Optimal Variational Asymptotic Method for Nonlinear Fractional Partial Differential Equations.

PubMed

Baranwal, Vipul K; Pandey, Ram K; Singh, Om P

2014-01-01

We propose optimal variational asymptotic method to solve time fractional nonlinear partial differential equations. In the proposed method, an arbitrary number of auxiliary parameters γ 0, γ 1, γ 2,… and auxiliary functions H 0(x), H 1(x), H 2(x),… are introduced in the correction functional of the standard variational iteration method. The optimal values of these parameters are obtained by minimizing the square residual error. To test the method, we apply it to solve two important classes of nonlinear partial differential equations: (1) the fractional advection-diffusion equation with nonlinear source term and (2) the fractional Swift-Hohenberg equation. Only few iterations are required to achieve fairly accurate solutions of both the first and second problems.

Remote sensing of the seasonal variation of coniferous forest structure and function

NASA Technical Reports Server (NTRS)

Spanner, Michael; Waring, Richard

1991-01-01

One of the objectives of the Oregon Transect Ecosystem Research (OTTER) project is the remotely sensed determination of the seasonal variation of leaf area index (LAI) and absorbed photosynthetically active radiation (APAR). These measurements are required for input into a forest ecosystem model which predicts net primary production evapotranspiration, and photosynthesis of coniferous forests. Details of the study are given.

The evolution of transcriptional regulation in eukaryotes

NASA Technical Reports Server (NTRS)

Wray, Gregory A.; Hahn, Matthew W.; Abouheif, Ehab; Balhoff, James P.; Pizer, Margaret; Rockman, Matthew V.; Romano, Laura A.

2003-01-01

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

Variational Calculations of Ro-Vibrational Energy Levels and Transition Intensities for Tetratomic Molecules

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

A description is given of an algorithm for computing ro-vibrational energy levels for tetratomic molecules. The expressions required for evaluating transition intensities are also given. The variational principle is used to determine the energy levels and the kinetic energy operator is simple and evaluated exactly. The computational procedure is split up into the determination of one dimensional radial basis functions, the computation of a contracted rotational-bending basis, followed by a final variational step coupling all degrees of freedom. An angular basis is proposed whereby the rotational-bending contraction takes place in three steps. Angular matrix elements of the potential are evaluated by expansion in terms of a suitable basis and the angular integrals are given in a factorized form which simplifies their evaluation. The basis functions in the final variational step have the full permutation symmetries of the identical particles. Sample results are given for HCCH and BH3.

Charge-transfer excited states: Seeking a balanced and efficient wave function ansatz in variational Monte Carlo

DOE PAGES

Blunt, Nick S.; Neuscamman, Eric

2017-11-16

We present a simple and efficient wave function ansatz for the treatment of excited charge-transfer states in real-space quantum Monte Carlo methods. Using the recently-introduced variation-after-response method, this ansatz allows a crucial orbital optimization step to be performed beyond a configuration interaction singles expansion, while only requiring calculation of two Slater determinant objects. As a result, we demonstrate this ansatz for the illustrative example of the stretched LiF molecule, for a range of excited states of formaldehyde, and finally for the more challenging ethylene-tetrafluoroethylene molecule.

Comparison of variational real-space representations of the kinetic energy operator

NASA Astrophysics Data System (ADS)

Skylaris, Chris-Kriton; Diéguez, Oswaldo; Haynes, Peter D.; Payne, Mike C.

2002-08-01

We present a comparison of real-space methods based on regular grids for electronic structure calculations that are designed to have basis set variational properties, using as a reference the conventional method of finite differences (a real-space method that is not variational) and the reciprocal-space plane-wave method which is fully variational. We find that a definition of the finite-difference method [P. Maragakis, J. Soler, and E. Kaxiras, Phys. Rev. B 64, 193101 (2001)] satisfies one of the two properties of variational behavior at the cost of larger errors than the conventional finite-difference method. On the other hand, a technique which represents functions in a number of plane waves which is independent of system size closely follows the plane-wave method and therefore also the criteria for variational behavior. Its application is only limited by the requirement of having functions strictly localized in regions of real space, but this is a characteristic of an increasing number of modern real-space methods, as they are designed to have a computational cost that scales linearly with system size.

Localized basis functions and other computational improvements in variational nonorthogonal basis function methods for quantum mechanical scattering problems involving chemical reactions

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Truhlar, Donald G.

1990-01-01

The Generalized Newton Variational Principle for 3D quantum mechanical reactive scattering is briefly reviewed. Then three techniques are described which improve the efficiency of the computations. First, the fact that the Hamiltonian is Hermitian is used to reduce the number of integrals computed, and then the properties of localized basis functions are exploited in order to eliminate redundant work in the integral evaluation. A new type of localized basis function with desirable properties is suggested. It is shown how partitioned matrices can be used with localized basis functions to reduce the amount of work required to handle the complex boundary conditions. The new techniques do not introduce any approximations into the calculations, so they may be used to obtain converged solutions of the Schroedinger equation.

Analysis of magnetic fields using variational principles and CELAS2 elements

NASA Technical Reports Server (NTRS)

Frye, J. W.; Kasper, R. G.

1977-01-01

Prospective techniques for analyzing magnetic fields using NASTRAN are reviewed. A variational principle utilizing a vector potential function is presented which has as its Euler equations, the required field equations and boundary conditions for static magnetic fields including current sources. The need for an addition to this variational principle of a constraint condition is discussed. Some results using the Lagrange multiplier method to apply the constraint and CELAS2 elements to simulate the matrices are given. Practical considerations of using large numbers of CELAS2 elements are discussed.

Multiple robustness in factorized likelihood models.

PubMed

Molina, J; Rotnitzky, A; Sued, M; Robins, J M

2017-09-01

We consider inference under a nonparametric or semiparametric model with likelihood that factorizes as the product of two or more variation-independent factors. We are interested in a finite-dimensional parameter that depends on only one of the likelihood factors and whose estimation requires the auxiliary estimation of one or several nuisance functions. We investigate general structures conducive to the construction of so-called multiply robust estimating functions, whose computation requires postulating several dimension-reducing models but which have mean zero at the true parameter value provided one of these models is correct.

Global variability in leaf respiration in relation to climate and leaf traits

NASA Astrophysics Data System (ADS)

Atkin, Owen K.

2015-04-01

Leaf respiration plays a vital role in regulating ecosystem functioning and the Earth's climate. Because of this, it is imperative that that Earth-system, climate and ecosystem-level models be able to accurately predict variations in rates of leaf respiration. In the field of photosynthesis research, the F/vC/B model has enabled modellers to accurately predict variations in photosynthesis through time and space. By contrast, we lack an equivalent biochemical model to predict variations in leaf respiration. Consequently, we need to rely on phenomenological approaches to model variations in respiration across the Earth's surface. Such approaches require that we develop a thorough understanding of how rates of respiration vary among species and whether global environmental gradients play a role in determining variations in leaf respiration. Dealing with these issues requires that data sets be assembled on rates of leaf respiration in biomes across the Earth's surface. In this talk, I will use a newly-assembled global database on leaf respiration and associated traits (including photosynthesis) to highlight variation in leaf respiration (and the balance between respiration and photosynthesis) across global gradients in growth temperature and aridity.

Exaggerated risk: prospect theory and probability weighting in risky choice.

PubMed

Kusev, Petko; van Schaik, Paul; Ayton, Peter; Dent, John; Chater, Nick

2009-11-01

In 5 experiments, we studied precautionary decisions in which participants decided whether or not to buy insurance with specified cost against an undesirable event with specified probability and cost. We compared the risks taken for precautionary decisions with those taken for equivalent monetary gambles. Fitting these data to Tversky and Kahneman's (1992) prospect theory, we found that the weighting function required to model precautionary decisions differed from that required for monetary gambles. This result indicates a failure of the descriptive invariance axiom of expected utility theory. For precautionary decisions, people overweighted small, medium-sized, and moderately large probabilities-they exaggerated risks. This effect is not anticipated by prospect theory or experience-based decision research (Hertwig, Barron, Weber, & Erev, 2004). We found evidence that exaggerated risk is caused by the accessibility of events in memory: The weighting function varies as a function of the accessibility of events. This suggests that people's experiences of events leak into decisions even when risk information is explicitly provided. Our findings highlight a need to investigate how variation in decision content produces variation in preferences for risk.

DSMS Operations Concept

NASA Technical Reports Server (NTRS)

Spradlin, G.

2000-01-01

The concept provides an overview of operational roles and responsibilities in a service system environment. It describes changed and new interfaces between the customers and the service system, and variations on these interfaces as a function of the level of support required by the customer.

Controlled wavelet domain sparsity for x-ray tomography

NASA Astrophysics Data System (ADS)

Purisha, Zenith; Rimpeläinen, Juho; Bubba, Tatiana; Siltanen, Samuli

2018-01-01

Tomographic reconstruction is an ill-posed inverse problem that calls for regularization. One possibility is to require sparsity of the unknown in an orthonormal wavelet basis. This, in turn, can be achieved by variational regularization, where the penalty term is the sum of the absolute values of the wavelet coefficients. The primal-dual fixed point algorithm showed that the minimizer of the variational regularization functional can be computed iteratively using a soft-thresholding operation. Choosing the soft-thresholding parameter \

Global model of zenith tropospheric delay proposed based on EOF analysis

NASA Astrophysics Data System (ADS)

Sun, Langlang; Chen, Peng; Wei, Erhu; Li, Qinzheng

2017-07-01

Tropospheric delay is one of the main error budgets in Global Navigation Satellite System (GNSS) measurements. Many empirical correction models have been developed to compensate this delay, and models which do not require meteorological parameters have received the most attention. This study established a global troposphere zenith total delay (ZTD) model, called Global Empirical Orthogonal Function Troposphere (GEOFT), based on the empirical orthogonal function (EOF, also known as geographically weighted PCAs) analysis method and the Global Geodetic Observing System (GGOS) Atmosphere data from 2012 to 2015. The results showed that ZTD variation could be well represented by the characteristics of the EOF base function Ek and associated coefficients Pk. Here, E1 mainly signifies the equatorial anomaly; E2 represents north-south asymmetry, and E3 and E4 reflects regional variation. Moreover, P1 mainly reflects annual and semiannual variation components; P2 and P3 mainly contains annual variation components, and P4 displays semiannual variation components. We validated the proposed GEOFT model using tropospheric delay data of GGOS ZTD grid data and the tropospheric product of the International GNSS Service (IGS) over the year 2016. The results showed that GEOFT model has high accuracy with bias and RMS of -0.3 and 3.9 cm, respectively, with respect to the GGOS ZTD data, and of -0.8 and 4.1 cm, respectively, with respect to the global IGS tropospheric product. The accuracy of GEOFT demonstrating that the use of the EOF analysis method to characterize ZTD variation is reasonable.

Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations.

PubMed

Will, Jessica L; Kim, Hyun Seok; Clarke, Jessica; Painter, John C; Fay, Justin C; Gasch, Audrey P

2010-04-01

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw-tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function-providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments-contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.

Spatial dynamics of the vegetation community associated with an invasive emergent macrophyte in a regulated river.

USDA-ARS?s Scientific Manuscript database

Successful management of riverine ecosystems often requires mitigation of alien plant invasions. Understanding how environmental variation within watersheds influences distribution and spread of invasive plants is essential to restoring impacted ecological functions and conserving native plant commu...

Characterization of nonGaussian atmospheric turbulence for prediction of aircraft response statistics

NASA Technical Reports Server (NTRS)

Mark, W. D.

1977-01-01

Mathematical expressions were derived for the exceedance rates and probability density functions of aircraft response variables using a turbulence model that consists of a low frequency component plus a variance modulated Gaussian turbulence component. The functional form of experimentally observed concave exceedance curves was predicted theoretically, the strength of the concave contribution being governed by the coefficient of variation of the time fluctuating variance of the turbulence. Differences in the functional forms of response exceedance curves and probability densities also were shown to depend primarily on this same coefficient of variation. Criteria were established for the validity of the local stationary assumption that is required in the derivations of the exceedance curves and probability density functions. These criteria are shown to depend on the relative time scale of the fluctuations in the variance, the fluctuations in the turbulence itself, and on the nominal duration of the relevant aircraft impulse response function. Metrics that can be generated from turbulence recordings for testing the validity of the local stationary assumption were developed.

Metal-ligand delocalization and spin density in the CuCl2 and [CuCl4](2-) molecules: Some insights from wave function theory.

PubMed

Giner, Emmanuel; Angeli, Celestino

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl2 and [CuCl4](2-) systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that each valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.

Combining animal personalities with transcriptomics resolves individual variation within a wild-type zebrafish population and identifies underpinning molecular differences in brain function.

PubMed

Rey, S; Boltana, S; Vargas, R; Roher, N; Mackenzie, S

2013-12-01

Resolving phenotype variation within a population in response to environmental perturbation is central to understanding biological adaptation. Relating meaningful adaptive changes at the level of the transcriptome requires the identification of processes that have a functional significance for the individual. This remains a major objective towards understanding the complex interactions between environmental demand and an individual's capacity to respond to such demands. The interpretation of such interactions and the significance of biological variation between individuals from the same or different populations remain a difficult and under-addressed question. Here, we provide evidence that variation in gene expression between individuals in a zebrafish population can be partially resolved by a priori screening for animal personality and accounts for >9% of observed variation in the brain transcriptome. Proactive and reactive individuals within a wild-type population exhibit consistent behavioural responses over time and context that relates to underlying differences in regulated gene networks and predicted protein-protein interactions. These differences can be mapped to distinct regions of the brain and provide a foundation towards understanding the coordination of underpinning adaptive molecular events within populations. © 2013 John Wiley & Sons Ltd.

Feeding, evaluating, and controlling rumen function.

PubMed

Lean, Ian J; Golder, Helen M; Hall, Mary Beth

2014-11-01

Achieving optimal rumen function requires an understanding of feeds and systems of nutritional evaluation. Key influences on optimal function include achieving good dry matter intake. The function of feeds in the rumen depends on other factors including chemical composition, rate of passage, degradation rate of the feed, availability of other substrates and cofactors, and individual animal variation. This article discusses carbohydrate, protein, and fat metabolism in the rumen, and provides practical means of evaluation of rations in the field. Conditions under which rumen function is suboptimal (ie, acidosis and bloat) are discussed, and methods for control examined. Copyright © 2014 Elsevier Inc. All rights reserved.

Intraspecific variation in flight metabolic rate in the bumblebee Bombus impatiens: repeatability and functional determinants in workers and drones.

PubMed

Darveau, Charles-A; Billardon, Fannie; Bélanger, Kasandra

2014-02-15

The evolution of flight energetics requires that phenotypes be variable, repeatable and heritable. We studied intraspecific variation in flight energetics in order to assess the repeatability of flight metabolic rate and wingbeat frequency, as well as the functional basis of phenotypic variation in workers and drones of the bumblebee species Bombus impatiens. We showed that flight metabolic rate and wingbeat frequency were highly repeatable in workers, even when controlling for body mass variation using residual analysis. We did not detect significant repeatability in drones, but a smaller range of variation might have prevented us from finding significant values in our sample. Based on our results and previous findings, we associated the high repeatability of flight phenotypes in workers to the functional links between body mass, thorax mass, wing size, wingbeat frequency and metabolic rate. Moreover, differences between workers and drones were as predicted from these functional associations, where drones had larger wings for their size, lower wingbeat frequency and lower flight metabolic rate. We also investigated thoracic muscle metabolic phenotypes by measuring the activity of carbohydrate metabolism enzymes, and we found positive correlations between mass-independent metabolic rate and the activity of all enzymes measured, but in workers only. When comparing workers and drones that differ in flight metabolic rate, only the activity of the enzymes hexokinase and trehalase showed the predicted differences. Overall, our study indicates that there should be correlated evolution among physiological phenotypes at multiple levels of organization and morphological traits associated with flight.

Familial hypertrophic cardiomyopathy: functional variance among individual cardiomyocytes as a trigger of FHC-phenotype development

PubMed Central

Brenner, Bernhard; Seebohm, Benjamin; Tripathi, Snigdha; Montag, Judith; Kraft, Theresia

2014-01-01

Familial hypertrophic cardiomyopathy (FHC) is the most frequent inherited cardiac disease. It has been related to numerous mutations in many sarcomeric and even some non-sarcomeric proteins. So far, however, no common mechanism has been identified by which the many different mutations in different sarcomeric and non-sarcomeric proteins trigger development of the FHC phenotype. Here we show for different MYH7 mutations variance in force pCa-relations from normal to highly abnormal as a feature common to all mutations we studied, while direct functional effects of the different FHC-mutations, e.g., on force generation, ATPase or calcium sensitivity of the contractile system, can be quite different. The functional variation among individual M. soleus fibers of FHC-patients is accompanied by large variation in mutant vs. wildtype β-MyHC-mRNA. Preliminary results show a similar variation in mutant vs. wildtype β-MyHC-mRNA among individual cardiomyocytes. We discuss our previously proposed concept as to how different mutations in the β-MyHC and possibly other sarcomeric and non-sarcomeric proteins may initiate an FHC-phenotype by functional variation among individual cardiomyocytes that results in structural distortions within the myocardium, leading to cellular and myofibrillar disarray. In addition, distortions can activate stretch-sensitive signaling in cardiomyocytes and non-myocyte cells which is known to induce cardiac remodeling with interstitial fibrosis and hypertrophy. Such a mechanism will have major implications for therapeutic strategies to prevent FHC-development, e.g., by reducing functional imbalances among individual cardiomyocytes or by inhibition of their triggering of signaling paths initiating remodeling. Targeting increased or decreased contractile function would require selective targeting of mutant or wildtype protein to reduce functional imbalances. PMID:25346696

Intra- and inter-dairy heifer variation of cellular neutrophil functions

USDA-ARS?s Scientific Manuscript database

Immune competence of dairy cattle is difficult to determine as a healthy immune system requires the resolution of pathogen invasion without excessive host-tissue damage. Neutrophil phagocytosis (PG) is important for eliminating pathogens, but PG induces an oxidative burst (OB), which helps destroy t...

Flap Gear for Airplanes : A New Scheme in Which Variation is Automatic

NASA Technical Reports Server (NTRS)

Tiltman, A Hessell

1927-01-01

A variable flap gear, which would function automatically and require no attention during flight appeared to be an attractive idea even in its early stages of development. The advantages of variable camber are described as well as the designs of these automatic flaps.

Electron requirements for carbon incorporation along a diel light cycle in three marine diatom species.

PubMed

Morelle, Jérôme; Claquin, Pascal

2018-02-23

Diatoms account for about 40% of primary production in highly productive ecosystems. The development of a new generation of fluorometers has made it possible to improve estimation of the electron transport rate from photosystem II, which, when coupled with the carbon incorporation rate enables estimation of the electrons required for carbon fixation. The aim of this study was to investigate the daily dynamics of these electron requirements as a function of the diel light cycle in three relevant diatom species and to apprehend if the method of estimating the electron transport rate can lead to different pictures of the dynamics. The results confirmed the species-dependent capacity for photoacclimation under increasing light levels. Despite daily variations in the photosynthetic parameters, the results of this study underline the low daily variability of the electron requirements estimated using functional absorption of the photosystem II compared to an estimation based on a specific absorption cross section of chlorophyll a. The stability of the electron requirements throughout the day would suggest it is potentially possible to estimate high-frequency primary production by using autonomous variable fluorescence measurements from ships-of-opportunity or moorings, without taking potential daily variation in this parameter into consideration, but this result has to be confirmed on natural phytoplankton assemblages. The results obtained in this study confirm the low electron requirements of diatoms to perform photosynthesis, and suggest a potential additional source of energy for carbon fixation, as recently described in the literature for this class.

Vibrational self-consistent field theory using optimized curvilinear coordinates.

PubMed

Bulik, Ireneusz W; Frisch, Michael J; Vaccaro, Patrick H

2017-07-28

A vibrational SCF model is presented in which the functions forming the single-mode functions in the product wavefunction are expressed in terms of internal coordinates and the coordinates used for each mode are optimized variationally. This model involves no approximations to the kinetic energy operator and does not require a Taylor-series expansion of the potential. The non-linear optimization of coordinates is found to give much better product wavefunctions than the limited variations considered in most previous applications of SCF methods to vibrational problems. The approach is tested using published potential energy surfaces for water, ammonia, and formaldehyde. Variational flexibility allowed in the current ansätze results in excellent zero-point energies expressed through single-product states and accurate fundamental transition frequencies realized by short configuration-interaction expansions. Fully variational optimization of single-product states for excited vibrational levels also is discussed. The highlighted methodology constitutes an excellent starting point for more sophisticated treatments, as the bulk characteristics of many-mode coupling are accounted for efficiently in terms of compact wavefunctions (as evident from the accurate prediction of transition frequencies).

An evolving-requirements technology assessment process for advanced propulsion concepts

NASA Astrophysics Data System (ADS)

McClure, Erin Kathleen

The following dissertation investigates the development of a methodology suitable for the evaluation of advanced propulsion concepts. At early stages of development, both the future performance of these concepts and their requirements are highly uncertain, making it difficult to forecast their future value. Developing advanced propulsion concepts requires a huge investment of resources. The methodology was developed to enhance the decision-makers understanding of the concepts, so that they could mitigate the risks associated with developing such concepts. A systematic methodology to identify potential advanced propulsion concepts and assess their robustness is necessary to reduce the risk of developing advanced propulsion concepts. Existing advanced design methodologies have evaluated the robustness of technologies or concepts to variations in requirements, but they are not suitable to evaluate a large number of dissimilar concepts. Variations in requirements have been shown to impact the development of advanced propulsion concepts, and any method designed to evaluate these concepts must incorporate the possible variations of the requirements into the assessment. In order to do so, a methodology was formulated to be capable of accounting for two aspects of the problem. First, it had to systemically identify a probabilistic distribution for the future requirements. Such a distribution would allow decision-makers to quantify the uncertainty introduced by variations in requirements. Second, the methodology must be able to assess the robustness of the propulsion concepts as a function of that distribution. This dissertation describes in depth these enabling elements and proceeds to synthesize them into a new method, the Evolving Requirements Technology Assessment (ERTA). As a proof of concept, the ERTA method was used to evaluate and compare advanced propulsion systems that will be capable of powering a hurricane tracking, High Altitude, Long Endurance (HALE) unmanned aerial vehicle (UAV). The use of the ERTA methodology to assess HALE UAV propulsion concepts demonstrated that potential variations in requirements do significantly impact the assessment and selection of propulsion concepts. The proof of concept also demonstrated that traditional forecasting techniques, such as the cross impact analysis, could be used to forecast the requirements for advanced propulsion concepts probabilistically. "Fitness", a measure of relative goodness, was used to evaluate the concepts. Finally, stochastic optimizations were used to evaluate the propulsion concepts across the range of requirement sets that were considered.

