The Acquisition of German Relative Clauses: A Case Study

ERIC Educational Resources Information Center

Brand, Silke; Diessel, Holger; Tomasello, Michael

2008-01-01

This paper investigates the development of relative clauses in the speech of one German-speaking child aged 2 ; 0 to 5 ; 0. The earliest relative clauses we found in the data occur in topicalization constructions that are only a little different from simple sentences: they contain a single proposition, express the actor prior to other…

Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

PubMed

Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

2016-05-23

Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

Big words, halved brains and small worlds: complex brain networks of figurative language comprehension.

PubMed

Arzouan, Yossi; Solomon, Sorin; Faust, Miriam; Goldstein, Abraham

2011-04-27

Language comprehension is a complex task that involves a wide network of brain regions. We used topological measures to qualify and quantify the functional connectivity of the networks used under various comprehension conditions. To that aim we developed a technique to represent functional networks based on EEG recordings, taking advantage of their excellent time resolution in order to capture the fast processes that occur during language comprehension. Networks were created by searching for a specific causal relation between areas, the negative feedback loop, which is ubiquitous in many systems. This method is a simple way to construct directed graphs using event-related activity, which can then be analyzed topologically. Brain activity was recorded while subjects read expressions of various types and indicated whether they found them meaningful. Slightly different functional networks were obtained for event-related activity evoked by each expression type. The differences reflect the special contribution of specific regions in each condition and the balance of hemispheric activity involved in comprehending different types of expressions and are consistent with the literature in the field. Our results indicate that representing event-related brain activity as a network using a simple temporal relation, such as the negative feedback loop, to indicate directional connectivity is a viable option for investigation which also derives new information about aspects not reflected in the classical methods for investigating brain activity.

Mass as a Form of Energy in a Simple Example

ERIC Educational Resources Information Center

Dib, Claudio

2013-01-01

A major consequence of special relativity, expressed in the relation E[subscript 0] = mc[superscript 2], is that the total energy content of an object at rest, including its thermal motion and binding energy among its constituents, is a measure of its inertia, i.e., its mass. This relation was first stated by Einstein. He showed that, in order to…

A conformally flat realistic anisotropic model for a compact star

NASA Astrophysics Data System (ADS)

Ivanov, B. V.

2018-04-01

A physically realistic stellar model with a simple expression for the energy density and conformally flat interior is found. The relations between the different conditions are used without graphic proofs. It may represent a real pulsar.

Unveiling Angular Momentum

NASA Astrophysics Data System (ADS)

Robinson, Stephen

2015-03-01

Angular momentum is a notoriously difficult concept to grasp. Visualization often requires three-dimensional pictures of vectors pointing in seemingly arbitrary directions. A simple student-run laboratory experiment coupled with intuitive explanations by an instructor can clear up some of the inherent ambiguity of rotational motion. Specifically, the precessional period of a suspended spinning bicycle wheel can be related to the spinning frequency through a simple algebraic expression. An explanation of this precession apart from the concept of angular momentum will be given.

Simple and compact expressions for neutrino oscillation probabilities in matter

DOE PAGES

Minakata, Hisakazu; Parke, Stephen J.

2016-01-29

We reformulate perturbation theory for neutrino oscillations in matter with an expansion parameter related to the ratio of the solar to the atmospheric Δm 2 scales. Unlike previous works, use a renormalized basis in which certain first-order effects are taken into account in the zeroth-order Hamiltonian. Using this perturbation theory we derive extremely compact expressions for the neutrino oscillations probabilities in matter. We find, for example, that the ν e disappearance probability at this order is of a simple two flavor form with an appropriately identified mixing angle and Δm 2. Furthermore, despite exceptional simplicity in their forms they accommodatemore » all order effects θ 13 and the matter potential.« less

The Relation between Executive Function and Theory of Mind Is More than Skin Deep

ERIC Educational Resources Information Center

Carlson, Stephanie M.; Claxton, Laura J.; Moses, Louis J.

2015-01-01

A simple "expression" account of the relation between executive function (EF) and children's developing theory of mind (ToM) has difficulty accounting for the generality of the changes occurring in children's mental-state understanding during the preschool years. The current study of preschool children (N = 43) showed that EF--especially…

TA-GC cloning: A new simple and versatile technique for the directional cloning of PCR products for recombinant protein expression.

PubMed

Niarchos, Athanasios; Siora, Anastasia; Konstantinou, Evangelia; Kalampoki, Vasiliki; Lagoumintzis, George; Poulas, Konstantinos

2017-01-01

During the last few decades, the recombinant protein expression finds more and more applications. The cloning of protein-coding genes into expression vectors is required to be directional for proper expression, and versatile in order to facilitate gene insertion in multiple different vectors for expression tests. In this study, the TA-GC cloning method is proposed, as a new, simple and efficient method for the directional cloning of protein-coding genes in expression vectors. The presented method features several advantages over existing methods, which tend to be relatively more labour intensive, inflexible or expensive. The proposed method relies on the complementarity between single A- and G-overhangs of the protein-coding gene, obtained after a short incubation with T4 DNA polymerase, and T and C overhangs of the novel vector pET-BccI, created after digestion with the restriction endonuclease BccI. The novel protein-expression vector pET-BccI also facilitates the screening of transformed colonies for recombinant transformants. Evaluation experiments of the proposed TA-GC cloning method showed that 81% of the transformed colonies contained recombinant pET-BccI plasmids, and 98% of the recombinant colonies expressed the desired protein. This demonstrates that TA-GC cloning could be a valuable method for cloning protein-coding genes in expression vectors.

TA-GC cloning: A new simple and versatile technique for the directional cloning of PCR products for recombinant protein expression

PubMed Central

Niarchos, Athanasios; Siora, Anastasia; Konstantinou, Evangelia; Kalampoki, Vasiliki; Poulas, Konstantinos

2017-01-01

During the last few decades, the recombinant protein expression finds more and more applications. The cloning of protein-coding genes into expression vectors is required to be directional for proper expression, and versatile in order to facilitate gene insertion in multiple different vectors for expression tests. In this study, the TA-GC cloning method is proposed, as a new, simple and efficient method for the directional cloning of protein-coding genes in expression vectors. The presented method features several advantages over existing methods, which tend to be relatively more labour intensive, inflexible or expensive. The proposed method relies on the complementarity between single A- and G-overhangs of the protein-coding gene, obtained after a short incubation with T4 DNA polymerase, and T and C overhangs of the novel vector pET-BccI, created after digestion with the restriction endonuclease BccI. The novel protein-expression vector pET-BccI also facilitates the screening of transformed colonies for recombinant transformants. Evaluation experiments of the proposed TA-GC cloning method showed that 81% of the transformed colonies contained recombinant pET-BccI plasmids, and 98% of the recombinant colonies expressed the desired protein. This demonstrates that TA-GC cloning could be a valuable method for cloning protein-coding genes in expression vectors. PMID:29091919

Thickness-shear mode quartz crystal resonators in viscoelastic fluid media

NASA Astrophysics Data System (ADS)

Arnau, A.; Jiménez, Y.; Sogorb, T.

2000-10-01

An extended Butterworth-Van Dyke (EBVD) model to characterize a thickness-shear mode quartz crystal resonator in a semi-infinite viscoelastic medium is derived by means of analysis of the lumped elements model described by Cernosek et al. [R. W. Cernosek, S. J. Martin, A. R. Hillman, and H. L. Bandey, IEEE Trans. Ultrason. Ferroelectr. Freq. Control 45, 1399 (1998)]. The EBVD model parameters are related to the viscoelastic properties of the medium. A capacitance added to the motional branch of the EBVD model has to be included when the elastic properties of the fluid are considered. From this model, an explicit expression for the frequency shift of a quartz crystal sensor in viscoelastic media is obtained. By combining the expressions for shifts in the motional series resonant frequency and in the motional resistance, a simple equation that relates only one unknown (the loss factor of the fluid) to those measurable quantities, and two simple explicit expressions for determining the viscoelastic properties of semi-infinite fluid media have been derived. The proposed expression for the parameter Δf/ΔR is compared with the corresponding ratio obtained with data computed from the complete admittance model. Relative errors below 4.5%, 3%, and 1.2% (for the ratios of the load surface mechanical impedance to the quartz shear characteristic impedance of 0.3, 0.25, and 0.1, respectively), are obtained in the range of the cases analyzed. Experimental data from the literature are used to validate the model.

A pseudo-sound constitutive relationship for the dilatational covariances in compressible turbulence: An analytical theory

NASA Technical Reports Server (NTRS)

Ristorcelli, J. R.

1995-01-01

The mathematical consequences of a few simple scaling assumptions about the effects of compressibility are explored using a simple singular perturbation idea and the methods of statistical fluid mechanics. Representations for the pressure-dilation and dilatational dissipation covariances appearing in single-point moment closures for compressible turbulence are obtained. While the results are expressed in the context of a second-order statistical closure they provide some interesting and very clear physical metaphors for the effects of compressibility that have not been seen using more traditional linear stability methods. In the limit of homogeneous turbulence with quasi-normal large-scales the expressions derived are - in the low turbulent Mach number limit - asymptotically exact. The expressions obtained are functions of the rate of change of the turbulence energy, its correlation length scale, and the relative time scale of the cascade rate. The expressions for the dilatational covariances contain constants which have a precise and definite physical significance; they are related to various integrals of the longitudinal velocity correlation. The pressure-dilation covariance is found to be a nonequilibrium phenomena related to the time rate of change of the internal energy and the kinetic energy of the turbulence. Also of interest is the fact that the representation for the dilatational dissipation in turbulence, with or without shear, features a dependence on the Reynolds number. This article is a documentation of an analytical investigation of the implications of a pseudo-sound theory for the effects of compressibility.

Communication: Simple liquids' high-density viscosity

NASA Astrophysics Data System (ADS)

Costigliola, Lorenzo; Pedersen, Ulf R.; Heyes, David M.; Schrøder, Thomas B.; Dyre, Jeppe C.

2018-02-01

This paper argues that the viscosity of simple fluids at densities above that of the triple point is a specific function of temperature relative to the freezing temperature at the density in question. The proposed viscosity expression, which is arrived at in part by reference to the isomorph theory of systems with hidden scale invariance, describes computer simulations of the Lennard-Jones system as well as argon and methane experimental data and simulation results for an effective-pair-potential model of liquid sodium.

Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

PubMed Central

Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

2011-01-01

Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

On some stochastic formulations and related statistical moments of pharmacokinetic models.

PubMed

Matis, J H; Wehrly, T E; Metzler, C M

1983-02-01

This paper presents the deterministic and stochastic model for a linear compartment system with constant coefficients, and it develops expressions for the mean residence times (MRT) and the variances of the residence times (VRT) for the stochastic model. The expressions are relatively simple computationally, involving primarily matrix inversion, and they are elegant mathematically, in avoiding eigenvalue analysis and the complex domain. The MRT and VRT provide a set of new meaningful response measures for pharmacokinetic analysis and they give added insight into the system kinetics. The new analysis is illustrated with an example involving the cholesterol turnover in rats.

English in the Garment Shops.

ERIC Educational Resources Information Center

Verplaetse, Lorrie

This text for limited-English-speaking workers in the garment industry consits of illustrated vocabulary words, grammar lessons, narratives or brief readings, and exercises on employment-related topics. The first section focuses on shop talk, including job-specific vocabulary, simple expressions and explanations, social language, seeking and…

WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning.

PubMed

Lee, M M; Schiefelbein, J

1999-11-24

The formation of the root epidermis of Arabidopsis provides a simple and elegant model for the analysis of cell patterning. A novel gene, WEREWOLF (WER), is described here that is required for position-dependent patterning of the epidermal cell types. The WER gene encodes a MYB-type protein and is preferentially expressed within cells destined to adopt the non-hair fate. Furthermore, WER is shown to regulate the position-dependent expression of the GLABRA2 homeobox gene, to interact with a bHLH protein, and to act in opposition to the CAPRICE MYB. These results suggest a simple model to explain the specification of the two root epidermal cell types, and they provide insight into the molecular mechanisms used to control cell patterning.

On determinant representations of scalar products and form factors in the SoV approach: the XXX case

NASA Astrophysics Data System (ADS)

Kitanine, N.; Maillet, J. M.; Niccoli, G.; Terras, V.

2016-03-01

In the present article we study the form factors of quantum integrable lattice models solvable by the separation of variables (SoVs) method. It was recently shown that these models admit universal determinant representations for the scalar products of the so-called separate states (a class which includes in particular all the eigenstates of the transfer matrix). These results permit to obtain simple expressions for the matrix elements of local operators (form factors). However, these representations have been obtained up to now only for the completely inhomogeneous versions of the lattice models considered. In this article we give a simple algebraic procedure to rewrite the scalar products (and hence the form factors) for the SoV related models as Izergin or Slavnov type determinants. This new form leads to simple expressions for the form factors in the homogeneous and thermodynamic limits. To make the presentation of our method clear, we have chosen to explain it first for the simple case of the XXX Heisenberg chain with anti-periodic boundary conditions. We would nevertheless like to stress that the approach presented in this article applies as well to a wide range of models solved in the SoV framework.

Spectral properties of thermal fluctuations on simple liquid surfaces below shot-noise levels.

PubMed

Aoki, Kenichiro; Mitsui, Takahisa

2012-07-01

We study the spectral properties of thermal fluctuations on simple liquid surfaces, sometimes called ripplons. Analytical properties of the spectral function are investigated and are shown to be composed of regions with simple analytic behavior with respect to the frequency or the wave number. The derived expressions are compared to spectral measurements performed orders of magnitude below shot-noise levels, which is achieved using a novel noise reduction method. The agreement between the theory of thermal surface fluctuations and the experiment is found to be excellent, elucidating the spectral properties of the surface fluctuations. The measurement method requires relatively only a small sample both spatially (few μm) and temporally (~20 s). The method also requires relatively weak light power (~0.5 mW) so that it has a broad range of applicability, including local measurements, investigations of time-dependent phenomena, and noninvasive measurements.

Quantify spatial relations to discover handwritten graphical symbols

NASA Astrophysics Data System (ADS)

Li, Jinpeng; Mouchère, Harold; Viard-Gaudin, Christian

2012-01-01

To model a handwritten graphical language, spatial relations describe how the strokes are positioned in the 2-dimensional space. Most of existing handwriting recognition systems make use of some predefined spatial relations. However, considering a complex graphical language, it is hard to express manually all the spatial relations. Another possibility would be to use a clustering technique to discover the spatial relations. In this paper, we discuss how to create a relational graph between strokes (nodes) labeled with graphemes in a graphical language. Then we vectorize spatial relations (edges) for clustering and quantization. As the targeted application, we extract the repetitive sub-graphs (graphical symbols) composed of graphemes and learned spatial relations. On two handwriting databases, a simple mathematical expression database and a complex flowchart database, the unsupervised spatial relations outperform the predefined spatial relations. In addition, we visualize the frequent patterns on two text-lines containing Chinese characters.

Modeling gene expression measurement error: a quasi-likelihood approach

PubMed Central

Strimmer, Korbinian

2003-01-01

Background Using suitable error models for gene expression measurements is essential in the statistical analysis of microarray data. However, the true probabilistic model underlying gene expression intensity readings is generally not known. Instead, in currently used approaches some simple parametric model is assumed (usually a transformed normal distribution) or the empirical distribution is estimated. However, both these strategies may not be optimal for gene expression data, as the non-parametric approach ignores known structural information whereas the fully parametric models run the risk of misspecification. A further related problem is the choice of a suitable scale for the model (e.g. observed vs. log-scale). Results Here a simple semi-parametric model for gene expression measurement error is presented. In this approach inference is based an approximate likelihood function (the extended quasi-likelihood). Only partial knowledge about the unknown true distribution is required to construct this function. In case of gene expression this information is available in the form of the postulated (e.g. quadratic) variance structure of the data. As the quasi-likelihood behaves (almost) like a proper likelihood, it allows for the estimation of calibration and variance parameters, and it is also straightforward to obtain corresponding approximate confidence intervals. Unlike most other frameworks, it also allows analysis on any preferred scale, i.e. both on the original linear scale as well as on a transformed scale. It can also be employed in regression approaches to model systematic (e.g. array or dye) effects. Conclusions The quasi-likelihood framework provides a simple and versatile approach to analyze gene expression data that does not make any strong distributional assumptions about the underlying error model. For several simulated as well as real data sets it provides a better fit to the data than competing models. In an example it also improved the power of tests to identify differential expression. PMID:12659637

[Endometrial hyperplasia, diagnosis. Clinical, paraclinical exam and management].

PubMed

Pangal, Alexandra; Costăchescu, Gh; Aldea, Marie Jeanne

2010-01-01

Factors associated with unopposed estrogenic stimulation such as obesity, exogenous hormone use endometrial hyperplasia are related to the development of the most common form of endometrial carcinoma, that is, the endometroid subtype. We selected a group of patients diagnosed with endometrial hyperplasia by endometrial biopsy and histopathological examination. The main complaint in all cases was abnormal uterine bleeding. All patients had gynecological examination, vaginal ultrasound, hysteroscopy endometrial biopsy or D&C. 32 patients had also immunohistochemical staining for Ki67, EGF, ER, PGR. Cases with ages between 24-67 years were classified as: 100 simple hyperplasia, 10 complex hyperplasia, 43 atypical simple hyperplasia, 7 atypical complex hyperplasia. PR were 40-60% at all forms of hyperplasia, E2R were 30-40% in simple hyperplasia without atypia and 50-70% in complex hyperplasia without atypia. Correlation between immunohistochemical expression of E2R, PGR, Ki-67, EGF and body mass revealed an high immunohistochemical expression of E2R and Ki-67 in patients with hyperplasia without atypia and a low expression and high reactivity of EGF in cases with high body mass. Vaginal ultrasound and hysteroscopy are efficacious completion for histopathological diagnosis. We recommend an age/risk appropriate screening to detect risk factors and early disease in the asymptomatic patients.

Chemistry for Kids: What Do Chemists Do? A Program for Grades 1-3.

ERIC Educational Resources Information Center

Umland, Jean B.

1985-01-01

Proposes a simple solution to the problem of expressing graphically absolute configuration, racemic character, and relative configuration in molecules. As demonstrated by several examples, the proposed convention brings added clarity and simplicity to structural drawings and renders graphic displays of chiral molecules as explicit and information…

Virtual Characters: Visual Realism Affects Response Time and Decision-Making

ERIC Educational Resources Information Center

Sibuma, Bernadette

2012-01-01

This study integrates agent research with a neurocognitive technique to study how character faces affect cognitive processing. The N170 event-related potential (ERP) was used to study face processing during simple decision-making tasks. Twenty-five adults responded to facial expressions (fear/neutral) presented in three designs…

Retrieval-Induced Forgetting of Arithmetic Facts

ERIC Educational Resources Information Center

Campbell, Jamie I. D.; Thompson, Valerie A.

2012-01-01

Retrieval-induced forgetting (RIF) is a widely studied phenomenon of human memory, but RIF of arithmetic facts remains relatively unexplored. In 2 experiments, we investigated RIF of simple addition facts (2 + 3 = 5) from practice of their multiplication counterparts (2 x 3 = 6). In both experiments, robust RIF expressed in response times occurred…

Mathematical model of the solar radiation force and torques acting on the components of a spacecraft

NASA Technical Reports Server (NTRS)

Georgevic, R. M.

1971-01-01

General expressions for the solar radiation force and torques are derived in the vectorial form for any given reflecting surface, provided that the reflecting characteristics of the surface, as well as the value of the solar constant, are known. An appropriate choice of a spacecraft-fixed frame of reference leads to relatively simple expressions for the solar radiation forces and torques in terms of the functions of the sun-spacecraft-earth angle.

Expressions of the fundamental equation of gradient elution and a numerical solution of these equations under any gradient profile.

PubMed

Nikitas, P; Pappa-Louisi, A

2005-09-01

The original work carried out by Freiling and Drake in gradient liquid chromatography is rewritten in the current language of reversed-phase liquid chromatography. This allows for the rigorous derivation of the fundamental equation for gradient elution and the development of two alternative expressions of this equation, one of which is free from the constraint that the holdup time must be constant. In addition, the above derivation results in a very simple numerical solution of the various equations of gradient elution under any gradient profile. The theory was tested using eight catechol-related solutes in mobile phases modified with methanol, acetonitrile, or 2-propanol. It was found to be a satisfactory prediction of solute gradient retention behavior even if we used a simple linear description for the isocratic elution of these solutes.

Information and complexity measures in the interface of a metal and a superconductor

NASA Astrophysics Data System (ADS)

Moustakidis, Ch. C.; Panos, C. P.

2018-06-01

Fisher information, Shannon information entropy and Statistical Complexity are calculated for the interface of a normal metal and a superconductor, as a function of the temperature for several materials. The order parameter Ψ (r) derived from the Ginzburg-Landau theory is used as an input together with experimental values of critical transition temperature Tc and the superconducting coherence length ξ0. Analytical expressions are obtained for information and complexity measures. Thus Tc is directly related in a simple way with disorder and complexity. An analytical relation is found of the Fisher Information with the energy profile of superconductivity i.e. the ratio of surface free energy and the bulk free energy. We verify that a simple relation holds between Shannon and Fisher information i.e. a decomposition of a global information quantity (Shannon) in terms of two local ones (Fisher information), previously derived and verified for atoms and molecules by Liu et al. Finally, we find analytical expressions for generalized information measures like the Tsallis entropy and Fisher information. We conclude that the proper value of the non-extensivity parameter q ≃ 1, in agreement with previous work using a different model, where q ≃ 1.005.

Eye-Tracking and Corpus-Based Analyses of Syntax-Semantics Interactions in Complement Coercion

PubMed Central

Lowder, Matthew W.; Gordon, Peter C.

2016-01-01

Previous work has shown that the difficulty associated with processing complex semantic expressions is reduced when the critical constituents appear in separate clauses as opposed to when they appear together in the same clause. We investigated this effect further, focusing in particular on complement coercion, in which an event-selecting verb (e.g., began) combines with a complement that represents an entity (e.g., began the memo). Experiment 1 compared reading times for coercion versus control expressions when the critical verb and complement appeared together in a subject-extracted relative clause (SRC) (e.g., The secretary that began/wrote the memo) compared to when they appeared together in a simple sentence. Readers spent more time processing coercion expressions than control expressions, replicating the typical coercion cost. In addition, readers spent less time processing the verb and complement in SRCs than in simple sentences; however, the magnitude of the coercion cost did not depend on sentence structure. In contrast, Experiment 2 showed that the coercion cost was reduced when the complement appeared as the head of an object-extracted relative clause (ORC) (e.g., The memo that the secretary began/wrote) compared to when the constituents appeared together in an SRC. Consistent with the eye-tracking results of Experiment 2, a corpus analysis showed that expressions requiring complement coercion are more frequent when the constituents are separated by the clause boundary of an ORC compared to when they are embedded together within an SRC. The results provide important information about the types of structural configurations that contribute to reduced difficulty with complex semantic expressions, as well as how these processing patterns are reflected in naturally occurring language. PMID:28529960

Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism

PubMed Central

Abehsera, Shai; Glazer, Lilah; Tynyakov, Jenny; Plaschkes, Inbar; Chalifa-Caspi, Vered; Khalaila, Isam; Aflalo, Eliahu D.; Sagi, Amir

2015-01-01

In crustaceans, like all arthropods, growth is accompanied by a molting cycle. This cycle comprises major physiological events in which mineralized chitinous structures are built and degraded. These events are in turn governed by genes whose patterns of expression are presumably linked to the molting cycle. To study these genes we performed next generation sequencing and constructed a molt-related transcriptomic library from two exoskeletal-forming tissues of the crayfish Cherax quadricarinatus, namely the gastrolith and the mandible cuticle-forming epithelium. To simplify the study of such a complex process as molting, a novel approach, binary patterning of gene expression, was employed. This approach revealed that key genes involved in the synthesis and breakdown of chitin exhibit a molt-related pattern in the gastrolith-forming epithelium. On the other hand, the same genes in the mandible cuticle-forming epithelium showed a molt-independent pattern of expression. Genes related to the metabolism of glucosamine-6-phosphate, a chitin precursor synthesized from simple sugars, showed a molt-related pattern of expression in both tissues. The binary patterning approach unfolds typical patterns of gene expression during the molt cycle of a crustacean. The use of such a simplifying integrative tool for assessing gene patterning seems appropriate for the study of complex biological processes. PMID:25919476

A closed-form expression for the effect in breakthrough curves of biofilm development: enhanced dispersion

NASA Astrophysics Data System (ADS)

Sanchez-Vila, X.; Rodriguez-Escales, P.

2017-12-01

It has been widely reported that biofilm growth changes the hydraulic parameters in porous media. While the impact upon reduction of hydraulic conductivity has been widely explained and modeled, this has not been the case for the reported order(s) of magnitude increase in dispersion coefficient even when a minute percentage of biofilm is formed, and despite the effect of biofilm growth is to reduce specific discharge, producing a somewhat counterintuitive result. We develop here a simple yet practical expression for the evaluation of an effective dispersion coefficient caused by biomass colonization, based on the modification of the breakthrough curves (in terms of temporal moments) with respect to the biofilm-free porous media. The advantage of the expression is that it is written in terms of observables that are relatively easy to measure in the lab or the field, contrarily to existing expressions that relate the effect to channelization resulting in tortuosity being the driving term of effective dispersion. We have tested our simplified expression in a number of reported sites, where enhanced dispersion of 1-2 orders of magnitude has been reported, indirectly showing the relative importance of the terms included in the expression.

Expression of the glutamine metabolism-related proteins glutaminase 1 and glutamate dehydrogenase in canine mammary tumours.

PubMed

Ryu, J-E; Park, H-K; Choi, H-J; Lee, H-B; Lee, H-J; Lee, H; Yu, E-S; Son, W-C

2018-06-01

Glutamine metabolism is an important metabolic pathway for cancer cell survival, and there is a critical connection between tumour growth and glutamine metabolism. Because of their similarities, canine mammary carcinomas are useful for studying human breast cancer. Accordingly, we investigated the correlations between the expression of glutamine metabolism-related proteins and the pathological features of canine mammary tumours. We performed immunohistochemical and western blot analysis of 39 mammary tumour tissues. In immunohistochemical analysis, the expression of glutaminase 1 (GLS1) in the epithelial region increased according to the histological grade (P < .005). In the stromal region, complex-type tumours displayed significantly higher GLS1 intensity than simple-type tumours. However, glutamate dehydrogenase expression did not show the same tendencies as GLS1. The western blot results were consistent with the immunohistochemical findings. These results suggest that the expression of GLS1 is correlates with clinicopathological factors in canine mammary tumours and shows a similar pattern to human breast cancer. © 2017 John Wiley & Sons Ltd.

Approximate Expressions for the Period of a Simple Pendulum Using a Taylor Series Expansion

ERIC Educational Resources Information Center

Belendez, Augusto; Arribas, Enrique; Marquez, Andres; Ortuno, Manuel; Gallego, Sergi

2011-01-01

An approximate scheme for obtaining the period of a simple pendulum for large-amplitude oscillations is analysed and discussed. When students express the exact frequency or the period of a simple pendulum as a function of the oscillation amplitude, and they are told to expand this function in a Taylor series, they always do so using the…

The Value of Emoticons in Investigating Student Emotions Related to Mathematics Task Negotiation

ERIC Educational Resources Information Center

D'Agostin, Fabio

2014-01-01

"Emoticons" are simple face icons expressing common feelings such as happiness, interest and boredom and are popularly used in electronic communication. Emoticons were utilised in this study as experience sampling devices. Year 10 students selected emoticons to indicate their emotional states at set intervals during classroom tasks.…

Path Integration on the Upper Half-Plane

NASA Astrophysics Data System (ADS)

Kubo, R.

1987-10-01

Feynman's path integral is considered on the Poincaré upper half-plane. It is shown that the fundermental solution to the heat equation partial f/partial t=Delta_{H}f can be expressed in terms of a path integral. A simple relation between the path integral and the Selberg trace formula is discussed briefly.

Lipid overloading during liver regeneration causes delayed hepatocyte DNA replication by increasing ER stress in mice with simple hepatic steatosis.

PubMed

Hamano, Mina; Ezaki, Hisao; Kiso, Shinichi; Furuta, Kunimaro; Egawa, Mayumi; Kizu, Takashi; Chatani, Norihiro; Kamada, Yoshihiro; Yoshida, Yuichi; Takehara, Tetsuo

2014-02-01

Impaired fatty liver regeneration has already been reported in many genetic modification models. However, in diet-induced simple hepatic steatosis, which showed similar phenotype with clinical pathology, whether liver regeneration is impaired or not remains unclear. In this study, we evaluated liver regeneration in mice with diet-induced simple hepatic steatosis, and focused on excess lipid accumulation occurring during liver regeneration. Mice were fed high fat diet (HFD) or control diet for 9-10 weeks. We analyzed intrahepatic lipid accumulation, DNA replication, and various signaling pathways including cell proliferation and ER stress during liver regeneration after partial hepatectomy. In addition, some of mice were pretreated with tauroursodeoxycholic acid (TUDCA), a chemical chaperone which alleviates ER stress, and then we estimated TUDCA effects on liver regeneration. The peak of hepatocyte BrdU incorporation, the expression of proliferation cell nuclear antigen (PCNA) protein, and the expressions of cell cycle-related genes were observed in delayed time in HFD mice. The expression of phosphorylated Erk1/2 was also delayed in HFD mice. The amounts of liver triglyceride were at least twofold higher in HFD mice at each time point. Intrahepatic palmitic acid was increased especially in HFD mice. ER stress induced during liver regeneration was significantly higher in HFD mice. In HFD mice, pretreatment with TUDCA reduced ER stress and resulted in improvement of delayed liver regeneration. In simple hepatic steatosis, lipid overloading occurring during liver regeneration might be caused ER stress and results in delayed hepatocyte DNA replication.

Analytic expressions for the black-sky and white-sky albedos of the cosine lobe model.

PubMed

Goodin, Christopher

2013-05-01

The cosine lobe model is a bidirectional reflectance distribution function (BRDF) that is commonly used in computer graphics to model specular reflections. The model is both simple and physically plausible, but physical quantities such as albedo have not been related to the parameterization of the model. In this paper, analytic expressions for calculating the black-sky and white-sky albedos from the cosine lobe BRDF model with integer exponents will be derived, to the author's knowledge for the first time. These expressions for albedo can be used to place constraints on physics-based simulations of radiative transfer such as high-fidelity ray-tracing simulations.

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

PubMed Central

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest. PMID:19131380

A Simple Exact Error Rate Analysis for DS-CDMA with Arbitrary Pulse Shape in Flat Nakagami Fading

NASA Astrophysics Data System (ADS)

Rahman, Mohammad Azizur; Sasaki, Shigenobu; Kikuchi, Hisakazu; Harada, Hiroshi; Kato, Shuzo

A simple exact error rate analysis is presented for random binary direct sequence code division multiple access (DS-CDMA) considering a general pulse shape and flat Nakagami fading channel. First of all, a simple model is developed for the multiple access interference (MAI). Based on this, a simple exact expression of the characteristic function (CF) of MAI is developed in a straight forward manner. Finally, an exact expression of error rate is obtained following the CF method of error rate analysis. The exact error rate so obtained can be much easily evaluated as compared to the only reliable approximate error rate expression currently available, which is based on the Improved Gaussian Approximation (IGA).

Extended Poisson process modelling and analysis of grouped binary data.

PubMed

Faddy, Malcolm J; Smith, David M

2012-05-01

A simple extension of the Poisson process results in binomially distributed counts of events in a time interval. A further extension generalises this to probability distributions under- or over-dispersed relative to the binomial distribution. Substantial levels of under-dispersion are possible with this modelling, but only modest levels of over-dispersion - up to Poisson-like variation. Although simple analytical expressions for the moments of these probability distributions are not available, approximate expressions for the mean and variance are derived, and used to re-parameterise the models. The modelling is applied in the analysis of two published data sets, one showing under-dispersion and the other over-dispersion. More appropriate assessment of the precision of estimated parameters and reliable model checking diagnostics follow from this more general modelling of these data sets. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A general relaxation theory of simple liquids

NASA Technical Reports Server (NTRS)

Merilo, M.; Morgan, E. J.

1973-01-01

A relatively simple relaxation theory to account for the behavior of liquids under dynamic conditions was proposed. The general dynamical equations are similar in form to the phenomenological relaxation equations used in theories of viscoelasticity, however, they differ in that all the coefficients of the present equations are expressed in terms of thermodynamic and molecular quantities. The theory is based on the concept that flow in a liquid distorts both the radial and the velocity distribution functions, and that relaxation equations describing the return of these functions to their isotropic distributions, characterizing a stationary liquid, can be written. The theory was applied to the problems of steady and oscillatory shear flows and to the propagation of longitudinal waves. In all cases classical results are predicted for strain rates, and an expression for the viscosity of a liquid, simular to the Macedo-Litovitz equation, is obtained.

Critical power for self-focusing of optical beam in absorbing media

NASA Astrophysics Data System (ADS)

Qi, Pengfei; Zhang, Lin; Lin, Lie; Zhang, Nan; Wang, Yan; Liu, Weiwei

2018-04-01

Self-focusing effects are of central importance for most nonlinear optical effects. The critical power for self-focusing is commonly investigated theoretically without considering a material’s absorption. Although this is practicable for various materials, investigating the critical power for self-focusing in media with non-negligible absorption is also necessary, because this is the situation usually met in practice. In this paper, the simple analytical expressions describing the relationships among incident power, absorption coefficient and focal position are provided by a simple physical model based on the Fermat principle. Expressions for the absorption dependent critical power are also derived; these can play important roles in experimental and applied research on self-focusing-related nonlinear optical phenomena in absorbing media. Numerical results, based on the nonlinear wave equation—and which can predict experimental results perfectly—are also presented, and agree quantitatively with the analytical results proposed in this paper.

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

PubMed Central

Hui, Sheng; Silverman, Josh M; Chen, Stephen S; Erickson, David W; Basan, Markus; Wang, Jilong; Hwa, Terence; Williamson, James R

2015-01-01

A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies. PMID:25678603

Generalization of Wilemski-Fixman-Weiss decoupling approximation to the case involving multiple sinks of different sizes, shapes, and reactivities.

PubMed

Uhm, Jesik; Lee, Jinuk; Eun, Changsun; Lee, Sangyoub

2006-08-07

We generalize the Wilemski-Fixman-Weiss decoupling approximation to calculate the transient rate of absorption of point particles into multiple sinks of different sizes, shapes, and reactivities. As an application we consider the case involving two spherical sinks. We obtain a Laplace-transform expression for the transient rate that is in excellent agreement with computer simulations. The long-time steady-state rate has a relatively simple expression, which clearly shows the dependence on the diffusion constant of the particles and on the sizes and reactivities of sinks, and its numerical result is in good agreement with the known exact result that is given in terms of recursion relations.

A model for accretion of the terrestrial planets

NASA Technical Reports Server (NTRS)

Weidenschilling, S. J.

1974-01-01

One possible origin of the terrestrial planets involves their formation by gravitational accretion of particles originally in Keplerian orbits about the sun. Some implications of this theory are considered. A formal expression for the rate of mass accretion by a planet is developed. The formal singularity of the gravitational collision cross section for low relative velocities is shown to be without physical significance when the accreting bodies are in heliocentric orbits. The distribution of particle velocities relative to an accreting planet is considered; the mean velocity increases with time. The internal temperature of an accreting planet is shown to depend simply on the accretion rate. A simple and physically reasonable approximate expression for a planetary accretion rate is proposed.

Some correlations between sugar maple tree characteristics and sap and sugar yields

Treesearch

Barton M. Blum

1971-01-01

Simple correlation coefficients between various characteristics of sugar maple trees and sap sugar concentration, sap volume yield, and total sugar production are given for the 1968 sap season. Correlation coefficients in general indicated that individual tree characteristics that express tree and crown size are significantly related to sap volume yield and total sugar...

Application of the Homotopy Perturbation Method to the Nonlinear Pendulum

ERIC Educational Resources Information Center

Belendez, A.; Hernandez, A.; Belendez, T.; Marquez, A.

2007-01-01

The homotopy perturbation method is used to solve the nonlinear differential equation that governs the nonlinear oscillations of a simple pendulum, and an approximate expression for its period is obtained. Only one iteration leads to high accuracy of the solutions and the relative error for the approximate period is less than 2% for amplitudes as…

Mass, Momentum and Kinetic Energy of a Relativistic Particle

ERIC Educational Resources Information Center

Zanchini, Enzo

2010-01-01

A rigorous definition of mass in special relativity, proposed in a recent paper, is recalled and employed to obtain simple and rigorous deductions of the expressions of momentum and kinetic energy for a relativistic particle. The whole logical framework appears as the natural extension of the classical one. Only the first, second and third laws of…

HD CAG-correlated gene expression changes support a simple dominant gain of function

PubMed Central

Jacobsen, Jessie C.; Gregory, Gillian C.; Woda, Juliana M.; Thompson, Morgan N.; Coser, Kathryn R.; Murthy, Vidya; Kohane, Isaac S.; Gusella, James F.; Seong, Ihn Sik; MacDonald, Marcy E.; Shioda, Toshi; Lee, Jong-Min

2011-01-01

Huntington's disease is initiated by the expression of a CAG repeat-encoded polyglutamine region in full-length huntingtin, with dominant effects that vary continuously with CAG size. The mechanism could involve a simple gain of function or a more complex gain of function coupled to a loss of function (e.g. dominant negative-graded loss of function). To distinguish these alternatives, we compared genome-wide gene expression changes correlated with CAG size across an allelic series of heterozygous CAG knock-in mouse embryonic stem (ES) cell lines (HdhQ20/7, HdhQ50/7, HdhQ91/7, HdhQ111/7), to genes differentially expressed between Hdhex4/5/ex4/5 huntingtin null and wild-type (HdhQ7/7) parental ES cells. The set of 73 genes whose expression varied continuously with CAG length had minimal overlap with the 754-member huntingtin-null gene set but the two were not completely unconnected. Rather, the 172 CAG length-correlated pathways and 238 huntingtin-null significant pathways clustered into 13 shared categories at the network level. A closer examination of the energy metabolism and the lipid/sterol/lipoprotein metabolism categories revealed that CAG length-correlated genes and huntingtin-null-altered genes either were different members of the same pathways or were in unique, but interconnected pathways. Thus, varying the polyglutamine size in full-length huntingtin produced gene expression changes that were distinct from, but related to, the effects of lack of huntingtin. These findings support a simple gain-of-function mechanism acting through a property of the full-length huntingtin protein and point to CAG-correlative approaches to discover its effects. Moreover, for therapeutic strategies based on huntingtin suppression, our data highlight processes that may be more sensitive to the disease trigger than to decreased huntingtin levels. PMID:21536587

Expression of Simple Mucin Type Antigens and Lewis Type 1 and Type 2 Chain Antigens in the Thyroid Gland: An Immunohistochemical Study of Normal Thyroid Tissues, Benign Lesions, and Malignant Tumors.

PubMed

Fonseca, Elsa; Castanhas, Salome; Sobrinho-Simoes, Manuel

1996-01-01

In order to characterize the pattern of expression of carbohydrate structures in several types of thyroid tissues and to evaluate the putative usefulness of the detection of such antigens in diagnostic surgical pathology, we undertook the immunohistochemical study of simple mucin type antigens (T, Tn, and sialyl Tn), Lewis type I antigens (Lewis a, sialyl Lewis a, and Lewis b), and Lewis type 2 related antigens (precursor type 2, H type 2, Lewis x, sialyl Lewis x, and Lewis y) in thyroid samples obtained from 65 patients. The material consisted on paraffin sections of normal thyroid (n = 43), benign lesions (13 goiters/hyperplastic lesions and 15 adenomas), and malignant tumors (12 follicular carcinomas and 27 papillary carcinomas, 5 of which had lymph node metastases) of the thyroid follicular epithelium. Tn, T, and precursor type 2 antigens were the only antigens that were detected and very rarely in normal thyroid. Benign lesions were similar to normal thyroid despite displaying a higher prevalence of immunoreactivity for several antigens of the three groups. Thyroid carcinomas presented a significantly higher level of expression of all types of simple mucin, Lewis type 1, and Lewis type 2 antigens than the normal thyroid and benign lesions. The expression of sialyl Tn was restricted to malignant tumors, and the expression of sialyl Lewis x was closely associated, though not exclusively, to papillary carcinomas. The immunoreactivity was stronger and the number of positive cases was higher in papillary than in follicular carcinomas. No differences were found between primary tumors and the respective metastases. The existence of distinct patterns of expression of carbohydrate antigens in different types of thyroid lesions points to the usefulness of the detection of some of these antigens in thyroid surgical pathology. The putative role of such antigens in the peculiar metastatic properties of thyroid carcinomas remains unsettled.

Approximate stresses in 2-D flat elastic contact fretting problems

NASA Astrophysics Data System (ADS)

Urban, Michael Rene

Fatigue results from the cyclic loading of a solid body. If the body subject to fatigue is in contact with another body and relative sliding motion occurs between these two bodies, then rubbing surface damage can accelerate fatigue failure. The acceleration of fatigue failure is especially important if the relative motion between the two bodies results in surface damage without excessive surface removal via wear. The situation just described is referred to as fretting fatigue. Understanding of fretting fatigue is greatly enhanced if the stress state associated with fretting can be characterized. For Hertzian contact, this can readily be done. Unfortunately, simple stress formulae are not available for flat body contact. The primary result of the present research is the development of a new, reasonably accurate, approximate closed form expression for 2-dimensional contact stresses which has been verified using finite element modeling. This expression is also combined with fracture mechanics to provide a simple method of determining when a crack is long enough to no longer be affected by the contact stress field. Lower bounds on fatigue life can then easily be calculated using fracture mechanics. This closed form expression can also be used to calculate crack propagation within the contact stress field. The problem of determining the cycles required to generate an initial crack and what to choose as an initial crack size is unresolved as it is in non-fretting fatigue.

Response to emotional expressions in generalized social phobia and generalized anxiety disorder: evidence for separate disorders.

PubMed

Blair, Karina; Shaywitz, Jonathan; Smith, Bruce W; Rhodes, Rebecca; Geraci, Marilla; Jones, Matthew; McCaffrey, Daniel; Vythilingam, Meena; Finger, Elizabeth; Mondillo, Krystal; Jacobs, Madeline; Charney, Dennis S; Blair, R J R; Drevets, Wayne C; Pine, Daniel S

2008-09-01

Generalized social phobia involves fear/avoidance, specifically of social situations, whereas generalized anxiety disorder involves intrusive worry about diverse circumstances. It remains unclear the degree to which these two, often comorbid, conditions represent distinct disorders or alternative presentations of a single, core underlying pathology. Functional magnetic resonance imaging assessed the neural response to facial expressions in generalized social phobia and generalized anxiety disorder. Individuals matched on age, IQ, and gender with generalized social phobia without generalized anxiety disorder (N=17), generalized anxiety disorder (N=17), or no psychopathology (N=17) viewed neutral, fearful, and angry expressions while ostensibly making a simple gender judgment. The patients with generalized social phobia without generalized anxiety disorder showed increased activation to fearful relative to neutral expressions in several regions, including the amygdala, compared to healthy individuals. This increased amygdala response related to self-reported anxiety in patients with generalized social phobia without generalized anxiety disorder. In contrast, patients with generalized anxiety disorder showed significantly less activation to fearful relative to neutral faces compared to the healthy individuals. They did show significantly increased response to angry expressions relative to healthy individuals in a lateral region of the middle frontal gyrus. This increased lateral frontal response related to self-reported anxiety in patients with generalized anxiety disorder. These results suggest that neural circuitry dysfunctions differ in generalized social phobia and generalized anxiety disorder.

Fall in hematocrit per 1000 parasites cleared from peripheral blood: a simple method for estimating drug-related fall in hematocrit after treatment of malaria infections.

PubMed

Gbotosho, Grace Olusola; Okuboyejo, Titilope; Happi, Christian Tientcha; Sowunmi, Akintunde

2014-01-01

A simple method to estimate antimalarial drug-related fall in hematocrit (FIH) after treatment of Plasmodium falciparum infections in the field is described. The method involves numeric estimation of the relative difference in hematocrit at baseline (pretreatment) and the first 1 or 2 days after treatment begun as numerator and the corresponding relative difference in parasitemia as the denominator, and expressing it per 1000 parasites cleared from peripheral blood. Using the method showed that FIH/1000 parasites cleared from peripheral blood (cpb) at 24 or 48 hours were similar in artemether-lumefantrine and artesunate-amodiaquine-treated children (0.09; 95% confidence interval, 0.052-0.138 vs 0.10; 95% confidence interval, 0.069-0.139%; P = 0.75) FIH/1000 parasites cpb in patients with higher parasitemias were significantly (P < 0.0001) and five- to 10-fold lower than in patients with lower parasitemias suggesting conservation of hematocrit or red cells in patients with higher parasitemias treated with artesunate-amodiaquine or artemether-lumefantrine. FIH/1000 parasites cpb were similar in anemic and nonanemic children. Estimation of FIH/1000 parasites cpb is simple, allows estimation of relatively conserved hematocrit during treatment, and can be used in both observational studies and clinical trials involving antimalarial drugs.

A first immunohistochemistry study of transketolase and transketolase-like 1 expression in canine hyperplastic and neoplastic mammary lesions.

PubMed

Burrai, Giovanni Pietro; Tanca, Alessandro; Cubeddu, Tiziana; Abbondio, Marcello; Polinas, Marta; Addis, Maria Filippa; Antuofermo, Elisabetta

2017-01-31

Canine mammary tumors represent the most common neoplasm in female dogs, and the discovery of cancer biomarkers and their translation to clinical relevant assays is a key requirement in the war on cancer. Since the description of the 'Warburg effect', the reprogramming of metabolic pathways is considered a hallmark of pathological changes in cancer cells. In this study, we investigate the expression of two cancer-related metabolic enzymes, transketolase (TKT) and transketolase-like 1 (TKTL1), involved in the pentose phosphate pathway (PPP), an alternative metabolic pathway for glucose breakdown that could promote cancer by providing the precursors and energy required for rapidly growing cells. TKT and TKTL1 protein expression was investigated by immunohistochemistry in canine normal (N = 6) and hyperplastic glands (N = 3), as well as in benign (N = 11) and malignant mammary tumors (N = 17). TKT expression was higher in hyperplastic lesions and in both benign and malignant tumors compared to the normal mammary gland, while TKTL1 levels were remarkably higher in hyperplastic lesions, simple adenomas and simple carcinomas than in the normal mammary glands (P < 0.05). This study reveals that the expression of a key PPP enzyme varies along the evolution of canine mammary neoplastic lesions, and supports a role of metabolic changes in the development of canine mammary tumors.

Northwest Laboratory for Integrated Systems, University of Washington, Semiannual Technical Report Number 1, July 1-November 8, 1991

DTIC Science & Technology

1991-11-08

only simple bounds on delays but also relate the delays in linear inequalities so that tradeoffs are apparent. We model circuits as communicating...set of linear inequalities constraining the variables. These relations provide synthesis tools with information about tradeoffs between circuit delays...available to express the original circuit as a graph of elementary gates and then cover the graph’s fanout-free trees with collections of three-input

Method for Face-Emotion Retrieval Using A Cartoon Emotional Expression Approach

NASA Astrophysics Data System (ADS)

Kostov, Vlaho; Yanagisawa, Hideyoshi; Johansson, Martin; Fukuda, Shuichi

A simple method for extracting emotion from a human face, as a form of non-verbal communication, was developed to cope with and optimize mobile communication in a globalized and diversified society. A cartoon face based model was developed and used to evaluate emotional content of real faces. After a pilot survey, basic rules were defined and student subjects were asked to express emotion using the cartoon face. Their face samples were then analyzed using principal component analysis and the Mahalanobis distance method. Feature parameters considered as having relations with emotions were extracted and new cartoon faces (based on these parameters) were generated. The subjects evaluated emotion of these cartoon faces again and we confirmed these parameters were suitable. To confirm how these parameters could be applied to real faces, we asked subjects to express the same emotions which were then captured electronically. Simple image processing techniques were also developed to extract these features from real faces and we then compared them with the cartoon face parameters. It is demonstrated via the cartoon face that we are able to express the emotions from very small amounts of information. As a result, real and cartoon faces correspond to each other. It is also shown that emotion could be extracted from still and dynamic real face images using these cartoon-based features.

Comments on ""Contact Diffusion Interaction of Materials with Cladding''

NASA Technical Reports Server (NTRS)

Morris, J. F.

1972-01-01

A Russian paper by A. A. Babad-Zakhryapina contributes much to the understanding of fuel, clad interactions, and thus to nuclear thermionic technology. In that publication the basic diffusion expression is a simple one. A more general but complicated equation for this mass transport results from the present work. With appropriate assumptions, however, the new relation reduces to Babad-Zakhryapina's version.

Invariant target detection by a correlation radiometer

NASA Astrophysics Data System (ADS)

Murza, L. P.

1986-12-01

The paper is concerned with the problem of the optimal detection of a heat-emitting target by a two-channel radiometer with an unstable amplification circuit. An expression is obtained for an asymptotically sufficient detection statistic which is invariant to changes in the amplification coefficients of the channels. The algorithm proposed here can be implemented numerically using a relatively simple program.

Screening plant derived dietary phenolic compounds for bioactivity related to cardiovascular disease.

PubMed

Croft, Kevin D; Yamashita, Yoko; O'Donoghue, Helen; Shirasaya, Daishi; Ward, Natalie C; Ashida, Hitoshi

2018-04-01

The potential health benefits of phenolic acids found in food and beverages has been suggested from a number of large population studies. However, the mechanism of how these compounds may exert biological effects is less well established. It is also now recognised that many complex polyphenols in the diet are metabolised to simple phenolic acids which can be taken up in the circulation. In this paper a number of selected phenolic compounds have been tested for their bioactivity in two cell culture models. The expression and activity of endothelial nitric oxide synthase (eNOS) in human aortic endothelial cells and the uptake of glucose in muscle cells. Our data indicate that while none of the compounds tested had a significant effect on eNOS expression or activation in endothelial cells, several of the compounds increased glucose uptake in muscle cells. These compounds also enhanced the translocation of the glucose transporter GLUT4 to the plasma membrane, which may explain the observed increase in cellular glucose uptake. These results indicate that simple cell culture models may be useful to help understand the bioactivity of phenolic compounds in relation to cardiovascular protection. Copyright © 2017 Elsevier B.V. All rights reserved.

AUCTSP: an improved biomarker gene pair class predictor.

PubMed

Kagaris, Dimitri; Khamesipour, Alireza; Yiannoutsos, Constantin T

2018-06-26

The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule for classification and class prediction of gene expression profiles. The idea that differences in gene expression ranking are associated with presence or absence of disease is compelling and has strong biological plausibility. Nevertheless, the TSP formulation ignores significant available information which can improve classification accuracy and is vulnerable to selecting genes which do not have differential expression in the two conditions ("pivot" genes). We introduce the AUCTSP classifier as an alternative rank-based estimator of the magnitude of the ranking reversals involved in the original TSP. The proposed estimator is based on the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) and as such, takes into account the separation of the entire distribution of gene expression levels in gene pairs under the conditions considered, as opposed to comparing gene rankings within individual subjects as in the original TSP formulation. Through extensive simulations and case studies involving classification in ovarian, leukemia, colon, breast and prostate cancers and diffuse large b-cell lymphoma, we show the superiority of the proposed approach in terms of improving classification accuracy, avoiding overfitting and being less prone to selecting non-informative (pivot) genes. The proposed AUCTSP is a simple yet reliable and robust rank-based classifier for gene expression classification. While the AUCTSP works by the same principle as TSP, its ability to determine the top scoring gene pair based on the relative rankings of two marker genes across all subjects as opposed to each individual subject results in significant performance gains in classification accuracy. In addition, the proposed method tends to avoid selection of non-informative (pivot) genes as members of the top-scoring pair.

Fundamental formulae for wave-energy conversion

PubMed Central

Falnes, Johannes; Kurniawan, Adi

2015-01-01

The time-average wave power that is absorbed from an incident wave by means of a wave-energy conversion (WEC) unit, or by an array of WEC units—i.e. oscillating immersed bodies and/or oscillating water columns (OWCs)—may be mathematically expressed in terms of the WEC units' complex oscillation amplitudes, or in terms of the generated outgoing (diffracted plus radiated) waves, or alternatively, in terms of the radiated waves alone. Following recent controversy, the corresponding three optional expressions are derived, compared and discussed in this paper. They all provide the correct time-average absorbed power. However, only the first-mentioned expression is applicable to quantify the instantaneous absorbed wave power and the associated reactive power. In this connection, new formulae are derived that relate the ‘added-mass’ matrix, as well as a couple of additional reactive radiation-parameter matrices, to the difference between kinetic energy and potential energy in the water surrounding the immersed oscillating WEC array. Further, a complex collective oscillation amplitude is introduced, which makes it possible to derive, by a very simple algebraic method, various simple expressions for the maximum time-average wave power that may be absorbed by the WEC array. The real-valued time-average absorbed power is illustrated as an axisymmetric paraboloid defined on the complex collective-amplitude plane. This is a simple illustration of the so-called ‘fundamental theorem for wave power’. Finally, the paper also presents a new derivation that extends a recently published result on the direction-average maximum absorbed wave power to cases where the WEC array's radiation damping matrix may be singular and where the WEC array may contain OWCs in addition to oscillating bodies. PMID:26064612

Fundamental formulae for wave-energy conversion.

PubMed

Falnes, Johannes; Kurniawan, Adi

2015-03-01

The time-average wave power that is absorbed from an incident wave by means of a wave-energy conversion (WEC) unit, or by an array of WEC units-i.e. oscillating immersed bodies and/or oscillating water columns (OWCs)-may be mathematically expressed in terms of the WEC units' complex oscillation amplitudes, or in terms of the generated outgoing (diffracted plus radiated) waves, or alternatively, in terms of the radiated waves alone. Following recent controversy, the corresponding three optional expressions are derived, compared and discussed in this paper. They all provide the correct time-average absorbed power. However, only the first-mentioned expression is applicable to quantify the instantaneous absorbed wave power and the associated reactive power. In this connection, new formulae are derived that relate the 'added-mass' matrix, as well as a couple of additional reactive radiation-parameter matrices, to the difference between kinetic energy and potential energy in the water surrounding the immersed oscillating WEC array. Further, a complex collective oscillation amplitude is introduced, which makes it possible to derive, by a very simple algebraic method, various simple expressions for the maximum time-average wave power that may be absorbed by the WEC array. The real-valued time-average absorbed power is illustrated as an axisymmetric paraboloid defined on the complex collective-amplitude plane. This is a simple illustration of the so-called 'fundamental theorem for wave power'. Finally, the paper also presents a new derivation that extends a recently published result on the direction-average maximum absorbed wave power to cases where the WEC array's radiation damping matrix may be singular and where the WEC array may contain OWCs in addition to oscillating bodies.

Atmospheric refraction effects on baseline error in satellite laser ranging systems

NASA Technical Reports Server (NTRS)

Im, K. E.; Gardner, C. S.

1982-01-01

Because of the mathematical complexities involved in exact analyses of baseline errors, it is not easy to isolate atmospheric refraction effects; however, by making certain simplifying assumptions about the ranging system geometry, relatively simple expressions can be derived which relate the baseline errors directly to the refraction errors. The results indicate that even in the absence of other errors, the baseline error for intercontinental baselines can be more than an order of magnitude larger than the refraction error.

Colored knot polynomials for arbitrary pretzel knots and links

DOE PAGES

Galakhov, D.; Melnikov, D.; Mironov, A.; ...

2015-04-01

A very simple expression is conjectured for arbitrary colored Jones and HOMFLY polynomials of a rich (g+1)-parametric family of pretzel knots and links. The answer for the Jones and HOMFLY is fully and explicitly expressed through the Racah matrix of Uq(SU N), and looks related to a modular transformation of toric conformal block. Knot polynomials are among the hottest topics in modern theory. They are supposed to summarize nicely representation theory of quantum algebras and modular properties of conformal blocks. The result reported in the present letter, provides a spectacular illustration and support to this general expectation.

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.

PubMed

Plessis, Anne; Hafemeister, Christoph; Wilkins, Olivia; Gonzaga, Zennia Jean; Meyer, Rachel Sarah; Pires, Inês; Müller, Christian; Septiningsih, Endang M; Bonneau, Richard; Purugganan, Michael

2015-11-26

Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field.

Mutation of SIMPLE in Charcot–Marie–Tooth 1C alters production of exosomes

PubMed Central

Zhu, Hong; Guariglia, Sara; Yu, Raymond Y. L.; Li, Wenjing; Brancho, Deborah; Peinado, Hector; Lyden, David; Salzer, James; Bennett, Craig; Chow, Chi-Wing

2013-01-01

Charcot–Marie–Tooth (CMT) disease is an inherited neurological disorder. Mutations in the small integral membrane protein of the lysosome/late endosome (SIMPLE) account for the rare autosomal-dominant demyelination in CMT1C patients. Understanding the molecular basis of CMT1C pathogenesis is impeded, in part, by perplexity about the role of SIMPLE, which is expressed in multiple cell types. Here we show that SIMPLE resides within the intraluminal vesicles of multivesicular bodies (MVBs) and inside exosomes, which are nanovesicles secreted extracellularly. Targeting of SIMPLE to exosomes is modulated by positive and negative regulatory motifs. We also find that expression of SIMPLE increases the number of exosomes and secretion of exosome proteins. We engineer a point mutation on the SIMPLE allele and generate a physiological mouse model that expresses CMT1C-mutated SIMPLE at the endogenous level. We find that CMT1C mouse primary embryonic fibroblasts show decreased number of exosomes and reduced secretion of exosome proteins, in part due to improper formation of MVBs. CMT1C patient B cells and CMT1C mouse primary Schwann cells show similar defects. Together the data indicate that SIMPLE regulates the production of exosomes by modulating the formation of MVBs. Dysregulated endosomal trafficking and changes in the landscape of exosome-mediated intercellular communications may place an overwhelming burden on the nervous system and account for CMT1C molecular pathogenesis. PMID:23576546

Correlations for determining thermodynamic properties of hydrogen-helium gas mixtures at temperatures from 7,000 to 35,000 K

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Gnoffo, P. A.; Graves, R. A., Jr.

1976-01-01

Simple relations for determining the enthalpy and temperature of hydrogen-helium gas mixtures were developed for hydrogen volumetric compositions from 1.0 to 0.7. These relations are expressed as a function of pressure and density and are valid for a range of temperatures from 7,000 to 35,000 K and pressures from 0.10 to 3.14 MPa. The proportionality constant and exponents in the correlation equations were determined for each gas composition by applying a linear least squares curve fit to a large number of thermodynamic calculations obtained from a detailed computer code. Although these simple relations yielded thermodynamic properties suitable for many engineering applications, their accuracy was improved significantly by evaluating the proportionality constants at postshock conditions and correlating these values as a function of the gas composition and the product of freestream velocity and shock angle. The resulting equations for the proportionality constants in terms of velocity and gas composition and the corresponding simple realtions for enthalpy and temperature were incorporated into a flow field computational scheme. Comparison was good between the thermodynamic properties determined from these relations and those obtained by using a detailed computer code to determine the properties. Thus, an appreciable savings in computer time was realized with no significant loss in accuracy.

