomellini, Sara [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy); Strigari, Lidia [Department of Physics, Regina Elena National Cancer Institute, Rome (Italy); Arcangeli, Giorgio [Department of Radiation Oncology, Regina Elena National Cancer Institute, Rome (Italy)

2016-10-01

Purpose: 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. Methods and Materials: 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). Results: 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. Conclusions: MHRT was associated with a statistically significant increased risk of macroscopic hematuria compared with CFRT.

Macroscopic Hematuria After Conventional or Hypofractionated Radiation Therapy: Results From a Prospective Phase 3 Study

International Nuclear Information System (INIS)

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

2016-01-01

Purpose: 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. Methods and Materials: 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). Results: 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. Conclusions: MHRT was associated with a statistically significant increased risk of macroscopic hematuria compared with CFRT.

Grasping the second law of thermodynamics at university: The consistency of macroscopic and microscopic explanations

Directory of Open Access Journals (Sweden)

Risto Leinonen

2015-09-01

Full Text Available [This paper is part of the Focused Collection on Upper Division Physics Courses.] This study concentrates on evaluating the consistency of upper-division students’ use of the second law of thermodynamics at macroscopic and microscopic levels. Data were collected by means of a paper and pencil test (N=48 focusing on the macroscopic and microscopic features of the second law concerned with heat transfer processes. The data analysis was based on a qualitative content analysis where students’ responses to the macroscopic- and microscopic-level items were categorized to provide insight into the consistency of the students’ ideas; if students relied on the same idea at both levels, they ended up in the same category at both levels, and their use of the second law was consistent. The most essential finding is that a majority of students, 52%–69% depending on the physical system under evaluation, used the second law of thermodynamics consistently at macroscopic and microscopic levels; approximately 40% of the students used it correctly in terms of physics while others relied on erroneous ideas, such as the idea of conserving entropy. The most common inconsistency harbored by 10%–15% of the students (depending on the physical system under evaluation was students’ tendency to consider the number of accessible microstates to remain constant even if the entropy was stated to increase in a similar process; other inconsistencies were only seen in the answers of a few students. In order to address the observed inconsistencies, we would suggest that lecturers should utilize tasks that challenge students to evaluate phenomena at macroscopic and microscopic levels concurrently and tasks that would guide students in their search for contradictions in their thinking.

A macroscopic model for magnetic shape-memory single crystals

Czech Academy of Sciences Publication Activity Database

Bessoud, A. L.; Kružík, Martin; Stefanelli, U.

2013-01-01

Roč. 64, č. 2 (2013), s. 343-359 ISSN 0044-2275 R&D Projects: GA AV ČR IAA100750802; GA ČR GAP201/10/0357 Institutional support: RVO:67985556 Keywords : magnetostriction * evolution Subject RIV: BA - General Mathematics Impact factor: 1.214, year: 2013 http://library.utia.cas.cz/separaty/2012/MTR/kruzik-a macroscopic model for magnetic shape- memory single crystals.pdf

Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane

Science.gov (United States)

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

2011-01-01

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.

The Two-Time Interpretation and Macroscopic Time-Reversibility

Directory of Open Access Journals (Sweden)

Yakir Aharonov

2017-03-01

Full Text Available The two-state vector formalism motivates a time-symmetric interpretation of quantum mechanics that entails a resolution of the measurement problem. We revisit a post-selection-assisted collapse model previously suggested by us, claiming that unlike the thermodynamic arrow of time, it can lead to reversible dynamics at the macroscopic level. In addition, the proposed scheme enables us to characterize the classical-quantum boundary. We discuss the limitations of this approach and its broad implications for other areas of physics.

A probabilistic model of RNA conformational space

DEFF Research Database (Denmark)

Frellsen, Jes; Moltke, Ida; Thiim, Martin

2009-01-01

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......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows......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...

Epithelial Distribution and Replication of Foot-and-Mouth Disease Virus RNA in Infected Pigs

DEFF Research Database (Denmark)

Durand, S.; Murphy, C.; Zhang, Z.

2008-01-01

experimentally with FMDV serotype O UKG 34/2001 and tissue samples were collected from I to 4 clays post-infection. Samples were stored at -70 degrees C and frozen sections were prepared for in-situ hybridization (ISH). A digoxigenin-labelled RNA probe complementary to a coding part of the RNA-dependent RNA...... negative strand RNA was observed in basal cells above the basement membrane and along the dermal papillae. The basal cells therefore demonstrate the highest signal for detection of the FMDV positive and negative strand RNAs in both tongue and foot epithelium. These novel results Suggest that the epithelial...

Hydroxychloroquine-conjugated gold nanoparticles for improved siRNA activity.

Science.gov (United States)

Perche, F; Yi, Y; Hespel, L; Mi, P; Dirisala, A; Cabral, H; Miyata, K; Kataoka, K

2016-06-01

Current technology of siRNA delivery relies on pharmaceutical dosage forms to route maximal doses of siRNA to the tumor. However, this rationale does not address intracellular bottlenecks governing silencing activity. Here, we tested the impact of hydroxychloroquine conjugation on the intracellular fate and silencing activity of siRNA conjugated PEGylated gold nanoparticles. Addition of hydroxychloroquine improved endosomal escape and increased siRNA guide strand distribution to the RNA induced silencing complex (RISC), both crucial obstacles to the potency of siRNA. This modification significantly improved gene downregulation in cellulo. Altogether, our data suggest the benefit of this modification for the design of improved siRNA delivery systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Vascular flora and macroscopic fauna on the Fernow Experimental Forest

Science.gov (United States)

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

2002-01-01

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...

Macroscopic and microscopic findings in avascular necrosis of the femoral head.

Science.gov (United States)

Kamal, Diana; Alexandru, D O; Kamal, C K; Streba, C T; Grecu, D; Mogoantă, L

2012-01-01

The avascular necrosis of the femoral head is an illness induced by the cutoff of blood flow to the femoral head and it affects mostly young adults between the ages of 30 and 50 years, raising therapeutic and diagnostic issues. Many risk factors are incriminated in the development of avascular necrosis of the femoral head like: trauma, chronic alcohol consumption, smoking, administration of corticosteroid drugs, most of the cases are considered to be idiopathic. The main goal of our paper is to describe the macroscopic and microscopic variations of the bone structure, which occur in patients with avascular necrosis of the femoral head. The biological material needed for our study was obtained following hip arthroplasty surgery in 26 patients between the ages of 29 and 59 years, which previously were diagnosed with avascular necrosis of the femoral head and admitted in the Orthopedics Department of the Emergency County Hospital of Craiova (Romania) between 2010 and 2011. From a macroscopic point of view, we found well defined areas of necrosis, most of which were neatly demarcated of the adjacent viable tissue by hyperemic areas, loss of shape and contour of the femoral head and transformations of the articular cartilage above the area of necrosis. When examined under the microscope, we found vast areas of fibrosis, narrow bone trabeculae, obstructed blood vessels or blood vessels with clots inside, hypertrophic fat cells, bone sequestration but also small cells and pyknotic nuclei. The microscopic and macroscopic findings on the femoral head sections varied with the patients and the stage of the disease.

X-Inactivation: Xist RNA Uses Chromosome Contacts to Coat the X

OpenAIRE

Leung, Karen N.; Panning, Barbara

2014-01-01

The mechanisms by which Xist RNA associates with the X chromosome to mediate alterations in chromatin structure remain mysterious. Recent genome-wide Xist RNA distribution studies suggest that this long noncoding RNA uses 3-dimensional chromosome contacts to move to its sites of action.

State-space based analysis and forecasting of macroscopic road safety trends in Greece.

Science.gov (United States)

Antoniou, Constantinos; Yannis, George

2013-11-01

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.

On the origin and elimination of macroscopic defects in MBE films

Science.gov (United States)

Wood, C. E. C.; Rathbun, L.; Ohno, H.; DeSimone, D.

1981-02-01

Spitting of group III metal droplets from Knudsen type effusion cells has been found culpable for a genre of problematical macroscopic surface topographical defects observed in the growth of semiconductor films by molecular beam epitaxy. Successful precautions are described which virtually eliminate the problem.

Dynamic Heterogeneous Multiscale Filtration Model: Probing Micro- and Macroscopic Filtration Characteristics of Gasoline Particulate Filters.

Science.gov (United States)

Gong, Jian; Viswanathan, Sandeep; Rothamer, David A; Foster, David E; Rutland, Christopher J

2017-10-03

Motivated by high filtration efficiency (mass- and number-based) and low pressure drop requirements for gasoline particulate filters (GPFs), a previously developed heterogeneous multiscale filtration (HMF) model is extended to simulate dynamic filtration characteristics of GPFs. This dynamic HMF model is based on a probability density function (PDF) description of the pore size distribution and classical filtration theory. The microstructure of the porous substrate in a GPF is resolved and included in the model. Fundamental particulate filtration experiments were conducted using an exhaust filtration analysis (EFA) system for model validation. The particulate in the filtration experiments was sampled from a spark-ignition direct-injection (SIDI) gasoline engine. With the dynamic HMF model, evolution of the microscopic characteristics of the substrate (pore size distribution, porosity, permeability, and deposited particulate inside the porous substrate) during filtration can be probed. Also, predicted macroscopic filtration characteristics including particle number concentration and normalized pressure drop show good agreement with the experimental data. The resulting dynamic HMF model can be used to study the dynamic particulate filtration process in GPFs with distinct microstructures, serving as a powerful tool for GPF design and optimization.

Affinity labeling of Escherichia coli phenylalanyl-tRNA synthetase at the binding site for tRNA

International Nuclear Information System (INIS)

Hountondji, C.; Schmitter, J.M.; Beauvallet, C.; Blanquet, S.

1987-01-01

Periodate-oxidized tRNA/sup Phe/ (tRNA/sub ox//sup Phe/) behaves as a specific affinity label of tetrameric Escherichia coli phenylalanyl-tRNA synthetase (PheRS). Reaction of the α 2 β 2 enzyme with tRNA/sub ox//sup Phe/ results in the loss of tRNA/sup Phe/ aminoacylation activity with covalent attachment of 2 mol of tRNA dialdehyde/mol of enzyme, in agreement with the stoichiometry of tRNA binding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the PheRS-[ 14 C]tRNA/sub ox//sup Phe/ covalent complex indicates that the large (α, M/sub r/ 87K) subunit of the enzyme interacts with the 3'-adenosine of tRNA/sub ox//sup Phe/. The [ 14 C]tRNA-labeled chymotryptic peptides of PheRS were purified by both gel filtration and reverse-phase high-performance liquid chromatography. The radioactivity was almost equally distributed among three peptides: Met-Lys[Ado]-Phe, Ala-Asp-Lys[Ado]-Leu, and Lys-Ile-Lys[Ado]-Ala. These sequences correspond to residues 1-3, 59-62, and 104-107, respectively, in the N-terminal region of the 795 amino acid sequence of the α subunit. It is noticeable that the labeled peptide Ala-Asp-Lys-Leu is adjacent to residues 63-66 (Arg-Val-Thr-Lys). The latter sequence was just predicted to resemble the proposed consensus tRNA CCA binding region Lys-Met-Ser-Lys-Ser, as deduced from previous affinity labeling studies on E. coli methionyl- and tyrosyl-tRNA synthetases

Flux dynamics and magnetovoltage measurements in a macroscopic cylindrical hole drilled in BSCCO

International Nuclear Information System (INIS)

Yetis, H.; Altinkok, A.; Olutas, M.; Kilic, A.; Kilic, K.

2007-01-01

Slow transport relaxation measurements (V-t curves) and magnetovoltage measurements (V-H curves) were carried out in a polycrystalline sample of Bi 1.7 Pb 0.3 Sr 2 Ca 2 Cu 3 O x (BSCCO) with a macroscopic cylindrically drilled hole (CH). The time evolution of quenched state in V-t curves was interpreted in terms of enhancement of the superconducting order parameter and the relaxation of moving entity. Upon cycling of the external magnetic field with different sweep rates, unusual counter clockwise hysteresis effects and asymmetry in V-H curves are observed in BSCCO sample with CH, which can also be correlated to the trapping of the macroscopic flux bundles in CH

Flux dynamics and magnetovoltage measurements in a macroscopic cylindrical hole drilled in BSCCO

Science.gov (United States)

Yetiş, H.; Altinkok, A.; Olutaş, M.; Kiliç, A.; Kiliç, K.

2007-10-01

Slow transport relaxation measurements (V-t curves) and magnetovoltage measurements (V-H curves) were carried out in a polycrystalline sample of Bi1.7Pb0.3Sr2Ca2Cu3Ox (BSCCO) with a macroscopic cylindrically drilled hole (CH). The time evolution of quenched state in V-t curves was interpreted in terms of enhancement of the superconducting order parameter and the relaxation of moving entity. Upon cycling of the external magnetic field with different sweep rates, unusual counter clockwise hysteresis effects and asymmetry in V-H curves are observed in BSCCO sample with CH, which can also be correlated to the trapping of the macroscopic flux bundles in CH.

On disentanglement of quantum wave functions: Answer to a comment on ''Unified dynamics for microscopic and macroscopic systems''

International Nuclear Information System (INIS)

Ghirardi, G.C.; Rimini, A.; Weber, T.

1987-06-01

It is shown that the assumption of a stochastic localization process for the quantum wave function is essentially different from the suppression of coherence over macroscopic distances arising from the interaction with the environment and allows for a conceptually complete derivation of the classical behaviour of macroscopic bodies. (author). 4 refs

Mechanism of action of mRNA-based vaccines.

Science.gov (United States)

Iavarone, Carlo; O'hagan, Derek T; Yu, Dong; Delahaye, Nicolas F; Ulmer, Jeffrey B

2017-09-01

The present review summarizes the growing body of work defining the mechanisms of action of this exciting new vaccine technology that should allow rational approaches in the design of next generation mRNA vaccines. Areas covered: Bio-distribution of mRNA, localization of antigen production, role of the innate immunity, priming of the adaptive immune response, route of administration and effects of mRNA delivery systems. Expert commentary: In the last few years, the development of RNA vaccines had a fast growth, the rising number of proof will enable rational approaches to improving the effectiveness and safety of this modern class of medicine.

An exploration for the macroscopic physical meaning of entropy

Institute of Scientific and Technical Information of China (English)

无

2010-01-01

The macroscopic physical meaning of entropy is analyzed based on the exergy (availability) of a combined system (a closed system and its environment), which is the maximum amount of useful work obtainable from the system and the environment as the system is brought into equilibrium with the environment. The process the system experiences can be divided in two sequent sub-processes, the process at constant volume, which represents the heat interaction of the system with the environment, and the adiabatic process, which represents the work interaction of the system with the environment. It is shown that the macroscopic physical meaning of entropy is a measure of the unavailable energy of a closed system for doing useful work through heat interaction. This statement is more precise than those reported in prior literature. The unavailability function of a closed system can be defined as T0S and p0V in volume constant process and adiabatic process, respectively. Their changes, that is, AiTgS) and A (p0V) represent the unusable parts of the internal energy of a closed system for doing useful work in corresponding processes. Finally, the relation between Clausius entropy and Boltzmann entropy is discussed based on the comparison of their expressions for absolute entropy.

Dosimetry for synchrotron stereotactic radiotherapy: from a macroscopic approach to microscopic energy deposits consideration

International Nuclear Information System (INIS)

Edouard, M.

2010-01-01

Numerous therapeutic strategies are currently being evaluated to find a curative treatment for high grade glioma. Among them, radiation therapy is partially effective but limited by the insufficient differential effect that can be reached between the dose delivered to the tumor compared to the one received by the healthy tissues. Synchrotron stereotactic radiotherapy aims at increasing this differential effect with a localized dose boost obtained by low energy x-rays stereotactic irradiations (≤ 100 keV) in presence of heavy elements restricted to the target area. This PhD work takes place in the general context of the future clinical trials foreseen at the European Synchrotron Radiation Facility. The first objective was to optimize the dose delivery to the target, at a macroscopic scale. We have demonstrated in particular that an even number of weighted beams was required to homogenize the tumor dose distribution. Microdosimetry studies were then performed to evaluate the dose delivered at the cellular level, taking into account the fine high-Z element distribution. These theoretical results have been compared to in vitro studies. Cell survival studies were performed using either a 3D glioma model (spheroids) or cells irradiated in suspension in an iodinated medium. (author) [fr

Macroscopic quantum tunneling of the magnetic moment

Science.gov (United States)

Tejada, J.; Hernandez, J. M.; del Barco, E.

1999-05-01

In this paper we review the work done on magnetic relaxation during the last 10 years on both single-domain particles and magnetic molecules and its contribution to the discovery of quantum tunneling of the magnetic moment (Chudnovsky and Tejada, Macroscopic Quantum tunneling of the Magnetic moment, Cambridge University press, Cambridge, 1998). We present first the theoretical expressions and their connection to quantum relaxation and secondly, we show and discuss the experimental results. Finally, we discuss very recent hysteresis data on Mn 12Ac molecules at extremely large sweeping rate for the external magnetic field which suggest the existence of quantum spin—phonon avalanches.

Macroscopic quantum tunneling in a dc SQUID

International Nuclear Information System (INIS)

Chen, Y.C.

1986-01-01

The theory of macroscopic quantum tunneling is applied to a current-biased dc SQUID whose dynamics can be described by a two-dimensional mechanical system with a dissipative environment. Based on the phenomenological model proposed by Caldeira and Leggett, the dissipative environment is represented by a set of harmonic oscillators coupling to the system. After integrating out the environmental degrees of freedom, an effective Euclidean action is found for the two-dimensional system. The action is used to provide the quantum tunneling rate formalism for the dc SQUID. Under certain conditions, the tunneling rate reduces to that of a single current-biased Josephson junction with an adjustable effective critical current

Seismic scanning tunneling macroscope - Theory

KAUST Repository

Schuster, Gerard T.

2012-09-01

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.

Seismic scanning tunneling macroscope - Theory

KAUST Repository

Schuster, Gerard T.; Hanafy, Sherif M.; Huang, Yunsong

2012-01-01

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.

Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Science.gov (United States)

Vacchi-Suzzi, Caterina; Hahne, Florian; Scheubel, Philippe; Marcellin, Magali; Dubost, Valerie; Westphal, Magdalena; Boeglen, Catherine; Büchmann-Møller, Stine; Cheung, Ming Sin; Cordier, André; De Benedetto, Christopher; Deurinck, Mark; Frei, Moritz; Moulin, Pierre; Oakeley, Edward; Grenet, Olivier; Grevot, Armelle; Stull, Robert; Theil, Diethilde; Moggs, Jonathan G; Marrer, Estelle; Couttet, Philippe

2013-01-01

MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves) in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744) and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*). The relative abundance of myocardium-enriched (miR-1) and valve-enriched (miR-125b-5p and miR-204) microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Directory of Open Access Journals (Sweden)

Caterina Vacchi-Suzzi

Full Text Available MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744 and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*. The relative abundance of myocardium-enriched (miR-1 and valve-enriched (miR-125b-5p and miR-204 microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

Capturing microscopic features of bone remodeling into a macroscopic model based on biological rationales of bone adaptation.