On the calculation of charge transfer transitions with standard density functionals using constrained variational density functional theory.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo

2010-08-21

It is well known that time-dependent density functional theory (TD-DFT) based on standard gradient corrected functionals affords both a quantitative and qualitative incorrect picture of charge transfer transitions between two spatially separated regions. It is shown here that the well known failure can be traced back to the use of linear response theory. Further, it is demonstrated that the inclusion of higher order terms readily affords a qualitatively correct picture even for simple functionals based on the local density approximation. The inclusion of these terms is done within the framework of a newly developed variational approach to excitation energies called constrained variational density functional theory (CV-DFT). To second order [CV(2)-DFT] this theory is identical to adiabatic TD-DFT within the Tamm-Dancoff approximation. With inclusion of fourth order corrections [CV(4)-DFT] it affords a qualitative correct description of charge transfer transitions. It is finally demonstrated that the relaxation of the ground state Kohn-Sham orbitals to first order in response to the change in density on excitation together with CV(4)-DFT affords charge transfer excitations in good agreement with experiment. The new relaxed theory is termed R-CV(4)-DFT. The relaxed scheme represents an effective way in which to introduce double replacements into the description of single electron excitations, something that would otherwise require a frequency dependent kernel.

Understanding immune function as a pace of life trait requires environmental context.

PubMed

Tieleman, B Irene

2018-01-01

This article provides a brief historical perspective on the integration of physiology into the concept of the pace of life of birds, evaluates the fit of immune function into this framework, and asks what it will take to fruitfully understand immune functioning of birds in pace of life studies in the future. In the late 1970s, physiology started to seriously enter avian life history ecology, with energy as the main currency of interest, inspired by David Lack's work in the preceding decades emphasizing how food availability explained life history variation. In an effort to understand the trade-off between survival and reproduction, and specifically the mortality costs associated with hard work, in the 1980s and 1990s, other physiological phenomena entered the realm of animal ecologists, including endocrinology, oxidative stress, and immunology. Reviewing studies thus far to evaluate the role of immune function in a life history context and particularly to address the questions whether immune function (1) consistently varies with life history variation among free-living bird species and (2) mediates life history trade-offs in experiments with free-living bird species; I conclude that, unlike energy metabolism, the immune system does not closely covary with life history among species nor mediates the classical trade-offs within individuals. Instead, I propose that understanding the tremendous immunological variation uncovered among free-living birds over the past 25 years requires a paradigm shift. The paradigm should shift from viewing immune function as a costly trait involved in life history trade-offs to explicitly including the benefits of the immune system and placing it firmly in an environmental and ecological context. A first step forward will be to quantify the immunobiotic pressures presented by diverse environmental circumstances that both shape and challenge the immune system of free-living animals. Current developments in the fields of infectious wildlife diseases and host-microbe interactions provide promising steps in this direction.

The right-hand side of the Jacobi identity: to be naught or not to be ?

NASA Astrophysics Data System (ADS)

Kiselev, Arthemy V.

2016-01-01

The geometric approach to iterated variations of local functionals -e.g., of the (master-)action functional - resulted in an extension of the deformation quantisation technique to the set-up of Poisson models of field theory. It also allowed of a rigorous proof for the main inter-relations between the Batalin-Vilkovisky (BV) Laplacian Δ and variational Schouten bracket [,]. The ad hoc use of these relations had been a known analytic difficulty in the BV- formalism for quantisation of gauge systems; now achieved, the proof does actually not require the assumption of graded-commutativity. Explained in our previous work, geometry's self- regularisation is rendered by Gel'fand's calculus of singular linear integral operators supported on the diagonal. We now illustrate that analytic technique by inspecting the validity mechanism for the graded Jacobi identity which the variational Schouten bracket does satisfy (whence Δ2 = 0, i.e., the BV-Laplacian is a differential acting in the algebra of local functionals). By using one tuple of three variational multi-vectors twice, we contrast the new logic of iterated variations - when the right-hand side of Jacobi's identity vanishes altogether - with the old method: interlacing its steps and stops, it could produce some non-zero representative of the trivial class in the top- degree horizontal cohomology. But we then show at once by an elementary counterexample why, in the frames of the old approach that did not rely on Gel'fand's calculus, the BV-Laplacian failed to be a graded derivation of the variational Schouten bracket.

Music Tune Restoration Based on a Mother Wavelet Construction

NASA Astrophysics Data System (ADS)

Fadeev, A. S.; Konovalov, V. I.; Butakova, T. I.; Sobetsky, A. V.

2017-01-01

It is offered to use the mother wavelet function obtained from the local part of an analyzed music signal. Requirements for the constructed function are proposed and the implementation technique and its properties are described. The suggested approach allows construction of mother wavelet families with specified identifying properties. Consequently, this makes possible to identify the basic signal variations of complex music signals including local time-frequency characteristics of the basic one.

A variational data assimilation system for the range dependent acoustic model using the representer method: Theoretical derivations.

PubMed

Ngodock, Hans; Carrier, Matthew; Fabre, Josette; Zingarelli, Robert; Souopgui, Innocent

2017-07-01

This study presents the theoretical framework for variational data assimilation of acoustic pressure observations into an acoustic propagation model, namely, the range dependent acoustic model (RAM). RAM uses the split-step Padé algorithm to solve the parabolic equation. The assimilation consists of minimizing a weighted least squares cost function that includes discrepancies between the model solution and the observations. The minimization process, which uses the principle of variations, requires the derivation of the tangent linear and adjoint models of the RAM. The mathematical derivations are presented here, and, for the sake of brevity, a companion study presents the numerical implementation and results from the assimilation simulated acoustic pressure observations.

Isomer effects on polyimide properties

NASA Technical Reports Server (NTRS)

Stump, B. L.

1975-01-01

The effect of structure variation on the solubility and glass-transition temperature of polyimide polymers is investigated. The addition of alkyl substituents to an aromatic ring in the polymer molecule, the reduction in the number of imide rings per average polymer chain-length, and a variation in the symmetry of the polymer molecule are studied. The synthesis of key intermediates for the preparation of the monomers required in this investigation is reported along with progress made in the synthesis of polyimide-precursor amines that contain functional groups to allow for post-cure cross-linking.

Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The cancer transcriptome is shaped by genetic changes, variation in gene transcription, mRNA processing, editing and stability, and the cancer microbiome. Deciphering this variation and understanding its implications on tumorigenesis requires sophisticated computational analyses. Most RNA-Seq analyses rely on methods that first map short reads to a reference genome, and then compare them to annotated transcripts or assemble them. However, this strategy can be limited when the cancer genome is substantially different than the reference or for detecting sequences from the cancer microbiome.

Fast computation of the electrolyte-concentration transfer function of a lithium-ion cell model

NASA Astrophysics Data System (ADS)

Rodríguez, Albert; Plett, Gregory L.; Trimboli, M. Scott

2017-08-01

One approach to creating physics-based reduced-order models (ROMs) of battery-cell dynamics requires first generating linearized Laplace-domain transfer functions of all cell internal electrochemical variables of interest. Then, the resulting infinite-dimensional transfer functions can be reduced by various means in order to find an approximate low-dimensional model. These methods include Padé approximation or the Discrete-Time Realization algorithm. In a previous article, Lee and colleagues developed a transfer function of the electrolyte concentration for a porous-electrode pseudo-two-dimensional lithium-ion cell model. Their approach used separation of variables and Sturm-Liouville theory to compute an infinite-series solution to the transfer function, which they then truncated to a finite number of terms for reasons of practicality. Here, we instead use a variation-of-parameters approach to arrive at a different representation of the identical solution that does not require a series expansion. The primary benefits of the new approach are speed of computation of the transfer function and the removal of the requirement to approximate the transfer function by truncating the number of terms evaluated. Results show that the speedup of the new method can be more than 3800.

Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

PubMed Central

Gibbons, John G.; Branco, Alan T.; Godinho, Susana A.; Yu, Shoukai; Lemos, Bernardo

2015-01-01

Tandemly repeated ribosomal DNA (rDNA) arrays are among the most evolutionary dynamic loci of eukaryotic genomes. The loci code for essential cellular components, yet exhibit extensive copy number (CN) variation within and between species. CN might be partly determined by the requirement of dosage balance between the 5S and 45S rDNA arrays. The arrays are nonhomologous, physically unlinked in mammals, and encode functionally interdependent RNA components of the ribosome. Here we show that the 5S and 45S rDNA arrays exhibit concerted CN variation (cCNV). Despite 5S and 45S rDNA elements residing on different chromosomes and lacking sequence similarity, cCNV between these loci is strong, evolutionarily conserved in humans and mice, and manifested across individual genotypes in natural populations and pedigrees. Finally, we observe that bisphenol A induces rapid and parallel modulation of 5S and 45S rDNA CN. Our observations reveal a novel mode of genome variation, indicate that natural selection contributed to the evolution and conservation of cCNV, and support the hypothesis that 5S CN is partly determined by the requirement of dosage balance with the 45S rDNA array. We suggest that human disease variation might be traced to disrupted rDNA dosage balance in the genome. PMID:25583482

LPCAT1 controls phosphate homeostasis in a zinc-dependent manner

PubMed Central

Kisko, Mushtak; Bouain, Nadia; Safi, Alaeddine; Medici, Anna; Akkers, Robert C; Secco, David; Fouret, Gilles; Krouk, Gabriel; Aarts, Mark GM; Busch, Wolfgang

2018-01-01

All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation. PMID:29453864

Quantification of regional nonuniformity and paradoxical intramural mechanics in hypertrophic cardiomyopathy by high frame rate ultrasound myocardial strain mapping.

PubMed

Sengupta, Partho P; Mehta, Vimal; Arora, Ramesh; Mohan, Jagdish C; Khandheria, Bijoy K

2005-07-01

This study tested the hypothesis that linear mapping of regional myocardial strain comprehensively assesses variations in regional myocardial function in hypertrophic cardiomyopathy. Hypertrophic cardiomyopathy is characterized by disorganized myocardial architecture that results in spatial and temporal nonuniformity of regional function. Left ventricular deformation was quantified in 20 patients with hypertrophic cardiomyopathy and compared with 25 age- and sex-matched control subjects. Abnormalities in subendocardial strain ranged from reduced longitudinal shortening to paradoxical systolic lengthening and delayed regional longitudinal contractions that were often located in small subsegmental areas. These variations were underestimated significantly by arbitrary measurements compared with linear mapping, in which a region of interest was moved across the longitudinal length of left ventricle (difference of peak and least strain, 10.7% +/- 5.1% vs 17% +/- 5.5%; P < .001). Echocardiographic assessment of variations in regional strain requires careful mapping and may be inappropriately assessed if left ventricular segments are sampled at arbitrary focal locations.

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

Jones, M. L.; McLaughlin, M. A.; Lam, M. T.

We analyze dispersion measure (DM) variations of 37 millisecond pulsars in the nine-year North American Nanohertz Observatory for Gravitational Waves (NANOGrav) data release and constrain the sources of these variations. DM variations can result from a changing distance between Earth and the pulsar, inhomogeneities in the interstellar medium, and solar effects. Variations are significant for nearly all pulsars, with characteristic timescales comparable to or even shorter than the average spacing between observations. Five pulsars have periodic annual variations, 14 pulsars have monotonically increasing or decreasing trends, and 14 pulsars show both effects. Of the four pulsars with linear trends thatmore » have line-of-sight velocity measurements, three are consistent with a changing distance and require an overdensity of free electrons local to the pulsar. Several pulsars show correlations between DM excesses and lines of sight that pass close to the Sun. Mapping of the DM variations as a function of the pulsar trajectory can identify localized interstellar medium features and, in one case, an upper limit to the size of the dispersing region of 4 au. Four pulsars show roughly Kolmogorov structure functions (SFs), and another four show SFs less steep than Kolmogorov. One pulsar has too large an uncertainty to allow comparisons. We discuss explanations for apparent departures from a Kolmogorov-like spectrum, and we show that the presence of other trends and localized features or gradients in the interstellar medium is the most likely cause.« less

The Nanograv Nine-Year Data Set: Measurement and Analysis of Variations in Dispersion Measures

NASA Technical Reports Server (NTRS)

Jones, M. L.; McLaughlin, M. A.; Lam, M. T.; Cordes, J. M.; Levin, L.; Chatterjee, S.; Arzoumanian, Z.; Crowter, K.; Demorest, P. B.; Dolch, T.;

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Metal-ligand delocalization and spin density in the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} molecules: Some insights from wave function theory

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

Giner, Emmanuel, E-mail: gnrmnl@unife.it; Angeli, Celestino, E-mail: anc@unife.it

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that eachmore » valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.« less

Influence of speckle image reconstruction on photometric precision for large solar telescopes

NASA Astrophysics Data System (ADS)

Peck, C. L.; Wöger, F.; Marino, J.

2017-11-01

Context. High-resolution observations from large solar telescopes require adaptive optics (AO) systems to overcome image degradation caused by Earth's turbulent atmosphere. AO corrections are, however, only partial. Achieving near-diffraction limited resolution over a large field of view typically requires post-facto image reconstruction techniques to reconstruct the source image. Aims: This study aims to examine the expected photometric precision of amplitude reconstructed solar images calibrated using models for the on-axis speckle transfer functions and input parameters derived from AO control data. We perform a sensitivity analysis of the photometric precision under variations in the model input parameters for high-resolution solar images consistent with four-meter class solar telescopes. Methods: Using simulations of both atmospheric turbulence and partial compensation by an AO system, we computed the speckle transfer function under variations in the input parameters. We then convolved high-resolution numerical simulations of the solar photosphere with the simulated atmospheric transfer function, and subsequently deconvolved them with the model speckle transfer function to obtain a reconstructed image. To compute the resulting photometric precision, we compared the intensity of the original image with the reconstructed image. Results: The analysis demonstrates that high photometric precision can be obtained for speckle amplitude reconstruction using speckle transfer function models combined with AO-derived input parameters. Additionally, it shows that the reconstruction is most sensitive to the input parameter that characterizes the atmospheric distortion, and sub-2% photometric precision is readily obtained when it is well estimated.

Children's Requests to Unfamiliar Adults: Form, Social Function, Age Variation.

ERIC Educational Resources Information Center

Gordon, David Paul; And Others

Elementary school students were required to obtain objects from two adults engaged in conversation with each other. Results differed markedly between older and younger children. For the younger children, (1) there were three times as many statement requests (SRs) as interrogative requests (IRs); (2) almost 50% of requests were need statements; (3)…

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases.

PubMed

Townend, Gillian S; Ehrhart, Friederike; van Kranen, Henk J; Wilkinson, Mark; Jacobsen, Annika; Roos, Marco; Willighagen, Egon L; van Enckevort, David; Evelo, Chris T; Curfs, Leopold M G

2018-04-27

Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data. © 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc.

Comparison of Sequential and Variational Data Assimilation

NASA Astrophysics Data System (ADS)

Alvarado Montero, Rodolfo; Schwanenberg, Dirk; Weerts, Albrecht

2017-04-01

Data assimilation is a valuable tool to improve model state estimates by combining measured observations with model simulations. It has recently gained significant attention due to its potential in using remote sensing products to improve operational hydrological forecasts and for reanalysis purposes. This has been supported by the application of sequential techniques such as the Ensemble Kalman Filter which require no additional features within the modeling process, i.e. it can use arbitrary black-box models. Alternatively, variational techniques rely on optimization algorithms to minimize a pre-defined objective function. This function describes the trade-off between the amount of noise introduced into the system and the mismatch between simulated and observed variables. While sequential techniques have been commonly applied to hydrological processes, variational techniques are seldom used. In our believe, this is mainly attributed to the required computation of first order sensitivities by algorithmic differentiation techniques and related model enhancements, but also to lack of comparison between both techniques. We contribute to filling this gap and present the results from the assimilation of streamflow data in two basins located in Germany and Canada. The assimilation introduces noise to precipitation and temperature to produce better initial estimates of an HBV model. The results are computed for a hindcast period and assessed using lead time performance metrics. The study concludes with a discussion of the main features of each technique and their advantages/disadvantages in hydrological applications.

Canonical fluid thermodynamics. [variational principles of stability for compressible adiabatic flow

NASA Technical Reports Server (NTRS)

Schmid, L. A.

1974-01-01

The space-time integral of the thermodynamic pressure plays in a certain sense the role of the thermodynamic potential for compressible adiabatic flow. The stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and temperature to be generalized velocities. In the fluid context, the definition of proper-time differentiation involves the fluid velocity expressed in terms of three particle identity parameters. The pressure function is then converted into a functional which is the Lagrangian density of the variational principle. Being also a minimum principle, the variational principle provides a means for comparing the relative stability of different flows. For boundary conditions with a high degree of symmetry, as in the case of a uniformly expanding spherical gas box, the most stable flow is a rectilinear flow for which the world-trajectory of each particle is a straight line. Since the behavior of the interior of a freely expanding cosmic cloud may be expected to be similar to that of the fluid in the spherical box of gas, this suggests that the cosmic principle is a consequence of the laws of thermodynamics, rather than just an ad hoc postulate.

Approaches to Macroevolution: 1. General Concepts and Origin of Variation.

PubMed

Jablonski, David

2017-01-01

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.

Method for determining how to operate and control wind turbine arrays in utility systems

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

Javid, S.H.; Hauth, R.L.; Younkins, T.D.

1984-01-01

A method for determining how utility wind turbine arrays should be controlled and operated on the load frequency control time-scale is presented. Initial considerations for setting wind turbine control requirements are followed by a description of open loop operation and of closed loop and feed forward wind turbine array control concepts. The impact of variations in array output on meeting minimum criteria are developed. The method for determining the required control functions is then presented and results are tabulated. (LEW)

Mechanical Harvesting of Aquatic Plants. Report 2. Evaluation of Selected Handling Functions of Mechanical Control.

DTIC Science & Technology

1980-06-01

with the extracted plants. Pusher boats were used to feed the plants into the throat of the conveyor where they were then pulled onto the conveyor by...technique or variations of it that involve extracting from the river periodically on the Withlacoochee River or similar rivers, requires 48 that operations...way to readily estimate the land area required to stockpile the large volumes of material that must be extracted from the water in many operational

Diurnal variation in the functioning of cowpea nodules.

PubMed

Rainbird, R M; Atkins, C A; Pate, J S

1983-06-01

Nitrogenase (EC 1.7.99.2) activity of nodules of cowpea (Vigna unguiculata [L.] Walp), maintained under conditions of a 12-hour day at 30 degrees C and 800 to 1,000 microeinsteins per square meter per second (photosynthetically active radiation) and a 12-hour night at 20 degrees C, showed a marked diurnal variation with the total electron flux through the enzyme at night being 60% of that in the photoperiod. This diurnal pattern was, however, due to changes in hydrogen evolution. The rate of nitrogen fixation, measured by short-term (15)N(2) assimilation or estimated from the difference in hydrogen evolution in air or Ar:O(2) (80:20; v/v), showed no diurnal variation. Carbon dioxide released from nodules showed a diurnal variation synchronized with that of nitrogenase functioning and, as a consequence, the apparent ;respiratory cost' of nitrogen fixation in the photoperiod was almost double that at night (9.74 +/- 0.38 versus 5.70 +/- 0.90 moles CO(2) evolved per mole N(2) fixed). Separate carbon and nitrogen balances constructed for nodules during the photoperiod and dark period showed that, at night, nodule functioning required up to 40% less carbohydrate to achieve the same level of nitrogen fixation as during the photoperiod (2.4 versus 1.4 moles hexose per mole N(2) fixed).Stored reserves of nonstructural carbohydrate of the nodule only partly satisfied the requirement for carbon at night, and fixation was dependent on continued import of translocated assimilates at all times. Measurements of the soluble nitrogen pools of the nodule together with (15)N studies indicated that, both during the day and night, nitrogenous products of fixation were effectively translocated to all organs of the host plant despite low rates of transpiration at night. Reduced fluxes of water through the plant at night were apparently counteracted by increased concentration of nitrogen, especially as ureides, in the xylem stream.

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

PubMed Central

Will, Jessica L.; Kim, Hyun Seok; Clarke, Jessica; Painter, John C.; Fay, Justin C.; Gasch, Audrey P.

2010-01-01

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw–tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function—providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments—contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection. PMID:20369021

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

PubMed Central

Turner, Thomas L.; Stewart, Andrew D.; Fields, Andrew T.; Rice, William R.; Tarone, Aaron M.

2011-01-01

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size. PMID:21437274

The Role of Data Range in Linear Regression

ERIC Educational Resources Information Center

da Silva, M. A. Salgueiro; Seixas, T. M.

2017-01-01

Measuring one physical quantity as a function of another often requires making some choices prior to the measurement process. Two of these choices are: the data range where measurements should focus and the number (n) of data points to acquire in the chosen data range. Here, we consider data range as the interval of variation of the independent…

A modified variational method for nonlinear vibration analysis of rotating beams including Coriolis effects

NASA Astrophysics Data System (ADS)

Tian, Jiajin; Su, Jinpeng; Zhou, Kai; Hua, Hongxing

2018-07-01

This paper presents a general formulation for nonlinear vibration analysis of rotating beams. A modified variational method combined with a multi-segment partitioning technique is employed to derive the free and transient vibration behaviors of the rotating beams. The strain energy and kinetic energy functional are formulated based on the order truncation principle of the fully geometrically nonlinear beam theory. The Coriolis effects as well as nonlinear effects due to the coupling of bending-stretching, bending-twist and twist-stretching are taken into account. The present method relaxes the need to explicitly meet the requirements of the boundary conditions for the admissible functions, and allows the use of any linearly independent, complete basis functions as admissible functions for rotating beams. Moreover, the method is readily used to deal with the nonlinear transient vibration problems for rotating beams subjected to dynamic loads. The accuracy, convergence and efficiency of the proposed method are examined by numerical examples. The influences of Coriolis and centrifugal forces on the vibration behaviors of the beams with various hub radiuses and slenderness ratios and rotating at different angular velocities are also investigated.

Orbitals, Occupation Numbers, and Band Structure of Short One-Dimensional Cadmium Telluride Polymers.

PubMed

Valentine, Andrew J S; Talapin, Dmitri V; Mazziotti, David A

2017-04-27

Recent work found that soldering CdTe quantum dots together with a molecular CdTe polymer yielded field-effect transistors with much greater electron mobility than quantum dots alone. We present a computational study of the CdTe polymer using the active-space variational two-electron reduced density matrix (2-RDM) method. While analogous complete active-space self-consistent field (CASSCF) methods scale exponentially with the number of active orbitals, the active-space variational 2-RDM method exhibits polynomial scaling. A CASSCF calculation using the (48o,64e) active space studied in this paper requires 10 24 determinants and is therefore intractable, while the variational 2-RDM method in the same active space requires only 2.1 × 10 7 variables. Natural orbitals, natural-orbital occupations, charge gaps, and Mulliken charges are reported as a function of polymer length. The polymer, we find, is strongly correlated, despite possessing a simple sp 3 -hybridized bonding scheme. Calculations reveal the formation of a nearly saturated valence band as the polymer grows and a charge gap that decreases sharply with polymer length.

The notion of snow grain shape: Ambiguous definitions, retrievalfrom tomography and implications on remote sensing

NASA Astrophysics Data System (ADS)

Krol, Q. E.; Loewe, H.