Distinct responses of Purkinje neurons and roles of simple spikes during associative motor learning in larval zebrafish

PubMed Central

Harmon, Thomas C; Magaram, Uri; McLean, David L; Raman, Indira M

2017-01-01

To study cerebellar activity during learning, we made whole-cell recordings from larval zebrafish Purkinje cells while monitoring fictive swimming during associative conditioning. Fish learned to swim in response to visual stimulation preceding tactile stimulation of the tail. Learning was abolished by cerebellar ablation. All Purkinje cells showed task-related activity. Based on how many complex spikes emerged during learned swimming, they were classified as multiple, single, or zero complex spike (MCS, SCS, ZCS) cells. With learning, MCS and ZCS cells developed increased climbing fiber (MCS) or parallel fiber (ZCS) input during visual stimulation; SCS cells fired complex spikes associated with learned swimming episodes. The categories correlated with location. Optogenetically suppressing simple spikes only during visual stimulation demonstrated that simple spikes are required for acquisition and early stages of expression of learned responses, but not their maintenance, consistent with a transient, instructive role for simple spikes during cerebellar learning in larval zebrafish. DOI: http://dx.doi.org/10.7554/eLife.22537.001 PMID:28541889

Simple, Flexible, Trigonometric Taper Equations

Treesearch

Charles E. Thomas; Bernard R. Parresol

1991-01-01

There have been numerous approaches to modeling stem form in recent decades. The majority have concentrated on the simpler coniferous bole form and have become increasingly complex mathematical expressions. Use of trigonometric equations provides a simple expression of taper that is flexible enough to fit both coniferous and hard-wood bole forms. As an illustration, we...

Visualization and analysis for multidimensional gene expressions signature of cigarette smoking

NASA Astrophysics Data System (ADS)

Wang, Changbo; Xiao, Zhao; Zhang, Tianlun; Cui, Jin; Pang, Chenming

2011-11-01

Biologists often use gene chip to get massive experimental data in the field of bioscience and chemical sciences. Facing a large amount of experimental data, researchers often need to find out a few interesting data or simple regulations. This paper presents a set of methods to visualize and analyze the data for gene expression signatures of people who smoke. We use the latest research data from National Center for Biotechnology Information. Totally, there are more than 400 thousand expressions data. Using these data, we can use parallel coordinates method to visualize the different gene expressions between smokers and nonsmokers and we can distinguish non-smokers, former smokers and current smokers by using the different colors. It can be easy to find out which gene is more important during the lung cancer angiogenesis in the smoking people. In another way, we can use a hierarchical model to visualize the inner relation of different genes. The location of the nodes shows different expression moment and the distance to the root shows the sequence of the expression. We can use the ring layout to represent all the nodes, and connect the different nodes which are related with color lines. Combined with the parallel coordinates method, the visualization result show the important genes and some inner relation obviously, which is useful for examination and prevention of lung cancer.

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence

PubMed Central

Zhang, Linlin

2017-01-01

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring “black and blue” wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development. PMID:28923944

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence.

PubMed

Zhang, Linlin; Mazo-Vargas, Anyi; Reed, Robert D

2017-10-03

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring "black and blue" wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development.

Polymer Fluid Dynamics: Continuum and Molecular Approaches.

PubMed

Bird, R B; Giacomin, A J

2016-06-07

To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.

PubMed

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-08-25

Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

PubMed Central

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

Simple method for assembly of CRISPR synergistic activation mediator gRNA expression array.

PubMed

Vad-Nielsen, Johan; Nielsen, Anders Lade; Luo, Yonglun

2018-05-20

When studying complex interconnected regulatory networks, effective methods for simultaneously manipulating multiple genes expression are paramount. Previously, we have developed a simple method for generation of an all-in-one CRISPR gRNA expression array. We here present a Golden Gate Assembly-based system of synergistic activation mediator (SAM) compatible CRISPR/dCas9 gRNA expression array for the simultaneous activation of multiple genes. Using this system, we demonstrated the simultaneous activation of the transcription factors, TWIST, SNAIL, SLUG, and ZEB1 a human breast cancer cell line. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity

PubMed Central

Gaiti, Federico; Fernandez-Valverde, Selene L.; Nakanishi, Nagayasu; Calcino, Andrew D.; Yanai, Itai; Tanurdzic, Milos; Degnan, Bernard M.

2015-01-01

Long noncoding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals. Here, we undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically simple, early-branching metazoan. We combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic nonprotein coding RNAs, and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appears to be taxonomically restricted with no identifiable orthologs, we find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organization, and dynamic expression of sponge lncRNAs to their bilaterian counterparts, we propose that these noncoding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity. PMID:25976353

An Anharmonic Solution to the Equation of Motion for the Simple Pendulum

ERIC Educational Resources Information Center

Johannessen, Kim

2011-01-01

An anharmonic solution to the differential equation describing the oscillations of a simple pendulum at large angles is discussed. The solution is expressed in terms of functions not involving the Jacobi elliptic functions. In the derivation, a sinusoidal expression, including a linear and a Fourier sine series in the argument, has been applied.…

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments.

PubMed

Ganger, Michael T; Dietz, Geoffrey D; Ewing, Sarah J

2017-12-01

qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the statistical analysis of qPCR data are needed. Here we develop a mathematical model, termed the Common Base Method, for analysis of qPCR data based on threshold cycle values (C q ) and efficiencies of reactions (E). The Common Base Method keeps all calculations in the logscale as long as possible by working with log 10 (E) ∙ C q , which we call the efficiency-weighted C q value; subsequent statistical analyses are then applied in the logscale. We show how efficiency-weighted C q values may be analyzed using a simple paired or unpaired experimental design and develop blocking methods to help reduce unexplained variation. The Common Base Method has several advantages. It allows for the incorporation of well-specific efficiencies and multiple reference genes. The method does not necessitate the pairing of samples that must be performed using traditional analysis methods in order to calculate relative expression ratios. Our method is also simple enough to be implemented in any spreadsheet or statistical software without additional scripts or proprietary components.

Fock expansion of multimode pure Gaussian states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cariolaro, Gianfranco; Pierobon, Gianfranco, E-mail: gianfranco.pierobon@unipd.it

2015-12-15

The Fock expansion of multimode pure Gaussian states is derived starting from their representation as displaced and squeezed multimode vacuum states. The approach is new and appears to be simpler and more general than previous ones starting from the phase-space representation given by the characteristic or Wigner function. Fock expansion is performed in terms of easily evaluable two-variable Hermite–Kampé de Fériet polynomials. A relatively simple and compact expression for the joint statistical distribution of the photon numbers in the different modes is obtained. In particular, this result enables one to give a simple characterization of separable and entangled states, asmore » shown for two-mode and three-mode Gaussian states.« less

Plasma phospholipids and fatty acid composition differ between liver biopsy-proven nonalcoholic fatty liver disease and healthy subjects

PubMed Central

Ma, D W L; Arendt, B M; Hillyer, L M; Fung, S K; McGilvray, I; Guindi, M; Allard, J P

2016-01-01

Background: There is growing evidence that nonalcoholic fatty liver disease (NAFLD) is associated with perturbations in liver lipid metabolism. Liver phospholipid and fatty acid composition have been shown to be altered in NAFLD. However, detailed profiles of circulating lipids in the pathogenesis of NAFLD are lacking. Objective: Therefore, the objective of the present study was to examine circulating lipids and potential mechanisms related to hepatic gene expression between liver biopsy-proven simple steatosis (SS), nonalcoholic steatohepatitis (NASH) and healthy subjects. Subjects: Plasma phospholipid and fatty acid composition were determined in 31 healthy living liver donors as healthy controls (HC), 26 patients with simple hepatic steatosis (SS) and 20 with progressive NASH. Hepatic gene expression was analyzed by Illumina microarray in a subset of 22 HC, 16 SS and 14 NASH. Results: Concentrations of phosphatidylethanolamine (PE) increased relative to disease progression, HC

Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamano, Koichi; Bruno, Kenneth S.; Karagiosis, Sue A.

2013-01-01

Microbial production of fats and oils is being developedas a means of converting biomass to biofuels. Here we investigate enhancing expression of enzymes involved in the production of fatty acids and triglycerides as a means to increase production of these compounds in Aspergillusoryzae. Examination of the A.oryzaegenome demonstrates that it contains twofatty acid synthases and several other genes that are predicted to be part of this biosynthetic pathway. We enhancedthe expressionof fatty acid synthesis-related genes by replacing their promoters with thepromoter fromthe constitutively highly expressedgene tef1. We demonstrate that by simply increasing the expression of the fatty acid synthasegenes wemore » successfullyincreasedtheproduction of fatty acids and triglyceridesby more than two fold. Enhancement of expression of the fatty acid pathway genes ATP-citrate lyase and palmitoyl-ACP thioesteraseincreasedproductivity to a lesser extent.Increasing expression ofacetyl-CoA carboxylase caused no detectable change in fatty acid levels. Increases in message level for each gene were monitored usingquantitative real-time RT-PCR. Our data demonstrates that a simple increase in the abundance of fatty acid synthase genes can increase the detectable amount of fatty acids.« less

GC-Content Normalization for RNA-Seq Data

PubMed Central

2011-01-01

Background Transcriptome sequencing (RNA-Seq) has become the assay of choice for high-throughput studies of gene expression. However, as is the case with microarrays, major technology-related artifacts and biases affect the resulting expression measures. Normalization is therefore essential to ensure accurate inference of expression levels and subsequent analyses thereof. Results We focus on biases related to GC-content and demonstrate the existence of strong sample-specific GC-content effects on RNA-Seq read counts, which can substantially bias differential expression analysis. We propose three simple within-lane gene-level GC-content normalization approaches and assess their performance on two different RNA-Seq datasets, involving different species and experimental designs. Our methods are compared to state-of-the-art normalization procedures in terms of bias and mean squared error for expression fold-change estimation and in terms of Type I error and p-value distributions for tests of differential expression. The exploratory data analysis and normalization methods proposed in this article are implemented in the open-source Bioconductor R package EDASeq. Conclusions Our within-lane normalization procedures, followed by between-lane normalization, reduce GC-content bias and lead to more accurate estimates of expression fold-changes and tests of differential expression. Such results are crucial for the biological interpretation of RNA-Seq experiments, where downstream analyses can be sensitive to the supplied lists of genes. PMID:22177264

Emotional Expression in Simple Line Drawings of a Robot's Face Leads to Higher Offers in the Ultimatum Game.

PubMed

Terada, Kazunori; Takeuchi, Chikara

2017-01-01

In the present study, we investigated whether expressing emotional states using a simple line drawing to represent a robot's face can serve to elicit altruistic behavior from humans. An experimental investigation was conducted in which human participants interacted with a humanoid robot whose facial expression was shown on an LCD monitor that was mounted as its head (Study 1). Participants were asked to play the ultimatum game, which is usually used to measure human altruistic behavior. All participants were assigned to be the proposer and were instructed to decide their offer within 1 min by controlling a slider bar. The corners of the robot's mouth, as indicated by the line drawing, simply moved upward, or downward depending on the position of the slider bar. The results suggest that the change in the facial expression depicted by a simple line drawing of a face significantly affected the participant's final offer in the ultimatum game. The offers were increased by 13% when subjects were shown contingent changes of facial expression. The results were compared with an experiment in a teleoperation setting in which participants interacted with another person through a computer display showing the same line drawings used in Study 1 (Study 2). The results showed that offers were 15% higher if participants were shown a contingent facial expression change. Together, Studies 1 and 2 indicate that emotional expression in simple line drawings of a robot's face elicits the same higher offer from humans as a human telepresence does.

Emotional Expression in Simple Line Drawings of a Robot's Face Leads to Higher Offers in the Ultimatum Game

PubMed Central

Terada, Kazunori; Takeuchi, Chikara

2017-01-01

In the present study, we investigated whether expressing emotional states using a simple line drawing to represent a robot's face can serve to elicit altruistic behavior from humans. An experimental investigation was conducted in which human participants interacted with a humanoid robot whose facial expression was shown on an LCD monitor that was mounted as its head (Study 1). Participants were asked to play the ultimatum game, which is usually used to measure human altruistic behavior. All participants were assigned to be the proposer and were instructed to decide their offer within 1 min by controlling a slider bar. The corners of the robot's mouth, as indicated by the line drawing, simply moved upward, or downward depending on the position of the slider bar. The results suggest that the change in the facial expression depicted by a simple line drawing of a face significantly affected the participant's final offer in the ultimatum game. The offers were increased by 13% when subjects were shown contingent changes of facial expression. The results were compared with an experiment in a teleoperation setting in which participants interacted with another person through a computer display showing the same line drawings used in Study 1 (Study 2). The results showed that offers were 15% higher if participants were shown a contingent facial expression change. Together, Studies 1 and 2 indicate that emotional expression in simple line drawings of a robot's face elicits the same higher offer from humans as a human telepresence does. PMID:28588520

Salinity-related variation in gene expression in wild populations of the black-chinned tilapia from various West African coastal marine, estuarine and freshwater habitats

NASA Astrophysics Data System (ADS)

Tine, Mbaye; McKenzie, David J.; Bonhomme, François; Durand, Jean-Dominique

2011-01-01

This study measured the relative expression of the genes coding for Na +, K +-ATPase 1α(NAKA), voltage-dependent anion channel (VDAC), cytochrome c oxidase-1 (COX), and NADH dehydrogenase (NDH), in gills of six wild populations of a West African tilapia species, acclimatised to a range of seasonal (rainy or dry) salinities in coastal, estuarine and freshwater sites. Previous laboratory experiments have demonstrated that these genes, involved in active ion transport, oxidative phosphorylation, and intra-cellular ATP transport, are relatively over-expressed in gill tissues of this species acclimated to high salinity. Positive correlations between relative expression and ambient salinity were found for all genes in the wild populations (Spearman rank correlation, p < 0.05), although for some genes these were only significant in either the rainy season or dry season. Most significantly, however, relative expression was positively correlated amongst the four genes, indicating that they are functionally interrelated in adaptation of Sarotherodon melanotheron to salinity variations in its natural environment. In the rainy season, when salinity was unstable and ranged between zero and 37 psu across the sites, overall mean expression of the genes was higher than in the dry season, which may have reflected more variable particularly sudden fluctuations in salinity and poorer overall water quality. In the dry season, when the salinity is more stable but ranged between zero and 100 psu across the sites, NAKA, NDH and VDAC expression revealed U-shaped relationships with lowest relative expression at salinities approaching seawater, between 25 and 45 psu. Although it is not simple to establish direct relationship between gene expression levels and energy requirement for osmoregulation, these results may indicate that costs of adaptation to salinity are lowest in seawater, the natural environment of this species. While S. melanotheron can colonise environments with extremely high salinities, up to 100 psu, this was related to high relative expression for all genes studied, indicating that this imposes increased energy demand for osmotic homeostasis in gill tissues. This study is the first to demonstrate, in fish and in wild populations, that expression of NAKA, VDAC, NDH and COX are interrelated in gill tissues, and are involved in long-term acclimatisation to a salinity range between 0 and 100 psu.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

Effects of touch on emotional face processing: A study of event-related potentials, facial EMG and cardiac activity.

PubMed

Spapé, M M; Harjunen, Ville; Ravaja, N

2017-03-01

Being touched is known to affect emotion, and even a casual touch can elicit positive feelings and affinity. Psychophysiological studies have recently shown that tactile primes affect visual evoked potentials to emotional stimuli, suggesting altered affective stimulus processing. As, however, these studies approached emotion from a purely unidimensional perspective, it remains unclear whether touch biases emotional evaluation or a more general feature such as salience. Here, we investigated how simple tactile primes modulate event related potentials (ERPs), facial EMG and cardiac response to pictures of facial expressions of emotion. All measures replicated known effects of emotional face processing: Disgust and fear modulated early ERPs, anger increased the cardiac orienting response, and expressions elicited emotion-congruent facial EMG activity. Tactile primes also affected these measures, but priming never interacted with the type of emotional expression. Thus, touch may additively affect general stimulus processing, but it does not bias or modulate immediate affective evaluation. Copyright © 2017. Published by Elsevier B.V.

Determination of human insulin in dog plasma by a selective liquid chromatography-tandem mass spectrometry method: Application to a pharmacokinetic study.

PubMed

Dong, Shiqi; Zeng, Yong; Wei, Guangli; Si, Duanyun; Liu, Changxiao

2018-03-01

A simple, sensitive and selective LC-MS/MS method for quantitative analysis of human insulin was developed and validated in dog plasma. Insulin glargine was used as the internal standard. After a simple step of solid-phase extraction, the chromatographic separation of human insulin was achieved by using InertSustain Bio C18 column with a mobile phase of acetonitrile containing 1% formic acid (A)-water containing 1% formic acid (B). The detection was performed by positive ion electrospray ionization in multiple-reaction monitoring (MRM) mode. Good linearity was observed in the concentration range of 1-1000 μIU/mL (r 2  > 0.99), and the lower limit of quantification was 1 μIU/mL (equal to 38.46 pg/mL). The intra- and inter-day precision (expressed as relative standard deviation, RSD) of human insulin were ≤12.1% and ≤13.0%, respectively, and the accuracy (expressed as relative error, RE) was in the range of -7.23-11.9%. The recovery and matrix effect were both within acceptable limits. This method was successfully applied for the pharmacokinetic study of human insulin in dogs after subcutaneous administration. Copyright © 2018 Elsevier B.V. All rights reserved.

Argyres-Douglas theories, the Macdonald index, and an RG inequality

DOE PAGES

Buican, Matthew; Nishinaka, Takahiro

2016-02-24

Here we conjecture closed-form expressions for the Macdonald limits of the superconformal indices of the (A 1,A 2n₋3) and (A 1,D 2n) Argyres-Douglas (AD) theories in terms of certain simple deformations of Macdonald polynomials. As checks of our conjectures, we demonstrate compatibility with two S-dualities, we show symmetry enhancement for special values of n, and we argue that our expressions encode a non-trivial set of renormalization group flows. Moreover, we demonstrate that, for certain values of n, our conjectures imply simple operator relations involving composites built out of the SU(2) R currents and flavor symmetry moment maps, and we findmore » a consistent picture in which these relations give rise to certain null states in the corresponding chiral algebras. In addition, we show that the Hall-Littlewood limits of our indices are equivalent to the corresponding Higgs branch Hilbert series. We explain this fact by considering the S 1 reductions of our theories and showing that the equivalence follows from an inequality on monopole quantum numbers whose coefficients are fixed by data of the four-dimensional parent theories. Finally, we comment on the implications of our work for more general $N = 2$ superconformal field theories.« less

Quantifying shapes of volcanoes on Venus

NASA Technical Reports Server (NTRS)

Garvin, J. B.

1994-01-01

A large population of discrete volcanic edifices on Venus has been identified and cataloged by means of Magellan SAR images, and an extensive database describing thousands of such features is in final preparation. Those volcanoes categorized as Intermediate to Large in scale, while relatively small in number (approx. 400), nonetheless constitute a significant volumetric component (approx. 13 x 10(exp 6) cu km) of the total apparent crustal volume of Venus. For this reason, we have focused attention on the morphometry of a representative suite of the larger edifices on Venus and, in particular, on ways of constraining the eruptive histories of these possibly geologically youthful landforms. Our approach has been to determine a series of reproducible morphometric parameters for as many of the discrete volcanoes on Venus that have an obvious expression within the global altimetry data acquired by Magellan. In addition, we have attempted to objectively and systematically define the mathematical essence of the shapes of these larger volcanoes using a polynomial cross-section approximation involving only parameters easily measured from digital topography, as well as with simple surface cylindrical harmonic expansions. The goal is to reduce the topological complexities of the larger edifices to a few simple parameters which can then be related to similar expressions for well-studied terrestrial and martian features.

Argyres-Douglas theories, the Macdonald index, and an RG inequality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buican, Matthew; Nishinaka, Takahiro

Here we conjecture closed-form expressions for the Macdonald limits of the superconformal indices of the (A 1,A 2n₋3) and (A 1,D 2n) Argyres-Douglas (AD) theories in terms of certain simple deformations of Macdonald polynomials. As checks of our conjectures, we demonstrate compatibility with two S-dualities, we show symmetry enhancement for special values of n, and we argue that our expressions encode a non-trivial set of renormalization group flows. Moreover, we demonstrate that, for certain values of n, our conjectures imply simple operator relations involving composites built out of the SU(2) R currents and flavor symmetry moment maps, and we findmore » a consistent picture in which these relations give rise to certain null states in the corresponding chiral algebras. In addition, we show that the Hall-Littlewood limits of our indices are equivalent to the corresponding Higgs branch Hilbert series. We explain this fact by considering the S 1 reductions of our theories and showing that the equivalence follows from an inequality on monopole quantum numbers whose coefficients are fixed by data of the four-dimensional parent theories. Finally, we comment on the implications of our work for more general $N = 2$ superconformal field theories.« less

Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model.

PubMed

Hu, Jianhua; Wright, Fred A

2007-03-01

The identification of the genes that are differentially expressed in two-sample microarray experiments remains a difficult problem when the number of arrays is very small. We discuss the implications of using ordinary t-statistics and examine other commonly used variants. For oligonucleotide arrays with multiple probes per gene, we introduce a simple model relating the mean and variance of expression, possibly with gene-specific random effects. Parameter estimates from the model have natural shrinkage properties that guard against inappropriately small variance estimates, and the model is used to obtain a differential expression statistic. A limiting value to the positive false discovery rate (pFDR) for ordinary t-tests provides motivation for our use of the data structure to improve variance estimates. Our approach performs well compared to other proposed approaches in terms of the false discovery rate.

Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies.

PubMed

Cheng, Changde; Kirkpatrick, Mark

2016-09-01

Sexual dimorphism results from sex-biased gene expression, which evolves when selection acts differently on males and females. While there is an intimate connection between sex-biased gene expression and sex-specific selection, few empirical studies have studied this relationship directly. Here we compare the two on a genome-wide scale in humans and flies. We find a distinctive "Twin Peaks" pattern in humans that relates the strength of sex-specific selection, quantified by genetic divergence between male and female adults at autosomal loci, to the degree of sex-biased expression. Genes with intermediate degrees of sex-biased expression show evidence of ongoing sex-specific selection, while genes with either little or completely sex-biased expression do not. This pattern apparently results from differential viability selection in males and females acting in the current generation. The Twin Peaks pattern is also found in Drosophila using a different measure of sex-specific selection acting on fertility. We develop a simple model that successfully recapitulates the Twin Peaks. Our results suggest that many genes with intermediate sex-biased expression experience ongoing sex-specific selection in humans and flies.

Simple approximation of total emissivity of CO2-H2O mixture used in the zonal method of calculation of heat transfer by radiation

NASA Astrophysics Data System (ADS)

Lisienko, V. G.; Malikov, G. K.; Titaev, A. A.

2014-12-01

The paper presents a new simple-to-use expression to calculate the total emissivity of a mixture of gases CO2 and H2O used for modeling heat transfer by radiation in industrial furnaces. The accuracy of this expression is evaluated using the exponential wide band model. It is found that the time taken to calculate the total emissivity in this expression is 1.5 times less than in other approximation methods.

Simple cloning strategy using GFPuv gene as positive/negative indicator.

PubMed

Miura, Hiromi; Inoko, Hidetoshi; Inoue, Ituro; Tanaka, Masafumi; Sato, Masahiro; Ohtsuka, Masato

2011-09-15

Because construction of expression vectors is the first requisite in the functional analysis of genes, development of simple cloning systems is a major requirement during the postgenomic era. In the current study, we developed cloning vectors for gain- or loss-of-function studies by using the GFPuv gene as a positive/negative indicator of cloning. These vectors allow us to easily detect correct clones and obtain expression vectors from a simple procedure by means of the combined use of the GFPuv gene and a type IIS restriction enzyme. Copyright © 2011 Elsevier Inc. All rights reserved.

MOPED enables discoveries through consistently processed proteomics data

PubMed Central

Higdon, Roger; Stewart, Elizabeth; Stanberry, Larissa; Haynes, Winston; Choiniere, John; Montague, Elizabeth; Anderson, Nathaniel; Yandl, Gregory; Janko, Imre; Broomall, William; Fishilevich, Simon; Lancet, Doron; Kolker, Natali; Kolker, Eugene

2014-01-01

The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org), is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration, as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project’s efforts to generate chromosome and diseases specific proteomes by providing links from proteins to chromosome and disease information, as well as many complementary resources. MOPED supports a new omics metadata checklist in order to harmonize data integration, analysis and use. MOPED’s development is driven by the user community, which spans 90 countries guiding future development that will transform MOPED into a multi-omics resource. MOPED encourages users to submit data in a simple format. They can use the metadata a checklist generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries. PMID:24350770

Variable Combinations of Specific Ephrin Ligand/Eph Receptor Pairs Control Embryonic Tissue Separation

PubMed Central

Rohani, Nazanin; Parmeggiani, Andrea; Winklbauer, Rudolf; Fagotto, François

2014-01-01

Ephrins and Eph receptors are involved in the establishment of vertebrate tissue boundaries. The complexity of the system is puzzling, however in many instances, tissues express multiple ephrins and Ephs on both sides of the boundary, a situation that should in principle cause repulsion between cells within each tissue. Although co-expression of ephrins and Eph receptors is widespread in embryonic tissues, neurons, and cancer cells, it is still unresolved how the respective signals are integrated into a coherent output. We present a simple explanation for the confinement of repulsion to the tissue interface: Using the dorsal ectoderm–mesoderm boundary of the Xenopus embryo as a model, we identify selective functional interactions between ephrin–Eph pairs that are expressed in partial complementary patterns. The combined repulsive signals add up to be strongest across the boundary, where they reach sufficient intensity to trigger cell detachments. The process can be largely explained using a simple model based exclusively on relative ephrin and Eph concentrations and binding affinities. We generalize these findings for the ventral ectoderm–mesoderm boundary and the notochord boundary, both of which appear to function on the same principles. These results provide a paradigm for how developmental systems may integrate multiple cues to generate discrete local outcomes. PMID:25247423

Vector-based model of elastic bonds for simulation of granular solids.

PubMed

Kuzkin, Vitaly A; Asonov, Igor E

2012-11-01

A model (further referred to as the V model) for the simulation of granular solids, such as rocks, ceramics, concrete, nanocomposites, and agglomerates, composed of bonded particles (rigid bodies), is proposed. It is assumed that the bonds, usually representing some additional gluelike material connecting particles, cause both forces and torques acting on the particles. Vectors rigidly connected with the particles are used to describe the deformation of a single bond. The expression for potential energy of the bond and corresponding expressions for forces and torques are derived. Formulas connecting parameters of the model with longitudinal, shear, bending, and torsional stiffnesses of the bond are obtained. It is shown that the model makes it possible to describe any values of the bond stiffnesses exactly; that is, the model is applicable for the bonds with arbitrary length/thickness ratio. Two different calibration procedures depending on bond length/thickness ratio are proposed. It is shown that parameters of the model can be chosen so that under small deformations the bond is equivalent to either a Bernoulli-Euler beam or a Timoshenko beam or short cylinder connecting particles. Simple analytical expressions, relating parameters of the V model with geometrical and mechanical characteristics of the bond, are derived. Two simple examples of computer simulation of thin granular structures using the V model are given.

Variable combinations of specific ephrin ligand/Eph receptor pairs control embryonic tissue separation.

PubMed

Rohani, Nazanin; Parmeggiani, Andrea; Winklbauer, Rudolf; Fagotto, François

2014-09-01

Ephrins and Eph receptors are involved in the establishment of vertebrate tissue boundaries. The complexity of the system is puzzling, however in many instances, tissues express multiple ephrins and Ephs on both sides of the boundary, a situation that should in principle cause repulsion between cells within each tissue. Although co-expression of ephrins and Eph receptors is widespread in embryonic tissues, neurons, and cancer cells, it is still unresolved how the respective signals are integrated into a coherent output. We present a simple explanation for the confinement of repulsion to the tissue interface: Using the dorsal ectoderm-mesoderm boundary of the Xenopus embryo as a model, we identify selective functional interactions between ephrin-Eph pairs that are expressed in partial complementary patterns. The combined repulsive signals add up to be strongest across the boundary, where they reach sufficient intensity to trigger cell detachments. The process can be largely explained using a simple model based exclusively on relative ephrin and Eph concentrations and binding affinities. We generalize these findings for the ventral ectoderm-mesoderm boundary and the notochord boundary, both of which appear to function on the same principles. These results provide a paradigm for how developmental systems may integrate multiple cues to generate discrete local outcomes.

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

PubMed Central

Plessis, Anne; Hafemeister, Christoph; Wilkins, Olivia; Gonzaga, Zennia Jean; Meyer, Rachel Sarah; Pires, Inês; Müller, Christian; Septiningsih, Endang M; Bonneau, Richard; Purugganan, Michael

2015-01-01

Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field. DOI: http://dx.doi.org/10.7554/eLife.08411.001 PMID:26609814

Deployment Design of Wireless Sensor Network for Simple Multi-Point Surveillance of a Moving Target

PubMed Central

Tsukamoto, Kazuya; Ueda, Hirofumi; Tamura, Hitomi; Kawahara, Kenji; Oie, Yuji

2009-01-01

In this paper, we focus on the problem of tracking a moving target in a wireless sensor network (WSN), in which the capability of each sensor is relatively limited, to construct large-scale WSNs at a reasonable cost. We first propose two simple multi-point surveillance schemes for a moving target in a WSN and demonstrate that one of the schemes can achieve high tracking probability with low power consumption. In addition, we examine the relationship between tracking probability and sensor density through simulations, and then derive an approximate expression representing the relationship. As the results, we present guidelines for sensor density, tracking probability, and the number of monitoring sensors that satisfy a variety of application demands. PMID:22412326

BCR-ABL1 expression, RT-qPCR and treatment decisions in chronic myeloid leukaemia.

PubMed

Latham, Susan; Bartley, Paul A; Budgen, Bradley; Ross, David M; Hughes, Elizabeth; Branford, Susan; White, Deborah; Hughes, Timothy P; Morley, Alexander A

2016-09-01

RT-qPCR is used to quantify minimal residual disease (MRD) in chronic myeloid leukaemia (CML) in order to make decisions on treatment, but its results depend on the level of BCR-ABL1 expression as well as leukaemic cell number. The aims of the study were to quantify inter-individual differences in expression level, to determine the relationship between expression level and response to treatment, and to investigate the effect of expression level on interpretation of the RT-qPCR result. BCR-ABL1 expression was studied in 248 samples from 65 patients with CML by determining the difference between MRD quantified by RT-qPCR and DNA-qPCR. The results were analysed statistically and by simple indicative modelling. Inter-individual levels of expression approximated a normal distribution with an SD of 0.36 log. Expression at diagnosis correlated with expression during treatment. Response to treatment, as measured by the number of leukaemic cells after 3, 6 or 12 months of treatment, was not related to the level of expression. Indicative modelling suggested that interpretation of RT-qPCR results in relation to treatment guidelines could be affected by variation in expression when MRD was around 10% at 3 months and by both expression variation and Poisson variation when MRD was around or below the limit of detection of RT-qPCR. Variation between individuals in expression of BCR-ABL1 can materially affect interpretation of the RT-qPCR when this test is used to make decisions on treatment. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Increased Expression Profile and Functionality of TLR6 in Peripheral Blood Mononuclear Cells and Hepatocytes of Morbidly Obese Patients with Non-Alcoholic Fatty Liver Disease.

PubMed

Arias-Loste, María Teresa; Iruzubieta, Paula; Puente, Ángela; Ramos, David; Santa Cruz, Carolina; Estébanez, Ángel; Llerena, Susana; Alonso-Martín, Carmen; San Segundo, David; Álvarez, Lorena; López Useros, Antonio; Fábrega, Emilio; López-Hoyos, Marcos; Crespo, Javier

2016-11-10

Current evidence suggests that gut dysbiosis drives obesity and non-alcoholic fatty liver disease (NAFLD) pathogenesis. Toll-like receptor 2 (TLR2) and TLR6 specifically recognize components of Gram-positive bacteria. Despite the potential implications of TLR2 in NAFLD pathogenesis, the role of TLR6 has not been addressed. Our aim is to study a potential role of TLR6 in obesity-related NAFLD. Forty morbidly obese patients undergoing bariatric surgery were prospectively studied. Cell surface expression of TLR2 and TLR6 was assessed on peripheral blood mononuclear cells (PBMCs) by flow cytometry. Freshly isolated monocytes were cultured with specific TLR2/TLR6 agonists and intracellular production of cytokines was determined by flow-cytometry. In liver biopsies, the expression of TLR2 and TLR6 was analyzed by immunohistochemistry and cytokine gene expression using RT-qPCR. TLR6 expression in PBMCs from non-alcoholic steatohepatitis (NASH) patients was significantly higher when compared to those from simple steatosis. The production of pro-inflammatory cytokines in response to TLR2/TLR6 stimulation was also significantly higher in patients with lobular inflammation. Hepatocyte expression of TLR6 but not that of TLR2 was increased in NAFLD patients compared to normal liver histology. Deregulated expression and activity of peripheral TLR6 in morbidly obese patients can mirror the liver inflammatory events that are well known drivers of obesity-related NASH pathogenesis. Moreover, TLR6 is also significantly overexpressed in the hepatocytes of NAFLD patients compared to their normal counterparts. Thus, deregulated TLR6 expression may potentiate TLR2-mediated liver inflammation in NAFLD pathogenesis, and also serve as a potential peripheral biomarker of obesity-related NASH.

Modeling the plant-soil interaction in presence of heavy metal pollution and acidity variations.

PubMed

Guala, Sebastián; Vega, Flora A; Covelo, Emma F

2013-01-01

On a mathematical interaction model, developed to model metal uptake by plants and the effects on their growth, we introduce a modification which considers also effects on variations of acidity in soil. The model relates the dynamics of the uptake of metals from soil to plants and also variations of uptake according to the acidity level. Two types of relationships are considered: total and available metal content. We suppose simple mathematical assumptions in order to get as simple as possible expressions with the aim of being easily tested in experimental problems. This work introduces modifications to two versions of the model: on the one hand, the expression of the relationship between the metal in soil and the concentration of the metal in plants and, on the other hand, the relationship between the metal in the soil and total amount of the metal in plants. The fine difference of both versions is fundamental at the moment to consider the tolerance and capacity of accumulation of pollutants in the biomass from the soil.

Identifying EGFR-Expressed Cells and Detecting EGFR Multi-Mutations at Single-Cell Level by Microfluidic Chip

NASA Astrophysics Data System (ADS)

Li, Ren; Zhou, Mingxing; Li, Jine; Wang, Zihua; Zhang, Weikai; Yue, Chunyan; Ma, Yan; Peng, Hailin; Wei, Zewen; Hu, Zhiyuan

2018-03-01

EGFR mutations companion diagnostics have been proved to be crucial for the efficacy of tyrosine kinase inhibitor targeted cancer therapies. To uncover multiple mutations occurred in minority of EGFR-mutated cells, which may be covered by the noises from majority of un-mutated cells, is currently becoming an urgent clinical requirement. Here we present the validation of a microfluidic-chip-based method for detecting EGFR multi-mutations at single-cell level. By trapping and immunofluorescently imaging single cells in specifically designed silicon microwells, the EGFR-expressed cells were easily identified. By in situ lysing single cells, the cell lysates of EGFR-expressed cells were retrieved without cross-contamination. Benefited from excluding the noise from cells without EGFR expression, the simple and cost-effective Sanger's sequencing, but not the expensive deep sequencing of the whole cell population, was used to discover multi-mutations. We verified the new method with precisely discovering three most important EGFR drug-related mutations from a sample in which EGFR-mutated cells only account for a small percentage of whole cell population. The microfluidic chip is capable of discovering not only the existence of specific EGFR multi-mutations, but also other valuable single-cell-level information: on which specific cells the mutations occurred, or whether different mutations coexist on the same cells. This microfluidic chip constitutes a promising method to promote simple and cost-effective Sanger's sequencing to be a routine test before performing targeted cancer therapy.[Figure not available: see fulltext.

Determination of absolute expression profiles using multiplexed miRNA analysis

PubMed Central

Song, Jee Hoon; Cheng, Yulan; Saeui, Christopher T.; Cheung, Douglas G.; Croce, Carlo M.; Yarema, Kevin J.; Meltzer, Stephen J.; Liu, Kelvin J.; Wang, Tza-Huei

2017-01-01

Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR’s ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes. PMID:28704432

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

PubMed Central

Plantegenet, Stephanie; Weber, Johann; Goldstein, Darlene R; Zeller, Georg; Nussbaumer, Cindy; Thomas, Jérôme; Weigel, Detlef; Harshman, Keith; Hardtke, Christian S

2009-01-01

In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5′ regulatory sequence variation in the corresponding genes is indeed increased. However, ∼42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL. PMID:19225455

Unattended facial expressions asymmetrically bias the concurrent processing of nonemotional information.

PubMed

Maxwell, Jeffrey S; Shackman, Alexander J; Davidson, Richard J

2005-09-01

Planned and reflexive behaviors often occur in the presence of emotional stimuli and within the context of an individual's acute emotional state. Therefore, determining the manner in which emotion and attention interact is an important step toward understanding how we function in the real world. Participants in the current investigation viewed centrally displayed, task-irrelevant, face distractors (angry, neutral, happy) while performing a lateralized go/no-go continuous performance task. Lateralized go targets and no-go lures that did not spatially overlap with the faces were employed to differentially probe processing in the left (LH) and right (RH) cerebral hemispheres. There was a significant interaction between expression and hemisphere, with an overall pattern such that angry distractors were associated with relatively more RH inhibitory errors than neutral or happy distractors and happy distractors with relatively more LH inhibitory errors than angry or neutral distractors. Simple effects analyses confirmed that angry faces differentially interfered with RH relative to LH inhibition and with inhibition in the RH relative to happy faces. A significant three-way interaction further revealed that state anxiety moderated relations between emotional expression and hemisphere. Under conditions of low cognitive load, more intense anxiety was associated with relatively greater RH than LH impairment in the presence of both happy and threatening distractors. By contrast, under high load, only angry distractors produced greater RH than LH interference as a function of anxiety.

A microRNA detection system based on padlock probes and rolling circle amplification

PubMed Central

Jonstrup, Søren Peter; Koch, Jørn; Kjems, Jørgen

2006-01-01

The differential expression and the regulatory roles of microRNAs (miRNAs) are being studied intensively these years. Their minute size of only 19–24 nucleotides and strong sequence similarity among related species call for enhanced methods for reliable detection and quantification. Moreover, miRNA expression is generally restricted to a limited number of specific cells within an organism and therefore requires highly sensitive detection methods. Here we present a simple and reliable miRNA detection protocol based on padlock probes and rolling circle amplification. It can be performed without specialized equipment and is capable of measuring the content of specific miRNAs in a few nanograms of total RNA. PMID:16888321

Scaling laws for AC gas breakdown and implications for universality

NASA Astrophysics Data System (ADS)

Loveless, Amanda M.; Garner, Allen L.

2017-10-01

The reduced dependence on secondary electron emission and electrode surface properties makes radiofrequency (RF) and microwave (MW) plasmas advantageous over direct current (DC) plasmas for various applications, such as microthrusters. Theoretical models relating molecular constants to alternating current (AC) breakdown often fail due to incomplete understanding of both the constants and the mechanisms involved. This work derives simple analytic expressions for RF and MW breakdown, demonstrating the transition between these regimes at their high and low frequency limits, respectively. We further show that the limiting expressions for DC, RF, and MW breakdown voltage all have the same universal scaling dependence on pressure and gap distance at high pressure, agreeing with experiment.

A microRNA detection system based on padlock probes and rolling circle amplification.

PubMed

Jonstrup, Søren Peter; Koch, Jørn; Kjems, Jørgen

2006-09-01

The differential expression and the regulatory roles of microRNAs (miRNAs) are being studied intensively these years. Their minute size of only 19-24 nucleotides and strong sequence similarity among related species call for enhanced methods for reliable detection and quantification. Moreover, miRNA expression is generally restricted to a limited number of specific cells within an organism and therefore requires highly sensitive detection methods. Here we present a simple and reliable miRNA detection protocol based on padlock probes and rolling circle amplification. It can be performed without specialized equipment and is capable of measuring the content of specific miRNAs in a few nanograms of total RNA.

Rapid correction of electron microprobe data for multicomponent metallic systems

NASA Technical Reports Server (NTRS)

Gupta, K. P.; Sivakumar, R.

1973-01-01

This paper describes an empirical relation for the correction of electron microprobe data for multicomponent metallic systems. It evaluates the empirical correction parameter, a for each element in a binary alloy system using a modification of Colby's MAGIC III computer program and outlines a simple and quick way of correcting the probe data. This technique has been tested on a number of multicomponent metallic systems and the agreement with the results using theoretical expressions is found to be excellent. Limitations and suitability of this relation are discussed and a model calculation is also presented in the Appendix.

Fatigue-related crashes involving express buses in Malaysia: will the proposed policy of banning the early-hour operation reduce fatigue-related crashes and benefit overall road safety?

PubMed

Mohamed, Norlen; Mohd-Yusoff, Mohammad-Fadhli; Othman, Ilhamah; Zulkipli, Zarir-Hafiz; Osman, Mohd Rasid; Voon, Wong Shaw

2012-03-01

Fatigue-related crashes have long been the topic of discussion and study worldwide. The relationship between fatigue-related crashes and time of day is well documented. In Malaysia, the possibility of banning express buses from operating during the early-hours of the morning has emerged as an important consideration for passenger safety. This paper highlights the findings of an impact assessment study. The study was conducted to determine all possible impacts prior to the government making any decision on the proposed banning. This study is an example of a simple and inexpensive approach that may influence future policy-making process. The impact assessment comprised two major steps. The first step involved profiling existing operation scenarios, gathering information on crashes involving public express buses and stakeholders' views. The second step involved a qualitative impact assessment analysis using all information gathered during the profiling stage to describe the possible impacts. Based on the assessment, the move to ban early-hour operations could possibly result in further negative impacts on the overall road safety agenda. These negative impacts may occur if the fundamental issues, such as driving and working hours, and the need for rest and sleep facilities for drivers, are not addressed. In addition, a safer and more accessible public transportation system as an alternative for those who choose to travel at night would be required. The proposed banning of early-hour operations is also not a feasible solution for sustainability of express bus operations in Malaysia, especially for those operating long journeys. The paper concludes by highlighting the need to design a more holistic approach for preventing fatigue-related crashes involving express buses in Malaysia. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evaluating hepatocellular carcinoma cell lines for tumour samples using within-sample relative expression orderings of genes.

PubMed

Ao, Lu; Guo, You; Song, Xuekun; Guan, Qingzhou; Zheng, Weicheng; Zhang, Jiahui; Huang, Haiyan; Zou, Yi; Guo, Zheng; Wang, Xianlong

2017-11-01

Concerns are raised about the representativeness of cell lines for tumours due to the culture environment and misidentification. Liver is a major metastatic destination of many cancers, which might further confuse the origin of hepatocellular carcinoma cell lines. Therefore, it is of crucial importance to understand how well they can represent hepatocellular carcinoma. The HCC-specific gene pairs with highly stable relative expression orderings in more than 99% of hepatocellular carcinoma but with reversed relative expression orderings in at least 99% of one of the six types of cancer, colorectal carcinoma, breast carcinoma, non-small-cell lung cancer, gastric carcinoma, pancreatic carcinoma and ovarian carcinoma, were identified. With the simple majority rule, the HCC-specific relative expression orderings from comparisons with colorectal carcinoma and breast carcinoma could exactly discriminate primary hepatocellular carcinoma samples from both primary colorectal carcinoma and breast carcinoma samples. Especially, they correctly classified more than 90% of liver metastatic samples from colorectal carcinoma and breast carcinoma to their original tumours. Finally, using these HCC-specific relative expression orderings from comparisons with six cancer types, we identified eight of 24 hepatocellular carcinoma cell lines in the Cancer Cell Line Encyclopedia (Huh-7, Huh-1, HepG2, Hep3B, JHH-5, JHH-7, C3A and Alexander cells) that are highly representative of hepatocellular carcinoma. Evaluated with a REOs-based prognostic signature for hepatocellular carcinoma, all these eight cell lines showed the same metastatic properties of the high-risk metastatic hepatocellular carcinoma tissues. Caution should be taken for using hepatocellular carcinoma cell lines. Our results should be helpful to select proper hepatocellular carcinoma cell lines for biological experiments. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Glutaminolysis and carcinogenesis of oral squamous cell carcinoma.

PubMed

Cetindis, Marcel; Biegner, Thorsten; Munz, Adelheid; Teriete, Peter; Reinert, Siegmar; Grimm, Martin

2016-02-01

Glutaminolysis is a crucial factor for tumor metabolism in the carcinogenesis of several tumors but has not been clarified for oral squamous cell carcinoma (OSCC) yet. Expression of glutaminolysis-related solute carrier family 1, member 5 (SLC1A5)/neutral amino acid transporter (ASCT2), glutaminase (GLS), and glutamate dehydrogenase (GLDH) was analyzed in normal oral mucosa (n = 5), oral precursor lesions (simple hyperplasia, n = 11; squamous intraepithelial neoplasia, SIN I-III, n = 35), and OSCC specimen (n = 42) by immunohistochemistry. SLC1A5/ASCT2 and GLS were significantly overexpressed in the carcinogenesis of OSCC compared with normal tissue, while GLDH was weakly detected. Compared with SIN I-III SLC1A5/ASCT2 and GLS expression were significantly increased in OSCC. GLDH expression did not significantly differ from SIN I-III compared with OSCC. This study shows the first evidence of glutaminolysis-related SLC1A5/ASCT2, GLS, and GLDH expression in OSCC. The very weak GLDH expression indicates that glutamine metabolism is rather related to nucleotide or protein/hexosamine biosynthesis or to the function as an antioxidant (glutathione) than to energy production or generation of lactate through entering the tricarboxylic acid cycle. Overcoming glutaminolysis by targeting c-Myc oncogene (e.g. by natural compounds) and thereby cross-activation of mammalian target of rapamycin complex 1 or SLC1A5/ASCT2, GLS inhibitors may be a useful strategy to sensitize cancer cells to common OSCC cancer therapies.

Dispersion of TE modes in slab waveguides with reference to double heterostructure semiconductor lasers

NASA Astrophysics Data System (ADS)

Buus, J.

1980-06-01

The group index for TE modes in an asymmetrical slab waveguide is investigated, and a simple analytical expression is derived. It is shown that the product of the phase and group indices is related to the power fraction in each of the three layers of the waveguide. The results are of interest in the analysis of double heterostructure semiconductor lasers. Theoretical and experimental results for lasers emitting at 1.55 microns are compared.

E-cadherin immunohistochemical expression in mammary gland neoplasms in bitches.

PubMed

Rodo, A; Malicka, E

2008-01-01

The aim of the study was to investigate E-cadherin expression in correlation with other neoplasm traits such as: histological type, the differentiation grade and proliferative activity. Material for the investigation comprised mammary gland tumours, collected from dogs, the patients of veterinary clinics, during surgical procedures and archival samples. All together 21 adenomas, 32 complex carcinomas, 35 simple carcinomas and 13 solid carcinomas were qualified for further investigation. E-cadherin expression was higher in adenomas as compared with carcinomas but lower in solid carcinomas as compared with simple and complex carcinomas. More over, the expression of E-cadherin decreased with the increase in the neoplasm malignancy and proliferative activity (value of the mitotic index and number of cells showing Ki67). The study has shown that the expression of E-cadherin can be used as a prognostic factor.

Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

PubMed

Wang, Xi; Gardiner, Erin J; Cairns, Murray J

2015-05-01

Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies

PubMed Central

Kirkpatrick, Mark

2016-01-01

Sexual dimorphism results from sex-biased gene expression, which evolves when selection acts differently on males and females. While there is an intimate connection between sex-biased gene expression and sex-specific selection, few empirical studies have studied this relationship directly. Here we compare the two on a genome-wide scale in humans and flies. We find a distinctive “Twin Peaks” pattern in humans that relates the strength of sex-specific selection, quantified by genetic divergence between male and female adults at autosomal loci, to the degree of sex-biased expression. Genes with intermediate degrees of sex-biased expression show evidence of ongoing sex-specific selection, while genes with either little or completely sex-biased expression do not. This pattern apparently results from differential viability selection in males and females acting in the current generation. The Twin Peaks pattern is also found in Drosophila using a different measure of sex-specific selection acting on fertility. We develop a simple model that successfully recapitulates the Twin Peaks. Our results suggest that many genes with intermediate sex-biased expression experience ongoing sex-specific selection in humans and flies. PMID:27658217

Antimicrobial peptide gene expression in periodontitis patients: A pilot study.

PubMed

Jourdain, Marie-Laure; Pierrard, Loïc; Kanagaratnam, Lukshe; Velard, Frédéric; Sergheraert, Johan; Lefèvre, Benoît; Gangloff, Sophie C; Braux, Julien

2018-05-01

Antimicrobial peptides (AMPs) are one of the most active components of innate immunity and have characteristics that could place them at the heart of the pathogenesis of periodontal disease. This study investigated differences in the expression of AMP coding genes obtained using a simple harvesting technique, gingival smear, between two groups of patients: chronic periodontitis subjects versus healthy ones. Twenty-three patients were enrolled in two groups: 12 were diagnosed with moderate or severe generalized chronic periodontitis, and 11 were diagnosed as clinically healthy. Gingival smears were retrieved and studied using reverse transcription-quantitative PCR (RT-qPCR) after mRNA purification. Fifteen gene expressions were obtained using real-time RT-qPCR. Three AMP genes, histatin 3 (HTN3), α-defensin 4 (DEFA4) and lysozyme C (LYZ), presented different expression levels in periodontitis patients compared with healthy subjects. The relative expression level of DEFA4 appeared to be a protective factor against periodontitis. Gingival smears studied by RT-qPCR may be used to assess the expression of AMPs coding genes. A lack of expression of DEFA4 could be a potential indicator of periodontitis status. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Type of supplemented simple sugar, not merely calorie intake, determines adverse effects on metabolism and aortic function in female rats

PubMed Central

Sangüesa, Gemma; Shaligram, Sonali; Akther, Farjana; Roglans, Núria; Laguna, Juan C.; Rahimian, Roshanak

2017-01-01

High consumption of simple sugars causes adverse cardiometabolic effects. We investigated the mechanisms underlying the metabolic and vascular effects of glucose or fructose intake and determined whether these effects are exclusively related to increased calorie consumption. Female Sprague-Dawley rats were supplemented with 20% wt/vol glucose or fructose for 2 mo, and plasma analytes and aortic response to vasodilator and vasoconstrictor agents were determined. Expression of molecules associated with lipid metabolism, insulin signaling, and vascular response were evaluated in hepatic and/or aortic tissues. Caloric intake was increased in both sugar-supplemented groups vs. control and in glucose- vs. fructose-supplemented rats. Hepatic lipogenesis was induced in both groups. Plasma triglycerides were increased only in the fructose group, together with decreased expression of carnitine palmitoyltransferase-1A and increased microsomal triglyceride transfer protein expression in the liver. Plasma adiponectin and peroxisome proliferator-activated receptor (PPAR)-α expression was increased only by glucose supplementation. Insulin signaling in liver and aorta was impaired in both sugar-supplemented groups, but the effect was more pronounced in the fructose group. Fructose supplementation attenuated aortic relaxation response to a nitric oxide (NO) donor, whereas glucose potentiated it. Phenylephrine-induced maximal contractions were reduced in the glucose group, which could be related to increased endothelial NO synthase (eNOS) phosphorylation and subsequent elevated basal NO in the glucose group. In conclusion, despite higher caloric intake in glucose-supplemented rats, fructose caused worse metabolic and vascular responses. This may be because of the elevated adiponectin level and the subsequent enhancement of PPARα and eNOS phosphorylation in glucose-supplemented rats. NEW & NOTEWORTHY This is the first study comparing the effects of glucose and fructose consumption on metabolic factors and aortic function in female rats. Our results show that, although total caloric consumption was higher in glucose-supplemented rats, fructose ingestion had a greater impact in inducing metabolic and aortic dysfunction. PMID:27923787

Simple and cost-effective fluorescent labeling of 5-hydroxymethylcytosine

NASA Astrophysics Data System (ADS)

Shahal, Tamar; Green, Ori; Hananel, Uri; Michaeli, Yael; Shabat, Doron; Ebenstein, Yuval

2016-12-01

The nucleobase 5-hydroxymethylcytosine (5-hmC), a modified form of cytosine, is an important epigenetic mark related to regulation of gene expression. 5-hmC levels are highly dynamic during early development and are modulated during the progression of neurodegenerative disease and cancer. We describe a spectroscopic method for the global quantification of 5-hmC in genomic DNA. This method relies on the enzymatic glucosylation of 5-hmC, followed by a glucose oxidation step that results in the formation of aldehyde moieties that are covalently linked to a fluorescent reporter by oxime ligation. The fluorescence intensity of the labeled sample is directly proportional to its 5-hmC content. We show that this simple and cost-effective technique is suitable for quantification of 5-hmC content in different mouse tissues.

Teachers and artificial intelligence. The Logo connection.

PubMed

Merbler, J B

1990-12-01

This article describes a three-phase program for training special education teachers to teach Logo and artificial intelligence. Logo is derived from the LISP computer language and is relatively simple to learn and use, and it is argued that these factors make it an ideal tool for classroom experimentation in basic artificial intelligence concepts. The program trains teachers to develop simple demonstrations of artificial intelligence using Logo. The material that the teachers learn to teach is suitable as an advanced level topic for intermediate- through secondary-level students enrolled in computer competency or similar courses. The material emphasizes problem-solving and thinking skills using a nonverbal expressive medium (Logo), thus it is deemed especially appropriate for hearing-impaired children. It is also sufficiently challenging for academically talented children, whether hearing or deaf. Although the notion of teachers as programmers is controversial, Logo is relatively easy to learn, has direct implications for education, and has been found to be an excellent tool for empowerment-for both teachers and children.

Obtaining natural-like flow releases in diverted river reaches from simple riparian benefit economic models.

PubMed

Perona, Paolo; Dürrenmatt, David J; Characklis, Gregory W

2013-03-30

We propose a theoretical river modeling framework for generating variable flow patterns in diverted-streams (i.e., no reservoir). Using a simple economic model and the principle of equal marginal utility in an inverse fashion we first quantify the benefit of the water that goes to the environment in relation to that of the anthropic activity. Then, we obtain exact expressions for optimal water allocation rules between the two competing uses, as well as the related statistical distributions. These rules are applied using both synthetic and observed streamflow data, to demonstrate that this approach may be useful in 1) generating more natural flow patterns in the river reach downstream of the diversion, thus reducing the ecodeficit; 2) obtaining a more enlightened economic interpretation of Minimum Flow Release (MFR) strategies, and; 3) comparing the long-term costs and benefits of variable versus MFR policies and showing the greater ecological sustainability of this new approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

Introducing Improvisational Skills Through Rhythm Tap: Whether Used in a Dance Class or in a Physical Education Dance Unit, These Simple Exercises Will Overcome Students' Inhibitions and Encourage Their Creative Abilities

ERIC Educational Resources Information Center

West, Colleen N.

2005-01-01

Rhythm tap is sweeping the nation as an outlet for self-expression. Also known as "jazz tap" or "percussive tap," this art form's dominant focus is musicality, improvisation, simple-to-complex rhythms, and new styles. It reaches beyond technique and serves as an outlet for self-expression, independence, and spontaneity. Rhythm tap incorporates an…

Transient heating of expressed breast milk up to 65°C inactivates HIV-1 in milk: a simple, rapid, and cost-effective method to prevent postnatal transmission.

PubMed

Hoque, Sheikh Ariful; Hoshino, Hiroo; Anwar, Kazi Selim; Tanaka, Atsushi; Shinagawa, Masahiko; Hayakawa, Yuko; Okitsu, Shoko; Wada, Yuichi; Ushijima, Hiroshi

2013-02-01

The postnatal transmission of human immunodeficiency virus (HIV) from mothers to children occurs through breastfeeding. Although heat treatment of expressed breast milk is a promising approach to make breastfeeding safer, it is still not popular, mainly because the recommended procedures are difficult to follow, or time-consuming, or because mothers do not know which temperature is sufficient to inactivate HIV without destroying the nutritional elements of milk. To overcome these drawbacks, a simple and rapid method of heat treatment that a mother could perform with regular household materials applying her day-to-day art of cooking was examined. This structured experiment has demonstrated that both cell-free and cell-associated HIV type 1 (HIV-1) in expressed breast milk could be inactivated once the temperature of milk reached 65°C. Furthermore, a heating method as simple as heating the milk in a pan over a stove to 65°C inhibited HIV-1 transmission retaining milk's nutritional key elements, for example, total protein, IgG, IgA, and vitamin B(12) . This study has highlighted a simple, handy, and cost-effective method of heat treatment of expressed breast milk that mothers infected with HIV could apply easily and with more confidence. Copyright © 2012 Wiley Periodicals, Inc.

Symmetrical treatment of "Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition", for major depressive disorders.

PubMed

Sawamura, Jitsuki; Morishita, Shigeru; Ishigooka, Jun

2016-01-01

We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5, the current version), is frequently used for diagnosis in daily psychiatric treatments and biological research. The diagnostic criteria of DSM-5 contain simple binominal items relating to the presence or absence of specific symptoms. In spite of its simple form, the practical structure of the DSM-5 system is not sufficiently systemized for data to be treated in a more rationally sophisticated way. To view the disease states in terms of symmetry in the manner of abstract algebra is considered important for the future systematization of clinical medicine. We provide a simple idea for the practical treatment of the psychiatric diagnosis/score of DSM-5 using depressive symptoms in line with our previously proposed method. An expression is given employing modulo-2 and -7 arithmetic (in particular, additive group theory) for Criterion A of a 'major depressive episode' that must be met for the diagnosis of 'major depressive disorder' in DSM-5. For this purpose, the novel concept of an imaginary value 0 that can be recognized as an explicit 0 or implicit 0 was introduced to compose the model. The zeros allow the incorporation or deletion of an item between any other symptoms if they are ordered appropriately. Optionally, a vector-like expression can be used to rate/select only specific items when modifying the criterion/scale. Simple examples are illustrated concretely. Further development of the proposed method for the criteria/scale of a disease is expected to raise the level of formalism of clinical medicine to that of other fields of natural science.

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

PubMed Central

Klesmith, Justin R.; Detwiler, Emily E.; Tomek, Kyle J.; Whitehead, Timothy A.

2014-01-01

In exponentially growing bacteria, expression of heterologous protein impedes cellular growth rates. Quantitative understanding of the relationship between expression and growth rate will advance our ability to forward engineer bacteria, important for metabolic engineering and synthetic biology applications. Recently, a work described a scaling model based on optimal allocation of ribosomes for protein translation. This model quantitatively predicts a linear relationship between microbial growth rate and heterologous protein expression with no free parameters. With the aim of validating this model, we have rigorously quantified the fitness cost of gene expression by using a library of synthetic constitutive promoters to drive expression of two separate proteins (eGFP and amiE) in E. coli in different strains and growth media. In all cases, we demonstrate that the fitness cost is consistent with the previous findings. We expand upon the previous theory by introducing a simple promoter activity model to quantitatively predict how basal promoter strength relates to growth rate and protein expression. We then estimate the amount of protein expression needed to support high flux through a heterologous metabolic pathway and predict the sizable fitness cost associated with enzyme production. This work has broad implications across applied biological sciences because it allows for prediction of the interplay between promoter strength, protein expression, and the resulting cost to microbial growth rates. PMID:25286161

Temporal Asthma Patterns Using Repeated Questionnaires over 13 Years in a Large French Cohort of Women

PubMed Central

Sanchez, Margaux; Bousquet, Jean; Le Moual, Nicole; Jacquemin, Bénédicte; Clavel-Chapelon, Françoise; Humbert, Marc; Kauffmann, Francine; Tubert-Bitter, Pascale; Varraso, Raphaëlle

2013-01-01

Variable expression is one aspect of the heterogeneity of asthma. We aimed to define a variable pattern, which is relevant in general health epidemiological cohorts. Our objectives were to assess whether: 1) asthma patterns defined using simple asthma questions through repeated measurements could reflect disease variability 2) these patterns may further be classified according to asthma severity/control. Among 70,428 French women, we used seven questionnaires (1992–2005) and a comprehensive reimbursement database (2004–2009) to define three reliable asthma patterns based on repeated positive answers to the ever asthma attack question: “never asthma” (n = 64,061); “inconsistent” (“yes” followed by “no”, n = 3,514); “consistent” (fully consistent positive answers, n = 2,853). The “Inconsistent” pattern was related to both long-term (childhood-onset asthma with remission in adulthood) and short-term (reported asthma attack in the last 12 months, associated with asthma medication) asthma variability, showing that repeated questions are relevant markers of the variable expression of asthma. Furthermore, in this pattern, the number of positive responses (1992–2005) predicted asthma drug consumption in subsequent years, a marker of disease severity. The “Inconsistent” pattern is a phenotype that may capture the variable expression of asthma. Repeated answers, even to a simple question, are too often neglected. PMID:23741466

Prediction of Petermann I and II Spot Sizes for Single-mode Dispersion-shifted and Dispersion-flattened Fibers by a Simple Technique

NASA Astrophysics Data System (ADS)

Kamila, Kiranmay; Panda, Anup Kumar; Gangopadhyay, Sankar

2013-09-01

Employing the series expression for the fundamental modal field of dispersion-shifted trapezoidal and dispersion-flattened graded and step W fibers, we present simple but accurate analytical expressions for Petermann I and II spot sizes of such kind of fibers. Choosing some typical dispersion-shifted trapezoidal and dispersion-flattened graded and step W fibers as examples, we show that our estimations match excellently with the exact numerical results. The evaluation of the concerned propagation parameters by our formalism needs very little computations. This accurate but simple formalism will benefit the system engineers working in the field of all optical technology.