Science.gov (United States)

Kim, Young Kwan; Kameo, Yoshitaka; Tanaka, Sakae; Adachi, Taiji

2017-10-01

To understand Wolff's law, bone adaptation by remodeling at the cellular and tissue levels has been discussed extensively through experimental and simulation studies. For the clinical application of a bone remodeling simulation, it is significant to establish a macroscopic model that incorporates clarified microscopic mechanisms. In this study, we proposed novel macroscopic models based on the microscopic mechanism of osteocytic mechanosensing, in which the flow of fluid in the lacuno-canalicular porosity generated by fluid pressure gradients plays an important role, and theoretically evaluated the proposed models, taking biological rationales of bone adaptation into account. The proposed models were categorized into two groups according to whether the remodeling equilibrium state was defined globally or locally, i.e., the global or local uniformity models. Each remodeling stimulus in the proposed models was quantitatively evaluated through image-based finite element analyses of a swine cancellous bone, according to two introduced criteria associated with the trabecular volume and orientation at remodeling equilibrium based on biological rationales. The evaluation suggested that nonuniformity of the mean stress gradient in the local uniformity model, one of the proposed stimuli, has high validity. Furthermore, the adaptive potential of each stimulus was discussed based on spatial distribution of a remodeling stimulus on the trabecular surface. The theoretical consideration of a remodeling stimulus based on biological rationales of bone adaptation would contribute to the establishment of a clinically applicable and reliable simulation model of bone remodeling.

Negative heat capacity at phase-separation in macroscopic systems

OpenAIRE

Gross, D. H. E.

2005-01-01

Systems with long-range as well with short-range interactions should necessarily have a convex entropy S(E) at proper phase transitions of first order, i.e. when a separation of phases occurs. Here the microcanonical heat capacity c(E)= -\\frac{(\\partial S/\\partial E)^2}{\\partial^2S/\\partial E^2} is negative. This should be observable even in macroscopic systems when energy fluctuations with the surrounding world can be sufficiently suppressed.

How can macroscopically normal peritoneum contribute to the pathogenesis of endometriosis?

Science.gov (United States)

Fassbender, Amelie; Overbergh, Lut; Verdrengh, Eefje; Kyama, Cleophas M; Vodolazakaia, Alexandra; Bokor, Attila; Meuleman, Christel; Peeraer, Karen; Tomassetti, Carla; Waelkens, Etienne; Mathieu, Chantal; D'Hooghe, Thomas

2011-09-01

This study indicates that the immunobiology of macroscopically normal peritoneum is relevant to understand the pathogenesis of endometriosis. Peritoneal interleukin 6, interleukin 12, and ferritin were differentially expressed in women with and without endometriosis. Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

A simple vibrating sample magnetometer for macroscopic samples

Science.gov (United States)

Lopez-Dominguez, V.; Quesada, A.; Guzmán-Mínguez, J. C.; Moreno, L.; Lere, M.; Spottorno, J.; Giacomone, F.; Fernández, J. F.; Hernando, A.; García, M. A.

2018-03-01

We here present a simple model of a vibrating sample magnetometer (VSM). The system allows recording magnetization curves at room temperature with a resolution of the order of 0.01 emu and is appropriated for macroscopic samples. The setup can be mounted with different configurations depending on the requirements of the sample to be measured (mass, saturation magnetization, saturation field, etc.). We also include here examples of curves obtained with our setup and comparison curves measured with a standard commercial VSM that confirms the reliability of our device.

NBLDA: negative binomial linear discriminant analysis for RNA-Seq data.

Science.gov (United States)

Dong, Kai; Zhao, Hongyu; Tong, Tiejun; Wan, Xiang

2016-09-13

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (Annals Appl Stat 5:2493-2518, 2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as the negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than or equal to the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated. In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes' rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze two real RNA-Seq data sets to demonstrate the advantages of our method in real-world applications. We have developed a new classifier using the negative binomial model for RNA-seq data classification. Our simulation results show that our proposed classifier has a better performance than existing works. The proposed classifier can serve as an effective tool for classifying RNA-seq data. Based on the comparison results, we have provided some guidelines for scientists to decide which method should be used in the discriminant analysis of RNA-Seq data

All-carbon nanotube diode and solar cell statistically formed from macroscopic network

Institute of Scientific and Technical Information of China (English)

Albert G. Nasibulin[1,2,3; Adinath M. Funde[3,4; Ilya V. Anoshkin[3; Igor A. Levitskyt[5,6

2015-01-01

Schottky diodes and solar cells are statistically created in the contact area between two macroscopic films of single-walled carbon nanotubes （SWNTs） at the junction of semiconducting and quasi-metallic bundles consisting of several high quality tubes. The n-doping of one of the films allows for photovoltaic action, owing to an increase in the built-in potential at the bundle-to-bundle interface. Statistical analysis demonstrates that the Schottky barrier device contributes significantly to the I-V characteristics, compared to the p-n diode. The upper limit of photovoltaic conversion efficiency has been estimated at N20%, demonstrating that the light energy conversion is very efficient for such a unique solar cell. While there have been multiple studies on rectifying SWNT diodes in the nanoscale environment, this is the first report of a macroscopic all-carbon nanotube diode and solar cell.

Laparoscopic vs open total mesorectal excision for rectal cancer: an evaluation of the mesorectum's macroscopic quality.

Science.gov (United States)

Breukink, S O; Grond, A J K; Pierie, J P E N; Hoff, C; Wiggers, T; Meijerink, W J H J

2005-03-01

Next to surgical margins, yield of lymph nodes, and length of bowel resected, macroscopic completeness of mesorectal excision may serve as another quality control of total mesorectal excision (TME). In this study, the macroscopic completeness of laparoscopic TME was evaluated. A series of 25 patients with rectal cancer were managed laparoscopically (LTME) and included in this study. The pathologic specimens of the LTME group were prospectively examined and matched with a historical group of resection specimens from patients who had undergone open TME (OTME). The two groups were matched for gender and type of resection (low anterior or abdominoperineal resection). Special care was given to the macroscopic judgment concerning the completeness of the mesorectum. A three-grade scoring system showed no differences between the LTME and OTME groups. The current study supports the hypothesis that oncologic resection using laparoscopic TME is feasible and adequate.

Electrically and mechanically induced macroscopic body couple, a newly recognized phenomenon of electromechanical interaction

International Nuclear Information System (INIS)

Chen, P.J.

1986-01-01

Microscopically, when the molecules of certain materials are under the influence of external stimuli such as mechanical and electrical forces, several processes can happen. In particular, the centers of charge of the positive and negative ions of a molecule may displace with respect to each other. This notion leads to the macroscopic concept of polarization which has been exploited in the classical studies of piezoelectric and ferroelectric materials. In addition, the ions of the molecule may also rotate angularly relative to one another. Here an entirely new macroscopic concept of body couple which differs from the classical concept is introduced. It is shown that the simplest representations of the proposed constitutive relations lead to an equation within the context of the classical bending theory of thin plates whose solution is in remarkable agreement with recent experimental results concerning the bending of thin virgin ferroelectric ceramic discs under the action of small d.c. voltages. These experimental results cannot be explained by the classical notion of polarization. Therefore, the concept of macroscopic body couple introduced here is a fundamental feature which must be taken into account in the considerations of electromechanical interactions

Gecko toe and lamellar shear adhesion on macroscopic, engineered rough surfaces.

Science.gov (United States)

Gillies, Andrew G; Henry, Amy; Lin, Hauwen; Ren, Angela; Shiuan, Kevin; Fearing, Ronald S; Full, Robert J

2014-01-15

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.

Transport coefficients in Lorentz plasmas with the power-law kappa-distribution

International Nuclear Information System (INIS)

Jiulin, Du

2013-01-01

Transport coefficients in Lorentz plasma with the power-law κ-distribution are studied by means of using the transport equation and macroscopic laws of Lorentz plasma without magnetic field. Expressions of electric conductivity, thermoelectric coefficient, and thermal conductivity for the power-law κ-distribution are accurately derived. It is shown that these transport coefficients are significantly modified by the κ-parameter, and in the limit of the parameter κ→∞ they are reduced to the standard forms for a Maxwellian distribution

Macroscopic Spatial Complexity of the Game of Life Cellular Automaton: A Simple Data Analysis

Science.gov (United States)

Hernández-Montoya, A. R.; Coronel-Brizio, H. F.; Rodríguez-Achach, M. E.

In this chapter we present a simple data analysis of an ensemble of 20 time series, generated by averaging the spatial positions of the living cells for each state of the Game of Life Cellular Automaton (GoL). We show that at the macroscopic level described by these time series, complexity properties of GoL are also presented and the following emergent properties, typical of data extracted complex systems such as financial or economical come out: variations of the generated time series following an asymptotic power law distribution, large fluctuations tending to be followed by large fluctuations, and small fluctuations tending to be followed by small ones, and fast decay of linear correlations, however, the correlations associated to their absolute variations exhibit a long range memory. Finally, a Detrended Fluctuation Analysis (DFA) of the generated time series, indicates that the GoL spatial macro states described by the time series are not either completely ordered or random, in a measurable and very interesting way.

A comparison of macroscopic models describing the collective response of sedimenting rod-like particles in shear flows

KAUST Repository

Helzel, Christiane; Tzavaras, Athanasios

2016-01-01

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.

A comparison of macroscopic models describing the collective response of sedimenting rod-like particles in shear flows

KAUST Repository

Helzel, Christiane

2016-07-22

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.

Complexity on Acute Myeloid Leukemia mRNA Transcript Variant

Directory of Open Access Journals (Sweden)

Carlo Cattani

2011-01-01

Full Text Available This paper deals with the sequence analysis of acute myeloid leukemia mRNA. Six transcript variants of mlf1 mRNA, with more than 2000 bps, are analyzed by focusing on the autocorrelation of each distribution. Through the correlation matrix, some patches and similarities are singled out and commented, with respect to similar distributions. The comparison of Kolmogorov fractal dimension will be also given in order to classify the six variants. The existence of a fractal shape, patterns, and symmetries are discussed as well.

Flux dynamics and magnetovoltage measurements in a macroscopic cylindrical hole drilled in BSCCO

Energy Technology Data Exchange (ETDEWEB)

Yetis, H.; Altinkok, A.; Olutas, M. [Abant Izzet Baysal University, Department of Physics, Turgut Gulez Research Laboratory, 14280 Bolu (Turkey); Kilic, A. [Abant Izzet Baysal University, Department of Physics, Turgut Gulez Research Laboratory, 14280 Bolu (Turkey)], E-mail: kilic_a@ibu.edu.tr; Kilic, K. [Abant Izzet Baysal University, Department of Physics, Turgut Gulez Research Laboratory, 14280 Bolu (Turkey)

2007-10-01

Slow transport relaxation measurements (V-t curves) and magnetovoltage measurements (V-H curves) were carried out in a polycrystalline sample of Bi{sub 1.7}Pb{sub 0.3}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub x} (BSCCO) with a macroscopic cylindrically drilled hole (CH). The time evolution of quenched state in V-t curves was interpreted in terms of enhancement of the superconducting order parameter and the relaxation of moving entity. Upon cycling of the external magnetic field with different sweep rates, unusual counter clockwise hysteresis effects and asymmetry in V-H curves are observed in BSCCO sample with CH, which can also be correlated to the trapping of the macroscopic flux bundles in CH.

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

Indian Academy of Sciences (India)

Physics Department, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria. E-mail: pscientific@aec.org.sy. MS received 10 June 2012; revised 18 October 2012; accepted 12 December 2012. Abstract. The effect of isovector coupling channel on the macroscopic part of the nuclear binding energy is studied ...

New nuclear data set ABBN-90 and its testing on macroscopic experiments

International Nuclear Information System (INIS)

Kosh'cheev, V.N.; Manturov, G.N.; Nikolaev, M.N.; Rineyskiy, A.A.; Sinitsa, V.V.; Tsyboolya, A.M.; Zabrodskaya, S.V.

1993-01-01

The new group constant set ABBN-90 is developed now. It based on the FOND-2 evaluated neutron data library processed with the code GRUCON. Some results of the testing ABBN-90 set in different macroscopic experiments are presented. (author)

X-inactivation: Xist RNA uses chromosome contacts to coat the X.

Science.gov (United States)

Leung, Karen N; Panning, Barbara

2014-01-20

The mechanisms by which Xist RNA associates with the X chromosome to mediate alterations in chromatin structure remain mysterious. Recent genome-wide Xist RNA distribution studies suggest that this long noncoding RNA uses 3-dimensional chromosome contacts to move to its sites of action. Copyright © 2014 Elsevier Ltd. All rights reserved.

Macroscopic Biological Characteristics of Individualized Therapy in Chinese Mongolian Osteopathy

Science.gov (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.

Ensemble distribution for immiscible two-phase flow in porous media.

Science.gov (United States)

Savani, Isha; Bedeaux, Dick; Kjelstrup, Signe; Vassvik, Morten; Sinha, Santanu; Hansen, Alex

2017-02-01

We construct an ensemble distribution to describe steady immiscible two-phase flow of two incompressible fluids in a porous medium. The system is found to be ergodic. The distribution is used to compute macroscopic flow parameters. In particular, we find an expression for the overall mobility of the system from the ensemble distribution. The entropy production at the scale of the porous medium is shown to give the expected product of the average flow and its driving force, obtained from a black-box description. We test numerically some of the central theoretical results.

Extension of Seismic Scanning Tunneling Macroscope to Elastic Waves

KAUST Repository

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

2017-01-01

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.

Extension of Seismic Scanning Tunneling Macroscope to Elastic Waves

KAUST Repository

Tarhini, Ahmad

2017-11-06

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.

Peptidomimetics with beta-peptoid resudies as carriers for intracellular delivery of small interfering RNA (siRNA)

DEFF Research Database (Denmark)

Foged, Camilla

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 si...... 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...... a negative zeta potential (-24 to -31 mV). At higher N/P ratios, larger aggregates with zeta potential close to neutral were formed. However, the complexes were not able to silence the expression of enhanced green fluorescent protein (EGFP) in HeLa-cells stably expressing EGFP, which was measured by flow...

Phage-mediated counting by the naked eye of miRNA molecules at attomolar concentrations in a Petri dish

Science.gov (United States)

Zhou, Xin; Cao, Peng; Zhu, Ye; Lu, Wuguang; Gu, Ning; Mao, Chuanbin

2015-10-01

The ability to count biomolecules such as cancer-biomarker miRNAs with the naked eye is seemingly impossible in molecular diagnostics. Here, we show an ultrasensitive naked-eye-counting strategy for quantifying miRNAs by employing T7 phage--a bacteria-specific virus nanoparticle--as a surrogate. The phage is genetically engineered to become fluorescent and capable of binding a miRNA-capturing gold nanoparticle (GNP) in a one-to-one manner. Target miRNAs crosslink the resultant phage-GNP couple and miRNA-capturing magnetic microparticles, forming a sandwich complex containing equimolar phage and miRNA. The phage is then released from the complex and developed into one macroscopic fluorescent plaque in a Petri dish by plating it in a host bacterial medium. Counting the plaques by the naked eye enables the quantification of miRNAs with detection limits of ~3 and ~5 aM for single-target and two-target miRNAs, respectively. This approach offers ultrasensitive and convenient quantification of disease biomarkers by the naked eye.

Partitioning a macroscopic system into independent subsystems

Science.gov (United States)

Delle Site, Luigi; Ciccotti, Giovanni; Hartmann, Carsten

2017-08-01

We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several fields of theoretical and applied physics. The thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e. particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA.

KAUST Repository

Cesana, Marcella

2011-10-01

Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA.

KAUST Repository

Cesana, Marcella; Cacchiarelli, Davide; Legnini, Ivano; Santini, Tiziana; Sthandier, Olga; Chinappi, Mauro; Tramontano, Anna; Bozzoni, Irene

2011-01-01

Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.

Exploration of miRNA families for hypotheses generation.

KAUST Repository

Kamanu, T.K.

2013-10-15

Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

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.

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)

2010-07-01

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.

Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerases in HeLa nuclei.

Science.gov (United States)

Roberge, M; Dahmus, M E; Bradbury, E M

1988-06-05

The relative distribution of transcriptionally active and inactive RNA polymerases I and II between the nuclear matrix/scaffold and chromosomal loops of HeLa cells was determined. Total RNA polymerase was assessed by immunoblotting and transcribing RNA polymerase by a photoaffinity labeling technique in isolated nuclei. Nuclear matrix/scaffold was isolated by three methods using high-salt, intermediate-salt or low-salt extraction. The distribution of RNA polymerases I and II were very similar within each of the methods, but considerable differences in distributions were found between the different preparation methods. Either intermediate-salt or high-salt treatment of DNase I-digested nuclei showed significant association of RNA polymerases with the nuclear matrix. However, intermediate-salt followed by high-salt treatment released all transcribing and non-transcribing RNA polymerases. Nuclear scaffolds isolated with lithium diiodosalicylate (low-salt) contained very little of the RNA polymerases. This treatment, however, caused the dissociation of RNA polymerase II transcription complexes. These results show unambiguously that RNA polymerases, both in their active and inactive forms, are not nuclear matrix proteins. The data support models in which the transcriptional machinery moves around DNA loops during transcription.

Macroscopic description of complex adaptive networks coevolving with dynamic node states

Science.gov (United States)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

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 coevolution 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 mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.

CH-π Interaction Driven Macroscopic Property Transition on Smart Polymer Surface

Science.gov (United States)

Li, Minmin; Qing, Guangyan; Xiong, Yuting; Lai, Yuekun; Sun, Taolei

2015-10-01

Life systems have evolved to utilize weak noncovalent interactions, particularly CH-π interaction, to achieve various biofunctions, for example cellular communication, immune response, and protein folding. However, for artificial materials, it remains a great challenge to recognize such weak interaction, further transform it into tunable macroscopic properties and realize special functions. Here we integrate monosaccharide-based CH-π receptor capable of recognizing aromatic peptides into a smart polymer with three-component “Recognition-Mediating-Function” design, and report the CH-π interaction driven surface property switching on smart polymer film, including wettability, adhesion, viscoelasticity and stiffness. Detailed studies indicate that, the CH-π interaction induces the complexation between saccharide unit and aromatic peptide, which breaks the initial amphiphilic balance of the polymer network, resulting in contraction-swelling conformational transition for polymer chains and subsequent dramatic switching in surface properties. This work not only presents a new approach to control the surface property of materials, but also points to a broader research prospect on CH-π interaction at a macroscopic level.

Toward a superconducting quantum computer. Harnessing macroscopic quantum coherence.

Science.gov (United States)

Tsai, Jaw-Shen

2010-01-01

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.

Distribution of 16S rRNA Methylases Among Different Species of Aminoglycoside-Resistant Enterobacteriaceae in a Tertiary Care Hospital in Poland.