2016-12-01

Grain shape is known to influence the effective physical properties of snow and therefore included in the international classification of seasonal snow. Accordingly, snowpack models account for phenomenological shape parameters (sphericity, dendricity) to capture shape variations. These parameters are however difficult to validate due to the lack of clear-cut definitions from the 3D microstucture and insufficient links to physical properties. While the definition of traditional shape was tailored to the requirements of observers, a more objective definition should be tailored to the requirements of physical properties, by analyzing geometrical (shape) corrections in existing theoretical formulations directly. To this end we revisited the autocorrelation function (ACF) and the chord length distribution (CLD) of snow. Both functions capture size distributions of the microstructure, can be calculated from X-ray tomography and are related to various physical properties. Both functions involve the optical equivalent diameter as dominant quantity, however the respective higher-order geometrical correction differ. We have analyzed these corrections, namely interfacial curvatures for the ACF and the second moment for the CLD, using an existing data set of 165 tomography samples. To unify the notion of shape, we derived various statistical relations between the length scales. Our analysis bears three key practical implications. First, we derived a significantly improved relation between the exponential correlation length and the optical diameter by taking curvatures into account. This adds to the understanding of linking "microwave grain size" and "optical grain size" of snow for remote sensing. Second, we retrieve the optical shape parameter (commonly referred to as B) from tomography images via the moment of the CLD. Third, shape variations seen by observers do not necessarily correspond to shape variations probed by physical properties.

Defining restoration targets for water depth and salinity in wind-dominated Spartina patens (Ait.) Muhl. coastal marshes

USGS Publications Warehouse

Nyman, J.A.; LaPeyre, Megan K.; Caldwell, Andral W.; Piazza, Sarai C.; Thom, C.; Winslow, C.

2009-01-01

Coastal wetlands provide valued ecosystem functions but the sustainability of those functions often is threatened by artificial hydrologic conditions. It is widely recognized that increased flooding and salinity can stress emergent plants, but there are few measurements to guide restoration, management, and mitigation. Marsh flooding can be estimated over large areas with few data where winds have little effect on water levels, but quantifying flooding requires hourly measurements over long time periods where tides are wind-dominated such as the northern Gulf of Mexico. Estimating salinity of flood water requires direct daily measurements because coastal marshes are characterized by dynamic salinity gradients. We analyzed 399,772 hourly observations of water depth and 521,561 hourly observations of water salinity from 14 sites in Louisiana coastal marshes dominated by Spartina patens (Ait.) Muhl. Unlike predicted water levels, observed water levels varied monthly and annually. We attributed those observed variations to variations in river runoff and winds. In stable marshes with slow wetland loss rates, we found that marsh elevation averaged 1 cm above mean high water, 15 cm above mean water, and 32 cm above mean low water levels. Water salinity averaged 3.7 ppt during April, May, and June, and 5.4 ppt during July, August, and September. The daily, seasonal, and annual variation in water levels and salinity that were evident would support the contention that such variation be retained when designing and operating coastal wetland management and restoration projects. Our findings might be of interest to scientists, engineers, and managers involved in restoration, management, and restoration in other regions where S. patens or similar species are common but local data are unavailable.

Defining restoration targets for water depth and salinity in wind-dominated Spartina patens (Ait.) Muhl. coastal marshes

USGS Publications Warehouse

Nyman, J.A.; La Peyre, M.K.; Caldwell, A.; Piazza, S.; Thom, C.; Winslow, C.

2009-01-01

Coastal wetlands provide valued ecosystem functions but the sustainability of those functions often is threatened by artificial hydrologic conditions. It is widely recognized that increased flooding and salinity can stress emergent plants, but there are few measurements to guide restoration, management, and mitigation. Marsh flooding can be estimated over large areas with few data where winds have little effect on water levels, but quantifying flooding requires hourly measurements over long time periods where tides are wind-dominated such as the northern Gulf of Mexico. Estimating salinity of flood water requires direct daily measurements because coastal marshes are characterized by dynamic salinity gradients. We analyzed 399,772 hourly observations of water depth and 521,561 hourly observations of water salinity from 14 sites in Louisiana coastal marshes dominated by Spartina patens (Ait.) Muhl. Unlike predicted water levels, observed water levels varied monthly and annually. We attributed those observed variations to variations in river runoff and winds. In stable marshes with slow wetland loss rates, we found that marsh elevation averaged 1 cm above mean high water, 15 cm above mean water, and 32 cm above mean low water levels. Water salinity averaged 3.7 ppt during April, May, and June, and 5.4 ppt during July, August, and September. The daily, seasonal, and annual variation in water levels and salinity that were evident would support the contention that such variation be retained when designing and operating coastal wetland management and restoration projects. Our findings might be of interest to scientists, engineers, and managers involved in restoration, management, and restoration in other regions where S. patens or similar species are common but local data are unavailable. ?? 2009 Elsevier B.V.

The Pilin N-terminal Domain Maintains Neisseria gonorrhoeae Transformation Competence during Pilus Phase Variation

PubMed Central

2016-01-01

The obligate human pathogen Neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection, gonorrhea. Required for gonococcal infection, Type IV pili (Tfp) mediate many functions including adherence, twitching motility, defense against neutrophil killing, and natural transformation. Critical for immune escape, the gonococcal Tfp undergoes antigenic variation, a recombination event at the pilE locus that varies the surface exposed residues of the major pilus subunit PilE (pilin) in the pilus fiber. This programmed recombination system has the potential to produce thousands of pilin variants and can produce strains with unproductive pilin molecules that are completely unable to form Tfp. Saturating mutagenesis of the 3’ third of the pilE gene identified 68 unique single nucleotide mutations that each resulted in an underpiliated colony morphology. Notably, all isolates, including those with undetectable levels of pilin protein and no observable surface-exposed pili, retained an intermediate level of transformation competence not exhibited in ΔpilE strains. Site-directed, nonsense mutations revealed that only the first 38 amino acids of the mature pilin N-terminus (the N-terminal domain or Ntd) are required for transformation competence, and microscopy, ELISAs and pilus purification demonstrate that extended Tfp are not required for competence. Transformation in strains producing only the pilin Ntd has the same genetic determinants as wild-type transformation. The Ntd corresponds to the alternative product of S-pilin cleavage, a specific proteolysis unique to pathogenic Neisseria. Mutation of the S-pilin cleavage site demonstrated that S-pilin cleavage mediated release of the Ntd is required for competence when a strain produces unproductive pilin molecules that cannot assemble into a Tfp through mutation or antigenic variation. We conclude that S-pilin cleavage evolved as a mechanism to maintain competence in nonpiliated antigenic variants and suggest there are alternate forms of the Tfp assembly apparatus that mediate various functions including transformation. PMID:27213957

A Rare SNP Identified a TCP Transcription Factor Essential for Tendril Development in Cucumber.

PubMed

Wang, Shenhao; Yang, Xueyong; Xu, Mengnan; Lin, Xingzhong; Lin, Tao; Qi, Jianjian; Shao, Guangjin; Tian, Nana; Yang, Qing; Zhang, Zhonghua; Huang, Sanwen

2015-12-07

Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber (Cucumis sativus L.). In a collection of >3000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and, therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide polymorphism. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a protein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcriptomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

On the penetration of a hot diapir through a strongly temperature-dependent viscosity medium

NASA Technical Reports Server (NTRS)

Daly, S. F.; Raefsky, A.

1985-01-01

The ascent of a hot spherical body through a fluid with a strongly temperature-dependent viscosity has been studied using an axisymmetric finite element method. Numerical solutions range over Peclet numbers of 0.1 - 1000 from constant viscosity up to viscosity variations of 100,000. Both rigid and stress-free boundary conditions were applied at the surface of the sphere. The dependence of drag on viscosity variation was shown to have no dependence on the stress boundary condition except for a Stokes flow scaling factor. A Nusselt number parameterization based on the stress-free constant viscosity functional dependence on the Peclet number scaled by a parameter depending on the viscosity structure fits both stress-free and rigid boundary condition data above viscosity variations of 100. The temperature scale height was determined as a function of sphere radius. For the simple physical model studied in this paper pre-heating is required to reduce the ambient viscosity of the country rock to less than 10 to the 22nd sq cm/s in order for a 10 km diapir to penetrate a distance of several radii.

The immune system: a target for functional foods?

PubMed

Calder, Philip C; Kew, Samantha

2002-11-01

The immune system acts to protect the host from infectious agents that exist in the environment (bacteria, viruses, fungi, parasites) and from other noxious insults. The immune system is constantly active, acting to discriminate 'non-self' from 'self'. The immune system has two functional divisions: the innate and the acquired. Both components involve various blood-borne factors (complement, antibodies, cytokines) and cells. A number of methodologies exist to assess aspects of immune function; many of these rely upon studying cells in culture ex vivo. There are large inter-individual variations in many immune functions even among the healthy. Genetics, age, gender, smoking habits, habitual levels of exercise, alcohol consumption, diet, stage in the female menstrual cycle, stress, history of infections and vaccinations, and early life experiences are likely to be important contributors to the observed variation. While it is clear that individuals with immune responses significantly below 'normal' are more susceptible to infectious agents and exhibit increased infectious morbidity and mortality, it is not clear how the variation in immune function among healthy individuals relates to variation in susceptibility to infection. Nutrient status is an important factor contributing to immune competence: undernutrition impairs the immune system, suppressing immune functions that are fundamental to host protection. Undernutrition leading to impairment of immune function can be due to insufficient intake of energy and macronutrients and/or due to deficiencies in specific micronutrients. Often these occur in combination. Nutrients that have been demonstrated (in either animal or human studies) to be required for the immune system to function efficiently include essential amino acids, the essential fatty acid linoleic acid, vitamin A, folic acid, vitamin B6, vitamin B12, vitamin C, vitamin E, Zn, Cu, Fe and Se. Practically all forms of immunity may be affected by deficiencies in one or more of these nutrients. Animal and human studies have demonstrated that adding the deficient nutrient back to the diet can restore immune function and resistance to infection. Among the nutrients studied most in this regard are vitamin E and Zn. Increasing intakes of some nutrients above habitual and recommended levels can enhance some aspects of immune function. However, excess amounts of some nutrients also impair immune function. There is increasing evidence that probiotic bacteria improve host immune function. The effect of enhancing immune function on host resistance to infection in healthy individuals is not clear.

Overset grid implementation of the complex Kohn variational method for electron-polyatomic molecule scattering

NASA Astrophysics Data System (ADS)

McCurdy, C. William; Lucchese, Robert L.; Greenman, Loren

2017-04-01

The complex Kohn variational method, which represents the continuum wave function in each channel using a combination of Gaussians and Bessel or Coulomb functions, has been successful in numerous applications to electron-polyatomic molecule scattering and molecular photoionization. The hybrid basis representation limits it to relatively low energies (< 50 eV) , requires an approximation to exchange matrix elements involving continuum functions, and hampers its coupling to modern electronic structure codes for the description of correlated target states. We describe a successful implementation of the method using completely adaptive overset grids to describe continuum functions, in which spherical subgrids are placed on every atomic center to complement a spherical master grid that describes the behavior at large distances. An accurate method for applying the free-particle Green's function on the grid eliminates the need to operate explicitly with the kinetic energy, enabling a rapidly convergent Arnoldi algorithm for solving linear equations on the grid, and no approximations to exchange operators are made. Results for electron scattering from several polyatomic molecules will be presented. Army Research Office, MURI, WN911NF-14-1-0383 and U. S. DOE DE-SC0012198 (at Texas A&M).

Thermal consequences of colour and near-infrared reflectance.

PubMed

Stuart-Fox, Devi; Newton, Elizabeth; Clusella-Trullas, Susana

2017-07-05

The importance of colour for temperature regulation in animals remains controversial. Colour can affect an animal's temperature because all else being equal, dark surfaces absorb more solar energy than do light surfaces, and that energy is converted into heat. However, in reality, the relationship between colour and thermoregulation is complex and varied because it depends on environmental conditions and the physical properties, behaviour and physiology of the animal. Furthermore, the thermal effects of colour depend as much on absorptance of near-infrared ((NIR), 700-2500 nm) as visible (300-700 nm) wavelengths of direct sunlight; yet the NIR is very rarely considered or measured. The few available data on NIR reflectance in animals indicate that the visible reflectance is often a poor predictor of NIR reflectance. Adaptive variation in animal coloration (visible reflectance) reflects a compromise between multiple competing functions such as camouflage, signalling and thermoregulation. By contrast, adaptive variation in NIR reflectance should primarily reflect thermoregulatory requirements because animal visual systems are generally insensitive to NIR wavelengths. Here, we assess evidence and identify key research questions regarding the thermoregulatory function of animal coloration, and specifically consider evidence for adaptive variation in NIR reflectance.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).

Common Variation in the DOPA Decarboxylase (DDC) Gene and Human Striatal DDC Activity In Vivo.

PubMed

Eisenberg, Daniel P; Kohn, Philip D; Hegarty, Catherine E; Ianni, Angela M; Kolachana, Bhaskar; Gregory, Michael D; Masdeu, Joseph C; Berman, Karen F

2016-08-01

The synthesis of multiple amine neurotransmitters, such as dopamine, norepinephrine, serotonin, and trace amines, relies in part on DOPA decarboxylase (DDC, AADC), an enzyme that is required for normative neural operations. Because rare, loss-of-function mutations in the DDC gene result in severe enzymatic deficiency and devastating autonomic, motor, and cognitive impairment, DDC common genetic polymorphisms have been proposed as a source of more moderate, but clinically important, alterations in DDC function that may contribute to risk, course, or treatment response in complex, heritable neuropsychiatric illnesses. However, a direct link between common genetic variation in DDC and DDC activity in the living human brain has never been established. We therefore tested for this association by conducting extensive genotyping across the DDC gene in a large cohort of 120 healthy individuals, for whom DDC activity was then quantified with [(18)F]-FDOPA positron emission tomography (PET). The specific uptake constant, Ki, a measure of DDC activity, was estimated for striatal regions of interest and found to be predicted by one of five tested haplotypes, particularly in the ventral striatum. These data provide evidence for cis-acting, functional common polymorphisms in the DDC gene and support future work to determine whether such variation might meaningfully contribute to DDC-mediated neural processes relevant to neuropsychiatric illness and treatment.

Leaf traits within communities: context may affect the mapping of traits to function.

PubMed

Funk, Jennifer L; Cornwell, William K

2013-09-01

The leaf economics spectrum (LES) has revolutionized the way many ecologists think about quantifying plant ecological trade-offs. In particular, the LES has connected a clear functional trade-off (long-lived leaves with slow carbon capture vs. short-lived leaves with fast carbon capture) to a handful of easily measured leaf traits. Building on this work, community ecologists are now able to quickly assess species carbon-capture strategies, which may have implications for community-level patterns such as competition or succession. However, there are a number of steps in this logic that require careful examination, and a potential danger arises when interpreting leaf-trait variation among species within communities where trait relationships are weak. Using data from 22 diverse communities, we show that relationships among three common functional traits (photosynthetic rate, leaf nitrogen concentration per mass, leaf mass per area) are weak in communities with low variation in leaf life span (LLS), especially communities dominated by herbaceous or deciduous woody species. However, globally there are few LLS data sets for communities dominated by herbaceous or deciduous species, and more data are needed to confirm this pattern. The context-dependent nature of trait relationships at the community level suggests that leaf-trait variation within communities, especially those dominated by herbaceous and deciduous woody species, should be interpreted with caution.

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

Demonstrating Principles of Spectrophotometry by Constructing a Simple, Low-Cost, Functional Spectrophotometer Utilizing the Light Sensor on a Smartphone

ERIC Educational Resources Information Center

Hosker, Bill S.

2018-01-01

A highly simplified variation on the do-it-yourself spectrophotometer using a smartphone's light sensor as a detector and an app to calculate and display absorbance values was constructed and tested. This simple version requires no need for electronic components or postmeasurement spectral analysis. Calibration graphs constructed from two…

Onset of natural convection in a continuously perturbed system

NASA Astrophysics Data System (ADS)

Ghorbani, Zohreh; Riaz, Amir

2017-11-01

The convective mixing triggered by gravitational instability plays an important role in CO2 sequestration in saline aquifers. The linear stability analysis and the numerical simulation concerning convective mixing in porous media requires perturbations of small amplitude to be imposed on the concentration field in the form of an initial shape function. In aquifers, however, the instability is triggered by local porosity and permeability. In this work, we consider a canonical 2D homogeneous system where perturbations arise due to spatial variation of porosity in the system. The advantage of this approach is not only the elimination of the required initial shape function, but it also serves as a more realistic approach. Using a reduced nonlinear method, we first explore the effect of harmonic variations of porosity in the transverse and streamwise direction on the onset time of convection and late time behavior. We then obtain the optimal porosity structure that minimizes the convection onset. We further examine the effect of a random porosity distribution, that is independent of the spatial mode of porosity structure, on the convection onset. Using high-order pseudospectral DNS, we explore how the random distribution differs from the modal approach in predicting the onset time.

Functional diversity of the superfamily of K⁺ transporters to meet various requirements.

PubMed

Diskowski, Marina; Mikusevic, Vedrana; Stock, Charlott; Hänelt, Inga

2015-09-01

The superfamily of K+ transporters unites proteins from plants, fungi, bacteria, and archaea that translocate K+ and/or Na+ across membranes. These proteins are key components in osmotic regulation, pH homeostasis, and resistance to high salinity and dryness. The members of the superfamily are closely related to K+ channels such as KcsA but also show several striking differences that are attributed to their altered functions. This review highlights these functional differences, focusing on the bacterial superfamily members KtrB, TrkH, and KdpA. The functional variations within the family and comparison to MPM-type K+ channels are discussed in light of the recently solved structures of the Ktr and Trk systems.

EVIDENCE FOR A CONSTANT IMF IN EARLY-TYPE GALAXIES BASED ON THEIR X-RAY BINARY POPULATIONS

NASA Astrophysics Data System (ADS)

Zepf, Stephen E.; Maccarone, T. J.; Kundu, A.; Gonzalez, A. H.; Lehmer, B.; Maraston, C.

2014-01-01

A number of recent studies have proposed that the stellar initial mass function (IMF) of early type galaxies varies systematically as a function of galaxy mass, with higher mass galaxies having steeper IMFs. These steeper IMFs have more low-mass stars relative to the number of high mass stars, and therefore naturally result in proportionally fewer neutron stars and black holes. In this paper, we specifically predict the variation in the number of black holes and neutron stars in early type galaxies based on the IMF variation required to reproduce the observed mass-to-light ratio trends with galaxy mass. We then test whether such variations are observed by studying the field low-mass X-ray binary populations (LMXBs) of nearby early-type galaxies. These binaries are field neutron stars or black holes accreting from a low-mass donor star. We specifically compare the number of field LMXBs per K-band light in a well-studied sample of elliptical galaxies, and use this result to distinguish between an invariant IMF and one that is Kroupa/Chabrier-like at low masses and steeper at high masses. We discuss how these observations constrain the possible forms of the IMF variations and how future Chandra observations can enable sharper tests of the IMF.

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

A biological sub-micron thickness optical broadband reflector characterized using both light and microwaves

PubMed Central

Vukusic, P.; Kelly, R.; Hooper, I.

2008-01-01

Broadband optical reflectors generally function through coherent scattering from systems comprising one of three designs: overlapped; chirped; or chaotic multilayer reflectors. For each, the requirement to scatter a broad band of wavelengths is met through the presence of a variation in nanostructural periodicity running perpendicular to the systems' outer surfaces. Consequently, the requisite total thickness of the multilayer can often be in excess of 50 μm. Here, we report the discovery and the microwave-assisted characterization of a natural system that achieves excellent optical broadband reflectivity but that is less than 1 μm thick. This system, found on the wing scales of the butterfly Argyrophorus argenteus, comprises a distinctive variation in periodicity that runs parallel to the reflecting surface, rather than perpendicular to it. In this way, the requirement for an extensively thick system is removed. PMID:19042180

Water quality assessment of the Li Canal using a functional fuzzy synthetic evaluation model.

PubMed

Feng, Yan; Ling, Liu

2014-07-01

Through introducing functional data analysis (FDA) theory into the conventional fuzzy synthetic evaluation (FSE) method, the functional fuzzy synthetic evaluation (FFSE) model is established. FFSE keeps the property of the conventional FSE that the fuzziness in the water quality condition can be suitably measured. Furthermore, compared with FSE, FFSE has the following advantages: (1) FFSE requires fewer conditions for observation, for example, pollutants can be monitored at different times, and missing data is accepted; (2) the dynamic variation of the water quality condition can be represented more comprehensively and intuitively. The procedure of FFSE is discussed and the water quality of the Li Canal in 2012 is evaluated as an illustration. The synthetic classification of the Li Canal is "II" in January, February and July, and "I" in other months, which can satisfy the requirement of the Chinese South-to-North Water Diversion Project.

A unifying theory for genetic epidemiological analysis of binary disease data

PubMed Central

2014-01-01

Background Genetic selection for host resistance offers a desirable complement to chemical treatment to control infectious disease in livestock. Quantitative genetics disease data frequently originate from field studies and are often binary. However, current methods to analyse binary disease data fail to take infection dynamics into account. Moreover, genetic analyses tend to focus on host susceptibility, ignoring potential variation in infectiousness, i.e. the ability of a host to transmit the infection. This stands in contrast to epidemiological studies, which reveal that variation in infectiousness plays an important role in the progression and severity of epidemics. In this study, we aim at filling this gap by deriving an expression for the probability of becoming infected that incorporates infection dynamics and is an explicit function of both host susceptibility and infectiousness. We then validate this expression according to epidemiological theory and by simulating epidemiological scenarios, and explore implications of integrating this expression into genetic analyses. Results Our simulations show that the derived expression is valid for a range of stochastic genetic-epidemiological scenarios. In the particular case of variation in susceptibility only, the expression can be incorporated into conventional quantitative genetic analyses using a complementary log-log link function (rather than probit or logit). Similarly, if there is moderate variation in both susceptibility and infectiousness, it is possible to use a logarithmic link function, combined with an indirect genetic effects model. However, in the presence of highly infectious individuals, i.e. super-spreaders, the use of any model that is linear in susceptibility and infectiousness causes biased estimates. Thus, in order to identify super-spreaders, novel analytical methods using our derived expression are required. Conclusions We have derived a genetic-epidemiological function for quantitative genetic analyses of binary infectious disease data, which, unlike current approaches, takes infection dynamics into account and allows for variation in host susceptibility and infectiousness. PMID:24552188

A unifying theory for genetic epidemiological analysis of binary disease data.