Generation of ΔF508-CFTR T84 cell lines by CRISPR/Cas9-mediated genome editing.

PubMed

Chung, Woo Young; Song, Myungjae; Park, Jinhong; Namkung, Wan; Lee, Jinu; Kim, Hyongbum; Lee, Min Goo; Kim, Joo Young

2016-12-01

To provide a simple method to make a stable ΔF508-CFTR-expressing T84 cell line that can be used as an efficient screening model system for ΔF508-CFTR rescue. CFTR knockout cell lines were generated by Cas9 with a single-guide RNA (sgRNA) targeting exon 1 of the CFTR genome, which produced indels that abolished CFTR protein expressions. Next, stable ΔF508-CFTR expression was achieved by genome integration of ΔF508-CFTR via the lentivirus infection system. Finally, we showed functional rescue of ΔF508-CFTR not only by growing the cells at a low temperature, but also incubating with VX-809, a ΔF508-CFTR corrector, in the established T84 cells expressing ΔF508-CFTR. This cell system provides an appropriate screening platform for rescue of ΔF508-CFTR, especially related to protein folding, escaped from endoplasmic-reticulum-associated protein degradation, and membrane transport.

Detection of Dystrophin Dp71 in Human Skeletal Muscle Using an Automated Capillary Western Assay System.

PubMed

Kawaguchi, Tatsuya; Niba, Emma Tabe Eko; Rani, Abdul Qawee Mahyoob; Onishi, Yoshiyuki; Koizumi, Makoto; Awano, Hiroyuki; Matsumoto, Masaaki; Nagai, Masashi; Yoshida, Shinobu; Sakakibara, Sachiko; Maeda, Naoyuki; Sato, Osamu; Nishio, Hisahide; Matsuo, Masafumi

2018-05-23

Dystrophin Dp71 is one of the isoforms produced by the DMD gene which is mutated in patients with Duchenne muscular dystrophy (DMD). Although Dp71 is expressed ubiquitously, it has not been detected in normal skeletal muscle. This study was performed to assess the expression of Dp71 in human skeletal muscle. Human skeletal muscle RNA and tissues were obtained commercially. Mouse skeletal muscle was obtained from normal and DMD mdx mice. Dp71 mRNA and protein were determined by reverse-transcription PCR and an automated capillary Western assay system, the Simple Western, respectively. Dp71 was over-expressed or suppressed using a plasmid expressing Dp71 or antisense oligonucleotide, respectively. Full-length Dp71 cDNA was PCR amplified as a single product from human skeletal muscle RNA. A ca. 70 kDa protein peak detected by the Simple Western was determined as Dp71 by over-expressing Dp71 in HEK293 cells, or suppressing Dp71 expression with antisense oligonucleotide in rhabdomyosarcoma cells. The Simple Western assay detected Dp71 in the skeletal muscles of both normal and DMD mice. In human skeletal muscle, Dp71 was also detected. The ratio of Dp71 to vinculin of human skeletal muscle samples varied widely, indicating various levels of Dp71 expression. Dp71 protein was detected in human skeletal muscle using a highly sensitive capillary Western blotting system.

Preferential amygdala reactivity to the negative assessment of neutral faces.

PubMed

Blasi, Giuseppe; Hariri, Ahmad R; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R; Mattay, Venkata S

2009-11-01

Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues.

Preferential Amygdala Reactivity to the Negative Assessment of Neutral Faces

PubMed Central

Blasi, Giuseppe; Hariri, Ahmad R.; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R.; Mattay, Venkata S.

2010-01-01

Background Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. Methods During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Results Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Conclusions Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues. PMID:19709644

Sunspots and Their Simple Harmonic Motion

ERIC Educational Resources Information Center

Ribeiro, C. I.

2013-01-01

In this paper an example of a simple harmonic motion, the apparent motion of sunspots due to the Sun's rotation, is described, which can be used to teach this subject to high-school students. Using real images of the Sun, students can calculate the star's rotation period with the simple harmonic motion mathematical expression.

An efficient method to identify differentially expressed genes in microarray experiments

PubMed Central

Qin, Huaizhen; Feng, Tao; Harding, Scott A.; Tsai, Chung-Jui; Zhang, Shuanglin

2013-01-01

Motivation Microarray experiments typically analyze thousands to tens of thousands of genes from small numbers of biological replicates. The fact that genes are normally expressed in functionally relevant patterns suggests that gene-expression data can be stratified and clustered into relatively homogenous groups. Cluster-wise dimensionality reduction should make it feasible to improve screening power while minimizing information loss. Results We propose a powerful and computationally simple method for finding differentially expressed genes in small microarray experiments. The method incorporates a novel stratification-based tight clustering algorithm, principal component analysis and information pooling. Comprehensive simulations show that our method is substantially more powerful than the popular SAM and eBayes approaches. We applied the method to three real microarray datasets: one from a Populus nitrogen stress experiment with 3 biological replicates; and two from public microarray datasets of human cancers with 10 to 40 biological replicates. In all three analyses, our method proved more robust than the popular alternatives for identification of differentially expressed genes. Availability The C++ code to implement the proposed method is available upon request for academic use. PMID:18453554

Isotope labeling of proteins in insect cells.

PubMed

Skora, Lukasz; Shrestha, Binesh; Gossert, Alvar D

2015-01-01

Protein targets of contemporary research are often membrane proteins, multiprotein complexes, secreted proteins, or other proteins of human origin. These are difficult to express in the standard expression host used for most nuclear magnetic resonance (NMR) studies, Escherichia coli. Insect cells represent an attractive alternative, since they have become a well-established expression system and simple solutions have been developed for generation of viruses to efficiently introduce the target protein DNA into cells. Insect cells enable production of a larger fraction of the human proteome in a properly folded way than bacteria, as insect cells have a very similar set of cytosolic chaperones and a closely related secretory pathway. Here, the limited and defined glycosylation pattern that insect cells produce is an advantage for structural biology studies. For these reasons, insect cells have been established as the most widely used eukaryotic expression host for crystallographic studies. In the past decade, significant advancements have enabled amino acid type-specific as well as uniform isotope labeling of proteins in insect cells, turning them into an attractive expression host for NMR studies. © 2015 Elsevier Inc. All rights reserved.

The difference between two random mixed quantum states: exact and asymptotic spectral analysis

NASA Astrophysics Data System (ADS)

Mejía, José; Zapata, Camilo; Botero, Alonso

2017-01-01

We investigate the spectral statistics of the difference of two density matrices, each of which is independently obtained by partially tracing a random bipartite pure quantum state. We first show how a closed-form expression for the exact joint eigenvalue probability density function for arbitrary dimensions can be obtained from the joint probability density function of the diagonal elements of the difference matrix, which is straightforward to compute. Subsequently, we use standard results from free probability theory to derive a relatively simple analytic expression for the asymptotic eigenvalue density (AED) of the difference matrix ensemble, and using Carlson’s theorem, we obtain an expression for its absolute moments. These results allow us to quantify the typical asymptotic distance between the two random mixed states using various distance measures; in particular, we obtain the almost sure asymptotic behavior of the operator norm distance and the trace distance.

Photokinesis and Djopsin gene expression analysis during the regeneration of planarian eyes.

PubMed

Dong, Zimei; Yuwen, Yanqing; Sima, Yingxu; Dong, Yanping; Zhan, Huina; Chen, Guangwen; Liu, Dezeng

2017-03-01

Planarians provide the ideal model for studying eye development, with their simple eye structure and exceptionally rapid regeneration. Here, we observed the eye morphogenesis, photophobic behavior, spectral sensitivity and expression pattern of Djopsin in the freshwater planarian Dugesia japonica. The results showed that: (i) Djopsin encoding the putative protein belonged to the rhabdomeric opsins group and displayed high conservation during animal evolution; (ii) planarians displayed diverse photophobic response to different visible wavelengths and were more sensitive to light blue (495 nm) and yellow (635 nm); (iii) the morphogenesis and functional recovery of eyes were related to the expression pattern of Djopsin during head regeneration; and (iv) Djopsin gene plays a major role in functional recovery during eye regeneration and visual system maintenance in adult planarians. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Ccdc85C, a causative protein for hydrocephalus and subcortical heterotopia, is expressed in the systemic epithelia with proliferative activity in rats.

PubMed

Tanaka, Natsuki; Izawa, Takeshi; Takenaka, Shigeo; Yamate, Jyoji; Kuwamura, Mitsuru

2015-07-01

Coiled-coil domain containing 85c (Ccdc85c) is a causative gene for spontaneous mutant mouse with non-obstructive hydrocephalus and subcortical heterotopia. Detailed functions of Ccdc85C protein have not been clarified. To reveal roles of Ccdc85C, we examined the distribution and expression pattern of Ccdc85C in the systemic developing organs in rats. Ccdc85C was expressed in various simple epithelia but not stratified epithelia. In the various epithelia, Ccdc85C was localized at cell-cell junctions and its expression was strong at apical junctions. Furthermore, intense expression was seen at developing period and gradually decreased with advancing development. Distribution of Ccdc85C coincides with that of proliferating epithelial cells. These results suggest that Ccdc85C plays an important role in the proliferative property of simple epithelia.

Microarray-based cancer prediction using soft computing approach.

PubMed

Wang, Xiaosheng; Gotoh, Osamu

2009-05-26

One of the difficulties in using gene expression profiles to predict cancer is how to effectively select a few informative genes to construct accurate prediction models from thousands or ten thousands of genes. We screen highly discriminative genes and gene pairs to create simple prediction models involved in single genes or gene pairs on the basis of soft computing approach and rough set theory. Accurate cancerous prediction is obtained when we apply the simple prediction models for four cancerous gene expression datasets: CNS tumor, colon tumor, lung cancer and DLBCL. Some genes closely correlated with the pathogenesis of specific or general cancers are identified. In contrast with other models, our models are simple, effective and robust. Meanwhile, our models are interpretable for they are based on decision rules. Our results demonstrate that very simple models may perform well on cancerous molecular prediction and important gene markers of cancer can be detected if the gene selection approach is chosen reasonably.

Correlation of Mixture Temperature Data Obtained from Bare Intake-manifold Thermocouples

NASA Technical Reports Server (NTRS)

White, H. Jack; Gammon, Goldie L

1946-01-01

A relatively simple equation has been found to express with fair accuracy, variation in manifold-charge temperature with charge in engine operating conditions. This equation and associated curves have been checked by multi cylinder-engine data, both test stand and flight, over a wide range of operating conditions. Average mixture temperatures, predicted by the equations of this report, agree reasonably well with results within the same range of carburetor-air temperatures from laboratories and test stands other than the NACA.

Statecharts Via Process Algebra

NASA Technical Reports Server (NTRS)

Luttgen, Gerald; vonderBeeck, Michael; Cleaveland, Rance

1999-01-01

Statecharts is a visual language for specifying the behavior of reactive systems. The Language extends finite-state machines with concepts of hierarchy, concurrency, and priority. Despite its popularity as a design notation for embedded system, precisely defining its semantics has proved extremely challenging. In this paper, a simple process algebra, called Statecharts Process Language (SPL), is presented, which is expressive enough for encoding Statecharts in a structure-preserving and semantic preserving manner. It is establish that the behavioral relation bisimulation, when applied to SPL, preserves Statecharts semantics

Mechanical Properties of Transcription

NASA Astrophysics Data System (ADS)

Sevier, Stuart A.; Levine, Herbert

2017-06-01

The mechanical properties of transcription have recently been shown to play a central role in gene expression. However, a full physical characterization of this central biological process is lacking. In this Letter, we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation, and DNA supercoiling are coupled. The resulting framework describes the relative amount of RNA polymerase rotation and DNA supercoiling that occurs during RNA elongation. Asymptotic behavior is derived and can be used to experimentally extract unknown mechanical parameters of transcription. Mechanical limits to transcription are incorporated through the addition of a DNA supercoiling-dependent RNA polymerase velocity. This addition can lead to transcriptional stalling and resulting implications for gene expression, chromatin structure and genome organization are discussed.

Performance Analysis of Blind Subspace-Based Signature Estimation Algorithms for DS-CDMA Systems with Unknown Correlated Noise

NASA Astrophysics Data System (ADS)

Zarifi, Keyvan; Gershman, Alex B.

2006-12-01

We analyze the performance of two popular blind subspace-based signature waveform estimation techniques proposed by Wang and Poor and Buzzi and Poor for direct-sequence code division multiple-access (DS-CDMA) systems with unknown correlated noise. Using the first-order perturbation theory, analytical expressions for the mean-square error (MSE) of these algorithms are derived. We also obtain simple high SNR approximations of the MSE expressions which explicitly clarify how the performance of these techniques depends on the environmental parameters and how it is related to that of the conventional techniques that are based on the standard white noise assumption. Numerical examples further verify the consistency of the obtained analytical results with simulation results.

Light-Responsive Cryptochromes from a Simple Multicellular Animal, the Coral Acropora millepora

NASA Astrophysics Data System (ADS)

Levy, O.; Appelbaum, L.; Leggat, W.; Gothlif, Y.; Hayward, D. C.; Miller, D. J.; Hoegh-Guldberg, O.

2007-10-01

Hundreds of species of reef-building corals spawn synchronously over a few nights each year, and moonlight regulates this spawning event. However, the molecular elements underpinning the detection of moonlight remain unknown. Here we report the presence of an ancient family of blue-light-sensing photoreceptors, cryptochromes, in the reef-building coral Acropora millepora. In addition to being cryptochrome genes from one of the earliest-diverging eumetazoan phyla, cry1 and cry2 were expressed preferentially in light. Consistent with potential roles in the synchronization of fundamentally important behaviors such as mass spawning, cry2 expression increased on full moon nights versus new moon nights. Our results demonstrate phylogenetically broad roles of these ancient circadian clock-related molecules in the animal kingdom.

GAPTrap: A Simple Expression System for Pluripotent Stem Cells and Their Derivatives.

PubMed

Kao, Tim; Labonne, Tanya; Niclis, Jonathan C; Chaurasia, Ritu; Lokmic, Zerina; Qian, Elizabeth; Bruveris, Freya F; Howden, Sara E; Motazedian, Ali; Schiesser, Jacqueline V; Costa, Magdaline; Sourris, Koula; Ng, Elizabeth; Anderson, David; Giudice, Antonietta; Farlie, Peter; Cheung, Michael; Lamande, Shireen R; Penington, Anthony J; Parish, Clare L; Thomson, Lachlan H; Rafii, Arash; Elliott, David A; Elefanty, Andrew G; Stanley, Edouard G

2016-09-13

The ability to reliably express fluorescent reporters or other genes of interest is important for using human pluripotent stem cells (hPSCs) as a platform for investigating cell fates and gene function. We describe a simple expression system, designated GAPTrap (GT), in which reporter genes, including GFP, mCherry, mTagBFP2, luc2, Gluc, and lacZ are inserted into the GAPDH locus in hPSCs. Independent clones harboring variations of the GT vectors expressed remarkably consistent levels of the reporter gene. Differentiation experiments showed that reporter expression was reliably maintained in hematopoietic cells, cardiac mesoderm, definitive endoderm, and ventral midbrain dopaminergic neurons. Similarly, analysis of teratomas derived from GT-lacZ hPSCs showed that β-galactosidase expression was maintained in a spectrum of cell types representing derivatives of the three germ layers. Thus, the GAPTrap vectors represent a robust and straightforward tagging system that enables indelible labeling of PSCs and their differentiated derivatives. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Generalized moment analysis of magnetic field correlations for accumulations of spherical and cylindrical magnetic pertubers

NASA Astrophysics Data System (ADS)

Kurz, Felix; Kampf, Thomas; Buschle, Lukas; Schlemmer, Heinz-Peter; Bendszus, Martin; Heiland, Sabine; Ziener, Christian

2016-12-01

In biological tissue, an accumulation of similarly shaped objects with a susceptibility difference to the surrounding tissue generates a local distortion of the external magnetic field in magnetic resonance imaging. It induces stochastic field fluctuations that characteristically influence proton spin diffusion in the vicinity of these magnetic perturbers. The magnetic field correlation that is associated with such local magnetic field inhomogeneities can be expressed in the form of a dynamic frequency autocorrelation function that is related to the time evolution of the measured magnetization. Here, an eigenfunction expansion for two simple magnetic perturber shapes, that of spheres and cylinders, is considered for restricted spin diffusion in a simple model geometry. Then, the concept of generalized moment analysis, an approximation technique that is applied in the study of (non-)reactive processes that involve Brownian motion, allows to provide analytical expressions for the correlation function for different exponential decay forms. Results for the biexponential decay for both spherical and cylindrical magnetized objects are derived and compared with the frequently used (less accurate) monoexponential decay forms. They are in asymptotic agreement with the numerically exact value of the correlation function for long and short times.

Development and validation of a simple GC-MS method for the simultaneous determination of 11 anticholinesterase pesticides in blood--clinical and forensic toxicology applications.

PubMed

Papoutsis, Ioannis; Mendonis, Marcela; Nikolaou, Panagiota; Athanaselis, Sotirios; Pistos, Constantinos; Maravelias, Constantinos; Spiliopoulou, Chara

2012-05-01

Anticholinesterase pesticides are widely used, and as a result they are involved in numerous acute and even fatal poisonings. The aim of this study was the development, optimization, and validation of a simple, rapid, specific, and sensitive gas chromatography-mass spectrometry method for the determination of 11 anticholinesterase pesticides (aldicarb, azinphos methyl, carbofuran, chlorpyrifos, dialifos, diazinon, malathion, methamidophos, methidathion, methomyl, and terbufos) in blood. Only 500 μL of blood was used, and the recoveries after liquid-liquid extraction (toluene/chloroform, 4:1, v/v) were more than 65.6%. The calibration curves were linear (R(2) ≥ 0.996). Limit of detections and limit of quantifications were found to be between 1.00-10.0 and 3.00-30.0 μg/L, respectively. Accuracy expressed as the %E(r) was found to be between -11.0 and 7.8%. Precision expressed as the percent relative standard deviation was found to be <9.4%. The developed method can be applied for the investigation of both forensic and clinical cases of accidental or suicidal poisoning with these pesticides. © 2011 American Academy of Forensic Sciences.

Carrier removal and defect behavior in p-type InP

NASA Technical Reports Server (NTRS)

Weinberg, I.; Swartz, C. K.; Drevinsky, P. J.

1992-01-01

A simple expression, obtained from the rate equation for defect production, was used to relate carrier removal to defect production and hole trapping rates in p-type InP after irradiation by 1-MeV electrons. Specific contributions to carrier removal from defect levels H3, H4, and H5 were determined from combined deep-level transient spectroscopy (DLTS) and measured carrier concentrations. An additional contribution was attributed to one or more defects not observed by the present DLTS measurements. The high trapping rate observed for H5 suggests that this defect, if present in relatively high concentration, could be dominant in p-type InP.

Fine-tuning gene networks using simple sequence repeats

PubMed Central

Egbert, Robert G.; Klavins, Eric

2012-01-01

The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch’s behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis—suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks. PMID:22927382

Occupation probabilities and fluctuations in the asymmetric simple inclusion process

NASA Astrophysics Data System (ADS)

Reuveni, Shlomi; Hirschberg, Ori; Eliazar, Iddo; Yechiali, Uri

2014-04-01

The asymmetric simple inclusion process (ASIP), a lattice-gas model of unidirectional transport and aggregation, was recently proposed as an "inclusion" counterpart of the asymmetric simple exclusion process. In this paper we present an exact closed-form expression for the probability that a given number of particles occupies a given set of consecutive lattice sites. Our results are expressed in terms of the entries of Catalan's trapezoids—number arrays which generalize Catalan's numbers and Catalan's triangle. We further prove that the ASIP is asymptotically governed by the following: (i) an inverse square-root law of occupation, (ii) a square-root law of fluctuation, and (iii) a Rayleigh law for the distribution of interexit times. The universality of these results is discussed.

Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting.

PubMed

Cowley, Michael; de Burca, Anna; McCole, Ruth B; Chahal, Mandeep; Saadat, Ghazal; Oakey, Rebecca J; Schulz, Reiner

2011-04-20

Genomic imprinting is a form of gene dosage regulation in which a gene is expressed from only one of the alleles, in a manner dependent on the parent of origin. The mechanisms governing imprinted gene expression have been investigated in detail and have greatly contributed to our understanding of genome regulation in general. Both DNA sequence features, such as CpG islands, and epigenetic features, such as DNA methylation and non-coding RNAs, play important roles in achieving imprinted expression. However, the relative importance of these factors varies depending on the locus in question. Defining the minimal features that are absolutely required for imprinting would help us to understand how imprinting has evolved mechanistically. Imprinted retrogenes are a subset of imprinted loci that are relatively simple in their genomic organisation, being distinct from large imprinting clusters, and have the potential to be used as tools to address this question. Here, we compare the repeat element content of imprinted retrogene loci with non-imprinted controls that have a similar locus organisation. We observe no significant differences that are conserved between mouse and human, suggesting that the paucity of SINEs and relative abundance of LINEs at imprinted loci reported by others is not a sequence feature universally required for imprinting.

Induction of CYP2E1 in non-alcoholic fatty liver diseases

PubMed Central

Aljomah, Ghanim; Baker, Susan S.; Liu, Wensheng; Kozielski, Rafal; Oluwole, Janet; Lupu, Benita; Baker, Robert D.; Zhu, Lixin

2015-01-01

Mounting evidence supports a contribution of endogenous alcohol metabolism in the pathogenesis of non-alcoholic steatohepatitis (NASH). However, it is not known whether the expression of alcohol metabolism genes is altered in the livers of simple steatosis. There is also a current debate on whether fatty acids induce CYP2E1 in fatty livers. In this study, expression of alcohol metabolizing genes in the liver biopsies of simple steatosis patients was examined by quantitative real-time PCR (qRT-PCR), in comparison to biopsies of NASH livers and normal controls. Induction of alcohol metabolizing genes was also examined in cultured HepG2 cells treated with ethanol or oleic acid, by qRT-PCR and Western blots. We found that the mRNA expression of alcohol metabolizing genes including ADH1C, ADH4, ADH6, catalase and CYP2E1 were elevated in the livers of simple steatosis, to similar levels found in NASH livers. In cultured HepG2 cells, ethanol induced the expression of CYP2E1 mRNA and protein, but not ADH4 or ADH6; oleic acid did not induce any of these genes. These results suggest that elevated alcohol metabolism may contribute to the pathogenesis of NAFLD at the stage of simple steatosis as well as more severe stages. Our in vitro data support that CYP2E1 is induced by endogenous alcohol but not by fatty acids. PMID:26551085

Mucin gene expression in intraductal papillary-mucinous pancreatic tumours and related lesions.

PubMed

Terris, Benoît; Dubois, Sylvie; Buisine, Marie-Pierre; Sauvanet, Alain; Ruszniewski, Philippe; Aubert, Jean-Pierre; Porchet, Nicole; Couvelard, Anne; Degott, Claude; Fléjou, Jean-Francois

2002-08-01

Intraductal papillary-mucinous tumours (IPMTs) of the pancreas are heterogeneous proliferations characterized by a malignant potential. The molecular mechanisms underlying the tumourigenesis process are not well understood. Recently, it has been shown that IPMTs secreting the mucin antigen MUC2 have a better prognosis, but the complete pattern of MUC gene expression has not yet been established. The aims of this study were to evaluate the mucin gene expression in 57 IPMTs and eight related lesions surgically resected and to relate MUC gene expression to the histological diagnosis. In situ hybridization (ISH) was performed in 28 cases with probes specific for the MUC1, MUC2, MUC3, MUC4, MUC5AC, MUC5B, MUC6, and MUC7 genes. An immunohistochemical analysis was carried in all 65 cases and in 90 conventional ductal adenocarcinomas of the pancreas using MUC1, MUC2, and MUC5AC antibodies. IPMTs of adenoma (dysplasia) type exhibited high expression of MUC2 (93%), MUC5AC (97%), and, to a lesser extent, of MUC4 (71%), all of which were also observed in colloid carcinomas associated with IPMTs. In contrast, IPMTs with simple hyperplasia, intraductal oncocytic papillary neoplasms, and pyloric glandular adenomas exhibited little or no expression of MUC2. The mucin expression profile supports the existence of two types of invasive tumour associated with IPMTs: a colloid and an ordinary form. The latter shows a pattern similar to the conventional ductal adenocarcinomas with a loss of MUC2 and a gain of MUC1 and has a greater tendency to metastasize. In conclusion, the altered expression of mucin, characteristic of IPMT of adenoma type and of colloid carcinomas, may contribute to the better clinical outcome of these neoplasms, compared to conventional pancreatic ductal adenocarcinomas. Copyright 2002 John Wiley & Sons, Ltd.

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

PubMed Central

Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

2015-01-01

Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5′ transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5′UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5′end can modulate protein levels up to 160%–300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple rules for engineering synthetic gene expression in eukaryotes. PMID:26176266

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.

PubMed

Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

2015-01-01

Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5' transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5'UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5'end can modulate protein levels up to 160%-300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple rules for engineering synthetic gene expression in eukaryotes.

Neuroendocrine control of seasonal plasticity in the auditory and vocal systems of fish

PubMed Central

Forlano, Paul M.; Sisneros, Joseph A.; Rohmann, Kevin N.; Bass, Andrew H.

2014-01-01

Seasonal changes in reproductive-related vocal behavior are widespread among fishes. This review highlights recent studies of the vocal plainfin midshipman fish, Porichthys notatus, a neuroethological model system used for the past two decades to explore neural and endocrine mechanisms of vocal-acoustic social behaviors shared with tetrapods. Integrative approaches combining behavior, neurophysiology, neuropharmacology, neuroanatomy, and gene expression methodologies have taken advantage of simple, stereotyped and easily quantifiable behaviors controlled by discrete neural networks in this model system to enable discoveries such as the first demonstration of adaptive seasonal plasticity in the auditory periphery of a vertebrate as well as rapid steroid and neuropeptide effects on vocal physiology and behavior. This simple model system has now revealed cellular and molecular mechanisms underlying seasonal and steroid-driven auditory and vocal plasticity in the vertebrate brain. PMID:25168757

A simple expression for the cold compression curve.

NASA Astrophysics Data System (ADS)

Čelebonović, V.

1996-10-01

The aim of this contribution is to present expressions for the bulk modulus of a material and its pressure derivative obtained by using the semi-classical theory of dense matter proposed by P. Savić and R. Kašanin. Some possibilities for the application of these expressions are briefly discussed.

Phonon scattering in nanoscale systems: lowest order expansion of the current and power expressions

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2006-04-01

We use the non-equilibrium Green's function method to describe the effects of phonon scattering on the conductance of nano-scale devices. Useful and accurate approximations are developed that both provide (i) computationally simple formulas for large systems and (ii) simple analytical models. In addition, the simple models can be used to fit experimental data and provide physical parameters.

Characterization of growth and reproduction performance, transgene integration, expression and transmission patterns in transgenic pigs produced by piggyBac transposition-mediated gene transfer

PubMed Central

Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

2016-01-01

Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance, and characterized the transgene insertion, transmission and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favourable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition. PMID:27565868

Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State.

PubMed

Gao, Wen; Yin, Jun; Bao, Lichen; Wang, Qun; Hou, Shan; Yue, Yali; Yao, Wenbing; Gao, Xiangdong

2018-05-18

Escherichia coli extracellular expression systems have a number of advantages over other systems, such as lower pyrogen levels and a simple purification process. Various approaches, such as the generation of leaky mutants via chromosomal engineering, have been explored for this expression system. However, extracellular protein yields in leaky mutants are relatively low compared to that in intracellular expression systems and therefore need to be improved. In this work, we describe the construction, characterization, and mechanism of enhanced extracellular expression in Escherichia coli. On the basis of the localizations, functions, and transcription levels of cell envelope proteins, we systematically elucidated the effects of multiple gene deletions on cell growth and extracellular expression using modified CRISPR/Cas9-based genome editing and a FlAsH labeling assay. High extracellular yields of heterologous proteins of different sizes were obtained by screening multiple gene mutations. The enhancement of extracellular secretion was associated with the derepression of translation and translocation. This work utilized universal methods in the design of extracellular expression systems for genes not directly associated with protein synthesis that were used to generate strains with higher protein expression capability. We anticipate that extracellular expression systems may help to shed light on the poorly understood aspects of these secretion processes as well as to further assist in the construction of engineered prokaryotic cells for efficient extracellular production of heterologous proteins.

Tinkering with the C-Function: A Molecular Frame for the Selection of Double Flowers in Cultivated Roses

PubMed Central

Dubois, Annick; Raymond, Olivier; Maene, Marion; Baudino, Sylvie; Langlade, Nicolas B.; Boltz, Véronique; Vergne, Philippe; Bendahmane, Mohammed

2010-01-01

Background Roses have been cultivated for centuries and a number of varieties have been selected based on flower traits such as petal form, color, and number. Wild-type roses have five petals (simple flowers), whereas high numbers of petals (double flowers) are typical attributes of most of the cultivated roses. Here, we investigated the molecular mechanisms that could have been selected to control petal number in roses. Methodology/Principal Findings We have analyzed the expression of several candidate genes known to be involved in floral organ identity determination in roses from similar genetic backgrounds but exhibiting contrasting petal numbers per flower. We show that the rose ortholog of AGAMOUS (RhAG) is differentially expressed in double flowers as compared to simple flowers. In situ hybridization experiments confirm the differential expression of RhAG and demonstrate that in the double-flower roses, the expression domain of RhAG is restricted toward the center of the flower. Conversely, in simple-flower roses, RhAG expression domain is wider. We further show that the border of RhAG expression domain is labile, which allows the selection of rose flowers with increased petal number. Double-flower roses were selected independently in the two major regions for domestication, China and the peri-Mediterranean areas. Comparison of RhAG expression in the wild-type ancestors of cultivated roses and their descendants both in the European and Chinese lineages corroborates the correlation between the degree of restriction of RhAG expression domain and the number of petals. Our data suggests that a restriction of RhAG expression domain is the basis for selection of double flowers in both the Chinese and peri-Mediterranean centers of domestication. Conclusions/Significance We demonstrate that a shift in RhAG expression domain boundary occurred in rose hybrids, causing double-flower phenotype. This molecular event was selected independently during rose domestication in Europe/Middle East and in China. PMID:20174587

75 FR 2545 - Call for Collaborating Partners for National Women's Health Week

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-15

... expressions of interest by February 28, 2010. ADDRESSES: Expressions of interest, comments, and questions may... simple steps for a longer, healthier and happier life. For more information about National Women's Health...

Python/Lua Benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Busby, L.

This is an adaptation of the pre-existing Scimark benchmark code to a variety of Python and Lua implementations. It also measures performance of the Fparser expression parser and C and C++ code on a variety of simple scientific expressions.

Algebraic Turbulence-Chemistry Interaction Model

NASA Technical Reports Server (NTRS)

Norris, Andrew T.

2012-01-01

The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

Free fall and harmonic oscillations: analyzing trampoline jumps

NASA Astrophysics Data System (ADS)

Pendrill, Ann-Marie; Eager, David

2015-01-01

Trampolines can be found in many gardens and also in some playgrounds. They offer an easily accessible vertical motion that includes free fall. In this work, the motion on a trampoline is modelled by assuming a linear relation between force and deflection, giving harmonic oscillations for small amplitudes. An expression for the cycle-time is obtained in terms of maximum normalized force from the trampoline and the harmonic frequency. A simple expression is obtained for the ratio between air-time and harmonic period, and the maximum g-factor. The results are compared to experimental results, including accelerometer data showing 7g during bounces on a small trampoline in an amusement park play area. Similar results are obtained on a larger garden trampoline, and even larger accelerations have been measured for gymnastic trampolines.

Cellular reprogramming dynamics follow a simple 1D reaction coordinate

NASA Astrophysics Data System (ADS)

Teja Pusuluri, Sai; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

2018-01-01

Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a ‘barrier-crossing’ process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an ‘optimal path’ in gene expression space for reprogramming.

Cytokeratins in normal and malignant transitional epithelium. Maintenance of expression of urothelial differentiation features in transitional cell carcinomas and bladder carcinoma cell culture lines.

PubMed Central

Moll, R.; Achtstätter, T.; Becht, E.; Balcarova-Ständer, J.; Ittensohn, M.; Franke, W. W.

1988-01-01

The pattern of cytokeratins expressed in normal urothelium has been compared with that of various forms of transitional cell carcinomas (TCCs; 21 cases) and cultured bladder carcinoma cell lines, using immunolocalization and gel electrophoretic techniques. In normal urothelium, all simple-epithelium-type cytokeratins (polypeptides 7, 8, 18, 19) were detected in all cell layers, whereas antibodies to cytokeratins typical for stratified epithelia reacted with certain basal cells only or, in the case of cytokeratin 13, with cells of the basal and intermediate layers. This pattern was essentially maintained in low-grade (G1, G1/2) TCCs but was remarkably modified in G2 TCCs. In G3 TCCs simple-epithelial cytokeratins were predominant whereas the amounts of component 13 were greatly reduced. Squamous metaplasia was accompanied generally by increased or new expression of some stratified-epithelial cytokeratins. The cytokeratin patterns of cell culture lines RT-112 and RT-4 resembled those of G1 and G2 TCCs, whereas cell line T-24 was comparable to G3 carcinomas. The cell line EJ showed a markedly different pattern. The results indicate that, in the cell layers of the urothelium, the synthesis of stratification-related cytokeratins such as component 13 is inversely oriented compared with that in other stratified epithelia where these proteins are suprabasally expressed, that TCCs retain certain intrinsic cytoskeletal features of urothelium, and that different TCCs can be distinguished by their cytokeratin patterns. The potential value of these observations in histopathologic and cytologic diagnoses is discussed. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 PMID:2456018

Evaluation of bed load transport subject to high shear stress fluctuations

NASA Astrophysics Data System (ADS)

Cheng, Nian-Sheng; Tang, Hongwu; Zhu, Lijun

2004-05-01

Many formulas available in the literature for computing sediment transport rates are often expressed in terms of time mean variables such as time mean bed shear stress or flow velocity, while effects of turbulence intensity, e.g., bed shear stress fluctuation, on sediment transport were seldom considered. This may be due to the fact that turbulence fluctuation is relatively limited in laboratory open-channel flows, which are often used for conducting sediment transport experiments. However, turbulence intensity could be markedly enhanced in practice. This note presents an analytical method to compute bed load transport by including effects of fluctuations in the bed shear stress. The analytical results obtained show that the transport rate enhanced by turbulence can be expressed as a simple function of the relative fluctuation of the bed shear stress. The results are also verified using data that were collected recently from specifically designed laboratory experiments. The present analysis is applicable largely for the condition of a flat bed that is comprised of uniform sand particles subject to unidirectional flows.

Optimized theory for simple and molecular fluids.

PubMed

Marucho, M; Montgomery Pettitt, B

2007-03-28

An optimized closure approximation for both simple and molecular fluids is presented. A smooth interpolation between Perkus-Yevick and hypernetted chain closures is optimized by minimizing the free energy self-consistently with respect to the interpolation parameter(s). The molecular version is derived from a refinement of the method for simple fluids. In doing so, a method is proposed which appropriately couples an optimized closure with the variant of the diagrammatically proper integral equation recently introduced by this laboratory [K. M. Dyer et al., J. Chem. Phys. 123, 204512 (2005)]. The simplicity of the expressions involved in this proposed theory has allowed the authors to obtain an analytic expression for the approximate excess chemical potential. This is shown to be an efficient tool to estimate, from first principles, the numerical value of the interpolation parameters defining the aforementioned closure. As a preliminary test, representative models for simple fluids and homonuclear diatomic Lennard-Jones fluids were analyzed, obtaining site-site correlation functions in excellent agreement with simulation data.

77 FR 15371 - Announcement of Call for Collaborating Partners for National Women's Health Week

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-15

... expressions of interest by April 13, 2012. ADDRESSES: Expressions of interest, comments, and questions may be... simple steps for a longer, healthier, and happier life. For more information about National Women's...

Immunohistochemical analysis of cytokeratin and human milk fat globulin expression in mucinous carcinoma of the skin.

PubMed

Ohnishi, Takamitsu; Takizawa, Hajime; Watanabe, Shinichi

2002-01-01

Mucinous carcinoma of the skin (MCS) is a rare epithelial tumor which arises primarily in the skin. Metastatic MC from extracutaneous sites, especially breast or colon, mimics MCS and cannot be differentiated from MCS by routine histology alone. Nine cases of MCS were analyzed immunohistochemically using monoclonal antibodies against cytokeratins (CKs) and human milk fat globulin 1 (HMFG) in order to clarify their nature and compare the immunophenotypes with those of other MCs studied in the literature. Expression of simple epithelial CKs in most of the tumor cells of all cases studied and co-expression of simple and stratified epithelial CKs in some tumor cells of two cases were recognized. CK 20 expression could not detected in any tumor cells. Focal HMFG expression in the luminal or outer surface of the nests was observed in three cases. From CKs expression, MCS was speculated to differentiated mainly toward the secretory cells of the sweat glands, and some tumor cells toward the transient portion between the dermal duct and the secretory portion. Focal HMFG expression suggested either a consequence of malignant transformation or apocrine differentiation. No expression of CK 20 in MCS suggests that we may exclude the diagnosis of metastatic colorectal MC which expressed CK 20.

The NIST Simple Guide for Evaluating and Expressing Measurement Uncertainty

NASA Astrophysics Data System (ADS)

Possolo, Antonio

2016-11-01

NIST has recently published guidance on the evaluation and expression of the uncertainty of NIST measurement results [1, 2], supplementing but not replacing B. N. Taylor and C. E. Kuyatt's (1994) Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results (NIST Technical Note 1297) [3], which tracks closely the Guide to the expression of uncertainty in measurement (GUM) [4], originally published in 1995 by the Joint Committee for Guides in Metrology of the International Bureau of Weights and Measures (BIPM). The scope of this Simple Guide, however, is much broader than the scope of both NIST Technical Note 1297 and the GUM, because it attempts to address several of the uncertainty evaluation challenges that have arisen at NIST since the 1990s, for example to include molecular biology, greenhouse gases and climate science measurements, and forensic science. The Simple Guide also expands the scope of those two other guidance documents by recognizing observation equations (that is, statistical models) as bona fide measurement models. These models are indispensable to reduce data from interlaboratory studies, to combine measurement results for the same measurand obtained by different methods, and to characterize the uncertainty of calibration and analysis functions used in the measurement of force, temperature, or composition of gas mixtures. This presentation reviews the salient aspects of the Simple Guide, illustrates the use of models and methods for uncertainty evaluation not contemplated in the GUM, and also demonstrates the NIST Uncertainty Machine [5] and the NIST Consensus Builder, which are web-based applications accessible worldwide that facilitate evaluations of measurement uncertainty and the characterization of consensus values in interlaboratory studies.

The effects of gratitude expression on neural activity.

PubMed

Kini, Prathik; Wong, Joel; McInnis, Sydney; Gabana, Nicole; Brown, Joshua W

2016-03-01

Gratitude is a common aspect of social interaction, yet relatively little is known about the neural bases of gratitude expression, nor how gratitude expression may lead to longer-term effects on brain activity. To address these twin issues, we recruited subjects who coincidentally were entering psychotherapy for depression and/or anxiety. One group participated in a gratitude writing intervention, which required them to write letters expressing gratitude. The therapy-as-usual control group did not perform a writing intervention. After three months, subjects performed a "Pay It Forward" task in the fMRI scanner. In the task, subjects were repeatedly endowed with a monetary gift and then asked to pass it on to a charitable cause to the extent they felt grateful for the gift. Operationalizing gratitude as monetary gifts allowed us to engage the subjects and quantify the gratitude expression for subsequent analyses. We measured brain activity and found regions where activity correlated with self-reported gratitude experience during the task, even including related constructs such as guilt motivation and desire to help as statistical controls. These were mostly distinct from brain regions activated by empathy or theory of mind. Also, our between groups cross-sectional study found that a simple gratitude writing intervention was associated with significantly greater and lasting neural sensitivity to gratitude - subjects who participated in gratitude letter writing showed both behavioral increases in gratitude and significantly greater neural modulation by gratitude in the medial prefrontal cortex three months later. Copyright © 2015 Elsevier Inc. All rights reserved.

A convenient basis for the Izergin-Korepin model

NASA Astrophysics Data System (ADS)

Qiao, Yi; Zhang, Xin; Hao, Kun; Cao, Junpeng; Li, Guang-Liang; Yang, Wen-Li; Shi, Kangjie

2018-05-01

We propose a convenient orthogonal basis of the Hilbert space for the quantum spin chain associated with the A2(2) algebra (or the Izergin-Korepin model). It is shown that compared with the original basis the monodromy-matrix elements acting on this basis take relatively simple forms, which is quite similar as that for the quantum spin chain associated with An algebra in the so-called F-basis. As an application of our general results, we present the explicit recursive expressions of the Bethe states in this basis for the Izergin-Korepin model.

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.

PubMed

Gruel, Jérémy; LeBorgne, Michel; LeMeur, Nolwenn; Théret, Nathalie

2011-09-12

Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

PubMed Central

2011-01-01

Background Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Results Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Conclusions Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks. PMID:21910886

Acculturation matters in the relation between ambivalence over emotional expressions and well-being among Chinese American breast cancer survivors.

PubMed

Tsai, William; Lu, Qian

2017-10-01

Ambivalence over emotional expression (AEE) is the inner conflict of desiring emotion expression and fearing consequence of emotion expression. Few studies to date have examined the effects of AEE within an ethnic group that prioritizes emotional self-control. The present study examined the associations between AEE and well-being (viz., quality of life and depressive symptoms) as a function of acculturation among a sample of Chinese American breast cancer survivors. Ninety-six Chinese breast cancer survivors (M age  = 54.64 years old, SD = 7.98) were recruited from Southern California. Participants filled out a paper-pen questionnaire containing the Ambivalence over Emotional Expression Questionnaire (AEQ), the Functional Assessment of Cancer Therapy-Breast (FACT-B), and the Center for Epidemiologic Studies Depression Scale-Short Form (CESD-10). Acculturation was a statistically significant moderator of the relations between AEE and depressive symptoms, and a statistically marginally significant moderator of the relations between AEE and quality of life. Simple slopes revealed that AEE was negatively associated with quality of life (B = -.45, p < .001) and depressive symptoms (B = .20, p < .001) for women with high acculturation, but not associated for women with low acculturation (Bs = -.15 and .04, ps > .05, for quality of life and depressive symptoms, respectively). These results suggest that less acculturated Chinese breast cancer survivors are protected by Chinese cultural values of emotional self-control and restraint, and thus do not experience the detrimental effects of AEE on their depressive symptoms and quality of life. Implications are discussed.

GENE EXPRESSION NETWORKS

EPA Science Inventory

"Gene expression network" is the term used to describe the interplay, simple or complex, between two or more gene products in performing a specific cellular function. Although the delineation of such networks is complicated by the existence of multiple and subtle types of intera...

Microbial risk assessment in heterogeneous aquifers: 1. Pathogen transport

NASA Astrophysics Data System (ADS)

Molin, S.; Cvetkovic, V.

2010-05-01

Pathogen transport in heterogeneous aquifers is investigated for microbial risk assessment. A point source with time-dependent input of pathogens is assumed, exemplified as a simple on-site sanitation installation, intermingled with water supply wells. Any pathogen transmission pathway (realization) to the receptor from a postulated infection hazard is viewed as a random event, with the hydraulic conductivity varying spatially. For aquifers where VAR[lnK] < 1 and the integral scale is finite, we provide relatively simple semianalytical expressions for pathogen transport that incorporate the colloid filtration theory. We test a wide range of Damkohler numbers in order to assess the significance of rate limitations on the aquifer barrier function. Even slow immobile inactivation may notably affect the retention of pathogens. Analytical estimators for microbial peak discharge are evaluated and are shown to be applicable using parameters representative of rotavirus and Hepatitis A with input of 10-20 days duration.

Would you like to play together? Adults' attachment and the mirror game.

PubMed

Feniger-Schaal, Rinat; Noy, Lior; Hart, Yuval; Koren-Karie, Nina; Mayo, Avraham E; Alon, Uri

2016-01-01

Why is it easy for some people to play together and difficult for others? In this interdisciplinary pilot study, we looked at dyadic interaction in motion as a paradigm to explore the expression of attachment in adulthood. We used a device that gives simple, quantitative and automated indicators for the quality of interaction while playing the mirror game. Forty-seven participants played the mirror game with the same gender-matched expert players. In addition, participants were interviewed on the Adult Attachment Interview to assess their quality of attachment. Using high resolution kinematic measures, we found that secure attachment was correlated with high complexity of the game and low synchrony compared to insecure attachment. The findings suggest that security of attachment is related to a more exploratory and less rigid game than insecure-dismissing attachment. These preliminary findings imply that high resolution analysis of simple movement interaction could carry information about attachment behavior.

Asymptotic Linear Spectral Statistics for Spiked Hermitian Random Matrices

NASA Astrophysics Data System (ADS)

Passemier, Damien; McKay, Matthew R.; Chen, Yang

2015-07-01

Using the Coulomb Fluid method, this paper derives central limit theorems (CLTs) for linear spectral statistics of three "spiked" Hermitian random matrix ensembles. These include Johnstone's spiked model (i.e., central Wishart with spiked correlation), non-central Wishart with rank-one non-centrality, and a related class of non-central matrices. For a generic linear statistic, we derive simple and explicit CLT expressions as the matrix dimensions grow large. For all three ensembles under consideration, we find that the primary effect of the spike is to introduce an correction term to the asymptotic mean of the linear spectral statistic, which we characterize with simple formulas. The utility of our proposed framework is demonstrated through application to three different linear statistics problems: the classical likelihood ratio test for a population covariance, the capacity analysis of multi-antenna wireless communication systems with a line-of-sight transmission path, and a classical multiple sample significance testing problem.

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages

NASA Astrophysics Data System (ADS)

Tian, Caihong; Tek Tay, Wee; Feng, Hongqiang; Wang, Ying; Hu, Yongmin; Li, Guoping

2015-06-01

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages

PubMed Central

Tian, Caihong; Tek Tay, Wee; Feng, Hongqiang; Wang, Ying; Hu, Yongmin; Li, Guoping

2015-01-01

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs. PMID:26047353

dREL: a relational expression language for dictionary methods.

PubMed

Spadaccini, Nick; Castleden, Ian R; du Boulay, Doug; Hall, Sydney R

2012-08-27

The provision of precise metadata is an important but a largely underrated challenge for modern science [Nature 2009, 461, 145]. We describe here a dictionary methods language dREL that has been designed to enable complex data relationships to be expressed as formulaic scripts in data dictionaries written in DDLm [Spadaccini and Hall J. Chem. Inf. Model.2012 doi:10.1021/ci300075z]. dREL describes data relationships in a simple but powerful canonical form that is easy to read and understand and can be executed computationally to evaluate or validate data. The execution of dREL expressions is not a substitute for traditional scientific computation; it is to provide precise data dependency information to domain-specific definitions and a means for cross-validating data. Some scientific fields apply conventional programming languages to methods scripts but these tend to inhibit both dictionary development and accessibility. dREL removes the programming barrier and encourages the production of the metadata needed for seamless data archiving and exchange in science.

Simple expression for the quantum Fisher information matrix

NASA Astrophysics Data System (ADS)

Šafránek, Dominik

2018-04-01

Quantum Fisher information matrix (QFIM) is a cornerstone of modern quantum metrology and quantum information geometry. Apart from optimal estimation, it finds applications in description of quantum speed limits, quantum criticality, quantum phase transitions, coherence, entanglement, and irreversibility. We derive a surprisingly simple formula for this quantity, which, unlike previously known general expression, does not require diagonalization of the density matrix, and is provably at least as efficient. With a minor modification, this formula can be used to compute QFIM for any finite-dimensional density matrix. Because of its simplicity, it could also shed more light on the quantum information geometry in general.

Evolving phage vectors for cell targeted gene delivery.

PubMed

Larocca, David; Burg, Michael A; Jensen-Pergakes, Kristen; Ravey, Edward Prenn; Gonzalez, Ana Maria; Baird, Andrew

2002-03-01

We adapted filamentous phage vectors for targeted gene delivery to mammalian cells by inserting a mammalian reporter gene expression cassette (GFP) into the vector backbone and fusing the pIII coat protein to a cell targeting ligand (i.e. FGF2, EGF). Like transfection with animal viral vectors, targeted phage gene delivery is concentration, time, and ligand dependent. Importantly, targeted phage particles are specific for the appropriate target cell surface receptor. Phage have distinct advantages over existing gene therapy vectors because they are simple, economical to produce at high titer, have no intrinsic tropism for mammalian cells, and are relatively simple to genetically modify and evolve. Initially transduction by targeted phage particles was low resulting in foreign gene expression in 1-2% of transfected cells. We increased transduction efficiency by modifying both the transfection protocol and vector design. For example, we stabilized the display of the targeting ligand to create multivalent phagemid-based vectors with transduction efficiencies of up to 45% in certain cell lines when combined with genotoxic treatment. Taken together, these studies establish that the efficiency of phage-mediated gene transfer can be significantly improved through genetic modification. We are currently evolving phage vectors with enhanced cell targeting, increased stability, reduced immunogenicity and other properties suitable for gene therapy.

Unmixing of spectral components affecting AVIRIS imagery of Tampa Bay

NASA Astrophysics Data System (ADS)

Carder, Kendall L.; Lee, Z. P.; Chen, Robert F.; Davis, Curtiss O.

1993-09-01

According to Kirk's as well as Morel and Gentili's Monte Carlo simulations, the popular simple expression, R approximately equals 0.33 bb/a, relating subsurface irradiance reflectance (R) to the ratio of the backscattering coefficient (bb) to absorption coefficient (a), is not valid for bb/a > 0.25. This means that it may no longer be valid for values of remote-sensing reflectance (above-surface ratio of water-leaving radiance to downwelling irradiance) where Rrs4/ > 0.01. Since there has been no simple Rrs expression developed for very turbid waters, we developed one based in part on Monte Carlo simulations and empirical adjustments to an Rrs model and applied it to rather turbid coastal waters near Tampa Bay to evaluate its utility for unmixing the optical components affecting the water- leaving radiance. With the high spectral (10 nm) and spatial (20 m2) resolution of Airborne Visible-InfraRed Imaging Spectrometer (AVIRIS) data, the water depth and bottom type were deduced using the model for shallow waters. This research demonstrates the necessity of further research to improve interpretations of scenes with highly variable turbid waters, and it emphasizes the utility of high spectral-resolution data as from AVIRIS for better understanding complicated coastal environments such as the west Florida shelf.

Noise in gene expression is coupled to growth rate.

PubMed

Keren, Leeat; van Dijk, David; Weingarten-Gabbay, Shira; Davidi, Dan; Jona, Ghil; Weinberger, Adina; Milo, Ron; Segal, Eran

2015-12-01

Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle-regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications. © 2015 Keren et al.; Published by Cold Spring Harbor Laboratory Press.

Noise in gene expression is coupled to growth rate

PubMed Central

Keren, Leeat; van Dijk, David; Weingarten-Gabbay, Shira; Davidi, Dan; Jona, Ghil; Weinberger, Adina; Milo, Ron; Segal, Eran

2015-01-01

Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle–regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications. PMID:26355006

A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays.

PubMed

McLachlan, G J; Bean, R W; Jones, L Ben-Tovim

2006-07-01

An important problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. We provide a straightforward and easily implemented method for estimating the posterior probability that an individual gene is null. The problem can be expressed in a two-component mixture framework, using an empirical Bayes approach. Current methods of implementing this approach either have some limitations due to the minimal assumptions made or with more specific assumptions are computationally intensive. By converting to a z-score the value of the test statistic used to test the significance of each gene, we propose a simple two-component normal mixture that models adequately the distribution of this score. The usefulness of our approach is demonstrated on three real datasets.

Swearing, Euphemisms, and Linguistic Relativity

PubMed Central

Bowers, Jeffrey S.; Pleydell-Pearce, Christopher W.

2011-01-01

Participants read aloud swear words, euphemisms of the swear words, and neutral stimuli while their autonomic activity was measured by electrodermal activity. The key finding was that autonomic responses to swear words were larger than to euphemisms and neutral stimuli. It is argued that the heightened response to swear words reflects a form of verbal conditioning in which the phonological form of the word is directly associated with an affective response. Euphemisms are effective because they replace the trigger (the offending word form) by another word form that expresses a similar idea. That is, word forms exert some control on affect and cognition in turn. We relate these findings to the linguistic relativity hypothesis, and suggest a simple mechanistic account of how language may influence thinking in this context. PMID:21799832

Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii

PubMed Central

Zhang, Shouan; Gao, Muqiang; Zaitlin, David

2012-01-01

Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a “modified backcross” involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062 cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina. PMID:22936937

Structure of the conversion laws in quantum integrable spin chains with short range interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grabowski, M.P.; Mathieu, P.

1995-11-01

The authors present a detailed analysis of the structure of the conservation laws in quantum integrable chains of the XYZ-type and in the Hubbard model. The essential tool for the former class of models is the boost operator, which provides a recursive way of calculating the integrals of motion. With its help, they establish the general form of the XYZ conserved charges in terms of simple polynomials in spin variables and derive recursion relations for the relative coefficients of these polynomials. Although these relations are difficult to solve in general, a subset of the coefficients can be determined. Moreover, formore » two submodels of the XYZ chain, namely the XXX and XY cases, all the charges can be calculated in closed form. Using this approach, the authors rederive the known expressions for the XY charges in a novel way. For the XXX case. a simple description of conserved charges is found in terms of a Catalan tree. This construction is generalized for the su(M) invariant integrable chain. They also investigate the circumstances permitting the existence of a recursive (ladder) operator in general quantum integrable systems. They indicate that a quantum ladder operator can be traced back to the presence of a Hamiltonian mastersymmetry of degree one in the classical continuous version of the model. In this way, quantum chains endowed with a recursive structure can be identified from the properties of their classical relatives. The authors also show that in the quantum continuous limits of the XYZ model, the ladder property of the boost operator disappears. For the Hubbard model they demonstrate the nonexistence of a ladder operator. Nevertheless, the general structure of the conserved charges is indicated, and the expression for the terms linear in the model`s free parameter for all charges is derived in closed form. 62 refs., 4 figs.« less

Regulation of nitrogen metabolism by GATA zinc finger transcription factors in Yarrowia lipolytica

DOE PAGES

Pomraning, Kyle R.; Bredeweg, Erin L.; Baker, Scott E.; ...

2017-02-15

Here, fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeast Yarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism in Y. lipolytica. Deletion of the GATA transcription factor genes gzf3 and gzf2 resulted in nitrogen source-specific growth defects and greatermore » accumulation of lipids when the cells were growing on a simple nitrogen source. Deletion of gzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion of gzf3 results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, while gzf2 is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressor mig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism.« less

Regulation of nitrogen metabolism by GATA zinc finger transcription factors in Yarrowia lipolytica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pomraning, Kyle R.; Bredeweg, Erin L.; Baker, Scott E.

Here, fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeast Yarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism in Y. lipolytica. Deletion of the GATA transcription factor genes gzf3 and gzf2 resulted in nitrogen source-specific growth defects and greatermore » accumulation of lipids when the cells were growing on a simple nitrogen source. Deletion of gzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion of gzf3 results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, while gzf2 is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressor mig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism.« less

s -wave scattering length of a Gaussian potential

NASA Astrophysics Data System (ADS)

Jeszenszki, Peter; Cherny, Alexander Yu.; Brand, Joachim

2018-04-01

We provide accurate expressions for the s -wave scattering length for a Gaussian potential well in one, two, and three spatial dimensions. The Gaussian potential is widely used as a pseudopotential in the theoretical description of ultracold-atomic gases, where the s -wave scattering length is a physically relevant parameter. We first describe a numerical procedure to compute the value of the s -wave scattering length from the parameters of the Gaussian, but find that its accuracy is limited in the vicinity of singularities that result from the formation of new bound states. We then derive simple analytical expressions that capture the correct asymptotic behavior of the s -wave scattering length near the bound states. Expressions that are increasingly accurate in wide parameter regimes are found by a hierarchy of approximations that capture an increasing number of bound states. The small number of numerical coefficients that enter these expressions is determined from accurate numerical calculations. The approximate formulas combine the advantages of the numerical and approximate expressions, yielding an accurate and simple description from the weakly to the strongly interacting limit.

Understanding network concepts in modules

PubMed Central

2007-01-01

Background Network concepts are increasingly used in biology and genetics. For example, the clustering coefficient has been used to understand network architecture; the connectivity (also known as degree) has been used to screen for cancer targets; and the topological overlap matrix has been used to define modules and to annotate genes. Dozens of potentially useful network concepts are known from graph theory. Results Here we study network concepts in special types of networks, which we refer to as approximately factorizable networks. In these networks, the pairwise connection strength (adjacency) between 2 network nodes can be factored into node specific contributions, named node 'conformity'. The node conformity turns out to be highly related to the connectivity. To provide a formalism for relating network concepts to each other, we define three types of network concepts: fundamental-, conformity-based-, and approximate conformity-based concepts. Fundamental concepts include the standard definitions of connectivity, density, centralization, heterogeneity, clustering coefficient, and topological overlap. The approximate conformity-based analogs of fundamental network concepts have several theoretical advantages. First, they allow one to derive simple relationships between seemingly disparate networks concepts. For example, we derive simple relationships between the clustering coefficient, the heterogeneity, the density, the centralization, and the topological overlap. The second advantage of approximate conformity-based network concepts is that they allow one to show that fundamental network concepts can be approximated by simple functions of the connectivity in module networks. Conclusion Using protein-protein interaction, gene co-expression, and simulated data, we show that a) many networks comprised of module nodes are approximately factorizable and b) in these types of networks, simple relationships exist between seemingly disparate network concepts. Our results are implemented in freely available R software code, which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/ModuleConformity/ModuleNetworks PMID:17547772

Task-dependent and task-independent neurovascular responses to syntactic processing⋆

PubMed Central

Caplan, David; Chen, Evan; Waters, Gloria

2008-01-01

The neural basis for syntactic processing was studied using event-related fMRI to determine the locations of BOLD signal increases in the contrast of syntactically complex sentences with center-embedded, object-extracted relative clauses and syntactically simple sentences with right-branching, subject-extracted relative clauses in a group of 15 participants in three tasks. In a sentence verification task, participants saw a target sentence in one of these two syntactic forms, followed by a probe in a simple active form, and determined whether the probe expressed a proposition in the target. In a plausibility judgment task, participants determined whether a sentence in one of these two syntactic forms was plausible or implausible. Finally, in a non-word detection task, participants determined whether a sentence in one of these two syntactic forms contained only real words or a non-word. BOLD signal associated with the syntactic contrast increased in the left posterior inferior frontal gyrus in non-word detection and in a widespread set of areas in the other two tasks. We conclude that the BOLD activity in the left posterior inferior frontal gyrus reflects syntactic processing independent of concurrent cognitive operations and the more widespread areas of activation reflect the use of strategies and the use of the products of syntactic processing to accomplish tasks. PMID:18387556

Method for Constructing Composite Response Surfaces by Combining Neural Networks with Polynominal Interpolation or Estimation Techniques

NASA Technical Reports Server (NTRS)

Rai, Man Mohan (Inventor); Madavan, Nateri K. (Inventor)

2007-01-01

A method and system for data modeling that incorporates the advantages of both traditional response surface methodology (RSM) and neural networks is disclosed. The invention partitions the parameters into a first set of s simple parameters, where observable data are expressible as low order polynomials, and c complex parameters that reflect more complicated variation of the observed data. Variation of the data with the simple parameters is modeled using polynomials; and variation of the data with the complex parameters at each vertex is analyzed using a neural network. Variations with the simple parameters and with the complex parameters are expressed using a first sequence of shape functions and a second sequence of neural network functions. The first and second sequences are multiplicatively combined to form a composite response surface, dependent upon the parameter values, that can be used to identify an accurate mode

Experience-based human perception of facial expressions in Barbary macaques (Macaca sylvanus).