Science.gov (United States)

Piekarska, Katarzyna; Zacharczuk, Katarzyna; Wołkowicz, Tomasz; Rzeczkowska, Magdalena; Bareja, Elżbieta; Olak, Monika; Gierczyński, Rafał

2016-01-01

Aminoglycosides are a group of antimicrobial agents still the most commonly used in the treatment of life-threatening bacterial infections in human and animals. The emergence and spread of 16S rRNA methylases, which confer high-level resistance to the majority of clinically relevant aminoglycosides, constitute a major public health concern. Our goal was to evaluate the distribution of 16S rRNA methylases among different species of Enterobacteriaceae during a five month-long survey in a tertiary hospital in Warszawa, Poland. In the survey, a total of 1770 non-duplicate clinical isolates were collected from all hospital wards in a tertiary hospital in Warszawa, Poland. The survey was conducted between 19 April and 19 September 2010. The ability to produce 16S rRNA methylase was examined by determining MICs for gentamicin, kanamycin, amikacin by means of the agar dilution method. The isolates resistant to high concentration of aminoglycosides were PCR tested for genes: armA, rmtA, rmtB and rmtC. PCR products were subjected to DNA sequencing by the Sanger method. The genetic similarity of the ArmA-producing isolates was analysed by pulsed-filed gel electrophoresis (PFGE). ArmA was the only 16S rRNA methylase detected in 20 of 1770 tested isolates. The overall prevalence rate of ArmA was 1.13%. In K. pneumoniae (n = 742), P. mirabilis (n = 130), and E. cloacae (n = 253) collected in the survey, the prevalence of ArmA was 0.4%, 0.8% and 5.9%, respectively. The PFGE revealed both horizontal and clonal spread of the armA gene in the hospital. The prevalence of 16S rRNA methylase ArmA reported in this study is significantly higher than observed in other countries in Europe.

Distribution of precursor amyloid-β-protein messenger RNA in human cerebral cortex: relationship to neurofibrillary tangles and neuritic plaques

International Nuclear Information System (INIS)

Lewis, D.A.; Higgins, G.A.; Young, W.G.; Goldgaber, D.; Gajdusek, D.C.; Wilson, M.C.; Morrison, J.H.

1988-01-01

Neurofibrillary tangles (NFT) and neuritic plaques (NP), two neuropathological markers of Alzheimer disease, may both contain peptide fragments derived from the human amyloid β protein. However, the nature of the relationship between NFT and NP and the source of the amyloid β proteins found in each have remained unclear. The authors used in situ hybridization techniques to map the anatomical distribution of precursor amyloid-β-protein mRNA in the neocortex of brains from three subjects with no known neurologic disease and from five patients with Alzheimer disease. In brains from control subjects, positively hybridizing neurons were present in cortical regions and layers that contain a high density of neuropathological markers in Alzheimer disease, as well as in those loci that contain NP but few NFT. Quantitative analyses of in situ hybridization patterns within layers III and V of the superior frontal cortex revealed that the presence of high numbers of NFT in Alzheimer-diseased brains was associated with a decrease in the number of positively hybridizing neurons compared to controls and Alzheimer-diseased brains with few NFT. These findings suggest that the expression of precursor amyloid-β-protein mRNA may be a necessary but is clearly not a sufficient prerequisite for NFT formation. In addition, these results may indicate that the amyloid β protein, present in NP in a given region or layer of cortex, is not derived from the resident neuronal cell bodies that express the mRNA for the precursor protein

Significant effect of grain size distribution on compaction rates in granular aggregates

NARCIS (Netherlands)

Niemeijer, André|info:eu-repo/dai/nl/370832132; Elsworth, Derek; Marone, Chris

2009-01-01

We investigate the role of pressure solution in deformation of upper- to mid-crustal rocks using aggregates of halite as a room temperature analog for fluid-assisted deformation processes in the Earth's crust. Experiments evaluate the effects of initial grain size distribution on macroscopic

Evaluation of healing potential of autogenous, macroscopic fat deposited or fat free, omental graft in experimental radius bone defect in rabbit: Radiological study

International Nuclear Information System (INIS)

Masouleh, M.N.; Haghdoost, I.S.; Heydari, G.A.C.; Raissi, A.; Mohitmafi, S.

2011-01-01

This study was designed for evaluation of the difference between the ability of greater omentum graft with or without macroscopic fat deposition in acceleration of bone healing process. Adult female New Zealand white rabbits (n=15) were randomly divided into three equal groups. In groups A and B, the drilled hole on the left radius was filled by the omentum without and with macroscopic fat deposition, respectively while drilled hole on the right radius left intact for consideration as control. In group C, the drilled hole on the left and right radius was filled by the omentum sample with and without macroscopic fat deposition, respectively. Experimental bone defects on the radiuses were secured by the pieces of greater omentum, with or without macroscopic fat deposition, which obtained as an autogenous graft from each rabbit in accompany with control samples. Standardized serial radiography for evaluation of bone healing was performed and the difference in bone healing process in three groups of study was determined. According to the obtained data, the radius bones which filled by omentum without macroscopic fat deposition showed faster healing process than the radius bones which filled by omentum with macroscopic fat deposition (P<0.05). (author)

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

Directory of Open Access Journals (Sweden)

Guorong Xu

Full Text Available High-throughput RNA sequencing (RNA-seq has become an instrumental assay for the analysis of multiple aspects of an organism's transcriptome. Further, the analysis of a biological specimen's associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs generated by the infection of naïve B-cells with the Epstein Barr virus (EBV, while another 23 samples were derived from Burkitt's lymphomas (BL, some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype from the LCLs (which have a blast-like phenotype with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely

Nonequilibrium Microscopic Distribution of Thermal Current in Particle Systems

KAUST Repository

Yukawa, Satoshi

2009-02-15

A nonequilibrium distribution function of microscopic thermal current is studied by a direct numerical simulation in a thermal conducting steady state of particle systems. Two characteristic temperatures of the thermal current are investigated on the basis of the distribution. It is confirmed that the temperature depends on the current direction; Parallel temperature to the heat-flux is higher than antiparallel one. The difference between the parallel temperature and the antiparallel one is proportional to a macroscopic temperature gradient. ©2009 The Physical Society of Japan.

Nonequilibrium Microscopic Distribution of Thermal Current in Particle Systems

KAUST Repository

Yukawa, Satoshi; Shimada, Takashi; Ogushi, Fumiko; Ito, Nobuyasu

2009-01-01

A nonequilibrium distribution function of microscopic thermal current is studied by a direct numerical simulation in a thermal conducting steady state of particle systems. Two characteristic temperatures of the thermal current are investigated on the basis of the distribution. It is confirmed that the temperature depends on the current direction; Parallel temperature to the heat-flux is higher than antiparallel one. The difference between the parallel temperature and the antiparallel one is proportional to a macroscopic temperature gradient. ©2009 The Physical Society of Japan.

Comparison of prevalence estimation of Mycobacterium avium subsp. paratuberculosis infection by sampling slaughtered cattle with macroscopic lesions vs. systematic sampling.

Science.gov (United States)

Elze, J; Liebler-Tenorio, E; Ziller, M; Köhler, H

2013-07-01

The objective of this study was to identify the most reliable approach for prevalence estimation of Mycobacterium avium ssp. paratuberculosis (MAP) infection in clinically healthy slaughtered cattle. Sampling of macroscopically suspect tissue was compared to systematic sampling. Specimens of ileum, jejunum, mesenteric and caecal lymph nodes were examined for MAP infection using bacterial microscopy, culture, histopathology and immunohistochemistry. MAP was found most frequently in caecal lymph nodes, but sampling more tissues optimized the detection rate. Examination by culture was most efficient while combination with histopathology increased the detection rate slightly. MAP was detected in 49/50 animals with macroscopic lesions representing 1.35% of the slaughtered cattle examined. Of 150 systematically sampled macroscopically non-suspect cows, 28.7% were infected with MAP. This indicates that the majority of MAP-positive cattle are slaughtered without evidence of macroscopic lesions and before clinical signs occur. For reliable prevalence estimation of MAP infection in slaughtered cattle, systematic random sampling is essential.

Energetic macroscopic representation and inversion-based control of a CVT-based HEV

NARCIS (Netherlands)

Chouhou, M.; Grée, F.; Jivan, C.; Bouscayrol, A.; Hofman, T.

2014-01-01

A Continuous Variable Transmission (CVT) is introduced in the simulation model of a Hybrid Electric Vehicle (HEV). The CVT-based vehicle simulation and its control are deduced from the Energetic Macroscopic Representation (EMR). Simulations are provided to show the interest of the CVT in term of

Energetic macroscopic representation and inversion- based control of a CVT-based HEV

NARCIS (Netherlands)

Chouhou, M.; Grée, F.; Jivan, C.; Bouscayrol, A.; Hofman, T.

2013-01-01

A Continuous Variable Transmission (CVT) is introduced in the simulation model of a Hybrid Electric Vehicle (HEV). The CVT-based vehicle simulation and its control are deduced from the Energetic Macroscopic Representation (EMR). Simulations are provided to show the interest of the CVT in term of

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

International Nuclear Information System (INIS)

Law, T.C.; Chong, S.F.; Lu, P.P.; Mak, K.H.

1998-01-01

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

Lability of Nanoparticulate Metal Complexes at a Macroscopic Metal Responsive (Bio)interface

NARCIS (Netherlands)

Duval, Jérôme F.L.; Town, Raewyn M.; Leeuwen, Van Herman P.

2018-01-01

The lability of metal complexes expresses the extent of the dissociative contribution of the complex species to the flux of metal ions toward a macroscopic metal-responsive (bio)interface, for example, an electrodic sensor or an organism. While the case of molecular ligands is well-established, it

Self-similar drag reduction in plug-flow of suspensions of macroscopic fibers

NARCIS (Netherlands)

Gillissen, J.J.J.; Hoving, J.P.

2012-01-01

Pipe flow experiments show that turbulent drag reduction in plug-flow of concentrated suspensions of macroscopic fibers is a self-similar function of the wall shear stress over the fiber network yield stress. We model the experimental observations, by assuming a central fiber network plug, whose

The influence of microscopic and macroscopic non-stoichiometry on interfacial planarity during the solid-phase epitaxial growth of amorphized GaAs

International Nuclear Information System (INIS)

Belay, K.B.; Ridgway, M.C.; Llewellyn, D.J.

1996-01-01

The influence of microscopic and macroscopic non-stoichiometry on the Solid-Phase Epitaxial Growth of GaAs has been studied. Ion implantation has been employed to produce microscopic non-stoichiometry via Ga and As implants and macroscopic non-stoichiometry via Ga or As implants. In-situ Time Resolved Reflectivity and Transmission Electron Microscopy and ex-situ Rutherford Backscattering Spectroscopy and Channeling have been used to investigate the regrowth of amorphized GaAs layers. As non-stoichiometry shifts from microscopic to macroscopic the interface loses its planar nature and subsequently gets rougher. 7 refs., 3 figs

The influence of microscopic and macroscopic non-stoichiometry on interfacial planarity during the solid-phase epitaxial growth of amorphized GaAs

Energy Technology Data Exchange (ETDEWEB)

Belay, K.B.; Ridgway, M.C.; Llewellyn, D.J. [Australian National Univ., Canberra, ACT (Australia). Dept. of Physics

1996-12-31

The influence of microscopic and macroscopic non-stoichiometry on the Solid-Phase Epitaxial Growth of GaAs has been studied. Ion implantation has been employed to produce microscopic non-stoichiometry via Ga and As implants and macroscopic non-stoichiometry via Ga or As implants. In-situ Time Resolved Reflectivity and Transmission Electron Microscopy and ex-situ Rutherford Backscattering Spectroscopy and Channeling have been used to investigate the regrowth of amorphized GaAs layers. As non-stoichiometry shifts from microscopic to macroscopic the interface loses its planar nature and subsequently gets rougher. 7 refs., 3 figs.

The influence of microscopic and macroscopic non-stoichiometry on interfacial planarity during the solid-phase epitaxial growth of amorphized GaAs

Energy Technology Data Exchange (ETDEWEB)

Belay, K B; Ridgway, M C; Llewellyn, D J [Australian National Univ., Canberra, ACT (Australia). Dept. of Physics

1997-12-31

The influence of microscopic and macroscopic non-stoichiometry on the Solid-Phase Epitaxial Growth of GaAs has been studied. Ion implantation has been employed to produce microscopic non-stoichiometry via Ga and As implants and macroscopic non-stoichiometry via Ga or As implants. In-situ Time Resolved Reflectivity and Transmission Electron Microscopy and ex-situ Rutherford Backscattering Spectroscopy and Channeling have been used to investigate the regrowth of amorphized GaAs layers. As non-stoichiometry shifts from microscopic to macroscopic the interface loses its planar nature and subsequently gets rougher. 7 refs., 3 figs.

Estimation of the tritium retention in ITER tungsten divertor target using macroscopic rate equations simulations

Science.gov (United States)

Hodille, E. A.; Bernard, E.; Markelj, S.; Mougenot, J.; Becquart, C. S.; Bisson, R.; Grisolia, C.

2017-12-01

Based on macroscopic rate equation simulations of tritium migration in an actively cooled tungsten (W) plasma facing component (PFC) using the code MHIMS (migration of hydrogen isotopes in metals), an estimation has been made of the tritium retention in ITER W divertor target during a non-uniform exponential distribution of particle fluxes. Two grades of materials are considered to be exposed to tritium ions: an undamaged W and a damaged W exposed to fast fusion neutrons. Due to strong temperature gradient in the PFC, Soret effect’s impacts on tritium retention is also evaluated for both cases. Thanks to the simulation, the evolutions of the tritium retention and the tritium migration depth are obtained as a function of the implanted flux and the number of cycles. From these evolutions, extrapolation laws are built to estimate the number of cycles needed for tritium to permeate from the implantation zone to the cooled surface and to quantify the corresponding retention of tritium throughout the W PFC.

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

Directory of Open Access Journals (Sweden)

Zhenqing Wang

2013-01-01

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.

The Secret Life of RNA: Lessons from Emerging Methodologies.

Science.gov (United States)

Medioni, Caroline; Besse, Florence

2018-01-01

The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression. Remarkably, the development of systems-level studies has been accompanied by tremendous progress in the visualization of individual RNA molecules in single cells, such that it is now possible to image RNA species with a single-molecule resolution from birth to translation or decay. Monitoring quantitatively, with unprecedented spatiotemporal resolution, the fate of individual molecules has been key to understanding the molecular mechanisms underlying the different steps of RNA regulation. This has also revealed biologically relevant, intracellular and intercellular heterogeneities in RNA distribution or regulation. More recently, the convergence of imaging and high-throughput technologies has led to the emergence of spatially resolved transcriptomic techniques that provide a means to perform large-scale analyses while preserving spatial information. By generating transcriptome-wide data on single-cell RNA content, or even subcellular RNA distribution, these methodologies are opening avenues to a wide range of network-level studies at the cell and organ-level, and promise to strongly improve disease diagnostic and treatment.In this introductory chapter, we highlight how recently developed technologies aiming at detecting and visualizing RNA molecules have contributed to

Tumour control probability (TCP) for non-uniform activity distribution in radionuclide therapy

International Nuclear Information System (INIS)

Uusijaervi, Helena; Bernhardt, Peter; Forssell-Aronsson, Eva

2008-01-01

Non-uniform radionuclide distribution in tumours will lead to a non-uniform absorbed dose. The aim of this study was to investigate how tumour control probability (TCP) depends on the radionuclide distribution in the tumour, both macroscopically and at the subcellular level. The absorbed dose in the cell nuclei of tumours was calculated for 90 Y, 177 Lu, 103m Rh and 211 At. The radionuclides were uniformly distributed within the subcellular compartment and they were uniformly, normally or log-normally distributed among the cells in the tumour. When all cells contain the same amount of activity, the cumulated activities required for TCP = 0.99 (A-tilde TCP=0.99 ) were 1.5-2 and 2-3 times higher when the activity was distributed on the cell membrane compared to in the cell nucleus for 103m Rh and 211 At, respectively. TCP for 90 Y was not affected by different radionuclide distributions, whereas for 177 Lu, it was slightly affected when the radionuclide was in the nucleus. TCP for 103m Rh and 211 At were affected by different radionuclide distributions to a great extent when the radionuclides were in the cell nucleus and to lesser extents when the radionuclides were distributed on the cell membrane or in the cytoplasm. When the activity was distributed in the nucleus, A-tilde TCP=0.99 increased when the activity distribution became more heterogeneous for 103m Rh and 211 At, and the increase was large when the activity was normally distributed compared to log-normally distributed. When the activity was distributed on the cell membrane, A-tilde TCP=0.99 was not affected for 103m Rh and 211 At when the activity distribution became more heterogeneous. A-tilde TCP=0.99 for 90 Y and 177 Lu were not affected by different activity distributions, neither macroscopic nor subcellular

Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics.

Science.gov (United States)

Kaneko, Kunihiko; Furusawa, Chikara

2018-05-20

We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. First, linear approximation in intracellular reaction dynamics is used to demonstrate proportional changes in the expression of all cellular components in response to a given environmental stress, with the proportion coefficient determined by the change in growth rate as a consequence of the steady growth of cells. We further demonstrate that this relationship is supported through adaptation experiments of bacteria, perhaps too well as this proportionality is held even across cultures of different types of conditions. On the basis of simulations of cell models, we further show that this global proportionality is a consequence of evolution in which expression changes in response to environmental or genetic perturbations are constrained along a unique one-dimensional curve, which is a result of evolutionary robustness. It then follows that the expression changes induced by environmental changes are proportionally reduced across different components of a cell by evolution, which is akin to the Le Chatelier thermodynamics principle. Finally, with the aid of a fluctuation-response relationship, this proportionality is shown to hold between fluctuations caused by genetic changes and those caused by noise. Overall, these results and support from the theoretical and experimental literature suggest a formulation of cellular systems akin to thermodynamics, in which a macroscopic potential is given by the growth rate (or fitness) represented as a function of environmental and evolutionary changes.

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

NARCIS (Netherlands)

Nijhuis, E.H.J.

2013-01-01

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

GRUCAL, a computer program for calculating macroscopic group constants

International Nuclear Information System (INIS)

Woll, D.

1975-06-01

Nuclear reactor calculations require material- and composition-dependent, energy averaged nuclear data to describe the interaction of neutrons with individual isotopes in material compositions of reactor zones. The code GRUCAL calculates these macroscopic group constants for given compositions from the material-dependent data of the group constant library GRUBA. The instructions for calculating group constants are not fixed in the program, but will be read at the actual execution time from a separate instruction file. This allows to accomodate GRUCAL to various problems or different group constant concepts. (orig.) [de

Monitoring road traffic congestion using a macroscopic traffic model and a statistical monitoring scheme

KAUST Repository

Zeroual, Abdelhafid; Harrou, Fouzi; Sun, Ying; Messai, Nadhir

2017-01-01

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.

Monitoring road traffic congestion using a macroscopic traffic model and a statistical monitoring scheme

KAUST Repository

Zeroual, Abdelhafid

2017-08-19

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.

Characterization of Mangifera indica cultivars in Thailand based on macroscopic, microscopic, and genetic characters

Directory of Open Access Journals (Sweden)

Aunyachulee Ganogpichayagrai

2016-01-01

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.