PubMed

Lipschutz-Powell, Debby; Woolliams, John A; Doeschl-Wilson, Andrea B

2014-02-19

Genetic selection for host resistance offers a desirable complement to chemical treatment to control infectious disease in livestock. Quantitative genetics disease data frequently originate from field studies and are often binary. However, current methods to analyse binary disease data fail to take infection dynamics into account. Moreover, genetic analyses tend to focus on host susceptibility, ignoring potential variation in infectiousness, i.e. the ability of a host to transmit the infection. This stands in contrast to epidemiological studies, which reveal that variation in infectiousness plays an important role in the progression and severity of epidemics. In this study, we aim at filling this gap by deriving an expression for the probability of becoming infected that incorporates infection dynamics and is an explicit function of both host susceptibility and infectiousness. We then validate this expression according to epidemiological theory and by simulating epidemiological scenarios, and explore implications of integrating this expression into genetic analyses. Our simulations show that the derived expression is valid for a range of stochastic genetic-epidemiological scenarios. In the particular case of variation in susceptibility only, the expression can be incorporated into conventional quantitative genetic analyses using a complementary log-log link function (rather than probit or logit). Similarly, if there is moderate variation in both susceptibility and infectiousness, it is possible to use a logarithmic link function, combined with an indirect genetic effects model. However, in the presence of highly infectious individuals, i.e. super-spreaders, the use of any model that is linear in susceptibility and infectiousness causes biased estimates. Thus, in order to identify super-spreaders, novel analytical methods using our derived expression are required. We have derived a genetic-epidemiological function for quantitative genetic analyses of binary infectious disease data, which, unlike current approaches, takes infection dynamics into account and allows for variation in host susceptibility and infectiousness.

Relative velocity change measurement based on seismic noise analysis in exploration geophysics

NASA Astrophysics Data System (ADS)

Corciulo, M.; Roux, P.; Campillo, M.; Dubuq, D.

2011-12-01

Passive monitoring techniques based on noise cross-correlation analysis are still debated in exploration geophysics even if recent studies showed impressive performance in seismology at larger scale. Time evolution of complex geological structure using noise data includes localization of noise sources and measurement of relative velocity variations. Monitoring relative velocity variations only requires the measurement of phase shifts of seismic noise cross-correlation functions computed for successive time recordings. The existing algorithms, such as the Stretching and the Doublet, classically need great efforts in terms of computation time, making them not practical when continuous dataset on dense arrays are acquired. We present here an innovative technique for passive monitoring based on the measure of the instantaneous phase of noise-correlated signals. The Instantaneous Phase Variation (IPV) technique aims at cumulating the advantages of the Stretching and Doublet methods while proposing a faster measurement of the relative velocity change. The IPV takes advantage of the Hilbert transform to compute in the time domain the phase difference between two noise correlation functions. The relative velocity variation is measured through the slope of the linear regression of the phase difference curve as a function of correlation time. The large amount of noise correlation functions, classically available at exploration scale on dense arrays, allows for a statistical analysis that further improves the precision of the estimation of the velocity change. In this work, numerical tests first aim at comparing the IPV performance to the Stretching and Doublet techniques in terms of accuracy, robustness and computation time. Then experimental results are presented using a seismic noise dataset with five days of continuous recording on 397 geophones spread on a ~1 km-squared area.

Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis.

PubMed

Bentsink, Leónie; Jowett, Jemma; Hanhart, Corrie J; Koornneef, Maarten

2006-11-07

Genetic variation for seed dormancy in nature is a typical quantitative trait controlled by multiple loci on which environmental factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a major scientific challenge, which also has relevance for agriculture and ecology. In this study we describe the identification of the DELAY OF GERMINATION 1 (DOG1) gene previously identified as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated by a combination of positional cloning and mutant analysis and is absolutely required for the induction of seed dormancy. DOG1 is a member of a small gene family of unknown molecular function, with five members in Arabidopsis. The functional natural allelic variation present in Arabidopsis is caused by polymorphisms in the cis-regulatory region of the DOG1 gene and results in considerable expression differences between the DOG1 alleles of the accessions analyzed.

Validation of Variations in Mental Workload as a Function of Scenario Difficulty: Traffic Density and Visibility

NASA Technical Reports Server (NTRS)

2003-01-01

Fluctuations in mental workload can be expected as a function of traffic density and visibility. The aim of the current investigation was to establish simulation scenarios that differed in attentional processing requirements. Four scenarios were created and tested representing two levels of traffic density (urban versus freeway) and two levels of visibility (clear versus foggy). An array of mental workload assessment measures were used to exam changes in attentional processing requirements in each scenario. The assessment array consisted of physiological (P300 amplitude and latency) and behavioral (RT and accuracy) indices. Preliminary results indicate that workload differs significantly as a function of traffic density in rural versus freeway scenarios. Workload also differs significantly in rural versus freeway scenarios as a function of visibility as observed by a significant interaction between the two variables of interest. Results are discussed in terms of their application for validating the difficulty level of simulation scenarios as a format for examining mental workload.

A Dynamic Time Warping based covariance function for Gaussian Processes signature identification

NASA Astrophysics Data System (ADS)

Silversides, Katherine L.; Melkumyan, Arman

2016-11-01

Modelling stratiform deposits requires a detailed knowledge of the stratigraphic boundaries. In Banded Iron Formation (BIF) hosted ores of the Hamersley Group in Western Australia these boundaries are often identified using marker shales. Both Gaussian Processes (GP) and Dynamic Time Warping (DTW) have been previously proposed as methods to automatically identify marker shales in natural gamma logs. However, each method has different advantages and disadvantages. We propose a DTW based covariance function for the GP that combines the flexibility of the DTW with the probabilistic framework of the GP. The three methods are tested and compared on their ability to identify two natural gamma signatures from a Marra Mamba type iron ore deposit. These tests show that while all three methods can identify boundaries, the GP with the DTW covariance function combines and balances the strengths and weaknesses of the individual methods. This method identifies more positive signatures than the GP with the standard covariance function, and has a higher accuracy for identified signatures than the DTW. The combined method can handle larger variations in the signature without requiring multiple libraries, has a probabilistic output and does not require manual cut-off selections.

Sensitive subgroups and normal variation in pulmonary function response to air pollution episodes.

PubMed Central

Brunekreef, B; Kinney, P L; Ware, J H; Dockery, D; Speizer, F E; Spengler, J D; Ferris, B G

1991-01-01

The Clean Air Act requires that sensitive subgroups of exposed populations be protected from adverse health effects of air pollution exposure. Hence, data suggesting the existence of sensitive subgroups can have an important impact on regulatory decisions. Some investigators have interpreted differences among individuals in observed pulmonary function response to air pollution episodes as evidence that individuals differ in their sensitivity. An alternative explanation is that the differences are due entirely to normal variation in repeated pulmonary function measurements. This paper investigates this question by reanalyzing data from three studies of children exposed to air pollution episodes to determine whether the observed variability in pulmonary function response indicates differences in sensitivity or natural interoccasion variability. One study investigated exposures to total suspended particulates (TSP), the other two investigated exposure to ozone. In all studies, each child's response to air pollution exposures was summarized by regressing that child's set of pulmonary function measurements on the air pollution concentrations on the day or days before measurement. The within-child and between-child variances of these slopes were used to test the hypothesis of variable sensitivity. Regression slopes did not vary significantly among children exposed to episodes of high TSP concentration, but there was evidence of heterogeneity in both studies of ozone exposures. The finding of heterogeneous response to ozone exposure is consistent with the epidemiologic and chamber studies of ozone exposures, but the lack of evidence for heterogeneous response to TSP exposures implies that observed variation in response can be explained by sampling variability rather than the presence of sensitive subgroup. PMID:2050060

Arachidonic acid and DHA status in pregnant women is not associated with cognitive performance of their children at 4 or 6-7 years.

PubMed

Crozier, Sarah R; Sibbons, Charlene M; Fisk, Helena L; Godfrey, Keith M; Calder, Philip C; Gale, Catharine R; Robinson, Sian M; Inskip, Hazel M; Baird, Janis; Harvey, Nicholas C; Cooper, Cyrus; Burdge, Graham C

2018-06-01

Arachidonic acid (ARA) and DHA, supplied primarily from the mother, are required for early development of the central nervous system. Thus, variations in maternal ARA or DHA status may modify neurocognitive development. We investigated the relationship between maternal ARA and DHA status in early (11·7 weeks) or late (34·5 weeks) pregnancy on neurocognitive function at the age of 4 years or 6-7 years in 724 mother-child pairs from the Southampton Women's Survey cohort. Plasma phosphatidylcholine fatty acid composition was measured in early and late pregnancy. ARA concentration in early pregnancy predicted 13 % of the variation in ARA concentration in late pregnancy (β=0·36, P<0·001). DHA concentration in early pregnancy predicted 21 % of the variation in DHA concentration in late pregnancy (β=0·46, P<0·001). Children's cognitive function at the age of 4 years was assessed by the Wechsler Preschool and Primary Scale of Intelligence and at the age of 6-7 years by the Wechsler Abbreviated Scale of Intelligence. Executive function at the age of 6-7 years was assessed using elements of the Cambridge Neuropsychological Test Automated Battery. Neither DHA nor ARA concentrations in early or late pregnancy were associated significantly with neurocognitive function in children at the age of 4 years or the age of 6-7 years. These findings suggest that ARA and DHA status during pregnancy in the range found in this cohort are unlikely to have major influences on neurocognitive function in healthy children.

Reduce, reuse, and recycle: developmental evolution of trait diversification.

PubMed

Preston, Jill C; Hileman, Lena C; Cubas, Pilar

2011-03-01

A major focus of evolutionary developmental (evo-devo) studies is to determine the genetic basis of variation in organismal form and function, both of which are fundamental to biological diversification. Pioneering work on metazoan and flowering plant systems has revealed conserved sets of genes that underlie the bauplan of organisms derived from a common ancestor. However, the extent to which variation in the developmental genetic toolkit mirrors variation at the phenotypic level is an active area of research. Here we explore evidence from the angiosperm evo-devo literature supporting the frugal use of genes and genetic pathways in the evolution of developmental patterning. In particular, these examples highlight the importance of genetic pleiotropy in different developmental modules, thus reducing the number of genes required in growth and development, and the reuse of particular genes in the parallel evolution of ecologically important traits.

Permeabilization of brain tissue in situ enables multiregion analysis of mitochondrial function in a single mouse brain.

PubMed

Herbst, Eric A F; Holloway, Graham P

2015-02-15

Mitochondrial function in the brain is traditionally assessed through analysing respiration in isolated mitochondria, a technique that possesses significant tissue and time requirements while also disrupting the cooperative mitochondrial reticulum. We permeabilized brain tissue in situ to permit analysis of mitochondrial respiration with the native mitochondrial morphology intact, removing the need for isolation time and minimizing tissue requirements to ∼2 mg wet weight. The permeabilized brain technique was validated against the traditional method of isolated mitochondria and was then further applied to assess regional variation in the mouse brain with ischaemia-reperfusion injuries. A transgenic mouse model overexpressing catalase within mitochondria was applied to show the contribution of mitochondrial reactive oxygen species to ischaemia-reperfusion injuries in different brain regions. This technique enhances the accessibility of addressing physiological questions in small brain regions and in applying transgenic mouse models to assess mechanisms regulating mitochondrial function in health and disease. Mitochondria function as the core energy providers in the brain and symptoms of neurodegenerative diseases are often attributed to their dysregulation. Assessing mitochondrial function is classically performed in isolated mitochondria; however, this process requires significant isolation time, demand for abundant tissue and disruption of the cooperative mitochondrial reticulum, all of which reduce reliability when attempting to assess in vivo mitochondrial bioenergetics. Here we introduce a method that advances the assessment of mitochondrial respiration in the brain by permeabilizing existing brain tissue to grant direct access to the mitochondrial reticulum in situ. The permeabilized brain preparation allows for instant analysis of mitochondrial function with unaltered mitochondrial morphology using significantly small sample sizes (∼2 mg), which permits the analysis of mitochondrial function in multiple subregions within a single mouse brain. Here this technique was applied to assess regional variation in brain mitochondrial function with acute ischaemia-reperfusion injuries and to determine the role of reactive oxygen species in exacerbating dysfunction through the application of a transgenic mouse model overexpressing catalase within mitochondria. Through creating accessibility to small regions for the investigation of mitochondrial function, the permeabilized brain preparation enhances the capacity for examining regional differences in mitochondrial regulation within the brain, as the majority of genetic models used for unique approaches exist in the mouse model. © 2014 The Authors. The Journal of Physiology © 2014 The Physiological Society.

Do key dimensions of seed and seedling functional trait variation capture variation in recruitment probability?

USDA-ARS?s Scientific Manuscript database

1. Plant functional traits provide a mechanistic basis for understanding ecological variation among plant species and the implications of this variation for species distribution, community assembly and restoration. 2. The bulk of our functional trait understanding, however, is centered on traits rel...

Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation.

PubMed

Yang, Shuzhi; Cai, Qunfeng; Bard, Jonathan; Jamison, Jennifer; Wang, Jianmin; Yang, Weiping; Hu, Bo Hua

2015-12-01

Individual variation in the susceptibility of the auditory system to acoustic overstimulation has been well-documented at both the functional and structural levels. However, the molecular mechanism responsible for this variation is unclear. The current investigation was designed to examine the variation patterns of cochlear gene expression using RNA-seq data and to identify the genes with expression variation that increased following acoustic trauma. This study revealed that the constitutive expressions of cochlear genes displayed diverse levels of gene-specific variation. These variation patterns were altered by acoustic trauma; approximately one-third of the examined genes displayed marked increases in their expression variation. Bioinformatics analyses revealed that the genes that exhibited increased variation were functionally related to cell death, biomolecule metabolism, and membrane function. In contrast, the stable genes were primarily related to basic cellular processes, including protein and macromolecular syntheses and transport. There was no functional overlap between the stable and variable genes. Importantly, we demonstrated that glutamate metabolism is related to the variation in the functional response of the cochlea to acoustic overstimulation. Taken together, the results indicate that our analyses of the individual variations in transcriptome changes of cochlear genes provide important information for the identification of genes that potentially contribute to the generation of individual variation in cochlear responses to acoustic overstimulation. Copyright © 2015 Elsevier B.V. All rights reserved.

Domain Derivatives in Dielectric Rough Surface Scattering

DTIC Science & Technology

2015-01-01

and require the gradient of the objective function in the unknown model parameter vector at each stage of iteration. For large N, finite...differencing becomes numerically intensive, and an efficient alternative is domain differentiation in which the full gradient is obtained by solving a single...derivative calculation of the gradient for a locally perturbed dielectric interface. The method is non-variational, and algebraic in nature in that it

Qualifying variability: patterns in water quality and biota from a long-term, multi-stream dataset

Treesearch

Camille Flinders; Douglas McLaughlin

2016-01-01

Effective water resources assessment and management requires quantitative information on the variability of ambient and biological conditions in aquatic communities. Although it is understood that natural systems are variable, robust estimates of variation in water quality and biotic endpoints (e.g. community-based structure and function metrics) are rare in US waters...

Variant Interpretation: Functional Assays to the Rescue.

PubMed

Starita, Lea M; Ahituv, Nadav; Dunham, Maitreya J; Kitzman, Jacob O; Roth, Frederick P; Seelig, Georg; Shendure, Jay; Fowler, Douglas M

2017-09-07

Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic. Experimentally measuring a variant's functional consequences can provide clearer guidance, but individual assays performed only after the discovery of the variant are both time and resource intensive. Here, we discuss how multiplex assays of variant effect (MAVEs) can be used to measure the functional consequences of all possible variants in disease-relevant loci for a variety of molecular and cellular phenotypes. The resulting large-scale functional data can be combined with machine learning and clinical knowledge for the development of "lookup tables" of accurate pathogenicity predictions. A coordinated effort to produce, analyze, and disseminate large-scale functional data generated by multiplex assays could be essential to addressing the variant-interpretation crisis. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

A Blocked Linear Method for Optimizing Large Parameter Sets in Variational Monte Carlo

DOE PAGES

Zhao, Luning; Neuscamman, Eric

2017-05-17

We present a modification to variational Monte Carlo’s linear method optimization scheme that addresses a critical memory bottleneck while maintaining compatibility with both the traditional ground state variational principle and our recently-introduced variational principle for excited states. For wave function ansatzes with tens of thousands of variables, our modification reduces the required memory per parallel process from tens of gigabytes to hundreds of megabytes, making the methodology a much better fit for modern supercomputer architectures in which data communication and per-process memory consumption are primary concerns. We verify the efficacy of the new optimization scheme in small molecule tests involvingmore » both the Hilbert space Jastrow antisymmetric geminal power ansatz and real space multi-Slater Jastrow expansions. Satisfied with its performance, we have added the optimizer to the QMCPACK software package, with which we demonstrate on a hydrogen ring a prototype approach for making systematically convergent, non-perturbative predictions of Mott-insulators’ optical band gaps.« less

Variation, Repetition, And Choice

PubMed Central

Abreu-Rodrigues, Josele; Lattal, Kennon A; dos Santos, Cristiano V; Matos, Ricardo A

2005-01-01

Experiment 1 investigated the controlling properties of variability contingencies on choice between repeated and variable responding. Pigeons were exposed to concurrent-chains schedules with two alternatives. In the REPEAT alternative, reinforcers in the terminal link depended on a single sequence of four responses. In the VARY alternative, a response sequence in the terminal link was reinforced only if it differed from the n previous sequences (lag criterion). The REPEAT contingency generated low, constant levels of sequence variation whereas the VARY contingency produced levels of sequence variation that increased with the lag criterion. Preference for the REPEAT alternative tended to increase directly with the degree of variation required for reinforcement. Experiment 2 examined the potential confounding effects in Experiment 1 of immediacy of reinforcement by yoking the interreinforcer intervals in the REPEAT alternative to those in the VARY alternative. Again, preference for REPEAT was a function of the lag criterion. Choice between varying and repeating behavior is discussed with respect to obtained behavioral variability, probability of reinforcement, delay of reinforcement, and switching within a sequence. PMID:15828592

The variational method in quantum mechanics: an elementary introduction

NASA Astrophysics Data System (ADS)

Borghi, Riccardo

2018-05-01

Variational methods in quantum mechanics are customarily presented as invaluable techniques to find approximate estimates of ground state energies. In the present paper a short catalogue of different celebrated potential distributions (both 1D and 3D), for which an exact and complete (energy and wavefunction) ground state determination can be achieved in an elementary way, is illustrated. No previous knowledge of calculus of variations is required. Rather, in all presented cases the exact energy functional minimization is achieved by using only a couple of simple mathematical tricks: ‘completion of square’ and integration by parts. This makes our approach particularly suitable for undergraduates. Moreover, the key role played by particle localization is emphasized through the entire analysis. This gentle introduction to the variational method could also be potentially attractive for more expert students as a possible elementary route toward a rather advanced topic on quantum mechanics: the factorization method. Such an unexpected connection is outlined in the final part of the paper.

Correlation functions from a unified variational principle: Trial Lie groups

NASA Astrophysics Data System (ADS)

Balian, R.; Vénéroni, M.

2015-11-01

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces the original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie-Poisson structure. At second order, the variational expression for two-time correlation functions separates-as does its exact counterpart-the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.

Uncertainty and operational considerations in mass prophylaxis workforce planning.

PubMed

Hupert, Nathaniel; Xiong, Wei; King, Kathleen; Castorena, Michelle; Hawkins, Caitlin; Wu, Cindie; Muckstadt, John A

2009-12-01

The public health response to an influenza pandemic or other large-scale health emergency may include mass prophylaxis using multiple points of dispensing (PODs) to deliver countermeasures rapidly to affected populations. Computer models created to date to determine "optimal" staffing levels at PODs typically assume stable patient demand for service. The authors investigated POD function under dynamic and uncertain operational environments. The authors constructed a Monte Carlo simulation model of mass prophylaxis (the Dynamic POD Simulator, or D-PODS) to assess the consequences of nonstationary patient arrival patterns on POD function under a variety of POD layouts and staffing plans. Compared are the performance of a standard POD layout under steady-state and variable patient arrival rates that may mimic real-life variation in patient demand. To achieve similar performance, PODs functioning under nonstationary patient arrival rates require higher staffing levels than would be predicted using the assumption of stationary arrival rates. Furthermore, PODs may develop severe bottlenecks unless staffing levels vary over time to meet changing patient arrival patterns. Efficient POD networks therefore require command and control systems capable of dynamically adjusting intra- and inter-POD staff levels to meet demand. In addition, under real-world operating conditions of heightened uncertainty, fewer large PODs will require a smaller total staff than many small PODs to achieve comparable performance. Modeling environments that capture the effects of fundamental uncertainties in public health disasters are essential for the realistic evaluation of response mechanisms and policies. D-PODS quantifies POD operational efficiency under more realistic conditions than have been modeled previously. The authors' experiments demonstrate that effective POD staffing plans must be responsive to variation and uncertainty in POD arrival patterns. These experiments highlight the need for command and control systems to be created to manage emergency response successfully.

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

A fast solver for the Helmholtz equation based on the generalized multiscale finite-element method

NASA Astrophysics Data System (ADS)

Fu, Shubin; Gao, Kai

2017-11-01

Conventional finite-element methods for solving the acoustic-wave Helmholtz equation in highly heterogeneous media usually require finely discretized mesh to represent the medium property variations with sufficient accuracy. Computational costs for solving the Helmholtz equation can therefore be considerably expensive for complicated and large geological models. Based on the generalized multiscale finite-element theory, we develop a novel continuous Galerkin method to solve the Helmholtz equation in acoustic media with spatially variable velocity and mass density. Instead of using conventional polynomial basis functions, we use multiscale basis functions to form the approximation space on the coarse mesh. The multiscale basis functions are obtained from multiplying the eigenfunctions of a carefully designed local spectral problem with an appropriate multiscale partition of unity. These multiscale basis functions can effectively incorporate the characteristics of heterogeneous media's fine-scale variations, thus enable us to obtain accurate solution to the Helmholtz equation without directly solving the large discrete system formed on the fine mesh. Numerical results show that our new solver can significantly reduce the dimension of the discrete Helmholtz equation system, and can also obviously reduce the computational time.

Occupancy analysis: design and operational energy studies in a new high-rise office building. Volume 3

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

Not Available

1983-10-01

The objective of this analysis, is simply to: determine how energy consumption varies as a function of building occupancy and utilization. This analysis is primarily involved with the relationship between occupancy patterns and energy consumption. It also addresses the relationship between building functional use (e.g., office, computer, parking, and food service) and energy consumption. This study investigates variations in use and energy consumption during (1) the period of building startup from pre-occupancy through initial occupancy to full occupancy, and (2) daily and night occupancy for weekdays, weekends, holidays, and vacation periods. The report includes an investigation of the relationship betweenmore » specific functional uses, systems requirements for those functions, and energy consumption.« less

Identification of the fitness determinants of budding yeast on a natural substrate.

PubMed

Filteau, Marie; Charron, Guillaume; Landry, Christian R

2017-04-01

The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway.

(e, 2e) simple ionization of {{\\rm{H}}}_{3}^{+} by fast electron impact: use of triangular three-center continuum and bound state wave functions

NASA Astrophysics Data System (ADS)

Obeid, S.; Chuluunbaatar, O.; Joulakian, B. B.

2017-07-01

The variation of the multiply differential cross section of the (e, 2e) simple ionization of {{{H}}}3+, with the incident and ejection energy values, as well as the directions of the ejected and scattered electrons, is studied. The calculations have been performed in the frame of the perturbative first Born procedure, which has required the development of equilateral triangular three center bound and continuum state wave functions. The results explore the optimal conditions and the particularities of the triangular targets, such as the appearance of interference patterns in the variation of the four fold differential cross section (FDCS) with the scattering angle for a fixed orientation of the molecule. The comparison between the results obtained by two H3 + ground wave functions, with and without a correlation term r 12, shows that the effect of correlation on the magnitude of the triple differential cross section is not large, but it produces some modification in the structure of the FDCS.