PubMed

Maréchal, Laëtitia; Levy, Xandria; Meints, Kerstin; Majolo, Bonaventura

2017-01-01

Facial expressions convey key cues of human emotions, and may also be important for interspecies interactions. The universality hypothesis suggests that six basic emotions (anger, disgust, fear, happiness, sadness, and surprise) should be expressed by similar facial expressions in close phylogenetic species such as humans and nonhuman primates. However, some facial expressions have been shown to differ in meaning between humans and nonhuman primates like macaques. This ambiguity in signalling emotion can lead to an increased risk of aggression and injuries for both humans and animals. This raises serious concerns for activities such as wildlife tourism where humans closely interact with wild animals. Understanding what factors (i.e., experience and type of emotion) affect ability to recognise emotional state of nonhuman primates, based on their facial expressions, can enable us to test the validity of the universality hypothesis, as well as reduce the risk of aggression and potential injuries in wildlife tourism. The present study investigated whether different levels of experience of Barbary macaques, Macaca sylvanus , affect the ability to correctly assess different facial expressions related to aggressive, distressed, friendly or neutral states, using an online questionnaire. Participants' level of experience was defined as either: (1) naïve: never worked with nonhuman primates and never or rarely encountered live Barbary macaques; (2) exposed: shown pictures of the different Barbary macaques' facial expressions along with the description and the corresponding emotion prior to undertaking the questionnaire; (3) expert: worked with Barbary macaques for at least two months. Experience with Barbary macaques was associated with better performance in judging their emotional state. Simple exposure to pictures of macaques' facial expressions improved the ability of inexperienced participants to better discriminate neutral and distressed faces, and a trend was found for aggressive faces. However, these participants, even when previously exposed to pictures, had difficulties in recognising aggressive, distressed and friendly faces above chance level. These results do not support the universality hypothesis as exposed and naïve participants had difficulties in correctly identifying aggressive, distressed and friendly faces. Exposure to facial expressions improved their correct recognition. In addition, the findings suggest that providing simple exposure to 2D pictures (for example, information signs explaining animals' facial signalling in zoos or animal parks) is not a sufficient educational tool to reduce tourists' misinterpretations of macaque emotion. Additional measures, such as keeping a safe distance between tourists and wild animals, as well as reinforcing learning via videos or supervised visits led by expert guides, could reduce such issues and improve both animal welfare and tourist experience.

Make Your Workflows Smarter

NASA Technical Reports Server (NTRS)

Jones, Corey; Kapatos, Dennis; Skradski, Cory

2012-01-01

Do you have workflows with many manual tasks that slow down your business? Or, do you scale back workflows because there are simply too many manual tasks? Basic workflow robots can automate some common tasks, but not everything. This presentation will show how advanced robots called "expression robots" can be set up to perform everything from simple tasks such as: moving, creating folders, renaming, changing or creating an attribute, and revising, to more complex tasks like: creating a pdf, or even launching a session of Creo Parametric and performing a specific modeling task. Expression robots are able to utilize the Java API and Info*Engine to do almost anything you can imagine! Best of all, these tools are supported by PTC and will work with later releases of Windchill. Limited knowledge of Java, Info*Engine, and XML are required. The attendee will learn what task expression robots are capable of performing. The attendee will learn what is involved in setting up an expression robot. The attendee will gain a basic understanding of simple Info*Engine tasks

A statistical method for measuring activation of gene regulatory networks.

PubMed

Esteves, Gustavo H; Reis, Luiz F L

2018-06-13

Gene expression data analysis is of great importance for modern molecular biology, given our ability to measure the expression profiles of thousands of genes and enabling studies rooted in systems biology. In this work, we propose a simple statistical model for the activation measuring of gene regulatory networks, instead of the traditional gene co-expression networks. We present the mathematical construction of a statistical procedure for testing hypothesis regarding gene regulatory network activation. The real probability distribution for the test statistic is evaluated by a permutation based study. To illustrate the functionality of the proposed methodology, we also present a simple example based on a small hypothetical network and the activation measuring of two KEGG networks, both based on gene expression data collected from gastric and esophageal samples. The two KEGG networks were also analyzed for a public database, available through NCBI-GEO, presented as Supplementary Material. This method was implemented in an R package that is available at the BioConductor project website under the name maigesPack.

Association of cancer metabolism-related proteins with oral carcinogenesis – indications for chemoprevention and metabolic sensitizing of oral squamous cell carcinoma?

PubMed Central

2014-01-01

Background Tumor metabolism is a crucial factor for the carcinogenesis of oral squamous cell carcinoma (OSCC). Methods Expression of IGF-R1, glycolysis-related proteins (GLUT-1, HK 2, PFK-1, LDHA, TKTL1), mitochondrial enzymes (SDHA, SDHB, ATP synthase) were analyzed in normal oral mucosa (n = 5), oral precursor lesions (simple hyperplasia, n = 11; squamous intraepithelial neoplasia, SIN I-III, n = 35), and OSCC specimen (n = 42) by immunohistochemistry and real-time polymerase chain reaction (qPCR) analysis in OSCC cell lines. Metabolism-related proteins were correlated with proliferation activity (Ki-67) and apoptotic properties (TUNEL assay) in OSCC. Specificity of antibodies was confirmed by western blotting in cancer cell lines. Results Expression of IGF-R1, glycolysis-related proteins (GLUT-1, HK 2, LDHA, TKTL1), and mitochondrial enzymes (SDHA, SDHB, ATP synthase) were significantly increased in the carcinogenesis of OSCC. Metabolic active regions of OSCC were strongly correlated with proliferating cancer (Ki-67+) cells without detection of apoptosis (TUNEL assay). Conclusions This study provides the first evidence of the expression of IGF-R1, glycolysis-related proteins GLUT-1, HK 2, PFK-1, LDHA, and TKTL1, as well as mitochondrial enzymes SDHA, SDHB, and ATP synthase in the multi-step carcinogenesis of OSCC. Both, hypoxia-related glucose metabolism and mitochondrial oxidative phosphorylation characteristics are associated with the carcinogenesis of OSCC. Acidosis and OXPHOS may drive a metabolic shift towards the pentose phosphate pathway (PPP). Therefore, inhibition of the PPP, glycolysis, and targeted anti-mitochondrial therapies (ROS generation) by natural compounds or synthetic vitamin derivatives may act as sensitizer for apoptosis in cancer cells mediated by adjuvant therapies in OSCC. PMID:25048361

A Simple Method for Constructing Artificial Promoters Activated in Response to Ultrasound Stimulation.

PubMed

Ogawa, Ryohei; Kagiya, Go; Watanabe, Akihiko; Morii, Akihiro; Cui, Zheng-Guo; Kondo, Takashi

2017-01-01

It has been pointed out that ultrasound could be used as a controller for bioprocesses including gene expression since its energy can noninvasively reach deep in the body. Gene expression may be timely and spatially controlled by ultrasound, thus providing necessary bioactive proteins for the targeted tissue in a timely fashion. Although there are many processes involved in gene expression control, one of the most important processes is transcription, and the promoter plays an essential role in it. There are several promoters known to be activated in response to ultrasound irradiation . However, in our opinion, an artificial promoter is more suitable for clinical use. We herein describe simple methods to construct promoters that are responsive to ultrasound irradiation by randomly combining cis-elements (transcription factor binding motifs) and thereby improve its reactivity to ultrasound irradiation .

Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.

PubMed

Bekiaris, Pavlos Stephanos; Tekath, Tobias; Staiger, Dorothee; Danisman, Selahattin

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.

Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

PubMed Central

Staiger, Dorothee

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, “Exploration of Distinctive CREs and CRMs” (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, “CRM Network Generator” (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression. PMID:29298348

A simple framework for relating variations in runoff to variations in climatic conditions and catchment properties

NASA Astrophysics Data System (ADS)

Roderick, Michael L.; Farquhar, Graham D.

2011-12-01

We use the Budyko framework to calculate catchment-scale evapotranspiration (E) and runoff (Q) as a function of two climatic factors, precipitation (P) and evaporative demand (Eo = 0.75 times the pan evaporation rate), and a third parameter that encodes the catchment properties (n) and modifies how P is partitioned between E and Q. This simple theory accurately predicted the long-term evapotranspiration (E) and runoff (Q) for the Murray-Darling Basin (MDB) in southeast Australia. We extend the theory by developing a simple and novel analytical expression for the effects on E and Q of small perturbations in P, Eo, and n. The theory predicts that a 10% change in P, with all else constant, would result in a 26% change in Q in the MDB. Future climate scenarios (2070-2099) derived using Intergovernmental Panel on Climate Change AR4 climate model output highlight the diversity of projections for P (±30%) with a correspondingly large range in projections for Q (±80%) in the MDB. We conclude with a qualitative description about the impact of changes in catchment properties on water availability and focus on the interaction between vegetation change, increasing atmospheric [CO2], and fire frequency. We conclude that the modern version of the Budyko framework is a useful tool for making simple and transparent estimates of changes in water availability.

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.

PubMed

Rue-Albrecht, Kévin; McGettigan, Paul A; Hernández, Belinda; Nalpas, Nicolas C; Magee, David A; Parnell, Andrew C; Gordon, Stephen V; MacHugh, David E

2016-03-11

Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.

Collaboratively Conceived, Designed and Implemented: Matching Visualization Tools with Geoscience Data Collections and Geoscience Data Collections with Visualization Tools via the ToolMatch Service.

NASA Astrophysics Data System (ADS)

Hoebelheinrich, N. J.; Lynnes, C.; West, P.; Ferritto, M.

2014-12-01

Two problems common to many geoscience domains are the difficulties in finding tools to work with a given dataset collection, and conversely, the difficulties in finding data for a known tool. A collaborative team from the Earth Science Information Partnership (ESIP) has gotten together to design and create a web service, called ToolMatch, to address these problems. The team began their efforts by defining an initial, relatively simple conceptual model that addressed the two uses cases briefly described above. The conceptual model is expressed as an ontology using OWL (Web Ontology Language) and DCterms (Dublin Core Terms), and utilizing standard ontologies such as DOAP (Description of a Project), FOAF (Friend of a Friend), SKOS (Simple Knowledge Organization System) and DCAT (Data Catalog Vocabulary). The ToolMatch service will be taking advantage of various Semantic Web and Web standards, such as OpenSearch, RESTful web services, SWRL (Semantic Web Rule Language) and SPARQL (Simple Protocol and RDF Query Language). The first version of the ToolMatch service was deployed in early fall 2014. While more complete testing is required, a number of communities besides ESIP member organizations have expressed interest in collaborating to create, test and use the service and incorporate it into their own web pages, tools and / or services including the USGS Data Catalog service, DataONE, the Deep Carbon Observatory, Virtual Solar Terrestrial Observatory (VSTO), and the U.S. Global Change Research Program. In this session, presenters will discuss the inception and development of the ToolMatch service, the collaborative process used to design, refine, and test the service, and future plans for the service.

Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.

PubMed

Chao, Anne; Jost, Lou; Hsieh, T C; Ma, K H; Sherwin, William B; Rollins, Lee Ann

2015-01-01

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Simple suspension culture system of human iPS cells maintaining their pluripotency for cardiac cell sheet engineering.

PubMed

Haraguchi, Yuji; Matsuura, Katsuhisa; Shimizu, Tatsuya; Yamato, Masayuki; Okano, Teruo

2015-12-01

In this study, a simple three-dimensional (3D) suspension culture method for the expansion and cardiac differentiation of human induced pluripotent stem cells (hiPSCs) is reported. The culture methods were easily adapted from two-dimensional (2D) to 3D culture without any additional manipulations. When hiPSCs were directly applied to 3D culture from 2D in a single-cell suspension, only a few aggregated cells were observed. However, after 3 days, culture of the small hiPSC aggregates in a spinner flask at the optimal agitation rate created aggregates which were capable of cell passages from the single-cell suspension. Cell numbers increased to approximately 10-fold after 12 days of culture. The undifferentiated state of expanded hiPSCs was confirmed by flow cytometry, immunocytochemistry and quantitative RT-PCR, and the hiPSCs differentiated into three germ layers. When the hiPSCs were subsequently cultured in a flask using cardiac differentiation medium, expression of cardiac cell-specific genes and beating cardiomyocytes were observed. Furthermore, the culture of hiPSCs on Matrigel-coated dishes with serum-free medium containing activin A, BMP4 and FGF-2 enabled it to generate robust spontaneous beating cardiomyocytes and these cells expressed several cardiac cell-related genes, including HCN4, MLC-2a and MLC-2v. This suggests that the expanded hiPSCs might maintain the potential to differentiate into several types of cardiomyocytes, including pacemakers. Moreover, when cardiac cell sheets were fabricated using differentiated cardiomyocytes, they beat spontaneously and synchronously, indicating electrically communicative tissue. This simple culture system might enable the generation of sufficient amounts of beating cardiomyocytes for use in cardiac regenerative medicine and tissue engineering. Copyright © 2013 John Wiley & Sons, Ltd.

A simple expression for quantifying bacterial chemotaxis using capillary assay data: application to the analysis of enhanced chemotactic responses from growth-limited cultures.

PubMed

Ford, R M; Lauffenburger, D A

1992-05-01

An individual cell-based mathematical model of Rivero et al. provides a framework for determining values of the chemotactic sensitivity coefficient chi 0, an intrinsic cell population parameter that characterizes the chemotactic response of bacterial populations. This coefficient can theoretically relate the swimming behavior of individual cells to the resulting migration of a bacterial population. When this model is applied to the commonly used capillary assay, an approximate solution can be obtained for a particular range of chemotactic strengths yielding a very simple analytical expression for estimating the value of chi 0, [formula: see text] from measurements of cell accumulation in the capillary, N, when attractant uptake is negligible. A0 and A infinity are the dimensionless attractant concentrations initially present at the mouth of the capillary and far into the capillary, respectively, which are scaled by Kd, the effective dissociation constant for receptor-attractant binding. D is the attractant diffusivity, and mu is the cell random motility coefficient. NRM is the cell accumulation in the capillary in the absence of an attractant gradient, from which mu can be determined independently as mu = (pi/4t)(NRM/pi r2bc)2, with r the capillary tube radius and bc the bacterial density initially in the chamber. When attractant uptake is significant, a slightly more involved procedure requiring a simple numerical integration becomes necessary. As an example, we apply this approach to quantitatively characterize, in terms of the chemotactic sensitivity coefficient chi 0, data from Terracciano indicating enhanced chemotactic responses of Escherichia coli to galactose when cultured under growth-limiting galactose levels in a chemostat.

Functional network in posttranslational modifications: Glyco-Net in Glycoconjugate Data Bank.

PubMed

Miura, Nobuaki; Okada, Takuya; Murayama, Daisuke; Hirose, Kazuko; Sato, Taku; Hashimoto, Ryo; Fukushima, Nobuhiro

2015-01-01

Elucidating pathways related to posttranslational modifications (PTMs) such as glycosylation is of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids, and various biological events, are considered extremely valuable and convenient tools for the systematic investigation of PTMs. Glyco-Net (http://bibi.sci.hokudai.ac.jp/functions/) can dynamically make network figures among various biological molecules and biological events. A certain molecule or event is expressed with a node, and the relationship between the molecule and the event is indicated by arrows in the network figures. In this chapter, we mention the features and current status of the Glyco-Net and a simple example of the search with the Glyco-Net.

Dynamics of entanglement and uncertainty relation in coupled harmonic oscillator system: exact results

NASA Astrophysics Data System (ADS)

Park, DaeKil

2018-06-01

The dynamics of entanglement and uncertainty relation is explored by solving the time-dependent Schrödinger equation for coupled harmonic oscillator system analytically when the angular frequencies and coupling constant are arbitrarily time dependent. We derive the spectral and Schmidt decompositions for vacuum solution. Using the decompositions, we derive the analytical expressions for von Neumann and Rényi entropies. Making use of Wigner distribution function defined in phase space, we derive the time dependence of position-momentum uncertainty relations. To show the dynamics of entanglement and uncertainty relation graphically, we introduce two toy models and one realistic quenched model. While the dynamics can be conjectured by simple consideration in the toy models, the dynamics in the realistic quenched model is somewhat different from that in the toy models. In particular, the dynamics of entanglement exhibits similar pattern to dynamics of uncertainty parameter in the realistic quenched model.

Leveraging the UML Metamodel: Expressing ORM Semantics Using a UML Profile

DOE Office of Scientific and Technical Information (OSTI.GOV)

CUYLER,DAVID S.

2000-11-01

Object Role Modeling (ORM) techniques produce a detailed domain model from the perspective of the business owner/customer. The typical process begins with a set of simple sentences reflecting facts about the business. The output of the process is a single model representing primarily the persistent information needs of the business. This type of model contains little, if any reference to a targeted computerized implementation. It is a model of business entities not of software classes. Through well-defined procedures, an ORM model can be transformed into a high quality objector relational schema.

A Transversely Isotropic Thermoelastic Theory

NASA Technical Reports Server (NTRS)

Arnold, S. M.

1989-01-01

A continuum theory is presented for representing the thermoelastic behavior of composites that can be idealized as transversely isotropic. This theory is consistent with anisotropic viscoplastic theories being developed presently at NASA Lewis Research Center. A multiaxial statement of the theory is presented, as well as plane stress and plane strain reductions. Experimental determination of the required material parameters and their theoretical constraints are discussed. Simple homogeneously stressed elements are examined to illustrate the effect of fiber orientation on the resulting strain distribution. Finally, the multiaxial stress-strain relations are expressed in matrix form to simplify and accelerate implementation of the theory into structural analysis codes.

The neutronic basis for elemental substitution in martensitic steels

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Butterworth, G. J.

1994-09-01

A simple graphical approach has been developed to facilitate the design of low-activation steels by elemental tailoring. Noting that the iron base provides the best achievable target, the influence of candidate alloying elements becomes readily apparent when the contribution each makes to a particular activation parameter such as specific activity, dose rate or decay power, is expressed relative to the contribution from the iron base. This approach highlights the most critical activation parameters and times after shutdown with respect to safety and environmental objectives. Its application to the design of low activation martensitic stainless steels is discussed.

Note on the stability of viscous roll waves

NASA Astrophysics Data System (ADS)

Barker, Blake; Johnson, Mathew A.; Noble, Pascal; Rodrigues, Luis Miguel; Zumbrun, Kevin

2017-02-01

In this note, we announce a complete classification of the stability of periodic roll-wave solutions of the viscous shallow water equations, from their onset at Froude number F ≈ 2 up to the infinite Froude limit. For intermediate Froude numbers, we obtain numerically a particularly simple power-law relation between F and the boundaries of the region of stable periods, which appears potentially useful in hydraulic engineering applications. In the asymptotic regime F → 2 (onset), we provide an analytic expression of the stability boundaries, whereas in the limit F → ∞, we show that roll waves are always unstable.

Efficiency equations of the railgun

NASA Astrophysics Data System (ADS)

Sadedin, D. R.

1984-03-01

The feasibility of an employment of railguns for large scale applications, such as space launching, will ultimately be determined by efficiency considerations. The present investigation is concerned with the calculation of the efficiencies for constant current railguns. Elementary considerations are discussed, taking into account a simple condition for high efficiency, the magnetic field of the rails, and the acceleration force on the projectile. The loss in a portion of the rails is considered along with rail loss comparisons, applications to the segmented gun, rail losses related to the constant resistance per unit length, efficiency expressions, and arc, or muzzle voltage energy.

On the analytical form of the Earth's magnetic attraction expressed as a function of time

NASA Technical Reports Server (NTRS)

Carlheim-Gyllenskold, V.

1983-01-01

An attempt is made to express the Earth's magnetic attraction in simple analytical form using observations during the 16th to 19th centuries. Observations of the magnetic inclination in the 16th and 17th centuries are discussed.

A combinatorial model of malware diffusion via bluetooth connections.

PubMed

Merler, Stefano; Jurman, Giuseppe

2013-01-01

We outline here the mathematical expression of a diffusion model for cellphones malware transmitted through Bluetooth channels. In particular, we provide the deterministic formula underlying the proposed infection model, in its equivalent recursive (simple but computationally heavy) and closed form (more complex but efficiently computable) expression.

Hepatic gene expression of Caucasian and African-American patients with obesity-related non-alcoholic fatty liver disease.

PubMed

Stepanova, Maria; Hossain, Noreen; Afendy, Arian; Perry, Kellie; Goodman, Zachary D; Baranova, Ancha; Younossi, Zobair

2010-05-01

There is increasing data suggesting that African Americans with NAFLD tend to have less progressive liver disease. The aim of this study is to assess differences in the hepatic gene expression of African-American and Caucasian patients with NAFLD who had undergone bariatric surgery. A total of 94 patients (81 NAFLD and 13 weight-matched controls with normal liver biopsy) were included. Of the entire cohort, 73 were Caucasians and 21 were African Americans. All patients were undergoing bariatric surgery. Two liver biopsies were obtained at the time of surgery. One biopsy was snap-frozen for gene expression and the other biopsy was stained for pathologic assessment. Liver biopsy confirmed that 24 patients from our cohort had NASH while 57 had only simple steatosis. Snap-frozen liver biopsy specimens of these patients were then used for the RNA extraction. cDNA probes were hybridized with customized microarray gene chips containing 5,220 relevant genes. Gene expression profiles were compared between groups using significance analysis of microarrays algorithm. In comparison to all Caucasian patients, African-American patients had over-expression of EPB41L1, IGF2, FAH, ACSL4, FUT4, CYP3A (q values < 10(-4)). In comparison to Caucasian NAFLD patients, African-American NAFLD patients showed over-expression of EPB41L1 and ACSL4 genes. Finally, in comparison to Caucasian NASH patients, African-American NASH patients showed over-expression of GSTM 2, GSTM4 and GSTM5 as well as FH and ASCL4 genes. Some genes highlighted by this analysis, particularly cytochrome CYP3A and glutathione transferases GSTM2, 4, 5, were previously implicated in the pathogenesis of NASH. African-American patients with biopsy-proven obesity-related NAFLD and NASH have a specific hepatic gene expression pattern that may explain their differences from Caucasian patients with NAFLD in developing progressive liver disease.

A triplex ribozyme expression system based on a single hairpin ribozyme.

PubMed

Aquino-Jarquin, Guillermo; Benítez-Hess, María Luisa; DiPaolo, Joseph A; Alvarez-Salas, Luis M

2008-09-01

Triplex ribozyme (RZ) configurations allow for the individual activity of trans-acting RZs in multiple expression cassettes (multiplex), thereby increasing target cleavage relative to conventionally expressed RZs. Although hairpin RZs have been advantageously compared to hammerhead RZs, their longer size and structural features complicated triplex design. We present a triplex expression system based on a single hairpin RZ with transcleavage capability and simple engineering. The system was tested in vitro using cis- and trans-cleavage kinetic assays against a known target RNA from HPV-16 E6/E7 mRNA. Single and multiplex triplex RZ constructs were more efficient in cleaving the target than tandem-cloned hairpin RZs, suggesting that the release of individual RZs enhanced trans-cleavage kinetics. Multiplex systems constructed with two different hairpin RZs resulted in better trans-cleavage compared to standard double-RZ constructs. In addition, the triplex RZ performed cis- and trans-cleavage in cervical cancer cells. The use of triplex configurations with multiplex RZs permit differential targeting of the same or different RNA, thus improving potential use against unstable targets. This prototype will provide the basis for the development of future RZ-based therapies and technologies.

Functional and evolutionary insights from the Ciona notochord transcriptome.

PubMed

Reeves, Wendy M; Wu, Yuye; Harder, Matthew J; Veeman, Michael T

2017-09-15

The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about notochord evolution. The full set of Ciona notochord genes provides a foundation for systems-level studies of notochord gene regulation and morphogenesis. We find only modest overlap between this set of notochord-enriched transcripts and the genes upregulated by ectopic expression of the key notochord transcription factor Brachyury, indicating that Brachyury is not a notochord master regulator gene as strictly defined. © 2017. Published by The Company of Biologists Ltd.

Impact of waste disposal on health of a poor urban community in Zimbambwe.

PubMed

Makoni, F S; Ndamba, J; Mbati, P A; Manase, G

2004-08-01

To assess excreta and waste disposal facilities available and their impact on sanitation related diseases in Epworth, an informal settlement on the outskirts of Harare. Descriptive cross-sectional survey. This was a community based study of Epworth informal settlement. A total of 308 households were interviewed. Participating households were randomly selected from the three communities of Epworth. Secondary medical archival data on diarrhoeal disease prevalence was collected from local clinics and district health offices in the study areas. Only 7% of households were connected to the sewer system. The study revealed that in Zinyengere extension 13% had no toilet facilities, 48% had simple pits and 37% had Blair VIP latrines. In Overspill 2% had no toilet facilities, 28% had simple latrines and 36% had Blair VIP latrines while in New Gada 20% had no toilet facilities, 24% had simple pits and 23% had Blair VIP latrines. Although a significant percentage had latrines (83.2%), over 50% of the population were not satisfied with the toilet facilities they were using. All the respondents expressed dissatisfaction with their domestic waste disposal practices with 46.6% admitting to have indiscriminately dumped waste. According to the community, diarrhoeal diseases were the most prevalent diseases (50%) related to poor sanitation. Health statistics also indicated that diarrhoea was a major problem in this community. It is recommended that households and the local authorities concentrate on improving the provision of toilets, water and waste disposal facilities as a way of improving the health state of the community.

In vivo neuronal calcium imaging in C. elegans.

PubMed

Chung, Samuel H; Sun, Lin; Gabel, Christopher V

2013-04-10

The nematode worm C. elegans is an ideal model organism for relatively simple, low cost neuronal imaging in vivo. Its small transparent body and simple, well-characterized nervous system allows identification and fluorescence imaging of any neuron within the intact animal. Simple immobilization techniques with minimal impact on the animal's physiology allow extended time-lapse imaging. The development of genetically-encoded calcium sensitive fluorophores such as cameleon and GCaMP allow in vivo imaging of neuronal calcium relating both cell physiology and neuronal activity. Numerous transgenic strains expressing these fluorophores in specific neurons are readily available or can be constructed using well-established techniques. Here, we describe detailed procedures for measuring calcium dynamics within a single neuron in vivo using both GCaMP and cameleon. We discuss advantages and disadvantages of both as well as various methods of sample preparation (animal immobilization) and image analysis. Finally, we present results from two experiments: 1) Using GCaMP to measure the sensory response of a specific neuron to an external electrical field and 2) Using cameleon to measure the physiological calcium response of a neuron to traumatic laser damage. Calcium imaging techniques such as these are used extensively in C. elegans and have been extended to measurements in freely moving animals, multiple neurons simultaneously and comparison across genetic backgrounds. C. elegans presents a robust and flexible system for in vivo neuronal imaging with advantages over other model systems in technical simplicity and cost.

Global Study of the Simple Pendulum by the Homotopy Analysis Method

ERIC Educational Resources Information Center

Bel, A.; Reartes, W.; Torresi, A.

2012-01-01

Techniques are developed to find all periodic solutions in the simple pendulum by means of the homotopy analysis method (HAM). This involves the solution of the equations of motion in two different coordinate representations. Expressions are obtained for the cycles and periods of oscillations with a high degree of accuracy in the whole range of…

Improvements in the Approximate Formulae for the Period of the Simple Pendulum

ERIC Educational Resources Information Center

Turkyilmazoglu, M.

2010-01-01

This paper is concerned with improvements in some exact formulae for the period of the simple pendulum problem. Two recently presented formulae are re-examined and refined rationally, yielding more accurate approximate periods. Based on the improved expressions here, a particular new formula is proposed for the period. It is shown that the derived…

ASSESSING THE ROLE OF CASPASE ACTIVITY AND METACASPASE EXPRESSION ON VIRAL SUSCEPTIBILITY OF THE COCCOLITHOPHORE, EMILIANIA HUXLEYI (HAPTOPHYTA).

PubMed

Bidle, Kay D; Kwityn, Clifford J

2012-10-01

As part of their strategy to infect the globally important coccolithophore, Emiliania huxleyi (Lohmann) W.W. Hay & H.P. Mohler, Coccolithoviruses trigger and regulate the host's programmed cell death (PCD) machinery during lytic infection. The induction and recruitment of host metacaspases, specialized, ancestral death proteases that facilitate viral lysis, suggests they may be important subcellular determinants to infection. We examined the "basal" levels and patterns of caspase activity and metacaspase expression in exponentially growing resistant and sensitive E. huxleyi strains and linked them with susceptibility to E. huxleyi virus 1 (EhV1). Resistant E. huxleyi strains were consistently characterized by low caspase specific activity and a relatively simple metacaspase expression profile. In contrast, sensitive E. huxleyi strains had markedly elevated caspase specific activity and consistently expressed more diverse metacaspase proteins. Using pooled data sets from triplicate experiments, we observed statistically significant linear correlations between infectivity, caspase activity, and metacaspase expression, with each strain forming distinct clusters, within a gradient in viral susceptibility. At the same time, we observed positive correlations between the expression of a subset of metacaspase proteins and lower susceptibility, suggestive of potential protective roles. Our findings implicate the importance of subtle differences in the basal physiological regulation of the PCD machinery to viral resistance or sensitivity and cell fate. © 2012 Phycological Society of America.

Early Dysregulation of Cell Adhesion and Extracellular Matrix Pathways in Breast Cancer Progression

PubMed Central

Emery, Lyndsey A.; Tripathi, Anusri; King, Chialin; Kavanah, Maureen; Mendez, Jane; Stone, Michael D.; de las Morenas, Antonio; Sebastiani, Paola; Rosenberg, Carol L.

2009-01-01

Proliferative breast lesions, such as simple ductal hyperplasia (SH) and atypical ductal hyperplasia (ADH), are candidate precursors to ductal carcinoma in situ (DCIS) and invasive cancer. To better understand the relationship of breast lesions to more advanced disease, we used microdissection and DNA microarrays to profile the gene expression of patient-matched histologically normal (HN), ADH, and DCIS from 12 patients with estrogen receptor positive sporadic breast cancer. SH were profiled from a subset of cases. We found 837 differentially expressed genes between DCIS-HN and 447 between ADH-HN, with >90% of the ADH-HN genes also present among the DCIS-HN genes. Only 61 genes were identified between ADH-DCIS. Expression differences were reproduced in an independent cohort of patient-matched lesions by quantitative real-time PCR. Many breast cancer-related genes and pathways were dysregulated in ADH and maintained in DCIS. Particularly, cell adhesion and extracellular matrix interactions were overrepresented. Focal adhesion was the top pathway in each gene set. We conclude that ADH and DCIS share highly similar gene expression and are distinct from HN. In contrast, SH appear more similar to HN. These data provide genetic evidence that ADH (but not SH) are often precursors to cancer and suggest cancer-related genetic changes, particularly adhesion and extracellular matrix pathways, are dysregulated before invasion and even before malignancy is apparent. These findings could lead to novel risk stratification, prevention, and treatment approaches. PMID:19700746

Motor and sensory neuropathy due to myelin infolding and paranodal damage in a transgenic mouse model of Charcot–Marie–Tooth disease type 1C

PubMed Central

Lee, Samuel M.; Sha, Di; Mohammed, Anum A.; Asress, Seneshaw; Glass, Jonathan D.; Chin, Lih-Shen; Li, Lian

2013-01-01

Charcot–Marie–Tooth disease type 1C (CMT1C) is a dominantly inherited motor and sensory neuropathy. Despite human genetic evidence linking missense mutations in SIMPLE to CMT1C, the in vivo role of CMT1C-linked SIMPLE mutations remains undetermined. To investigate the molecular mechanism underlying CMT1C pathogenesis, we generated transgenic mice expressing either wild-type or CMT1C-linked W116G human SIMPLE. Mice expressing mutant, but not wild type, SIMPLE develop a late-onset motor and sensory neuropathy that recapitulates key clinical features of CMT1C disease. SIMPLE mutant mice exhibit motor and sensory behavioral impairments accompanied by decreased motor and sensory nerve conduction velocity and reduced compound muscle action potential amplitude. This neuropathy phenotype is associated with focally infolded myelin loops that protrude into the axons at paranodal regions and near Schmidt–Lanterman incisures of peripheral nerves. We find that myelin infolding is often linked to constricted axons with signs of impaired axonal transport and to paranodal defects and abnormal organization of the node of Ranvier. Our findings support that SIMPLE mutation disrupts myelin homeostasis and causes peripheral neuropathy via a combination of toxic gain-of-function and dominant-negative mechanisms. The results from this study suggest that myelin infolding and paranodal damage may represent pathogenic precursors preceding demyelination and axonal degeneration in CMT1C patients. PMID:23359569

The Helium Atom and Isoelectronic Ions in Two Dimensions

ERIC Educational Resources Information Center

Patil, S. H.

2008-01-01

The energy levels of the helium atom and isoelectronic ions in two dimensions are considered. The difficulties encountered in the analytical evaluation of the perturbative and variational expressions for the ground state, promote an interesting factorization of the inter-electronic interaction, leading to simple expressions for the energy. This…

A Combinatorial Model of Malware Diffusion via Bluetooth Connections

PubMed Central

Merler, Stefano; Jurman, Giuseppe

2013-01-01

We outline here the mathematical expression of a diffusion model for cellphones malware transmitted through Bluetooth channels. In particular, we provide the deterministic formula underlying the proposed infection model, in its equivalent recursive (simple but computationally heavy) and closed form (more complex but efficiently computable) expression. PMID:23555677

Radar scattering mechanisms within the meteor crater ejecta blanket: Geologic implications and relevance to Venus

NASA Technical Reports Server (NTRS)

Garvin, J. B.; Campbell, B. A.; Zisk, S. H.; Schaber, Gerald G.; Evans, C.

1989-01-01

Simple impact craters are known to occur on all of the terrestrial planets and the morphologic expression of their ejecta blankets is a reliable indicator of their relative ages on the Moon, Mars, Mercury, and most recently for Venus. It will be crucial for the interpretation of the geology of Venus to develop a reliable means of distinguishing smaller impact landforms from volcanic collapse and explosion craters, and further to use the observed SAR characteristics of crater ejecta blankets (CEB) as a means of relative age estimation. With these concepts in mind, a study was initiated of the quantitative SAR textural characteristics of the ejecta blanket preserved at Meteor Crater, Arizona, the well studied 1.2 km diameter simple crater that formed approx. 49,000 years ago from the impact of an octahedrite bolide. While Meteor Crater was formed as the result of an impact into wind and water lain sediments and has undergone recognizable water and wind related erosion, it nonetheless represents the only well studied simple impact crater on Earth with a reasonably preserved CEB. Whether the scattering behavior of the CEB can provide an independent perspective on its preservation state and style of erosion is explored. Finally, airborne laser altimeter profiles of the microtopography of the Meteor Crater CEB were used to further quantify the subradar pizel scale topographic slopes and RMS height variations for comparisons with the scattering mechanisms computed from SAR polarimetry. A preliminary assessment was summarized of the L-band radar scattering mechanisms within the Meteor Crater CEB as derived from a NASA/JPL DC-8 SAR Polarimetry dataset acquired in 1988, and the dominant scattering behavior was compared with microtopographic data (laser altimeter profiles and 1:10,000 scale topographic maps).

Using heterologous expression systems to characterize potassium and sodium transport activities.

PubMed

Rodríguez, Alonso; Benito, Begoña; Cagnac, Olivier

2012-01-01

The expression of plant transporters in simple well-characterized cell systems is an irreplaceable technique for gaining insights into the kinetic and energetic features of plant transporters. Among all the available expression systems, yeast cells offer the highest simplicity and have the capacity to mimic the in vivo properties of plant transporters. Here, we describe the use of yeast mutants to express K(+) and Na(+) plant transporters and discuss some experimental problems that can produce misleading results.

New Expression for Collisionless Magnetic Reconnection Rate

NASA Technical Reports Server (NTRS)

Klimas, Alexander J.

2014-01-01

For 2D, symmetric, anti-parallel, collisionless magnetic reconnection, a new expression for the reconnection rate in the electron diffusion region is introduced. It is shown that this expression can be derived in just a few simple steps from a physically intuitive starting point; the derivation is given in its entirety and the validity of each step is confirmed. The predictions of this expression are compared to the results of several long-duration, open-boundary PIC reconnection simulations to demonstrate excellent agreement.

Simple Sugars to Complex Disease—Mucin-Type O-Glycans in Cancer

PubMed Central

Kudelka, Matthew R.; Ju, Tongzhong; Heimburg-Molinaro, Jamie; Cummings, Richard D.

2017-01-01

Mucin-type O-glycans are a class of glycans initiated with N-acetylgalactosamine (GalNAc) α-linked primarily to Ser/Thr residues within glycoproteins and often extended or branched by sugars or saccharides. Most secretory and membrane-bound proteins receive this modification, which is important in regulating many biological processes. Alterations in mucin-type O-glycans have been described across tumor types and include expression of relatively small-sized, truncated O-glycans and altered terminal structures, both of which are associated with patient prognosis. New discoveries in the identity and expression of tumor-associated O-glycans are providing new avenues for tumor detection and treatment. This chapter describes mucin-type O-glycan biosynthesis, altered mucin-type O-glycans in primary tumors, including mechanisms for structural changes and contributions to the tumor phenotype, and clinical approaches to detect and target altered O-glycans for cancer treatment and management. PMID:25727146

Facial attractiveness impressions precede trustworthiness inferences: lower detection thresholds and faster decision latencies.

PubMed

Gutiérrez-García, Aida; Beltrán, David; Calvo, Manuel G

2018-02-26

Prior research has found a relationship between perceived facial attractiveness and perceived personal trustworthiness. We examined the time course of attractiveness relative to trustworthiness evaluation of emotional and neutral faces. This served to explore whether attractiveness might be used as an easily accessible cue and a quick shortcut for judging trustworthiness. Detection thresholds and judgment latencies as a function of expressive intensity were measured. Significant correlations between attractiveness and trustworthiness consistently held for six emotional expressions at four intensities, and neutral faces. Importantly, perceived attractiveness preceded perceived trustworthiness, with lower detection thresholds and shorter decision latencies. This reveals a time course advantage for attractiveness, and suggests that earlier attractiveness impressions could bias trustworthiness inferences. A heuristic cognitive mechanism is hypothesised to ease processing demands by relying on simple and observable clues (attractiveness) as a substitute for more complex and not easily accessible information (trustworthiness).

A technique for computation of noise temperature due to a beam waveguide shroud

NASA Technical Reports Server (NTRS)

Veruttipong, W.; Franco, M. M.

1993-01-01

Direct analytical computation of the noise temperature of real beam waveguide (BWG) systems, including all mirrors and the surrounding shroud, is an extremely complex problem and virtually impossible to achieve. Yet the DSN antennas are required to be ultra low-noise in order to be effective, and a reasonably accurate prediction is essential. This article presents a relatively simple technique to compute a real BWG system noise temperature by combining analytical techniques with data from experimental tests. Specific expressions and parameters for X-band (8.45-GHz) BWG noise computation are obtained for DSS 13 and DSS 24, now under construction. These expressions are also valid for various conditions of the BWG feed systems, including horn sizes and positions, and mirror sizes, curvatures, and positions. Parameters for S- and Ka-bands (2.3 and 32.0 GHz) have not been determined; however, those can be obtained following the same procedure as for X-band.

Regular paths in SparQL: querying the NCI Thesaurus.

PubMed

Detwiler, Landon T; Suciu, Dan; Brinkley, James F

2008-11-06

OWL, the Web Ontology Language, provides syntax and semantics for representing knowledge for the semantic web. Many of the constructs of OWL have a basis in the field of description logics. While the formal underpinnings of description logics have lead to a highly computable language, it has come at a cognitive cost. OWL ontologies are often unintuitive to readers lacking a strong logic background. In this work we describe GLEEN, a regular path expression library, which extends the RDF query language SparQL to support complex path expressions over OWL and other RDF-based ontologies. We illustrate the utility of GLEEN by showing how it can be used in a query-based approach to defining simpler, more intuitive views of OWL ontologies. In particular we show how relatively simple GLEEN-enhanced SparQL queries can create views of the OWL version of the NCI Thesaurus that match the views generated by the web-based NCI browser.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

The soil water characteristic as new class of closed-form parametric expressions for the flow duration curve

NASA Astrophysics Data System (ADS)

Sadegh, M.; Vrugt, J. A.; Gupta, H. V.; Xu, C.

2016-04-01

The flow duration curve is a signature catchment characteristic that depicts graphically the relationship between the exceedance probability of streamflow and its magnitude. This curve is relatively easy to create and interpret, and is used widely for hydrologic analysis, water quality management, and the design of hydroelectric power plants (among others). Several mathematical expressions have been proposed to mimic the FDC. Yet, these efforts have not been particularly successful, in large part because available functions are not flexible enough to portray accurately the functional shape of the FDC for a large range of catchments and contrasting hydrologic behaviors. Here, we extend the work of Vrugt and Sadegh (2013) and introduce several commonly used models of the soil water characteristic as new class of closed-form parametric expressions for the flow duration curve. These soil water retention functions are relatively simple to use, contain between two to three parameters, and mimic closely the empirical FDCs of 430 catchments of the MOPEX data set. We then relate the calibrated parameter values of these models to physical and climatological characteristics of the watershed using multivariate linear regression analysis, and evaluate the regionalization potential of our proposed models against those of the literature. If quality of fit is of main importance then the 3-parameter van Genuchten model is preferred, whereas the 2-parameter lognormal, 3-parameter GEV and generalized Pareto models show greater promise for regionalization.

Differential Brain Activation to Angry Faces by Elite Warfighters: Neural Processing Evidence for Enhanced Threat Detection

PubMed Central

Paulus, Martin P.; Simmons, Alan N.; Fitzpatrick, Summer N.; Potterat, Eric G.; Van Orden, Karl F.; Bauman, James; Swain, Judith L.

2010-01-01

Background Little is known about the neural basis of elite performers and their optimal performance in extreme environments. The purpose of this study was to examine brain processing differences between elite warfighters and comparison subjects in brain structures that are important for emotion processing and interoception. Methodology/Principal Findings Navy Sea, Air, and Land Forces (SEALs) while off duty (n = 11) were compared with n = 23 healthy male volunteers while performing a simple emotion face-processing task during functional magnetic resonance imaging. Irrespective of the target emotion, elite warfighters relative to comparison subjects showed relatively greater right-sided insula, but attenuated left-sided insula, activation. Navy SEALs showed selectively greater activation to angry target faces relative to fearful or happy target faces bilaterally in the insula. This was not accounted for by contrasting positive versus negative emotions. Finally, these individuals also showed slower response latencies to fearful and happy target faces than did comparison subjects. Conclusions/Significance These findings support the hypothesis that elite warfighters deploy greater processing resources toward potential threat-related facial expressions and reduced processing resources to non-threat-related facial expressions. Moreover, rather than expending more effort in general, elite warfighters show more focused neural and performance tuning. In other words, greater neural processing resources are directed toward threat stimuli and processing resources are conserved when facing a nonthreat stimulus situation. PMID:20418943

A discrete Markov metapopulation model for persistence and extinction of species.

PubMed

Thompson, Colin J; Shtilerman, Elad; Stone, Lewi

2016-09-07

A simple discrete generation Markov metapopulation model is formulated for studying the persistence and extinction dynamics of a species in a given region which is divided into a large number of sites or patches. Assuming a linear site occupancy probability from one generation to the next we obtain exact expressions for the time evolution of the expected number of occupied sites and the mean-time to extinction (MTE). Under quite general conditions we show that the MTE, to leading order, is proportional to the logarithm of the initial number of occupied sites and in precise agreement with similar expressions for continuous time-dependent stochastic models. Our key contribution is a novel application of generating function techniques and simple asymptotic methods to obtain a second order asymptotic expression for the MTE which is extremely accurate over the entire range of model parameter values. Copyright © 2016 Elsevier Ltd. All rights reserved.

Expression of brain derived-neurotrophic factor and granulocyte-colony stimulating factor in the urothelium: relation with voiding function.

PubMed

Yuk, Seung Mo; Shin, Ju Hyun; Song, Ki Hak; Na, Yong Gil; Lim, Jae Sung; Sul, Chong Koo

2015-05-08

We designed this experiment to elucidate the relationship between the expression of brain derived-neurotrophic factor (BDNF), the expression of granulocyte-colony stimulating factor (G-CSF), and the development of overactive bladder (OAB). In our previous study, the urothelium was observed to be more than a simple mechanosensory receptor and was found to be a potential therapeutic target for OAB. Moreover, neuregulin-1 and BDNF were found to be potential new biomarkers of OAB. Here, we investigated the relationship between changes in the voiding pattern and the expression of BDNF and G-CSF in the urothelium and evaluated the effects of 5-hydroxymethyl tolterodine (5-HMT) on rats with bladder outlet obstruction (BOO). A total of 100 Sprague-Dawley rats were divided into the following groups: 20 control rats; 40 BOO rats; and 40 BOO rats administered 5-HMT (0.1 mg/kg). After BOO was induced for 4 weeks, the rats were assessed by cystometrography. The changes in BDNF and G-CSF expression were examined in both separated urothelial tissues and in cultured urothelial cells by reverse transcription polymerase chain reaction (RT-PCR). BOO rats showed increased non-voiding activity [NVA; (number/10 voidings)] and bladder weight and decreased micturition volume (MV), micturition interval (MI), and micturition time (MT) relative to the controls. Moreover, the 5-HMT administration rats showed decreased NVA and bladder weight and increased MV and MI in comparison to the BOO rats. BDNF and G-CSF expression was increased in BOO rats and decreased following 5-HMT administration. In this model, voiding dysfunction developed as a result of BOO. As a therapeutic agent for OAB, the administration of 5-HMT improved the voiding dysfunction. BDNF and G-CSF might modulate voiding patterns through micturition pathways and might be involved only in the urothelium. Moreover, the expression of both genes in the urothelium might be related to voiding dysfunction in OAB patients. Thus, the urothelium has an important role in the manifestation of voiding symptoms.

De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy.

PubMed

Zhang, Senhao; Shi, Yinghua; Cheng, Ningning; Du, Hongqi; Fan, Wenna; Wang, Chengzhang

2015-01-01

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa.

De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy

PubMed Central

Cheng, Ningning; Du, Hongqi; Fan, Wenna; Wang, Chengzhang

2015-01-01

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa. PMID:25799491

Evaluation of certain food additives.

PubMed

2012-01-01

This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, with a view to concluding as to safety concerns and to preparing specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of and assessment of dietary exposure to food additives, including flavouring agents. A summary follows of the Committee's evaluations of technical, toxicological and dietary exposure data for five food additives (magnesium dihydrogen diphosphate; mineral oil (medium and low viscosity) classes II and III; 3-phytase from Aspergillus niger expressed in Aspergillus niger; serine protease (chymotrypsin) from Nocardiopsis prasina expressed in Bacillus licheniformis; and serine protease (trypsin) from Fusarium oxysporum expressed in Fusarium venenatum) and 16 groups of flavouring agents (aliphatic and aromatic amines and amides; aliphatic and aromatic ethers; aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers containing furan substitution; aliphatic linear alpha,beta-unsaturated aldehydes, acids and related alcohols, acetals and esters; amino acids and related substances; epoxides; furfuryl alcohol and related substances; linear and branched-chain aliphatic, unsaturated, unconjugated alcohols, aldehydes, acids and related esters; miscellaneous nitrogen-containing substances; phenol and phenol derivatives; pyrazine derivatives; pyridine, pyrrole and quinoline derivatives; saturated aliphatic acyclic branched-chain primary alcohols, aldehydes and acids; simple aliphatic and aromatic sulfides and thiols; sulfur-containing heterocyclic compounds; and sulfur-substituted furan derivatives). Specifications for the following food additives were revised: ethyl cellulose, mineral oil (medium viscosity), modified starches and titanium dioxide. Annexed to the report are tables summarizing the Committee's recommendations for dietary exposures to and toxicological evaluations of the food additives and flavouring agents considered.

Multi-Tasking and Choice of Training Data Influencing Parietal ERP Expression and Single-Trial Detection-Relevance for Neuroscience and Clinical Applications.

PubMed

Kirchner, Elsa A; Kim, Su Kyoung

2018-01-01

Event-related potentials (ERPs) are often used in brain-computer interfaces (BCIs) for communication or system control for enhancing or regaining control for motor-disabled persons. Especially results from single-trial EEG classification approaches for BCIs support correlations between single-trial ERP detection performance and ERP expression. Hence, BCIs can be considered as a paradigm shift contributing to new methods with strong influence on both neuroscience and clinical applications. Here, we investigate the relevance of the choice of training data and classifier transfer for the interpretability of results from single-trial ERP detection. In our experiments, subjects performed a visual-motor oddball task with motor-task relevant infrequent ( targets ), motor-task irrelevant infrequent ( deviants ), and motor-task irrelevant frequent ( standards ) stimuli. Under dual-task condition, a secondary senso-motor task was performed, compared to the simple-task condition. For evaluation, average ERP analysis and single-trial detection analysis with different numbers of electrodes were performed. Further, classifier transfer was investigated between simple and dual task. Parietal positive ERPs evoked by target stimuli (but not by deviants) were expressed stronger under dual-task condition, which is discussed as an increase of task emphasis and brain processes involved in task coordination and change of task set. Highest classification performance was found for targets irrespective whether all 62, 6 or 2 parietal electrodes were used. Further, higher detection performance of targets compared to standards was achieved under dual-task compared to simple-task condition in case of training on data from 2 parietal electrodes corresponding to results of ERP average analysis. Classifier transfer between tasks improves classification performance in case that training took place on more varying examples (from dual task). In summary, we showed that P300 and overlaying parietal positive ERPs can successfully be detected while subjects are performing additional ongoing motor activity. This supports single-trial detection of ERPs evoked by target events to, e.g., infer a patient's attentional state during therapeutic intervention.

Multi-Tasking and Choice of Training Data Influencing Parietal ERP Expression and Single-Trial Detection—Relevance for Neuroscience and Clinical Applications

PubMed Central

Kirchner, Elsa A.; Kim, Su Kyoung

2018-01-01

Event-related potentials (ERPs) are often used in brain-computer interfaces (BCIs) for communication or system control for enhancing or regaining control for motor-disabled persons. Especially results from single-trial EEG classification approaches for BCIs support correlations between single-trial ERP detection performance and ERP expression. Hence, BCIs can be considered as a paradigm shift contributing to new methods with strong influence on both neuroscience and clinical applications. Here, we investigate the relevance of the choice of training data and classifier transfer for the interpretability of results from single-trial ERP detection. In our experiments, subjects performed a visual-motor oddball task with motor-task relevant infrequent (targets), motor-task irrelevant infrequent (deviants), and motor-task irrelevant frequent (standards) stimuli. Under dual-task condition, a secondary senso-motor task was performed, compared to the simple-task condition. For evaluation, average ERP analysis and single-trial detection analysis with different numbers of electrodes were performed. Further, classifier transfer was investigated between simple and dual task. Parietal positive ERPs evoked by target stimuli (but not by deviants) were expressed stronger under dual-task condition, which is discussed as an increase of task emphasis and brain processes involved in task coordination and change of task set. Highest classification performance was found for targets irrespective whether all 62, 6 or 2 parietal electrodes were used. Further, higher detection performance of targets compared to standards was achieved under dual-task compared to simple-task condition in case of training on data from 2 parietal electrodes corresponding to results of ERP average analysis. Classifier transfer between tasks improves classification performance in case that training took place on more varying examples (from dual task). In summary, we showed that P300 and overlaying parietal positive ERPs can successfully be detected while subjects are performing additional ongoing motor activity. This supports single-trial detection of ERPs evoked by target events to, e.g., infer a patient's attentional state during therapeutic intervention. PMID:29636660

A simple method for calculating growth rates of petroleum hydrocarbon plumes

USGS Publications Warehouse

Bekins, B.A.; Cozzarelli, I.M.; Curtis, G.P.

2005-01-01

Consumption of aquifer Fe(III) during biodegradation of ground water contaminants may result in expansion of a contaminant plume, changing the outlook for monitored natural attenuation. Data from two research sites contaminated with petroleum hydrocarbons show that toluene and xylenes degrade under methanogenic conditions, but the benzene and ethylbenzene plumes grow as aquifer Fe(III) supplies are depleted. By considering a one-dimensional reaction front in a constant unidirectional flow field, it is possible to derive a simple expression for the growth rate of a benzene plume. The method balances the mass flux of benzene with the Fe(III) content of the aquifer, assuming that the biodegradation reaction is instantaneous. The resulting expression shows that the benzene front migration is retarded relative to the ground water velocity by a factor that depends on the concentrations of hydrocarbon and bioavailable Fe(III). The method provides good agreement with benzene plumes at a crude oil study site in Minnesota and a gasoline site in South Carolina. Compared to the South Carolina site, the Minnesota site has 25% higher benzene flux but eight times the Fe(III), leading to about one-sixth the expansion rate. Although it was developed for benzene, toluene, ethylbenzene, and xylenes, the growth-rate estimation method may have applications to contaminant plumes from other persistent contaminant sources. Copyright ?? 2005 National Ground Water Association.

Parametrizing growth in dark energy and modified gravity models

NASA Astrophysics Data System (ADS)

Resco, Miguel Aparicio; Maroto, Antonio L.

2018-02-01

It is well known that an extremely accurate parametrization of the growth function of matter density perturbations in Λ CDM cosmology, with errors below 0.25%, is given by f (a )=Ωmγ(a ) with γ ≃0.55 . In this work, we show that a simple modification of this expression also provides a good description of growth in modified gravity theories. We consider the model-independent approach to modified gravity in terms of an effective Newton constant written as μ (a ,k )=Geff/G and show that f (a )=β (a )Ωmγ(a ) provides fits to the numerical solutions with similar accuracy to that of Λ CDM . In the time-independent case with μ =μ (k ), simple analytic expressions for β (μ ) and γ (μ ) are presented. In the time-dependent (but scale-independent) case μ =μ (a ), we show that β (a ) has the same time dependence as μ (a ). As an example, explicit formulas are provided in the Dvali-Gabadadze-Porrati (DGP) model. In the general case, for theories with μ (a ,k ), we obtain a perturbative expansion for β (μ ) around the general relativity case μ =1 which, for f (R ) theories, reaches an accuracy below 1%. Finally, as an example we apply the obtained fitting functions in order to forecast the precision with which future galaxy surveys will be able to measure the μ parameter.

Falling head ponded infiltration in the nonlinear limit

NASA Astrophysics Data System (ADS)

Triadis, D.

2014-12-01

The Green and Ampt infiltration solution represents only an extreme example of behavior within a larger class of very nonlinear, delta function diffusivity soils. The mathematical analysis of these soils is greatly simplified by the existence of a sharp wetting front below the soil surface. Solutions for more realistic delta function soil models have recently been presented for infiltration under surface saturation without ponding. After general formulation of the problem, solutions for a full suite of delta function soils are derived for ponded surface water depleted by infiltration. Exact expressions for the cumulative infiltration as a function of time, or the drainage time as a function of the initial ponded depth may take implicit or parametric forms, and are supplemented by simple asymptotic expressions valid for small times, and small and large initial ponded depths. As with surface saturation without ponding, the Green-Ampt model overestimates the effect of the soil hydraulic conductivity. At the opposing extreme, a low-conductivity model is identified that also takes a very simple mathematical form and appears to be more accurate than the Green-Ampt model for larger ponded depths. Between these two, the nonlinear limit of Gardner's soil is recommended as a physically valid first approximation. Relative discrepancies between different soil models are observed to reach a maximum for intermediate values of the dimensionless initial ponded depth, and in general are smaller than for surface saturation without ponding.

Analytical expressions for stability regions in the Ince-Strutt diagram of Mathieu equation

NASA Astrophysics Data System (ADS)

Butikov, Eugene I.

2018-04-01

Simple analytical expressions are suggested for transition curves that separate, in the Ince-Strutt diagram, different types of solutions to the famous Mathieu equation. The derivations of these expressions in this paper rely on physically meaningful periodic solutions describing various regular motions of a familiar nonlinear mechanical system—a rigid planar pendulum with a vertically oscillating pivot. The paper is accompanied by a relevant simulation program.

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

PubMed

Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

2017-07-21

Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

Engineering modular ‘ON’ RNA switches using biological components

PubMed Central

Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

2013-01-01

Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

Temperature dependence of ion transport: the compensated Arrhenius equation.

PubMed

Petrowsky, Matt; Frech, Roger

2009-04-30

The temperature-dependent conductivity originating in a thermally activated process is often described by a simple Arrhenius expression. However, this expression provides a poor description of the data for organic liquid electrolytes and amorphous polymer electrolytes. Here, we write the temperature dependence of the conductivity as an Arrhenius expression and show that the experimentally observed non-Arrhenius behavior is due to the temperature dependence of the dielectric constant contained in the exponential prefactor. Scaling the experimentally measured conductivities to conductivities at a chosen reference temperature leads to a "compensated" Arrhenius equation that provides an excellent description of temperature-dependent conductivities. A plot of the prefactors as a function of the solvent dielectric constant results in a single master curve for each family of solvents. These data suggest that ion transport in these and related systems is governed by a single activated process differing only in the activation energy for each family of solvents. Connection is made to the shift factor used to describe electrical and mechanical relaxation in a wide range of phenomena, suggesting that this scaling procedure might have broad applications.

Analytic expressions for Atomic Layer Deposition: coverage, throughput, and materials utilization in cross-flow, particle coating, and spatial ALD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yanguas-Gil, Angel; Elam, Jeffrey W.

2014-05-01

In this work, the authors present analytic models for atomic layer deposition (ALD) in three common experimental configurations: cross-flow, particle coating, and spatial ALD. These models, based on the plug-flow and well-mixed approximations, allow us to determine the minimum dose times and materials utilization for all three configurations. A comparison between the three models shows that throughput and precursor utilization can each be expressed by universal equations, in which the particularity of the experimental system is contained in a single parameter related to the residence time of the precursor in the reactor. For the case of cross-flow reactors, the authorsmore » show how simple analytic expressions for the reactor saturation profiles agree well with experimental results. Consequently, the analytic model can be used to extract information about the ALD surface chemistry (e. g., the reaction probability) by comparing the analytic and experimental saturation profiles, providing a useful tool for characterizing new and existing ALD processes. (C) 2014 American Vacuum Society« less

The ethic of care: recapturing social work's first voice.