Overcoming drug resistance of MCF-7/ADR cells by altering intracellular distribution of doxorubicin via MVP knockdown with a novel siRNA polyamidoamine-hyaluronic acid complex.

Science.gov (United States)

Han, Min; Lv, Qing; Tang, Xin-Jiang; Hu, Yu-Lan; Xu, Dong-Hang; Li, Fan-Zhu; Liang, Wen-Quan; Gao, Jian-Qing

2012-10-28

Drug resistance is one of the critical reasons leading to failure in chemotherapy. Enormous studies have been focused on increasing intracellular drug accumulation through inhibiting P-glycoprotein (Pgp). Meanwhile, we found that major vault protein (MVP) may be also involved in drug resistance of human breast cancer MCF-7/ADR cells by transporting doxorubicin (DOX) from the action target (i.e. nucleus) to cytoplasma. Herein polyamidoamine (PAMAM) dendrimers was functionalized by a polysaccharide hyaluronic acid (HA) to effectively deliver DOX as well as MVP targeted small-interfering RNA (MVP-siRNA) to down regulate MVP expression and improve DOX chemotherapy in MCF-7/ADR cells. In comparison with DOX solution (IC50=48.5 μM), an enhanced cytotoxicity could be observed for DOX PAMAM-HA (IC50=11.3 μM) as well as enhanced tumor target, higher intracellular accumulation, increased blood circulating time and less in vivo toxicity. Furthermore, codelivery of siRNA and DOX by PAMAM-HA exhibited satisfactory gene silencing effect as well as enhanced stability and efficient intracellular delivery of siRNA, which allowed DOX access to nucleus and induced subsequent much more cytotoxicity than siRNA absent case as a result of MVP knockdown. This observation highlights a promising application of novel nanocarrier PAMAM-HA, which could co-deliver anticancer drug and siRNA, in reversing drug resistance by altering intracellular drug distribution. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparison of GLUT1, GLUT3, and GLUT4 mRNA and the subcellular distribution of their proteins in normal human muscle

Science.gov (United States)

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

2000-01-01

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.

siRNA-loaded liposomes: Inhibition of encystment of Acanthamoeba and toxicity on the eye surface.

Science.gov (United States)

Faber, Kathrin; Zorzi, Giovanni K; Brazil, Nathalya T; Rott, Marilise B; Teixeira, Helder F

2017-09-01

Current treatments for Acanthamoeba keratitis are unspecific. Because of the presence of the resilient cyst form of the parasite, the infection is persistent. Silencing the key protein of cyst formation, glycogen phosphorylase, has shown potential for reducing encystment processes of the Acanthamoeba trophozoite. However, a suitable carrier to protect and deliver siRNA sequences is still needed. DOPE:DSPE-PEG liposomes were prepared by three different techniques and used to associate a therapeutic siRNA sequence. Liposomes prepared by film hydration followed by membrane extrusion were considered the most adequate ones with average size of 250 nm and zeta potential of +45 mV, being able to associate siRNA for at least 24 hr in culture medium. siRNA-liposomes could inhibit up to 66% of the encystment process. Cell viability studies demonstrated MTT reduction capacity higher than 80% after 3 hr incubation with this formulation. After 24 hr of incubation, LDH activity ranged for both the formulations from around 4% to 40%. In vivo tolerance studies in mice showed no macroscopic alteration in the eye structures up to 24 hr after eight administrations during 1 day. Histological studies showed regular tissue architecture without any morphological alteration. Overall, these results suggest that the formulations developed are a promising new strategy for the treatment of ocular keratitis caused by Acanthamoeba spp. © 2017 John Wiley & Sons A/S.

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

1998-05-01

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.

Macroscopic balance model for wave rotors

Science.gov (United States)

Welch, Gerard E.

1996-01-01

A mathematical model for multi-port wave rotors is described. The wave processes that effect energy exchange within the rotor passage are modeled using one-dimensional gas dynamics. Macroscopic mass and energy balances relate volume-averaged thermodynamic properties in the rotor passage control volume to the mass, momentum, and energy fluxes at the ports. Loss models account for entropy production in boundary layers and in separating flows caused by blade-blockage, incidence, and gradual opening and closing of rotor passages. The mathematical model provides a basis for predicting design-point wave rotor performance, port timing, and machine size. Model predictions are evaluated through comparisons with CFD calculations and three-port wave rotor experimental data. A four-port wave rotor design example is provided to demonstrate model applicability. The modeling approach is amenable to wave rotor optimization studies and rapid assessment of the trade-offs associated with integrating wave rotors into gas turbine engine systems.

Theory of superfluidity macroscopic quantum waves

International Nuclear Information System (INIS)

Ventura, I.

1978-10-01

A new description of superfluidity is proposed, based upon the fact that Bogoliubov's theory of superfluidity exhibits some so far unsuspected macroscopic quantum waves (MQWs), which have a topological nature and travel within the fluid at subsonic velocities. To quantize the bounded quasi-particles the field theoretic version of the Bohr-Sommerfeld quantization rule, is employed and also resort to a variational computation. In an instantaneous configuration the MQWs cut the condensate into blocks of phase, providing, by analogy with ferromagnetism, a nice explanation of what could be the lambda-transition. A crude estimate of the critical temperature gives T sub(c) approximately equal to 2-4K. An attempt is made to understand Tisza's two-fluid model in terms of the MQWs, and we rise the conjecture that they play an important role in the motion of second. We present also a qualitative prediction concerning to the behavior of the 'phononroton' peak below 1.0K, and propose two experiments to look for MQWs [pt

RNA detection in situ with FISH-STICs.

Science.gov (United States)

Sinnamon, John R; Czaplinski, Kevin

2014-02-01

The ability to detect RNA molecules in situ has long had important applications for molecular biological studies. Enzyme or dye-labeled antisense in vitro runoff transcripts and synthetic oligodeoxynucleotides (ODN) both have a proven track record of success, but each of these also has scientific and practical drawbacks and limitations to its use. We devised a means to use commercially synthesized oligonucleotides as RNA-FISH probes without further modification and show that such probes work well for detection of RNA in cultured cells. This approach can bind a high concentration of fluorescent ODN to a short stretch of an RNA using commercial DNA synthesis outlets available to any laboratory. We call this approach for creating in situ hybridization probes Fluorescence In Situ Hybridization with Sequential Tethered and Intertwined ODN Complexes (FISH-STICs). We demonstrate that one FISH-STIC probe can detect mRNA molecules in culture, and that probe detection can be improved by the addition of multiple probes that can be easily adapted for robust mRNA quantification. Using FISH-STICs, we demonstrate a nonoverlapping distribution for β-actin and γ-actin mRNA in cultured fibroblasts, and the detection of neuron-specific transcripts within cultured primary hippocampal neurons.

Towards an Einstein–Podolsky–Rosen paradox between two macroscopic atomic ensembles at room temperature

International Nuclear Information System (INIS)

He, Q Y; Reid, M D

2013-01-01

Experiments have reported the entanglement of two spatially separated macroscopic atomic ensembles at room temperature (Krauter et al 2011 Phys. Rev. Lett. 107 080503; Julsgaard et al 2001 Nature 413 400). We show how an Einstein–Podolsky–Rosen (EPR) paradox is realizable with this experiment. Our proposed test involves violation of an inferred Heisenberg uncertainty principle, which is a sufficient condition for an EPR paradox. This is a stronger test of nonlocality than entanglement. Our proposal would enable the first definitive confirmation of quantum EPR paradox correlations between two macroscopic objects at room temperature. This is a necessary intermediate step towards a nonlocal experiment with causal measurement separations. As well as having fundamental significance, the realization of an atomic EPR paradox could provide a resource for novel applications in quantum technology. (paper)

Towards an Einstein-Podolsky-Rosen paradox between two macroscopic atomic ensembles at room temperature

Science.gov (United States)

He, Q. Y.; Reid, M. D.

2013-06-01

Experiments have reported the entanglement of two spatially separated macroscopic atomic ensembles at room temperature (Krauter et al 2011 Phys. Rev. Lett. 107 080503; Julsgaard et al 2001 Nature 413 400). We show how an Einstein-Podolsky-Rosen (EPR) paradox is realizable with this experiment. Our proposed test involves violation of an inferred Heisenberg uncertainty principle, which is a sufficient condition for an EPR paradox. This is a stronger test of nonlocality than entanglement. Our proposal would enable the first definitive confirmation of quantum EPR paradox correlations between two macroscopic objects at room temperature. This is a necessary intermediate step towards a nonlocal experiment with causal measurement separations. As well as having fundamental significance, the realization of an atomic EPR paradox could provide a resource for novel applications in quantum technology.

Large-time behavior of solutions to a reaction-diffusion system with distributed microstructure

NARCIS (Netherlands)

Muntean, A.

2009-01-01

Abstract We study the large-time behavior of a class of reaction-diffusion systems with constant distributed microstructure arising when modeling diffusion and reaction in structured porous media. The main result of this Note is the following: As t ¿ 8 the macroscopic concentration vanishes, while

Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

Directory of Open Access Journals (Sweden)

Miguel Fribourg

2017-02-01

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

Localization of foot-and-mouth disease - RNA synthesis on newly formed cellular smooth membranous vacuoles

International Nuclear Information System (INIS)

Polatnick, J.; Wool, S.H.

1982-01-01

Viral RNA synthesis in foot-and-mouth disease infected bovine kidney cell cultures was associated throughout the infectious period with newly formed smooth membranous vacuoles. Membrane formation was measured by choline uptake. The site of RNA synthesis was determined by electron microscopic examination of autoradiograms of incorporated [ 3 H] uridine. Both membrane formation and RNA synthesis became signifcant at 2.5 hours postinfection, but membrane formation increased steadily to 4.5 hours while RNA synthesis peaked at 3.5 hours. Percent density distributions of developed silver grains on autoradiograms showed that almost all RNA synthesis was concentrated on the smooth vacuoles of infected cells. Histogram analysis of grain density distributions established that the site of RNA synthesis was the vacuolar membrane. The newly formed smooth membrane-bound vacuoles were not seen to coalesce into the large vacuolated areas typical of poliovirus cytopathogenicity. (Author)

Localization of foot-and-mouth disease - RNA synthesis on newly formed cellular smooth membranous vacuoles

Energy Technology Data Exchange (ETDEWEB)

Polatnick, J.; Wool, S.H. (United States Department of Agriculture, Science and Education, Greenport, New York (USA). Agricultural Research, Plum Island Animal Disease Center)

1982-01-01

Viral RNA synthesis in foot-and-mouth disease infected bovine kidney cell cultures was associated throughout the infectious period with newly formed smooth membranous vacuoles. Membrane formation was measured by choline uptake. The site of RNA synthesis was determined by electron microscopic examination of autoradiograms of incorporated (/sup 3/H) uridine. Both membrane formation and RNA synthesis became signifcant at 2.5 hours postinfection, but membrane formation increased steadily to 4.5 hours while RNA synthesis peaked at 3.5 hours. Percent density distributions of developed silver grains on autoradiograms showed that almost all RNA synthesis was concentrated on the smooth vacuoles of infected cells. Histogram analysis of grain density distributions established that the site of RNA synthesis was the vacuolar membrane. The newly formed smooth membrane-bound vacuoles were not seen to coalesce into the large vacuolated areas typical of poliovirus cytopathogenicity.

Macroscopic Description of Pressure-anisotropy-driven Collective Instability in Intense Charged Particle Beams

International Nuclear Information System (INIS)

Strasburg, Sean; Davidson, Ronald C.

2000-01-01

The macroscopic warm-fluid model developed by Lund and Davidson [Phys.Plasmas 5, 3028 (1998)] is used in the smooth-focusing approximation to investigate detailed stability properties of an intense charged particle beam with pressure anisotropy, assuming small-amplitude electrostatic perturbations about a waterbag equilibrium

Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

Directory of Open Access Journals (Sweden)

Hiraku Takada

Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

Macroscopic quantum tunneling of a Bose-Einstein condensate through double Gaussian barriers

Science.gov (United States)

Maeda, Kenji; Urban, Gregor; Weidemüller, Matthias; Carr, Lincoln D.

2015-05-01

Macroscopic quantum tunneling is one of the great manifestations of quantum physics, not only showing passage through a potential barrier but also emerging in a many-body wave function. We study a quasi-1D Bose-Einstein condensate of Lithium, confined by two Gaussian barriers, and show that in an experimentally realistic potential tens of thousands of atoms tunnel on time scales of 10 to 100 ms. Using a combination of variational and WKB approximations based on the Gross-Pitaevskii or nonlinear Schrödinger equation, we show that many unusual tunneling features appear due to the nonlinearity, including the number of trapped atoms exhibiting non-exponential decay, severe distortion of the barriers by the mean field, and even formation of a triple barrier in certain regimes. In the first 10ms, nonlinear many-body effects make the tunneling rates significantly larger than background loss rates, from 10 to 70 Hz. Thus we conclude that macroscopic quantum tunneling can be observed on experimental time scales. Funded by NSF, AFOSR, the Alexander von Humboldt foundation, and the Heidelberg Center for Quantum Dynamics.

Propagation of acoustic waves in a one-dimensional macroscopically inhomogeneous poroelastic material.

Science.gov (United States)

Gautier, G; Kelders, L; Groby, J P; Dazel, O; De Ryck, L; Leclaire, P

2011-09-01

Wave propagation in macroscopically inhomogeneous porous materials has received much attention in recent years. The wave equation, derived from the alternative formulation of Biot's theory of 1962, was reduced and solved recently in the case of rigid frame inhomogeneous porous materials. This paper focuses on the solution of the full wave equation in which the acoustic and the elastic properties of the poroelastic material vary in one-dimension. The reflection coefficient of a one-dimensional macroscopically inhomogeneous porous material on a rigid backing is obtained numerically using the state vector (or the so-called Stroh) formalism and Peano series. This coefficient can then be used to straightforwardly calculate the scattered field. To validate the method of resolution, results obtained by the present method are compared to those calculated by the classical transfer matrix method at both normal and oblique incidence and to experimental measurements at normal incidence for a known two-layers porous material, considered as a single inhomogeneous layer. Finally, discussion about the absorption coefficient for various inhomogeneity profiles gives further perspectives. © 2011 Acoustical Society of America

Modeling two-stage bunch compression with wakefields: Macroscopic properties and microbunching instability

Directory of Open Access Journals (Sweden)

R. A. Bosch

2008-09-01

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.

Correlation of macroscopic osteoarthrotic changes and radiographic findings in the acromioclavicular joint

International Nuclear Information System (INIS)

Stenlund, B.; Marions, O.; Engstroem, K.F.; Goldie, I.; Soedersjukhuset, Stockholm; Karolinska Sjukhuset, Stockholm

1988-01-01

In a total of 108 acromioclavicular articulations from cadavers the osteoarthrotic changes were studied. The articulations were macroscopically and radiographically ranked according to their grade of osteoarthrosis. The two ranking lines were correlated statistically and showed a rank correlation of 0.741. In 38 articulations tomography was also carried out. These articulations were classified into five grades of osteoarthrosis and the macroscopic, conventional radiographic and tomographic gradings were compared. The correlation coefficient for tomography versus macroscopy was 0.714. Tomography versus standard radiography showed a correlation of 0.767 and standard radiography versus macroscopy a correlation of 0.841. The standard radiographic investigation reveals moderate and severe osteoarthrotic changes in the acromioclavicular joint but cannot depict smaller changes. Tomography does not seem to improve the specificity. There is a need for a better radiologic technique in the examination of the acromioclavicular joint. Radiography during some kind of loading might be a practical way of improving the specificity and make it possible to show early osteoarthrosis in the acromioclavicular articulation. (orig.)

Correlation of macroscopic osteoarthrotic changes and radiographic findings in the acromioclavicular joint

Energy Technology Data Exchange (ETDEWEB)

Stenlund, B.; Marions, O.; Engstroem, K.F.; Goldie, I.

In a total of 108 acromioclavicular articulations from cadavers the osteoarthrotic changes were studied. The articulations were macroscopically and radiographically ranked according to their grade of osteoarthrosis. The two ranking lines were correlated statistically and showed a rank correlation of 0.741. In 38 articulations tomography was also carried out. These articulations were classified into five grades of osteoarthrosis and the macroscopic, conventional radiographic and tomographic gradings were compared. The correlation coefficient for tomography versus macroscopy was 0.714. Tomography versus standard radiography showed a correlation of 0.767 and standard radiography versus macroscopy a correlation of 0.841. The standard radiographic investigation reveals moderate and severe osteoarthrotic changes in the acromioclavicular joint but cannot depict smaller changes. Tomography does not seem to improve the specificity. There is a need for a better radiologic technique in the examination of the acromioclavicular joint. Radiography during some kind of loading might be a practical way of improving the specificity and make it possible to show early osteoarthrosis in the acromioclavicular articulation.

The RNA gene information: retroelement-microRNA entangling as the RNA quantum code.

Science.gov (United States)

Fujii, Yoichi Robertus

2013-01-01

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.

Computational optimization of catalyst distributions at the nano-scale

International Nuclear Information System (INIS)

Ström, Henrik

2017-01-01

Highlights: • Macroscopic data sampled from a DSMC simulation contain statistical scatter. • Simulated annealing is evaluated as an optimization algorithm with DSMC. • Proposed method is more robust than a gradient search method. • Objective function uses the mass transfer rate instead of the reaction rate. • Combined algorithm is more efficient than a macroscopic overlay method. - Abstract: Catalysis is a key phenomenon in a great number of energy processes, including feedstock conversion, tar cracking, emission abatement and optimizations of energy use. Within heterogeneous, catalytic nano-scale systems, the chemical reactions typically proceed at very high rates at a gas–solid interface. However, the statistical uncertainties characteristic of molecular processes pose efficiency problems for computational optimizations of such nano-scale systems. The present work investigates the performance of a Direct Simulation Monte Carlo (DSMC) code with a stochastic optimization heuristic for evaluations of an optimal catalyst distribution. The DSMC code treats molecular motion with homogeneous and heterogeneous chemical reactions in wall-bounded systems and algorithms have been devised that allow optimization of the distribution of a catalytically active material within a three-dimensional duct (e.g. a pore). The objective function is the outlet concentration of computational molecules that have interacted with the catalytically active surface, and the optimization method used is simulated annealing. The application of a stochastic optimization heuristic is shown to be more efficient within the present DSMC framework than using a macroscopic overlay method. Furthermore, it is shown that the performance of the developed method is superior to that of a gradient search method for the current class of problems. Finally, the advantages and disadvantages of different types of objective functions are discussed.

The "G-Spot" Is Not a Structure Evident on Macroscopic Anatomic Dissection of the Vaginal Wall.