The efficacy of elastic therapeutic tape variations on measures of ankle function and performance.

PubMed

Brogden, Christopher Michael; Marrin, Kelly; Page, Richard Michael; Greig, Matt

2018-04-23

To investigate the effects of different variations of elastic therapeutic taping (ETT) on tests used to screen for ankle injury risk and function. Randomized crossover. Laboratory. Twelve professional male soccer players completed three experimental trials: No tape (NT), RockTape™ (RT), and Kinesio™ Tape (KT) applied to the ankle complex. Clinical and functional ankle screening tests were used to assess the effects of ETT on measures of joint position sense, postural stability and ground reaction forces. KT (P = 0.04) and RT (P = 0.01) demonstrated significant improvements in end range joint position sense. When compared to NT, RT significantly (P = 0.02) improved mid-range joint position sense at 15°, and time to complete a drop landing task. No significant differences were observed for measures of postural stability (P ≥ 0.12) nor ground reaction force variables (P ≥ 0.33). Results advocate the use of ETT for proprioceptive and functional tasks when applied to the ankles of healthy male soccer players. However, a greater number of practical and significant differences were observed when RT only was applied, indicating that practitioners may potentially advocate the use of RT for tasks requiring proprioception and functional performance. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Common Variation in the DOPA Decarboxylase (DDC) Gene and Human Striatal DDC Activity In Vivo

PubMed Central

Eisenberg, Daniel P; Kohn, Philip D; Hegarty, Catherine E; Ianni, Angela M; Kolachana, Bhaskar; Gregory, Michael D; Masdeu, Joseph C; Berman, Karen F

2016-01-01

The synthesis of multiple amine neurotransmitters, such as dopamine, norepinephrine, serotonin, and trace amines, relies in part on DOPA decarboxylase (DDC, AADC), an enzyme that is required for normative neural operations. Because rare, loss-of-function mutations in the DDC gene result in severe enzymatic deficiency and devastating autonomic, motor, and cognitive impairment, DDC common genetic polymorphisms have been proposed as a source of more moderate, but clinically important, alterations in DDC function that may contribute to risk, course, or treatment response in complex, heritable neuropsychiatric illnesses. However, a direct link between common genetic variation in DDC and DDC activity in the living human brain has never been established. We therefore tested for this association by conducting extensive genotyping across the DDC gene in a large cohort of 120 healthy individuals, for whom DDC activity was then quantified with [18F]-FDOPA positron emission tomography (PET). The specific uptake constant, Ki, a measure of DDC activity, was estimated for striatal regions of interest and found to be predicted by one of five tested haplotypes, particularly in the ventral striatum. These data provide evidence for cis-acting, functional common polymorphisms in the DDC gene and support future work to determine whether such variation might meaningfully contribute to DDC-mediated neural processes relevant to neuropsychiatric illness and treatment. PMID:26924680

Mining a sea of data: deducing the environmental controls of ocean chlorophyll.

PubMed

Irwin, Andrew J; Finkel, Zoe V

2008-01-01

Chlorophyll biomass in the surface ocean is regulated by a complex interaction of physiological, oceanographic, and ecological factors and in turn regulates the rates of primary production and export of organic carbon to the deep ocean. Mechanistic models of phytoplankton responses to climate change require the parameterization of many processes of which we have limited knowledge. We develop a statistical approach to estimate the response of remote-sensed ocean chlorophyll to a variety of physical and chemical variables. Irradiance over the mixed layer depth, surface nitrate, sea-surface temperature, and latitude and longitude together can predict 83% of the variation in log chlorophyll in the North Atlantic. Light and nitrate regulate biomass through an empirically determined minimum function explaining nearly 50% of the variation in log chlorophyll by themselves and confirming that either light or macronutrients are often limiting and that much of the variation in chlorophyll concentration is determined by bottom-up mechanisms. Assuming the dynamics of the future ocean are governed by the same processes at work today, we should be able to apply these response functions to future climate change scenarios, with changes in temperature, nutrient distributions, irradiance, and ocean physics.

Variation in multiring basic structures as a function of impact angle

NASA Technical Reports Server (NTRS)

Wichman, R. W.; Schultz, P. H.

1992-01-01

Previous studies have demonstrated that the impact process in the laboratory varies as a function of impact angle. This variation is attributed to changes in energy partitioning and projectile failure during the impact and, in simple craters, produces a sequence of progressively smaller and more asymmetric crater forms as impact angle decreases from approximately 20 degrees. Variations in impact angle can produce differences in the appearance of multiring impact basins. Comparisons of Orientale to the more oblique impact structure at Crisium also suggests that these differences primarily reflect the degree of cavity collapse. The relative changes in massif ring topography, basin scarp relief, and the distribution of peripheral mare units are consistent with a reduction in degree of cavity collapse with decreasing impact angle. The prominent uprange basin scarps and the restriction of tectonically derived peripheral mare units along uprange ring structures also may indicate an uprange enhancement of failure during cavity collapse. Finally, although basin ring faults appear to be preferred pathways for mare volcanism, fault-controlled peripheral mare volcanism occurs most readily uprange of an oblique impact; elsewhere such volcanism apparently requires superposition of an impact structure on the ring fault.

Quantification of atrial dynamics using cardiovascular magnetic resonance: inter-study reproducibility.

PubMed

Kowallick, Johannes T; Morton, Geraint; Lamata, Pablo; Jogiya, Roy; Kutty, Shelby; Hasenfuß, Gerd; Lotz, Joachim; Nagel, Eike; Chiribiri, Amedeo; Schuster, Andreas

2015-05-17

Cardiovascular magnetic resonance (CMR) offers quantification of phasic atrial functions based on volumetric assessment and more recently, on CMR feature tracking (CMR-FT) quantitative strain and strain rate (SR) deformation imaging. Inter-study reproducibility is a key requirement for longitudinal studies but has not been defined for CMR-based quantification of left atrial (LA) and right atrial (RA) dynamics. Long-axis 2- and 4-chamber cine images were acquired at 9:00 (Exam A), 9:30 (Exam B) and 14:00 (Exam C) in 16 healthy volunteers. LA and RA reservoir, conduit and contractile booster pump functions were quantified by volumetric indexes as derived from fractional volume changes and by strain and SR as derived from CMR-FT. Exam A and B were compared to assess the inter-study reproducibility. Morning and afternoon scans were compared to address possible diurnal variation of atrial function. Inter-study reproducibility was within acceptable limits for all LA and RA volumetric, strain and SR parameters. Inter-study reproducibility was better for volumetric indexes and strain than for SR parameters and better for LA than for RA dynamics. For the LA, reservoir function showed the best reproducibility (intraclass correlation coefficient (ICC) 0.94-0.97, coefficient of variation (CoV) 4.5-8.2%), followed by conduit (ICC 0.78-0.97, CoV 8.2-18.5%) and booster pump function (ICC 0.71-0.95, CoV 18.3-22.7). Similarly, for the RA, reproducibility was best for reservoir function (ICC 0.76-0.96, CoV 7.5-24.0%) followed by conduit (ICC 0.67-0.91, CoV 13.9-35.9) and booster pump function (ICC 0.73-0.90, CoV 19.4-32.3). Atrial dynamics were not measurably affected by diurnal variation between morning and afternoon scans. Inter-study reproducibility for CMR-based derivation of LA and RA functions is acceptable using either volumetric, strain or SR parameters with LA function showing higher reproducibility than RA function assessment. Amongst the different functional components, reservoir function is most reproducibly assessed by either technique followed by conduit and booster pump function, which needs to be considered in future longitudinal research studies.

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

PubMed Central

2012-01-01

The increasing size and complexity of exome/genome sequencing data requires new tools for clinical geneticists to discover disease-causing variants. Bottlenecks in identifying the causative variation include poor cross-sample querying, constantly changing functional annotation and not considering existing knowledge concerning the phenotype. We describe a methodology that facilitates exploration of patient sequencing data towards identification of causal variants under different genetic hypotheses. Annotate-it facilitates handling, analysis and interpretation of high-throughput single nucleotide variant data. We demonstrate our strategy using three case studies. Annotate-it is freely available and test data are accessible to all users at http://www.annotate-it.org. PMID:23013645

Multidimensional motion measurement of a bimorph-type piezoelectric actuator using a diffraction grating target

NASA Astrophysics Data System (ADS)

Kim, Jong-Ahn; Bae, Eui Won; Kim, Soo Hyun; Kwak, Yoon Keun

2001-09-01

Precision actuators, such as pick-up actuators for HDDs or CD-ROMs, mostly show multidimensional motion. So, to evaluate them more completely, multidimensional measurement is required. Through structural variation and optimization of the design index, the performance of a measurement system can be improved to satisfy the requirement of this application, and so the resolution of each axis is higher than 0.1 μm for translation and 0.5 arcsec for rotation. Using this measurement system, the multidimensional motion and frequency transfer functions of a bimorph-type piezoelectric actuator are obtained.

Temporal Gain Correction for X-Ray Calorimeter Spectrometers

NASA Technical Reports Server (NTRS)

Porter, F. S.; Chiao, M. P.; Eckart, M. E.; Fujimoto, R.; Ishisaki, Y.; Kelley, R. L.; Kilbourne, C. A.; Leutenegger, M. A.; McCammon, D.; Mitsuda, K.

2016-01-01

Calorimetric X-ray detectors are very sensitive to their environment. The boundary conditions can have a profound effect on the gain including heat sink temperature, the local radiation temperature, bias, and the temperature of the readout electronics. Any variation in the boundary conditions can cause temporal variations in the gain of the detector and compromise both the energy scale and the resolving power of the spectrometer. Most production X-ray calorimeter spectrometers, both on the ground and in space, have some means of tracking the gain as a function of time, often using a calibration spectral line. For small gain changes, a linear stretch correction is often sufficient. However, the detectors are intrinsically non-linear and often the event analysis, i.e., shaping, optimal filters etc., add additional non-linearity. Thus for large gain variations or when the best possible precision is required, a linear stretch correction is not sufficient. Here, we discuss a new correction technique based on non-linear interpolation of the energy-scale functions. Using Astro-HSXS calibration data, we demonstrate that the correction can recover the X-ray energy to better than 1 part in 104 over the entire spectral band to above 12 keV even for large-scale gain variations. This method will be used to correct any temporal drift of the on-orbit per-pixel gain using on-board calibration sources for the SXS instrument on the Astro-H observatory.

The neural dynamics of competition resolution for language production in the prefrontal cortex.

PubMed

Bourguignon, Nicolas J; Ohashi, Hiroki; Nguyen, Don; Gracco, Vincent L

2018-03-01

Previous research suggests a pivotal role of the prefrontal cortex (PFC) in word selection during tasks of confrontation naming (CN) and verb generation (VG), both of which feature varying degrees of competition between candidate responses. However, discrepancies in prefrontal activity have also been reported between the two tasks, in particular more widespread and intense activation in VG extending into (left) ventrolateral PFC, the functional significance of which remains unclear. We propose that these variations reflect differences in competition resolution processes tied to distinct underlying lexico-semantic operations: Although CN involves selecting lexical entries out of limited sets of alternatives, VG requires exploration of possible semantic relations not readily evident from the object itself, requiring prefrontal areas previously shown to be recruited in top-down retrieval of information from lexico-semantic memory. We tested this hypothesis through combined independent component analysis of functional imaging data and information-theoretic measurements of variations in selection competition associated with participants' performance in overt CN and VG tasks. Selection competition during CN engaged the anterior insula and surrounding opercular tissue, while competition during VG recruited additional activity of left ventrolateral PFC. These patterns remained after controlling for participants' speech onset latencies indicative of possible task differences in mental effort. These findings have implications for understanding the neural-computational dynamics of cognitive control in language production and how it relates to the functional architecture of adaptive behavior. © 2017 Wiley Periodicals, Inc.

Spacecraft design sensitivity for a disaster warning satellite system

NASA Technical Reports Server (NTRS)

Maloy, J. E.; Provencher, C. E.; Leroy, B. E.; Braley, R. C.; Shumaker, H. A.

1977-01-01

A disaster warning satellite (DWS) is described for warning the general public of impending natural catastrophes. The concept is responsive to NOAA requirements and maximizes the use of ATS-6 technology. Upon completion of concept development, the study was extended to establishing the sensitivity of the DWSS spacecraft power, weight, and cost to variations in both warning and conventional communications functions. The results of this sensitivity analysis are presented.

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

Zhao, Luning; Neuscamman, Eric

We present a modification to variational Monte Carlo’s linear method optimization scheme that addresses a critical memory bottleneck while maintaining compatibility with both the traditional ground state variational principle and our recently-introduced variational principle for excited states. For wave function ansatzes with tens of thousands of variables, our modification reduces the required memory per parallel process from tens of gigabytes to hundreds of megabytes, making the methodology a much better fit for modern supercomputer architectures in which data communication and per-process memory consumption are primary concerns. We verify the efficacy of the new optimization scheme in small molecule tests involvingmore » both the Hilbert space Jastrow antisymmetric geminal power ansatz and real space multi-Slater Jastrow expansions. Satisfied with its performance, we have added the optimizer to the QMCPACK software package, with which we demonstrate on a hydrogen ring a prototype approach for making systematically convergent, non-perturbative predictions of Mott-insulators’ optical band gaps.« less

Adaptive variational mode decomposition method for signal processing based on mode characteristic

NASA Astrophysics Data System (ADS)

Lian, Jijian; Liu, Zhuo; Wang, Haijun; Dong, Xiaofeng

2018-07-01

Variational mode decomposition is a completely non-recursive decomposition model, where all the modes are extracted concurrently. However, the model requires a preset mode number, which limits the adaptability of the method since a large deviation in the number of mode set will cause the discard or mixing of the mode. Hence, a method called Adaptive Variational Mode Decomposition (AVMD) was proposed to automatically determine the mode number based on the characteristic of intrinsic mode function. The method was used to analyze the simulation signals and the measured signals in the hydropower plant. Comparisons have also been conducted to evaluate the performance by using VMD, EMD and EWT. It is indicated that the proposed method has strong adaptability and is robust to noise. It can determine the mode number appropriately without modulation even when the signal frequencies are relatively close.

Average of delta: a new quality control tool for clinical laboratories.

PubMed

Jones, Graham R D

2016-01-01

Average of normals is a tool used to control assay performance using the average of a series of results from patients' samples. Delta checking is a process of identifying errors in individual patient results by reviewing the difference from previous results of the same patient. This paper introduces a novel alternate approach, average of delta, which combines these concepts to use the average of a number of sequential delta values to identify changes in assay performance. Models for average of delta and average of normals were developed in a spreadsheet application. The model assessed the expected scatter of average of delta and average of normals functions and the effect of assay bias for different values of analytical imprecision and within- and between-subject biological variation and the number of samples included in the calculations. The final assessment was the number of patients' samples required to identify an added bias with 90% certainty. The model demonstrated that with larger numbers of delta values, the average of delta function was tighter (lower coefficient of variation). The optimal number of samples for bias detection with average of delta was likely to be between 5 and 20 for most settings and that average of delta outperformed average of normals when the within-subject biological variation was small relative to the between-subject variation. Average of delta provides a possible additional assay quality control tool which theoretical modelling predicts may be more valuable than average of normals for analytes where the group biological variation is wide compared with within-subject variation and where there is a high rate of repeat testing in the laboratory patient population. © The Author(s) 2015.

The diastolic function to cyclic variation of myocardial ultrasonic backscatter relation: the influence of parameterized diastolic filling (PDF) formalism determined chamber properties.

PubMed

Lloyd, Christopher W; Shmuylovich, Leonid; Holland, Mark R; Miller, James G; Kovács, Sándor J

2011-08-01

Myocardial tissue characterization represents an extension of currently available echocardiographic imaging. The systematic variation of backscattered energy during the cardiac cycle (the "cyclic variation" of backscatter) has been employed to characterize cardiac function in a wide range of investigations. However, the mechanisms responsible for observed cyclic variation remain incompletely understood. As a step toward determining the features of cardiac structure and function that are responsible for the observed cyclic variation, the present study makes use of a kinematic approach of diastolic function quantitation to identify diastolic function determinants that influence the magnitude and timing of cyclic variation. Echocardiographic measurements of 32 subjects provided data for determination of the cyclic variation of backscatter to diastolic function relation characterized in terms of E-wave determined, kinematic model-based parameters of chamber stiffness, viscosity/relaxation and load. The normalized time delay of cyclic variation appears to be related to the relative viscoelasticity of the chamber and predictive of the kinematic filling dynamics as determined using the parameterized diastolic filling formalism (with r-values ranging from .44 to .59). The magnitude of cyclic variation does not appear to be strongly related to the kinematic parameters. Copyright © 2011 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Variations of response time in a selective attention task are linked to variations of functional connectivity in the attentional network.

PubMed

Prado, Jérôme; Carp, Joshua; Weissman, Daniel H

2011-01-01

Although variations of response time (RT) within a particular experimental condition are typically ignored, they may sometimes reflect meaningful changes in the efficiency of cognitive and neural processes. In the present study, we investigated whether trial-by-trial variations of response time (RT) in a cross-modal selective attention task were associated with variations of functional connectivity between brain regions that are thought to underlie attention. Sixteen healthy young adults performed an audiovisual selective attention task, which involved attending to a relevant visual letter while ignoring an irrelevant auditory letter, as we recorded their brain activity using functional magnetic resonance imaging (fMRI). In line with predictions, variations of RT were associated with variations of functional connectivity between the anterior cingulate cortex and various other brain regions that are posited to underlie attentional control, such as the right dorsolateral prefrontal cortex and bilateral regions of the posterior parietal cortex. They were also linked to variations of functional connectivity between anatomically early and anatomically late regions of the relevant-modality visual cortex whose communication is thought to be modulated by attentional control processes. By revealing that variations of RT in a selective attention task are linked to variations of functional connectivity in the attentional network, the present findings suggest that variations of attention may contribute to trial-by-trial fluctuations of behavioral performance. Copyright © 2010 Elsevier Inc. All rights reserved.

[Offered income, salary expectations, and the economic activity of married women: an analytic model].

PubMed

Lollivier, S

1984-06-01

This study uses data from tax declarations for 40,000 French households for 1975 to propose a model that permits quantification of the effects of certain significant factors on the economic activity of married women. The PROBIT model of analysis of variance was used to determine the specific effect of several variables, including age of the woman, number of children under 25 years of age in the household, the age of the youngest child, husband's income and socioprofessional status, wife's level and type of education, size of community of residence and region of residence. The principal factors influencing activity rates were found to be educational level, age, and to those of childless women, but activity rates dropped by about 30% for mothers of 2 and even more for mothers of 3 or more children. Influence of the place of residence and the husband's income were associated with lesser disparities. The reasons for variations in female labor force participation can be viewed as analogous to a balance. Underlying factors can increase or decrease the income the woman hopes to earn (offered income) as well as the minimum income for which she will work (required salary). A TOBIT model was constructed in which income was a function of age, education, geographic location, and number of children, and salary required was a function of the variables related to the husband including income and socioprofessional status. For most of the effects considered, the observed variation in activity rates resulted from variations in offered income. The husband's income influences only the desired salary. The offered income decreases and the required salary increases when the number of children is 2 or more, reducing the rate of activity. More educated women have slightly greater salary expectations, but command much higher salaries, resulting in an increased rate of professional activity.

Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics.

PubMed

Miller, Charlotte N; Harper, Andrea L; Trick, Martin; Werner, Peter; Waldron, Keith; Bancroft, Ian

2016-07-16

The current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse (lodge) under the weight of its grain is based on reducing stem height via the introduction of Rht genes. However, these reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Identification of alternative height-control loci is therefore of key interest. In addition, the improvement of stem mechanical strength provides a further way through which lodging can be reduced. To investigate the prospects for genetic alternatives to Rht, we assessed variation for plant height and stem strength properties in a training genetic diversity panel of 100 wheat accessions fixed for Rht. Using mRNAseq data derived from RNA purified from leaves, functional genotypes were developed for the panel comprising 42,066 Single Nucleotide Polymorphism (SNP) markers and 94,060 Gene Expression Markers (GEMs). In the first application in wheat of the recently-developed method of Associative Transcriptomics, we identified associations between trait variation and both SNPs and GEMs. Analysis of marker-trait associations revealed candidates for the causative genes underlying the trait variation, implicating xylan acetylation and the COP9 signalosome as contributing to stem strength and auxin in the control of the observed variation for plant height. Predictive capabilities of key markers for stem strength were validated using a test genetic diversity panel of 30 further wheat accessions. This work illustrates the power of Associative Transcriptomics for the exploration of complex traits of high agronomic importance in wheat. The careful selection of genotypes included in the analysis, allowed for high resolution mapping of novel trait-controlling loci in this staple crop. The use of Gene Expression markers coupled with the more traditional sequence-based markers, provides the power required to understand the biological context of the marker-trait associations observed. This not only adds to the wealth of knowledge that we strive to accumulate regarding gene function and plant adaptation, but also provides breeders with the information required to make more informed decisions regarding the potential consequences of incorporating the use of particular markers into future breeding programmes.

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm

PubMed Central

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis. PMID:27959895

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

PubMed

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

Multichannel blind iterative image restoration.

PubMed

Sroubek, Filip; Flusser, Jan

2003-01-01

Blind image deconvolution is required in many applications of microscopy imaging, remote sensing, and astronomical imaging. Unfortunately in a single-channel framework, serious conceptual and numerical problems are often encountered. Very recently, an eigenvector-based method (EVAM) was proposed for a multichannel framework which determines perfectly convolution masks in a noise-free environment if channel disparity, called co-primeness, is satisfied. We propose a novel iterative algorithm based on recent anisotropic denoising techniques of total variation and a Mumford-Shah functional with the EVAM restoration condition included. A linearization scheme of half-quadratic regularization together with a cell-centered finite difference discretization scheme is used in the algorithm and provides a unified approach to the solution of total variation or Mumford-Shah. The algorithm performs well even on very noisy images and does not require an exact estimation of mask orders. We demonstrate capabilities of the algorithm on synthetic data. Finally, the algorithm is applied to defocused images taken with a digital camera and to data from astronomical ground-based observations of the Sun.

Using an expanding nondirect product harmonic basis with an iterative eigensolver to compute vibrational energy levels with as many as seven atoms.

PubMed

Brown, James; Carrington, Tucker

2016-10-14

We demonstrate that it is possible to use a variational method to compute 50 vibrational levels of ethylene oxide (a seven-atom molecule) with convergence errors less than 0.01 cm -1 . This is done by beginning with a small basis and expanding it to include product basis functions that are deemed to be important. For ethylene oxide a basis with fewer than 3 × 10 6 functions is large enough. Because the resulting basis has no exploitable structure we use a mapping to evaluate the matrix-vector products required to use an iterative eigensolver. The expanded basis is compared to bases obtained from pre-determined pruning condition. Similar calculations are presented for molecules with 3, 4, 5, and 6 atoms. For the 6-atom molecule, CH 3 CH, the required expanded basis has about 106 000 functions and is about an order of magnitude smaller than bases made with a pre-determined pruning condition.