PubMed

Dybicz, Phillip

2012-07-01

This article examines the dynamic between expressions of care--that is, simple acts of kindness and consideration that make up friendly relations--and professional expertise. During the 20th century, social work based its expertise on a solid scientific foundation. Within the embrace of scientific expertise, expressions of care are assigned the vital, but limited, role of ameliorating the sterile application of scientific knowledge, mainly through the application of social work values. This role is limited, however, because social workers are cautioned to avoid dual relationships; one cannot be both a professional and a friend to the client. This was not always the case. Working from a different paradigm, Charity Organization Society workers and settlement house workers each actively embraced and nurtured the notion of being a friend and neighbor to those they served. Post-modern practices--also stemming from a different paradigm and embracing an expertise in critical consciousness, in turn--seek to redefine the client-social worker relationship along this dimension. Expressions of care, propagated through a genuine (albeit circumscribed) friendship, actively contribute to treatment planning and a more fruitful outcome.

GAPD and tubulin are suitable internal controls for qPCR analysis of oral squamous cell carcinoma cell lines.

PubMed

Campos, M S; Rodini, C O; Pinto-Júnior, D S; Nunes, F D

2009-02-01

The selection of housekeeping genes is critical for gene expression studies. To address this issue, four candidate housekeeping genes, including several commonly used ones, were investigated in oral squamous cell carcinoma cell lines. A simple quantitative RT-PCR approach was employed by comparing relative expression of the four candidate genes within two cancerous cell lines (HN6 and HN31) and one noncancerous cell line (HaCaT) treated or not with EGF and TGF-beta1. Data were analyzed using ANOVA followed by the NormFinder software program. On this basis, stability of the candidate housekeeping genes was ranked and non statistical differences were found using ANOVA test. On the other hand, the NormFinder was able to show that GAPD and TUBB presented the less variable results, representing appropriated housekeeping genes for the samples and conditions analyzed. In conclusion, this study suggests that the GAPD and the TUBB represent adequate normalizers for gene profiling studies in OSCC cell lines, covering, respectively, high and low expression levels genes.

3D-printed gelatin scaffolds of differing pore geometry modulate hepatocyte function and gene expression.

PubMed

Lewis, Phillip L; Green, Richard M; Shah, Ramille N

2018-03-15

Three dimensional (3D) printing is highly amenable to the fabrication of tissue-engineered organs of a repetitive microstructure such as the liver. The creation of uniform and geometrically repetitive tissue scaffolds can also allow for the control over cellular aggregation and nutrient diffusion. However, the effect of differing geometries, while controlling for pore size, has yet to be investigated in the context of hepatocyte function. In this study, we show the ability to precisely control pore geometry of 3D-printed gelatin scaffolds. An undifferentiated hepatocyte cell line (HUH7) demonstrated high viability and proliferation when seeded on 3D-printed scaffolds of two different geometries. However, hepatocyte specific functions (albumin secretion, CYP activity, and bile transport) increases in more interconnected 3D-printed gelatin cultures compared to a less interconnected geometry and to 2D controls. Additionally, we also illustrate the disparity between gene expression and protein function in simple 2D culture modes, and that recreation of a physiologically mimetic 3D environment is necessary to induce both expression and function of cultured hepatocytes. Three dimensional (3D) printing provides tissue engineers the ability spatially pattern cells and materials in precise geometries, however the biological effects of scaffold geometry on soft tissues such as the liver have not been rigorously investigated. In this manuscript, we describe a method to 3D print gelatin into well-defined repetitive geometries that show clear differences in biological effects on seeded hepatocytes. We show that a relatively simple and widely used biomaterial, such as gelatin, can significantly modulate biological processes when fabricated into specific 3D geometries. Furthermore, this study expands upon past research into hepatocyte aggregation by demonstrating how it can be manipulated to enhance protein function, and how function and expression may not precisely correlate in 2D models. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Bacterial Expression of a Single-Chain Variable Fragment (scFv) Antibody against Ganoderic Acid A: A Cost-Effective Approach for Quantitative Analysis Using the scFv-Based Enzyme-Linked Immunosorbent Assay.

PubMed

Yusakul, Gorawit; Nuntawong, Poomraphie; Sakamoto, Seiichi; Ratnatilaka Na Bhuket, Pahweenvaj; Kohno, Toshitaka; Kikkawa, Nao; Rojsitthisak, Pornchai; Shimizu, Kuniyoshi; Tanaka, Hiroyuki; Morimoto, Satoshi

2017-01-01

Due to the highly specific binding between an antibody and its target, superior analytical performances was obtained by immunoassays for phytochemical analysis over conventional chromatographic techniques. Here, we describe a simple method for producing a functional single-chain variable fragment (scFv) antibody against ganoderic acid A (GAA), a pharmacologically active metabolite from Ganoderma lingzhi. The Escherichia coli BL21(DE3) strain produced a large amount of anti-GAA scFv. However, in vitro refolding steps, which partially recovered the reactivity of the scFv, were required. Interestingly, the functional scFv was expressed as a soluble and active form in the cytoplasm of an engineered E. coli SHuffle ® strain. Purified anti-GAA scFv, which yielded 2.56 mg from 1 L of culture medium, was obtained from simple and inexpensive procedures for expression and purification. The anti-GAA scFv-based indirect competitive enzyme-linked immunosorbent assay (icELISA) exhibited high sensitivity (linearity: 0.078-1.25 µg/mL) with precision (CV: ≤6.20%) and reliability (recovery: 100.1-101.8%) for GAA determination. In summary, the approach described here is an inexpensive, simple, and efficient expression system that extends the application of anti-GAA scFv-based immunoassays. In addition, when in vitro refolding steps can be skipped, the cost and complexity of scFv antibody production can be minimized.

Binding in pair potentials of liquid simple metals from nonlocality in electronic kinetic energy

NASA Technical Reports Server (NTRS)

Perrot, F.; March, N. H.

1990-01-01

The paper presents an explicit expression for the pair potential in liquid simple metals from low-order density-gradient theory when the superposition of single-center displaced charges is employed. Numerical results are presented for the gradient expansion pair interaction in liquid Na and Be. The low-order density-gradient equation for the pair potential is presented.

An approximate theoretical treatment of ion transfer processes at asymmetric microscopic and nanoscopic liquid-liquid interfaces: Single and double potential pulse techniques

NASA Astrophysics Data System (ADS)

Molina, A.; Laborda, E.; Compton, R. G.

2014-03-01

Simple theory for the electrochemical study of reversible ion transfer processes at micro- and nano-liquid|liquid interfaces supported on a capillary is presented. Closed-form expressions are obtained for the response in normal pulse and differential double pulse voltammetries, which describe adequately the particular behaviour of these systems due to the ‘asymmetric’ ion diffusion inside and outside the capillary. The use of different potential pulse techniques for the determination of the formal potential and diffusion coefficients of the ion is examined. For this, very simple analytical expressions are presented for the half-wave potential in NPV and the peak potential in DDPV.

Macroscopic Fluctuation Theory for Stationary Non-Equilibrium States

NASA Astrophysics Data System (ADS)

Bertini, L.; de Sole, A.; Gabrielli, D.; Jona-Lasinio, G.; Landim, C.

2002-05-01

We formulate a dynamical fluctuation theory for stationary non-equilibrium states (SNS) which is tested explicitly in stochastic models of interacting particles. In our theory a crucial role is played by the time reversed dynamics. Within this theory we derive the following results: the modification of the Onsager-Machlup theory in the SNS; a general Hamilton-Jacobi equation for the macroscopic entropy; a non-equilibrium, nonlinear fluctuation dissipation relation valid for a wide class of systems; an H theorem for the entropy. We discuss in detail two models of stochastic boundary driven lattice gases: the zero range and the simple exclusion processes. In the first model the invariant measure is explicitly known and we verify the predictions of the general theory. For the one dimensional simple exclusion process, as recently shown by Derrida, Lebowitz, and Speer, it is possible to express the macroscopic entropy in terms of the solution of a nonlinear ordinary differential equation; by using the Hamilton-Jacobi equation, we obtain a logically independent derivation of this result.

Expression of the transmembrane mucins, MUC1, MUC4 and MUC16, in normal endometrium and in endometriosis.

PubMed

Dharmaraj, N; Chapela, P J; Morgado, M; Hawkins, S M; Lessey, B A; Young, S L; Carson, D D

2014-08-01

Are the transmembrane mucins, MUC1, MUC4 and MUC16, differentially expressed in endometriosis compared with normal endometrium? This study revealed that transmembrane mucin expression does not vary significantly in normal endometrium during the menstrual cycle and is not altered in endometriosis relative to the epithelial marker, cytokeratin-18 (KRT18). Increased serum levels of the transmembrane mucin fragments MUC1, MUC4 and MUC16 that normally dominate the apical surface of simple epithelia are found in several pathological conditions, including endometriosis. Altered mucin expression in gynecologic diseases may promote infertility or endometrial pathologies. This was a laboratory-based study of samples from 12 endometriosis patients as well as non-endometriosis control samples obtained from 31 patients. Total RNA was isolated from endometrial biopsies of ectopic and eutopic endometrium from women with endometriosis and control patients from different stages of the menstrual cycle. Quantitative (q)-RT-PCR analyses were performed for the mucins, MUC1, MUC4 and MUC16, relative to the epithelial marker, cytokeratin-18 (KRT18), or β-actin (ACTB). Frozen sections from endometrial biopsies of proliferative and mid-secretory stage women with endometriosis were immunostained for MUC1, MUC4 and MUC16. qRT-PCR analyses of MUC1 and MUC16 mRNA revealed that these mucins do not vary significantly during the menstrual cycle nor are they altered in women with endometriosis relative to the epithelial marker, KRT18. MUC4 mRNA is expressed at very low levels relative to MUC1 and MUC16 under all conditions. There was little difference in MUC1 and MUC16 expression between eutopic endometrial and ectopic endometriotic tissues. MUC4 expression also was not significantly higher in the ectopic endometriotic tissues. Immunostaining for all three mucins reveals robust expression of MUC1 and MUC16 at the apical surfaces of endometrial epithelia, but little to no staining for MUC4. qRT-PCR analysis was the main method used for mucin detection. Additional studies with stage III-IV endometriotic tissue would be useful to determine if changes in MUC1 and MUC16 expression occur, or if MUC4 expression increases, at later stages of endometriosis. We report a comprehensive comparative profile of the major transmembrane mucins, MUC1, MUC4 and MUC16, relative to the epithelial marker, KRT18, in normal cycling endometrium and in endometriosis, and indicate constitutive expression. Previous studies have profiled the expression of individual mucins relative to β-actin and indicate accumulation in the luteal phase. Thus, these differences in interpretation appear to reflect the increased epithelial content of endometrium during the luteal phase. This study was supported by: NIH R01HD29963 to D.D.C.; NIH U54HD007495 to S.M.H.; and NIH R01HD067721 to S.L.Y. and B.A.L. The authors have no competing interests to declare. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Frequency domain analysis of noise in simple gene circuits

NASA Astrophysics Data System (ADS)

Cox, Chris D.; McCollum, James M.; Austin, Derek W.; Allen, Michael S.; Dar, Roy D.; Simpson, Michael L.

2006-06-01

Recent advances in single cell methods have spurred progress in quantifying and analyzing stochastic fluctuations, or noise, in genetic networks. Many of these studies have focused on identifying the sources of noise and quantifying its magnitude, and at the same time, paying less attention to the frequency content of the noise. We have developed a frequency domain approach to extract the information contained in the frequency content of the noise. In this article we review our work in this area and extend it to explicitly consider sources of extrinsic and intrinsic noise. First we review applications of the frequency domain approach to several simple circuits, including a constitutively expressed gene, a gene regulated by transitions in its operator state, and a negatively autoregulated gene. We then review our recent experimental study, in which time-lapse microscopy was used to measure noise in the expression of green fluorescent protein in individual cells. The results demonstrate how changes in rate constants within the gene circuit are reflected in the spectral content of the noise in a manner consistent with the predictions derived through frequency domain analysis. The experimental results confirm our earlier theoretical prediction that negative autoregulation not only reduces the magnitude of the noise but shifts its content out to higher frequency. Finally, we develop a frequency domain model of gene expression that explicitly accounts for extrinsic noise at the transcriptional and translational levels. We apply the model to interpret a shift in the autocorrelation function of green fluorescent protein induced by perturbations of the translational process as a shift in the frequency spectrum of extrinsic noise and a decrease in its weighting relative to intrinsic noise.

Stability of the line preserving flows

NASA Astrophysics Data System (ADS)

Figura, Przemysław

2017-11-01

We examine the equations that are used to describe flows which preserve field lines. We study what happens if we introduce perturbations to the governing equations. The stability of the line preserving flows in the case of the magneto-fluids permeated by magnetic fields is strictly connected to the non-null magnetic reconnection processes. In most of our study we use the Euler potential representation of the external magnetic field. We provide general expressions for the perturbations of the Euler potentials that describe the magnetic field. Similarly, we provide expressions for the case of steady flow as well as we obtain certain conditions required for the stability of the flow. In addition, for steady flows we formulate conditions under which the perturbations of the external field are negligible and the field may be described by its initial unperturbed form. Then we consider the flow equation that transforms quantities from the laboratory coordinate system to the related external field coordinate system. We introduce perturbations to the equation and obtain its simplified versions for the case of a steady flow. For a given system, use of this method allows us to simplify the considerations provided that some part of the system may be described as a perturbation. Next, to study regions favourable for the magnetic reconnection to occur we introduce a deviation vector to the basic line preserving flows condition equation. We provide expressions of the vector for some simplifying cases. This method allows us to examine if given perturbations either stabilise the system or induce magnetic reconnection. To illustrate some of our results we study two examples, namely a simple laboratory plasma flow and a simple planetary magnetosphere model.

Nonlocal electrostatics in ionic liquids: The key to an understanding of the screening decay length and screened interactions.

PubMed

Kjellander, Roland

2016-09-28

Screened electrostatic interactions in ionic liquids are investigated by means of exact statistical mechanical analysis combined with physical arguments that enhance the transparency and conceptual accessibility of the analysis and results. The constituent ions and immersed particles in the liquid can have arbitrary shapes and any internal charge distributions. The decay of the screened electrostatic potential and the free energy of interaction in ionic liquids can be exponentially damped oscillatory (like in molten simple salts) as well as plain exponential and long-ranged (like in dilute electrolyte solutions). Both behaviors are in agreement with the exact statistical mechanical analysis and reasons for their appearances are investigated. Exact but surprisingly simple expressions for the decay parameter κ of the screened electrostatics are obtained, which replace the classical expression for the Debye-Hückel parameter κ DH (the reciprocal Debye length). The expressions are applicable both for cases with plain exponential and oscillatory behaviors. The key importance of nonlocal electrostatics is thereby demonstrated explicitly. Dielectric properties of ionic liquids and other electrolytes are investigated, in particular the static dielectric function ϵ̃(k) and some effective relative permittivities (E r eff and E r ∗ ), which take roles that the dielectric constant ε r has for polar liquids consisting of electroneutral molecules. The dielectric constant in the latter case, which is the limit of ϵ̃(k) when the wave number k → 0, can be expressed solely in terms of dipolar features of the molecules. In contrast to this, the effective dielectric permittivities of ionic liquids have contributions also from quadrupolar, octupolar, and higher multipolar features of the constituent ions. The "dielectric constant" of electrolytes does not exist since ϵ̃(k)→∞ when k → 0, a well-known effect of perfect screening. The effective relative permittivities, E r eff , and E r ∗ of ionic liquids are obtained from the non-diverging part of ϵ̃(k), but not as a k → 0 limit. Influences of ion associations, especially pairing, are investigated for screened electrostatics and these permittivities. A general, multipolar expansion of ϵ̃(k) is derived and used to analyze dielectric properties of ionic liquids and other electrolytes.

Nonlocal electrostatics in ionic liquids: The key to an understanding of the screening decay length and screened interactions

NASA Astrophysics Data System (ADS)

Kjellander, Roland

2016-09-01

Screened electrostatic interactions in ionic liquids are investigated by means of exact statistical mechanical analysis combined with physical arguments that enhance the transparency and conceptual accessibility of the analysis and results. The constituent ions and immersed particles in the liquid can have arbitrary shapes and any internal charge distributions. The decay of the screened electrostatic potential and the free energy of interaction in ionic liquids can be exponentially damped oscillatory (like in molten simple salts) as well as plain exponential and long-ranged (like in dilute electrolyte solutions). Both behaviors are in agreement with the exact statistical mechanical analysis and reasons for their appearances are investigated. Exact but surprisingly simple expressions for the decay parameter κ of the screened electrostatics are obtained, which replace the classical expression for the Debye-Hückel parameter κDH (the reciprocal Debye length). The expressions are applicable both for cases with plain exponential and oscillatory behaviors. The key importance of nonlocal electrostatics is thereby demonstrated explicitly. Dielectric properties of ionic liquids and other electrolytes are investigated, in particular the static dielectric function ɛ ˜ ( k ) and some effective relative permittivities ( Er eff and Er ∗ ), which take roles that the dielectric constant ɛr has for polar liquids consisting of electroneutral molecules. The dielectric constant in the latter case, which is the limit of ɛ ˜ ( k ) when the wave number k → 0, can be expressed solely in terms of dipolar features of the molecules. In contrast to this, the effective dielectric permittivities of ionic liquids have contributions also from quadrupolar, octupolar, and higher multipolar features of the constituent ions. The "dielectric constant" of electrolytes does not exist since ɛ ˜ ( k ) → ∞ when k → 0, a well-known effect of perfect screening. The effective relative permittivities, Er eff , and Er ∗ of ionic liquids are obtained from the non-diverging part of ɛ ˜ ( k ) , but not as a k → 0 limit. Influences of ion associations, especially pairing, are investigated for screened electrostatics and these permittivities. A general, multipolar expansion of ɛ ˜ ( k ) is derived and used to analyze dielectric properties of ionic liquids and other electrolytes.

Evaluation of anonymous and expressed sequence tag derived polymorphic microsatellite markers in the tobacco budworm Heliothis virescens (Lepidoptera: noctuidae)

USDA-ARS?s Scientific Manuscript database

Polymorphic genetic markers were identified and characterized using a partial genomic library of Heliothis virescens enriched for simple sequence repeats (SSR) and nucleotide sequences of expressed sequence tags (EST). Nucleotide sequences of 192 clones from the partial genomic library yielded 147 u...

Desmoplakin II expression is not restricted to stratified epithelia.

PubMed

Angst, B D; Nilles, L A; Green, K J

1990-10-01

Desmosomes are major intercellular junctions found in association with intermediate filaments in epithelial, cardiac and arachnoidal tissue. Desmoplakins I and II (DPI and II) are highly related proteins localized in the innermost part of the desmosomal plaque and are candidates for linking intermediate filaments (IF) to the desmosomal complex. While investigators agree that DPI is present in all epithelia, they disagree on the distribution of DPII. Some have reported DPII to be restricted to stratified tissue and have furthermore suggested that the expression of DPII may be linked to stratification. We have compared the expression of DPI and II at the mRNA and protein levels in cell lines derived from simple, transitional and stratified epithelia. Northern blot analysis revealed DPI and II mRNA to be present in all cell lines as well as simple and stratified epithelial tissues. However, DPII mRNA could not be detected in cardiac muscle tissue. Immunoblotting and immunoprecipitation demonstrated the presence of DPI and II in all cell lines at the whole-cell protein level as well as in association with cytoskeletal fractions. Immunofluorescence staining was used to correlate the biochemical findings with the localization of DPI and II. While most cell lines exhibited typical intercellular and in many cases cytoplasmic DP staining, T24 cells exhibited predominantly diffuse and dotty cytoplasmic staining. In addition, we investigated whether changes in DPI and II expression occurred following calcium-induced cell contact formation and stratification in the human pharyngeal cell line, FaDu. No significant changes in mRNA or whole-cell protein levels were observed during a period of 5 days following the calcium switch. However, immunoblotting revealed a significant increase in DPI and II levels in the insoluble protein pool during desmosome formation. These observations indicated a possible recruitment of soluble DPI/II into an insoluble pool after induction of desmosome assembly by the calcium switch, consistent with earlier reports for MDCK cells. In summary, our results suggest that the expression of DPII is not strictly linked to stratification or differentiation; however, the apparent absence of DPII mRNA from cardiac muscle suggests it may not be a constituent of all desmosomes.

Resonant Drag Instability of Grains Streaming in Fluids

NASA Astrophysics Data System (ADS)

Squire, J.; Hopkins, P. F.

2018-03-01

We show that grains streaming through a fluid are generically unstable if their velocity, projected along some direction, matches the phase velocity of a fluid wave (linear oscillation). This can occur whenever grains stream faster than any fluid wave. The wave itself can be quite general—sound waves, magnetosonic waves, epicyclic oscillations, and Brunt–Väisälä oscillations each generate instabilities, for example. We derive a simple expression for the growth rates of these “resonant drag instabilities” (RDI). This expression (i) illustrates why such instabilities are so virulent and generic and (ii) allows for simple analytic computation of RDI growth rates and properties for different fluids. As examples, we introduce several new instabilities, which could see application across a variety of physical systems from atmospheres to protoplanetary disks, the interstellar medium, and galactic outflows. The matrix-based resonance formalism we introduce can also be applied more generally in other (nonfluid) contexts, providing a simple means for calculating and understanding the stability properties of interacting systems.

An unexpected way forward: towards a more accurate and rigorous protein-protein binding affinity scoring function by eliminating terms from an already simple scoring function.

PubMed

Swanson, Jon; Audie, Joseph

2018-01-01

A fundamental and unsolved problem in biophysical chemistry is the development of a computationally simple, physically intuitive, and generally applicable method for accurately predicting and physically explaining protein-protein binding affinities from protein-protein interaction (PPI) complex coordinates. Here, we propose that the simplification of a previously described six-term PPI scoring function to a four term function results in a simple expression of all physically and statistically meaningful terms that can be used to accurately predict and explain binding affinities for a well-defined subset of PPIs that are characterized by (1) crystallographic coordinates, (2) rigid-body association, (3) normal interface size, and hydrophobicity and hydrophilicity, and (4) high quality experimental binding affinity measurements. We further propose that the four-term scoring function could be regarded as a core expression for future development into a more general PPI scoring function. Our work has clear implications for PPI modeling and structure-based drug design.

A path-oriented matrix-based knowledge representation system

NASA Technical Reports Server (NTRS)

Feyock, Stefan; Karamouzis, Stamos T.

1993-01-01

Experience has shown that designing a good representation is often the key to turning hard problems into simple ones. Most AI (Artificial Intelligence) search/representation techniques are oriented toward an infinite domain of objects and arbitrary relations among them. In reality much of what needs to be represented in AI can be expressed using a finite domain and unary or binary predicates. Well-known vector- and matrix-based representations can efficiently represent finite domains and unary/binary predicates, and allow effective extraction of path information by generalized transitive closure/path matrix computations. In order to avoid space limitations a set of abstract sparse matrix data types was developed along with a set of operations on them. This representation forms the basis of an intelligent information system for representing and manipulating relational data.

Delay in polling systems in heavy traffic

NASA Astrophysics Data System (ADS)

van der Mei, Robert D.

1998-10-01

We study the delay in asymmetric cyclic polling systems with general mixtures of gated and exhaustive service, with generally distributed service times and switch-over times, in heavy traffic. We obtain closed-form expressions for all moments of the delay incurred at each of the queues. The expressions are strikingly simple and can even be expressed as finite products of known factors. The results provide new insights into the heavy-traffic behavior of polling systems.

The effect of ambient pressure on the evaporation rate of materials

NASA Technical Reports Server (NTRS)

Naumann, R. J.; Russell, W. M.

1972-01-01

A simple expression is obtained using a diffusion model for the effect of ambient pressure on the outgassing or evaporation rate of materials. The correctness of the expression is demonstrated by comparing the estimates from this expression with actual weight loss measurements. It is shown that the rate of mass loss is governed by the ratio of mean free path to the characteristic dimension of the surface in question.

[Electroacupuncture Combined with Clomiphene Promotes Pregnancy and Blastocyst Implantation Possibly by Up-regulating Expression of Insulin Receptor and Insulin Receptor Substrate 1 Proteins in Endometrium in Rats with PCOS].

PubMed

Lai, Mao-Hua; Ma, Hong-Xia; Song, Xing-Hua

2016-10-25

To observe the effect of electroacupuncture (EA) intervention combined with clomiphene critate (CC) on the blastocyst implantation and pregnancy rate and expression of insulin receptor (INSR) and insulin receptor substrate 1 (IRS 1) proteins in the endometrium in rats with polycystic ovary syndrome (PCOS), so as to reveal its mechanisms underlying improvement of PCOS. One hundred and twenty-five female SD rats were randomly divided into normal control, PCOS model, medication (CC), EA and EA+CC groups ( n =25 in each group, 15 for checking blastocyst implantation, and 10 for Western blot). The PCOS model was established by subcutaneous injection of Dehydroepiandrosterone (DHEA) and fed with high-fat diet. Rats of the normal control group were treated by subcutaneous injection of sesame oil and fed with the normal forage. EA stimulation was applied to "Zhongwan" (CV 12), "Guanyuan" (CV 4) and bilateral "Tianshu" (ST 25) for 30 min, 3 times a week, 5 weeks altogether. Rats of the CC and EA+CC groups were fed with CC (100 mg·kg -1 ·d -1 ) for 2 days after regular restriction (30 min, 3 times a week, 5 weeks altogether). The pregnancy was determined by vaginal smear tests and the number of blastocyst implantation determined by examination of the uterus after execution. The expression of INSR and IRS 1 proteins in the endometrium was detected by Western blot. The pregnancy rate and the number of blastocyst implantation were significantly lower in the model group than in the normal control group ( P <0.05), and remarkably increased after EA and EA+CC interventions ( P <0.05). The effects of EA+CC were obviously superior to those of simple EA and simple medication in raising the pregnancy rate and the number of blastocyst implantation ( P <0.05). No significant differences were found between the EA and CC groups in the pregnancy rate and the number of blastocyst implantation ( P >0.05). The relative expression levels of both INSR and IRS 1 proteins were markedly lower in the model group than in the normal control group ( P <0.05), and significantly higher in both EA and EA+CC groups than in the model group ( P <0.05). No significant differences were found between the model and the CC groups and between the EA and EA+CC groups in the expression levels of INSR and IRS 1 proteins ( P >0.05). EA intervention can improve pregnancy rate and the number of blastocyst implantation in PCOS rats, which may be related to its effects in up-regulating the expression of INSR and IRS 1 proteins in the endometrium.

Social Cohesion, Structural Holes, and a Tale of Two Measures

NASA Astrophysics Data System (ADS)

Latora, V.; Nicosia, V.; Panzarasa, P.

2013-05-01

In the social sciences, the debate over the structural foundations of social capital has long vacillated between two positions on the relative benefits associated with two types of social structures: closed structures, rich in third-party relationships, and open structures, rich in structural holes and brokerage opportunities. In this paper, we engage with this debate by focusing on the measures typically used for formalising the two conceptions of social capital: clustering and effective size. We show that these two measures are simply two sides of the same coin, as they can be expressed one in terms of the other through a simple functional relation. Building on this relation, we then attempt to reconcile closed and open structures by proposing a new measure, Simmelian brokerage, that captures opportunities of brokerage between otherwise disconnected cohesive groups of contacts. Implications of our findings for research on social capital and complex networks are discussed.

Experience-based human perception of facial expressions in Barbary macaques (Macaca sylvanus)

PubMed Central

Levy, Xandria; Meints, Kerstin; Majolo, Bonaventura

2017-01-01

Background Facial expressions convey key cues of human emotions, and may also be important for interspecies interactions. The universality hypothesis suggests that six basic emotions (anger, disgust, fear, happiness, sadness, and surprise) should be expressed by similar facial expressions in close phylogenetic species such as humans and nonhuman primates. However, some facial expressions have been shown to differ in meaning between humans and nonhuman primates like macaques. This ambiguity in signalling emotion can lead to an increased risk of aggression and injuries for both humans and animals. This raises serious concerns for activities such as wildlife tourism where humans closely interact with wild animals. Understanding what factors (i.e., experience and type of emotion) affect ability to recognise emotional state of nonhuman primates, based on their facial expressions, can enable us to test the validity of the universality hypothesis, as well as reduce the risk of aggression and potential injuries in wildlife tourism. Methods The present study investigated whether different levels of experience of Barbary macaques, Macaca sylvanus, affect the ability to correctly assess different facial expressions related to aggressive, distressed, friendly or neutral states, using an online questionnaire. Participants’ level of experience was defined as either: (1) naïve: never worked with nonhuman primates and never or rarely encountered live Barbary macaques; (2) exposed: shown pictures of the different Barbary macaques’ facial expressions along with the description and the corresponding emotion prior to undertaking the questionnaire; (3) expert: worked with Barbary macaques for at least two months. Results Experience with Barbary macaques was associated with better performance in judging their emotional state. Simple exposure to pictures of macaques’ facial expressions improved the ability of inexperienced participants to better discriminate neutral and distressed faces, and a trend was found for aggressive faces. However, these participants, even when previously exposed to pictures, had difficulties in recognising aggressive, distressed and friendly faces above chance level. Discussion These results do not support the universality hypothesis as exposed and naïve participants had difficulties in correctly identifying aggressive, distressed and friendly faces. Exposure to facial expressions improved their correct recognition. In addition, the findings suggest that providing simple exposure to 2D pictures (for example, information signs explaining animals’ facial signalling in zoos or animal parks) is not a sufficient educational tool to reduce tourists’ misinterpretations of macaque emotion. Additional measures, such as keeping a safe distance between tourists and wild animals, as well as reinforcing learning via videos or supervised visits led by expert guides, could reduce such issues and improve both animal welfare and tourist experience. PMID:28584731

Introducing a Simple Equation to Express Oxidation States as an Alternative to Using Rules Associated with Words Alone

ERIC Educational Resources Information Center

Minkiewicz, Piotr; Darewicz, Malgorzata; Iwaniak, Anna

2018-01-01

A simple equation to calculate the oxidation states (oxidation numbers) of individual atoms in molecules and ions may be introduced instead of rules associated with words alone. The equation includes two of three categories of bonds, classified as proposed by Goodstein: number of bonds with more electronegative atoms and number of bonds with less…

Multi-Mode Analysis of Dual Ridged Waveguide Systems for Material Characterization

DTIC Science & Technology

2015-09-17

characterization is the process of determining the dielectric, magnetic, and magnetoelectric properties of a material. For simple (i.e., linear ...field expressions in terms of elementary functions (sines, cosines, exponentials and Bessel functions) and corresponding propagation constants of the...with material parameters 0 and µ0. • The MUT is simple ( linear , isotropic, homogeneous), and the sample has a uniform thickness. • The waveguide

Expression of an Msx homeobox gene in ascidians: insights into the archetypal chordate expression pattern.

PubMed

Ma, L; Swalla, B J; Zhou, J; Dobias, S L; Bell, J R; Chen, J; Maxson, R E; Jeffery, W R

1996-03-01

The Msx homeobox genes are expressed in complex patterns during vertebrate development in conjunction with inductive tissue interactions. As a means of understanding the archetypal role of Msx genes in chordates, we have isolated and characterized an Msx gene in ascidians, protochordates with a relatively simple body plan. The Mocu Msx-a and McMsx-a genes, isolated from the ascidians Molgula oculata and Molgula citrina, respectively, have homeodomains that place them in the msh-like subclass of Msx genes. Therefore, the Molgula Msx-a genes are most closely related to the msh genes previously identified in a number of invertebrates. Southern blot analysis suggests that there are one or two copies of the Msx-a gene in the Molgula genome. Northern blot and RNase protection analysis indicate that Msx-a transcripts are restricted to the developmental stages of the life cycle. In situ hybridization showed that Msx-a mRNA first appears just before gastrulation in the mesoderm (presumptive notochord and muscle) and ectoderm (neural plate) cells. Transcript levels decline in mesoderm cells after the completion of gastrulation, but are enhanced in the folding neural plate during neurulation. Later, Msx-a mRNA is also expressed in the posterior ectoderm and in a subset of the tail muscle cells. The ectoderm and mesoderm cells that express Msx-a are undergoing morphogenetic movements during gastrulation, neurulation, and tail formation. Msx-a expression ceases after these cells stop migrating. The ascidian M. citrina, in which adult tissues and organs begin to develop precociously in the larva, was used to study Msx-a expression during adult development. Msx-a transcripts are expressed in the heart primordium and the rudiments of the ampullae, epidermal protrusions with diverse functions in the juvenile. The heart and ampullae develop in regions where mesenchyme cells interact with endodermal or epidermal epithelia. A comparison of the expression patterns of the Molgula genes with those of their vertebrate congeners suggests that the archetypal roles of the Msx genes may be in morphogenetic movements during embryogenesis and in mesenchymal-epithelial interactions during organogenesis.

[Conversion methods of freshwater snail tissue dry mass and ash free dry mass].

PubMed

Zhao, Wei-Hua; Wang, Hai-Jun; Wang, Hong-Zhu; Liu, Xue-Qin

2009-06-01

Mollusk biomass is usually expressed as wet mass with shell, but this expression fails to represent real biomass due to the high calcium carbonate content in shells. Tissue dry mass and ash free dry mass are relatively close to real biomass. However, the determination process of these two parameters is very complicated, and thus, it is necessary to establish simple and practical conversion methods for these two parameters. A total of six taxa of freshwater snails (Bellamya sp., Alocinma longicornis, Parafossarulus striatulus, Parafossarulus eximius, Semisulcospira cancellata, and Radix sp.) common in the Yangtze Basin were selected to explore the relations of their five shell dimension parameters, dry and wet mass with shells with their tissue dry mass and ash free dry mass. The regressions of the tissue dry mass and ash free dry mass with the five shell dimension parameters were all exponential (y = ax(b)). Among them, shell width and shell length were more precise (the average percentage error between observed and predicted value being 22.0% and 22.5%, respectively) than the other three parameters in the conversion of dry mass. Wet mass with shell could be directly converted to tissue dry mass and ash free dry mass, with an average percentage error of 21.7%. According to the essence of definition and the errors of conversion, ash free dry mass would be the optimum parameter to express snail biomass.

ICL: The Image Composition Language

NASA Technical Reports Server (NTRS)

Foley, James D.; Kim, Won Chul

1986-01-01

The Image Composition Language (ICL) provides a convenient way for programmers of interactive graphics application programs to define how the video look-up table of a raster display system is to be loaded. The ICL allows one or several images stored in the frame buffer to be combined in a variety of ways. The ICL treats these images as variables, and provides arithematic, relational, and conditional operators to combine the images, scalar variables, and constants in image composition expressions. The objective of ICL is to provide programmers with a simple way to compose images, to relieve the tedium usually associated with loading the video look-up table to obtain desired results.

Enhanced thermoelectric response in the fractional quantum Hall effect

NASA Astrophysics Data System (ADS)

Roura-Bas, Pablo; Arrachea, Liliana; Fradkin, Eduardo

2018-02-01

We study the linear thermoelectric response of a quantum dot embedded in a constriction of a quantum Hall bar with fractional filling factors ν =1 /m within Laughlin series. We calculate the figure of merit Z T for the maximum efficiency at a fixed temperature difference. We find a significant enhancement of this quantity in the fractional filling in relation to the integer-filling case, which is a direct consequence of the fractionalization of the electron in the fractional quantum Hall state. We present simple theoretical expressions for the Onsager coefficients at low temperatures, which explicitly show that Z T and the Seebeck coefficient increase with m .

Automated Reporting of DXA Studies Using a Custom-Built Computer Program.

PubMed

England, Joseph R; Colletti, Patrick M

2018-06-01

Dual-energy x-ray absorptiometry (DXA) scans are a critical population health tool and relatively simple to interpret but can be time consuming to report, often requiring manual transfer of bone mineral density and associated statistics into commercially available dictation systems. We describe here a custom-built computer program for automated reporting of DXA scans using Pydicom, an open-source package built in the Python computer language, and regular expressions to mine DICOM tags for patient information and bone mineral density statistics. This program, easy to emulate by any novice computer programmer, has doubled our efficiency at reporting DXA scans and has eliminated dictation errors.

Breeding based remobilization of Tol2 transposon in Xenopus tropicalis.

PubMed

Lane, Maura A; Kimber, Megan; Khokha, Mustafa K

2013-01-01

Xenopus is a powerful model for studying a diverse array of biological processes. However, despite multiple methods for transgenesis, relatively few transgenic reporter lines are available and commonly used. Previous work has demonstrated that transposon based strategies are effective for generating transgenic lines in both invertebrate and vertebrate systems. Here we show that the Tol2 transposon can be remobilized in the genome of X. tropicalis and passed through the germline via a simple breeding strategy of crossing transposase expressing and transposon lines. This remobilization system provides another tool to exploit transgenesis and opens new opportunities for gene trap and enhancer trap strategies.

Optimization of optical systems.

PubMed

Champagne, E B

1966-11-01

The power signal-to-noise ratios for coherent and noncoherent optical detection are presented, with the expression for noncoherent detection being examined in detail. It is found that for the long range optical system to compete with its microwave counterpart it is necessary to optimize the optical system. The optical system may be optimized by using coherent detection, or noncoherent detection if the signal is the dominate noise factor. A design procedure is presented which, in principle, always allows one to obtain signal shot-noise limited operation with noncoherent detection if pulsed operation is used. The technique should make reasonable extremely long range, high data rate systems of relatively simple design.

An asymptotic analysis of the laminar-turbulent transition of yield stress fluids in pipes

NASA Astrophysics Data System (ADS)

Myers, Tim G.; Mitchell, Sarah L.; Slatter, Paul

2017-02-01

The work in this paper concerns the axisymmetric pipe flow of a Herschel-Bulkley fluid, with the aim of determining a relation between the critical velocity (defining the transition between laminar and turbulent flow) and the pipe diameter in terms of the Reynolds number Re 3. The asymptotic behaviour for large and small pipes is examined and simple expressions for the leading order terms are presented. Results are then compared with experimental data. A nonlinear regression analysis shows that for the tested fluids the transition occurs at similar values to the Newtonian case, namely in the range 2100 < Re 3 < 2500.

Generation and Analysis of Expressed Sequence Tags (ESTs) from Halophyte Atriplex canescens to Explore Salt-Responsive Related Genes

PubMed Central

Li, Jingtao; Sun, Xinhua; Yu, Gang; Jia, Chengguo; Liu, Jinliang; Pan, Hongyu

2014-01-01

Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources. PMID:24960361

Constitutive Activity among Orphan Class-A G Protein Coupled Receptors.

PubMed

Martin, Adam L; Steurer, Michael A; Aronstam, Robert S

2015-01-01

The purpose of this study was to evaluate the extent of constitutive activity among orphan class-A G protein coupled receptors within the cAMP signaling pathway. Constitutive signaling was revealed by changes in gene expression under control of the cAMP response element. Gene expression was measured in Chinese hamster ovary cells transiently co-transfected with plasmids containing a luciferase reporter and orphan receptor. Criteria adopted for defining constitutive activation were: 1) 200% elevation over baseline reporter gene expression; 2) 40% inhibition of baseline expression; and 3) 40% inhibition of expression stimulated by 3 μM forskolin. Five patterns of activity were noted: 1) inhibition under both baseline and forskolin stimulated expression (GPR15, GPR17, GPR18, GPR20, GPR25, GPR27, GPR31, GPR32, GPR45, GPR57, GPR68, GPR83, GPR84, GPR132, GPR150, GPR176); 2) no effect on baseline expression, but inhibition of forskolin stimulated expression (GPR4, GPR26, GPR61, GPR62, GPR78, GPR101, GPR119); 3) elevation of baseline signaling coupled with inhibition of forskolin stimulated expression (GPR6, GPR12); 4) elevation of baseline signaling without inhibition of forskolin stimulated expression (GPR3, GPR21, GPR52, GPR65); and 5) no effect on expression (GPR1, GPR19, GPR22, GPR34, GPR35, GPR39, GPR63, GPR82, GPR85, GPR87). Constitutive activity was observed in 75% of the orphan class-A receptors examined (30 of 40). This constitutive signaling cannot be explained by simple overexpression of the receptor. Inhibition of cAMP mediated expression was far more common (65%) than stimulation of expression (15%). Orphan receptors that were closely related based on amino acid homology tended to have similar effects on gene expression. These results suggest that identification of inverse agonists may be a fruitful approach for categorizing these orphan receptors and targeting them for pharmacological intervention.

Constitutive Activity among Orphan Class-A G Protein Coupled Receptors

PubMed Central

Martin, Adam L.; Steurer, Michael A.; Aronstam, Robert S.

2015-01-01

The purpose of this study was to evaluate the extent of constitutive activity among orphan class-A G protein coupled receptors within the cAMP signaling pathway. Constitutive signaling was revealed by changes in gene expression under control of the cAMP response element. Gene expression was measured in Chinese hamster ovary cells transiently co-transfected with plasmids containing a luciferase reporter and orphan receptor. Criteria adopted for defining constitutive activation were: 1) 200% elevation over baseline reporter gene expression; 2) 40% inhibition of baseline expression; and 3) 40% inhibition of expression stimulated by 3 μM forskolin. Five patterns of activity were noted: 1) inhibition under both baseline and forskolin stimulated expression (GPR15, GPR17, GPR18, GPR20, GPR25, GPR27, GPR31, GPR32, GPR45, GPR57, GPR68, GPR83, GPR84, GPR132, GPR150, GPR176); 2) no effect on baseline expression, but inhibition of forskolin stimulated expression (GPR4, GPR26, GPR61, GPR62, GPR78, GPR101, GPR119); 3) elevation of baseline signaling coupled with inhibition of forskolin stimulated expression (GPR6, GPR12); 4) elevation of baseline signaling without inhibition of forskolin stimulated expression (GPR3, GPR21, GPR52, GPR65); and 5) no effect on expression (GPR1, GPR19, GPR22, GPR34, GPR35, GPR39, GPR63, GPR82, GPR85, GPR87). Constitutive activity was observed in 75% of the orphan class-A receptors examined (30 of 40). This constitutive signaling cannot be explained by simple overexpression of the receptor. Inhibition of cAMP mediated expression was far more common (65%) than stimulation of expression (15%). Orphan receptors that were closely related based on amino acid homology tended to have similar effects on gene expression. These results suggest that identification of inverse agonists may be a fruitful approach for categorizing these orphan receptors and targeting them for pharmacological intervention. PMID:26384023

Using Synthetic Biology to Distinguish and Overcome Regulatory and Functional Barriers Related to Nitrogen Fixation

PubMed Central

Wang, Xia; Yang, Jian-Guo; Chen, Li; Wang, Ji-Long; Cheng, Qi; Dixon, Ray; Wang, Yi-Ping

2013-01-01

Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ∼100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase–LacI expression system was used to replace the σ54-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ∼42% of the nitrogenase activity of the σ54-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology. PMID:23935879

Defect of the well-known (classical) expression for the ionization rate in gas-discharge plasma and its modification

NASA Astrophysics Data System (ADS)

Litvinov, I. I.

2015-11-01

A critical analysis is given of the well-known expression for the electron-impact ionization rate constant α i of neutral atoms and ions, derived by linearization of the ionization cross section σ i (ɛ) as a function of the electron energy near the threshold I and containing the characteristic factor ( I + 2 kT). Using the classical Thomson expression for the ionization cross section, it is shown that in addition to the linear slope of σ i (ɛ), it is also necessary to take into account the large negative curvature of this function near the threshold. In this case, the second term in parentheses changes its sign, which means that the commonly used expression for α i (˜4 kT/I) already at moderate values of the temperature ( kT/I ˜ 0.1). The source of this error lies in a mathematical mistake in the original approach and is related to the incorrect choice of the sequential orders of terms small in the parameter kT/I. On the basis of a large amount of experimental data and considerations similar to the Gryzinski theory, a universal two-parameter modification of the Thomson formula (as well as the Bethe—Born formula) is proposed and a new simple expression for the ionization rate constant for arbitrary values of kT/I is derived.

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia

2014-08-28

The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigatedmore » preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results.« less

MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms

PubMed Central

2011-01-01

Background Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge. Therefore, a reverse strategy, which identifies functionally important SNPs by virtue of the bimodal abundance across the human population of the SNP-related mRNAs will be useful. Those mRNA transcripts that are expressed at two distinct abundances in proportion to SNP allele frequency may warrant further study. Matrix metalloproteinase 1 (MMP1) is important in both normal development and in numerous pathologies. Although much research has been conducted to investigate the expression of MMP1 in many different cell types and conditions, the regulation of its expression is still not fully understood. Results In this study, we used a novel but straightforward method based on agglomerative hierarchical clustering to identify bimodally expressed transcripts in human umbilical vein endothelial cell (HUVEC) microarray data from 15 individuals. We found that MMP1 mRNA abundance was bimodally distributed in un-treated HUVECs and showed a bimodal response to inflammatory mediator treatment. RT-PCR and MMP1 activity assays confirmed the bimodal regulation and DNA sequencing of 69 individuals identified an MMP1 gene promoter polymorphism that segregated precisely with the MMP1 bimodal expression. Chromatin immunoprecipation (ChIP) experiments indicated that the transcription factors (TFs) ETS1, ETS2 and GATA3, bind to the MMP1 promoter in the region of this polymorphism and may contribute to the bimodal expression. Conclusions We describe a simple method to identify putative bimodally expressed RNAs from transcriptome data that is effective yet easy for non-statisticans to understand and use. This method identified bimodal endothelial cell expression of MMP1, which appears to be biologically significant with implications for inflammatory disease. (271 Words) PMID:21244711

Expression of Prox1 defines regions of the avian otocyst that give rise to sensory or neural cells

NASA Technical Reports Server (NTRS)

Stone, Jennifer S.; Shang, Jia-Lin; Tomarev, Stanislav

2003-01-01

The simple primordium of the inner ear (otocyst) differentiates into many cell types, including sensory neurons and hair cells. We examined expression of the divergent homeobox transcription factor, cProx1, during otocyst development in chickens. Nuclear cProx1 protein is not evident in the otic placode but emerges in the otic cup by stage 12. At stage 16, cProx1-positive nuclei are scattered continuously throughout the neuroepithelium, from anteroventral to posteromedial. These labeled cells are neural precursors; they express betaIII-tubulin and migrate to the cochleovestibular ganglion between stages 13 and 21. By stage 18, two areas develop a dense pattern of cProx1 expression in which every nucleus is labeled. These areas emerge at the anterior and posterior extremes of the band of scattered cProx1 expression and express the sensory markers cSerrate1 and Cath1 by stage 23. Four discrete patches of dense cProx1 expression appear by stage 23 that correspond to the future superior crista, lateral crista, saccular macula, and posterior crista, as confirmed by immunolabeling for hair cell antigen (HCA) by stage 29. The remaining sensory epithelia display a dense pattern of cProx1 expression and label for HCA by stage 29. In the basilar papilla, nuclear cProx1 expression is down-regulated in most hair cells by stage 37 and in many supporting cells by stage 40. Our findings show that regions of the otocyst that give rise to neurons or hair cells are distinguished by their relative density of cProx1-positive nuclei, and suggest a role for cProx1 in the genesis of these cell types.

A LEAFY co-regulator encoded by UNUSUAL FLORAL ORGANS.

PubMed

Lee, I; Wolfe, D S; Nilsson, O; Weigel, D

1997-02-01

. Development of petals and stamens in Arabidopsis flowers requires the function of the organ-identity gene APETALA3 (AP3), whose RNA is expressed specifically in petal and stamen primordia. AP3 expression is positively regulated by the meristem-identity gene LEAFY (LFY), which is expressed ubiquitously in young flowers. It is unknown how the transition from ubiquitous expression of LFY to region-specific expression of AP3 is made. It has previously been proposed for Antirrhinum that another gene, FIMBRIATA (FIM), mediates between the LFY and AP3 orthologs, with the three genes acting in a simple regulatory hierarchy. FIM is activated later than the LFY ortholog, and its expression is more restricted than that of the LFY ortholog. . We have tested whether the model proposed for Antirrhinum applies to Arabidopsis, by creating transgenic plants in which the FIM ortholog UNUSUAL FLORAL ORGANS (UFO) was expressed constitutively from the promoter of the cauliflower mosaic virus 35S gene. In 35S::UFO flowers, AP3 was expressed precociously and ectopically, confirming that UFO is an upstream regulator of AP3. However, 35S::UFO could not restore petal and stamen development in lfy mutants, indicating that UFO can only function in the presence of LFY activity. The failure of 35S::UFO to rescue lfy mutants is consistent with our observation that UFO expression levels are not markedly changed in lfy mutants. . We conclude that UFO is not a simple mediator between meristem- and organ-identity genes, but is likely to be a partially dispensable co-regulator that acts together with LFY. The interplay between LFY and UFO provides a paradigm for how a global regulator such as LFY activates selected target genes only in restricted regions within its expression domain.

Identification of novel candidate maternal serum protein markers for Down syndrome by integrated proteomic and bioinformatic analysis.

PubMed

Kang, Yuan; Dong, Xinran; Zhou, Qiongjie; Zhang, Ying; Cheng, Yan; Hu, Rong; Su, Cuihong; Jin, Hong; Liu, Xiaohui; Ma, Duan; Tian, Weidong; Li, Xiaotian

2012-03-01

This study aimed to identify candidate protein biomarkers from maternal serum for Down syndrome (DS) by integrated proteomic and bioinformatics analysis. A pregnancy DS group of 18 women and a control group with the same number were prepared, and the maternal serum proteins were analyzed by isobaric tags for relative and absolute quantitation and mass spectrometry, to identify DS differentially expressed maternal serum proteins (DS-DEMSPs). Comprehensive bioinformatics analysis was then employed to analyze DS-DEMSPs both in this paper and seven related publications. Down syndrome differentially expressed maternal serum proteins from different studies are significantly enriched with common Gene Ontology functions, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, transcription factor binding sites, and Pfam protein domains, However, the DS-DEMSPs are less functionally related to known DS-related genes. These evidences suggest that common molecular mechanisms induced by secondary effects may be present upon DS carrying. A simple scoring scheme revealed Alpha-2-macroglobulin, Apolipoprotein A1, Apolipoprotein E, Complement C1s subcomponent, Complement component 5, Complement component 8, alpha polypeptide, Complement component 8, beta polypeptide and Fibronectin as potential DS biomarkers. The integration of proteomics and bioinformatics studies provides a novel approach to develop new prenatal screening methods for noninvasive yet accurate diagnosis of DS. Copyright © 2012 John Wiley & Sons, Ltd.

Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters.

PubMed

Lukashin, A V; Fuchs, R

2001-05-01

Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

The Use of Standard Tasks to Measure Achievement in Reading, Spelling, and Written Expression: A Normative and Developmental Study.

ERIC Educational Resources Information Center

Deno, Stanley; And Others

Simple measures of reading, spelling, and written expression were administered to 566 elementary students from the states of Minnesota, Pennsylvania, and Washington. Each child was individually administered three reading word lists, three reading passages, two dictated spelling lists, and two story starters. Approximately 25 minutes was needed for…

Fisher classifier and its probability of error estimation

NASA Technical Reports Server (NTRS)

Chittineni, C. B.

1979-01-01

Computationally efficient expressions are derived for estimating the probability of error using the leave-one-out method. The optimal threshold for the classification of patterns projected onto Fisher's direction is derived. A simple generalization of the Fisher classifier to multiple classes is presented. Computational expressions are developed for estimating the probability of error of the multiclass Fisher classifier.

An Efficient Method for Generation of Knockout Human Embryonic Stem Cells Using CRISPR/Cas9 System.

PubMed

Bohaciakova, Dasa; Renzova, Tereza; Fedorova, Veronika; Barak, Martin; Kunova Bosakova, Michaela; Hampl, Ales; Cajanek, Lukas

2017-11-01

Human embryonic stem cells (hESCs) represent a promising tool to study functions of genes during development, to model diseases, and to even develop therapies when combined with gene editing techniques such as CRISPR/CRISPR-associated protein-9 nuclease (Cas9) system. However, the process of disruption of gene expression by generation of null alleles is often inefficient and tedious. To circumvent these limitations, we developed a simple and efficient protocol to permanently downregulate expression of a gene of interest in hESCs using CRISPR/Cas9. We selected p53 for our proof of concept experiments. The methodology is based on series of hESC transfection, which leads to efficient downregulation of p53 expression even in polyclonal population (p53 Low cells), here proven by a loss of regulation of the expression of p53 target gene, microRNA miR-34a. We demonstrate that our approach achieves over 80% efficiency in generating hESC clonal sublines that do not express p53 protein. Importantly, we document by a set of functional experiments that such genetically modified hESCs do retain typical stem cells characteristics. In summary, we provide a simple and robust protocol to efficiently target expression of gene of interest in hESCs that can be useful for laboratories aiming to employ gene editing in their hESC applications/protocols.

Kinetic models of gene expression including non-coding RNAs

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2011-03-01

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

Vitronectin-Based, Biomimetic Encapsulating Hydrogel Scaffolds Support Adipogenesis of Adipose Stem Cells

PubMed Central

Clevenger, Tracy N.; Hinman, Cassidy R.; Ashley Rubin, Rebekah K.; Smither, Kate; Burke, Daniel J.; Hawker, Craig J.; Messina, Darin; Van Epps, Dennis

2016-01-01

Soft tissue defects are relatively common, yet currently used reconstructive treatments have varying success rates, and serious potential complications such as unpredictable volume loss and reabsorption. Human adipose-derived stem cells (ASCs), isolated from liposuction aspirate have great potential for use in soft tissue regeneration, especially when combined with a supportive scaffold. To design scaffolds that promote differentiation of these cells down an adipogenic lineage, we characterized changes in the surrounding extracellular environment during adipogenic differentiation. We found expression changes in both extracellular matrix proteins, including increases in expression of collagen-IV and vitronectin, as well as changes in the integrin expression profile, with an increase in expression of integrins such as αVβ5 and α1β1. These integrins are known to specifically interact with vitronectin and collagen-IV, respectively, through binding to an Arg-Gly-Asp (RGD) sequence. When three different short RGD-containing peptides were incorporated into three-dimensional (3D) hydrogel cultures, it was found that an RGD-containing peptide derived from vitronectin provided strong initial attachment, maintained the desired morphology, and created optimal conditions for in vitro 3D adipogenic differentiation of ASCs. These results describe a simple, nontoxic encapsulating scaffold, capable of supporting the survival and desired differentiation of ASCs for the treatment of soft tissue defects. PMID:26956095

Expression of Innate Immunity Genes in Epithelial Cells of Hypertrophic Adenoids with and without Pediatric Chronic Rhinosinusitis: A Preliminary Report

PubMed Central

Qu, Xiao-Peng; Huang, Zhen-Xiao; Sun, Yan; Ye, Ting; Cui, Shun-Jiu; Huang, Qian; Ma, Li-Jing; Yang, Qing-Wen; Wang, Hong; Fan, Er-Zhong; Li, Ying; Zhang, Liang; Zhou, Bing

2015-01-01

Background: Adenoid hypertrophy (AH) is associated with pediatric chronic rhinosinusitis (pCRS), but its role in the inflammatory process of pCRS is unclear. It is thought that innate immunity gene expression is disrupted in the epithelium of patients with chronic rhinosinusitis (CRS), including antimicrobial peptides and pattern recognition receptors (PRRs). The aim of this preliminary study was to detect the expression of innate immunity genes in epithelial cells of hypertrophic adenoids with and without pCRS to better understand their role in pCRS. Methods: Nine pCRS patients and nine simple AH patients undergoing adenoidectomy were recruited for the study. Adenoidal epithelium was isolated, and real-time quantitative polymerase chain reaction (RT-qPCR) was employed to measure relative expression levels of the following messenger RNAs in hypertrophic adenoid epithelial cells of pediatric patients with and without CRS: Human β-defensin (HBD) 2 and 3, surfactant protein (SP)-A and D, toll-like receptors 1–10, nucleotide-binding oligomerization domain (NOD)-like receptors NOD 1, NOD 2, and NACHT, LRR and PYD domains-containing protein 3, retinoic acid-induced gene 1, melanoma differentiation-associated gene 5, and nuclear factor-κB (NF-κB). RT-qPCR data from two groups were analyzed by independent sample t-tests and Mann-Whitney U-tests. Results: The relative expression of SP-D in adenoidal epithelium of pCRS group was significantly lower than that in AH group (pCRS 0.73 ± 0.10 vs. AH 1.21 ± 0.15; P = 0.0173, t = 2.654). The relative expression levels of all tested PRRs and NF-κB, as well as HBD-2, HBD-3, and SP-A, showed no statistically significant differences in isolated adenoidal epithelium between pCRS group and AH group. Conclusions: Down-regulated SP-D levels in adenoidal epithelium may contribute to the development of pCRS. PRRs, however, are unlikely to play a significant role in the inflammatory process of pCRS. PMID:26521790

A novel dual-marker expression panel for easy and accurate risk stratification of patients with gastric cancer.

PubMed

Kanda, Mitsuro; Murotani, Kenta; Tanaka, Haruyoshi; Miwa, Takashi; Umeda, Shinichi; Tanaka, Chie; Kobayashi, Daisuke; Hayashi, Masamichi; Hattori, Norifumi; Suenaga, Masaya; Yamada, Suguru; Nakayama, Goro; Fujiwara, Michitaka; Kodera, Yasuhiro

2018-05-07

Development of specific biomarkers is necessary for individualized management of patients with gastric cancer. The aim of this study was to design a simple expression panel comprising novel molecular markers for precise risk stratification. Patients (n = 200) who underwent gastrectomy for gastric cancer were randomly assigned into learning and validation sets. Tissue mRNA expression levels of 15 candidate molecular markers were determined using quantitative PCR analysis. A dual-marker expression panel was created according to concordance index (C-index) values of overall survival for all 105 combinations of two markers in the learning set. The reproducibility and clinical significance of the dual-marker expression panel were evaluated in the validation set. The patient characteristics of the learning and validation sets were well balanced. The C-index values of combinations were significantly higher compared with those of single markers. The panel with the highest C-index (0.718) of the learning set comprised SYT8 and MAGED2, which clearly stratified patients into low-, intermediate-, and high-risk groups. The reproducibility of the panel was demonstrated in the validation set. High expression scores were significantly associated with larger tumor size, vascular invasion, lymph node metastasis, peritoneal metastasis, and advanced disease. The dual-marker expression panel provides a simple tool that clearly stratifies patients with gastric cancer into low-, intermediate-, and high risk after gastrectomy. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

A set for relational reasoning: Facilitation of algebraic modeling by a fraction task.

PubMed

DeWolf, Melissa; Bassok, Miriam; Holyoak, Keith J

2016-12-01

Recent work has identified correlations between early mastery of fractions and later math achievement, especially in algebra. However, causal connections between aspects of reasoning with fractions and improved algebra performance have yet to be established. The current study investigated whether relational reasoning with fractions facilitates subsequent algebraic reasoning using both pre-algebra students and adult college students. Participants were first given either a relational reasoning fractions task or a fraction algebra procedures control task. Then, all participants solved word problems and constructed algebraic equations in either multiplication or division format. The word problems and the equation construction tasks involved simple multiplicative comparison statements such as "There are 4 times as many students as teachers in a classroom." Performance on the algebraic equation construction task was enhanced for participants who had previously completed the relational fractions task compared with those who completed the fraction algebra procedures task. This finding suggests that relational reasoning with fractions can establish a relational set that promotes students' tendency to model relations using algebraic expressions. Copyright © 2016 Elsevier Inc. All rights reserved.

A simple and robust vector-based shRNA expression system used for RNA interference.

PubMed

Wang, Xue-jun; Li, Ying; Huang, Hai; Zhang, Xiu-juan; Xie, Pei-wen; Hu, Wei; Li, Dan-dan; Wang, Sheng-qi

2013-01-01

RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful genetic tool for conducting functional studies. Previously, vector-based shRNA-expression strategies capable of inducing RNAi in viable cells have been developed, however, these vector systems have some disadvantages, either because they were error-prone or cost prohibitive. In this report we described the development of a simple, robust shRNA expression system utilizing 1 long oligonucleotide or 2 short oligonucleotides for half the cost of conventional shRNA construction methods and with a >95% cloning success rate. The shRNA loop sequence and stem structure were also compared and carefully selected for better RNAi efficiency. Furthermore, an easier strategy was developed based on isocaudomers which permit rapid combination of the most efficient promoter-shRNA cassettes. Finally, using this method, the conservative target sites for hepatitis B virus (HBV) knockdown were systemically screened and HBV antigen expression shown to be successfully suppressed in the presence of connected multiple shRNAs both in vitro and in vivo. This novel design describes an inexpensive and effective way to clone and express single or multiple shRNAs from the same vector with the capacity for potent and effective silencing of target genes.

Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicumstrains.

PubMed

Tummala, Seshu B; Junne, Stefan G; Paredes, Carlos J; Papoutsakis, Eleftherios T

2003-12-30

Antisense RNA (asRNA) downregulation alters protein expression without changing the regulation of gene expression. Downregulation of primary metabolic enzymes possibly combined with overexpression of other metabolic enzymes may result in profound changes in product formation, and this may alter the large-scale transcriptional program of the cells. DNA-array based large-scale transcriptional analysis has the potential to elucidate factors that control cellular fluxes even in the absence of proteome data. These themes are explored in the study of large-scale transcriptional analysis programs and the in vivo primary-metabolism fluxes of several related recombinant C. acetobutylicum strains: C. acetobutylicum ATCC 824(pSOS95del) (plasmid control; produces high levels of butanol snd acetone), 824(pCTFB1AS) (expresses antisense RNA against CoA transferase (ctfb1-asRNA); produces very low levels of butanol and acetone), and 824(pAADB1) (expresses ctfb1-asRNA and the alcohol-aldehyde dahydrogenase gene (aad); produce high alcohol and low acetone levels). DNA-array based transcriptional analysis revealed that the large changes in product concentrations (snd notably butanol concentration) due to ctfb1-asRNA expression alone and in combination with aad overexpression resulted in dramatic changes of the cellular transcriptome. Cluster analysis and gene expression patterns of established and putative operons involved in stress response, motility, sporulation, and fatty-acid biosynthesis indicate that these simple genetic changes dramatically alter the cellular programs of C. acetobutylicum. Comparison of gene expression and flux analysis data may point to possible flux-controling steps and suggest unknown regulatory mechanisms. Copyright 2003; Wiley Periodicals, Inc.

Normal uniform mixture differential gene expression detection for cDNA microarrays

PubMed Central

Dean, Nema; Raftery, Adrian E

2005-01-01

Background One of the primary tasks in analysing gene expression data is finding genes that are differentially expressed in different samples. Multiple testing issues due to the thousands of tests run make some of the more popular methods for doing this problematic. Results We propose a simple method, Normal Uniform Differential Gene Expression (NUDGE) detection for finding differentially expressed genes in cDNA microarrays. The method uses a simple univariate normal-uniform mixture model, in combination with new normalization methods for spread as well as mean that extend the lowess normalization of Dudoit, Yang, Callow and Speed (2002) [1]. It takes account of multiple testing, and gives probabilities of differential expression as part of its output. It can be applied to either single-slide or replicated experiments, and it is very fast. Three datasets are analyzed using NUDGE, and the results are compared to those given by other popular methods: unadjusted and Bonferroni-adjusted t tests, Significance Analysis of Microarrays (SAM), and Empirical Bayes for microarrays (EBarrays) with both Gamma-Gamma and Lognormal-Normal models. Conclusion The method gives a high probability of differential expression to genes known/suspected a priori to be differentially expressed and a low probability to the others. In terms of known false positives and false negatives, the method outperforms all multiple-replicate methods except for the Gamma-Gamma EBarrays method to which it offers comparable results with the added advantages of greater simplicity, speed, fewer assumptions and applicability to the single replicate case. An R package called nudge to implement the methods in this paper will be made available soon at . PMID:16011807

In Vivo Functional Genomic Studies of Sterol Carrier Protein-2 Gene in the Yellow Fever Mosquito

PubMed Central

Peng, Rong; Maklokova, Vilena I.; Chandrashekhar, Jayadevi H.; Lan, Que

2011-01-01

A simple and efficient DNA delivery method to introduce extrachromosomal DNA into mosquito embryos would significantly aid functional genomic studies. The conventional method for delivery of DNA into insects is to inject the DNA directly into the embryos. Taking advantage of the unique aspects of mosquito reproductive physiology during vitellogenesis and an in vivo transfection reagent that mediates DNA uptake in cells via endocytosis, we have developed a new method to introduce DNA into mosquito embryos vertically via microinjection of DNA vectors in vitellogenic females without directly manipulating the embryos. Our method was able to introduce inducible gene expression vectors transiently into F0 mosquitoes to perform functional studies in vivo without transgenic lines. The high efficiency of expression knockdown was reproducible with more than 70% of the F0 individuals showed sufficient gene expression suppression (<30% of the controls' levels). At the cohort level, AeSCP-2 expression knockdown in early instar larvae resulted in detectable phenotypes of the expression deficiency such as high mortality, lowered fertility, and distorted sex ratio after induction of AeSCP-2 siRNA expression in vivo. The results further confirmed the important role of AeSCP-2 in the development and reproduction of A. aegypti. In this study, we proved that extrachromosaomal transient expression of an inducible gene from a DNA vector vertically delivered via vitellogenic females can be used to manipulate gene expression in F0 generation. This new method will be a simple and efficient tool for in vivo functional genomic studies in mosquitoes. PMID:21437205

INTERNATIONAL CONFERENCE ON SEMICONDUCTOR INJECTION LASERS SELCO-87: Simple formula for the thermal conductivity of a quaternary solid solution

NASA Astrophysics Data System (ADS)

Nakwaski, W.

1988-11-01

An analysis is made of the thermal conductivity of quaternary solid solutions (alloys) allowing for their disordered structure on the basis of a phenomenological analysis proposed by Abeles. This method is applied to a quaternary solid solution In1 - xGaxAsyP1 - y. A simple analytic expression is derived for the thermal conductivity of this material.

Coulomb explosion of uniformly charged spheroids

NASA Astrophysics Data System (ADS)

Grech, M.; Nuter, R.; Mikaberidze, A.; di Cintio, P.; Gremillet, L.; Lefebvre, E.; Saalmann, U.; Rost, J. M.; Skupin, S.

2011-11-01

A simple, semianalytical model is proposed for nonrelativistic Coulomb explosion of a uniformly charged spheroid. This model allows us to derive the time-dependent particle energy distributions. Simple expressions are also given for the characteristic explosion time and maximum particle energies in the limits of extreme prolate and oblate spheroids as well as for the sphere. Results of particle simulations are found to be in remarkably good agreement with the model.

Climate system properties determining the social cost of carbon

NASA Astrophysics Data System (ADS)

Otto, Alexander; Todd, Benjamin J.; Bowerman, Niel; Frame, David J.; Allen, Myles R.

2013-06-01

The choice of an appropriate scientific target to guide global mitigation efforts is complicated by uncertainties in the temperature response to greenhouse gas emissions. Much climate policy discourse has been based on the equilibrium global mean temperature increase following a concentration stabilization scenario. This is determined by the equilibrium climate sensitivity (ECS) which, in many studies, shows persistent, fat-tailed uncertainty. However, for many purposes, the equilibrium response is less relevant than the transient response. Here, we show that one prominent policy variable, the social cost of carbon (SCC), is generally better constrained by the transient climate response (TCR) than by the ECS. Simple analytic expressions show the SCC to be directly proportional to the TCR under idealized assumptions when the rate at which we discount future damage equals 2.8%. Using ensemble simulations of a simple climate model we find that knowing the true value of the TCR can reduce the relative uncertainty in the SCC substantially more, up to a factor of 3, than knowing the ECS under typical discounting assumptions. We conclude that the TCR, which is better constrained by observations, less subject to fat-tailed uncertainty and more directly related to the SCC, is generally preferable to the ECS as a single proxy for the climate response in SCC calculations.

State relations for a two-phase mixture of reacting explosives and applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kubota, Shiro; Saburi, Tei; Ogata, Yuji

2007-10-15

To assess the assumptions behind the two phase mixture rule for reacting explosives, the shock-to-detonation transition process was calculated for high explosives using a finite difference method. An ignition and growth model and the Jones-Wilkins-Lee (JWL) equations of state were employed. The simple mixture rule assumes that the reacting explosive is a simple mixture of the reactant and product components. Four different assumptions, such as that of thermal equilibrium and isotropy, were adopted to calculate the pressure. The main purpose of this paper is to present the answer to the question of why the numerical results of shock-initiation are insensitivemore » to the assumptions adopted. The equations of state for reactants and products were assessed by considering plots of the specific internal energy E and specific volume V. If the slopes of the constant-pressure lines for both components in the E-V plane are almost the same, it is demonstrated that the numerical results are insensitive to the assumptions adopted. We have found that the relation for the specific volumes of the two components can be approximately expressed by a single curve of the specific volume of the reactant vs that of the products. We discuss this relationship in terms of the results of the numerical simulation. (author)« less

Chemosignals, hormones, and amphibian reproduction.

PubMed

Woodley, Sarah

2015-02-01

This article is part of a Special Issue "Chemosignals and Reproduction". Amphibians are often thought of as relatively simple animals especially when compared to mammals. Yet the chemosignaling systems used by amphibians are varied and complex. Amphibian chemosignals are particularly important in reproduction, in both aquatic and terrestrial environments. Chemosignaling is most evident in salamanders and newts, but increasing evidence indicates that chemical communication facilitates reproduction in frogs and toads as well. Reproductive hormones shape the production, dissemination, detection, and responsiveness to chemosignals. A large variety of chemosignals have been identified, ranging from simple, invariant chemosignals to complex, variable blends of chemosignals. Although some chemosignals elicit straightforward responses, others have relatively subtle effects. Review of amphibian chemosignaling reveals a number of issues to be resolved, including: 1) the significance of the complex, individually variable blends of courtship chemosignals found in some salamanders, 2) the behavioral and/or physiological functions of chemosignals found in anuran "breeding glands", 3) the ligands for amphibian V2Rs, especially V2Rs expressed in the main olfactory epithelium, and 4) the mechanism whereby transdermal delivery of chemosignals influences behavior. To date, only a handful of the more than 7000 species of amphibians has been examined. Further study of amphibians should provide additional insight to the role of chemosignals in reproduction. Copyright © 2014 Elsevier Inc. All rights reserved.

A simple approach for human recombinant apolipoprotein E4 expression and purification.

PubMed

Argyri, Letta; Skamnaki, Vassiliki; Stratikos, Efstratios; Chroni, Angeliki

2011-10-01

We report a simple expression and purification procedure for the production of recombinant apolipoprotein E4 (apoE4), an important protein for the lipid homeostasis in humans that plays critical roles in the pathogenesis of cardiovascular and neurodegenerative diseases. Our approach is based on the expression of a thioredoxin-apoE4 fusion construct in bacterial cells and subsequent removal of the fused thioredoxin using the highly specific 3C protease, avoiding costly and laborious lipidation-delipidation steps used before. Our approach results in rapid, high-yield production of structurally and functionally competent apoE4 as evidenced by secondary structure measurements, thermal and chemical melting profiles and the kinetic profile of solubilization of dimyristoyl-phosphatidylcholine (DMPC) vesicles. This protocol is appropriate for laboratories with little experience in apolipoprotein biochemistry and will facilitate future studies on the role of apoE4 in the pathogenesis of cardiovascular disease and neurodegenerative diseases, including Alzheimer's disease. Copyright © 2011 Elsevier Inc. All rights reserved.

Lensing in the geodesic light-cone coordinates and its (exact) illustration to an off-center observer in Lemaȋtre-Tolman-Bondi models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanizza, G.; Nugier, F., E-mail: giuseppe.fanizza@ba.infn.it, E-mail: fabienjean.nugier@unibo.it

We present in this paper a new application of the geodesic light-cone (GLC) gauge for weak lensing calculations. Using interesting properties of this gauge, we derive an exact expression of the amplification matrix—involving convergence, magnification and shear—and of the deformation matrix—involving the optical scalars. These expressions are simple and non-perturbative as long as no caustics are created on the past light-cone and are, by construction, free from the thin lens approximation. We apply these general expressions on the example of an Lemaȋtre-Tolman-Bondi (LTB) model with an off-center observer and obtain explicit forms for the lensing quantities as a direct consequencemore » of the non-perturbative transformation between GLC and LTB coordinates. We show their evolution in redshift after a numerical integration, for underdense and overdense LTB models, and interpret their respective variations in the simple non-curvature case.« less

A Comparative Proteomic Analysis of the Simple Amino Acid Repeat Distributions in Plasmodia Reveals Lineage Specific Amino Acid Selection

PubMed Central

Dalby, Andrew R.

2009-01-01

Background Microsatellites have been used extensively in the field of comparative genomics. By studying microsatellites in coding regions we have a simple model of how genotypic changes undergo selection as they are directly expressed in the phenotype as altered proteins. The simplest of these tandem repeats in coding regions are the tri-nucleotide repeats which produce a repeat of a single amino acid when translated into proteins. Tri-nucleotide repeats are often disease associated, and are also known to be unstable to both expansion and contraction. This makes them sensitive markers for studying proteome evolution, in closely related species. Results The evolutionary history of the family of malarial causing parasites Plasmodia is complex because of the life-cycle of the organism, where it interacts with a number of different hosts and goes through a series of tissue specific stages. This study shows that the divergence between the primate and rodent malarial parasites has resulted in a lineage specific change in the simple amino acid repeat distribution that is correlated to A–T content. The paper also shows that this altered use of amino acids in SAARs is consistent with the repeat distributions being under selective pressure. Conclusions The study shows that simple amino acid repeat distributions can be used to group related species and to examine their phylogenetic relationships. This study also shows that an outgroup species with a similar A–T content can be distinguished based only on the amino acid usage in repeats, and suggest that this might be a useful feature for proteome clustering. The lineage specific use of amino acids in repeat regions suggests that comparative studies of SAAR distributions between proteomes gives an insight into the mechanisms of expansion and the selective pressures acting on the organism. PMID:19597555

Characterizing the Grape Transcriptome. Analysis of Expressed Sequence Tags from Multiple Vitis Species and Development of a Compendium of Gene Expression during Berry Development1[w

PubMed Central

Silva, Francisco Goes da; Iandolino, Alberto; Al-Kayal, Fadi; Bohlmann, Marlene C.; Cushman, Mary Ann; Lim, Hyunju; Ergul, Ali; Figueroa, Rubi; Kabuloglu, Elif K.; Osborne, Craig; Rowe, Joan; Tattersall, Elizabeth; Leslie, Anna; Xu, Jane; Baek, JongMin; Cramer, Grant R.; Cushman, John C.; Cook, Douglas R.

2005-01-01

We report the analysis and annotation of 146,075 expressed sequence tags from Vitis species. The majority of these sequences were derived from different cultivars of Vitis vinifera, comprising an estimated 25,746 unique contig and singleton sequences that survey transcription in various tissues and developmental stages and during biotic and abiotic stress. Putatively homologous proteins were identified for over 17,752 of the transcripts, with 1,962 transcripts further subdivided into one or more Gene Ontology categories. A simple structured vocabulary, with modules for plant genotype, plant development, and stress, was developed to describe the relationship between individual expressed sequence tags and cDNA libraries; the resulting vocabulary provides query terms to facilitate data mining within the context of a relational database. As a measure of the extent to which characterized metabolic pathways were encompassed by the data set, we searched for homologs of the enzymes leading from glycolysis, through the oxidative/nonoxidative pentose phosphate pathway, and into the general phenylpropanoid pathway. Homologs were identified for 65 of these 77 enzymes, with 86% of enzymatic steps represented by paralogous genes. Differentially expressed transcripts were identified by means of a stringent believability index cutoff of ≥98.4%. Correlation analysis and two-dimensional hierarchical clustering grouped these transcripts according to similarity of expression. In the broadest analysis, 665 differentially expressed transcripts were identified across 29 cDNA libraries, representing a range of developmental and stress conditions. The groupings revealed expected associations between plant developmental stages and tissue types, with the notable exception of abiotic stress treatments. A more focused analysis of flower and berry development identified 87 differentially expressed transcripts and provides the basis for a compendium that relates gene expression and annotation to previously characterized aspects of berry development and physiology. Comparison with published results for select genes, as well as correlation analysis between independent data sets, suggests that the inferred in silico patterns of expression are likely to be an accurate representation of transcript abundance for the conditions surveyed. Thus, the combined data set reveals the in silico expression patterns for hundreds of genes in V. vinifera, the majority of which have not been previously studied within this species. PMID:16219919

Expression of the transmembrane mucins, MUC1, MUC4 and MUC16, in normal endometrium and in endometriosis

PubMed Central

Dharmaraj, N.; Chapela, P.J.; Morgado, M.; Hawkins, S.M.; Lessey, B.A.; Young, S.L.; Carson, D.D.

2014-01-01

STUDY QUESTION Are the transmembrane mucins, MUC1, MUC4 and MUC16, differentially expressed in endometriosis compared with normal endometrium? SUMMARY ANSWER This study revealed that transmembrane mucin expression does not vary significantly in normal endometrium during the menstrual cycle and is not altered in endometriosis relative to the epithelial marker, cytokeratin-18 (KRT18). WHAT IS KNOWN ALREADY Increased serum levels of the transmembrane mucin fragments MUC1, MUC4 and MUC16 that normally dominate the apical surface of simple epithelia are found in several pathological conditions, including endometriosis. Altered mucin expression in gynecologic diseases may promote infertility or endometrial pathologies. STUDY DESIGN, SIZE, DURATION This was a laboratory-based study of samples from 12 endometriosis patients as well as non-endometriosis control samples obtained from 31 patients. PARTICIPANTS/MATERIALS, SETTING, METHODS Total RNA was isolated from endometrial biopsies of ectopic and eutopic endometrium from women with endometriosis and control patients from different stages of the menstrual cycle. Quantitative (q)-RT–PCR analyses were performed for the mucins, MUC1, MUC4 and MUC16, relative to the epithelial marker, cytokeratin-18 (KRT18), or β-actin (ACTB). Frozen sections from endometrial biopsies of proliferative and mid-secretory stage women with endometriosis were immunostained for MUC1, MUC4 and MUC16. MAIN RESULTS AND THE ROLE OF CHANCE qRT–PCR analyses of MUC1 and MUC16 mRNA revealed that these mucins do not vary significantly during the menstrual cycle nor are they altered in women with endometriosis relative to the epithelial marker, KRT18. MUC4 mRNA is expressed at very low levels relative to MUC1 and MUC16 under all conditions. There was little difference in MUC1 and MUC16 expression between eutopic endometrial and ectopic endometriotic tissues. MUC4 expression also was not significantly higher in the ectopic endometriotic tissues. Immunostaining for all three mucins reveals robust expression of MUC1 and MUC16 at the apical surfaces of endometrial epithelia, but little to no staining for MUC4. LIMITATIONS, REASONS FOR CAUTION qRT–PCR analysis was the main method used for mucin detection. Additional studies with stage III–IV endometriotic tissue would be useful to determine if changes in MUC1 and MUC16 expression occur, or if MUC4 expression increases, at later stages of endometriosis. WIDER IMPLICATIONS OF THE FINDINGS We report a comprehensive comparative profile of the major transmembrane mucins, MUC1, MUC4 and MUC16, relative to the epithelial marker, KRT18, in normal cycling endometrium and in endometriosis, and indicate constitutive expression. Previous studies have profiled the expression of individual mucins relative to β-actin and indicate accumulation in the luteal phase. Thus, these differences in interpretation appear to reflect the increased epithelial content of endometrium during the luteal phase. STUDY FUNDING This study was supported by: NIH R01HD29963 to D.D.C.; NIH U54HD007495 to S.M.H.; and NIH R01HD067721 to S.L.Y. and B.A.L. The authors have no competing interests to declare. PMID:24939955

DOE Office of Scientific and Technical Information (OSTI.GOV)

French, Jarrod B.; Yates, Phillip A.; Soysa, D.Radika

The final two steps of de novo uridine 5'-monophosphate (UMP) biosynthesis are catalyzed by orotate phosphoribosyltransferase (OPRT) and orotidine 5'-monophosphate decarboxylase (OMPDC). In most prokaryotes and simple eukaryotes these two enzymes are encoded by separate genes, whereas in mammals they are expressed as a bifunctional gene product called UMP synthase (UMPS), with OPRT at the N terminus and OMPDC at the C terminus. Leishmania and some closely related organisms also express a bifunctional enzyme for these two steps, but the domain order is reversed relative to mammalian UMPS. In this work we demonstrate that L. donovani UMPS (LdUMPS) is anmore » essential enzyme in promastigotes and that it is sequestered in the parasite glycosome. We also present the crystal structure of the LdUMPS in complex with its product, UMP. This structure reveals an unusual tetramer with two head to head and two tail to tail interactions, resulting in two dimeric OMPDC and two dimeric OPRT functional domains. In addition, we provide structural and biochemical evidence that oligomerization of LdUMPS is controlled by product binding at the OPRT active site. We propose a model for the assembly of the catalytically relevant LdUMPS tetramer and discuss the implications for the structure of mammalian UMPS.« less

Off-energy-shell p-p scattering at sub-Coulomb energies via the Trojan horse method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumino, A.; Dipartimento di Metodologie Fisiche e Chimiche per l'Ingegneria, Universita di Catania, Catania; Universita Kore di Enna, Enna

2008-12-15

Two-proton scattering at sub-Coulomb energies has been measured indirectly via the Trojan horse method applied to the p + d{yields}p + p + n reaction to investigate off-energy shell effects for scattering processes. The three-body experiment was performed at 5 and 4.7 MeV corresponding to a p-p relative energy ranging from 80 to 670 keV. The free p-p cross section exhibits a deep minimum right within this relative energy region due to Coulomb plus nuclear destructive interference. No minimum occurs instead in the Trojan horse p-p cross section, which was extracted by employing a simple plane-wave impulse approximation. A detailedmore » formalism was developed to build up the expression of the theoretical half-off-shell p-p cross section. Its behavior agrees with the Trojan horse data and in turn formally fits the n-n, n-p, and nuclear p-p cross sections given the fact that in its expression the Coulomb amplitude is negligible with respect to the nuclear one. These results confirm the Trojan horse suppression of the Coulomb amplitude for scattering due to the off-shell character of the process.« less

Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues.

PubMed

Almeida, Tânia; Menéndez, Esther; Capote, Tiago; Ribeiro, Teresa; Santos, Conceição; Gonçalves, Sónia

2013-01-15

The molecular processes associated with cork development in Quercus suber L. are poorly understood. A previous molecular approach identified a list of genes potentially important for cork formation and differentiation, providing a new basis for further molecular studies. This report is the first molecular characterization of one of these candidate genes, QsMYB1, coding for an R2R3-MYB transcription factor. The R2R3-MYB gene sub-family has been described as being involved in the phenylpropanoid and lignin pathways, both involved in cork biosynthesis. The results showed that the expression of QsMYB1 is putatively mediated by an alternative splicing (AS) mechanism that originates two different transcripts (QsMYB1.1 and QsMYB1.2), differing only in the 5'-untranslated region, due to retention of the first intron in one of the variants. Moreover, within the retained intron, a simple sequence repeat (SSR) was identified. The upstream regulatory region of QsMYB1 was extended by a genome walking approach, which allowed the identification of the putative gene promoter region. The relative expression pattern of QsMYB1 transcripts determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR) revealed that both transcripts were up-regulated in cork tissues; the detected expression was several times higher in newly formed cork harvested from trees producing virgin, second or reproduction cork when compared with wood. Moreover, the expression analysis of QsMYB1 in several Q. suber organs showed very low expression in young branches and roots, whereas in leaves, immature acorns or male flowers, no expression was detected. These preliminary results suggest that QsMYB1 may be related to secondary growth and, in particular, with the cork biosynthesis process with a possible alternative splicing mechanism associated with its regulatory function. Copyright © 2012 Elsevier GmbH. All rights reserved.

A novel strategy of integrated microarray analysis identifies CENPA, CDK1 and CDC20 as a cluster of diagnostic biomarkers in lung adenocarcinoma.

PubMed

Liu, Wan-Ting; Wang, Yang; Zhang, Jing; Ye, Fei; Huang, Xiao-Hui; Li, Bin; He, Qing-Yu

2018-07-01

Lung adenocarcinoma (LAC) is the most lethal cancer and the leading cause of cancer-related death worldwide. The identification of meaningful clusters of co-expressed genes or representative biomarkers may help improve the accuracy of LAC diagnoses. Public databases, such as the Gene Expression Omnibus (GEO), provide rich resources of valuable information for clinics, however, the integration of multiple microarray datasets from various platforms and institutes remained a challenge. To determine potential indicators of LAC, we performed genome-wide relative significance (GWRS), genome-wide global significance (GWGS) and support vector machine (SVM) analyses progressively to identify robust gene biomarker signatures from 5 different microarray datasets that included 330 samples. The top 200 genes with robust signatures were selected for integrative analysis according to "guilt-by-association" methods, including protein-protein interaction (PPI) analysis and gene co-expression analysis. Of these 200 genes, only 10 genes showed both intensive PPI network and high gene co-expression correlation (r > 0.8). IPA analysis of this regulatory networks suggested that the cell cycle process is a crucial determinant of LAC. CENPA, as well as two linked hub genes CDK1 and CDC20, are determined to be potential indicators of LAC. Immunohistochemical staining showed that CENPA, CDK1 and CDC20 were highly expressed in LAC cancer tissue with co-expression patterns. A Cox regression model indicated that LAC patients with CENPA + /CDK1 + and CENPA + /CDC20 + were high-risk groups in terms of overall survival. In conclusion, our integrated microarray analysis demonstrated that CENPA, CDK1 and CDC20 might serve as novel cluster of prognostic biomarkers for LAC, and the cooperative unit of three genes provides a technically simple approach for identification of LAC patients. Copyright © 2018 Elsevier B.V. All rights reserved.

Candidate gene prioritization by network analysis of differential expression using machine learning approaches

PubMed Central

2010-01-01

Background Discovering novel disease genes is still challenging for diseases for which no prior knowledge - such as known disease genes or disease-related pathways - is available. Performing genetic studies frequently results in large lists of candidate genes of which only few can be followed up for further investigation. We have recently developed a computational method for constitutional genetic disorders that identifies the most promising candidate genes by replacing prior knowledge by experimental data of differential gene expression between affected and healthy individuals. To improve the performance of our prioritization strategy, we have extended our previous work by applying different machine learning approaches that identify promising candidate genes by determining whether a gene is surrounded by highly differentially expressed genes in a functional association or protein-protein interaction network. Results We have proposed three strategies scoring disease candidate genes relying on network-based machine learning approaches, such as kernel ridge regression, heat kernel, and Arnoldi kernel approximation. For comparison purposes, a local measure based on the expression of the direct neighbors is also computed. We have benchmarked these strategies on 40 publicly available knockout experiments in mice, and performance was assessed against results obtained using a standard procedure in genetics that ranks candidate genes based solely on their differential expression levels (Simple Expression Ranking). Our results showed that our four strategies could outperform this standard procedure and that the best results were obtained using the Heat Kernel Diffusion Ranking leading to an average ranking position of 8 out of 100 genes, an AUC value of 92.3% and an error reduction of 52.8% relative to the standard procedure approach which ranked the knockout gene on average at position 17 with an AUC value of 83.7%. Conclusion In this study we could identify promising candidate genes using network based machine learning approaches even if no knowledge is available about the disease or phenotype. PMID:20840752

Non-linear control of the output stage of a solar microinverter

NASA Astrophysics Data System (ADS)

Lopez-Santos, Oswaldo; Garcia, Germain; Martinez-Salamero, Luis; Avila-Martinez, Juan C.; Seguier, Lionel

2017-01-01

This paper presents a proposal to control the output stage of a two-stage solar microinverter to inject real power into the grid. The input stage of the microinverter is used to extract the maximum available power of a photovoltaic module enforcing a power source behavior in the DC-link to feed the output stage. The work here reported is devoted to control a grid-connected power source inverter with a high power quality level at the grid side ensuring the power balance of the microinverter regulating the voltage of the DC-link. The proposed control is composed of a sinusoidal current reference generator and a cascade type controller composed by a current tracking loop and a voltage regulation loop. The current reference is obtained using a synchronized generator based on phase locked loop (PLL) which gives the shape, the frequency and phase of the current signal. The amplitude of the reference is obtained from a simple controller regulating the DC-link voltage. The tracking of the current reference is accomplished by means of a first-order sliding mode control law. The solution takes advantage of the rapidity and inherent robustness of the sliding mode current controller allowing a robust behavior in the regulation of the DC-link using a simple linear controller. The analytical expression to determine the power quality indicators of the micro-inverter's output is theoretically solved giving expressions relating the converter parameters. The theoretical approach is validated using simulation and experimental results.

Two-degree-of-freedom fractional order-PID controllers design for fractional order processes with dead-time.

PubMed

Li, Mingjie; Zhou, Ping; Zhao, Zhicheng; Zhang, Jinggang

2016-03-01

Recently, fractional order (FO) processes with dead-time have attracted more and more attention of many researchers in control field, but FO-PID controllers design techniques available for the FO processes with dead-time suffer from lack of direct systematic approaches. In this paper, a simple design and parameters tuning approach of two-degree-of-freedom (2-DOF) FO-PID controller based on internal model control (IMC) is proposed for FO processes with dead-time, conventional one-degree-of-freedom control exhibited the shortcoming of coupling of robustness and dynamic response performance. 2-DOF control can overcome the above weakness which means it realizes decoupling of robustness and dynamic performance from each other. The adjustable parameter η2 of FO-PID controller is directly related to the robustness of closed-loop system, and the analytical expression is given between the maximum sensitivity specification Ms and parameters η2. In addition, according to the dynamic performance requirement of the practical system, the parameters η1 can also be selected easily. By approximating the dead-time term of the process model with the first-order Padé or Taylor series, the expressions for 2-DOF FO-PID controller parameters are derived for three classes of FO processes with dead-time. Moreover, compared with other methods, the proposed method is simple and easy to implement. Finally, the simulation results are given to illustrate the effectiveness of this method. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Familial hypofibrinogenaemia associated with heterozygous substitution of a conserved arginine residue; Bbeta255 Arg-->His (Fibrinogen Merivale).

PubMed

Maghzal, Ghassan J; Brennan, Stephen O; Fellowes, Andrew P; Spearing, Ruth; George, Peter M

2003-02-21

Sequencing of all three fibrinogen genes from an individual with hypofibrinogenaemia led to the identification of two new point mutations in the Bbeta gene. Family studies showed the mutations Bbeta255 Arg-->His (Fibrinogen Merivale) and Bbeta148 Lys-->Asn (Fibrinogen Merivale II) were on different alleles and that only the Bbeta255 Arg-->His mutation segregated with hypofibrinogenaemia. Three simple heterozygotes for this mutation had mean fibrinogen concentrations of 1.4 mg/ml, while heterozygotes for the Bbeta148 Lys-->Asn mutation had normal fibrinogen concentrations. ESI MS analysis of endoproteinase Asp-N digests of Bbeta chains showed that the Bbeta255 Arg-->His substitution was not expressed in plasma, confirming it as the cause of the hypofibrinogenaemia. The Bbeta148 Lys-->Asn chains, on the other hand, were equally expressed with wild-type Bbeta chains in simple heterozygotes. Genotype analysis failed to detect either substitution in 182 healthy controls. Arg(255) is located in the first strand of the five-stranded sheet that forms the main feature of the betaD domain and appears to form an essential H bond with Gly(414). Both the Arg and Gly are absolutely conserved, not only in all known Bbeta chains, but also in all homologous alphaE and gamma chains and in all fibrinogen-related proteins. Protein instability from loss of this contact could easily explain the association of this mutation with hypofibrinogenaemia.

Internal (Annular) and Compressible External (Flat Plate) Turbulent Flow Heat Transfer Correlations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dechant, Lawrence; Smith, Justin

Here we provide a discussion regarding the applicability of a family of traditional heat transfer correlation based models for several (unit level) heat transfer problems associated with flight heat transfer estimates and internal flow heat transfer associated with an experimental simulation design (Dobranich 2014). Variability between semi-empirical free-flight models suggests relative differences for heat transfer coefficients on the order of 10%, while the internal annular flow behavior is larger with differences on the order of 20%. We emphasize that these expressions are strictly valid only for the geometries they have been derived for e.g. the fully developed annular flow ormore » simple external flow problems. Though, the application of flat plate skin friction estimate to cylindrical bodies is a traditional procedure to estimate skin friction and heat transfer, an over-prediction bias is often observed using these approximations for missile type bodies. As a correction for this over-estimate trend, we discuss a simple scaling reduction factor for flat plate turbulent skin friction and heat transfer solutions (correlations) applied to blunt bodies of revolution at zero angle of attack. The method estimates the ratio between axisymmetric and 2-d stagnation point heat transfer skin friction and Stanton number solution expressions for sub-turbulent Reynolds numbers %3C1x10 4 . This factor is assumed to also directly influence the flat plate results applied to the cylindrical portion of the flow and the flat plate correlations are modified by« less

Relativistically correct DD and DT neutron spectra

NASA Astrophysics Data System (ADS)

Appelbe, B.; Chittenden, J.

2014-06-01

We use relativistic kinematics to derive an expression for the energy spectrum of neutrons produced by fusion reactions in deuterium and deuterium-tritium thermal plasmas. The derivation does not require approximations and the obtained expression gives the exact shape of the spectrum. It is shown that the high-energy tail of the neutron spectrum is highly sensitive to the plasma temperature. Simple expressions for the plasma temperature as a function of the neutron spectrum full width at half maximum (FWHM) are given.

Usage Automata

NASA Astrophysics Data System (ADS)

Bartoletti, Massimo

Usage automata are an extension of finite stata automata, with some additional features (e.g. parameters and guards) that improve their expressivity. Usage automata are expressive enough to model security requirements of real-world applications; at the same time, they are simple enough to be statically amenable, e.g. they can be model-checked against abstractions of program usages. We study here some foundational aspects of usage automata. In particular, we discuss about their expressive power, and about their effective use in run-time mechanisms for enforcing usage policies.

Understanding advanced theory of mind and empathy in high-functioning adults with autism spectrum disorder.

PubMed

Mathersul, Danielle; McDonald, Skye; Rushby, Jacqueline A

2013-01-01

It has been argued that higher functioning individuals with autism spectrum disorders (ASDs) have specific deficits in advanced but not simple theory of mind (ToM), yet the questionable ecological validity of some tasks reduces the strength of this assumption. The present study employed The Awareness of Social Inference Test (TASIT), which uses video vignettes to assess comprehension of subtle conversational inferences (sarcasm, lies/deception). Given the proposed relationships between advanced ToM and cognitive and affective empathy, these associations were also investigated. As expected, the high-functioning adults with ASDs demonstrated specific deficits in comprehending the beliefs, intentions, and meaning of nonliteral expressions. They also had significantly lower cognitive and affective empathy. Cognitive empathy was related to ToM and group membership whereas affective empathy was only related to group membership.

Developmental Changes in the Relationship Between the Infant's Attention and Emotion During Early Face-to-Face Communication: The 2-Month Transition

ERIC Educational Resources Information Center

Lavelli, Manuela; Fogel, Alan

2005-01-01

Weekly observations documented developmental changes in mother-infant face-to-face communication between birth and 3 months. Developmental trajectories for each dyad of the duration of infant facial expressions showed a change from the dominance of Simple Attention (without other emotion expressions) to active and emotionally positive forms of…

Simple Analytic Expressions for the Magnetic Field of a Circular Current Loop

NASA Technical Reports Server (NTRS)

Simpson, James C.; Lane, John E.; Immer, Christopher D.; Youngquist, Robert C.

2001-01-01

Analytic expressions for the magnetic induction (magnetic flux density, B) of a simple planar circular current loop have been published in Cartesian and cylindrical coordinates [1,2], and are also known implicitly in spherical coordinates [3]. In this paper, we present explicit analytic expressions for B and its spatial derivatives in Cartesian, cylindrical, and spherical coordinates for a filamentary current loop. These results were obtained with extensive use of Mathematica "TM" and are exact throughout all space outside of the conductor. The field expressions reduce to the well-known limiting cases and satisfy V · B = 0 and V x B = 0 outside the conductor. These results are general and applicable to any model using filamentary circular current loops. Solenoids of arbitrary size may be easily modeled by approximating the total magnetic induction as the sum of those for the individual loops. The inclusion of the spatial derivatives expands their utility to magnetohydrodynamics where the derivatives are required. The equations can be coded into any high-level programming language. It is necessary to numerically evaluate complete elliptic integrals of the first and second kind, but this capability is now available with most programming packages.

Simple formula for the surface area of the body and a simple model for anthropometry.

PubMed

Reading, Bruce D; Freeman, Brian

2005-03-01

The body surface area (BSA) of any adult, when derived from the arithmetic mean of the different values calculated from four independent accepted formulae, can be expressed accurately in Systeme International d'Unites (SI) units by the simple equation BSA = 1/6(WH)0.5, where W is body weight in kg, H is body height in m, and BSA is in m2. This formula, which is derived in part by modeling the body as a simple solid of revolution or a prolate spheroid (i.e., a stretched ellipsoid of revolution) gives students, teachers, and clinicians a simple rule for the rapid estimation of surface area using rational units. The formula was tested independently for human subjects by using it to predict body volume and then comparing this prediction against the actual volume measured by Archimedes' principle. Copyright 2005 Wiley-Liss, Inc.

Analytical model for the radio-frequency sheath

NASA Astrophysics Data System (ADS)

Czarnetzki, Uwe

2013-12-01

A simple analytical model for the planar radio-frequency (rf) sheath in capacitive discharges is developed that is based on the assumptions of a step profile for the electron front, charge exchange collisions with constant cross sections, negligible ionization within the sheath, and negligible ion dynamics. The continuity, momentum conservation, and Poisson equations are combined in a single integro-differential equation for the square of the ion drift velocity, the so called sheath equation. Starting from the kinetic Boltzmann equation, special attention is paid to the derivation and the validity of the approximate fluid equation for momentum balance. The integrals in the sheath equation appear in the screening function which considers the relative contribution of the temporal mean of the electron density to the space charge in the sheath. It is shown that the screening function is quite insensitive to variations of the effective sheath parameters. The two parameters defining the solution are the ratios of the maximum sheath extension to the ion mean free path and the Debye length, respectively. A simple general analytic expression for the screening function is introduced. By means of this expression approximate analytical solutions are obtained for the collisionless as well as the highly collisional case that compare well with the exact numerical solution. A simple transition formula allows application to all degrees of collisionality. In addition, the solutions are used to calculate all static and dynamic quantities of the sheath, e.g., the ion density, fields, and currents. Further, the rf Child-Langmuir laws for the collisionless as well as the collisional case are derived. An essential part of the model is the a priori knowledge of the wave form of the sheath voltage. This wave form is derived on the basis of a cubic charge-voltage relation for individual sheaths, considering both sheaths and the self-consistent self-bias in a discharge with arbitrary symmetry. The externally applied rf voltage is assumed to be sinusoidal, although the model can be extended to arbitrary wave forms, e.g., for dual-frequency discharges. The model calculates explicitly the cubic correction parameter in the charge-voltage relation for the case of highly asymmetric discharges. It is shown that the cubic correction is generally moderate but more pronounced in the collisionless case. The analytical results are compared to experimental data from the literature obtained by laser electric field measurements of the mean and dynamic fields in the capacitive sheath for various gases and pressures. Very good agreement is found throughout.

Analytical model for the radio-frequency sheath.

PubMed

Czarnetzki, Uwe

2013-12-01

A simple analytical model for the planar radio-frequency (rf) sheath in capacitive discharges is developed that is based on the assumptions of a step profile for the electron front, charge exchange collisions with constant cross sections, negligible ionization within the sheath, and negligible ion dynamics. The continuity, momentum conservation, and Poisson equations are combined in a single integro-differential equation for the square of the ion drift velocity, the so called sheath equation. Starting from the kinetic Boltzmann equation, special attention is paid to the derivation and the validity of the approximate fluid equation for momentum balance. The integrals in the sheath equation appear in the screening function which considers the relative contribution of the temporal mean of the electron density to the space charge in the sheath. It is shown that the screening function is quite insensitive to variations of the effective sheath parameters. The two parameters defining the solution are the ratios of the maximum sheath extension to the ion mean free path and the Debye length, respectively. A simple general analytic expression for the screening function is introduced. By means of this expression approximate analytical solutions are obtained for the collisionless as well as the highly collisional case that compare well with the exact numerical solution. A simple transition formula allows application to all degrees of collisionality. In addition, the solutions are used to calculate all static and dynamic quantities of the sheath, e.g., the ion density, fields, and currents. Further, the rf Child-Langmuir laws for the collisionless as well as the collisional case are derived. An essential part of the model is the a priori knowledge of the wave form of the sheath voltage. This wave form is derived on the basis of a cubic charge-voltage relation for individual sheaths, considering both sheaths and the self-consistent self-bias in a discharge with arbitrary symmetry. The externally applied rf voltage is assumed to be sinusoidal, although the model can be extended to arbitrary wave forms, e.g., for dual-frequency discharges. The model calculates explicitly the cubic correction parameter in the charge-voltage relation for the case of highly asymmetric discharges. It is shown that the cubic correction is generally moderate but more pronounced in the collisionless case. The analytical results are compared to experimental data from the literature obtained by laser electric field measurements of the mean and dynamic fields in the capacitive sheath for various gases and pressures. Very good agreement is found throughout.

Construction of a simple biocatalyst using psychrophilic bacterial cells and its application for efficient 3-hydroxypropionaldehyde production from glycerol.

PubMed

Tajima, Takahisa; Fuki, Koji; Kataoka, Naoya; Kudou, Daizou; Nakashimada, Yutaka; Kato, Junichi

2013-12-05

Most whole cell biocatalysts have some problems with yields and productivities because of various metabolites produced as byproducts and limitations of substrate uptake. We propose a psychrophile-based simple biocatalyst for efficient bio-production using mesophilic enzymes expressed in psychrophilic Shewanella livingstonensis Ac10 cells whose basic metabolism was inactivated by heat treatment. The 45°C heat-treated cells expressing lacZ showed maximum beta-galactosidase activity as well as chloroform/SDS-treated cells to increase membrane permeability. The fluorescent dye 5-cyano-2,3-ditolyl-tetrazolium chloride staining indicated that most basic metabolism of Ac10 was lost by heat treatment at 45˚C for 10 min. The simple biocatalyst was applied for 3-HPA production by using Klebsiella pneumoniae dhaB genes. 3-HPA was stoichiometrically produced with the complete consumption of glycerol at a high production rate of 8.85 mmol 3-HPA/g dry cell/h. The amount of 3-HPA production increased by increasing the concentrations of biocatalyst and glycerol. Furthermore, it could convert biodiesel-derived crude glycerol to 3-HPA.

Conditions and Linear Stability Analysis at the Transition to Synchronization of Three Coupled Phase Oscillators in a Ring

NASA Astrophysics Data System (ADS)

El-Nashar, Hassan F.

2017-06-01

We consider a system of three nonidentical coupled phase oscillators in a ring topology. We explore the conditions that must be satisfied in order to obtain the phases at the transition to a synchrony state. These conditions lead to the correct mathematical expressions of phases that aid to find a simple analytic formula for critical coupling when the oscillators transit to a synchronization state having a common frequency value. The finding of a simple expression for the critical coupling allows us to perform a linear stability analysis at the transition to the synchronization stage. The obtained analytic forms of the eigenvalues show that the three coupled phase oscillators with periodic boundary conditions transit to a synchrony state when a saddle-node bifurcation occurs.

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments

PubMed Central

Wang, Yuling; Zhang, Xinfu; Wang, Ran; Bai, Yingxin; Liu, Chenglian; Yuan, Yongbing; Yang, Yingjie; Yang, Shaolan

2017-01-01

Preharvest bagging is a simple, grower-friendly and safe physical protection technique commonly applied to many fruits, and the application of different fruit bags can have various effects. To explore the molecular mechanisms underlying the fruit quality effects of different bagging treatments, digital gene expression (DGE) profiling of bagged and unbagged ‘Chili’ (Pyrus bretschneideri Rehd.) pear pericarp during development was performed. Relative to unbagged fruit, a total of 3022 and 769 differentially expressed genes (DEGs) were detected in the polyethylene (PE)-bagged and non-woven fabric-bagged fruit, respectively. DEGs annotated as photosynthesis-antenna proteins and photosynthesis metabolism pathway were upregulated in non-woven fabric-bagged fruit but downregulated in the PE-bagged fruit. Non-woven fabric bagging inhibited lignin synthesis in ‘Chili’ pear pericarp by downregulating DEGs involved in phenylpropanoid biosynthesis; consequently, the fruit lenticels in non-woven fabric-bagged fruit were smaller than those in the other treatments. The results indicate that the non-woven fabric bagging method has a positive effect on the appearance of ‘Chili’ pear fruit but neither of the two bagging treatments is conducive to the accumulation of soluble sugar. PMID:28280542

A Graphene-enhanced imaging of microRNA with enzyme-free signal amplification of catalyzed hairpin assembly in living cells.

PubMed

Liu, Haiyun; Tian, Tian; Ji, Dandan; Ren, Na; Ge, Shenguang; Yan, Mei; Yu, Jinghua

2016-11-15

In situ imaging of miRNA in living cells could help us to monitor the miRNA expression in real time and obtain accurate information for studying miRNA related bioprocesses and disease. Given the low-level expression of miRNA, amplification strategies for intracellular miRNA are imperative. Here, we propose an amplification strategy with a non-destructive enzyme-free manner in living cells using catalyzed hairpin assembly (CHA) based on graphene oxide (GO) for cellular miRNA imaging. The enzyme-free CHA exhibits stringent recognition and excellent signal amplification of miRNA in the living cells. GO is a good candidate as a fluorescence quencher and cellular carrier. Taking the advantages of the CHA and GO, we can monitor the miRNA at low level in living cells with a simple, sensitive and real-time manner. Finally, imaging of miRNAs in the different expression cells is realized. The novel method could supply an effective tool to visualize intracellular low-level miRNAs and help us to further understand the role of miRNAs in cellular processes. Copyright © 2016 Elsevier B.V. All rights reserved.

Cell of Origin: Exploring an Alternative Contributor to Ovarian Cancer

DTIC Science & Technology

2015-12-01

of 60 mice). We previously reported that we conducted simple preliminary studies to assess the potential impact of the retroviral infections on...using primers designed to specifically detect exogenous TP53 gene expression. 12. Simple preliminary studies assessing the potential impact of exogenous...Award was ending and we were delinquent with respect to submission of the Closure report and no longer had access to the funds. Since there was such a

Modelling formulations using gene expression programming--a comparative analysis with artificial neural networks.

PubMed

Colbourn, E A; Roskilly, S J; Rowe, R C; York, P

2011-10-09

This study has investigated the utility and potential advantages of gene expression programming (GEP)--a new development in evolutionary computing for modelling data and automatically generating equations that describe the cause-and-effect relationships in a system--to four types of pharmaceutical formulation and compared the models with those generated by neural networks, a technique now widely used in the formulation development. Both methods were capable of discovering subtle and non-linear relationships within the data, with no requirement from the user to specify the functional forms that should be used. Although the neural networks rapidly developed models with higher values for the ANOVA R(2) these were black box and provided little insight into the key relationships. However, GEP, although significantly slower at developing models, generated relatively simple equations describing the relationships that could be interpreted directly. The results indicate that GEP can be considered an effective and efficient modelling technique for formulation data. Copyright © 2011 Elsevier B.V. All rights reserved.

Diagrammatic technique for calculating matrix elements of collective operators in superradiance. [eigenstates for N two-level atom systems

NASA Technical Reports Server (NTRS)

Lee, C. T.

1975-01-01

Adopting the so-called genealogical construction, one can express the eigenstates of collective operators corresponding to a specified mode for an N-atom system in terms of those for an (N-1) atom system. Using these Dicke states as bases and using the Wigner-Eckart theorem, a matrix element of a collective operator of an arbitrary mode can be written as the product of an m-dependent factor and an m-independent reduced matrix element (RME). A set of recursion formulas for the RME is obtained. A graphical representation of the RME on the branching diagram for binary irreducible representations of permutation groups is then introduced. This gives a simple and systematic way of calculating the RME. This method is especially useful when the cooperation number r is close to N/2, where almost exact asymptotic expressions can be obtained easily. The result shows explicity the geometry dependence of superradiance and the relative importance of r-conserving and r-nonconserving processes.

A Potential Role for Drosophila Mucins in Development and Physiology

PubMed Central

Syed, Zulfeqhar A.; Härd, Torleif; Uv, Anne; van Dijk-Härd, Iris F.

2008-01-01

Vital vertebrate organs are protected from the external environment by a barrier that to a large extent consists of mucins. These proteins are characterized by poorly conserved repeated sequences that are rich in prolines and potentially glycosylated threonines and serines (PTS). We have now used the characteristics of the PTS repeat domain to identify Drosophila mucins in a simple bioinformatics approach. Searching the predicted protein database for proteins with at least 4 repeats and a high ST content, more than 30 mucin-like proteins were identified, ranging from 300–23000 amino acids in length. We find that Drosophila mucins are present at all stages of the fly life cycle, and that their transcripts localize to selective organs analogous to sites of vertebrate mucin expression. The results could allow for addressing basic questions about human mucin-related diseases in this model system. Additionally, many of the mucins are expressed in selective tissues during embryogenesis, thus revealing new potential functions for mucins as apical matrix components during organ morphogenesis. PMID:18725942

Variable Refractive Index Effects on Radiation in Semitransparent Scattering Multilayered Regions

NASA Technical Reports Server (NTRS)

Siegel, R.; Spuckler, C. M.

1993-01-01

A simple set of equations is derived for predicting the temperature distribution and radiative energy flow in a semitransparent layer consisting of an arbitrary number of laminated sublayers that absorb, emit, and scatter radiation. Each sublayer can have a different refractive index and optical thickness. The plane composite region is heated on each exterior side by a different amount of incident radiation. The results are for the limiting case where heat conduction within the layers is very small relative to radiative transfer, and is neglected. The interfaces are assumed diffuse, and all interface reflections are included in the analysis. The thermal behavior is readily calculated from the analytical expressions that are obtained. By using many sublayers, expressions provide the temperature distribution and heat flow for a diffusing medium with a continually varying refractive index, including internal reflection effects caused by refractive index gradients. Temperature and heat flux results are given to show the effect of variations in refractive index and optical thickness through the multilayer laminate.

Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

PubMed

Lakatos, Eszter; Salehi-Reyhani, Ali; Barclay, Michael; Stumpf, Michael P H; Klug, David R

2017-01-01

We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

A new variance stabilizing transformation for gene expression data analysis.

PubMed

Kelmansky, Diana M; Martínez, Elena J; Leiva, Víctor

2013-12-01

In this paper, we introduce a new family of power transformations, which has the generalized logarithm as one of its members, in the same manner as the usual logarithm belongs to the family of Box-Cox power transformations. Although the new family has been developed for analyzing gene expression data, it allows a wider scope of mean-variance related data to be reached. We study the analytical properties of the new family of transformations, as well as the mean-variance relationships that are stabilized by using its members. We propose a methodology based on this new family, which includes a simple strategy for selecting the family member adequate for a data set. We evaluate the finite sample behavior of different classical and robust estimators based on this strategy by Monte Carlo simulations. We analyze real genomic data by using the proposed transformation to empirically show how the new methodology allows the variance of these data to be stabilized.

A time-dependent model to determine the thermal conductivity of a nanofluid

NASA Astrophysics Data System (ADS)

Myers, T. G.; MacDevette, M. M.; Ribera, H.

2013-07-01

In this paper, we analyse the time-dependent heat equations over a finite domain to determine expressions for the thermal diffusivity and conductivity of a nanofluid (where a nanofluid is a fluid containing nanoparticles with average size below 100 nm). Due to the complexity of the standard mathematical analysis of this problem, we employ a well-known approximate solution technique known as the heat balance integral method. This allows us to derive simple analytical expressions for the thermal properties, which appear to depend primarily on the volume fraction and liquid properties. The model is shown to compare well with experimental data taken from the literature even up to relatively high concentrations and predicts significantly higher values than the Maxwell model for volume fractions approximately >1 %. The results suggest that the difficulty in reproducing the high values of conductivity observed experimentally may stem from the use of a static heat flow model applied over an infinite domain rather than applying a dynamic model over a finite domain.

Pharmacological assessment of methamphetamine-induced behavioral hyperactivity mediated by dopaminergic transmission in planarian Dugesia japonica.

PubMed

Tashiro, Natsuka; Nishimura, Kaneyasu; Daido, Kanako; Oka, Tomoe; Todo, Mio; Toshikawa, Asami; Tsushima, Jun; Takata, Kazuyuki; Ashihara, Eishi; Yoshimoto, Kanji; Agata, Kiyokazu; Kitamura, Yoshihisa

2014-07-11

The freshwater planarian Dugesia japonica has a simple central nervous system (CNS) and can regenerate complete organs, even a functional brain. Recent studies demonstrated that there is a great variety of neuronal-related genes, specifically expressed in several domains of the planarian brain. We identified a planarian dat gene, named it D. japonica dopamine transporter (Djdat), and analyzed its expression and function. Both in situ hybridization and immunofluorescence revealed that localization of Djdat mRNA and protein was the same as that of D. japonica tyrosine hydroxylase (DjTH). Although, dopamine (DA) content in Djdat(RNAi) planarians was not altered, Djdat(RNAi) planarians showed increased spontaneous locomotion. The hyperactivity in the Djdat(RNAi) planarians was significantly suppressed by SCH23390 or sulpiride pretreatment, which are D1 or D2 receptor antagonists, respectively. These results suggest that planarians have a Djdat ortholog and the ability to regulate dopaminergic neurotransmission and association with spontaneous locomotion. Copyright © 2014 Elsevier Inc. All rights reserved.

The many faces of the quantum Liouville exponentials

NASA Astrophysics Data System (ADS)

Gervais, Jean-Loup; Schnittger, Jens

1994-01-01

First, it is proven that the three main operator approaches to the quantum Liouville exponentials—that is the one of Gervais-Neveu (more recently developed further by Gervais), Braaten-Curtright-Ghandour-Thorn, and Otto-Weigt—are equivalent since they are related by simple basis transformations in the Fock space of the free field depending upon the zero-mode only. Second, the GN-G expressions for quantum Liouville exponentials, where the U q( sl(2)) quantum-group structure is manifest, are shown to be given by q-binomial sums over powers of the chiral fields in the J = {1}/{2} representation. Third, the Liouville exponentials are expressed as operator tau functions, whose chiral expansion exhibits a q Gauss decomposition, which is the direct quantum analogue of the classical solution of Leznov and Saveliev. It involves q exponentials of quantum-group generators with group "parameters" equal to chiral components of the quantum metric. Fourth, we point out that the OPE of the J = {1}/{2} Liouville exponential provides the quantum version of the Hirota bilinear equation.

Variable Refractive Index Effects on Radiation in Semitransparent Scattering Multilayered Regions

NASA Technical Reports Server (NTRS)

Siegel, R.; Spuckler, C. M.

1993-01-01

A simple set of equations is derived for predicting the temperature distribution and radiative energy flow in a semitransparent layer consisting of an arbitrary number of laminated sublayers that absorb, emit, and scatter radiation. Each sublayer can have a different refractive index and optical thickness. The plane composite region is heated on each exterior side by a different amount of incident radiation. The results are for the limiting case where heat conduction within the layers is very small relative to radiative transfer, and is neglected. The interfaces are assumed diffuse, and all interface reflections are included in the analysis. The thermal behavior is readily calculated from the analytical expressions that are obtained. By using many sublayers, the analytical expressions provide the temperature distribution and heat flow for a diffusing medium with a continuously varying refractive index, including internal reflection effects caused by refractive index gradients. Temperature and heat flux results are given to show the effect of variations in refractive index and optical thickness through the multilayer laminate.

Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

PubMed

Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

2010-02-01

Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

Bacterial RNA Biology on a Genome Scale.

PubMed

Hör, Jens; Gorski, Stanislaw A; Vogel, Jörg

2018-06-07

Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. Copyright © 2017 Elsevier Inc. All rights reserved.

On the connection coefficients and recurrence relations arising from expansions in series of Laguerre polynomials

NASA Astrophysics Data System (ADS)

Doha, E. H.

2003-05-01

A formula expressing the Laguerre coefficients of a general-order derivative of an infinitely differentiable function in terms of its original coefficients is proved, and a formula expressing explicitly the derivatives of Laguerre polynomials of any degree and for any order as a linear combination of suitable Laguerre polynomials is deduced. A formula for the Laguerre coefficients of the moments of one single Laguerre polynomial of certain degree is given. Formulae for the Laguerre coefficients of the moments of a general-order derivative of an infinitely differentiable function in terms of its Laguerre coefficients are also obtained. A simple approach in order to build and solve recursively for the connection coefficients between Jacobi-Laguerre and Hermite-Laguerre polynomials is described. An explicit formula for these coefficients between Jacobi and Laguerre polynomials is given, of which the ultra-spherical polynomials of the first and second kinds and Legendre polynomials are important special cases. An analytical formula for the connection coefficients between Hermite and Laguerre polynomials is also obtained.

Green-Kubo relations for the viscosity of biaxial nematic liquid crystals

NASA Astrophysics Data System (ADS)

Sarman, Sten

1996-09-01

We derive Green-Kubo relations for the viscosities of a biaxial nematic liquid crystal. In this system there are seven shear viscosities, three twist viscosities, and three cross coupling coefficients between the antisymmetric strain rate and the symmetric traceless pressure tensor. According to the Onsager reciprocity relations these couplings are equal to the cross couplings between the symmetric traceless strain rate and the antisymmetric pressure. Our method is based on a comparison of the microscopic linear response generated by the SLLOD equations of motion for planar Couette flow (so named because of their close connection to the Doll's tensor Hamiltonian) and the macroscopic linear phenomenological relations between the pressure tensor and the strain rate. In order to obtain simple Green-Kubo relations we employ an equilibrium ensemble where the angular velocities of the directors are identically zero. This is achieved by adding constraint torques to the equations for the molecular angular accelerations. One finds that all the viscosity coefficients can be expressed as linear combinations of time correlation function integrals (TCFIs). This is much simpler compared to the expressions in the conventional canonical ensemble, where the viscosities are complicated rational functions of the TCFIs. The reason for this is, that in the constrained angular velocity ensemble, the thermodynamic forces are given external parameters whereas the thermodynamic fluxes are ensemble averages of phase functions. This is not the case in the canonical ensemble. The simplest way of obtaining numerical estimates of viscosity coefficients of a particular molecular model system is to evaluate these fluctuation relations by equilibrium molecular dynamics simulations.

Generalized thermodynamic relations for a system experiencing heat and mass diffusion in the far-from-equilibrium realm based on steepest entropy ascent.

PubMed

Li, Guanchen; von Spakovsky, Michael R

2016-09-01

This paper presents a nonequilibrium thermodynamic model for the relaxation of a local, isolated system in nonequilibrium using the principle of steepest entropy ascent (SEA), which can be expressed as a variational principle in thermodynamic state space. The model is able to arrive at the Onsager relations for such a system. Since no assumption of local equilibrium is made, the conjugate fluxes and forces are intrinsic to the subspaces of the system's state space and are defined using the concepts of hypoequilibrium state and nonequilibrium intensive properties, which describe the nonmutual equilibrium status between subspaces of the thermodynamic state space. The Onsager relations are shown to be a thermodynamic kinematic feature of the system independent of the specific details of the micromechanical dynamics. Two kinds of relaxation processes are studied with different constraints (i.e., conservation laws) corresponding to heat and mass diffusion. Linear behavior in the near-equilibrium region as well as nonlinear behavior in the far-from-equilibrium region are discussed. Thermodynamic relations in the equilibrium and near-equilibrium realm, including the Gibbs relation, the Clausius inequality, and the Onsager relations, are generalized to the far-from-equilibrium realm. The variational principle in the space spanned by the intrinsic conjugate fluxes and forces is expressed via the quadratic dissipation potential. As an application, the model is applied to the heat and mass diffusion of a system represented by a single-particle ensemble, which can also be applied to a simple system of many particles. Phenomenological transport coefficients are also derived in the near-equilibrium realm.