Science.gov (United States)

Hoag, Nathan; Keast, Janet R; O'Connell, Helen E

2017-12-01

Controversy exists in the literature regarding the presence or absence of an anatomic "G-spot." However, few studies have examined the detailed topographic or histologic anatomy of the putative G-spot location. To determine the anatomy of the anterior vaginal wall and present detailed, systematic, accessible findings from female cadaveric dissections to provide anatomic clarity with respect to this location. Systematic anatomic dissections were performed on 13 female cadavers (32-97 years old, 8 fixed and 5 fresh) to characterize the gross anatomy of the anterior vaginal wall. Digital photography was used to document dissections. Dissection preserved the anterior vaginal wall, urethra, and clitoris. In 9 cadavers, the vaginal epithelial layer was reflected to expose the underlying urethral wall and associated tissues. In 4 cadavers, the vaginal wall was left intact before preservation. Once photographed, 8 specimens were transversely sectioned for macroscopic inspection and histologic examination. The presence or absence of a macroscopic anatomic structure at detailed cadaveric pelvis dissection that corresponds to the previously described G-spot and gross anatomic description of the anterior vaginal wall. Deep to the lining epithelium of the anterior vaginal wall is the urethra. There is no macroscopic structure other than the urethra and vaginal wall lining in the location of the putative G-spot. Specifically, there is no apparent erectile or "spongy" tissue in the anterior vaginal wall, except where the urethra abuts the clitoris distally. The absence of an anatomic structure corresponding to the putative G-spot helps clarify the controversy on this subject. Limitations to this study include limited access to specimens immediately after death and potential for observational bias. In addition, age, medical history, and cause of death are not publishable for privacy reasons. However, it is one of the most thorough and complete anatomic evaluations documenting the

Determination of the macroscopic chloride diffusivity in cementitious by porous materials coupling periodic homogenization of Nernst-Planck equation with experimental protocol

Directory of Open Access Journals (Sweden)

Olivier Millet

2008-03-01

Full Text Available In this paper, we propose a macroscopic migration model for cementitious porous media obtained from periodic homogenization technique. The dimensional analysis of Nernst-Planck equation leads to dimensionless numbers characterizing the problem. According to the order of magnitude of the dimensionless numbers, the homogenization of Nernst-Planck equation leads at the leading order to a macroscopic model where several rates can be coupled or not. For a large applied electrical field accelerating the transfer of ionic species, we obtain a macroscopic model only involving migration. A simple experimental procedure of measurement of the homogenized chlorides diffusivity is then proposed for cement-based materials.

Coherence and entanglement in the ground state of a bosonic Josephson junction: From macroscopic Schroedinger cat states to separable Fock states

International Nuclear Information System (INIS)

Mazzarella, G.; Toigo, F.; Salasnich, L.; Parola, A.

2011-01-01

We consider a bosonic Josephson junction made of N ultracold and dilute atoms confined by a quasi-one-dimensional double-well potential within the two-site Bose-Hubbard model framework. The behavior of the system is investigated at zero temperature by varying the interatomic interaction from the strongly attractive regime to the repulsive one. We show that the ground state exhibits a crossover from a macroscopic Schroedinger-cat state to a separable Fock state through an atomic coherent regime. By diagonalizing the Bose-Hubbard Hamiltonian we characterize the emergence of the macroscopic cat states by calculating the Fisher information F, the coherence by means of the visibility α of the interference fringes in the momentum distribution, and the quantum correlations by using the entanglement entropy S. Both Fisher information and visibility are shown to be related to the ground-state energy by employing the Hellmann-Feynman theorem. This result, together with a perturbative calculation of the ground-state energy, allows simple analytical formulas for F and α to be obtained over a range of interactions, in excellent agreement with the exact diagonalization of the Bose-Hubbard Hamiltonian. In the attractive regime the entanglement entropy attains values very close to its upper limit for a specific interaction strength lying in the region where coherence is lost and self-trapping sets in.

New potential markers of in vitro tomato morphogenesis identified by mRNA differential display.

Science.gov (United States)

Torelli, A; Soragni, E; Bolchi, A; Petrucco, S; Ottonello, S; Branca, C

1996-12-01

The identification of plant genes involved in early phases of in vitro morphogenesis can not only contribute to our understanding of the processes underlying growth regulator-controlled determination, but also provide novel markers for evaluating the outcome of in vitro regeneration experiments. To search for such genes and to monitor changes in gene expression accompanying in vitro regeneration, we have adapted the mRNA differential display technique to the comparative analysis of a model system of tomato cotyledons that can be driven selectively toward either shoot or callus formation by means of previously determined growth regulator supplementations. Hormone-independent transcriptional modulation (mainly down-regulation) has been found to be the most common event, indicating that a non-specific reprogramming of gene expression quantitatively predominates during the early phases of in vitro culture. However, cDNA fragments representative of genes that are either down-regulated or induced in a programme-specific manner could also be identified, and two of them (G35, G36) were further characterized. One of these cDNA fragments, G35, corresponds to an mRNA that is down-regulated much earlier in callus- (day 2) than in shoot-determined explants (day 6). The other, G36, identifies an mRNA that is transiently expressed in shoot-determined explants only, well before any macroscopic signs of differentiation become apparent, and thus exhibits typical features of a morphogenetic marker.

Building the library of RNA 3D nucleotide conformations using the clustering approach

Directory of Open Access Journals (Sweden)

Zok Tomasz

2015-09-01

Full Text Available An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i backbone- and (ii ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.

TBI server: a web server for predicting ion effects in RNA folding.

Science.gov (United States)

Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

2015-01-01

Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects. The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects. By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

TBI server: a web server for predicting ion effects in RNA folding.

Directory of Open Access Journals (Sweden)

Yuhong Zhu

Full Text Available Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects.The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects.By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

Linking stress with macroscopic and microscopic leaf response in trees: New diagnostic perspectives

Energy Technology Data Exchange (ETDEWEB)

Guenthardt-Goerg, Madeleine S. [Swiss Federal Institute for Forest, Snow and Landscape Research, WSL, Zuercherstrasse 111, CH-8903 Birmensdorf (Switzerland)]. E-mail: madeleine.goerg@wsl.ch; Vollenweider, Pierre [Swiss Federal Institute for Forest, Snow and Landscape Research, WSL, Zuercherstrasse 111, CH-8903 Birmensdorf (Switzerland)

2007-06-15

Visible symptoms in tree foliage can be used for stress diagnosis once validated with microscopical analyses. This paper reviews and illustrates macroscopical and microscopical markers of stress with a biotic (bacteria, fungi, insects) or abiotic (frost, drought, mineral deficiency, heavy metal pollution in the soil, acidic deposition and ozone) origin helpful for the validation of symptoms in broadleaved and conifer trees. Differentiation of changes in the leaf or needle physiology, through ageing, senescence, accelerated cell senescence, programmed cell death and oxidative stress, provides additional clues raising diagnosis efficiency, especially in combination with information about the target of the stress agent at the tree, leaf/needle, tissue, cell and ultrastructural level. Given the increasing stress in a changing environment, this review discusses how integrated diagnostic approaches lead to better causal analysis to be applied for specific monitoring of stress factors affecting forest ecosystems. - Macroscopic leaf symptoms and their microscopic analysis as stress bioindications.

Linking stress with macroscopic and microscopic leaf response in trees: New diagnostic perspectives

International Nuclear Information System (INIS)

Guenthardt-Goerg, Madeleine S.; Vollenweider, Pierre

2007-01-01

Visible symptoms in tree foliage can be used for stress diagnosis once validated with microscopical analyses. This paper reviews and illustrates macroscopical and microscopical markers of stress with a biotic (bacteria, fungi, insects) or abiotic (frost, drought, mineral deficiency, heavy metal pollution in the soil, acidic deposition and ozone) origin helpful for the validation of symptoms in broadleaved and conifer trees. Differentiation of changes in the leaf or needle physiology, through ageing, senescence, accelerated cell senescence, programmed cell death and oxidative stress, provides additional clues raising diagnosis efficiency, especially in combination with information about the target of the stress agent at the tree, leaf/needle, tissue, cell and ultrastructural level. Given the increasing stress in a changing environment, this review discusses how integrated diagnostic approaches lead to better causal analysis to be applied for specific monitoring of stress factors affecting forest ecosystems. - Macroscopic leaf symptoms and their microscopic analysis as stress bioindications

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

1998-03-01

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)

The effect of learning multimedia on students’ understanding of macroscopic, sub-microscopic, and symbolic levels in electrolyte and nonelectrolyte

Science.gov (United States)

Eliyawati; Rohman, I.; Kadarohman, A.

2018-05-01

This research aims to investigate the effect of learning multimedia on students’ understanding of macroscopic, sub-microscopic, and symbolic levels in electrolyte and nonelectrolyte topic. The quasi-experimental with one group pre-test post-test design was used. Thirty-five students were experimental class and another thirty-five were control class. The instrument was used is three representation levels. The t-test was performed on average level of 95% to identify the significant difference between experimental class and control class. The results show that the normalized gain average of experimental class is 0.75 (high) and the normalized gain average of control class is 0.45 (moderate). There is significant difference in students’ understanding in sub-microscopic and symbolic levels and there is not significant difference of students’ understanding in macroscopic level between experimental class and control class. The normalized gain of students’ understanding of macroscopic, sub-microscopic and symbolic in experimental class are 0.6 (moderate), 0.75 (high), and 0.64 (moderate), while the normalized gain of students’ understanding of macroscopic, sub-microscopic and symbolic in control class are 0.49 (moderate), 0.39 (high), and 0.3 (moderate). Therefore, it can be concluded that learning multimedia can help in improving students’ understanding especially in sub-microscopic and symbolic levels.

Conductance fluctuations in a macroscopic 3-dimensional Anderson insulator

International Nuclear Information System (INIS)

Sanquer, M.

1990-01-01

We report magnetoconductance experiment on a amorphous Y x -Si 1-x alloy (∼0.3). which is an Anderson insulator where spin-orbit scattering is strong. Two principal and new features emerge from the data: the first one is an halving of the localization length by the application of a magnetic field of about 2.5 Teslas. This effect is predicted by a new approach of transport in Anderson insulators where basic symetry considerations are the most important ingredient. The second one is the observation of reproducible conductance fluctuations at very low temperature in this macroscopic 3 D amorphous material

Dicer uses distinct modules for recognizing dsRNA termini.

Science.gov (United States)

Sinha, Niladri K; Iwasa, Janet; Shen, Peter S; Bass, Brenda L

2018-01-19

Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Drosophila Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging termini are cleaved distributively. To understand this discrimination, we used cryo-electron microscopy to solve structures of Drosophila Dicer-2 alone and in complex with blunt dsRNA. Whereas the Platform-PAZ domains have been considered the only Dicer domains that bind dsRNA termini, unexpectedly, we found that the helicase domain is required for binding blunt, but not 3' overhanging, termini. We further showed that blunt dsRNA is locally unwound and threaded through the helicase domain in an adenosine triphosphate-dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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

Directory of Open Access Journals (Sweden)

V. Couvreur

2012-08-01

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 K_rs and the compensatory RWU conductance K_comp. 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.

Are the toroidal shapes of heavy-ion reactions seen in macroscopic drop collisions?

International Nuclear Information System (INIS)

Menchaca R, A.; Borunda, M.; Hidalgo, S.S.; Huidobro, F.; Michaelian, K.; Perez, A.; Rodriguez, V.

1996-01-01

Experiments involving the collisions of water, and mineral oil, drops are reported. The aim is to search for toroidal configurations predicted by, both, macroscopic fluid dynamic and nuclear models. Instead, we find the formation of thin liquid sheets surrounded by a somewhat thicker rim presenting a fingering instability. (Author)

Investigating the impact of uneven magnetic flux density distribution on core loss estimation

DEFF Research Database (Denmark)

Niroumand, Farideh Javidi; Nymand, Morten; Wang, Yiren

2017-01-01

is calculated according to an effective flux density value and the macroscopic dimensions of the cores. However, the flux distribution in the core can alter by core shapes and/or operating conditions due to nonlinear material properties. This paper studies the element-wise estimation of the loss in magnetic......There are several approaches for loss estimation in magnetic cores, and all these approaches highly rely on accurate information about flux density distribution in the cores. It is often assumed that the magnetic flux density evenly distributes throughout the core and the overall core loss...

Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

Science.gov (United States)

Brezinski, Mark E; Rupnick, Maria

2016-01-01

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

Electricity in foams: from one soapy interface to the macroscopic material

Science.gov (United States)

Biance, Anne-Laure

2017-11-01

Liquid foams (a dispersion of gas bubbles in a soapy solution) destabilize with time due to coarsening, coalescence and gravity driven drainage. We propose here to inhibit (or trigger) the foam destabilization by applying an electric field to the material. This effect is investigated at the different scales of the system: one soapy interface, one liquid film, the macroscopic foam. The generation of an electroosmotic flow near a soapy liquid/gas interface raises many issues. How does the flow affect surfactant repartition? Is there a Marangoni stress at the interface? At the scale of one soap film, how the electric field affects the film stability and deformation? In a macroscopic foam, one can wonder whether the electric field can indeed reverse gravity driven drainage and increase foam lifetime? These different issues are considered by developing new experimental techniques allowing us to probe surfactant repartition at liquid interfaces, soap film thicknesses and liquid foam properties when an electric field is applied. The results will be presented together with a comprehensive picture of the mechanisms arising at each scale of the material, to conclude with the potential use of electricity in liquid foams to control destabilization. Collaborators: Baptiste Blanc, Oriane Bonhomme, Laurent Joly, Christophe Ybert.

Effects of ultraviolet irradiation and postirradiation incubation on heterogeneous nuclear RNA size in murine cells

International Nuclear Information System (INIS)

Ali, R.; Sauerbier, W.

1978-01-01

We have analyzed the decrease in synthesis of individual size classes of heterogeneous nuclear RNA (hnRNA) in ultraviolet (uv)-irradiated Merwin plasmacytoma (MPC-11) cells at various times of postirradiation incubation. HnRNA from nonirradiated control cells is distributed over a wide range from approximately 60S to 5S, with 42S RNA carrying more label than any other size class. HnRNA from uv-irradiated cells shows a dose-dependent shift in size distribution toward lower molecular weight. The size distribution of hnRNA synthesized after prolonged times of postirradiation incubation is restored toward normal, i.e., synthesis of long RNA molecules increases relative to the synthesis of short ones. Analysis of the total number of hnRNA chains synthesized during a 20-min [ 3 H]uridine pulse shows a considerable eduction in their number with increasing uv dose. Murine cell lines are excision-repair-deficient but capable of post replication repair inhibited by caffeine. HnRNA transcripts of cells incubated in its presence were studied. The caffeine, which has no effect on hnRNA size in control cells, inhibits to a considerable extent the restoration of full-length transcripts during postirradiation incubation. The lack of excision repair in MPC-11 was confirmed by the analysis of pyrimidine dimers in trichloracetic acid-insoluble and soluble fractions within 8 h of postirradiation incubation. The size of parental and daughter strand DNA in uv-irradiated cells was correlated with RNA transcript size. The parental DNA in these experiments does not change its size as a consequence of uv exposure and postirradiation incubation. In contrast, daughter DNA strands are short in uv-irradiated cells and they increase in size during postirradiation incubation to reach the size of parental strands after 8 h

Macroscopic influence on the spontaneous symmetry breaking in quantum field

International Nuclear Information System (INIS)

Kirzhnitz, D.A.

1977-01-01

Major results of investigations concerning macroscopic influence (heating, compression, external field and current) on elementary particle systems with spontaneous symmetry breaking are briefly reviewed. The study of this problem has been stimulated by recent progress in the unified renormalizable theory of elementary particles. Typically it appears that at some values of external parameters a phase transition with symmetry restoration takes place. There exists a profound and far going analogy with phase transition in many-body physics especially with superconductivity phenomenon. Some applications to cosmology are also considered

The distribution of intervariant crystallographic planes in a lath martensite using five macroscopic parameters

International Nuclear Information System (INIS)

Beladi, Hossein; Rohrer, Gregory S.; Rollett, Anthony D.; Tari, Vahid; Hodgson, Peter D.

2014-01-01

Electron backscatter diffraction analysis was employed to compute the closest orientation relationship and the distribution of intervariant boundary character in a lath martensitic microstructure. The misorientations were close to the Kurdjumov–Sachs orientation relationship. The intervariant crystallographic plane distribution exhibited a relatively high anisotropy with a tendency for the lath interfaces to terminate on (1 1 0) planes. This results from the crystallographic constraints associated with the shear transformation rather than a low energy interface configuration. The lath martensite habit plane was determined to be mostly (1 1 0) or near (1 1 0). The relative populations of boundaries with [1 1 1] and [1 1 0] misorientations were greater than other high index misorientations, mostly characterized as (1 1 0) symmetric tilt and (1 1 0) twist boundary types, respectively. Analysis with homology metrics of the connectivity in the lath martensitic microstructure revealed the connectivity dominated by population of misorientation angle and boundary plane type

Small angle scattering study of the structure and organization of RNA and protein in Brome Mosaic Virus (BMV)

Science.gov (United States)

Das, Narayan C.; Warren, Garfield T.; Cheng, Si; Kao, C. Cheng; Ni, Peng; Dragnea, Bogdan; Sokol, Paul E.

2012-02-01

Brome mosaic virus (BMV) is a small icosahedral of the alpha virus-like superfamily of RNA with a segmented positive-strand RNA genome and a mean diameter ˜ 268å that offers high levels of RNA synthesis and virus production in plants. BMV also tightly regulates the packaging of its four RNAs (RNA1 through RNA4) into three separate particles; RNA1 and RNA2 are encapsidated separately while one copy each of RNA3 and RNA4 are normally packaged together. Small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) were applied to study the size, shape and protein-RNA organization of BMV. D2O/H2O mixture was used to enhance contrast in SANS measurement. The radial distribution of BMV from the Fourier transform of scattering spectrum gives a clear indication of RNA packing, and distribution and their structure in the BMV. The result reveals that the virus is about 266 å in diameter and is composed of RNA inside the virion coated with a protein shell.

BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.

Science.gov (United States)

Lee, Hyungro; Yang, Youngik; Chae, Heejoon; Nam, Seungyoon; Choi, Donghoon; Tangchaisin, Patanachai; Herath, Chathura; Marru, Suresh; Nephew, Kenneth P; Kim, Sun

2012-09-01

MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research. However, the ability to conduct genome-wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extended the BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by the XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an "as needed" basis; 4) distributed orchestration supports complex and long running workflows asynchronously. We believe that BioVLAB-MMIA will be an easy-to-use computing environment for researchers who plan to perform genome-wide microRNA-mRNA (gene) integrated analysis tasks.

iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

Directory of Open Access Journals (Sweden)

Jittrawan Thaiprasit

2016-03-01

Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA

Time-dependent mechanical behavior of human amnion: Macroscopic and microscopic characterization

OpenAIRE

2014-01-01

© 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Characterizing the mechanical response of the human amnion is essential to understand and to eventually prevent premature rupture of fetal membranes. In this study a large set of macroscopic and microscopic mechanical tests have been carried out on fresh unfixed amnion to gain insight into the time dependent material response and the underlying mechanisms. Creep and relaxation responses of amnion were characterized in...

Macroscopic angular-momentum stages of Bose-Einstein condensates in toroidal traps

International Nuclear Information System (INIS)

Benakli, M.; Raghavan, S.; Smerzi, A.; Fantoni, S.; Shenoy, S.R.