Modeling L2,3-Edge X-ray Absorption Spectroscopy with Real-Time Exact Two-Component Relativistic Time-Dependent Density Functional Theory.

PubMed

Kasper, Joseph M; Lestrange, Patrick J; Stetina, Torin F; Li, Xiaosong

2018-04-10

X-ray absorption spectroscopy is a powerful technique to probe local electronic and nuclear structure. There has been extensive theoretical work modeling K-edge spectra from first principles. However, modeling L-edge spectra directly with density functional theory poses a unique challenge requiring further study. Spin-orbit coupling must be included in the model, and a noncollinear density functional theory is required. Using the real-time exact two-component method, we are able to variationally include one-electron spin-orbit coupling terms when calculating the absorption spectrum. The abilities of different basis sets and density functionals to model spectra for both closed- and open-shell systems are investigated using SiCl 4 and three transition metal complexes, TiCl 4 , CrO 2 Cl 2 , and [FeCl 6 ] 3- . Although we are working in the real-time framework, individual molecular orbital transitions can still be recovered by projecting the density onto the ground state molecular orbital space and separating contributions to the time evolving dipole moment.

A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions

NASA Astrophysics Data System (ADS)

Song, Bongyong; Park, Justin C.; Song, William Y.

2014-11-01

The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7 s, further supporting its clinical applicability.

A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions.

PubMed

Song, Bongyong; Park, Justin C; Song, William Y

2014-11-07

The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires 'at most one function evaluation' in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a 'smoothed TV' or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7 s, further supporting its clinical applicability.

Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas.

PubMed

Irwin, Judith A; Soumpourou, Eleni; Lister, Clare; Ligthart, Jan-Dick; Kennedy, Sue; Dean, Caroline

2016-09-01

Variation in flowering time and response to overwintering has been exploited to breed brassica vegetables that can be harvested year-round. Our knowledge of flowering time control now enables the investigation of the molecular basis of this important variation. Here, we show that a major determinant of heading date variation in Brassica oleracea is from variation in vernalization response through allelic variation at FLOWERING LOCUS C.C2 (BoFLC4). We characterize two alleles of BoFLC.C2 that are both functional and confer a requirement for vernalization, but they show distinct expression dynamics in response to cold. Complementation experiments in Arabidopsis thaliana revealed that the allelic variation results from cis polymorphism at BoFLC.C2, which quantitatively influences the degree of cold-induced epigenetic silencing. This results in one allelic variant conferring consistently later heading under both glasshouse and field conditions through reduced environmental sensitivity. Our results suggest that breeding of brassica varieties for commercially valuable variation in heading date has been achieved through the selection of cis polymorphism at FLC, similar to that underpinning natural variation in A. thaliana. This understanding will allow for the selection of alleles with distinct sensitivities to cold and robust heading dates under variable climatic conditions, and will facilitate the breeding of varieties more resistant to climate change. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Seasonal and Inter-annual Variation in Wood Production in Tropical Trees on Barro Colorado Island, Panama, is Related to Local Climate and Species Functional Traits

NASA Astrophysics Data System (ADS)

Cushman, K.; Muller-Landau, H. C.; Kellner, J. R.; Wright, S. J.; Condit, R.; Detto, M.; Tribble, C. M.

2015-12-01

Tropical forest carbon budgets play a major role in global carbon dynamics, but the responses of tropical forests to current and future inter-annual climatic variation remains highly uncertain. Better predictions of future tropical forest carbon fluxes require an improved understanding of how different species of tropical trees respond to changes in climate at seasonal and inter-annual temporal scales. We installed dendrometer bands on a size-stratified sample of 2000 trees in old growth forest on Barro Colorado Island, Panama, a moist lowland forest that experiences an annual dry season of approximately four months. Tree diameters were measured at the beginning and end of the rainy season since 2008. Additionally, we recorded the canopy illumination level, canopy intactness, and liana coverage of all trees during each census. We used linear mixed-effects models to evaluate how tree growth was related to seasonal and interannual variation in local climate, tree condition, and species identity, and how species identity effects related to tree functional traits. Climatic variables considered included precipitation, solar radiation, soil moisture, and climatological water deficit, and were all calculated from high-quality on-site measurements. Functional traits considered included wood density, maximum adult stature, deciduousness, and drought tolerance. We found that annual wood production was positively related to water availability, with higher growth in wetter years. Species varied in their response to seasonal water availability, with some species showing more pronounced reduction of growth during the dry season when water availability is limited. Interspecific variation in seasonal and interannual growth patterns was related to life-history strategies and species functional traits. The finding of higher growth in wetter years is consistent with previous tree ring studies conducted on a small subset of species with reliable annual rings. Together with previous findings that seed production at this site is higher in sunnier (and drier) years, this suggests strong climate-related shifts in allocation. This study highlights the importance of considering forest species composition and potential allocational shifts when predicting carbon fluxes in response to local climate variation.

Variational Methods in Design Optimization and Sensitivity Analysis for Two-Dimensional Euler Equations

NASA Technical Reports Server (NTRS)

Ibrahim, A. H.; Tiwari, S. N.; Smith, R. E.

1997-01-01

Variational methods (VM) sensitivity analysis employed to derive the costate (adjoint) equations, the transversality conditions, and the functional sensitivity derivatives. In the derivation of the sensitivity equations, the variational methods use the generalized calculus of variations, in which the variable boundary is considered as the design function. The converged solution of the state equations together with the converged solution of the costate equations are integrated along the domain boundary to uniquely determine the functional sensitivity derivatives with respect to the design function. The application of the variational methods to aerodynamic shape optimization problems is demonstrated for internal flow problems at supersonic Mach number range. The study shows, that while maintaining the accuracy of the functional sensitivity derivatives within the reasonable range for engineering prediction purposes, the variational methods show a substantial gain in computational efficiency, i.e., computer time and memory, when compared with the finite difference sensitivity analysis.

Fault tolerant computer control for a Maglev transportation system

NASA Technical Reports Server (NTRS)

Lala, Jaynarayan H.; Nagle, Gail A.; Anagnostopoulos, George

1994-01-01

Magnetically levitated (Maglev) vehicles operating on dedicated guideways at speeds of 500 km/hr are an emerging transportation alternative to short-haul air and high-speed rail. They have the potential to offer a service significantly more dependable than air and with less operating cost than both air and high-speed rail. Maglev transportation derives these benefits by using magnetic forces to suspend a vehicle 8 to 200 mm above the guideway. Magnetic forces are also used for propulsion and guidance. The combination of high speed, short headways, stringent ride quality requirements, and a distributed offboard propulsion system necessitates high levels of automation for the Maglev control and operation. Very high levels of safety and availability will be required for the Maglev control system. This paper describes the mission scenario, functional requirements, and dependability and performance requirements of the Maglev command, control, and communications system. A distributed hierarchical architecture consisting of vehicle on-board computers, wayside zone computers, a central computer facility, and communication links between these entities was synthesized to meet the functional and dependability requirements on the maglev. Two variations of the basic architecture are described: the Smart Vehicle Architecture (SVA) and the Zone Control Architecture (ZCA). Preliminary dependability modeling results are also presented.

Integrating evolutionary and functional approaches to infer adaptation at specific loci.

PubMed

Storz, Jay F; Wheat, Christopher W

2010-09-01

Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally,population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation.

Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations

PubMed Central

Kumar, Sudhir; Dudley, Joel T.; Filipski, Alan; Liu, Li

2011-01-01

Modern technologies have made the sequencing of personal genomes routine. They have revealed thousands of nonsynonymous (amino-acid altering) single nucleotide variants (nSNVs) of protein coding DNA per genome. What do these variants foretell about an individual’s predisposition to diseases? The experimental technologies required to carry out such evaluations at a genomic scale are not yet available. Fortunately, the process of natural selection has lent us an almost infinite set of tests in nature. During the long-term evolution, new mutations and existing variations have been evaluated for their biological consequences in countless species, and outcomes were readily revealed by multispecies genome comparisons. We review studies that have investigated evolutionary characteristics and in silico functional diagnoses of nSNVs found in thousands of disease-associated genes. We conclude that the patterns of long-term evolutionary conservation and permissible divergence are essential and instructive modalities for functional assessment of human genetic variations. PMID:21764165

Genetic background effects in quantitative genetics: gene-by-system interactions.

PubMed

Sardi, Maria; Gasch, Audrey P

2018-04-11

Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype-phenotype relationships across individuals.

A Variational Approach to the Analysis of Dissipative Electromechanical Systems

PubMed Central

Allison, Andrew; Pearce, Charles E. M.; Abbott, Derek

2014-01-01

We develop a method for systematically constructing Lagrangian functions for dissipative mechanical, electrical, and electromechanical systems. We derive the equations of motion for some typical electromechanical systems using deterministic principles that are strictly variational. We do not use any ad hoc features that are added on after the analysis has been completed, such as the Rayleigh dissipation function. We generalise the concept of potential, and define generalised potentials for dissipative lumped system elements. Our innovation offers a unified approach to the analysis of electromechanical systems where there are energy and power terms in both the mechanical and electrical parts of the system. Using our novel technique, we can take advantage of the analytic approach from mechanics, and we can apply these powerful analytical methods to electrical and to electromechanical systems. We can analyse systems that include non-conservative forces. Our methodology is deterministic, and does does require any special intuition, and is thus suitable for automation via a computer-based algebra package. PMID:24586221

Mapping behavioural evolution onto brain evolution: the strategic roles of conserved organization in individuals and species.

PubMed

Finlay, Barbara L; Hinz, Flora; Darlington, Richard B

2011-07-27

The pattern of individual variation in brain component structure in pigs, minks and laboratory mice is very similar to variation across species in the same components, at a reduced scale. This conserved pattern of allometric scaling resembles robotic architectures designed to be robust to changes in computing power and task demands, and may reflect the mechanism by which both growing and evolving brains defend basic sensory, motor and homeostatic functions at multiple scales. Conserved scaling rules also have implications for species-specific sensory and social communication systems, motor competencies and cognitive abilities. The role of relative changes in neuron number in the central nervous system in producing species-specific behaviour is thus highly constrained, while changes in the sensory and motor periphery, and in motivational and attentional systems increase in probability as the principal loci producing important changes in functional neuroanatomy between species. By their nature, these loci require renewed attention to development and life history in the initial organization and production of species-specific behavioural abilities.

Functional variation in the gut microbiome of wild Drosophila populations.

PubMed

Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

2018-05-26

Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Individual variation and the endocrine regulation of behaviour and physiology in birds: a cellular/molecular perspective.

PubMed

Ball, Gregory F; Balthazart, Jacques

2008-05-12

Investigations of the cellular and molecular mechanisms of physiology and behaviour have generally avoided attempts to explain individual differences. The goal has rather been to discover general processes. However, understanding the causes of individual variation in many phenomena of interest to avian eco-physiologists will require a consideration of such mechanisms. For example, in birds, changes in plasma concentrations of steroid hormones are important in the activation of social behaviours related to reproduction and aggression. Attempts to explain individual variation in these behaviours as a function of variation in plasma hormone concentrations have generally failed. Cellular variables related to the effectiveness of steroid hormone have been useful in some cases. Steroid hormone target sensitivity can be affected by variables such as metabolizing enzyme activity, hormone receptor expression as well as receptor cofactor expression. At present, no general theory has emerged that might provide a clear guidance when trying to explain individual variability in birds or in any other group of vertebrates. One strategy is to learn from studies of large units of intraspecific variation such as population or sex differences to provide ideas about variables that might be important in explaining individual variation. This approach along with the use of newly developed molecular genetic tools represents a promising avenue for avian eco-physiologists to pursue.

Development of New Methods for Predicting the Bistatic Electromagnetic Scattering from Absorbing Shapes

DTIC Science & Technology

1990-01-01

least-squares sense by adding a penalty term proportional to the square of the divergence to the variational principle At the start of this project... principle required for stable solutions of the electromagnetic field: It must be possible to express the basis functions used in the finite element method as... principle to derive several different methods for computing stable solutions to electromagnetic field problems. To understand above principle , notice that

Model Sensitivity and Use of the Comparative Finite Element Method in Mammalian Jaw Mechanics: Mandible Performance in the Gray Wolf

PubMed Central

Tseng, Zhijie Jack; Mcnitt-Gray, Jill L.; Flashner, Henryk; Wang, Xiaoming; Enciso, Reyes

2011-01-01

Finite Element Analysis (FEA) is a powerful tool gaining use in studies of biological form and function. This method is particularly conducive to studies of extinct and fossilized organisms, as models can be assigned properties that approximate living tissues. In disciplines where model validation is difficult or impossible, the choice of model parameters and their effects on the results become increasingly important, especially in comparing outputs to infer function. To evaluate the extent to which performance measures are affected by initial model input, we tested the sensitivity of bite force, strain energy, and stress to changes in seven parameters that are required in testing craniodental function with FEA. Simulations were performed on FE models of a Gray Wolf (Canis lupus) mandible. Results showed that unilateral bite force outputs are least affected by the relative ratios of the balancing and working muscles, but only ratios above 0.5 provided balancing-working side joint reaction force relationships that are consistent with experimental data. The constraints modeled at the bite point had the greatest effect on bite force output, but the most appropriate constraint may depend on the study question. Strain energy is least affected by variation in bite point constraint, but larger variations in strain energy values are observed in models with different number of tetrahedral elements, masticatory muscle ratios and muscle subgroups present, and number of material properties. These findings indicate that performance measures are differentially affected by variation in initial model parameters. In the absence of validated input values, FE models can nevertheless provide robust comparisons if these parameters are standardized within a given study to minimize variation that arise during the model-building process. Sensitivity tests incorporated into the study design not only aid in the interpretation of simulation results, but can also provide additional insights on form and function. PMID:21559475

Atmospheric density models

NASA Technical Reports Server (NTRS)

Mueller, A. C.

1977-01-01

An atmospheric model developed by Jacchia, quite accurate but requiring a large amount of computer storage and execution time, was found to be ill-suited for the space shuttle onboard program. The development of a simple atmospheric density model to simulate the Jacchia model was studied. Required characteristics including variation with solar activity, diurnal variation, variation with geomagnetic activity, semiannual variation, and variation with height were met by the new atmospheric density model.

The role of interindividual variation in human carcinogenesis.

PubMed

Lai, C; Shields, P G

1999-02-01

The process of chemical carcinogenesis is a complex multistage process initiated by DNA damage in growth control genes. Carcinogens enter the body from a variety of sources, but most require metabolic activation before they can damage DNA. There are multiple protective processes that include detoxification and conjugation, DNA repair and programmed cell death. Most of these functions exhibit wide interindividual variation in the population and thus are thought to affect cancer risk. The role of gene-environment interactions is being explored, and current data indicate that genetic susceptibilities can modify carcinogen exposures from the diet and tobacco smoking, although much more data exist for the latter. This review addresses the relationships of human carcinogenesis to these interindividual differences of phase I, phase II and DNA repair enzymes.

Total pancreatectomy with islet autotransplantation: an overview

PubMed Central

Ong, Seok L; Gravante, Gianpiero; Pollard, Cristina A; Webb, M'Balu A; Illouz, Severine; Dennison, Ashley R

2009-01-01

Pain control is one of the most challenging aspects in the management of chronic pancreatitis. Total pancreatectomy can successfully relieve the intractable abdominal pain in these patients but will inevitably result in insulin-dependent diabetes. Islet autotransplantation aims to preserve, as far as possible, the insulin secretory function of the islet cell mass thereby reducing (or even removing) the requirement for exogenous insulin administration after a total pancreactomy. Despite the relatively small number of centres able to perform these procedures, there are important technical variations in the details of their approaches. The aim of this review is to provide details of the current surgical practice for total pancreatectomy combined with islet autotransplantation, and outline the potential advantages and disadvantages of the variations adopted in each centre. PMID:20495628

Born iterative reconstruction using perturbed-phase field estimates.

PubMed

Astheimer, Jeffrey P; Waag, Robert C

2008-10-01

A method of image reconstruction from scattering measurements for use in ultrasonic imaging is presented. The method employs distorted-wave Born iteration but does not require using a forward-problem solver or solving large systems of equations. These calculations are avoided by limiting intermediate estimates of medium variations to smooth functions in which the propagated fields can be approximated by phase perturbations derived from variations in a geometric path along rays. The reconstruction itself is formed by a modification of the filtered-backpropagation formula that includes correction terms to account for propagation through an estimated background. Numerical studies that validate the method for parameter ranges of interest in medical applications are presented. The efficiency of this method offers the possibility of real-time imaging from scattering measurements.

Variational and robust density fitting of four-center two-electron integrals in local metrics

NASA Astrophysics Data System (ADS)

Reine, Simen; Tellgren, Erik; Krapp, Andreas; Kjærgaard, Thomas; Helgaker, Trygve; Jansik, Branislav; Høst, Stinne; Salek, Paweł

2008-09-01

Density fitting is an important method for speeding up quantum-chemical calculations. Linear-scaling developments in Hartree-Fock and density-functional theories have highlighted the need for linear-scaling density-fitting schemes. In this paper, we present a robust variational density-fitting scheme that allows for solving the fitting equations in local metrics instead of the traditional Coulomb metric, as required for linear scaling. Results of fitting four-center two-electron integrals in the overlap and the attenuated Gaussian damped Coulomb metric are presented, and we conclude that density fitting can be performed in local metrics at little loss of chemical accuracy. We further propose to use this theory in linear-scaling density-fitting developments.

Variational and robust density fitting of four-center two-electron integrals in local metrics.

PubMed

Reine, Simen; Tellgren, Erik; Krapp, Andreas; Kjaergaard, Thomas; Helgaker, Trygve; Jansik, Branislav; Host, Stinne; Salek, Paweł

2008-09-14

Density fitting is an important method for speeding up quantum-chemical calculations. Linear-scaling developments in Hartree-Fock and density-functional theories have highlighted the need for linear-scaling density-fitting schemes. In this paper, we present a robust variational density-fitting scheme that allows for solving the fitting equations in local metrics instead of the traditional Coulomb metric, as required for linear scaling. Results of fitting four-center two-electron integrals in the overlap and the attenuated Gaussian damped Coulomb metric are presented, and we conclude that density fitting can be performed in local metrics at little loss of chemical accuracy. We further propose to use this theory in linear-scaling density-fitting developments.

Crushing motor patterns in drum (Teleostei: Sciaenidae): functional novelties associated with molluscivory.

PubMed

Grubich, J R

2000-10-01

This study explores the evolution of molluscivory in the marine teleost family Sciaenidae by comparing the motor activity patterns of the pharyngeal muscles of two closely related taxa, the molluscivorous black drum (Pogonias cromis) and the generalist red drum (Sciaenops ocellatus). Muscle activity patterns were recorded simultaneously from eight pharyngeal muscles. Electromyographic (EMG) activity was recorded during feeding on three prey types that varied in shell hardness. Canonical variate and discriminant function analyses were used to describe the distinctness of drum pharyngeal processing behaviors. Discriminant functions built of EMG timing variables were more accurate than muscle activity intensity at identifying cycles by prey type and species. Both drum species demonstrated the ability to modulate pharyngeal motor patterns in response to prey hardness. The mean motor patterns and the canonical variate space of crushing behavior indicated that black drum employed a novel motor pattern during molluscivory. The mollusc-crushing motor pattern of black drum is different from other neoteleost pharyngeal behaviors in lacking upper jaw retraction by the retractor dorsalis muscle. This functional modification suggests that crushing hard-shelled marine bivalves requires a 'vice-like' compression bite in contrast to the shearing forces that are applied to weaker-shelled fiddler crabs by red drum and to freshwater snails by redear sunfish.

Environmental drivers of fish functional diversity and composition in the Lower Colorado River Basin

USGS Publications Warehouse

Pool, T.K.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

2010-01-01

Freshwater conservation efforts require an understanding of how natural and anthropogenic factors shape the present-day biogeography of native and non-native species. This knowledge need is especially acute for imperiled native fishes in the highly modified Lower Colorado River Basin (LCRB), USA. In the present study we employed both a taxonomic and functional approach to explore how natural and human-related environmental drivers shape landscape-scale patterns of fish community composition in the LCRB. Our results showed that hydrologic alteration, watershed land use, and regional climate explained 30.3% and 44.7% of the total variation in fish community taxonomic and functional composition, respectively. Watersheds with greater dam densities and upstream storage capacity supported higher non-native functional diversity, suggesting that dams have provided additional "niche opportunities" for non-native equilibrium life-history strategists by introducing new reservoir habitat and modifying downstream flow and thermal regimes. By contrast, watersheds characterized by greater upstream land protection, lower dam densities, and higher variation in spring and summer precipitation supported fish communities with a strong complement of native species (opportunistic-periodic strategists). In conclusion, our study highlights the utility of a life-history approach to better understand the patterns and processes by which fish communities vary along environmental gradients.

Estimation and Simulation of Slow Crack Growth Parameters from Constant Stress Rate Data

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.; Weaver, Aaron S.

2003-01-01

Closed form, approximate functions for estimating the variances and degrees-of-freedom associated with the slow crack growth parameters n, D, B, and A(sup *) as measured using constant stress rate ('dynamic fatigue') testing were derived by using propagation of errors. Estimates made with the resulting functions and slow crack growth data for a sapphire window were compared to the results of Monte Carlo simulations. The functions for estimation of the variances of the parameters were derived both with and without logarithmic transformation of the initial slow crack growth equations. The transformation was performed to make the functions both more linear and more normal. Comparison of the Monte Carlo results and the closed form expressions derived with propagation of errors indicated that linearization is not required for good estimates of the variances of parameters n and D by the propagation of errors method. However, good estimates variances of the parameters B and A(sup *) could only be made when the starting slow crack growth equation was transformed and the coefficients of variation of the input parameters were not too large. This was partially a result of the skewered distributions of B and A(sup *). Parametric variation of the input parameters was used to determine an acceptable range for using closed form approximate equations derived from propagation of errors.

Autism Spectrum Disorder and intact executive functioning.

PubMed

Ferrara, R; Ansermet, F; Massoni, F; Petrone, L; Onofri, E; Ricci, P; Archer, T; Ricci, S

2016-01-01

Earliest notions concerning autism (Autism Spectrum Disorders, ASD) describe the disturbance in executive functioning. Despite altered definition, executive functioning, expressed as higher cognitive skills required complex behaviors linked to the prefrontal cortex, are defective in autism. Specific difficulties in children presenting autism or verbal disabilities at executive functioning levels have been identified. Nevertheless, the developmental deficit of executive functioning in autism is highly diversified with huge individual variation and may even be absent. The aim of the present study to examine the current standing of intact executive functioning intact in ASD. Analysis of ASD populations, whether high-functioning, Asperger's or autism Broad Phenotype, studied over a range of executive functions including response inhibition, planning, cognitive flexibility, cognitive inhibition, and alerting networks indicates an absence of damage/impairment compared to the typically-developed normal control subjects. These findings of intact executive functioning in ASD subjects provide a strong foundation on which to construct applications for growth environments and the rehabilitation of autistic subjects.

Quantifying heterogeneity in human tumours using MRI and PET.