Inferring molecular interactions pathways from eQTL data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rashid, Imran; McDermott, Jason E.; Samudrala, Ram

Analysis of expression quantitative trait loci (eQTL) helps elucidate the connection between genotype, gene expression levels, and phenotype. However, standard statistical genetics can only attribute changes in expression levels to loci on the genome, not specific genes. Each locus can contain many genes, making it very difficult to discover which gene is controlling the expression levels of other genes. Furthermore, it is even more difficult to find a pathway of molecular interactions responsible for controlling the expression levels. Here we describe a series of techniques for finding explanatory pathways by exploring graphs of molecular interactions. We show several simple methodsmore » can find complete pathways the explain the mechanism of differential expression in eQTL data.« less

New approach in the quantum statistical parton distribution

NASA Astrophysics Data System (ADS)

Sohaily, Sozha; Vaziri (Khamedi), Mohammad

2017-12-01

An attempt to find simple parton distribution functions (PDFs) based on quantum statistical approach is presented. The PDFs described by the statistical model have very interesting physical properties which help to understand the structure of partons. The longitudinal portion of distribution functions are given by applying the maximum entropy principle. An interesting and simple approach to determine the statistical variables exactly without fitting and fixing parameters is surveyed. Analytic expressions of the x-dependent PDFs are obtained in the whole x region [0, 1], and the computed distributions are consistent with the experimental observations. The agreement with experimental data, gives a robust confirm of our simple presented statistical model.

Asymptotic solutions for the case of nearly symmetric gravitational lens systems

NASA Astrophysics Data System (ADS)

Wertz, O.; Pelgrims, V.; Surdej, J.

2012-08-01

Gravitational lensing provides a powerful tool to determine the Hubble parameter H0 from the measurement of the time delay Δt between two lensed images of a background variable source. Nevertheless, knowledge of the deflector mass distribution constitutes a hurdle. We propose in the present work interesting solutions for the case of nearly symmetric gravitational lens systems. For the case of a small misalignment between the source, the deflector and the observer, we first consider power-law (ɛ) axially symmetric models for which we derive an analytical relation between the amplification ratio and source position which is independent of the power-law slope ɛ. According to this relation, we deduce an expression for H0 also irrespective of the value ɛ. Secondly, we consider the power-law axially symmetric lens models with an external large-scale gravitational field, the shear γ, resulting in the so-called ɛ-γ models, for which we deduce simple first-order equations linking the model parameters and the lensed image positions, the latter being observable quantities. We also deduce simple relations between H0 and observables quantities only. From these equations, we may estimate the value of the Hubble parameter in a robust way. Nevertheless, comparison between the ɛ-γ and singular isothermal ellipsoid (SIE) models leads to the conclusion that these models remain most often distinct. Therefore, even for the case of a small misalignment, use of the first-order equations and precise astrometric measurements of the positions of the lensed images with respect to the centre of the deflector enables one to discriminate between these two families of models. Finally, we confront the models with numerical simulations to evaluate the intrinsic error of the first-order expressions used when deriving the model parameters under the assumption of a quasi-alignment between the source, the deflector and the observer. From these same simulations, we estimate for the case of the ɛ-γ family of models that the standard deviation affecting H0 is ? which merely reflects the adopted astrometric uncertainties on the relative image positions, typically ? arcsec. In conclusions, we stress the importance of getting very accurate measurements of the relative positions of the multiple lensed images and of the time delays for the case of nearly symmetric gravitational lens systems, in order to derive robust and precise values of the Hubble parameter.

The Role of Metarepresentation in the Production and Resolution of Referring Expressions.

PubMed

Horton, William S; Brennan, Susan E

2016-01-01

In this paper we consider the potential role of metarepresentation-the representation of another representation, or as commonly considered within cognitive science, the mental representation of another individual's knowledge and beliefs-in mediating definite reference and common ground in conversation. Using dialogues from a referential communication study in which speakers conversed in succession with two different addressees, we highlight ways in which interlocutors work together to successfully refer to objects, and achieve shared conceptualizations. We briefly review accounts of how such shared conceptualizations could be represented in memory, from simple associations between label and referent, to "triple co-presence" representations that track interlocutors in an episode of referring, to more elaborate metarepresentations that invoke theory of mind, mutual knowledge, or a model of a conversational partner. We consider how some forms of metarepresentation, once created and activated, could account for definite reference in conversation by appealing to ordinary processes in memory. We conclude that any representations that capture information about others' perspectives are likely to be relatively simple and subject to the same kinds of constraints on attention and memory that influence other kinds of cognitive representations.

Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain.

PubMed

Koyama, Minoru; Kinkhabwala, Amina; Satou, Chie; Higashijima, Shin-ichi; Fetcho, Joseph

2011-01-18

The hindbrain of larval zebrafish contains a relatively simple ground plan in which the neurons throughout it are arranged into stripes that represent broad neuronal classes that differ in transmitter identity, morphology, and transcription factor expression. Within the stripes, neurons are stacked continuously according to age as well as structural and functional properties, such as axonal extent, input resistance, and the speed at which they are recruited during movements. Here we address the question of how particular networks among the many different sensory-motor networks in hindbrain arise from such an orderly plan. We use a combination of transgenic lines and pairwise patch recording to identify excitatory and inhibitory interneurons in the hindbrain network for escape behaviors initiated by the Mauthner cell. We map this network onto the ground plan to show that an individual hindbrain network is built by drawing components in predictable ways from the underlying broad patterning of cell types stacked within stripes according to their age and structural and functional properties. Many different specialized hindbrain networks may arise similarly from a simple early patterning.

The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks

PubMed Central

Chevalier, Michael; Venturelli, Ophelia; El-Samad, Hana

2015-01-01

Stochastic fluctuations in signaling and gene expression limit the ability of cells to sense the state of their environment, transfer this information along cellular pathways, and respond to it with high precision. Mutual information is now often used to quantify the fidelity with which information is transmitted along a cellular pathway. Mutual information calculations from experimental data have mostly generated low values, suggesting that cells might have relatively low signal transmission fidelity. In this work, we demonstrate that mutual information calculations might be artificially lowered by cell-to-cell variability in both initial conditions and slowly fluctuating global factors across the population. We carry out our analysis computationally using a simple signaling pathway and demonstrate that in the presence of slow global fluctuations, every cell might have its own high information transmission capacity but that population averaging underestimates this value. We also construct a simple synthetic transcriptional network and demonstrate using experimental measurements coupled to computational modeling that its operation is dominated by slow global variability, and hence that its mutual information is underestimated by a population averaged calculation. PMID:26484538

Theoretical study of production of unique glasses in space

NASA Technical Reports Server (NTRS)

Larsen, D. C.

1974-01-01

Analytical functional relationships describing homogeneous nucleation and crystallization in various supercooled liquids were developed. The time and temperature dependent relationships of nucleation and crystallization (intrinsic properties) are being used to relate glass forming tendency to extrinsic parameters such as cooling rate through computer simulation. Single oxide systems are being studied initially to aid in developing workable kinetic models and to indicate the primary materials parameters affecting glass formation. The theory and analytical expressions developed for simple systems is then extended to complex oxide systems. A thorough understanding of nucleation and crystallization kinetics of glass forming systems provides a priori knowledge of the ability of a given system to form a glass.

Collective modes in two-dimensional one-component-plasma with logarithmic interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khrapak, Sergey A.; Forschungsgruppe Komplexe Plasmen, Deutsches Zentrum für Luft- und Raumfahrt, Oberpfaffenhofen; Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow

The collective modes of a familiar two-dimensional one-component-plasma with the repulsive logarithmic interaction between the particles are analysed using the quasi-crystalline approximation (QCA) combined with the molecular dynamic simulation of the equilibrium structural properties. It is found that the dispersion curves in the strongly coupled regime are virtually independent of the coupling strength. Arguments based on the excluded volume consideration for the radial distribution function allow us to derive very simple expressions for the dispersion relations, which show excellent agreement with the exact QCA dispersion over the entire domain of wavelengths. Comparison with the results of the conventional fluid analysismore » is performed, and the difference is explained.« less

Mathematical Modeling Of Life-Support Systems

NASA Technical Reports Server (NTRS)

Seshan, Panchalam K.; Ganapathi, Balasubramanian; Jan, Darrell L.; Ferrall, Joseph F.; Rohatgi, Naresh K.

1994-01-01

Generic hierarchical model of life-support system developed to facilitate comparisons of options in design of system. Model represents combinations of interdependent subsystems supporting microbes, plants, fish, and land animals (including humans). Generic model enables rapid configuration of variety of specific life support component models for tradeoff studies culminating in single system design. Enables rapid evaluation of effects of substituting alternate technologies and even entire groups of technologies and subsystems. Used to synthesize and analyze life-support systems ranging from relatively simple, nonregenerative units like aquariums to complex closed-loop systems aboard submarines or spacecraft. Model, called Generic Modular Flow Schematic (GMFS), coded in such chemical-process-simulation languages as Aspen Plus and expressed as three-dimensional spreadsheet.

Simplified sonic-boom prediction. [using aerodynamic configuration charts and calculators or slide rules

NASA Technical Reports Server (NTRS)

Carlson, H. W.

1978-01-01

Sonic boom overpressures and signature duration may be predicted for the entire affected ground area for a wide variety of supersonic airplane configurations and spacecraft operating at altitudes up to 76 km in level flight or in moderate climbing or descending flight paths. The outlined procedure relies to a great extent on the use of charts to provide generation and propagation factors for use in relatively simple expressions for signature calculation. Computational requirements can be met by hand-held scientific calculators, or even by slide rules. A variety of correlations of predicted and measured sonic-boom data for airplanes and spacecraft serve to demonstrate the applicability of the simplified method.

Signal velocity in oscillator arrays

NASA Astrophysics Data System (ADS)

Cantos, C. E.; Veerman, J. J. P.; Hammond, D. K.

2016-09-01

We investigate a system of coupled oscillators on the circle, which arises from a simple model for behavior of large numbers of autonomous vehicles where the acceleration of each vehicle depends on the relative positions and velocities between itself and a set of local neighbors. After describing necessary and sufficient conditions for asymptotic stability, we derive expressions for the phase velocity of propagation of disturbances in velocity through this system. We show that the high frequencies exhibit damping, which implies existence of well-defined signal velocitiesc+ > 0 and c- < 0 such that low frequency disturbances travel through the flock as f+(x - c+t) in the direction of increasing agent numbers and f-(x - c-t) in the other.

Thermo-elasto-viscoplastic analysis of problems in extension and shear

NASA Technical Reports Server (NTRS)

Riff, R.; Simitses, G. J.

1987-01-01

The problems of extension and shear behavior of structural elements made of carbon steel and subjected to large thermomechanical loads are investigated. The analysis is based on nonlinear geometric and constitutive relations, and is expressed in a rate form. The material constitutive equations are capable of reproducing all nonisothermal, elasto-viscoplastic characteristics. The results of the test problems show that: (1) the formulation can accommodate very large strains and rotations; (2) the model incorporates the simplification associated with rate-insensitive elastic response without losing the ability to model a rate-temperature dependent yield strength and plasticity; and (3) the formulation does not display oscillatory behavior in the stresses for the simple shear problem.

Testing the Effects of SIAH Ubiquitin E3 Ligases on Lysine Acetyl Transferases.

PubMed

Hagenbucher, Jan; Stekman, Hilda; Rodriguez-Gil, Alfonso; Kracht, Michael; Schmitz, M Lienhard

2017-01-01

The family of seven-in-absentia (SIAH) ubiquitin E3 ligases functions in the control of numerous key signaling pathways. These enzymes belong to the RING (really interesting new gene) group of E3 ligases and mediate the attachment of ubiquitin chains to substrates, which then leads to their proteasomal degradation. Here, we describe a protocol that allows measuring SIAH-mediated ubiquitination and degradation of its client proteins as exemplified by acetyl transferases using simple overexpression experiments. The impact of SIAH expression on the relative amounts of target proteins and their mRNAs can be quantified by Western blotting and quantitative PCR (qPCR) as described here.

Role of carbon source in the shift from oxidative to hydrolytic wood decomposition by Postia placenta.

PubMed

Zhang, Jiwei; Schilling, Jonathan S

2017-09-01

Brown rot fungi initiate wood decay using oxidative pretreatments to improve access for cellulolytic enzymes. These pretreatments are incompatible with enzymes, and we recently showed that Postia placenta overcomes this issue by delaying glycoside hydrolase (GH) gene upregulation briefly (<48h) until expression of oxidoreductases (ORs) is repressed. This implies an inducible cellulase system rather than a constitutive system, as often reported, and it remains unclear what cues this transition. To address this, we grew P. placenta along wood wafers and spatially mapped expression (via quantitative PCR) of twelve ORs and GHs targeted using functional genomics analyses. By layering expression patterns over solubilized sugar data (via HPLC) from wood, we observed solubilization of wood glucose, cellobiose, mannose, and xylose coincident with the OR-GH transition. We then tested effects of these soluble sugars, plus polymeric carbon sources (spruce powder, cellulose), on P. placenta gene expression in liquid cultures. Expression of ORs was strictly (aox1, cro5) or progressively repressed over time (qrd1, lcc1) by all soluble sugars, including cellobiose, but not by polymeric sources. Simple sugars repressed hemicellulase gene expression over time, but these sugars did not repress cellulases. Cellulase genes were upregulated, however, along with hemicellulases in the presence of soluble cellobiose and in the presence of polymeric carbon sources, relative to starvation (carbon-free). This verifies an inducible cellulase system in P. placenta that lacks carbon catabolite repression (CCR), and it suggests that brown rot fungi use soluble sugars, particularly cellobiose, to cue a critical oxidative-hydrolytic transition. Copyright © 2017 Elsevier Inc. All rights reserved.

On readout of vibrational qubits using quantum beats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shyshlov, Dmytro; Babikov, Dmitri, E-mail: Dmitri.Babikov@mu.edu; Berrios, Eduardo

2014-12-14

Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl{sub 2}, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. Themore » resulting oscillation of population of the readout state is then detected as a function of time delay. In principle, fitting the quantum beat signal by an analytical expression should allow extracting the values of probability amplitudes and the relative phases of the vibrational qubit states. However, we found that if this procedure is implemented using the standard analytic expression for quantum beats, a non-negligible phase error is obtained. We discuss the origin and properties of this phase error, and propose a new analytical expression to correct the phase error. The corrected expression fits the quantum beat signal very accurately, which may permit reading out the final state of vibrational qubits in experiments by combining the analytic fitting expression with numerical modelling of the readout process. The new expression is also useful as a simple model for fitting any quantum beat experiments where more accurate phase information is desired.« less

A cost-effective assay for antioxidant using simple cotton thread combining paper based device with mobile phone detection.

PubMed

Sateanchok, Suphasinee; Wangkarn, Sunanta; Saenjum, Chalermpong; Grudpan, Kate

2018-01-15

A cost-effective assay for antioxidant using simple cotton thread combining paper based device with mobile phone detection has been investigated. Standard and sample solutions flow along a bunch of cotton thread treated with sodium hydroxide via microfluidic behaviors without external pumping. The analyte solution reacts with the reagents that have been immobilized on the paper strip fixed at the end of the cotton bunch. The developed platforms were used for the assays of total phenolic content and antioxidant capacity by employing Folin-Ciocalteu and 2, 2-diphenyl-1-picryhydrazyl (DPPH) respectively. Simple detection can be made by employing a mobile phone camera (iPhone 4S) with Image J or Photoshop for image processing and evaluation. Gallic acid was used as a reference standard in this work, as its polyphenol structures can be found in many plants. The total phenolic content is expressed as gallic acid equivalents (GAE) (mg/g material). Inhibition capacity is calculated by the equation: % I = [(I o - I s )/ I o ] × 100, where I s is the relative magenta intensity (CMYK mode) of sample, and I o the relative magenta intensity of DPPH•. IC 50 inhibition can be estimated from the graph and can be used for the antioxidant capacity consideration. Applications to the assay green tea samples were demonstrated. The total phenolic contents in the green tea samples were found to be 48-105mg/g, with %RSD of less than 10 for that of higher 50 GAE mg/g and IC 50 values of the samples studied were 25-50mg/L. The results obtained by the developed methods agree with that of the standard methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparative in vitro flow study of 3 different Ex-PRESS miniature glaucoma device models.

PubMed

Estermann, Stephan; Yuttitham, Kanokwan; Chen, Julie A; Lee, On-Tat; Stamper, Robert L

2013-03-01

To determine the flow characteristics of the 3 different models of the Ex-PRESS miniature glaucoma device in a controlled laboratory study. The 3 different Ex-PRESS models (P-50, R-50, and P-200; Optonol Ltd; now Alcon Lab) were tested using a gravity-driven flow test. Three samples of each of the 3 Ex-PRESS models were subjected to a constant gravitational force of fluid at 5 different pressure levels (5 to 25 mm Hg). Four measurements per sample were taken at each pressure level. The main outcome measure was flow rate (Q) (µL/min). Resistance (R) was calculated by dividing pressure (P) by the measured flow (Q). The flow rate was primarily pressure dependent. The P-200 model (internal diameter 200 µm) showed a statistically significant higher flow rate and lower resistance compared with both the P-50 and R-50 models (internal diameter 50 µm) (P<0.0001). The P-50 and R-50 models demonstrated similar flow rates (P=0.08) despite their difference in tube length (2.64 vs. 2.94 mm). The 3 models of the Ex-PRESS mini shunt behaved in vitro as simple flow resistors by creating a relatively constant resistance to flow. Tube diameter was the only parameter with significant impact on flow and resistance. All models demonstrated flow rates per unit of pressure much higher than the outflow facility of a healthy human eye.

Msn2 Coordinates a Stoichiometric Gene Expression Program

PubMed Central

Stewart-Ornstein, Jacob; Nelson, Christopher; DeRisi, Joe; Weissman, Jonathan S.; El-Samad, Hana

2014-01-01

Summary Background Many cellular processes operate in an “analog” regime in which the magnitude of the response is precisely tailored to the intensity of the stimulus. In order to maintain the coherence of such responses, the cell must provide for proportional expression of multiple target genes across a wide dynamic range of induction states. Our understanding of the strategies used to achieve graded gene regulation is limited. Results In this work, we document a relationship between stress responsive gene expression and the transcription factor Msn2 that is graded over a large range of Msn2 cocnentrations. We use computational modeling, in vivo, and in vitro analysis to dissect the roots of this relationship. Our studies reveal a simple and general strategy based on non-cooperative low-affinity interactions between Msn2 and its cognate binding sites, as well as competition over a large number of Msn2 binding sites in the genome relative to the number of Msn2 molecules. Conclusions In addition to enabling precise tuning of gene expression to the state of the environment, this strategy ensures co-linear activation of target genes, allowing for stoichiometric expression of large groups of genes without extensive promoter tuning. Furthermore, such a strategy enables precise modulation of the activity of any given promoter by addition of binding sites without altering the qualitative relationship between different genes in a regulon. This feature renders a given regulon highly ‘evolvable’. PMID:24210615

Analytical performance evaluation of SAR ATR with inaccurate or estimated models

NASA Astrophysics Data System (ADS)

DeVore, Michael D.

2004-09-01

Hypothesis testing algorithms for automatic target recognition (ATR) are often formulated in terms of some assumed distribution family. The parameter values corresponding to a particular target class together with the distribution family constitute a model for the target's signature. In practice such models exhibit inaccuracy because of incorrect assumptions about the distribution family and/or because of errors in the assumed parameter values, which are often determined experimentally. Model inaccuracy can have a significant impact on performance predictions for target recognition systems. Such inaccuracy often causes model-based predictions that ignore the difference between assumed and actual distributions to be overly optimistic. This paper reports on research to quantify the effect of inaccurate models on performance prediction and to estimate the effect using only trained parameters. We demonstrate that for large observation vectors the class-conditional probabilities of error can be expressed as a simple function of the difference between two relative entropies. These relative entropies quantify the discrepancies between the actual and assumed distributions and can be used to express the difference between actual and predicted error rates. Focusing on the problem of ATR from synthetic aperture radar (SAR) imagery, we present estimators of the probabilities of error in both ideal and plug-in tests expressed in terms of the trained model parameters. These estimators are defined in terms of unbiased estimates for the first two moments of the sample statistic. We present an analytical treatment of these results and include demonstrations from simulated radar data.

Gene expression models for prediction of longitudinal dispersion coefficient in streams

NASA Astrophysics Data System (ADS)

Sattar, Ahmed M. A.; Gharabaghi, Bahram

2015-05-01

Longitudinal dispersion is the key hydrologic process that governs transport of pollutants in natural streams. It is critical for spill action centers to be able to predict the pollutant travel time and break-through curves accurately following accidental spills in urban streams. This study presents a novel gene expression model for longitudinal dispersion developed using 150 published data sets of geometric and hydraulic parameters in natural streams in the United States, Canada, Europe, and New Zealand. The training and testing of the model were accomplished using randomly-selected 67% (100 data sets) and 33% (50 data sets) of the data sets, respectively. Gene expression programming (GEP) is used to develop empirical relations between the longitudinal dispersion coefficient and various control variables, including the Froude number which reflects the effect of reach slope, aspect ratio, and the bed material roughness on the dispersion coefficient. Two GEP models have been developed, and the prediction uncertainties of the developed GEP models are quantified and compared with those of existing models, showing improved prediction accuracy in favor of GEP models. Finally, a parametric analysis is performed for further verification of the developed GEP models. The main reason for the higher accuracy of the GEP models compared to the existing regression models is that exponents of the key variables (aspect ratio and bed material roughness) are not constants but a function of the Froude number. The proposed relations are both simple and accurate and can be effectively used to predict the longitudinal dispersion coefficients in natural streams.

Divergence and Necessary Conditions for Extremums

NASA Technical Reports Server (NTRS)

Quirein, J. A.

1973-01-01

The problem is considered of finding a dimension reducing transformation matrix B that maximizes the divergence in the reduced dimension for multi-class cases. A comparitively simple expression for the gradient of the average divergence with respect to B is developed. The developed expression for the gradient contains no eigenvectors or eigenvalues; also, all matrix inversions necessary to evaluate the gradient are available from computing the average divergence.

Simple and Flexible Classification of Gene Expression Microarrays Via Swirls and Ripples | Division of Cancer Prevention

Cancer.gov

By Stuart G. Baker The program requires Mathematica 7.01.0 The key function is Classify [datalist,options] where datalist={data, genename, dataname} data ={matrix for class 0, matrix for class 1}, matrix is gene expression by specimen genename a list of names of genes, dataname ={name of data set, name of class0, name of class1} |

Early Detection of Breast Cancer Using Molecular Beacons

DTIC Science & Technology

2008-01-01

a molecular beacon (MB)-based approach for direct examination of gene expression in viable and fixed cells (2, 3). This objective of proposed study ...can be distinguished from normal cells (dark) (Figure 1) (2, 3, 8). Recently, a class of new fluorescent emitting nanoparticles, semiconductor ...morphological classification. This method may offer a simple and fast procedure to detect biomarker gene expression in clinical samples. Our study results

Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pomraning, Kyle R.; Bredeweg, Erin L.; Baker, Scott E.

ABSTRACT Fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeastYarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism inY. lipolytica. Deletion of the GATA transcription factor genesgzf3andgzf2resulted in nitrogen source-specific growth defects and greater accumulation of lipids when the cells weremore » growing on a simple nitrogen source. Deletion ofgzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion ofgzf3results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, whilegzf2is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressormig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism. IMPORTANCENitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeastY. lipolyticato determine how the nitrogen source regulates lipid metabolism. We show that disruption of both activators and repressors of nitrogen catabolite repression leads to increased lipid accumulation via activation of carbon catabolite repression through an as yet uncharacterized method.« less

Investigation of the feasibility of a simple method for verifying the motion of a binary multileaf collimator synchronized with the rotation of the gantry for helical tomotherapy

PubMed Central

Uematsu, Masahiro; Ito, Makiko; Hama, Yukihiro; Inomata, Takayuki; Fujii, Masahiro; Nishio, Teiji; Nakamura, Naoki; Nakagawa, Keiichi

2012-01-01

In this paper, we suggest a new method for verifying the motion of a binary multileaf collimator (MLC) in helical tomotherapy. For this we used a combination of a cylindrical scintillator and a general‐purpose camcorder. The camcorder records the light from the scintillator following photon irradiation, which we use to track the motion of the binary MLC. The purpose of this study is to demonstrate the feasibility of this method as a binary MLC quality assurance (QA) tool. First, the verification was performed using a simple binary MLC pattern with a constant leaf open time; secondly, verification using the binary MLC pattern used in a clinical setting was also performed. Sinograms of simple binary MLC patterns, in which leaves that were open were detected as “open” from the measured light, define the sensitivity which, in this case, was 1.000. On the other hand, the specificity, which gives the fraction of closed leaves detected as “closed”, was 0.919. The leaf open error identified by our method was −1.3±7.5%. The 68.6% of observed leaves were performed within ± 3% relative error. The leaf open error was expressed by the relative errors calculated on the sinogram. In the clinical binary MLC pattern, the sensitivity and specificity were 0.994 and 0.997, respectively. The measurement could be performed with −3.4±8.0% leaf open error. The 77.5% of observed leaves were performed within ± 3% relative error. With this method, we can easily verify the motion of the binary MLC, and the measurement unit developed was found to be an effective QA tool. PACS numbers: 87.56.Fc, 87.56.nk PMID:22231222

An 8-gene qRT-PCR-based gene expression score that has prognostic value in early breast cancer

PubMed Central

2010-01-01

Background Gene expression profiling may improve prognostic accuracy in patients with early breast cancer. Our objective was to demonstrate that it is possible to develop a simple molecular signature to predict distant relapse. Methods We included 153 patients with stage I-II hormonal receptor-positive breast cancer. RNA was isolated from formalin-fixed paraffin-embedded samples and qRT-PCR amplification of 83 genes was performed with gene expression assays. The genes we analyzed were those included in the 70-Gene Signature, the Recurrence Score and the Two-Gene Index. The association among gene expression, clinical variables and distant metastasis-free survival was analyzed using Cox regression models. Results An 8-gene prognostic score was defined. Distant metastasis-free survival at 5 years was 97% for patients defined as low-risk by the prognostic score versus 60% for patients defined as high-risk. The 8-gene score remained a significant factor in multivariate analysis and its performance was similar to that of two validated gene profiles: the 70-Gene Signature and the Recurrence Score. The validity of the signature was verified in independent cohorts obtained from the GEO database. Conclusions This study identifies a simple gene expression score that complements histopathological prognostic factors in breast cancer, and can be determined in paraffin-embedded samples. PMID:20584321

Nonlinear Curvature Expressions for Combined Flapwise Bending, Chordwise Bending, Torsion and Extension of Twisted Rotor Blades

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.; Kaza, K. R. V.

1976-01-01

The nonlinear curvature expressions for a twisted rotor blade or a beam undergoing transverse bending in two planes, torsion, and extension were developed. The curvature expressions were obtained using simple geometric considerations. The expressions were first developed in a general manner using the geometrical nonlinear theory of elasticity. These general nonlinear expressions were then systematically reduced to four levels of approximation by imposing various simplifying assumptions, and in each of these levels the second degree nonlinear expressions were given. The assumptions were carefully stated and their implications with respect to the nonlinear theory of elasticity as applied to beams were pointed out. The transformation matrices between the deformed and undeformed blade-fixed coordinates, which were needed in the development of the curvature expressions, were also given for three of the levels of approximation. The present curvature expressions and transformation matrices were compared with corresponding expressions existing in the literature.

Slip and barodiffusion phenomena in slow flows of a gas mixture

NASA Astrophysics Data System (ADS)

Zhdanov, V. M.

2017-03-01

The slip and barodiffusion problems for the slow flows of a gas mixture are investigated on the basis of the linearized moment equations following from the Boltzmann equation. We restrict ourselves to the set of the third-order moment equations and state two general relations (resembling conservation equations) for the moments of the distribution function similar to the conditions used by Loyalka [S. K. Loyalka, Phys. Fluids 14, 2291 (1971), 10.1063/1.1693331] in his approximation method (the modified Maxwell method). The expressions for the macroscopic velocities of the gas mixture species, the partial viscous stress tensors, and the reduced heat fluxes for the stationary slow flow of a gas mixture in the semi-infinite space over a plane wall are obtained as a result of the exact solution of the linearized moment equations in the 10- and 13-moment approximations. The general expression for the slip velocity and the simple and accurate expressions for the viscous, thermal, diffusion slip, and baroslip coefficients, which are given in terms of the basic transport coefficients, are derived by using the modified Maxwell method. The solutions of moment equations are also used for investigation of the flow and diffusion of a gas mixture in a channel formed by two infinite parallel plates. A fundamental result is that the barodiffusion factor in the cross-section-averaged expression for the diffusion flux contains contributions associated with the viscous transfer of momentum in the gas mixture and the effect of the Knudsen layer. Our study revealed that the barodiffusion factor is equal to the diffusion slip coefficient (correct to the opposite sign). This result is consistent with the Onsager's reciprocity relations for kinetic coefficients following from nonequilibrium thermodynamics of the discontinuous systems.

Generation of WNK1 knockout cell lines by CRISPR/Cas-mediated genome editing.

PubMed

Roy, Ankita; Goodman, Joshua H; Begum, Gulnaz; Donnelly, Bridget F; Pittman, Gabrielle; Weinman, Edward J; Sun, Dandan; Subramanya, Arohan R

2015-02-15

Sodium-coupled SLC12 cation chloride cotransporters play important roles in cell volume and chloride homeostasis, epithelial fluid secretion, and renal tubular salt reabsorption. These cotransporters are phosphorylated and activated indirectly by With-No-Lysine (WNK) kinases through their downstream effector kinases, Ste20- and SPS1-related proline alanine-rich kinase (SPAK) and oxidative stress-responsive kinase 1 (OSR1). Multiple WNK kinases can coexist within a single cell type, although their relative contributions to SPAK/OSR1 activation and salt transport remain incompletely understood. Deletion of specific WNKs from cells that natively express a functional WNK-SPAK/OSR1 network will help resolve these knowledge gaps. Here, we outline a simple method to selectively knock out full-length WNK1 expression from mammalian cells using RNA-guided clustered regularly interspaced short palindromic repeats/Cas9 endonucleases. Two clonal cell lines were generated by using a single-guide RNA (sgRNA) targeting exon 1 of the WNK1 gene, which produced indels that abolished WNK1 protein expression. Both cell lines exhibited reduced endogenous WNK4 protein abundance, indicating that WNK1 is required for WNK4 stability. Consistent with an on-target effect, the reduced WNK4 abundance was associated with increased expression of the KLHL3/cullin-3 E3 ubiquitin ligase complex and was rescued by exogenous WNK1 overexpression. Although the morphology of the knockout cells was indistinguishable from control, they exhibited low baseline SPAK/OSR1 activity and failed to trigger regulatory volume increase after hypertonic stress, confirming an essential role for WNK1 in cell volume regulation. Collectively, our data show how this new, powerful, and accessible gene-editing technology can be used to dissect and analyze WNK signaling networks.

The suitability of human adipose-derived stem cells for the engineering of ligament tissue.

PubMed

Eagan, Michael J; Zuk, Patricia A; Zhao, Ke-Wei; Bluth, Benjamin E; Brinkmann, Elyse J; Wu, Benjamin M; McAllister, David R

2012-10-01

Rupture of the anterior cruciate ligament (ACL) is the one of the most common sports-related injuries. With its poor healing capacity, surgical reconstruction using either autografts or allografts is currently required to restore function. However, serious complications are associated with graft reconstructions and the number of such reconstructions has steadily risen over the years, necessitating the search for an alternative approach to ACL repair. Such an approach may likely be tissue engineering. Recent engineering approaches using ligament-derived fibroblasts have been promising, but the slow growth rate of such fibroblasts in vitro may limit their practical application. More promising results are being achieved using bone marrow mesenchymal stem cells (MSCs). The adipose-derived stem cell (ASC) is often proposed as an alternative choice to the MSC and, as such, may be a suitable stem cell for ligament engineering. However, the use of ASCs in ligament engineering still remains relatively unexplored. Therefore, in this study, the potential use of human ASCs in ligament tissue engineering was initially explored by examining their ability to express several ligament markers under growth factor treatment. ASC populations treated for up to 4 weeks with TGFβ1 or IGF1 did not show any significant and consistent upregulation in the expression of collagen types 1 and 3, tenascin C and scleraxis. While treatment with EGF or bFGF resulted in increased tenascin C expression, increased expression of collagens 1 and 3 were never observed. Therefore, simple in vitro treatment of human ASC populations with growth factors may not stimulate their ligament differentiative potential. Copyright © 2011 John Wiley & Sons, Ltd.

Exact expressions and accurate approximations for the dependences of radius and index of refraction of solutions of inorganic solutes on relative humidity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, E.R.; Schwartz, S.

2010-03-15

Light scattering by aerosols plays an important role in Earth’s radiative balance, and quantification of this phenomenon is important in understanding and accounting for anthropogenic influences on Earth’s climate. Light scattering by an aerosol particle is determined by its radius and index of refraction, and for aerosol particles that are hygroscopic, both of these quantities vary with relative humidity RH. Here exact expressions are derived for the dependences of the radius ratio (relative to the volume-equivalent dry radius) and index of refraction on RH for aqueous solutions of single solutes. Both of these quantities depend on the apparent molal volumemore » of the solute in solution and on the practical osmotic coefficient of the solution, which in turn depend on concentration and thus implicitly on RH. Simple but accurate approximations are also presented for the RH dependences of both radius ratio and index of refraction for several atmospherically important inorganic solutes over the entire range of RH values for which these substances can exist as solution drops. For all substances considered, the radius ratio is accurate to within a few percent, and the index of refraction to within ~0.02, over this range of RH. Such parameterizations will be useful in radiation transfer models and climate models.« less

Gyrochronology relating star age to rotational period is derived from first principles through a novel time dual for thermodynamics, named lingerdynamics

NASA Astrophysics Data System (ADS)

Feria, Erlan H.

2017-10-01

Gyrochronology estimates the age of a low-mass star from its rotational period, which is found from changes in brightness caused by dark star spots. First revealed as an insight in (Skumanich, A. 1972, The Astrophysical Journal. 171: 565) it allows astronomers to find true sun-like stars that may harbor life in its planets (Meibom, S. et. al., Nature. 517: 589-591). Here a simple expression for the age of a star is derived through a novel linger thermo theory (LTT) integrating thermodynamics with its revealed time-dual, named lingerdynamics. This expression relates the star age to the ratio of past and present rotational period metrics (RPM) of lingerdynamics. LTT has been used earlier to derive a simple expression for the finding of the entropy of spherical-homogeneous mediums (Feria, E. H. Nov. 19, 2016, Linger Thermo Theory, IEEE Int’l Conf. on Smart Cloud, 18 pages, DOI 10.1109/SmartCloud.2016.57, Colombia Univ., N.Y., N.Y. and Feria, E. H. June 7th 2017, AAS 340th Meeting). In LTT the lifespan of system operation τ is given by: τ = (2Π /3v3)G2M2 x RPM where G is the gravitational constant, Π is the pace of mass-energy retention in s/m3 units (e.g., for our current sun it is given by 5 billion ‘future’ years over its volume), and v is the perpetual radial speed about the point-mass M. Since in LTT a star is modeled as a point mass at the center of its spherical volume, its RPM is not the same as the measured rotational period of an actual star. For instance, for our sun its equator rotational period is approximately 25.34 days, while in lingerdynamics it is a fraction of a day, i.e., 0.116 days, where this value is derived from the RPM expression 2πrsun/(GMsun / rsun)1/2 where 2πrsun is the circumference of the sun, (GMsun/rsun)1/2 is the perpetual radial speed v for our point-mass modeled sun, and rsun and Msun are the sun radius and point-mass, respectively. However, using conservation of angular momentum arguments it is assumed that the ratio of the ‘actual past and present rotational periods’ matches that of our theoretical lingerdynamic’s rotational period metrics. Using this key enabling theoretical assumption one then sensibly arrives at gyrochronology from our first principles LTT perspective.

A Simple Optical Waveguide Experiment.

ERIC Educational Resources Information Center

Phelps, J.; Sambles, J. R.

1989-01-01

Describes a thin film rectangular dielectric waveguide and its laboratory use. Discusses the theory of uniaxial thin film waveguides with mathematical expressions and the laboratory procedures for a classroom experiment with diagrams. (Author/YP)

Understanding space weather with new physical, mathematical and philosophical approaches

NASA Astrophysics Data System (ADS)

Mateev, Lachezar; Velinov, Peter; Tassev, Yordan

2016-07-01

The actual problems of solar-terrestrial physics, in particular of space weather are related to the prediction of the space environment state and are solved by means of different analyses and models. The development of these investigations can be considered also from another side. This is the philosophical and mathematical approach towards this physical reality. What does it constitute? We have a set of physical processes which occur in the Sun and interplanetary space. All these processes interact with each other and simultaneously participate in the general process which forms the space weather. Let us now consider the Leibniz's monads (G.W. von Leibniz, 1714, Monadologie, Wien; Id., 1710, Théodicée, Amsterdam) and use some of their properties. There are total 90 theses for monads in the Leibniz's work (1714), f.e. "(1) The Monad, of which we shall here speak, is nothing but a simple substance, which enters into compounds. By 'simple' is meant 'without parts'. (Theod. 10.); … (56) Now this connexion or adaptation of all created things to each and of each to all, means that each simple substance has relations which express all the others, and, consequently, that it is a perpetual living mirror of the universe. (Theod. 130, 360.); (59) … this universal harmony, according to which every substance exactly expresses all others through the relations it has with them. (63) … every Monad is, in its own way, a mirror of the universe, and the universe is ruled according to a perfect order. (Theod. 403.)", etc. Let us introduce in the properties of monads instead of the word "monad" the word "process". We obtain the following statement: Each process reflects all other processes and all other processes reflect this process. This analogy is not formal at all, it reflects accurately the relation between the physical processes and their unity. The category monad which in the Leibniz's Monadology reflects generally the philosophical sense is fully identical with the physical one, in our case. The corresponding mathematical relations are needed for the application of this analogy in the solar-terrestrial physics and space weather. For this purpose in the contemporary categories theory in the algebra a whole field for it exists - the theory of monads (M. Barr, Ch. Wells, 1985, Toposes, Triples and Theories, Springer-Verlag, 278, p. 82). This theory is generated by analogous elements as in the Leibniz's Monadology. As it is known the categories theory and in particular the monad theory (also named triple or triad theory) tends to make axioms in mathematics. This approach would be very useful for such complex systems and processes as these in the solar-terrestrial physics and space weather. Here some methods for algebraic data structures could be introduced. Or some imperative programs can be embedded in a purely functional program for modeling, respectively. All these problems are principally considered in the proposed report.

Immunohistochemistry Study of P53 and C-erbB-2 Expression in Trophoblastic Tissue and Their Predictive Values in Diagnosing Malignant Progression of Simple Molar Pregnancy

PubMed Central

Hasanzadeh, Malihe; Sharifi, Norrie; Farazestanian, Marjaneh; Nazemian, Seyed Saman; Madani Sani, Faezeh

2016-01-01

Background Finding a tumor marker to predict the aggressive behavior of molar pregnancy in early stages has yet been a topic for studies. Objectives In this survey we planned to study patients with molar pregnancy to 1) assess the p53 and c-erbB-2 expression in trophoblastic tissue, 2) to study the relationship between their expression intensity and progression of a molar pregnancy to gestational trophoblastic neoplasia, and 3) to determine a cut off value for the amount of p53 and c-erbB-2 expression which might correlate with aggressive behavior of molar pregnancy. Patients and Methods In a prospective cross sectional study by using a high accuracy technique EnVision Tm system for immunohistochemistry staining of molar pregnancy samples, we evaluated p53 and c-erbB-2 expression in cytotrophoblast and syncytiotrophoblast and the correlation of their expression with progression of molar pregnancy to gestational trophoblastic neoplasia (GTN). Normal prostatic tissue and Breast cancer tissue were used as positive controls. Results We studied 28 patients with simple molar pregnancy (SMP) and 30 with GTN. Cytotrophobalst had significantly higher expression of p53 and c-erbB-2 and syncytiotrophoblast had greater expression of p53 in GTN group as compared to SMP group. The cut off values for percentage of p53 positive immunostained cytotrophoblast and syncytiotrophoblast were 5.5% and 2.5%. In c-erbB-2 positive membranous stained cytotrophoblast the cut off was 12.5%. Conclusions Our data suggests that over expression of p53 and c-erbB-2 is associated with malignant progression of molar pregnancy. We encountered that high expression of p53 and c-erbB-2 in trophoblastic cells could predict gestational trophoblastic neoplasia during the early stages. PMID:27703642

Remodeling a tissue: subtraction adds insight.

PubMed

Axelrod, Jeffrey D

2012-11-27

Sculpting a body plan requires both patterning of gene expression and translating that pattern into morphogenesis. Developmental biologists have made remarkable strides in understanding gene expression patterning, but despite a long history of fascination with the mechanics of morphogenesis, knowledge of how patterned gene expression drives the emergence of even simple shapes and forms has grown at a slower pace. The successful merging of approaches from cell biology, developmental biology, imaging, engineering, and mathematical and computational sciences is now accelerating progress toward a fuller and better integrated understanding of the forces shaping morphogenesis.

Analytical expressions for the nonlinear interference in dispersion managed transmission coherent optical systems

NASA Astrophysics Data System (ADS)

Qiao, Yaojun; Li, Ming; Yang, Qiuhong; Xu, Yanfei; Ji, Yuefeng

2015-01-01

Closed-form expressions of nonlinear interference of dense wavelength-division-multiplexed (WDM) systems with dispersion managed transmission (DMT) are derived. We carry out a simulative validation by addressing an ample and significant set of the Nyquist-WDM systems based on polarization multiplexed quadrature phase-shift keying (PM-QPSK) subcarriers at a baud rate of 32 Gbaud per channel. Simulation results show the simple closed-form analytical expressions can provide an effective tool for the quick and accurate prediction of system performance in DMT coherent optical systems.

Expression-invariant representations of faces.

PubMed

Bronstein, Alexander M; Bronstein, Michael M; Kimmel, Ron

2007-01-01

Addressed here is the problem of constructing and analyzing expression-invariant representations of human faces. We demonstrate and justify experimentally a simple geometric model that allows to describe facial expressions as isometric deformations of the facial surface. The main step in the construction of expression-invariant representation of a face involves embedding of the facial intrinsic geometric structure into some low-dimensional space. We study the influence of the embedding space geometry and dimensionality choice on the representation accuracy and argue that compared to its Euclidean counterpart, spherical embedding leads to notably smaller metric distortions. We experimentally support our claim showing that a smaller embedding error leads to better recognition.

RADIATION-INDUCED GENETIC DAMAGE IN THE MEXICAN TOAD (BUFO VALLICEPS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blair, W.F.

1960-10-01

Lines of Mexican toads (Bufo valliceps) bearing x-ray induced genetic damage were established by mating normal females with males that had received gonadal x-ray doses ranging from 300 to 3000 r. Survival in the first generation was inversely proportional to dose,-as was expected. Toads of the 300-r and l000- r lines were inbred, and toads of these lines and of the 700-r line were outcrossed to normal ones. Two crosses were made between toads of the 500-r and 1000-r lines. Developmental abnormalities of various kinds appeared at life history stages rangthg from early embryonic development to post-metamorphic life in bothmore » inbred and outcross generations. These included abnormal gastrulation and neurulation, larval and post-metamorphic edema, abnormally positioned or missing limbs, optical deficiencies, prognathous jaw due to excessive elongation of the lower jaw, and melanin deficiency. The prognathous jaw, in its extreme expression, would probably be lethal in natural populations because of difficulty of feeding. The melanin deficiency, in its extreme expression, is lethal as metamorphosis fails to occur, and in lesser expression, it appears to be lethal or detrimental. The various abnormalities do not appear to be inherited in any simple way, but instead they vary in expression both within and between generations, possibly in relation to genotype and environment. (auth)« less

Affinity ranking of antibodies using flow cytometry: application in antibody phage display-based target discovery.

PubMed

Geuijen, Cecilia A W; Clijsters-van der Horst, Marieke; Cox, Freek; Rood, Pauline M L; Throsby, Mark; Jongeneelen, Mandy A C; Backus, Harold H J; van Deventer, Els; Kruisbeek, Ada M; Goudsmit, Jaap; de Kruif, John

2005-07-01

Application of antibody phage display to the identification of cell surface antigens with restricted expression patterns is often complicated by the inability to demonstrate specific binding to a certain cell type. The specificity of an antibody can only be properly assessed when the antibody is of sufficient high affinity to detect low-density antigens on cell surfaces. Therefore, a robust and simple assay for the prediction of relative antibody affinities was developed and compared to data obtained using surface plasmon resonance (SPR) technology. A panel of eight anti-CD46 antibody fragments with different affinities was selected from phage display libraries and reformatted into complete human IgG1 molecules. SPR was used to determine K(D) values for these antibodies. The association and dissociation of the antibodies for binding to CD46 expressed on cell surfaces were analysed using FACS-based assays. We show that ranking of the antibodies based on FACS data correlates well with ranking based on K(D) values as measured by SPR and can therefore be used to discriminate between high- and low-affinity antibodies. Finally, we show that a low-affinity antibody may only detect high expression levels of a surface marker while failing to detect lower expression levels of this molecule, which may lead to a false interpretation of antibody specificity.

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

PubMed Central

2011-01-01

Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes. PMID:21333005

Turning around Newton's Second Law

ERIC Educational Resources Information Center

Goff, John Eric

2004-01-01

Conceptual and quantitative difficulties surrounding Newton's second law often arise among introductory physics students. Simply turning around how one expresses Newton's second law may assist students in their understanding of a deceptively simple-looking equation.

Sub-core permeability and relative permeability characterization with Positron Emission Tomography

NASA Astrophysics Data System (ADS)

Zahasky, C.; Benson, S. M.

2017-12-01

This study utilizes preclinical micro-Positron Emission Tomography (PET) to image and quantify the transport behavior of pulses of a conservative aqueous radiotracer injected during single and multiphase flow experiments in a Berea sandstone core with axial parallel bedding heterogeneity. The core is discretized into streamtubes, and using the micro-PET data, expressions are derived from spatial moment analysis for calculating sub-core scale tracer flux and pore water velocity. Using the flux and velocity data, it is then possible to calculate porosity and saturation from volumetric flux balance, and calculate permeability and water relative permeability from Darcy's law. Full 3D simulations are then constructed based on this core characterization. Simulation results are compared with experimental results in order to test the assumptions of the simple streamtube model. Errors and limitations of this analysis will be discussed. These new methods of imaging and sub-core permeability and relative permeability measurements enable experimental quantification of transport behavior across scales.

Light propagation and the distance-redshift relation in a realistic inhomogeneous universe

NASA Technical Reports Server (NTRS)

Futamase, Toshifumi; Sasaki, Misao

1989-01-01

The propagation of light rays in a clumpy universe constructed by cosmological version of the post-Newtonian approximation was investigated. It is shown that linear approximation to the propagation equations is valid in the region where zeta is approximately less than 1 even if the density contrast is much larger than unity. Based on a gerneral order-of-magnitude statistical consideration, it is argued that the linear approximation is still valid where zeta is approximately greater than 1. A general formula for the distance-redshift relation in a clumpy universe is given. An explicit expression is derived for a simplified situation in which the effect of the gravitational potential of inhomogeneities dominates. In the light of the derived relation, the validity of the Dyer-Roeder distance is discussed. Also, statistical properties of light rays are investigated for a simple model of an inhomogeneous universe. The result of this example supports the validity of the linear approximation.

Determination of alkenylbenzenes and related flavour compounds in food samples by on-column preconcentration-capillary liquid chromatography.

PubMed

Avila, Mónica; Zougagh, Mohammed; Escarpa, Alberto; Ríos, Angel

2009-10-23

A new, simple and versatile method is presented for the determination of different concentration levels of alkenylbenzenes (eugenol, isoeugenol, eugenol methyl ether, myristicin, anethole and estragole) and the related flavour compounds (coumarin and pulegone) in food samples. The method involves the use of a stationary phase (capillary column) for the enrichment with appropriate elution. After the sample had completely passed through the capillary column the eluent was changed and the separation/detection was achieved. Excellent linearity was obtained under the proposed conditions for a direct determination method and a method including on-line preconcentration. The limits of detection were in the ranges 97-148 and 9.5-14.2 ng/mL, respectively. Evidence for a matrix effect was not found and recoveries between 92 and 110% were obtained. The precision of the method, expressed as relative standard deviation values, was below 5% in all cases. The applicability of this methodology was tested by analyzing synthetic and real food samples.

Speeding up ontology creation of scientific terms

NASA Astrophysics Data System (ADS)

Bermudez, L. E.; Graybeal, J.

2005-12-01

An ontology is a formal specification of a controlled vocabulary. Ontologies are composed of classes (similar to categories), individuals (members of classes) and properties (attributes of the individuals). Having vocabularies expressed in a formal specification like the Web Ontology Language (OWL) enables interoperability due to the comprehensiveness of OWL by software programs. Two main non-inclusive strategies exist when constructing an ontology: an up-down approach and a bottom-up approach. The former one is directed towards the creation of top classes first (main concepts) and then finding the required subclasses and individuals. The later approach starts from the individuals and then finds similar properties promoting the creation of classes. At the Marine Metadata Interoperability (MMI) Initiative we used a bottom-up approach to create ontologies from simple-vocabularies (those that are not expressed in a conceptual way). We found that the vocabularies were available in different formats (relational data bases, plain files, HTML, XML, PDF) and sometimes were composed of thousands of terms, making the ontology creation process a very time consuming activity. To expedite the conversion process we created a tool VOC2OWL that takes a vocabulary in a table like structure (CSV or TAB format) and a conversion-property file to create automatically an ontology. We identified two basic structures of simple-vocabularies: Flat vocabularies (e.g., phone directory) and hierarchical vocabularies (e.g., taxonomies). The property file defines a list of attributes for the conversion process for each structure type. The attributes included metadata information (title, description, subject, contributor, urlForMoreInformation) and conversion flags (treatAsHierarchy, generateAutoIds) and other conversion information needed to create the ontology (columnForPrimaryClass, columnsToCreateClassesFrom, fileIn, fileOut, namespace, format). We created more than 50 ontologies and generated more than 250,000 statements (or triples). The previous ontologies allowed domain experts to create 800 relations allowing to infer 2200 more relations among different vocabularies in the MMI workshop "Advancing Domain Vocabularies" held in Boulder Aug, 2005.

Production of human insulin in an E. coli system with Met-Lys-human proinsulin as the expressed precursor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin-Qiu Chen; Hong-Tao Zhang; Mei-Hao Hu

1995-10-01

The construction of a gene encoding Lys-human proinsulin, its direct expression in E.coli, and the simple purification procedure are described here. The temperature inducible promotor was employed for induction in a very short time. The expression level could reach 20-30%. After a simple downstream processing and only one step of Sephadex G50 purification, 150 mg recombinant Lys-human proinsulin with a purity of up to 90% could be obtained easily from 1 L of high density fermentation medium. The obtained product is in the form of Met-Lys-human proinsulin because of the failure of the bacterial host to remove the initiator methioninemore » residue. The Lys-human proinsulin could be changed into human insulin by tryspin and carboxypeptidase B treatment in later steps. After separation with DEAE Sephadex A25, human insulin with expected amino acid composition and full native biological activity could be obtained with a yield of 50 mg/L fermentation medium. 20 refs., 5 figs., 4 tabs.« less

Analytical study of the critical behavior of the nonlinear pendulum

NASA Astrophysics Data System (ADS)

Lima, F. M. S.

2010-11-01

The dynamics of a simple pendulum consisting of a small bob and a massless rigid rod has three possible regimes depending on its total energy E: Oscillatory (when E is not enough for the pendulum to reach the top position), "perpetual ascent" when E is exactly the energy needed to reach the top, and nonoscillatory for greater energies. In the latter regime, the pendulum rotates periodically without velocity inversions. In contrast to the oscillatory regime, for which an exact analytic solution is known, the other two regimes are usually studied by solving the equation of motion numerically. By applying conservation of energy, I derive exact analytical solutions to both the perpetual ascent and nonoscillatory regimes and an exact expression for the pendulum period in the nonoscillatory regime. Based on Cromer's approximation for the large-angle pendulum period, I find a simple approximate expression for the decrease of the period with the initial velocity in the nonoscillatory regime, valid near the critical velocity. This expression is used to study the critical slowing down, which is observed near the transition between the oscillatory and nonoscillatory regimes.

Insect cells-baculovirus system for the production of difficult to express proteins.

PubMed

Osz-Papai, Judit; Radu, Laura; Abdulrahman, Wassim; Kolb-Cheynel, Isabelle; Troffer-Charlier, Nathalie; Birck, Catherine; Poterszman, Arnaud

2015-01-01

The production of sufficient quantities of homogenous protein not only is an essential prelude for structural investigations but also represents a rate-limiting step for many human functional studies. Although technologies for expression of recombinant proteins and complexes have been improved tremendously, in many cases, protein production remains a challenge and can be associated with considerable investment. This chapter describes simple and efficient protocols for expression screening and optimization of protein production in insect cells using the baculovirus expression system. We describe the procedure, starting from the cloning of a gene of interest into an expression transfer baculovirus vector, followed by generation of the recombinant virus by homologous recombination, evaluation of protein expression, and scale-up. Handling of insect cell cultures and preparation of bacmid for co-transfection are also detailed.

The Fringe-Imaging Skin Friction Technique PC Application User's Manual

NASA Technical Reports Server (NTRS)

Zilliac, Gregory G.

1999-01-01

A personal computer application (CXWIN4G) has been written which greatly simplifies the task of extracting skin friction measurements from interferograms of oil flows on the surface of wind tunnel models. Images are first calibrated, using a novel approach to one-camera photogrammetry, to obtain accurate spatial information on surfaces with curvature. As part of the image calibration process, an auxiliary file containing the wind tunnel model geometry is used in conjunction with a two-dimensional direct linear transformation to relate the image plane to the physical (model) coordinates. The application then applies a nonlinear regression model to accurately determine the fringe spacing from interferometric intensity records as required by the Fringe Imaging Skin Friction (FISF) technique. The skin friction is found through application of a simple expression that makes use of lubrication theory to relate fringe spacing to skin friction.

Structure and effective interactions in three-component hard sphere liquids.

PubMed

König, A; Ashcroft, N W

2001-04-01

Complete and simple analytical expressions for the partial structure factors of the ternary hard sphere mixture are obtained within the Percus-Yevick approximation and presented as functions of relative packing fractions and relative hard sphere diameters. These solutions follow from the Laplace transform method as applied to multicomponent systems by Lebowitz [Phys. Rev. 133, A895 (1964)]. As an important application, we examine effective interactions in hard sphere liquid mixtures using the microscopic information contained in their partial structure factors. Thus the ensuring pair potential for an effective one-component system is obtained from the correlation functions by using an approximate inversion, and examples of effective potentials for three-component hard sphere mixtures are given. These mixtures may be of particular interest for the study of the packing aspects of melts that form glasses or quasicrystals, since noncrystalline solids often emerge from melts with at least three atomic constituents.

Modal sound transmission loss of a single leaf panel: Asymptotic solutions.

PubMed

Wang, Chong

2015-12-01

In a previously published paper [C. Wang, J. Acoust. Soc. Am. 137(6), 3514-3522 (2015)], the modal sound transmission coefficients of a single leaf panel were discussed with regard to the inter-modal coupling effects. By incorporating such effect into the equivalent modal radiation impedance, which is directly related to the modal sound transmission coefficient of each mode, the overall sound transmission loss for both normal and randomized sound incidences was computed through a simple modal superposition. Benefiting from the analytical expressions of the equivalent modal impedance and modal transmission coefficients, in this paper, behaviors of modal sound transmission coefficients in several typical frequency ranges are discussed in detail. Asymptotic solutions are also given for the panels with relatively low bending stiffnesses, for which the sound transmission loss has been assumed to follow the mass law of a limp panel. Results are also compared to numerical analysis and the renowned mass law theories.

Effect of deposition rate and NNN interactions on adatoms mobility in epitaxial growth

NASA Astrophysics Data System (ADS)

Hamouda, Ajmi B. H.; Mahjoub, B.; Blel, S.

2017-07-01

This paper provides a detailed analysis of the surface diffusion problem during epitaxial step-flow growth using a simple theoretical model for the diffusion equation of adatoms concentration. Within this framework, an analytical expression for the adatom mobility as a function of the deposition rate and the Next-Nearest-Neighbor (NNN) interactions is derived and compared with the effective mobility computed from kinetic Monte Carlo (kMC) simulations. As far as the 'small' step velocity or relatively weak deposition rate commonly used for copper growth is concerned, an excellent quantitative agreement with the theoretical prediction is found. The effective adatoms mobility is shown to exhibit an exponential decrease with NNN interactions strength and increases in roughly linear behavior versus deposition rate F. The effective step stiffness and the adatoms mobility are also shown to be closely related to the concentration of kinks.

Tandem carrying, a new foraging strategy in ants: description, function, and adaptive significance relative to other described foraging strategies

NASA Astrophysics Data System (ADS)

Guénard, Benoit; Silverman, Jules

2011-08-01

An important aspect of social insect biology lies in the expression of collective foraging strategies developed to exploit food. In ants, four main types of foraging strategies are typically recognized based on the intensity of recruitment and the importance of chemical communication. Here, we describe a new type of foraging strategy, "tandem carrying", which is also one of the most simple recruitment strategies, observed in the Ponerinae species Pachycondyla chinensis. Within this strategy, workers are directly carried individually and then released on the food resource by a successful scout. We demonstrate that this recruitment is context dependent and based on the type of food discovered and can be quickly adjusted as food quality changes. We did not detect trail marking by tandem-carrying workers. We conclude by discussing the importance of tandem carrying in an evolutionary context relative to other modes of recruitment in foraging and nest emigration.

The condition of a finite Markov chain and perturbation bounds for the limiting probabilities

NASA Technical Reports Server (NTRS)

Meyer, C. D., Jr.

1979-01-01

The inequalities bounding the relative error the norm of w- w squiggly/the norm of w are exhibited by a very simple function of E and A. Let T denote the transition matrix of an ergodic chain, C, and let A = I - T. Let E be a perturbation matrix such that T squiggly = T - E is also the transition matrix of an ergodic chain, C squiggly. Let w and w squiggly denote the limiting probability (row) vectors for C and C squiggly. The inequality is the best one possible. This bound can be significant in the numerical determination of the limiting probabilities for an ergodic chain. In addition to presenting a sharp bound for the norm of w-w squiggly/the norm of w an explicit expression for w squiggly will be derived in which w squiggly is given as a function of E, A, w and some other related terms.

Model systems for the study of kidney development: use of the pronephros in the analysis of organ induction and patterning.

PubMed

Vize, P D; Seufert, D W; Carroll, T J; Wallingford, J B

1997-08-15

Most vertebrate organs, once formed, continue to perform the function for which they were generated until the death of the organism. The kidney is a notable exception to this rule. Vertebrates, even those that do not undergo metamorphosis, utilize a progression of more complex kidneys as they grow and develop. This is presumably due to the changing conditions to which the organism must respond to retain what Homer Smith referred to as our physiological freedom. To quote, "Recognizing that we have the kind of blood we have because we have the kind of kidneys we have, we must acknowledge that our kidneys constitute the major foundation of our physiological freedom. Only because they work the way they do has it become possible for us to have bones, muscles, glands, and brains. Superficially, it might be said that the function of the kidneys is to make urine; but in a more considered view one can say that the kidneys make the stuff of philosophy itself" ("From Fish to Philosopher," Little, Brown and Co., Boston, 1953). Different kidneys are used to make the stuff of philosophy at different stages of development depending on the age and needs of the organism, rather than the usual approach of simply making embryonic organs larger as the animal grows. Although evolution has provided the higher vertebrates with complex adult kidneys, they continue to utilize simple kidneys in embryogenesis. In lower vertebrates with simple adult kidneys, even more simple versions are used during early developmental stages. In this review the anatomy, development, and gene expression patterns of the embryonic kidney, the pronephros, will be described and compared to the more complex kidney forms. Despite some differences in anatomy, similar developmental pathways seem to be responsible for the induction and the response to induction in both evanescent and permanent kidney forms. Gene expression patterns can, therefore, be added to the morphological and functional data indicating that all forms of the kidney are closely related structures. Given the similarities between the development of simple and complex kidneys, the embryonic kidneys may be an ideal model system in which to investigate the genesis of multicomponent organ systems.