2001-03-01

We study the stability of a rotating repulsive-atom Bose-Einstein condensate in a toroidal trap. The resulting macroscopic angular-momentum states with integer vorticity l spread radially, lowering rotational energies. These states are robust against vorticity-lowering decays, with estimated metastability barriers capable of sustaining large angular momenta (1 < or ∼ 10) for typical parameters. We identify the centrifugally squashed l-dependent density profile as a possible signature of condensate rotation and superfluidity. (author)

Efficient RNA extraction protocol for the wood mangrove species Laguncularia racemosa suited for next-generation RNA sequencing

International Nuclear Information System (INIS)

Wilwerth, M. W.; Rossetto, P.

2016-01-01

Mangrove flora and habitat have immeasurable importance in marine and coastal ecology as well as in the economy. Despite their importance, they are constantly threatened by oil spill accidents and environmental contamination; therefore, it is crucial to understand the changes in gene expression to better predict toxicity in these plants. Among the species of Atlantic coast mangrove (Americas and Africa), Laguncularia racemosa, or white mangrove, is a conspicuous species. The wide distribution of L. racemosa in areas where marine oil exploration is rapidly increasing make it a candidate mangrove species model to uncover the impact of oil spills at the molecular level with the use of massive transcriptome sequencing. However, for this purpose, the RNA extraction protocol should ensure low levels of contaminants and structure integrity. In this study, eight RNA extraction methods were tested and analysed using downstream applications. The InviTrap Spin Plant RNA Mini Kit performed best with regard to purity and integrity. Moreover, the obtained RNA was submitted to cDNA synthesis and RT-PCR, successfully generating amplification products of the expected size. These Results show the applicability of the RNA obtained here for downstream methodologies, such as the construction of cDNA libraries for the Illumina Hi-seq platform. (author)

Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

Science.gov (United States)

Tan, M K

1991-08-01

A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

Science.gov (United States)

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

Generation of macroscopic singlet states in atomic ensembles

Science.gov (United States)

Tóth, Géza; Mitchell, Morgan W.

2010-05-01

We study squeezing of the spin uncertainties by quantum non-demolition (QND) measurement in non-polarized spin ensembles. Unlike the case of polarized ensembles, the QND measurements can be performed with negligible back-action, which allows, in principle, perfect spin squeezing as quantified by Tóth et al (2007 Phys. Rev. Lett. 99 250405). The generated spin states approach many-body singlet states and contain a macroscopic number of entangled particles even when individual spin is large. We introduce the Gaussian treatment of unpolarized spin states and use it to estimate the achievable spin squeezing for realistic experimental parameters. Our proposal might have applications for magnetometry with a high spatial resolution or quantum memories storing information in decoherence free subspaces.

Catalytic Growth of Macroscopic Carbon Nanofibers Bodies with Activated Carbon

Science.gov (United States)

Abdullah, N.; Rinaldi, A.; Muhammad, I. S.; Hamid, S. B. Abd.; Su, D. S.; Schlogl, R.

2009-06-01

Carbon-carbon composite of activated carbon and carbon nanofibers have been synthesized by growing Carbon nanofiber (CNF) on Palm shell-based Activated carbon (AC) with Ni catalyst. The composites are in an agglomerated shape due to the entanglement of the defective CNF between the AC particles forming a macroscopic body. The macroscopic size will allow the composite to be used as a stabile catalyst support and liquid adsorbent. The preparation of CNT/AC nanocarbon was initiated by pre-treating the activated carbon with nitric acid, followed by impregnation of 1 wt% loading of nickel (II) nitrate solutions in acetone. The catalyst precursor was calcined and reduced at 300° C for an hour in each step. The catalytic growth of nanocarbon in C2H4/H2 was carried out at temperature of 550° C for 2 hrs with different rotating angle in the fluidization system. SEM and N2 isotherms show the level of agglomeration which is a function of growth density and fluidization of the system. The effect of fluidization by rotating the reactor during growth with different speed give a significant impact on the agglomeration of the final CNF/AC composite and thus the amount of CNFs produced. The macrostructure body produced in this work of CNF/AC composite will have advantages in the adsorbent and catalyst support application, due to the mechanical and chemical properties of the material.

Combinatorics of RNA-RNA interaction

DEFF Research Database (Denmark)

Li, Thomas J X; Reidys, Christian

2012-01-01

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...

Macroscopic Magnetic Coupling Effect: The Physical Origination of a High-Temperature Superconducting Flux Pump

Science.gov (United States)

Wang, Wei; Coombs, Tim

2018-04-01

We have uncovered at the macroscopic scale a magnetic coupling phenomenon in a superconducting YBa2Cu3O7 -δ (YBCO) film, which physically explains the mechanism of the high-temperature superconducting flux pump. The coupling occurs between the applied magnetic poles and clusters of vortices induced in the YBCO film, with each cluster containing millions of vortices. The coupling energy is verified to originate from the inhomogeneous field of the magnetic poles, which reshapes the vortex distribution, aggregates millions of vortices into a single cluster, and accordingly moves with the poles. A contrast study is designed to verify that, to provide the effective coupling energy, the applied wavelength must be short while the field amplitude must be strong, i.e., local-field inhomogeneity is the crucial factor. This finding broadens our understanding of the collective vortex behavior in an applied magnetic field with strong local inhomogeneity. Moreover, this phenomenon largely increases the controlled vortex flow rate by several orders of magnitude compared with existing methods, providing motivation for and physical support to a new branch of wireless superconducting dc power sources, i.e., the high-temperature superconducting flux pump.

Collective motion of macroscopic spheres floating on capillary ripples: Dynamic heterogeneity and dynamic criticality

NARCIS (Netherlands)

Sanli, Ceyda; Saitoh, K.; Luding, Stefan; van der Meer, Roger M.

2014-01-01

When a densely packed monolayer of macroscopic spheres floats on chaotic capillary Faraday waves, a coexistence of large scale convective motion and caging dynamics typical for glassy systems is observed. We subtract the convective mean flow using a coarse graining (homogenization) method and reveal

Pinning of a curved flux line by macroscopic inclusions in a type II superconductor

International Nuclear Information System (INIS)

Shehata, L.N.; Saif, A.G.

1983-08-01

The pinning force is calculated as a function of the distance between a curved (or straight) flux line and the centre of a macroscopic superconducting (or normal) ellipsoidal inclusion. When the ellipsoidal tends to a spherical inclusion the results agree with those previously obtained. (author)

Derivation of some new distributions in statistical mechanics using maximum entropy approach

Directory of Open Access Journals (Sweden)

Ray Amritansu

2014-01-01

Full Text Available The maximum entropy principle has been earlier used to derive the Bose Einstein(B.E., Fermi Dirac(F.D. & Intermediate Statistics(I.S. distribution of statistical mechanics. The central idea of these distributions is to predict the distribution of the microstates, which are the particle of the system, on the basis of the knowledge of some macroscopic data. The latter information is specified in the form of some simple moment constraints. One distribution differs from the other in the way in which the constraints are specified. In the present paper, we have derived some new distributions similar to B.E., F.D. distributions of statistical mechanics by using maximum entropy principle. Some proofs of B.E. & F.D. distributions are shown, and at the end some new results are discussed.

Levitation of Bose-Einstein condensates induced by macroscopic non-adiabatic quantum tunneling

OpenAIRE

Nakamura, Katsuhiro; Kohi, Akihisa; Yamasaki, Hisatsugu; Perez-Garcia, Victor M.

2006-01-01

We study the dynamics of two-component Bose-Einstein condensates trapped in different vertical positions in the presence of an oscillating magnetic field. It is shown here how tuning appropriately the oscillation frequency of the magnetic field leads to the levitation of the system against gravity. This phenomenon is a manifestation of a macroscopic non-adiabatic tunneling in a system with internal degrees of freedom.

A macroscopic constitutive model of temperature-induced phase transition of polycrystalline Ni2MnGa by directional solidification

International Nuclear Information System (INIS)

Zhu, Yuping; Gu, Yunling; Liu, Hongguang

2015-01-01

Directional solidification technology has been widely used to improve the properties of polycrystalline Ni 2 MnGa materials. Mechanical training can adjust the internal organizational structures of the materials, reduce the stress of twin boundaries motion, and then result in larger strain at lower outfield levels. In this paper, we test the microscopic structure of Ni 2 MnGa polycrystalline ferromagnetic shape memory alloy produced by directional solidification and compress it along two axes successively for mechanical training. The influences of pre-compressive stresses on the temperature-induced strains are analyzed. The macroscopic mechanical behaviors show anisotropy. According to the generating mechanism of the macroscopic strain, a three-dimensional constitutive model is established. Based on thermodynamic method, the kinetic equations of the martensitic transformation and inverse transformation are presented considering the driving force and energy dissipation. The prediction curves of temperature-induce strains along two different directions are investigated. And the results coincide well with the experiment data. It well explains the macroscopic anisotropy mechanical behaviors and fits for using in engineering

A fortran code CVTRAN to provide cross-section file for TWODANT by using macroscopic file written by SRAC

International Nuclear Information System (INIS)

Yamane, Tsuyoshi; Tsuchihashi, Keichiro

1999-03-01

A code CVTRAN provides the macroscopic cross-sections in the format of XSLIB file which is one of Standard interface files for a two-dimensional Sn transport code TWODANT by reading a macroscopic cross section file in the PDS format which is prepared by SRAC execution. While a two-dimensional Sn transport code TWOTRAN published by LANL is installed as a module in the SRAC code system, several functions such as alpha search, concentration search, zone thickness search and various edits are suppressed. Since the TWODANT code was released from LANL, its short running time, stable convergence and plenty of edits have attracted many users. The code CVTRAN makes the TWODANT available to the SRAC user by providing the macroscopic cross-sections on a card-image file XSLIB. The CVTRAN also provides material dependent fission spectra into a card-image format file CVLIB, together with group velocities, group boundary energies and material names. The user can feed them into the TWODANT input, if necessary, by cut-and-paste command. (author)

Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

Science.gov (United States)

Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

2009-01-01

Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

Macroscopic quantum coherence in a magnetic nanoparticle above the surface of a superconductor

Science.gov (United States)

Chudnovsky; Friedman

2000-12-11

We study macroscopic quantum tunneling of the magnetic moment in a single-domain particle placed above the surface of a superconductor. Such a setup allows one to manipulate the height of the energy barrier, preserving the degeneracy of the ground state. The tunneling amplitude and the effect of the dissipation in the superconductor are computed.

Macroscopic Quantum Coherence in a Magnetic Nanoparticle Above the Surface of a Superconductor

Energy Technology Data Exchange (ETDEWEB)

Chudnovsky, Eugene M.; Friedman, Jonathan R.

2000-12-11

We study macroscopic quantum tunneling of the magnetic moment in a single-domain particle placed above the surface of a superconductor. Such a setup allows one to manipulate the height of the energy barrier, preserving the degeneracy of the ground state. The tunneling amplitude and the effect of the dissipation in the superconductor are computed.

Macroscopic Quantum Coherence in a Magnetic Nanoparticle Above the Surface of a Superconductor

International Nuclear Information System (INIS)

Chudnovsky, Eugene M.; Friedman, Jonathan R.

2000-01-01

We study macroscopic quantum tunneling of the magnetic moment in a single-domain particle placed above the surface of a superconductor. Such a setup allows one to manipulate the height of the energy barrier, preserving the degeneracy of the ground state. The tunneling amplitude and the effect of the dissipation in the superconductor are computed

Salvage radiotherapy for macroscopic local recurrences after radical prostatectomy. A national survey on patterns of practice

Energy Technology Data Exchange (ETDEWEB)

Dal Pra, Alan [Bern University Hospital, Inselspital Bern, Department of Radiation Oncology, Bern (Switzerland); Panje, Cedric; Glatzer, Markus; Putora, Paul Martin [Kantonsspital St. Gallen, Department of Radiation Oncology, St. Gallen (Switzerland); Zilli, Thomas [Hospitaux Universitaires de Geneve, Department of Radiation Oncology, Geneve (Switzerland); Arnold, Winfried [Luzerner Kantonsspital, Department of Radiation Oncology, Luzerner (Switzerland); Brouwer, Kathrin [Stadtspital Triemli, Department of Radiation Oncology, Zuerich (Switzerland); Garcia, Helena [Universitaetsspital Zuerich, Department of Radiation Oncology, Zuerich (Switzerland); Gomez, Silvia [Kantonsspital Aarau, Department of Radiation Oncology, Aarau (Switzerland); Herrera, Fernanda [Centre Hospitalier Universitaire Vaudois, Department of Radiation Oncology, Lausanne (Switzerland); Kaouthar, Khanfir [Hopital du Valais, Department of Radiation Oncology, Sion (Switzerland); Papachristofilou, Alexandros [Universitaetsspital Basel, Department of Radiation Oncology, Basel (Switzerland); Pesce, Gianfranco [EOC Bellinzona, Department of Radiation Oncology, Bellinzona (Switzerland); Reuter, Christiane [Kantonsspital Muensterlingen, Department of Radiation Oncology, Muensterlingen (Switzerland); Vees, Hansjoerg [Klinik Hirslanden, Department of Radiation Oncology, Zuerich (Switzerland); Zwahlen, Daniel Rudolf [Kantonsspital Graubuenden, Department of Radiation Oncology, Chur (Switzerland); Engeler, Daniel [Kantonsspital St. Gallen, Department of Urology, St. Gallen (Switzerland)

2018-01-15

Although salvage radiotherapy (SRT) for PSA recurrence after radical prostatectomy provides better oncological outcomes when delivered early, in the absence of detectable disease many patients are treated for macroscopic locally recurrent tumors. Due to limited data from prospective studies, we hypothesized an important variability in the SRT management of these patients. Our aim was to investigate current practice patterns of SRT for local macroscopic recurrence after radical prostatectomy. A total of 14 Swiss radiation oncology centers were asked to complete a survey on treatment specifications for macroscopic locally recurrent disease including information on pretherapeutic diagnostic procedures, dose prescription, radiation delivery techniques and androgen deprivation therapy (ADT). Treatment recommendations on ADT were analyzed using the objective consensus methodology. The majority of centers recommended pretreatment magnetic resonance imaging (MRI) of the pelvis and choline positron emission tomography (PET). The median prescribed dose to the prostate bed was 66 Gy (range 65-72 Gy) with a boost to the macroscopic lesion used by 79% of the centers with a median total dose of 72 Gy (range 70-80 Gy). Intensity-modulated rotational techniques were used by all centers and daily cone beam computed tomography (CT) was recommended by 43%. The use of concomitant ADT for any macroscopic recurrence was recommended by 43% of the centers while the remaining centers recommended it only for high-risk disease, which was not consistently defined. We observed a high variability of treatment paradigms when SRT is indicated for macroscopic local recurrences after prostatectomy. These data reflect the need for more standardized approaches and ultimately further research in this field. (orig.) [German] Obwohl die Evidenz fuer eine fruehzeitige Salvage-Radiotherapie (SRT) bei einem PSA-Rezidiv nach radikaler Prostatektomie spricht, werden viele Patienten erst bei einem

[Cartilage tissue reconstruction by the polymer biomaterials--early macroscopic and histological results].

Science.gov (United States)

Scierski, Wojciech; Polok, Aleksandra; Namysłowski, Grzegorz; Nozyński, Jerzy; Turecka, Lucyna; Urbaniec, Natalia; Pamuła, Elzbieta

2009-09-01

The surgical treatment of large cartilage defects in the region of head and neck is often impossible because of the atrophy of surrounding tissues and lack of suitable material for reconstruction. In the surgical treatment many of methods and reconstructive materials have been used. For many years the suitable synthetic material for the cartilage defects reconstruction has been searched for. Was to evaluate two different biomaterials with proper mechanical and biological features for the cartilage replacement. Two type of biomaterials in this study were used: resorbable polymer - poly(L-lactide-co-glycolide) (PLG) acting as a supportive matrix. A thin layer of sodium hyaluronate (Hyal) was also deposited on the surface as well in the pore walls of PLG scaffolds in order to provide biologically active molecules promoting differentiation and regeneration of the tissue. The studies were performed on the 50 animals--rabbits divided into 2 groups. The animals were operated in the general anaesthesia. The incision was done along the edge of the rabbit's auricle. Perichondrium and cartilage of the auricle on the surface 4 x 3 cm were prepared. Subperichondrically 1 x 1 cm fragment of the cartilage was removed by the scissors. This fragment was then replaced by the biomaterials: PLG in first group of 25 rabbits and PLG-Hyal in second group 25 rabbits. The tissues were sutured with polyglycolide Safil 3-0. The animals obtained Enrofloxacin for three days after the operation. Then 1, 4 and 12 weeks after the surgery the animals were painlessly euthanized by an overdose of Morbital. Implants and surrounding tissues were excised and observed macroscopically and using an optical microscope. In all the observation periods we observed proper macroscopic healing process of biomaterials. We didn't stated strong inflammatory process and necrosis around the implanted biomaterials. The histological and macroscopic examinations indicated that both materials developed in this study have

SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq Data

Directory of Open Access Journals (Sweden)

Yuxiang Tan

2015-01-01

Full Text Available The performance evaluation of fusion detection algorithms from high-throughput sequencing data crucially relies on the availability of data with known positive and negative cases of gene rearrangements. The use of simulated data circumvents some shortcomings of real data by generation of an unlimited number of true and false positive events, and the consequent robust estimation of accuracy measures, such as precision and recall. Although a few simulated fusion datasets from RNA Sequencing (RNA-Seq are available, they are of limited sample size. This makes it difficult to systematically evaluate the performance of RNA-Seq based fusion-detection algorithms. Here, we present SimFuse to address this problem. SimFuse utilizes real sequencing data as the fusions’ background to closely approximate the distribution of reads from a real sequencing library and uses a reference genome as the template from which to simulate fusions’ supporting reads. To assess the supporting read-specific performance, SimFuse generates multiple datasets with various numbers of fusion supporting reads. Compared to an extant simulated dataset, SimFuse gives users control over the supporting read features and the sample size of the simulated library, based on which the performance metrics needed for the validation and comparison of alternative fusion-detection algorithms can be rigorously estimated.

Induction of novel macroscopic properties by local symmetry violations in spin-spiral multiferroics

Science.gov (United States)

Meier, D.; Leo, N.; Becker, P.; Bohaty, L.; Ramesh, R.; Fiebig, M.

2011-03-01

Incommensurate (IC) structures are omnipresent in strongly correlated electron systems as high-TC superconductors, CMR manganites, as well as multiferroics. In each case they are origin of a pronounced symmetry reduction reflecting the complexity of the underlying microscopic interactions. Macroscopically, this can lead to new phases and possibilities to gain control of the host material. Here we report how the IC nature of a spin-spiral multiferroic induces new physical properties by renormalizing the relevant length scales of the system. Local symmetry violations directly manifest in the macroscopic response of the material and co-determine the multiferroic order giving rise to additional domain states. These usually hidden degrees of freedom become visible when non-homogenous fields are applied and condition for instance the second harmonic generation. Our study shows that incommensurabilities play a vital role in the discussion of the physical properties of multiferroics -- they represent a key ingredient for further enhancing the functionality of this class of materials. This work was supported by the DFG through the SFB 608. D.M. thanks the AvH for financial support.