PubMed

Asselin, Marie-Claude; O'Connor, James P B; Boellaard, Ronald; Thacker, Neil A; Jackson, Alan

2012-03-01

Most tumours, even those of the same histological type and grade, demonstrate considerable biological heterogeneity. Variations in genomic subtype, growth factor expression and local microenvironmental factors can result in regional variations within individual tumours. For example, localised variations in tumour cell proliferation, cell death, metabolic activity and vascular structure will be accompanied by variations in oxygenation status, pH and drug delivery that may directly affect therapeutic response. Documenting and quantifying regional heterogeneity within the tumour requires histological or imaging techniques. There is increasing evidence that quantitative imaging biomarkers can be used in vivo to provide important, reproducible and repeatable estimates of tumoural heterogeneity. In this article we review the imaging methods available to provide appropriate biomarkers of tumour structure and function. We also discuss the significant technical issues involved in the quantitative estimation of heterogeneity and the range of descriptive metrics that can be derived. Finally, we have reviewed the existing clinical evidence that heterogeneity metrics provide additional useful information in drug discovery and development and in clinical practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Schmidt, T.; Zimoch, D.

The operation of an APPLE II based undulator beamline with all its polarization states (linear horizontal and vertical, circular and elliptical, and continous variation of the linear vector) requires an effective description allowing an automated calculation of gap and shift parameter as function of energy and operation mode. The extension of the linear polarization range from 0 to 180 deg. requires 4 shiftable magnet arrrays, permitting use of the APU (adjustable phase undulator) concept. Studies for a pure fixed gap APPLE II for the SLS revealed surprising symmetries between circular and linear polarization modes allowing for simplified operation. A semi-analyticalmore » model covering all types of APPLE II and its implementation will be presented.« less

About APPLE II Operation

NASA Astrophysics Data System (ADS)

Schmidt, T.; Zimoch, D.

2007-01-01

The operation of an APPLE II based undulator beamline with all its polarization states (linear horizontal and vertical, circular and elliptical, and continous variation of the linear vector) requires an effective description allowing an automated calculation of gap and shift parameter as function of energy and operation mode. The extension of the linear polarization range from 0 to 180° requires 4 shiftable magnet arrrays, permitting use of the APU (adjustable phase undulator) concept. Studies for a pure fixed gap APPLE II for the SLS revealed surprising symmetries between circular and linear polarization modes allowing for simplified operation. A semi-analytical model covering all types of APPLE II and its implementation will be presented.

Information transfer satellite concept study. Volume 1: Summary

NASA Technical Reports Server (NTRS)

Bergin, P.; Kincade, C.; Kurpiewski, D.; Leinhaupel, F.; Millican, F.; Onstad, R.

1971-01-01

A wide range of information transfer demands were identified and analyzed. They were then combined into an appropriate set of requirements for satellite communication services. In this process the demands were ranked and combined into single and multipurpose satellite systems. A detailed analysis was performed on each satellite system to determine: total system cost, including both ground and space segments; sensitivities of the systems to various system tradeoffs; and forcing functions which control the system variations. A listing of candidate missions for detailed study is presented, along with a description of the conceptual system design and an identification of the technology developments required to bring these systems to fruition.

Identification of the fitness determinants of budding yeast on a natural substrate

PubMed Central

Filteau, Marie; Charron, Guillaume; Landry, Christian R

2017-01-01

The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway. PMID:27935595

Chemiresistive Graphene Sensors for Ammonia Detection.

PubMed

Mackin, Charles; Schroeder, Vera; Zurutuza, Amaia; Su, Cong; Kong, Jing; Swager, Timothy M; Palacios, Tomás

2018-05-09

The primary objective of this work is to demonstrate a novel sensor system as a convenient vehicle for scaled-up repeatability and the kinetic analysis of a pixelated testbed. This work presents a sensor system capable of measuring hundreds of functionalized graphene sensors in a rapid and convenient fashion. The sensor system makes use of a novel array architecture requiring only one sensor per pixel and no selector transistor. The sensor system is employed specifically for the evaluation of Co(tpfpp)ClO 4 functionalization of graphene sensors for the detection of ammonia as an extension of previous work. Co(tpfpp)ClO 4 treated graphene sensors were found to provide 4-fold increased ammonia sensitivity over pristine graphene sensors. Sensors were also found to exhibit excellent selectivity over interfering compounds such as water and common organic solvents. The ability to monitor a large sensor array with 160 pixels provides insights into performance variations and reproducibility-critical factors in the development of practical sensor systems. All sensors exhibit the same linearly related responses with variations in response exhibiting Gaussian distributions, a key finding for variation modeling and quality engineering purposes. The mean correlation coefficient between sensor responses was found to be 0.999 indicating highly consistent sensor responses and excellent reproducibility of Co(tpfpp)ClO 4 functionalization. A detailed kinetic model is developed to describe sensor response profiles. The model consists of two adsorption mechanisms-one reversible and one irreversible-and is shown capable of fitting experimental data with a mean percent error of 0.01%.

Methodology for Image-Based Reconstruction of Ventricular Geometry for Patient-Specific Modeling of Cardiac Electrophysiology

PubMed Central

Prakosa, A.; Malamas, P.; Zhang, S.; Pashakhanloo, F.; Arevalo, H.; Herzka, D. A.; Lardo, A.; Halperin, H.; McVeigh, E.; Trayanova, N.; Vadakkumpadan, F.

2014-01-01

Patient-specific modeling of ventricular electrophysiology requires an interpolated reconstruction of the 3-dimensional (3D) geometry of the patient ventricles from the low-resolution (Lo-res) clinical images. The goal of this study was to implement a processing pipeline for obtaining the interpolated reconstruction, and thoroughly evaluate the efficacy of this pipeline in comparison with alternative methods. The pipeline implemented here involves contouring the epi- and endocardial boundaries in Lo-res images, interpolating the contours using the variational implicit functions method, and merging the interpolation results to obtain the ventricular reconstruction. Five alternative interpolation methods, namely linear, cubic spline, spherical harmonics, cylindrical harmonics, and shape-based interpolation were implemented for comparison. In the thorough evaluation of the processing pipeline, Hi-res magnetic resonance (MR), computed tomography (CT), and diffusion tensor (DT) MR images from numerous hearts were used. Reconstructions obtained from the Hi-res images were compared with the reconstructions computed by each of the interpolation methods from a sparse sample of the Hi-res contours, which mimicked Lo-res clinical images. Qualitative and quantitative comparison of these ventricular geometry reconstructions showed that the variational implicit functions approach performed better than others. Additionally, the outcomes of electrophysiological simulations (sinus rhythm activation maps and pseudo-ECGs) conducted using models based on the various reconstructions were compared. These electrophysiological simulations demonstrated that our implementation of the variational implicit functions-based method had the best accuracy. PMID:25148771

Variability at the FCGR locus: characterization in Black South Africans and evidence for ethnic variation in and out of Africa.

PubMed

Lassaunière, R; Tiemessen, C T

2016-03-01

This study set out to comprehensively investigate all known functional FcγR variants in South African Black and Caucasian individuals. Population diversity was further assessed using data from the 1000 Genomes Project. In our cohort, Black South Africans neither possessed the haplotypes previously associated with increased surface densities of FcγRIIb and FcγRIIIa nor the FCGR2C haplotype recently associated with increased vaccine efficacy in the RV144 HIV-1 vaccine trial (despite 48.7% bearing the c.134-96T tag allele). Moreover, Africans (South Africans, Luhya Kenyans and Yoruba Nigerians) lack the FCGR2C c.798+1G splice-site allele required for the expression of functional FcγRIIc. Although the presence or absence of surface FcγRIIc did not affect natural killer cell-mediated antibody-dependent cellular cytotoxicity capability, this may be significant for other FcγRIIc-mediated functions. Overall, allele distribution and linkage disequilibrium in Africans and Caucasians differed in a manner that would suggest a differentially maintained balance of FcγR-mediated cell activation in these populations. Finally, significant variation observed among different African populations precludes the use of any one African population as a proxy for FcγR diversity in Africans. In conclusion, the findings of this study highlight further ethnic variation at the FCGR gene locus, in particular for FCGR2C, a gene with increasingly recognized clinical significance.

Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.

PubMed

Cohen, Sarah; Tirindelli, Joëlle; Gomez-Chiarri, Marta; Nacci, Diane

2006-12-01

Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under strong directional selection by pathogens have revealed fascinating cases of MHC allelic disease linkage. More generally in genetically diverse species, however, these linkages may be hard to find. In this paper, we review approaches for assessing functional variation in MHC and discuss their potential use for discovering smaller-scale intraspecific spatial and temporal patterns of MHC variation. Then, we describe and illustrate an approach using the structural model to produce a population composite of variation in antigen-binding regions by mapping population-specific substitutions onto functional regions of the molecule. We are producing models of variation in major histocompatibility (MH) loci for populations of non-migratory fish (killifish, Fundulus heteroclitus) resident at sites that vary dramatically in environmental quality. We discuss the goal of relating MH population variation to functional differences in disease susceptibility such as those inferred by observations of parasitic infection and direct measurement of bacterial challenges in the laboratory. Our study has focused on relatively well-studied killifish populations, including those resident in a highly disturbed, chemically contaminated estuary and nearby less contaminated sites. Population-specific genetic changes at MHC antigen-binding loci are described, and evidence relevant to functional implications of these changes is reviewed. Population-specific patterns of variation in antigen-binding regions in combination with a range of assessments of immune function will provide a powerful new approach to reveal functional changes in MHC.

Variations in body morphology explain sex differences in thermoeffector function during compensable heat stress.

PubMed

Notley, Sean R; Park, Joonhee; Tagami, Kyoko; Ohnishi, Norikazu; Taylor, Nigel A S

2017-05-01

What is the central question of this study? Can sex-related differences in cutaneous vascular and sudomotor responses be explained primarily by variations in the ratio between body surface area and mass during compensable exercise that elicits equivalent heat-loss requirements and mean body temperature changes across participants? What is the main finding and its importance? Mass-specific surface area was a significant determinant of vasomotor and sudomotor responses in men and women, explaining 10-48% of the individual thermoeffector variance. Nonetheless, after accounting for changes in mean body temperature and morphological differences, sex explained only 5% of that inter-individual variability. It was concluded that sex differences in thermoeffector function are morphologically dependent, but not sex dependent. Sex is sometimes thought to be an independent modulator of cutaneous vasomotor and sudomotor function during heat exposure. Nevertheless, it was hypothesized that, when assessed during compensable exercise that evoked equal heat-loss requirements across participants, sex differences in those thermoeffectors would be explained by variations in the ratio between body surface area and mass (specific surface area). To evaluate that possibility, vasomotor and sudomotor functions were assessed in 60 individuals (36 men and 24 women) with widely varying (overlapping) specific surface areas (range, 232.3-292.7 and 241.2-303.1 cm 2  kg -1 , respectively). Subjects completed two trials in compensable conditions (28°C, 36% relative humidity) involving rest (20 min) and steady-state cycling (45 min) at fixed, area-specific metabolic heat-production rates (light, ∼135 W m -2 ; moderate, ∼200 W m -2 ). Equivalent heat-loss requirements and mean body temperature changes were evoked across participants. Forearm blood flow and vascular conductance were positively related to specific surface area during light work in men (r = 0.67 and r = 0.66, respectively; both P < 0.05) and during both exercise intensities in women (light, r = 0.57 and r = 0.69; and moderate, r = 0.64 and r = 0.68; all P < 0.05). Whole-body and local sweat rates were negatively related to that ratio (correlation coefficient range, -0.33 to -0.62; all P < 0.05) during both work rates in men and women. Those relationships accounted for 10-48% of inter-individual thermoeffector variance (P < 0.05). Furthermore, after accounting for morphological differences, sex explained no more than 5% of that variability (P < 0.05). It was concluded that, when assessed during compensable exercise, sex differences in thermoeffector function were largely determined morphologically, rather than being sex dependent. © 2017 The Authors. Experimental Physiology © 2017 The Physiological Society.

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

PubMed Central

Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

2014-01-01

The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782

Conformal gravity holography in four dimensions.

PubMed

Grumiller, Daniel; Irakleidou, Maria; Lovrekovic, Iva; McNees, Robert

2014-03-21

We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a "partially massless response". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair.

The Cluster Variation Method: A Primer for Neuroscientists.

PubMed

Maren, Alianna J

2016-09-30

Effective Brain-Computer Interfaces (BCIs) require that the time-varying activation patterns of 2-D neural ensembles be modelled. The cluster variation method (CVM) offers a means for the characterization of 2-D local pattern distributions. This paper provides neuroscientists and BCI researchers with a CVM tutorial that will help them to understand how the CVM statistical thermodynamics formulation can model 2-D pattern distributions expressing structural and functional dynamics in the brain. The premise is that local-in-time free energy minimization works alongside neural connectivity adaptation, supporting the development and stabilization of consistent stimulus-specific responsive activation patterns. The equilibrium distribution of local patterns, or configuration variables , is defined in terms of a single interaction enthalpy parameter ( h ) for the case of an equiprobable distribution of bistate (neural/neural ensemble) units. Thus, either one enthalpy parameter (or two, for the case of non-equiprobable distribution) yields equilibrium configuration variable values. Modeling 2-D neural activation distribution patterns with the representational layer of a computational engine, we can thus correlate variational free energy minimization with specific configuration variable distributions. The CVM triplet configuration variables also map well to the notion of a M = 3 functional motif. This paper addresses the special case of an equiprobable unit distribution, for which an analytic solution can be found.

Systematic Analysis of the Genetic Variability That Impacts SUMO Conjugation and Their Involvement in Human Diseases

NASA Astrophysics Data System (ADS)

Xu, Hao-Dong; Shi, Shao-Ping; Chen, Xiang; Qiu, Jian-Ding

2015-07-01

Protein function has been observed to rely on select essential sites instead of requiring all sites to be indispensable. Small ubiquitin-related modifier (SUMO) conjugation or sumoylation, which is a highly dynamic reversible process and its outcomes are extremely diverse, ranging from changes in localization to altered activity and, in some cases, stability of the modified, has shown to be especially valuable in cellular biology. Motivated by the significance of SUMO conjugation in biological processes, we report here on the first exploratory assessment whether sumoylation related genetic variability impacts protein functions as well as the occurrence of diseases related to SUMO. Here, we defined the SUMOAMVR as sumoylation related amino acid variations that affect sumoylation sites or enzymes involved in the process of connectivity, and categorized four types of potential SUMOAMVRs. We detected that 17.13% of amino acid variations are potential SUMOAMVRs and 4.83% of disease mutations could lead to SUMOAMVR with our system. More interestingly, the statistical analysis demonstrates that the amino acid variations that directly create new potential lysine sumoylation sites are more likely to cause diseases. It can be anticipated that our method can provide more instructive guidance to identify the mechanisms of genetic diseases.

The Cluster Variation Method: A Primer for Neuroscientists

PubMed Central

Maren, Alianna J.

2016-01-01

Effective Brain–Computer Interfaces (BCIs) require that the time-varying activation patterns of 2-D neural ensembles be modelled. The cluster variation method (CVM) offers a means for the characterization of 2-D local pattern distributions. This paper provides neuroscientists and BCI researchers with a CVM tutorial that will help them to understand how the CVM statistical thermodynamics formulation can model 2-D pattern distributions expressing structural and functional dynamics in the brain. The premise is that local-in-time free energy minimization works alongside neural connectivity adaptation, supporting the development and stabilization of consistent stimulus-specific responsive activation patterns. The equilibrium distribution of local patterns, or configuration variables, is defined in terms of a single interaction enthalpy parameter (h) for the case of an equiprobable distribution of bistate (neural/neural ensemble) units. Thus, either one enthalpy parameter (or two, for the case of non-equiprobable distribution) yields equilibrium configuration variable values. Modeling 2-D neural activation distribution patterns with the representational layer of a computational engine, we can thus correlate variational free energy minimization with specific configuration variable distributions. The CVM triplet configuration variables also map well to the notion of a M = 3 functional motif. This paper addresses the special case of an equiprobable unit distribution, for which an analytic solution can be found. PMID:27706022

Defining Genetic Risk for GVHD and Mortality Following Allogeneic Hematopoietic Stem Cell Transplantation

PubMed Central

Hansen, John A; Chien, Jason W; Warren, Edus H; Zhao, Lue Ping; Martin, Paul J

2011-01-01

Purpose of review To explore what is known about the genetics of hematopoietic stem cell transplantation (HCT) and how genetic polymorphism affects risk of graft-versus-host disease (GVHD) and mortality. Recent findings Genetic variation found across the human genome can impact HCT outcome by 1) causing genetic disparity between patient and donor, and 2) modifying gene function. Single nucleotide polymorphisms (SNP) and structural variation can result in mismatching for cellular peptides known as histocompatibility antigens (HA). At least 25 to 30 polymorphic genes are known to encode functional HA in mismatched individuals, but their individual contribution to clinical GVHD is unclear. HCT outcome may also be affected by polymorphism in donor or recipient. Association studies have implicated several genes with GVHD and mortality, however results have been inconsistent most likely due to limited sample size, and differences in racial diversity and clinical covariates. New technologies using DNA arrays genotyping for a million or more SNPs promise genome-wide discovery of HCT associated genes, however adequate statistical power requires study populations of several thousand patient-donor pairs. Summary Available data offers strong preliminary support for the impact that genetic variation has on risk of GVHD and mortality following HCT. Definitive results however await future genome-wide studies of large multi-center HCT cohorts. PMID:20827186

The Challenging Pupil in the Classroom: Child Effects on Teachers

PubMed Central

Houts, Renate M.; Caspi, Avshalom; Pianta, Robert C.; Arseneault, Louise; Moffitt, Terrie E.

2012-01-01

Teaching children requires effort and some children naturally require more effort than others. This study tests whether teacher effort devoted to individual children varies as a function of children’s personal characteristics. Using a nation-wide longitudinal study of twins followed between ages 5-12 years, we asked teachers about the effort they invested in each child enrolled in our study. We found that teacher effort was a function of heritable child characteristics; that children’s challenging behavior assessed at age 5 predicted teacher effort at age 12; and that challenging child behavior and teacher effort share common etiology in children’s genes. While child effects accounted for a significant proportion of variance in teacher effort, we also found variation that could not be attributed to children’s behavior. Treating children with challenging behavior and enhancing teachers’ skills in behavior management could increase the time and energy teachers have to deliver curriculum in their classrooms. PMID:21078897

Linking plant and ecosystem functional biogeography.

PubMed

Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D; Kattge, Jens; Baldocchi, Dennis D

2014-09-23

Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere-atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches.

Linking plant and ecosystem functional biogeography

PubMed Central

Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D.; Kattge, Jens; Baldocchi, Dennis D.

2014-01-01

Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere–atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches. PMID:25225392

Using the Screened Coulomb Potential to Illustrate the Variational Method

ERIC Educational Resources Information Center

Zuniga, Jose; Bastida, Adolfo; Requena, Alberto

2012-01-01

The screened Coulomb potential, or Yukawa potential, is used to illustrate the application of the single and linear variational methods. The trial variational functions are expressed in terms of Slater-type functions, for which the integrals needed to carry out the variational calculations are easily evaluated in closed form. The variational…

Silicon photonic integrated circuits with electrically programmable non-volatile memory functions.

PubMed

Song, J-F; Lim, A E-J; Luo, X-S; Fang, Q; Li, C; Jia, L X; Tu, X-G; Huang, Y; Zhou, H-F; Liow, T-Y; Lo, G-Q

2016-09-19

Conventional silicon photonic integrated circuits do not normally possess memory functions, which require on-chip power in order to maintain circuit states in tuned or field-configured switching routes. In this context, we present an electrically programmable add/drop microring resonator with a wavelength shift of 426 pm between the ON/OFF states. Electrical pulses are used to control the choice of the state. Our experimental results show a wavelength shift of 2.8 pm/ms and a light intensity variation of ~0.12 dB/ms for a fixed wavelength in the OFF state. Theoretically, our device can accommodate up to 65 states of multi-level memory functions. Such memory functions can be integrated into wavelength division mutiplexing (WDM) filters and applied to optical routers and computing architectures fulfilling large data downloading demands.

Quantitative secondary electron imaging for work function extraction at atomic level and layer identification of graphene

PubMed Central

Zhou, Yangbo; Fox, Daniel S; Maguire, Pierce; O’Connell, Robert; Masters, Robert; Rodenburg, Cornelia; Wu, Hanchun; Dapor, Maurizio; Chen, Ying; Zhang, Hongzhou

2016-01-01

Two-dimensional (2D) materials usually have a layer-dependent work function, which require fast and accurate detection for the evaluation of their device performance. A detection technique with high throughput and high spatial resolution has not yet been explored. Using a scanning electron microscope, we have developed and implemented a quantitative analytical technique which allows effective extraction of the work function of graphene. This technique uses the secondary electron contrast and has nanometre-resolved layer information. The measurement of few-layer graphene flakes shows the variation of work function between graphene layers with a precision of less than 10 meV. It is expected that this technique will prove extremely useful for researchers in a broad range of fields due to its revolutionary throughput and accuracy. PMID:26878907

Spatial variation and seasonal dynamics of leaf-area index in the arctic tundra-implications for linking ground observations and satellite images

NASA Astrophysics Data System (ADS)

Juutinen, Sari; Virtanen, Tarmo; Kondratyev, Vladimir; Laurila, Tuomas; Linkosalmi, Maiju; Mikola, Juha; Nyman, Johanna; Räsänen, Aleksi; Tuovinen, Juha-Pekka; Aurela, Mika

2017-09-01

Vegetation in the arctic tundra typically consists of a small-scale mosaic of plant communities, with species differing in growth forms, seasonality, and biogeochemical properties. Characterization of this variation is essential for understanding and modeling the functioning of the arctic tundra in global carbon cycling, as well as for evaluating the resolution requirements for remote sensing. Our objective was to quantify the seasonal development of the leaf-area index (LAI) and its variation among plant communities in the arctic tundra near Tiksi, coastal Siberia, consisting of graminoid, dwarf shrub, moss, and lichen vegetation. We measured the LAI in the field and used two very-high-spatial resolution multispectral satellite images (QuickBird and WorldView-2), acquired at different phenological stages, to predict landscape-scale patterns. We used the empirical relationships between the plant community-specific LAI and degree-day accumulation (0 °C threshold) and quantified the relationship between the LAI and satellite NDVI (normalized difference vegetation index). Due to the temporal difference between the field data and satellite images, the LAI was approximated for the imagery dates, using the empirical model. LAI explained variation in the NDVI values well (R 2 adj. 0.42-0.92). Of the plant functional types, the graminoid LAI showed the largest seasonal amplitudes and was the main cause of the varying spatial patterns of the NDVI and the related LAI between the two images. Our results illustrate how the short growing season, rapid development of the LAI, yearly climatic variation, and timing of the satellite data should be accounted for in matching imagery and field verification data in the Arctic region.