Tense and Aspect in Mandarin Chinese and Spanish: Contrasts Manifested in the Mandarin Translation of Javier Marias' Corazón Tan Blanco

ERIC Educational Resources Information Center

Hung, Yu-Ju

2016-01-01

Mandarin Chinese and Spanish are both considered aspect languages for the simple reason that they both mark grammatical aspect morphologically: the former attaches a particle expressing only aspectual meaning to the root of a verb, while the latter attaches a suffix expressing both aspectual and tense meaning to the root of a verb. Since tense…

Ribosomal Binding Site Switching: An Effective Strategy for High-Throughput Cloning Constructions

PubMed Central

Li, Yunlong; Zhang, Yong; Lu, Pei; Rayner, Simon; Chen, Shiyun

2012-01-01

Direct cloning of PCR fragments by TA cloning or blunt end ligation are two simple methods which would greatly benefit high-throughput (HTP) cloning constructions if the efficiency can be improved. In this study, we have developed a ribosomal binding site (RBS) switching strategy for direct cloning of PCR fragments. RBS is an A/G rich region upstream of the translational start codon and is essential for gene expression. Change from A/G to T/C in the RBS blocks its activity and thereby abolishes gene expression. Based on this property, we introduced an inactive RBS upstream of a selectable marker gene, and designed a fragment insertion site within this inactive RBS. Forward and reverse insertions of specifically tailed fragments will respectively form an active and inactive RBS, thus all background from vector self-ligation and fragment reverse insertions will be eliminated due to the non-expression of the marker gene. The effectiveness of our strategy for TA cloning and blunt end ligation are confirmed. Application of this strategy to gene over-expression, a bacterial two-hybrid system, a bacterial one-hybrid system, and promoter bank construction are also verified. The advantages of this simple procedure, together with its low cost and high efficiency, makes our strategy extremely useful in HTP cloning constructions. PMID:23185557

Relationship between p53 dysfunction, CD38 expression, and IgV(H) mutation in chronic lymphocytic leukemia.

PubMed

Lin, Ke; Sherrington, Paul D; Dennis, Michael; Matrai, Zoltan; Cawley, John C; Pettitt, Andrew R

2002-08-15

Established adverse prognostic factors in chronic lymphocytic leukemia (CLL) include CD38 expression, relative lack of IgV(H) mutation, and defects of the TP53 gene. However, disruption of the p53 pathway can occur through mechanisms other than TP53 mutation, and we have recently developed a simple screening test that detects p53 dysfunction due to mutation of the genes encoding either p53 or ATM, a kinase that regulates p53. The present study was conducted to examine the predictive value of this test and to establish the relationship between p53 dysfunction, CD38 expression, and IgV(H) mutation. CLL cells from 71 patients were examined for IgV(H) mutation, CD38 expression, and p53 dysfunction (detected as an impaired p53/p21 response to ionizing radiation). Survival data obtained from 69 patients were analyzed according to each of these parameters. Relative lack of IgV(H) mutation (less than 5%; n = 45), CD38 positivity (antigen expressed on more than 20% of malignant cells; n = 19), and p53 dysfunction (n = 19) were independently confirmed as adverse prognostic factors. Intriguingly, all p53-dysfunctional patients and all but one of the CD38(+) patients had less [corrected] than 5% IgV(H) mutation. Moreover, patients with p53 dysfunction and/or CD38 positivity (n = 31) accounted for the short survival of the less mutated group. These findings indicate that the poor outcome associated with having less than 5% IgV(H) mutation may be due to the overrepresentation of high-risk patients with p53 dysfunction and/or CD38 positivity within this group, and that CD38(-) patients with functionally intact p53 may have a prolonged survival regardless of the extent of IgV(H) mutation.

Theory of periodic swarming of bacteria: Application to Proteus mirabilis

NASA Astrophysics Data System (ADS)

Czirók, A.; Matsushita, M.; Vicsek, T.

2001-03-01

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth), a series of concentric rings are developed as the bacteria multiply and swarm following a scenario that periodically repeats itself. We have developed a theoretical description for this process in order to obtain a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. Our approach is based on simple assumptions directly related to the latest experimental observations on colony formation under various conditions. The corresponding one-dimensional model consists of two coupled differential equations investigated here both by numerical integrations and by analyzing the various expressions obtained from these equations using a few natural assumptions about the parameters of the model. We determine the phase diagram corresponding to systems exhibiting periodic swarming, and discuss in detail how the various stages of the colony development can be interpreted in our framework. We point out that all of our theoretical results are in excellent agreement with the complete set of available observations. Thus the present study represents one of the few examples where self-organized biological pattern formation is understood within a relatively simple theoretical approach, leading to results and predictions fully compatible with experiments.

The algebra of complex 2 × 2 matrices and a general closed Baker-Campbell-Hausdorff formula

NASA Astrophysics Data System (ADS)

Foulis, D. L.

2017-07-01

We derive a closed formula for the Baker-Campbell-Hausdorff series expansion in the case of complex 2×2 matrices. For arbitrary matrices A and B, and a matrix Z such that \\exp Z = \\exp A \\exp B , our result expresses Z as a linear combination of A and B, their commutator [A, B] , and the identity matrix I. The coefficients in this linear combination are functions of the traces and determinants of A and B, and the trace of their product. The derivation proceeds purely via algebraic manipulations of the given matrices and their products, making use of relations developed here, based on the Cayley-Hamilton theorem, as well as a characterization of the consequences of [A, B] and/or its determinant being zero or otherwise. As a corollary of our main result we also derive a closed formula for the Zassenhaus expansion. We apply our results to several special cases, most notably the parametrization of the product of two SU(2) matrices and a verification of the recent result of Van-Brunt and Visser (2015 J. Phys. A: Math. Theor. 48 225207) for complex 2×2 matrices, in this latter case deriving also the related Zassenhaus formula which turns out to be quite simple. We then show that this simple formula should be valid for all matrices and operators.

The relative importance of light and nutrient limitation of phytoplankton growth: A simple index of coastal ecosystem sensitivity to nutrient enrichment

USGS Publications Warehouse

Cloern, J.E.

1999-01-01

Anthropogenic nutrient enrichment of the coastal zone is now a well-established fact. However, there is still uncertainty about the mechanisms through which nutrient enrichment can disrupt biological communities and ecosystem processes in the coastal zone. For example, while some estuaries exhibit classic symptoms of acute eutrophication, including enhanced production of algal biomass, other nutrient-rich estuaries maintain low algal biomass and primary production. This implies that large differences exist among coastal ecosystems in the rates and patterns of nutrient assimilation and cycling. Part of this variability comes from differences among ecosystems in the other resource that can limit algal growth and production - the light energy required for photosynthesis. Complete understanding of the eutrophication process requires consideration of the interacting effects of light and nutrients, including the role of light availability as a regulator of the expression of eutrophication. A simple index of the relative strength of light and nutrient limitation of algal growth can be derived from models that describe growth rate as a function of these resources. This index can then be used as one diagnostic to classify the sensitivity of coastal ecosystems to the harmful effects of eutrophication. Here I illustrate the application of this diagnostic with light and nutrient measurements made in three California estuaries and two Dutch estuaries.

The fluorescence theatre: a cost-effective device using theatre gels for fluorescent protein and dye screening.

PubMed

Heil, John R; Nordeste, Ricardo F; Charles, Trevor C

2011-04-01

Here we report a simple cost-effective device for screening colonies on plates for expression of the monomeric red fluorescent protein mRFP1 and the fluorescent dye Nile red. This device can be built from any simple light source, in our case a Quebec Colony Counter, and cost-effective theatre gels. The device can be assembled in as little as 20 min, and it produces excellent results when screening a large number of colonies.

Some simple solutions of Schrödinger's equation for a free particle or for an oscillator

NASA Astrophysics Data System (ADS)

Andrews, Mark

2018-05-01

For a non-relativistic free particle, we show that the evolution of some simple initial wave functions made up of linear segments can be expressed in terms of Fresnel integrals. Examples include the square wave function and the triangular wave function. The method is then extended to wave functions made from quadratic elements. The evolution of all these initial wave functions can also be found for the harmonic oscillator by a transformation of the free evolutions.

How should spin-weighted spherical functions be defined?

NASA Astrophysics Data System (ADS)

Boyle, Michael

2016-09-01

Spin-weighted spherical functions provide a useful tool for analyzing tensor-valued functions on the sphere. A tensor field can be decomposed into complex-valued functions by taking contractions with tangent vectors on the sphere and the normal to the sphere. These component functions are usually presented as functions on the sphere itself, but this requires an implicit choice of distinguished tangent vectors with which to contract. Thus, we may more accurately say that spin-weighted spherical functions are functions of both a point on the sphere and a choice of frame in the tangent space at that point. The distinction becomes extremely important when transforming the coordinates in which these functions are expressed, because the implicit choice of frame will also transform. Here, it is proposed that spin-weighted spherical functions should be treated as functions on the spin or rotation groups, which simultaneously tracks the point on the sphere and the choice of tangent frame by rotating elements of an orthonormal basis. In practice, the functions simply take a quaternion argument and produce a complex value. This approach more cleanly reflects the geometry involved, and allows for a more elegant description of the behavior of spin-weighted functions. In this form, the spin-weighted spherical harmonics have simple expressions as elements of the Wigner 𝔇 representations, and transformations under rotation are simple. Two variants of the angular-momentum operator are defined directly in terms of the spin group; one is the standard angular-momentum operator L, while the other is shown to be related to the spin-raising operator ð.

Ca2+ current vs. Ca2+ channel cooperativity of exocytosis

PubMed Central

Matveev, Victor; Bertram, Richard; Sherman, Arthur

2009-01-01

Recently there has been significant interest and progress in the study of spatio-temporal dynamics of Ca2+ that triggers exocytosis at a fast chemical synapse, which requires understanding the contribution of individual calcium channels to the release of a single vesicle. Experimental protocols provide insight into this question by probing the sensitivity of exocytosis to Ca2+ influx. While varying extracellular or intracellular Ca2+ concentration assesses the intrinsic biochemical Ca2+ cooperativity of neurotransmitter release, varying the number of open Ca2+ channels using pharmacological channel block or the tail current titration probes the cooperativity between individual Ca2+ channels in triggering exocytosis. Despite the wide use of these Ca2+ sensitivity measurements, their interpretation often relies on heuristic arguments. Here we provide a detailed analysis of the Ca2+ sensitivity measures probed by these experimental protocols, present simple expressions for special cases, and demonstrate the distinction between the Ca2+ current cooperativity, defined by the relationship between exocytosis rate and the whole-terminal Ca2+ current magnitude, and the underlying Ca2+ channel cooperativity, defined as the average number of channels involved in the release of a single vesicle. We find simple algebraic expressions that show that the two are different but linearly related. Further, we use 3D computational modeling of buffered Ca2+ diffusion to analyze these distinct Ca2+ cooperativity measures, and demonstrate the role of endogenous Ca2+ buffers on such measures. We show that buffers can either increase or decrease the Ca2+ current cooperativity of exocytosis, depending on their concentration and the single-channel Ca2+ current. PMID:19793978

Construction and development of an auto-regulatory gene expression system in Bacillus subtilis.

PubMed

Guan, Chengran; Cui, Wenjing; Cheng, Jintao; Zhou, Li; Guo, Junling; Hu, Xu; Xiao, Guoping; Zhou, Zhemin

2015-09-21

Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression system that has an expression pattern that is split between cell-growth and over-expression, leading to an increase in cell density and elevating the overall expression levels of heterologously expressed proteins. The broad applicability of this system and inducer-free expression property in B. subtilis facilitate the industrial scale-up and medical applications for the over-production of a variety of desired proteins.

Semantic integration of gene expression analysis tools and data sources using software connectors

PubMed Central

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data. PMID:24341380

Semantic integration of gene expression analysis tools and data sources using software connectors.

PubMed

Miyazaki, Flávia A; Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

2013-10-25

The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

ENTRAINMENT MODELS

EPA Science Inventory

This presentation presented information on entrainment models. Entrainment models use entrainment hypotheses to express the continuity equation. The advantage is that plume boundaries are known. A major disadvantage is that the problems that can be solved are rather simple. The ...

How to Talk about Professional Communication: Metalanguage and Heuristic Power.

ERIC Educational Resources Information Center

Killingsworth, M. Jimmie

1989-01-01

Analyzes several examples of metalanguage from current literature on professional writing, applying three principles for evaluating metalanguage in industry and academe. Considers a potentially effective metalanguage based on simple grammatical expressions. (MM)

Rough Evaluation Structure: Application of Rough Set Theory to Generate Simple Rules for Inconsistent Preference Relation

NASA Astrophysics Data System (ADS)

Gehrmann, Andreas; Nagai, Yoshimitsu; Yoshida, Osamu; Ishizu, Syohei

Since management decision-making becomes complex and preferences of the decision-maker frequently becomes inconsistent, multi-attribute decision-making problems were studied. To represent inconsistent preference relation, the concept of evaluation structure was introduced. We can generate simple rules to represent inconsistent preference relation by the evaluation structures. Further rough set theory for the preference relation was studied and the concept of approximation was introduced. One of our main aims of this paper is to introduce a concept of rough evaluation structure for representing inconsistent preference relation. We apply rough set theory to the evaluation structure, and develop a method for generating simple rules for inconsistent preference relations. In this paper, we introduce concepts of totally ordered information system, similarity class of preference relation, upper and lower approximation of preference relations. We also show the properties of rough evaluation structure and provide a simple example. As an application of rough evaluation structure, we analyze questionnaire survey of customer preferences about audio players.

The nature of the colloidal 'glass' transition.

PubMed

Dawson, Kenneth A; Lawlor, A; DeGregorio, Paolo; McCullagh, Gavin D; Zaccarelli, Emanuela; Foffi, Giuseppe; Tartaglia, Piero

2003-01-01

The dynamically arrested state of matter is discussed in the context of athermal systems, such as the hard sphere colloidal arrest. We believe that the singular dynamical behaviour near arrest expressed, for example, in how the diffusion constant vanishes may be 'universal', in a sense to be discussed in the paper. Based on this we argue the merits of studying the problem with simple lattice models. This, by analogy with the the critical point of the Ising model, should lead us to clarify the questions, and begin the program of establishing the degree of universality to be expected. We deal only with 'ideal' athermal dynamical arrest transitions, such as those found for hard sphere systems. However, it is argued that dynamically available volume (DAV) is the relevant order parameter of the transition, and that universal mechanisms may be well expressed in terms of DAV. For simple lattice models we give examples of simple laws that emerge near the dynamical arrest, emphasising the idea of a near-ideal gas of 'holes', interacting to give the power law diffusion constant scaling near the arrest. We also seek to open the discussion of the possibility of an underlying weak coupling theory of the dynamical arrest transition, based on DAV.

[Effect of Inhibiting and Activating Wnt Signalling Pathway on NSC67657-inducing Monocytic Differentiation of HL-60 Cells].

PubMed

Wang, Wei-Jia; Zhang, Xiu-Ming; Zhang, Yan; Wang, Jin-Shu

2016-04-01

To investigate the effect of inhibiting and activating Wnt signalling pathway on monocyte differentiation of HL-60 cells induced with a new steroidal drug NSC67657 and its possible mechamism. The HL-60 cells were treated with 5, 10 and 20 µmol/L XAV-939 (inhibitor of Wnt signalling pathway) for 3 days, and with 10, 20 and 30 mmol/L LiCl (activator of Wnt signalling pathway) for 1 day; the expression levels of down-stream genes and proteins of Wnt signolling pathway were detected by RT-PCR and Western blot, respectively; the expression of cell surface differentiation antigen CD14 and early apoptosis of HL-60 cells was detected by flow cytometry, moreover the most suitable concentration of Wnt inhibitor and activator for HL-60 cells was determined. Then the HL-60 cells with inhibited and activated Wnt pathway were treated with NSC67657 of 10 µmol/L for 3 days; the expression levels of CD14 and down-stream target proteins of Wnt signalling pathway in blank control (culture mediam) group, simple NSC67657-treated group, NSC67657 combined with inhibitor group and NSC67657 combined activator group were compared and analyzed. 20 µmol/L XAV-939 and 20 mmol/L LiCl could effectively inhibit and activate Wnt signalling pathway of HL-60 cells respectively, could significantly down- and up-regulate the expression of cyclinD1, TCF1 and c-Jun genes (P < 0.05) and proteins (P < 0.05); moreover, the number of CD10(+) HL-60 cells in these conditions was below 1%, no early apoptosis of HL-60 cells was found. In the simple NSC67657-treated groups, the expression of cyclinD1, TCF1 and c-Jun proteins was down-regulated (P < 0.05), and the percentage of CD14(+) HL-60 cells accounted for 62.13 ± 9.44; after the HL-60 cells were treated with XAV-939, the NSC67657 could more significantly down-regulate the expression of cyclinD1, TCF1 and c-Jun proteins and the percentage of CD14(+) HL-60 cell accounted for 84.17 ± 5.39%, as compared with simple NSC67657-treated group; as compared with blank controls group, the expression of cyclinD1, TCF1 and c-Jun proteins was more obviously down-regulated and the percentage of CD14(+) HL-60 cells decreased to 33.99 ± 8.37% in NSC67657 combined LiC1 streated group, but which were higher than those in simple NSC67657-treated group (P < 0.05). 20 µmol/L XAV-939 and 20 mmol/L LiCl as effective inhabitor and activator of Wnt signalling pathway respectively can significantly down- and up-regulate the expression of Wnt down-stream pathway target genes and proteins. The influence of XAV-939 and LiC1 on differentiation of HL-60 cells induced by NSC67657 suggests that Wnt signalling pathway plays a key role in monocyte differentiction of HL-60 cells induced by NSC67657.

Theoretical and Numerical Investigations on Shallow Tunnelling in Unsaturated Soils

NASA Astrophysics Data System (ADS)

Soranzo, Enrico; Wu, Wei

2013-04-01

Excavation of shallow tunnels with the New Austrian Tunnelling Method (NATM) requires proper assessing of the tunnel face stability, to enable an open-face excavation, and the estimation of the correspondent surface settlements. Soils in a partially saturated condition exhibit a higher cohesion than in a fully saturated state, which can be taken into account when assessing the stability of the tunnel face. For the assessment of the face support pressure, different methods are used in engineering practice, varying from simple empirical and analytical formulations to advanced finite element analysis. Such procedures can be modified to account for the unsaturated state of soils. In this study a method is presented to incorporate the effect of partial saturation in the numerical analysis. The results are then compared with a simple analytical formulation derived from parametric studies. As to the numerical analysis, the variation of cohesion and of Young's modulus with saturation can be considered when the water table lies below the tunnel in a soil exhibiting a certain capillary rise, so that the tunnel is driven in a partially saturated layer. The linear elastic model with Mohr-Coulomb failure criterion can be extended to partially saturated states and calibrated with triaxial tests on unsaturated. In order to model both positive and negative pore water pressure (suction), Bishop's effective stress is incorporated into Mohr-Coulomb's failure criterion. The effective stress parameter in Bishop's formulation is related to the degree of saturation as suggested by Fredlund. If a linear suction distribution is assumed, the degree of saturation can be calculated from the Soil Water Characteristic Curve (SWCC). Expressions exist that relate the Young's modulus of unsaturated soils to the net mean stress and the matric suction. The results of the numerical computation can be compared to Vermeer & Ruse's closed-form formula that expresses the limit support pressure of the tunnel face. The expression is derived from parametric studies and predicts stability of the tunnel face when negative values are returned, suggesting that open-face tunnelling can be performed. The formula can be modified to account for the variation of cohesion along the tunnel face. The results obtained from both the numerical analysis and the analytical formulation are well in agreement and show that the stability of the tunnel face can greatly benefit from the enhanced cohesion of partially saturated soils.

Single-step colony assay for screening antibody libraries.

PubMed

Kato, Mieko; Hanyu, Yoshiro

2017-08-10

We describe a method, single-step colony assay, for simple and rapid screening of single-chain Fv fragment (scFv) libraries. Colonies of Escherichia coli expressing the scFv library are formed on a hydrophilic filter that is positioned in contact with a membrane coated with an antigen. scFv expression is triggered upon treatment of colonies with an induction reagent, following which scFvs are secreted from the cells and diffused to the antigen-coated membrane. scFvs that exhibit binding affinity for the antigen are captured by the membrane-immobilized antigen. Lastly, detection of scFv binding of the antigen on the membrane allows identification of the clones on the filter that express antigen-specific scFvs. We tested this methodology by using an anti-rabbit IgG scFv, scFv(A10B), and a rat immune scFv library. Experiments conducted using scFv(A10B) revealed that this method improves scFv expression during the colony assay. By using our method to screen an immune library of 3×10 3 scFv clones, we established several clones exhibiting affinity for the antigen. Moreover, we tested 7 other antigens, including peptides, and successfully identified positive clones. We believe that this simple procedure and controlled scFv expression of the single-step colony assay could make the antibody screening both rapid and reliable and lead to successful isolation of positive clones from antibody libraries. Copyright © 2017 Elsevier B.V. All rights reserved.

Acquisition and diversification of tendrilled leaves in Bignonieae (Bignoniaceae) involved changes in expression patterns of SHOOTMERISTEMLESS (STM), LEAFY/FLORICAULA (LFY/FLO), and PHANTASTICA (PHAN).

PubMed

Sousa-Baena, Mariane Silveira; Lohmann, Lúcia G; Rossi, Magdalena; Sinha, Neelima R

2014-02-01

Leaves have undergone structural modifications over evolutionary time, and presently exist in many forms. For instance, in Fabaceae and Bignoniaceae, leaf parts can be modified into tendrils. Currently, no data are available on genic control of tendrilled leaf development outside Fabaceae. Here, we conducted a detailed study of three representatives of Bignonieae: Amphilophium buccinatorium, Dolichandra unguis-cati, and Bignonia callistegioides, bearing multifid, trifid, and simple-tendrilled leaves, respectively. We investigated the structure of their petioles, petiolules, leaflets, and tendrils through histological analyses. Additionally, the expression of SHOOTMERISTEMLESS (STM), PHANTASTICA (PHAN), and LEAFY/FLORICAULA (LFY/FLO) during leaf development was analyzed by in situ hybridizations. Tendrils share some anatomical similarities with leaflets, but not with other leaf parts. Transcripts of both STM and LFY/FLO were detected in leaf primordia, associated with regions from which leaflets and tendril branches originate. PHAN expression was found to be polarized in branched tendrils, but not in simple tendrils. In Bignonieae, tendrils are modified leaflets that, as a result of premature completion of development, become bladeless organs. Bignonieae leaves develop differently from those of peas, as both LFY/FLO and STM are expressed in developing leaves of Bignonieae. Moreover, PHAN is probably involved in tendril diversification in Bignonieae, as it has distinct expression patterns in different leaf types. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

On the numerical dispersion of electromagnetic particle-in-cell code: Finite grid instability

NASA Astrophysics Data System (ADS)

Meyers, M. D.; Huang, C.-K.; Zeng, Y.; Yi, S. A.; Albright, B. J.

2015-09-01

The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the Electromagnetic PIC model. We rigorously derive the faithful 3-D numerical dispersion relation of the PIC model, for a simple, direct current deposition scheme, which does not conserve electric charge exactly. We then specialize to the Yee FDTD scheme. In particular, we clarify the presence of alias modes in an eigenmode analysis of the PIC model, which combines both discrete and continuous variables. The manner in which the PIC model updates and samples the fields and distribution function, together with the temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme, is explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1-D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction, which is then verified by simulation. We demonstrate that our analysis is readily extendable to charge conserving models.

On the numerical dispersion of electromagnetic particle-in-cell code: Finite grid instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyers, M.D., E-mail: mdmeyers@physics.ucla.edu; Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095; Huang, C.-K., E-mail: huangck@lanl.gov

The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the Electromagnetic PIC model. We rigorously derive the faithful 3-D numerical dispersion relation of the PIC model, for a simple, direct current deposition scheme, which does not conserve electric charge exactly. We then specialize to the Yee FDTDmore » scheme. In particular, we clarify the presence of alias modes in an eigenmode analysis of the PIC model, which combines both discrete and continuous variables. The manner in which the PIC model updates and samples the fields and distribution function, together with the temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme, is explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1-D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction, which is then verified by simulation. We demonstrate that our analysis is readily extendable to charge conserving models.« less

Virasoro constraints and polynomial recursion for the linear Hodge integrals

NASA Astrophysics Data System (ADS)

Guo, Shuai; Wang, Gehao

2017-04-01

The Hodge tau-function is a generating function for the linear Hodge integrals. It is also a tau-function of the KP hierarchy. In this paper, we first present the Virasoro constraints for the Hodge tau-function in the explicit form of the Virasoro equations. The expression of our Virasoro constraints is simply a linear combination of the Virasoro operators, where the coefficients are restored from a power series for the Lambert W function. Then, using this result, we deduce a simple version of the Virasoro constraints for the linear Hodge partition function, where the coefficients are restored from the Gamma function. Finally, we establish the equivalence relation between the Virasoro constraints and polynomial recursion formula for the linear Hodge integrals.

AdS Black Disk Model for Small-x Deep Inelastic Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cornalba, Lorenzo; Costa, Miguel S.; Penedones, Joao

2010-08-13

Using the approximate conformal invariance of QCD at high energies we consider a simple anti-de Sitter black disk model to describe saturation in deep inelastic scattering. Deep inside saturation the structure functions have the same power law scaling, F{sub T}{approx}F{sub L}{approx}x{sup -{omega}}, where {omega} is related to the expansion rate of the black disk with energy. Furthermore, the ratio F{sub L}/F{sub T} is given by the universal value (1+{omega}/3+{omega}), independently of the target. For {gamma}*-{gamma}* scattering at high energies we obtain explicit expressions and ratios for the total cross sections of transverse and longitudinal photons in terms of the singlemore » parameter {omega}.« less

Stability analysis of automobile driver steering control

NASA Technical Reports Server (NTRS)

Allen, R. W.

1981-01-01

In steering an automobile, the driver must basically control the direction of the car's trajectory (heading angle) and the lateral deviation of the car relative to a delineated pathway. A previously published linear control model of driver steering behavior which is analyzed from a stability point of view is considered. A simple approximate expression for a stability parameter, phase margin, is derived in terms of various driver and vehicle control parameters, and boundaries for stability are discussed. A field test study is reviewed that includes the measurement of driver steering control parameters. Phase margins derived for a range of vehicle characteristics are found to be generally consistent with known adaptive properties of the human operator. The implications of these results are discussed in terms of driver adaptive behavior.

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

Analysis and control of employee turnover.

PubMed

McConnell, Charles R

2007-01-01

Turnover is a relatively simple and easily described concept. However, considerable confusion often results when addressing turnover because of differences in how it is defined; that is, what is counted, how it is counted, and how the turnover rates are expressed. Turnover is also costly, although not enough attention is paid to its cost because so much of it is indirect, and thus, not readily visible. There are a variety of causes of turnover, some which can be corrected and some which cannot be avoided. Reducing or otherwise controlling turnover requires continuing management attention to its causes and constant recognition of what can and should be controlled and what cannot be controlled. Ongoing attention to turnover is an essential part of the department manager's role.

Dynamics of Aqueous Foam Drops

NASA Technical Reports Server (NTRS)

Akhatov, Iskander; McDaniel, J. Gregory; Holt, R. Glynn

2001-01-01

We develop a model for the nonlinear oscillations of spherical drops composed of aqueous foam. Beginning with a simple mixture law, and utilizing a mass-conserving bubble-in-cell scheme, we obtain a Rayleigh-Plesset-like equation for the dynamics of bubbles in a foam mixture. The dispersion relation for sound waves in a bubbly liquid is then coupled with a normal modes expansion to derive expressions for the frequencies of eigenmodal oscillations. These eigenmodal (breathing plus higher-order shape modes) frequencies are elicited as a function of the void fraction of the foam. A Mathieu-like equation is obtained for the dynamics of the higher-order shape modes and their parametric coupling to the breathing mode. The proposed model is used to explain recently obtained experimental data.

On the Mass Distribution of Animal Species

NASA Astrophysics Data System (ADS)

Redner, Sidney; Clauset, Aaron; Schwab, David

2009-03-01

We develop a simple diffusion-reaction model to account for the broad and asymmetric distribution of adult body masses for species within related taxonomic groups. The model assumes three basic evolutionary features that control body mass: (i) a fixed lower limit that is set by metabolic constraints, (ii) a species extinction risk that is a weakly increasing function of body mass, and (iii) cladogenetic diffusion, in which daughter species have a slight tendency toward larger mass. The steady-state solution for the distribution of species masses in this model can be expressed in terms of the Airy function. This solution gives mass distributions that are in good agreement with data on 4002 terrestrial mammal species from the late Quaternary and 8617 extant bird species.

A Simple And Rapid Minicircle DNA Vector Manufacturing System

PubMed Central

Kay, Mark A; He, Cheng-Yi; Chen, Zhi-Ying

2010-01-01

Minicircle DNA vectors consisting of a circular expression cassette devoid of the bacterial plasmid DNA backbone provides several advantages including sustained transgene expression in quiescent cells/tissues. Their use has been limited by labor-intensive production. We report on a strategy for making multiple genetic modifications in E.coli to construct a producer strain that stably expresses a set of inducible minicircle-assembly enzymes, the øC31-integrase and I-SceI homing-endonuclease. This bacterial strain is capable of producing highly purified minicircle yields in the same time frame as routine plasmid DNA. It is now feasible for minicircle DNA vectors to replace routine plasmids in mammalian transgene expression studies. PMID:21102455

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

PubMed Central

Prazak, Lisa; Fujioka, Miki; Gergen, J. Peter

2010-01-01

The relatively simple combinatorial rules responsible for establishing the initial metameric expression of sloppy-paired-1 (slp1) in the Drosophila blastoderm embryo make this system an attractive model for investigating the mechanism of regulation by pair rule transcription factors. This investigation of slp1 cis-regulatory architecture identifies two distinct elements, a proximal early stripe element (PESE) and a distal early stripe element (DESE) located from −3.1 kb to −2.5 kb and from −8.1 kb to −7.1 kb upstream of the slp1 promoter, respectively, that mediate this early regulation. The proximal element expresses only even-numbered stripes and mediates repression by Even-skipped (Eve) as well as by the combination of Runt and Fushi-tarazu (Ftz). A 272 basepair sub-element of PESE retains Eve-dependent repression, but is expressed throughout the even-numbered parasegments due to the loss of repression by Runt and Ftz. In contrast, the distal element expresses both odd and even-numbered stripes and also drives inappropriate expression in the anterior half of the odd-numbered parasegments due to an inability to respond to repression by Eve. Importantly, a composite reporter gene containing both early stripe elements recapitulates pair-rule gene-dependent regulation in a manner beyond what is expected from combining their individual patterns. These results indicate interactions involving distinct cis-elements contribute to the proper integration of pair-rule regulatory information. A model fully accounting for these results proposes that metameric slp1 expression is achieved through the Runt-dependent regulation of interactions between these two pair-rule response elements and the slp1 promoter. PMID:20435028

A Theoretical Lower Bound for Selection on the Expression Levels of Proteins

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2016-06-11

We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient.more » Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.« less

Identifying and engineering promoters for high level and sustainable therapeutic recombinant protein production in cultured mammalian cells.

PubMed

Ho, Steven C L; Yang, Yuansheng

2014-08-01

Promoters are essential on plasmid vectors to initiate transcription of the transgenes when generating therapeutic recombinant proteins expressing mammalian cell lines. High and sustained levels of gene expression are desired during therapeutic protein production while gene expression is useful for cell engineering. As many finely controlled promoters exhibit cell and product specificity, new promoters need to be identified, optimized and carefully evaluated before use. Suitable promoters can be identified using techniques ranging from simple molecular biology methods to modern high-throughput omics screenings. Promoter engineering is often required after identification to either obtain high and sustained expression or to provide a wider range of gene expression. This review discusses some of the available methods to identify and engineer promoters for therapeutic recombinant protein expression in mammalian cells.

A Theoretical Lower Bound for Selection on the Expression Levels of Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, Morgan N.; Arkin, Adam P.

We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient.more » Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.« less

Demonstrations Using a Fabry-Perot. I. Multiple-Slit Interference

ERIC Educational Resources Information Center

Roychoudhuri, Chandrasekhar

1975-01-01

Describes a demonstration technique for showing multiple-slit interference patterns with the use of a Fabry-Perot etalon and a laser beam. A simple derivation of the analytical expression for such fringes is presented. (Author/CP)

A Simple Method to Determine the Refractive Index of Glass.

ERIC Educational Resources Information Center

Mak, Se-yuen

1988-01-01

Describes an experiment for determining the refractive index. Discusses the experiment procedure and mathematical expression for calculating the index. Provides two geometrical diagrams and a graph for determining the index with a typical data. (YP)

Mechanisms Underlying Helper T cell Plasticity: Implications for Immune-mediated Disease

PubMed Central

Hirahara, Kiyoshi; Poholek, Amanda; Vahedi, Golnaz; Laurence, Arian; Kanno, Yuka; Milner, Joshua D.; O’Shea, John J.

2013-01-01

CD4 helper T cells are critical for proper immune cell homeostasis and host defense, but are also major contributes to immune and inflammatory disease. Arising from a simple, biphasic model of differentiation, Th1 and Th2 cells, a bewildering number of fates seem to possible for helper T cells. To what extent different helper cell subsets maintain their characteristic gene expression profiles or exhibit functional plasticity is a hotly debated topic. In this review, we will discuss how the expression of “signature cytokines” and “master regulator” transcription factors do not neatly conform to a simple T helper paradigm. While this may seem confusing, the good news is that the newly recognized complexity fits better with our understanding of immunopathogenesis. Finally, we will discuss factors include epigenetic regulation and metabolic alterations that contribute to helper cell specific and plasticity. PMID:23622118

Gauge Theories of Vector Particles

DOE R&D Accomplishments Database

Glashow, S. L.; Gell-Mann, M.

1961-04-24

The possibility of generalizing the Yang-Mills trick is examined. Thus we seek theories of vector bosons invariant under continuous groups of coordinate-dependent linear transformations. All such theories may be expressed as superpositions of certain "simple" theories; we show that each "simple theory is associated with a simple Lie algebra. We may introduce mass terms for the vector bosons at the price of destroying the gauge-invariance for coordinate-dependent gauge functions. The theories corresponding to three particular simple Lie algebras - those which admit precisely two commuting quantum numbers - are examined in some detail as examples. One of them might play a role in the physics of the strong interactions if there is an underlying super-symmetry, transcending charge independence, that is badly broken. The intermediate vector boson theory of weak interactions is discussed also. The so-called "schizon" model cannot be made to conform to the requirements of partial gauge-invariance.

Expression of cancer-associated simple mucin-type O-glycosylated antigens in parasites.

PubMed

Osinaga, Eduardo

2007-01-01

Simple mucin-type O-glycan structures, such as Tn, TF, sialyl-Tn and Tk antigens, are among of the most specific human cancer-associated structures. These antigens are involved in several types of receptor-ligand interactions, and they are potential targets for immunotherapy. In the last few years several simple mucin-type O-glycan antigens were identified in different species belonging to the main two helminth parasite phyla, and sialyl-Tn bearing glycoproteins were detected in Trypanosoma cruzi. These results are of interest to understand new aspects in parasite glycoimmunology and may help identify new biological characteristics of parasites as well of the host-parasite relationship. Considering that different groups reported a negative correlation between certain parasite infections and cancer development, we could hypothesize that simple mucin-type O-glycosylated antigens obtained from parasites could be good potential targets for cancer immunotherapy.

Identification of Proteins Related to Epigenetic Regulation in the Malignant Transformation of Aberrant Karyotypic Human Embryonic Stem Cells by Quantitative Proteomics

PubMed Central

Sun, Yi; Yang, Yixuan; Zeng, Sicong; Tan, Yueqiu; Lu, Guangxiu; Lin, Ge

2014-01-01

Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs. PMID:24465727

Different perceptual sensitivities for Chernoff's face between children and adults.

PubMed

Tsurusawa, Reimi; Goto, Yoshinobu; Mitsudome, Akihisa; Nakashima, Taisuke; Tobimatsu, Shozo

2008-02-01

The aim of this study was to investigate the differences between children and adults in recognizing facial expressions of simple line drawings of "Chernoff's face". First, the angles of the eyebrows and mouth of Chernoff's face were changed in a stepwise way with a personal computer, and the emotional response of the subjects was evaluated by a questionnaire. Second, three drawings of non-target stimuli (neutral face, angry face, and wheelchair) and target stimuli were used to elicit event-related potentials (ERPs). Children had higher scores for the facial expressions than adults, and relied much more on the angles of the eyebrows and mouth. The major ERP findings were (1) the latencies of P100 and N170 were significantly longer in children than adults, (2) the amplitudes of P100 were significantly larger in children than adults, but the N170 amplitudes were not significantly different, and (3) a slow negative shift was recorded with a latency of 240-460ms at the posterior-temporal site for angry face compared with neutral face in adults but not in children. These results suggest that the differences in the electrophysiological recognition of facial expressions can be set at 240ms after appearance of the Chernoff's face in adults but not in children.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silin, D.; Goloshubin, G.

Analysis of compression wave propagation in a poroelastic medium predicts a peak of reflection from a high-permeability layer in the low-frequency end of the spectrum. An explicit formula expresses the resonant frequency through the elastic moduli of the solid skeleton, the permeability of the reservoir rock, the fluid viscosity and compressibility, and the reservoir thickness. This result is obtained through a low-frequency asymptotic analysis of Biot's model of poroelasticity. A review of the derivation of the main equations from the Hooke's law, momentum and mass balance equations, and Darcy's law suggests an alternative new physical interpretation of some coefficients ofmore » the classical poroelasticity. The velocity of wave propagation, the attenuation factor, and the wave number, are expressed in the form of power series with respect to a small dimensionless parameter. The absolute value of this parameter is equal to the product of the kinematic reservoir fluid mobility and the wave frequency. Retaining only the leading terms of the series leads to explicit and relatively simple expressions for the reflection and transmission coefficients for a planar wave crossing an interface between two permeable media, as well as wave reflection from a thin highly-permeable layer (a lens). Practical applications of the obtained asymptotic formulae are seismic modeling, inversion, and at-tribute analysis.« less

Molecular pharming - VLPs made in plants.

PubMed

Marsian, Johanna; Lomonossoff, George P

2016-02-01

Plant-based expression offers a safe, inexpensive and potentially limitless way to produce therapeutics in a quick and flexible manner. Plants require only simple inorganic nutrients, water, carbon dioxide and sunlight for efficient growth. Virus-like particles (VLPs) are convincing look-alikes of viruses but without carrying infectious genomic material. However, they can still elicit a very potent immune response which makes them ideal vaccine candidates. In this review the different methods of plant expression are described together with the most recent developments in the field of transiently-expressed plant-made VLPs. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Zipf's Law in Gene Expression

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2003-02-01

Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1; i.e., they obey Zipf’s law. Furthermore, by simulations of a simple model with an intracellular reaction network, we found that Zipf’s law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.

Generalized recursive solutions to Ornstein-Zernike integral equations

NASA Astrophysics Data System (ADS)

Rossky, Peter J.; Dale, William D. T.

1980-09-01

Recursive procedures for the solution of a class of integral equations based on the Ornstein-Zernike equation are developed; the hypernetted chain and Percus-Yevick equations are two special cases of the class considered. It is shown that certain variants of the new procedures developed here are formally equivalent to those recently developed by Dale and Friedman, if the new recursive expressions are initialized in the same way as theirs. However, the computational solution of the new equations is significantly more efficient. Further, the present analysis leads to the identification of various graphical quantities arising in the earlier study with more familiar quantities related to pair correlation functions. The analysis is greatly facilitated by the use of several identities relating simple chain sums whose graphical elements can be written as a sum of two or more parts. In particular, the use of these identities permits renormalization of the equivalent series solution to the integral equation to be directly incorporated into the recursive solution in a straightforward manner. Formulas appropriate to renormalization with respect to long and short range parts of the pair potential, as well as more general components of the direct correlation function, are obtained. To further illustrate the utility of this approach, we show that a simple generalization of the hypernetted chain closure relation for the direct correlation function leads directly to the reference hypernetted chain (RHNC) equation due to Lado. The form of the correlation function used in the exponential approximation of Andersen and Chandler is then seen to be equivalent to the first estimate obtained from a renormalized RHNC equation.

Transmating: conjugative transfer of a new broad host range expression vector to various Bacillus species using a single protocol.

PubMed

Heinze, Simon; Kornberger, Petra; Grätz, Christian; Schwarz, Wolfgang H; Zverlov, Vladimir V; Liebl, Wolfgang

2018-06-08

The genus Bacillus includes a great variety of species with potential applications in biotechnology. While species such as B. subtilis or B. licheniformis are well-known and used to provide various products at industrial scale, other Bacillus species are less characterized and are not yet used in commercial processes. One reason for this is the fact that genetic manipulation of new isolates is usually complicated with conventional techniques which have to be adapted to each new strain. Even in well-established strains, the available transformation protocols often suffer from low efficiencies. In this paper, we provide a new broad host range E. coli/Bacillus shuttle vector, named pBACOV (Bacillus conjugation vector), that can be efficiently transferred to various Bacillus species using a single protocol. A variant of pBACOV carrying the sfGFP gene was successfully transferred to eight different species from the genus Bacillus and to one Paenibacillus species using triparental conjugation ("transmating"). This was achieved using a single protocol and worked for nine out of eleven tested acceptor species. The transmating procedure was used to test expression of the heterologous reporter gene sfGFP under control of the P aprE -promoter from B. subtilis in several Bacillus species in parallel. Expression of sfGFP was found in eight out of nine transmates. For several of the tested species, this is the first report of a method for genetic modification and heterologous gene expression. The expression level, analyzed by measuring the relative sfGFP-fluorescence normalized to the cell density of the cultures, was highest in B. mojavensis. The new shuttle vector pBACOV can be transferred to many different Bacillus and Paenibacillus species using a simple and efficient transmating protocol. It is a versatile tool facilitating the application of recombinant DNA technology in new as well as established strains, or selection of an ideal host for heterologous gene expression from a multitude of strains. This paves the way for the genetic modification and biotechnological exploitation of the broad diversity of species of Bacillus and related genera as well as different strains from these species.

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

PubMed Central

Erceg, Jelena; Saunders, Timothy E.; Girardot, Charles; Devos, Damien P.; Hufnagel, Lars; Furlong, Eileen E. M.

2014-01-01

Deciphering the specific contribution of individual motifs within cis-regulatory modules (CRMs) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation. But despite vast improvements in the ability to identify where transcription factors (TFs) bind throughout the genome, we are limited in our ability to relate information on motif occupancy to function from sequence alone. Here, we engineered 63 synthetic CRMs to systematically assess the relationship between variation in the content and spacing of motifs within CRMs to CRM activity during development using Drosophila transgenic embryos. In over half the cases, very simple elements containing only one or two types of TF binding motifs were capable of driving specific spatio-temporal patterns during development. Different motif organizations provide different degrees of robustness to enhancer activity, ranging from binary on-off responses to more subtle effects including embryo-to-embryo and within-embryo variation. By quantifying the effects of subtle changes in motif organization, we were able to model biophysical rules that explain CRM behavior and may contribute to the spatial positioning of CRM activity in vivo. For the same enhancer, the effects of small differences in motif positions varied in developmentally related tissues, suggesting that gene expression may be more susceptible to sequence variation in one tissue compared to another. This result has important implications for human eQTL studies in which many associated mutations are found in cis-regulatory regions, though the mechanism for how they affect tissue-specific gene expression is often not understood. PMID:24391522

The generation and functional characterization of induced pluripotent stem cells from human intervertebral disc nucleus pulposus cells.

PubMed

Zhu, Yanxia; Liang, Yuhong; Zhu, Hongxia; Lian, Cuihong; Wang, Liang; Wang, Yiwei; Gu, Hongsheng; Zhou, Guangqian; Yu, Xiaoping

2017-06-27

Disc degenerative disease (DDD) is believed to originate in the nucleus pulposus (NP) region therefore, it is important to obtain a greater number of active NP cells for the study and therapy of DDD. Human induced pluripotent stem cells (iPSCs) are a powerful tool for modeling the development of DDD in humans, and have the potential to be applied in regenerative medicine. NP cells were isolated from DDD patients following our improved method, and then the primary NP cells were reprogramed into iPSCs with Sendai virus vectors encoding 4 factors. Successful reprogramming of iPSCs was verified by the expression of surface markers and presence of teratoma. Differentiation of iPSCs into NP-like cells was performed in a culture plate or in hydrogel, whereby skin fibroblast derived-iPSCs were used as a control. Results demonstrated that iPSCs derived from NP cells displayed a normal karyotype, expressed pluripotency markers, and formed teratoma in nude mice. NP induction of iPSCs resulted in the expression of NP cell specific matrix proteins and related genes. Non-induced NP derived-iPSCs also showed some NP-like phenotype. Furthermore, NP-derived iPSCs differentiate much better in hydrogel than that in a culture plate. This is a novel method for the generation of iPSCs from NP cells of DDD patients, and we have successfully differentiated these iPSCs into NP-like cells in hydrogel. This method provides a novel treatment of DDD by using patient-specific NP cells in a relatively simple and straightforward manner.

Muscular dystrophy in the Japanese Spitz: an inversion disrupts the DMD and RPGR genes.

PubMed

Atencia-Fernandez, Sabela; Shiel, Robert E; Mooney, Carmel T; Nolan, Catherine M

2015-04-01

An X-linked muscular dystrophy, with deficiency of full-length dystrophin and expression of a low molecular weight dystrophin-related protein, has been described in Japanese Spitz dogs. The aim of this study was to identify the causative mutation and develop a specific test to identify affected cases and carrier animals. Gene expression studies in skeletal muscle of an affected animal indicated aberrant expression of the Duchenne muscular dystrophy (dystrophin) gene and an anomaly in intron 19 of the gene. Genome-walking experiments revealed an inversion that interrupts two genes on the X chromosome, the Duchenne muscular dystrophy gene and the retinitis pigmentosa GTPase regulator gene. All clinically affected dogs and obligate carriers that were tested had the mutant chromosome, and it is concluded that the inversion is the causative mutation for X-linked muscular dystrophy in the Japanese Spitz breed. A PCR assay that amplifies mutant and wild-type alleles was developed and proved capable of identifying affected and carrier individuals. Unexpectedly, a 7-year-old male animal, which had not previously come to clinical attention, was shown to possess the mutant allele and to have a relatively mild form of the disease. This observation indicates phenotypic heterogeneity in Japanese Spitz muscular dystrophy, a feature described previously in humans and Golden Retrievers. With the availability of a simple, fast and accurate test for Japanese Spitz muscular dystrophy, detection of carrier animals and selected breeding should help eliminate the mutation from the breed. © 2015 Stichting International Foundation for Animal Genetics.

Baculovirus-mediated gene transfer in butterfly wings in vivo: an efficient expression system with an anti-gp64 antibody.

PubMed

Dhungel, Bidur; Ohno, Yoshikazu; Matayoshi, Rie; Otaki, Joji M

2013-03-25

Candidate genes for color pattern formation in butterfly wings have been known based on gene expression patterns since the 1990s, but their functions remain elusive due to a lack of a functional assay. Several methods of transferring and expressing a foreign gene in butterfly wings have been reported, but they have suffered from low success rates or low expression levels. Here, we developed a simple, practical method to efficiently deliver and express a foreign gene using baculovirus-mediated gene transfer in butterfly wings in vivo. A recombinant baculovirus containing a gene for green fluorescent protein (GFP) was injected into pupae of the blue pansy butterfly Junonia orithya (Nymphalidae). GFP fluorescence was detected in the pupal wings and other body parts of the injected individuals three to five days post-injection at various degrees of fluorescence. We obtained a high GFP expression rate at relatively high virus titers, but it was associated with pupal death before color pattern formation in wings. To reduce the high mortality rate caused by the baculovirus treatment, we administered an anti-gp64 antibody, which was raised against baculovirus coat protein gp64, to infected pupae after the baculovirus injection. This treatment greatly reduced the mortality rate of the infected pupae. GFP fluorescence was observed in pupal and adult wings and other body parts of the antibody-treated individuals at various degrees of fluorescence. Importantly, we obtained completely developed wings with a normal color pattern, in which fluorescent signals originated directly from scales or the basal membrane after the removal of scales. GFP fluorescence in wing tissues spatially coincided with anti-GFP antibody staining, confirming that the fluorescent signals originated from the expressed GFP molecules. Our baculovirus-mediated gene transfer system with an anti-gp64 antibody is reasonably efficient, and it can be an invaluable tool to transfer, express, and functionally examine foreign genes in butterfly wings and also in other non-model insect systems.

Engineering N-Glycosylation Pathway in Insect Cells: Suppression of β-N-Acetylglucosaminidase and Expression of β-1,4-Galactosyltransferase.

PubMed

Kim, Yeon Kyu; Cha, Hyung Joon

2015-01-01

Most insect cells have a simple N-glycosylation process and consequently paucimannosidic or simple core glycans predominate. It has been proposed that β-N-acetylglucosaminidase (GlcNAcase), a hexosaminidase in the Golgi membrane which removes a terminal N-acetylglucosamine (GlcNAc), might contribute to simple N-glycosylation profile in several insect cells including Drosophila S2. Here, we describe GlcNAcase suppression strategy using RNA interference (RNAi) to avoid the formation of paucimannosidic glycans in insect S2 cells. In addition, we describe coexpression of β(1,4)-galactosyltransferase (GalT) as a strategy to improve N-glycosylation pattern and enable recombinant therapeutic proteins to be produced in S2 cells with more complex N-glycans.

Increased Expression of Simple Ganglioside Species GM2 and GM3 Detected by MALDI Imaging Mass Spectrometry in a Combined Rat Model of Aβ Toxicity and Stroke

PubMed Central

Caughlin, Sarah; Hepburn, Jeffrey D.; Park, Dae Hee; Jurcic, Kristina; Yeung, Ken K.-C.; Cechetto, David F.; Whitehead, Shawn N.

2015-01-01

The aging brain is often characterized by the presence of multiple comorbidities resulting in synergistic damaging effects in the brain as demonstrated through the interaction of Alzheimer’s disease (AD) and stroke. Gangliosides, a family of membrane lipids enriched in the central nervous system, may have a mechanistic role in mediating the brain’s response to injury as their expression is altered in a number of disease and injury states. Matrix-Assisted Laser Desorption Ionization (MALDI) Imaging Mass Spectrometry (IMS) was used to study the expression of A-series ganglioside species GD1a, GM1, GM2, and GM3 to determine alteration of their expression profiles in the presence of beta-amyloid (Aβ) toxicity in addition to ischemic injury. To model a stroke, rats received a unilateral striatal injection of endothelin-1 (ET-1) (stroke alone group). To model Aβ toxicity, rats received intracerebralventricular (icv) injections of the toxic 25-35 fragment of the Aβ peptide (Aβ alone group). To model the combination of Aβ toxicity with stroke, rats received both the unilateral ET-1 injection and the bilateral icv injections of Aβ₂₅₋₃₅ (combined Aβ/ET-1 group). By 3 d, a significant increase in the simple ganglioside species GM2 was observed in the ischemic brain region of rats who received a stroke (ET-1), with or without Aβ. By 21 d, GM2 levels only remained elevated in the combined Aβ/ET-1 group. GM3 levels however demonstrated a different pattern of expression. By 3 d GM3 was elevated in the ischemic brain region only in the combined Aβ/ET-1 group. By 21 d, GM3 was elevated in the ischemic brain region in both stroke alone and Aβ/ET-1 groups. Overall, results indicate that the accumulation of simple ganglioside species GM2 and GM3 may be indicative of a mechanism of interaction between AD and stroke. PMID:26086081

Increased Expression of Simple Ganglioside Species GM2 and GM3 Detected by MALDI Imaging Mass Spectrometry in a Combined Rat Model of Aβ Toxicity and Stroke.

PubMed

Caughlin, Sarah; Hepburn, Jeffrey D; Park, Dae Hee; Jurcic, Kristina; Yeung, Ken K-C; Cechetto, David F; Whitehead, Shawn N

2015-01-01

The aging brain is often characterized by the presence of multiple comorbidities resulting in synergistic damaging effects in the brain as demonstrated through the interaction of Alzheimer's disease (AD) and stroke. Gangliosides, a family of membrane lipids enriched in the central nervous system, may have a mechanistic role in mediating the brain's response to injury as their expression is altered in a number of disease and injury states. Matrix-Assisted Laser Desorption Ionization (MALDI) Imaging Mass Spectrometry (IMS) was used to study the expression of A-series ganglioside species GD1a, GM1, GM2, and GM3 to determine alteration of their expression profiles in the presence of beta-amyloid (Aβ) toxicity in addition to ischemic injury. To model a stroke, rats received a unilateral striatal injection of endothelin-1 (ET-1) (stroke alone group). To model Aβ toxicity, rats received intracerebralventricular (i.c.v.) injections of the toxic 25-35 fragment of the Aβ peptide (Aβ alone group). To model the combination of Aβ toxicity with stroke, rats received both the unilateral ET-1 injection and the bilateral icv injections of Aβ25-35 (combined Aβ/ET-1 group). By 3 d, a significant increase in the simple ganglioside species GM2 was observed in the ischemic brain region of rats who received a stroke (ET-1), with or without Aβ. By 21 d, GM2 levels only remained elevated in the combined Aβ/ET-1 group. GM3 levels however demonstrated a different pattern of expression. By 3 d GM3 was elevated in the ischemic brain region only in the combined Aβ/ET-1 group. By 21 d, GM3 was elevated in the ischemic brain region in both stroke alone and Aβ/ET-1 groups. Overall, results indicate that the accumulation of simple ganglioside species GM2 and GM3 may be indicative of a mechanism of interaction between AD and stroke.

Relation of squeezed states between damped harmonic and simple harmonic oscillators

NASA Technical Reports Server (NTRS)

Um, Chung-In; Yeon, Kyu-Hwang; George, Thomas F.; Pandey, Lakshmi N.

1993-01-01

The minimum uncertainty and other relations are evaluated in the framework of the coherent states of the damped harmonic oscillator. It is shown that the coherent states of the damped harmonic oscillator are the squeezed coherent states of the simple harmonic oscillator. The unitary operator is also constructed, and this connects coherent states with damped harmonic and simple harmonic oscillators.

Effect of the Four-Step Learning Cycle Model on Students' Understanding of Concepts Related to Simple Harmonic Motion

ERIC Educational Resources Information Center

Madu, B. C.

2012-01-01

The study explored the efficacy of four-step (4-E) learning cycle approach on students understanding of concepts related to Simple Harmonic Motion (SHM). 124 students (63 for experimental group and 61 for control group) participated in the study. The students' views and ideas in simple Harmonic Achievement test were analyzed qualitatively. The…

Simple and Complex Memory Spans and Their Relation to Fluid Abilities: Evidence from List-Length Effects

ERIC Educational Resources Information Center

Unsworth, Nash; Engle, Randall W.

2006-01-01

Complex (working memory) span tasks have generally shown larger and more consistent correlations with higher-order cognition than have simple (or short-term memory) span tasks. The relation between verbal complex and simple verbal span tasks to fluid abilities as a function of list-length was examined. The results suggest that the simple…

De novo transcriptome sequencing of Acer palmatum and comprehensive analysis of differentially expressed genes under salt stress in two contrasting genotypes.

PubMed

Rong, Liping; Li, Qianzhong; Li, Shushun; Tang, Ling; Wen, Jing

2016-04-01

Maple (Acer palmatum) is an important species for landscape planting worldwide. Salt stress affects the normal growth of the Maple leaf directly, leading to loss of esthetic value. However, the limited availability of Maple genomic information has hindered research on the mechanisms underlying this tolerance. In this study, we performed comprehensive analyses of the salt tolerance in two genotypes of Maple using RNA-seq. Approximately 146.4 million paired-end reads, representing 181,769 unigenes, were obtained. The N50 length of the unigenes was 738 bp, and their total length over 102.66 Mb. 14,090 simple sequence repeats and over 500,000 single nucleotide polymorphisms were identified, which represent useful resources for marker development. Importantly, 181,769 genes were detected in at least one library, and 303 differentially expressed genes (DEGs) were identified between salt-sensitive and salt-tolerant genotypes. Among these DEGs, 125 were upregulated and 178 were downregulated genes. Two MYB-related proteins and one LEA protein were detected among the first 10 most downregulated genes. Moreover, a methyltransferase-related gene was detected among the first 10 most upregulated genes. The three most significantly enriched pathways were plant hormone signal transduction, arginine and proline metabolism, and photosynthesis. The transcriptome analysis provided a rich genetic resource for gene discovery related to salt tolerance in Maple, and in closely related species. The data will serve as an important public information platform to further our understanding of the molecular mechanisms involved in salt tolerance in Maple.

Relativistic Corrections to the Bohr Model of the Atom

ERIC Educational Resources Information Center

Kraft, David W.

1974-01-01

Presents a simple means for extending the Bohr model to include relativistic corrections using a derivation similar to that for the non-relativistic case, except that the relativistic expressions for mass and kinetic energy are employed. (Author/GS)

Simple in vitro generation of human leukocyte antigen-G-expressing T-regulatory cells through pharmacological hypomethylation for adoptive cellular immunotherapy against graft-versus-host disease.

PubMed

Stamou, Panagiota; Marioli, Dimitra; Patmanidi, Alexandra L; Sgourou, Argyro; Vittoraki, Angeliki; Theofani, Efthymia; Pierides, Chryso; Taraviras, Stavros; Costeas, Paul A; Spyridonidis, Alexandros

2017-04-01

Major barriers in using classical FOXP3+ regulatory T cells (Tregs) in clinical practice are their low numbers in the circulation, the lack of specific cell surface markers for efficient purification and the loss of expression of Treg signature molecules and suppressive function after in vitro expansion or in a pro-inflammatory microenviroment. A surface molecule with potent immunosuppressive function is the human leukocyte antigen-G (HLA-G), which is normally expressed in placenta protecting the "semi-allogeneic" fetus from maternal immune attack. Because HLA-G expression is strongly regulated by methylation, we asked whether hypomethylating agents (HA) may be used in vitro to induce HLA-G expression on conventional T cells and convert them to Tregs. Human peripheral blood T cells were exposed to azacytidine/decitabine and analyzed for HLA-G expression and their in vitro suppressor properties. HA treatment induces de novo expression of HLA-G on T cells through hypomethylation of the HLA-G proximal promoter. The HA-induced CD4 + HLA-G pos T cells are FOXP3 negative and have potent in vitro suppression function, which is dependent to a large extent, but not exclusively, on the HLA-G molecule. Converted HLA-G pos suppressors retain their suppressor function in the presence of tumor necrosis factor (TNF) and preserve hypomethylated the HLA-G promoter for at least 2 days after azacytidine exposure. Decitabine-treated T cells suppressed ex vivo the proliferation of T cells isolated from patients suffering from graft-versus-host disease (GVHD). We propose, in vitro generation of HLA-G-expressing T cells through pharmacological hypomethylation as a simple, Good Manufacturing Practice (GMP)-compatible and efficient strategy to produce a stable Treg subset of a defined phenotype that can be easily purified for adoptive immunotherapy. Copyright © 2017 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.