Resistivity distribution of silicon single crystals using codoping

Science.gov (United States)

Wang, Jong Hoe

2005-07-01

Numerous studies including continuous Czochralski method and double crucible technique have been reported on the control of macroscopic axial resistivity distribution in bulk crystal growth. The simple codoping method for improving the productivity of silicon single-crystal growth by controlling axial specific resistivity distribution was proposed by Wang [Jpn. J. Appl. Phys. 43 (2004) 4079]. Wang [J. Crystal Growth 275 (2005) e73] demonstrated using numerical analysis and by experimental results that the axial specific resistivity distribution can be modified in melt growth of silicon crystals and relatively uniform profile is possible by B-P codoping method. In this work, the basic characteristic of 8 in silicon single crystal grown using codoping method is studied and whether proposed method has advantage for the silicon crystal growth is discussed.

Understanding Analysis Macroscopic, microscopic, and Acid-Base Titration Symbolic Student Class XI Science High School and Improvement Efforts Microscopy Approach

Directory of Open Access Journals (Sweden)

Putu Indrayani

2014-06-01

Full Text Available Analisis Pemahaman Makroskopik, Mikroskopik, dan Simbolik Titrasi Asam-Basa Siswa Kelas XI IPA SMA serta Upaya Perbaikannya dengan Pendekatan Mikroskopik Abstract: This study aims to determine: (1 the level of understanding of the macroscopic, microscopic and symbolic students; (2 the error understanding of macroscopic, microscopic and symbolic students; (3 the effectiveness of the microscopic approach in an effort to improve students' ability to solve the problems macroscopic, symbolic and microscopic material acid-base titration. This research uses descriptive research design and quasi-experimental research design. Data research is the understanding of macroscopic, symbolic and microscopic students on the material acid-base titration. Student comprehension test measured with instruments that include: (1 macroscopic comprehension tests, (2 test the understanding of symbolic, and (3 understanding of the microscopic tests. Content validity was tested by a team of experts and the reliability of test questions macroscopic and microscopic calculated using the Spearman-Brown while reliability symbolic test item was calculated using Cronbach's Alpha. Data were analyzed using descriptive analysis and statistical tests using Anacova. Results of the study are as follows. (1 The level of understanding of the macroscopic students is high, while the symbolic and microscopic levels of understanding of students is very low. (2 Errors identified macroscopic understanding is that students do not understand that the color shown by indicators related to the nature of the solution. Symbolic understanding of the identified errors are: (i the student can not write ionization reaction; and (ii students can not choose the formula used to calculate the pH of the solution. Errors identified microscopic understanding is that students can not provide a microscopic picture of a solution of a strong acid, strong base, weak acid, weak base, and salt solutions because they do

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

Distribution of HIV RNA in CSF and Blood is linked to CD4/CD8 Ratio During Acute HIV.

Science.gov (United States)

Chan, Phillip; Patel, Payal; Hellmuth, Joanna; Colby, Donn J; Kroon, Eugène; Sacdalan, Carlo; Pinyakorn, Suteeraporn; Jagodzinski, Linda; Krebs, Shelly; Ananworanich, Jintanat; Valcour, Victor; Spudich, Serena

2018-05-07

HIV RNA levels in the plasma and cerebrospinal fluid (CSF) are correlated in chronic HIV infection but their dynamics have not been characterized during acute infection. This study analyzed predictors of CSF HIV RNA and relative degree of CNS viral transmigration expressed as plasma minus CSF HIV log10 RNA (PCratio) during untreated acute HIV infection. CSF immune markers were compared between groups with different PCratio. 117 mostly male (97%) participants in the RV254 cohort in Bangkok, Thailand, had median age 28 years and an estimated median 18 days duration of infection; forty-three (37%) were Fiebig stages I/II. Twenty-seven (23%) had CSF HIV RNA CSF HIV RNA and PCratio of 3.76 and 2.36 Log10 copies/mL, respectively. HIV RNA peaked at Fiebig III in plasma and Fiebig IV in CSF. In multivariable analyses, plasma HIV RNA and CD4/CD8 ratio independently correlated with CSF HIV RNA (pCSF neopterin, sCD163, IL-6 and sCD14 levels (all pCSF HIV RNA and PCratio, suggesting that immune responses modulate CNS viral entry at early infection.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

Science.gov (United States)

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

On the inclusion of macroscopic theory in Monte Carlo simulation using game theory

International Nuclear Information System (INIS)

Tatarkiewicz, J.

1980-01-01

This paper presents the inclusion of macroscopic damage theory into Monte Carlo particle-range simulation using game theory. A new computer code called RADDI was developed on the basis of this inclusion. Results of Monte Carlo damage simulation after 6.3 MeV proton bombardment of silicon are compared with experimental data of Bulgakov et al. (orig.)

The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

Science.gov (United States)

Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

2017-01-01

RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

DSAP: deep-sequencing small RNA analysis pipeline.

Science.gov (United States)

Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

2010-07-01

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Assessing mRNA nuclear export in mammalian cells by microinjection.

Science.gov (United States)

Lee, Eliza S; Palazzo, Alexander F

2017-08-15

The nuclear export of mRNAs is an important yet little understood part of eukaryotic gene expression. One of the easiest methods for monitoring mRNA export in mammalian tissue culture cells is through the microinjection of DNA plasmids into the nucleus and monitoring the distribution of the transcribed product over time. Here we describe how to setup a microscope equipped with a micromanipulator used in cell microinjections, and we explain how to perform a nuclear mRNA export assay and obtain the nuclear export rate for any given mRNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Coarse and fine root plants affect pore size distributions differently

OpenAIRE

Bodner, G.; Leitner, D.; Kaul, H.-P.

2014-01-01

Aims Small scale root-pore interactions require validation of their impact on effective hydraulic processes at the field scale. Our objective was to develop an interpretative framework linking root effects on macroscopic pore parameters with knowledge at the rhizosphere scale. Methods A field experiment with twelve species from different families was conducted. Parameters of Kosugi?s pore size distribution (PSD) model were determined inversely from tension infiltrometer data. Measured root tr...

Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

International Nuclear Information System (INIS)

Lloyd, Richard E.

2015-01-01

Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication

Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

Energy Technology Data Exchange (ETDEWEB)

Lloyd, Richard E., E-mail: rlloyd@bcm.edu

2015-05-15

Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers

Science.gov (United States)

Feng, Li; Li, Feng; Sun, Zeguo; Wu, Tan; Shi, Xinrui; Li, Jing; Li, Xia

2016-01-01

Recent studies indicate that long noncoding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to indirectly regulate mRNAs through shared microRNAs, which represents a novel layer of RNA crosstalk and plays critical roles in the development of tumor. However, the global regulation landscape and characterization of these lncRNA related ceRNA crosstalk in cancers is still largely unknown. Here, we systematically characterized the lncRNA related ceRNA interactions across 12 major cancers and the normal physiological states by integrating multidimensional molecule profiles of more than 5000 samples. Our study suggest the large difference of ceRNA regulation between normal and tumor states and the higher similarity across similar tissue origin of tumors. The ceRNA related molecules have more conserved features in tumor networks and they play critical roles in both the normal and tumorigenesis processes. Besides, lncRNAs in the pan-cancer ceRNA network may be potential biomarkers of tumor. By exploring hub lncRNAs, we found that these conserved key lncRNAs dominate variable tumor hallmark processes across pan-cancers. Network dynamic analysis highlights the critical roles of ceRNA regulation in tumorigenesis. By analyzing conserved ceRNA interactions, we found that miRNA mediate ceRNA regulation showed different patterns across pan-cancer; while analyzing the cancer specific ceRNA interactions reveal that lncRNAs synergistically regulated tumor driver genes of cancer hallmarks. Finally, we found that ceRNA modules have the potential to predict patient survival. Overall, our study systematically dissected the lncRNA related ceRNA networks in pan-cancer that shed new light on understanding the molecular mechanism of tumorigenesis. PMID:27580177

Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

Science.gov (United States)

Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

2017-01-01

microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772

Designed Er(3+)-singly doped NaYF4 with double excitation bands for simultaneous deep macroscopic and microscopic upconverting bioimaging.

Science.gov (United States)

Wen, Xuanyuan; Wang, Baoju; Wu, Ruitao; Li, Nana; He, Sailing; Zhan, Qiuqiang

2016-06-01

Simultaneous deep macroscopic imaging and microscopic imaging is in urgent demand, but is challenging to achieve experimentally due to the lack of proper fluorescent probes. Herein, we have designed and successfully synthesized simplex Er(3+)-doped upconversion nanoparticles (UCNPs) with double excitation bands for simultaneous deep macroscopic and microscopic imaging. The material structure and the excitation wavelength of Er(3+)-singly doped UCNPs were further optimized to enhance the upconversion emission efficiency. After optimization, we found that NaYF4:30%Er(3+)@NaYF4:2%Er(3+) could simultaneously achieve efficient two-photon excitation (2PE) macroscopic tissue imaging and three-photon excitation (3PE) deep microscopic when excited by 808 nm continuous wave (CW) and 1480 nm CW lasers, respectively. In vitro cell imaging and in vivo imaging have also been implemented to demonstrate the feasibility and potential of the proposed simplex Er(3+)-doped UCNPs as bioprobe.

ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

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Yuttachon Promworn

Full Text Available Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance.We present Transformation of Nucleotide Enrichment Ratios (ToNER, a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR.ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a

ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

Science.gov (United States)

Promworn, Yuttachon; Kaewprommal, Pavita; Shaw, Philip J; Intarapanich, Apichart; Tongsima, Sissades; Piriyapongsa, Jittima

2017-01-01

Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance. We present Transformation of Nucleotide Enrichment Ratios (ToNER), a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR. ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a.biotec.or.th/GI/tools/toner) and Git

Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

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Yunpeng Zhang

2015-01-01

Full Text Available Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it is important to identify subtype specific miRNA-mRNA modules. In this study, we integrated the Ping-Pong algorithm and multiobjective genetic algorithm to identify subtype specific miRNA-mRNA functional regulatory modules (MFRMs through integrative analysis of three biological data sets: GO biological processes, miRNA target information, and matched miRNA and mRNA expression data. We applied our method on a heterogeneous disease, multiple myeloma (MM, to identify MM subtype specific MFRMs. The constructed miRNA-mRNA regulatory networks provide modular outlook at subtype specific miRNA-mRNA interactions. Furthermore, clustering analysis demonstrated that heterogeneous MFRMs were able to separate corresponding MM subtypes. These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment.

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

1993-01-01

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....

Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting

Science.gov (United States)

Piazza, Carol Lyn; Smith, Dorie

2018-01-01

Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns. PMID:29905149

From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

Science.gov (United States)

Michelini, Flavia; Jalihal, Ameya P; Francia, Sofia; Meers, Chance; Neeb, Zachary T; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G; Fagagna, Fabrizio d'Adda di

2018-03-30

Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.

Optimization of miRNA-seq data preprocessing.

Science.gov (United States)

Tam, Shirley; Tsao, Ming-Sound; McPherson, John D

2015-11-01

The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments. © The Author 2015. Published by Oxford University Press.

34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

African Journals Online (AJOL)

RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.

Light induced electrical and macroscopic changes in hydrogenated polymorphous silicon solar cells

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Roca i Cabarrocas P.

2012-07-01

Full Text Available We report on light-induced electrical and macroscopic changes in hydrogenated polymorphous silicon (pm-Si:H PIN solar cells. To explain the particular light-soaking behavior of such cells – namely an increase of the open circuit voltage (Voc and a rapid drop of the short circuit current density (Jsc – we correlate these effects to changes in hydrogen incorporation and structural properties in the layers of the cells. Numerous techniques such as current-voltage characteristics, infrared spectroscopy, hydrogen exodiffusion, Raman spectroscopy, atomic force microscopy, scanning electron microscopy and spectroscopic ellipsometry are used to study the light-induced changes from microscopic to macroscopic scales (up to tens of microns. Such comprehensive use of complementary techniques lead us to suggest that light-soaking produces the diffusion of molecular hydrogen, hydrogen accumulation at p-layer/substrate interface and localized delamination of the interface. Based on these results we propose that light-induced degradation of PIN solar cells has to be addressed from not only as a material issue, but also a device point of view. In particular we bring experimental evidence that localized delamination at the interface between the p-layer and SnO2 substrate by light-induced hydrogen motion causes the rapid drop of Jsc.

Macroscopic Rock Texture Image Classification Using a Hierarchical Neuro-Fuzzy Class Method

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Laercio B. Gonçalves

2010-01-01

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.

Intracellular distribution of histone mRNAs in human fibroblasts studied by in situ hybridization

International Nuclear Information System (INIS)

Lawrence, J.B.; Singer, R.H.; Villnave, C.A.; Stein, J.L.; Stein, G.S.

1988-01-01

We have used in situ hybridization to study the intracellular distribution of mRNAs for cell cycle-dependent core and H1 histone proteins in human WI-38 fibroblasts. Because histones are abundant nuclear proteins and histone mRNA expression is tightly coupled to DNA synthesis, it was of interest to determine whether histone mRNAs are localized near the nucleus. Cells were hybridized with tritiated DNA probes specific for either histone H1, histone H4, actin, or poly(A)+ mRNA and were processed for autoradiography. In exponentially growing cultures, the fraction of histone mRNA-positive cells correlated well with the fraction of cells in S phase and was eliminated by hydroxyurea inhibition of DNA synthesis. Within individual cells the label for histone mRNA was widely distributed throughout the cytoplasm and did not appear to be more heavily concentrated near the nucleus. However, histone mRNA appeared to exhibit patchy, nonhomogeneous localization, and a quantitative evaluation confirmed that grain distributions were not as uniform as they were after hybridizations to poly(A)+ mRNA. Actin mRNA in WI-38 cells was also widely distributed throughout the cytoplasm but differed from histone mRNA in that label for actin mRNA was frequently most dense at the outermost region of narrow cell extensions. The localization of actin mRNA was less pronounced but qualitatively very similar to that previously described for chicken embryonic myoblasts and fibroblasts. We conclude that localization of histones in WI-38 cells is not facilitated by localization of histone protein synthesis near the nucleus and that there are subtle but discrete and potentially functional differences in the distributions of histone, actin, and poly(A)+ mRNAs

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

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Enrico Sciubba

2017-11-01

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.

Ancient sedimentary structures in the Mars, that resemble macroscopic morphology, spatial associations, and temporal succession in terrestrial microbialites.

Science.gov (United States)

Noffke, Nora

2015-02-01

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.

Extracellular RNA Communication (ExRNA)

Data.gov (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...

GRUCAL: a program system for the calculation of macroscopic group constants

International Nuclear Information System (INIS)

Woll, D.

1984-01-01

Nuclear reactor calculations require material- and composition-dependent, energy-averaged neutron physical data in order to decribe the interaction between neutrons and isotopes. The multigroup cross section code GRUCAL calculates these macroscopic group constants for given material compositions from the material-dependent data of the group constant library GRUBA. The instructions for calculating group constants are not fixed in the program, but are read in from an instruction file. This makes it possible to adapt GRUCAL to various problems or different group constant concepts

RNA Crystallization

Science.gov (United States)

Golden, Barbara L.; Kundrot, Craig E.

2003-01-01

RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

Beta-Poisson model for single-cell RNA-seq data analyses.

Science.gov (United States)

Vu, Trung Nghia; Wills, Quin F; Kalari, Krishna R; Niu, Nifang; Wang, Liewei; Rantalainen, Mattias; Pawitan, Yudi

2016-07-15

Single-cell RNA-sequencing technology allows detection of gene expression at the single-cell level. One typical feature of the data is a bimodality in the cellular distribution even for highly expressed genes, primarily caused by a proportion of non-expressing cells. The standard and the over-dispersed gamma-Poisson models that are commonly used in bulk-cell RNA-sequencing are not able to capture this property. We introduce a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. We further integrate the model into the generalized linear model framework in order to perform differential expression analyses. The whole analytical procedure is called BPSC. The results from several real single-cell RNA-seq datasets indicate that ∼90% of the transcripts are well characterized by the beta-Poisson model; the model-fit from BPSC is better than the fit of the standard gamma-Poisson model in > 80% of the transcripts. Moreover, in differential expression analyses of simulated and real datasets, BPSC performs well against edgeR, a conventional method widely used in bulk-cell RNA-sequencing data, and against scde and MAST, two recent methods specifically designed for single-cell RNA-seq data. An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq data is available under GPL-3 license at https://github.com/nghiavtr/BPSC CONTACT: yudi.pawitan@ki.se or mattias.rantalainen@ki.se Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Identifying microRNA/mRNA dysregulations in ovarian cancer.

Science.gov (United States)

Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify

A macroscopic constitutive model of temperature-induced phase transition of polycrystalline Ni{sub 2}MnGa by directional solidification

Energy Technology Data Exchange (ETDEWEB)

Zhu, Yuping, E-mail: zhuyuping@126.com; Gu, Yunling; Liu, Hongguang

2015-02-25

Directional solidification technology has been widely used to improve the properties of polycrystalline Ni{sub 2}MnGa materials. Mechanical training can adjust the internal organizational structures of the materials, reduce the stress of twin boundaries motion, and then result in larger strain at lower outfield levels. In this paper, we test the microscopic structure of Ni{sub 2}MnGa polycrystalline ferromagnetic shape memory alloy produced by directional solidification and compress it along two axes successively for mechanical training. The influences of pre-compressive stresses on the temperature-induced strains are analyzed. The macroscopic mechanical behaviors show anisotropy. According to the generating mechanism of the macroscopic strain, a three-dimensional constitutive model is established. Based on thermodynamic method, the kinetic equations of the martensitic transformation and inverse transformation are presented considering the driving force and energy dissipation. The prediction curves of temperature-induce strains along two different directions are investigated. And the results coincide well with the experiment data. It well explains the macroscopic anisotropy mechanical behaviors and fits for using in engineering.

Using Non-linear Homogenization to Improve the Performance of Macroscopic Damage Models of Trabecular Bone.

Science.gov (United States)

Levrero-Florencio, Francesc; Pankaj, Pankaj

2018-01-01

Realistic macro-level finite element simulations of the mechanical behavior of trabecular bone, a cellular anisotropic material, require a suitable constitutive model; a model that incorporates the mechanical response of bone for complex loading scenarios and includes post-elastic phenomena, such as plasticity (permanent deformations) and damage (permanent stiffness reduction), which bone is likely to experience. Some such models have been developed by conducting homogenization-based multiscale finite element simulations on bone micro-structure. While homogenization has been fairly successful in the elastic regime and, to some extent, in modeling the macroscopic plastic response, it has remained a challenge with respect to modeling damage. This study uses a homogenization scheme to upscale the damage behavior from the tissue level (microscale) to the organ level (macroscale) and assesses the suitability of different damage constitutive laws. Ten cubic specimens were each subjected to 21 strain-controlled load cases for a small range of macroscopic post-elastic strains. Isotropic and anisotropic criteria were considered, density and fabric relationships were used in the formulation of the damage law, and a combined isotropic/anisotropic law with tension/compression asymmetry was formulated, based on the homogenized results, as a possible alternative to the currently used single scalar damage criterion. This computational study enhances the current knowledge on the macroscopic damage behavior of trabecular bone. By developing relationships of damage progression with bone's micro-architectural indices (density and fabric) the study also provides an aid for the creation of more precise macroscale continuum models, which are likely to improve clinical predictions.

Natural RNA circles function as efficient microRNA sponges

DEFF Research Database (Denmark)

Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

2013-01-01

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

RNA Origami

DEFF Research Database (Denmark)

Sparvath, Steffen Lynge

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...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

Branched RNA: A New Architecture for RNA Interference

Directory of Open Access Journals (Sweden)

Anna Aviñó

2011-01-01

Full Text Available Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.

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

Directory of Open Access Journals (Sweden)

Nasrollah Ghassemi Dehkordi

2012-06-01

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.

Plant RNA Regulatory Network and RNA Granules in Virus Infection

Directory of Open Access Journals (Sweden)

Kristiina Mäkinen

2017-12-01

Full Text Available Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and

Plant RNA Regulatory Network and RNA Granules in Virus Infection.

Science.gov (United States)

Mäkinen, Kristiina; Lõhmus, Andres; Pollari, Maija

2017-01-01

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual

EL-2 reactor: Thermal neutron flux distribution

International Nuclear Information System (INIS)

Rousseau, A.; Genthon, J.P.

1958-01-01

The flux distribution of thermal neutrons in EL-2 reactor is studied. The reactor core and lattices are described as well as the experimental reactor facilities, in particular, the experimental channels and special facilities. The measurement shows that the thermal neutron flux increases in the central channel when enriched uranium is used in place of natural uranium. However the thermal neutron flux is not perturbed in the other reactor channels by the fuel modification. The macroscopic flux distribution is measured according the radial positioning of fuel rods. The longitudinal neutron flux distribution in a fuel rod is also measured and shows no difference between enriched and natural uranium fuel rods. In addition, measurements of the flux distribution have been effectuated for rods containing other material as steel or aluminium. The neutron flux distribution is also studied in all the experimental channels as well as in the thermal column. The determination of the distribution of the thermal neutron flux in all experimental facilities, the thermal column and the fuel channels has been made with a heavy water level of 1825 mm and is given for an operating power of 1000 kW. (M.P.)

Methylated nucleosides in tRNA and tRNA methyltransferases

Directory of Open Access Journals (Sweden)

Hiroyuki eHori

2014-05-01

Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

International Nuclear Information System (INIS)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

2012-01-01

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Energy Technology Data Exchange (ETDEWEB)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

2012-04-15

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

MysiRNA-designer: a workflow for efficient siRNA design.

Directory of Open Access Journals (Sweden)

Mohamed Mysara

Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

Determination of crystallographic and macroscopic orientation of planar structures in TEM

DEFF Research Database (Denmark)

Huang, X.; Liu, Q.

1998-01-01

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...

Inverse Bayesian inference as a key of consciousness featuring a macroscopic quantum logical structure.

Science.gov (United States)

Gunji, Yukio-Pegio; Shinohara, Shuji; Haruna, Taichi; Basios, Vasileios

2017-02-01

To overcome the dualism between mind and matter and to implement consciousness in science, a physical entity has to be embedded with a measurement process. Although quantum mechanics have been regarded as a candidate for implementing consciousness, nature at its macroscopic level is inconsistent with quantum mechanics. We propose a measurement-oriented inference system comprising Bayesian and inverse Bayesian inferences. While Bayesian inference contracts probability space, the newly defined inverse one relaxes the space. These two inferences allow an agent to make a decision corresponding to an immediate change in their environment. They generate a particular pattern of joint probability for data and hypotheses, comprising multiple diagonal and noisy matrices. This is expressed as a nondistributive orthomodular lattice equivalent to quantum logic. We also show that an orthomodular lattice can reveal information generated by inverse syllogism as well as the solutions to the frame and symbol-grounding problems. Our model is the first to connect macroscopic cognitive processes with the mathematical structure of quantum mechanics with no additional assumptions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

RNA binding and replication by the poliovirus RNA polymerase

International Nuclear Information System (INIS)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region

Macroscopic chirality of a liquid crystal from nonchiral molecules

International Nuclear Information System (INIS)

Jakli, A.; Nair, G. G.; Lee, C. K.; Sun, R.; Chien, L. C.

2001-01-01

The transfer of chirality from nonchiral polymer networks to the racemic B2 phase of nonchiral banana-shaped molecules is demonstrated. This corresponds to the transfer of chirality from an achiral material to another achiral material. There are two levels of chirality transfers. (a) On a microscopic level the presence of a polymer network (chiral or nonchiral) favors a chiral state over a thermodynamically stable racemic state due to the inversion symmetry breaking at the polymer-liquid crystal interfaces. (b) A macroscopically chiral (enantimerically enriched) sample can be produced if the polymer network has a helical structure, and/or contains chemically chiral groups. The chirality transfer can be locally suppressed by exposing the liquid crystal to a strong electric field treatment

Theoretical models for electron conduction in polymer systems—I. Macroscopic calculations of d.c. transient conductivity after pulse irradiation

Science.gov (United States)

Bartczak, Witold M.; Kroh, Jerzy

The simulation of the transient d.c. conductivity in a quasi one-dimensional system of charges produced by a pulse of ionizing radiation in a solid sample has been performed. The simulation is based on the macroscopic conductivity equations and can provide physical insight into d.c. conductivity measurements, particularly for the case of transient currents in samples with internal space charge. We consider the system of mobile (negative) and immobile (positive) charges produced by a pulse of ionizing radiation in the sample under a fixed external voltage V0. The presence of space charge results in an electric field which is a function of both the spatial and the time variable: E( z, t). Given the space charge density, the electric field can be calculated from the Poisson equation. However, for an arbitrary space charge distribution, the corresponding equations can only be solved numerically. The two non-trivial cases for which approximate analytical solutions can be provided are: (i) The density of the current carriers n( z, t) is negligible in comparison with the density of immobile space charge N( z). A general analytical solution has been found for this case using Green's functions. The solutions for two cases, viz. the homogeneous distribution of space charge N( z) = N, and the non-homogeneous exponential distribution N( z) = A exp(- Bz), have been separately discussed. (ii) The space charge created in the pulse without any space charge present prior to the irradiation.

On the inherent self-excited macroscopic randomness of chaotic three-body system

OpenAIRE

Liao, Shijun; Li, Xiaoming

2014-01-01

What is the origin of macroscopic randomness (uncertainty)? This is one of the most fundamental open questions for human being. In this paper, 10000 samples of reliable (convergent), multiple-scale (from 1.0E-60 to 100) numerical simulations of a chaotic three-body system indicate that, without any external disturbance, the microscopic inherent uncertainty (in the level of 1.0E-60) due to physical fluctuation of initial positions of the three-body system enlarges exponentially into macroscopi...

RNA.

Science.gov (United States)

Darnell, James E., Jr.

1985-01-01

Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

OpenAIRE

Zhang, Yunpeng; Liu, Wei; Xu, Yanjun; Li, Chunquan; Wang, Yingying; Yang, Haixiu; Zhang, Chunlong; Su, Fei; Li, Yixue; Li, Xia

2015-01-01

Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it i...

NGScloud: RNA-seq analysis of non-model species using cloud computing.

Science.gov (United States)

Mora-Márquez, Fernando; Vázquez-Poletti, José Luis; López de Heredia, Unai

2018-05-03

RNA-seq analysis usually requires large computing infrastructures. NGScloud is a bioinformatic system developed to analyze RNA-seq data using the cloud computing services of Amazon that permit the access to ad hoc computing infrastructure scaled according to the complexity of the experiment, so its costs and times can be optimized. The application provides a user-friendly front-end to operate Amazon's hardware resources, and to control a workflow of RNA-seq analysis oriented to non-model species, incorporating the cluster concept, which allows parallel runs of common RNA-seq analysis programs in several virtual machines for faster analysis. NGScloud is freely available at https://github.com/GGFHF/NGScloud/. A manual detailing installation and how-to-use instructions is available with the distribution. unai.lopezdeheredia@upm.es.

microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

Science.gov (United States)

Pinder, Benjamin D; Smibert, Craig A

2013-01-01

Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

Directory of Open Access Journals (Sweden)

Andronescu Mirela

2008-08-01

Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

MicroRNA from tuberculosis RNA: A bioinformatics study

OpenAIRE

Wiwanitkit, Somsri; Wiwanitkit, Viroj

2012-01-01

The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

Science.gov (United States)

Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

2013-01-01

CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

Studying RNA-protein interactions in vivo by RNA immunoprecipitation

DEFF Research Database (Denmark)

Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

2011-01-01

and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.......The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases...

RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

OpenAIRE

Montano, Monty; Long, Kimberly

2010-01-01

In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...

Macroscopic local-field effects on photoabsorption processes

International Nuclear Information System (INIS)

Ma Xiaoguang; Gong Yubing; Wang Meishan; Wang Dehua

2008-01-01

The influence of the local-field effect on the photoabsorption cross sections of the atoms which are embedded in the macroscopic medium has been studied by a set of alternative expressions in detail. Some notes on the validity of some different local-field models used to study the photoabsorption cross sections of atoms in condensed matter have been given for the first time. Our results indicate that the local fields can have substantial and different influence on the photoabsorption cross section of atoms in condensed matter for different models. Clausius-Mossotti model and Onsager model have proved to be more reasonable to describe the local field in gas, liquid, or even some simple solid, while Glauber-Lewenstein model probably is wrong in these conditions except for the ideal gas. A procedure which can avoid the errors introduced by Kramers-Kronig transformation has been implemented in this work. This procedure can guarantee that the theoretical studies on the local field effects will not be influenced by the integral instability of the Kramers-Kronig transformation

Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

NARCIS (Netherlands)

Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

2012-01-01

MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

Localization of glucocorticoid receptor mRNA in the male rat brain by in situ hybridization

International Nuclear Information System (INIS)

Aronsson, M.; Fuxe, K.; Dong, Y.; Agnati, L.F.; Okret, S.; Gustafsson, J.A.

1988-01-01

The localization and distribution of mRNA encoding the glucocorticoid receptor (GR) was investigated in tissue sections of the adult male rat brain by in situ hybridization and RNA blot analysis. GR mRNA levels were measured by quantitative autoradiography with 35S- and 32P-labeled RNA probes, respectively. Strong labeling was observed within the pyramidal nerve cells of the CA1 and CA2 areas of the hippocampal formation, in the granular cells of the dentate gyrus, in the parvocellular nerve cells of the paraventricular hypothalamic nucleus, and in the cells of the arcuate nucleus, especially the parvocellular part. Moderate labeling of a large number of nerve cells was observed within layers II, III, and VI of the neocortex and in many thalamic nuclei, especially the anterior and ventral nuclear groups as well as several midline nuclei. Within the cerebellar cortex, strong labeling was observed all over the granular layer. In the lower brainstem, strong labeling was found within the entire locus coeruleus and within the mesencephalic raphe nuclei rich in noradrenaline and 5-hydroxytryptamine cell bodies, respectively. A close correlation was found between the distribution of GR mRNA and the distribution of previously described GR immunoreactivity. These studies open the possibility of obtaining additional information on in vivo regulation of GR synthesis and how the brain may alter its sensitivity to circulating glucocorticoids

Macroscopic Floquet topological crystalline steel and superconductor pump

Science.gov (United States)

Rossi, Anna M. E. B.; Bugase, Jonas; Fischer, Thomas M.

2017-08-01

The transport of a macroscopic steel sphere and a superconducting sphere on top of two-dimensional periodic magnetic patterns is studied experimentally and compared with the theory and with experiments on topological transport of magnetic colloids. Transport of the steel and superconducting sphere is achieved by moving an external permanent magnet on a closed loop around the two-dimensional crystal. The transport is topological, i.e., the spheres are transported by a primitive unit vector of the lattice when the external magnet loop winds around specific directions. We experimentally determine the set of directions the loops must enclose for nontrivial transport of the spheres into various directions. We show that the loops can be used to sort steel and superconducting spheres. We show that the topological transport is robust with respect to the scale of the system and therefore speculate on its down scalability to the molecular scale.

Theoretical analysis of the distribution of isolated particles in totally asymmetric exclusion processes: Application to mRNA translation rate estimation

Science.gov (United States)

Dao Duc, Khanh; Saleem, Zain H.; Song, Yun S.

2018-01-01

The Totally Asymmetric Exclusion Process (TASEP) is a classical stochastic model for describing the transport of interacting particles, such as ribosomes moving along the messenger ribonucleic acid (mRNA) during translation. Although this model has been widely studied in the past, the extent of collision between particles and the average distance between a particle to its nearest neighbor have not been quantified explicitly. We provide here a theoretical analysis of such quantities via the distribution of isolated particles. In the classical form of the model in which each particle occupies only a single site, we obtain an exact analytic solution using the matrix ansatz. We then employ a refined mean-field approach to extend the analysis to a generalized TASEP with particles of an arbitrary size. Our theoretical study has direct applications in mRNA translation and the interpretation of experimental ribosome profiling data. In particular, our analysis of data from Saccharomyces cerevisiae suggests a potential bias against the detection of nearby ribosomes with a gap distance of less than approximately three codons, which leads to some ambiguity in estimating the initiation rate and protein production flux for a substantial fraction of genes. Despite such ambiguity, however, we demonstrate theoretically that the interference rate associated with collisions can be robustly estimated and show that approximately 1% of the translating ribosomes get obstructed.

Detailed Simulation of Complex Hydraulic Problems with Macroscopic and Mesoscopic Mathematical Methods

Directory of Open Access Journals (Sweden)

Chiara Biscarini

2013-01-01

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.

On the macroscopic modeling of dilute emulsions under flow in the presence of particle inertia

Science.gov (United States)

Mwasame, Paul M.; Wagner, Norman J.; Beris, Antony N.

2018-03-01

Recently, Mwasame et al. ["On the macroscopic modeling of dilute emulsions under flow," J. Fluid Mech. 831, 433 (2017)] developed a macroscopic model for the dynamics and rheology of a dilute emulsion with droplet morphology in the limit of negligible particle inertia using the bracket formulation of non-equilibrium thermodynamics of Beris and Edwards [Thermodynamics of Flowing Systems: With Internal Microstructure (Oxford University Press on Demand, 1994)]. Here, we improve upon that work to also account for particle inertia effects. This advance is facilitated by using the bracket formalism in its inertial form that allows for the natural incorporation of particle inertia effects into macroscopic level constitutive equations, while preserving consistency to the previous inertialess approximation in the limit of zero inertia. The parameters in the resultant Particle Inertia Thermodynamically Consistent Ellipsoidal Emulsion (PITCEE) model are selected by utilizing literature-available mesoscopic theory for the rheology at small capillary and particle Reynolds numbers. At steady state, the lowest level particle inertia effects can be described by including an additional non-affine inertial term into the evolution equation for the conformation tensor, thereby generalizing the Gordon-Schowalter time derivative. This additional term couples the conformation and vorticity tensors and is a function of the Ohnesorge number. The rheological and microstructural predictions arising from the PITCEE model are compared against steady-shear simulation results from the literature. They show a change in the signs of the normal stress differences that is accompanied by a change in the orientation of the major axis of the emulsion droplet toward the velocity gradient direction with increasing Reynolds number, capturing the two main signatures of particle inertia reported in simulations.

Macroscopic Study of the Isthmus of the Thyroid Gland in Bangladeshi People: A Postmortem Study

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Fakhrul Amin Mohammad Hasanul Banna

2017-01-01

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.

MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

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Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

2010-04-08

RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

Searching for the nanoscopic–macroscopic boundary

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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: jmejia@puc.cl [Facultad de Física, Pontificia Universidad Católica de Chile, CEDENNA, Santiago (Chile)

2013-12-15

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%.

Polyadenylated mRNA from the photosynthetic procaryote Rhodospirillum rubrum

International Nuclear Information System (INIS)

Majumdar, P.K.; McFadden, B.A.

1984-01-01

Total cellular RNA extracted from Rhodospirillum rubrum cultured in butyrate-containing medium under strict photosynthetic conditions to the stationary phase of growth has been fractionated on an oligodeoxy-thymidylic acid-cellulose column into polyadenylated [poly(A) + ] RNA and poly(A) - RNA fractions. The poly(A) + fraction was 9 to 10% of the total bulk RNA isolated. Analysis of the poly(A) + RNA on a denaturing urea-polyacrylamide gel revealed four sharp bands of RNA distributed in heterodisperse fashion between 16S and 9S. Similar fractionation of the poly(A) - RNA resulted in the separation of 23, 16, and 5S rRNAs and 4S tRNA. Poly(A) + fragments isolated after combined digestion with pancreatic A and T 1 RNases and analysis by denaturing gel electrophoresis demonstrated two major components of 80 and 100 residues. Alkaline hydrolysis of the nuclease-resistant, purified residues showed AMP-rich nucleotides. Through the use of snake venom phosphodiesterase, poly(A) tracts were placed at the 3' end of poly(A) + RNA. Stimulation of [ 3 H]leucine incorporation into hot trichloroacetic acid-precipitable polypeptides in a cell-free system from wheat germ primed by the poly(A) + RNA mixture was found to be 220-fold higher than that for poly(A) - RNAs (on a unit mass basis), a finding which demonstrated that poly(A) + RNAs in R. rubrum are mRNAs. Gel electrophoretic analysis of the translation mixture revealed numerous 3 H-labeled products including a major band (M/sub r/, 52,000). The parent protein was precipitated by antibodies to ribulose bisphosphate carboxylase-oxygenase and comprised 6.5% of the total translation products

Plant RNA binding proteins for control of RNA virus infection

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Sung Un eHuh

2013-12-01

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.

Effective Anti-miRNA Oligonucleotides Show High Releasing Rate of MicroRNA from RNA-Induced Silencing Complex.

Science.gov (United States)

Ariyoshi, Jumpei; Matsuyama, Yohei; Kobori, Akio; Murakami, Akira; Sugiyama, Hiroshi; Yamayoshi, Asako

2017-10-01

MicroRNAs (miRNAs) regulate gene expression by forming RNA-induced silencing complexes (RISCs) and have been considered as promising therapeutic targets. MiRNA is an essential component of RISC for the modulation of gene expression. Therefore, the release of miRNA from RISC is considered as an effective method for the inhibition of miRNA functions. In our previous study, we reported that anti-miRNA oligonucleotides (AMOs), which are composed of the 2'-O-methyl (2'-OMe) RNA, could induce the release of miRNA from RISC. However, the mechanisms underlying the miRNA-releasing effects of chemically modified AMOs, which are conventionally used as anti-cancer drugs, are still unclear. In this study, we investigated the relationship between the miRNA releasing rate from RISC and the inhibitory effect on RISC activity (IC 50 ) using conventional chemically modified AMOs. We demonstrated that the miRNA-releasing effects of AMOs are directly proportional to the IC 50 values, and AMOs, which have an ability to promote the release of miRNA from RISC, can effectively inhibit RISC activity in living cells.

Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

DEFF Research Database (Denmark)

Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

2007-01-01

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....