Genetic enhancement of cognition in a kindred with cone–rod dystrophy due to RIMS1 mutation

PubMed Central

Sisodiya, Sanjay M; Thompson, Pamela J; Need, Anna; Harris, Sarah E; Weale, Michael E; Wilkie, Susan E; Michaelides, Michel; Free, Samantha L; Walley, Nicole; Gumbs, Curtis; Gerrelli, Dianne; Ruddle, Piers; Whalley, Lawrence J; Starr, John M; Hunt, David M; Goldstein, David B; Deary, Ian J; Moore, Anthony T

2007-01-01

Background The genetic basis of variation in human cognitive abilities is poorly understood. RIMS1 encodes a synapse active‐zone protein with important roles in the maintenance of normal synaptic function: mice lacking this protein have greatly reduced learning ability and memory function. Objective An established paradigm examining the structural and functional effects of mutations in genes expressed in the eye and the brain was used to study a kindred with an inherited retinal dystrophy due to RIMS1 mutation. Materials and methods Neuropsychological tests and high‐resolution MRI brain scanning were undertaken in the kindred. In a population cohort, neuropsychological scores were associated with common variation in RIMS1. Additionally, RIMS1 was sequenced in top‐scoring individuals. Evolution of RIMS1 was assessed, and its expression in developing human brain was studied. Results Affected individuals showed significantly enhanced cognitive abilities across a range of domains. Analysis suggests that factors other than RIMS1 mutation were unlikely to explain enhanced cognition. No association with common variation and verbal IQ was found in the population cohort, and no other mutations in RIMS1 were detected in the highest scoring individuals from this cohort. RIMS1 protein is expressed in developing human brain, but RIMS1 does not seem to have been subjected to accelerated evolution in man. Conclusions A possible role for RIMS1 in the enhancement of cognitive function at least in this kindred is suggested. Although further work is clearly required to explore these findings before a role for RIMS1 in human cognition can be formally accepted, the findings suggest that genetic mutation may enhance human cognition in some cases. PMID:17237123

27 CFR 25.52 - Variations from requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Variations from requirements. 25.52 Section 25.52 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS BEER Miscellaneous Provisions § 25.52 Variations from...

27 CFR 25.52 - Variations from requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Variations from requirements. 25.52 Section 25.52 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL BEER Miscellaneous Provisions § 25.52 Variations from...

27 CFR 25.52 - Variations from requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Variations from requirements. 25.52 Section 25.52 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS BEER Miscellaneous Provisions § 25.52 Variations from...

27 CFR 25.52 - Variations from requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Variations from requirements. 25.52 Section 25.52 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS BEER Miscellaneous Provisions § 25.52 Variations from...

Determination of wave-function functionals: The constrained-search variational method

NASA Astrophysics Data System (ADS)

Pan, Xiao-Yin; Sahni, Viraht; Massa, Lou

2005-09-01

In a recent paper [Phys. Rev. Lett. 93, 130401 (2004)], we proposed the idea of expanding the space of variations in variational calculations of the energy by considering the approximate wave function ψ to be a functional of functions χ , ψ=ψ[χ] , rather than a function. A constrained search is first performed over all functions χ such that the wave-function functional ψ[χ] satisfies a physical constraint or leads to the known value of an observable. A rigorous upper bound to the energy is then obtained via the variational principle. In this paper we generalize the constrained-search variational method, applicable to both ground and excited states, to the determination of arbitrary Hermitian single-particle operators as applied to two-electron atomic and ionic systems. We construct analytical three-parameter ground-state functionals for the H- ion and the He atom through the constraint of normalization. We present the results for the total energy E , the expectations of the single-particle operators W=∑irin , n=-2,-1,1,2 , W=∑iδ(ri) , and W=∑iδ(ri-r) , the structure of the nonlocal Coulomb hole charge ρc(rr') , and the expectations of the two particle operators u2,u,1/u,1/u2 , where u=∣ri-rj∣ . The results for all the expectation values are remarkably accurate when compared with the 1078-parameter wave function of Pekeris, and other wave functions that are not functionals. We conclude by describing our current work on how the constrained-search variational method in conjunction with quantal density-functional theory is being applied to the many-electron case.

Definition of Specific Functions and Procedural Skills Required by Cuban Specialists in Intensive Care and Emergency Medicine.

PubMed

Véliz, Pedro L; Berra, Esperanza M; Jorna, Ana R

2015-07-01

INTRODUCTION Medical specialties' core curricula should take into account functions to be carried out, positions to be filled and populations to be served. The functions in the professional profile for specialty training of Cuban intensive care and emergency medicine specialists do not include all the activities that they actually perform in professional practice. OBJECTIVE Define the specific functions and procedural skills required of Cuban specialists in intensive care and emergency medicine. METHODS The study was conducted from April 2011 to September 2013. A three-stage methodological strategy was designed using qualitative techniques. By purposive maximum variation sampling, 82 professionals were selected. Documentary analysis and key informant criteria were used in the first stage. Two expert groups were formed in the second stage: one used various group techniques (focus group, oral and written brainstorming) and the second used a three-round Delphi method. In the final stage, a third group of experts was questioned in semistructured in-depth interviews, and a two-round Delphi method was employed to assess priorities. RESULTS Ultimately, 78 specific functions were defined: 47 (60.3%) patient care, 16 (20.5%) managerial, 6 (7.7%) teaching, and 9 (11.5%) research. Thirty-one procedural skills were identified. The specific functions and procedural skills defined relate to the profession's requirements in clinical care of the critically ill, management of patient services, teaching and research at the specialist's different occupational levels. CONCLUSIONS The specific functions and procedural skills required of intensive care and emergency medicine specialists were precisely identified by a scientific method. This product is key to improving the quality of teaching, research, administration and patient care in this specialty in Cuba. The specific functions and procedural skills identified are theoretical, practical, methodological and social contributions to inform future curricular reform and to help intensive care specialists enhance their performance in comprehensive patient care. KEYWORDS Intensive care, urgent care, emergency medicine, continuing medical education, curriculum, diagnostic techniques and procedures, medical residency, Cuba.

From field to region yield predictions in response to pedo-climatic variations in Eastern Canada

NASA Astrophysics Data System (ADS)

JÉGO, G.; Pattey, E.; Liu, J.

2013-12-01

The increase in global population coupled with new pressures to produce energy and bioproducts from agricultural land requires an increase in crop productivity. However, the influence of climate and soil variations on crop production and environmental performance is not fully understood and accounted for to define more sustainable and economical management strategies. Regional crop modeling can be a great tool for understanding the impact of climate variations on crop production, for planning grain handling and for assessing the impact of agriculture on the environment, but it is often limited by the availability of input data. The STICS ("Simulateur mulTIdisciplinaire pour les Cultures Standard") crop model, developed by INRA (France) is a functional crop model which has a built-in module to optimize several input parameters by minimizing the difference between calculated and measured output variables, such as Leaf Area Index (LAI). STICS crop model was adapted to the short growing season of the Mixedwood Plains Ecozone using field experiments results, to predict biomass and yield of soybean, spring wheat and corn. To minimize the numbers of inference required for regional applications, 'generic' cultivars rather than specific ones have been calibrated in STICS. After the calibration of several model parameters, the root mean square error (RMSE) of yield and biomass predictions ranged from 10% to 30% for the three crops. A bit more scattering was obtained for LAI (20%

Intra-specific diversity of Serratia marcescens in Anopheles mosquito midgut defines Plasmodium transmission capacity

PubMed Central

Bando, Hironori; Okado, Kiyoshi; Guelbeogo, Wamdaogo M.; Badolo, Athanase; Aonuma, Hiroka; Nelson, Bryce; Fukumoto, Shinya; Xuan, Xuenan; Sagnon, N'Fale; Kanuka, Hirotaka

2013-01-01

A critical stage in malaria transmission occurs in the Anopheles mosquito midgut, when the malaria parasite, Plasmodium, ingested with blood, first makes contact with the gut epithelial surface. To understand the response mechanisms within the midgut environment, including those influenced by resident microbiota against Plasmodium, we focus on a midgut bacteria species' intra-specific variation that confers diversity to the mosquito's competency for malaria transmission. Serratia marcescens isolated from either laboratory-reared mosquitoes or wild populations in Burkina Faso shows great phenotypic variation in its cellular and structural features. Importantly, this variation is directly correlated with its ability to inhibit Plasmodium development within the mosquito midgut. Furthermore, this anti-Plasmodium function conferred by Serratia marcescens requires increased expression of the flagellum biosynthetic pathway that is modulated by the motility master regulatory operon, flhDC. These findings point to new strategies for controlling malaria through genetic manipulation of midgut bacteria within the mosquito. PMID:23571408

Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence.

PubMed

Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

2017-08-16

Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations. © 2017 Botanical Society of America.

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

Error Analysis of Wind Measurements for the University of Illinois Sodium Doppler Temperature System

NASA Technical Reports Server (NTRS)

Pfenninger, W. Matthew; Papen, George C.

1992-01-01

Four-frequency lidar measurements of temperature and wind velocity require accurate frequency tuning to an absolute reference and long term frequency stability. We quantify frequency tuning errors for the Illinois sodium system, to measure absolute frequencies and a reference interferometer to measure relative frequencies. To determine laser tuning errors, we monitor the vapor cell and interferometer during lidar data acquisition and analyze the two signals for variations as functions of time. Both sodium cell and interferometer are the same as those used to frequency tune the laser. By quantifying the frequency variations of the laser during data acquisition, an error analysis of temperature and wind measurements can be calculated. These error bounds determine the confidence in the calculated temperatures and wind velocities.

An interative solution of an integral equation for radiative transfer by using variational technique

NASA Technical Reports Server (NTRS)

Yoshikawa, K. K.

1973-01-01

An effective iterative technique is introduced to solve a nonlinear integral equation frequently associated with radiative transfer problems. The problem is formulated in such a way that each step of an iterative sequence requires the solution of a linear integral equation. The advantage of a previously introduced variational technique which utilizes a stepwise constant trial function is exploited to cope with the nonlinear problem. The method is simple and straightforward. Rapid convergence is obtained by employing a linear interpolation of the iterative solutions. Using absorption coefficients of the Milne-Eddington type, which are applicable to some planetary atmospheric radiation problems. Solutions are found in terms of temperature and radiative flux. These solutions are presented numerically and show excellent agreement with other numerical solutions.

Born iterative reconstruction using perturbed-phase field estimates

PubMed Central

Astheimer, Jeffrey P.; Waag, Robert C.

2008-01-01

A method of image reconstruction from scattering measurements for use in ultrasonic imaging is presented. The method employs distorted-wave Born iteration but does not require using a forward-problem solver or solving large systems of equations. These calculations are avoided by limiting intermediate estimates of medium variations to smooth functions in which the propagated fields can be approximated by phase perturbations derived from variations in a geometric path along rays. The reconstruction itself is formed by a modification of the filtered-backpropagation formula that includes correction terms to account for propagation through an estimated background. Numerical studies that validate the method for parameter ranges of interest in medical applications are presented. The efficiency of this method offers the possibility of real-time imaging from scattering measurements. PMID:19062873

Orion Burn Management, Nominal and Response to Failures

NASA Technical Reports Server (NTRS)

Odegard, Ryan; Goodman, John L.; Barrett, Charles P.; Pohlkamp, Kara; Robinson, Shane

2016-01-01

An approach for managing Orion on-orbit burn execution is described for nominal and failure response scenarios. The burn management strategy for Orion takes into account per-burn variations in targeting, timing, and execution; crew and ground operator intervention and overrides; defined burn failure triggers and responses; and corresponding on-board software sequencing functionality. Burn-to- burn variations are managed through the identification of specific parameters that may be updated for each progressive burn. Failure triggers and automatic responses during the burn timeframe are defined to provide safety for the crew in the case of vehicle failures, along with override capabilities to ensure operational control of the vehicle. On-board sequencing software provides the timeline coordination for performing the required activities related to targeting, burn execution, and responding to burn failures.

Does shape co-variation between the skull and the mandible have functional consequences? A 3D approach for a 3D problem

PubMed Central

Cornette, Raphaël; Baylac, Michel; Souter, Thibaud; Herrel, Anthony

2013-01-01

Morpho-functional patterns are important drivers of phenotypic diversity given their importance in a fitness-related context. Although modularity of the mandible and skull has been studied extensively in mammals, few studies have explored shape co-variation between these two structures. Despite being developmentally independent, the skull and mandible form a functionally integrated unit. In the present paper we use 3D surface geometric morphometric methods allowing us to explore the form of both skull and mandible in its 3D complexity using the greater white-toothed shrew as a model. This approach allows an accurate 3D description of zones devoid of anatomical landmarks that are functionally important. Two-block partial least-squares approaches were used to describe the co-variation of form between skull and mandible. Moreover, a 3D biomechanical model was used to explore the functional consequences of the observed patterns of co-variation. Our results show the efficiency of the method in investigations of complex morpho-functional patterns. Indeed, the description of shape co-variation between the skull and the mandible highlighted the location and the intensity of their functional relationships through the jaw adductor muscles linking these two structures. Our results also demonstrated that shape co-variation in form between the skull and mandible has direct functional consequences on the recruitment of muscles during biting. PMID:23964811

Defibrillation depends on conductivity fluctuations and the degree of disorganization in reentry patterns.

PubMed

Plank, Gernot; Leon, L Joshua; Kimber, Shane; Vigmond, Edward J

2005-02-01

Defibrillation depends on conductivity and disorganization. Cardiac fibrillation is the deterioration of the heart's normally well-organized activity into one or more meandering spiral waves, which subsequently break up into many meandering wave fronts. Delivery of an electric shock (defibrillation) is the only effective way of restoring the normal rhythm. This study focuses on examining whether higher degrees of disorganization requires higher shock strengths to defibrillate and whether microscopic conductivity fluctuations favor shock success. We developed a three-dimensional computer bidomain model of a block of cardiac tissue with straight fibers immersed in a conductive bath. The membrane behavior was described by the Courtemanche human atrial action potential model incorporating electroporation and an acetylcholine- (ACh) dependent potassium current. Intracellular conductivities were varied stochastically around nominal values with variations of up to 50%. A single rotor reentry was initiated and, by adjusting the spatial ACh variation, the level of organization could be controlled. The single rotor could be stabilized or spiral wave breakup could be provoked leading to fibrillatory-like activity. For each level of organization, multiple shock timings and strengths were applied to compute the probability of shock success as a function of shock strength. Our results suggest that the level of the small-scale conductivity fluctuations is a very important factor in defibrillation. A higher variation significantly lowers the required shock strength. Further, we demonstrated that success also heavily depends on the level of organization of the fibrillatory episode. In general, higher levels of disorganization require higher shock strengths to defibrillate.

Higher biodiversity is required to sustain multiple ecosystem processes across temperature regimes

PubMed Central

Perkins, Daniel M; Bailey, R A; Dossena, Matteo; Gamfeldt, Lars; Reiss, Julia; Trimmer, Mark; Woodward, Guy

2015-01-01

Biodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1–4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive-based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment. PMID:25131335

Tuning up mind's pattern to nature's own idea: Eddington's early twenties case for variational derivatives

NASA Astrophysics Data System (ADS)

Smadja, Ivahn

This paper sets out to show how Eddington's early twenties case for variational derivatives significantly bears witness to a steady and consistent shift in focus from a resolute striving for objectivity towards "selective subjectivism" and structuralism. While framing his so-called "Hamiltonian derivatives" along the lines of previously available variational methods allowing to derive gravitational field equations from an action principle, Eddington assigned them a theoretical function of his own devising in The Mathematical Theory of Relativity (1923). I make clear that two stages should be marked out in Eddington's train of thought if the meaning of such variational derivatives is to be adequately assessed. As far as they were originally intended to embody the mind's collusion with nature by linking atomicity of matter with atomicity of action, variational derivatives were at first assigned a dual role requiring of them not only to express mind's craving for permanence but also to tune up mind's privileged pattern to "Nature's own idea". Whereas at a later stage, as affine field theory would provide a framework for world-building, such "Hamiltonian differentiation" would grow out of tune through gauge-invariance and, by disregarding how mathematical theory might precisely come into contact with actual world, would be turned into a mere heuristic device for structural knowledge.

Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms

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

Pederson, Mark R., E-mail: mark.pederson@science.doe.gov

2015-02-14

A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeitmore » slightly too low.« less

The design and function of birds' nests

PubMed Central

Mainwaring, Mark C; Hartley, Ian R; Lambrechts, Marcel M; Deeming, D Charles

2014-01-01

All birds construct nests in which to lay eggs and/or raise offspring. Traditionally, it was thought that natural selection and the requirement to minimize the risk of predation determined the design of completed nests. However, it is becoming increasingly apparent that sexual selection also influences nest design. This is an important development as while species such as bowerbirds build structures that are extended phenotypic signals whose sole purpose is to attract a mate, nests contain eggs and/or offspring, thereby suggesting a direct trade-off between the conflicting requirements of natural and sexual selection. Nest design also varies adaptively in order to both minimize the detrimental effects of parasites and to create a suitable microclimate for parents and developing offspring in relation to predictable variation in environmental conditions. Our understanding of the design and function of birds' nests has increased considerably in recent years, and the evidence suggests that nests have four nonmutually exclusive functions. Consequently, we conclude that the design of birds' nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s. PMID:25505520

Genetics of Inflammatory Bowel Diseases

PubMed Central

McGovern, Dermot; Kugathasan, Subra; Cho, Judy H.

2015-01-01

In this Review, we provide an update on genome-wide association studies (GWAS) in inflammatory bowel disease (IBD). In addition, we summarize progress in defining the functional consequences of associated alleles for coding and non-coding genetic variation. In the small minority of loci where major association signals correspond to non-synonymous variation, we summarize studies defining their functional effects and implications for therapeutic targeting. Importantly, the large majority of GWAS-associated loci involve non-coding variation, many of which modulate levels of gene expression. Recent expression quantitative trait loci (eQTL) studies have established that expression of the large majority of human genes is regulated by non-coding genetic variation. Significant advances in defining the epigenetic landscape have demonstrated that IBD GWAS signals are highly enriched within cell-specific active enhancer marks. Studies in European ancestry populations have dominated the landscape of IBD genetics studies, but increasingly, studies in Asian and African-American populations are being reported. Common variation accounts for only a modest fraction of the predicted heritability and the role of rare genetic variation of higher effects (i.e. odds ratios markedly deviating from one) is increasingly being identified through sequencing efforts. These sequencing studies have been particularly productive in very-early onset, more severe cases. A major challenge in IBD genetics will be harnessing the vast array of genetic discovery for clinical utility, through emerging precision medicine initiatives. We discuss the rapidly evolving area of direct to consumer genetic testing, as well as the current utility of clinical exome sequencing, especially in very early onset, severe IBD cases. We summarize recent progress in the pharmacogenetics of IBD with respect of partitioning patient responses to anti-TNF and thiopurine therapies. Highly collaborative studies across research centers and across subspecialties and disciplines will be required to fully realize the promise of genetic discovery in IBD. PMID:26255561

Molecular characterization of phosphorylcholine expression on the lipooligosaccharide of Histophilus somni.

PubMed

Elswaifi, Shaadi F; St Michael, Frank; Sreenivas, Avula; Cox, Andrew; Carman, George M; Inzana, Thomas J

2009-10-01

Histophilus somni (Haemophilus somnus) is an important pathogen of cattle that is responsible for respiratory disease, septicemia, and systemic diseases such as thrombotic meningoencephalitis, myocarditis, and abortion. A variety of virulence factors have been identified in H. somni, including compositional and antigenic variation of the lipooligosaccharide (LOS). Phosphorylcholine (ChoP) has been identified as one of the components of H. somni LOS that undergoes antigenic variation. In this study, five genes (lic1ABCD(Hs) and glpQ) with homology to genes responsible for ChoP expression in Haemophilus influenzae LOS were identified in the H. somni genome. An H. somni open reading frame (ORF) with homology to H. influenzae lic1A (lic1A(Hi)) contained a variable number of tandem repeats (VNTR). However, whereas the tetranucleotide repeat 5'-CAAT-3' is present in lic1A(Hi), the VNTR in H. somni lic1A (lic1A(Hs)) consisted of 5'-AACC-3'. Due to the propensity of VNTR to vary during replication and cause the ORF to shift in and out of frame with the upstream start codon, the VNTR were deleted from lic1A(Hs) to maintain the gene constitutively on. This construct was cloned into Escherichia coli, and functional enzyme assays confirmed that lic1A(Hs) encoded a choline kinase, and that the VNTR were not required for expression of a functional gene product. Variation in the number of VNTR in lic1A(Hs) correlated with antigenic variation of ChoP expression in H. somni strain 124P. However, antigenic variation of ChoP expression in strain 738 predominately occurred through variable extension/truncation of the LOS outer core. These results indicated that the lic1(Hs) genes controlled expression of ChoP on the LOS, but that in H. somni there are two potential mechanisms that account for antigenic variation of ChoP.

Molecular characterization of phosphorylcholine expression on the lipooligosaccharide of Histophilus somni

PubMed Central

Elswaifi, Shaadi F.; St. Michael, Frank; Sreenivas, Avula; Cox, Andrew; Carman, George M.; Inzana, Thomas J.

2013-01-01

Histophilus somni (Haemophilus somnus) is an important pathogen of cattle that is responsible for respiratory disease, septicemia, and systemic diseases such as thrombotic meningoencephalitis, myocarditis, and abortion. A variety of virulence factors have been identified in H. somni, including compositional and antigenic variation of the lipooligosaccharide (LOS). Phosphorylcholine (ChoP) has been identified as one of the components of H. somni LOS that undergoes antigenic variation. In this study, five genes (lic1ABCDHs and glpQ) with homology to genes responsible for ChoP expression in Haemophilus influenzae LOS were identified in the H. somni genome. An H. somni open reading frame (ORF) with homology to H. influenzae lic1A (lic1AHi) contained a variable number of tandem repeats (VNTR). However, whereas the tetranucleotide repeat 5′-CAAT-3′ is present in lic1AHi, the VNTR in H. somni lic1A (lic1AHs) consisted of 5′-AACC-3′. Due to the propensity of VNTR to vary during replication and cause the ORF to shift in and out of frame with the upstream start codon, the VNTR were deleted from lic1AHs to maintain the gene constitutively on. This construct was cloned into Escherichia coli, and functional enzyme assays confirmed that lic1AHs encoded a choline kinase, and that the VNTR were not required for expression of a functional gene product. Variation in the number of VNTR in lic1AHs correlated with antigenic variation of ChoP expression in H. somni strain 124P. However, antigenic variation of ChoP expression in strain 738 predominately occurred through variable extension/truncation of the LOS outer core. These results indicated that the lic1Hs genes controlled expression of ChoP on the LOS, but that in H. somni there are two potential mechanisms that account for antigenic variation of ChoP. PMID:19682567

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

PubMed

Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

2010-02-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer

PubMed Central

Wojcik, Sylwia E.; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S.; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z.; Rai, Kanti R.; Kipps, Thomas J.; Keating, Michael J.

2010-01-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas. PMID:19926640

Extrinsic Sources of Scatter in the Richness-mass Relation of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Rozo, Eduardo; Rykoff, Eli; Koester, Benjamin; Nord, Brian; Wu, Hao-Yi; Evrard, August; Wechsler, Risa

2011-10-01

Maximizing the utility of upcoming photometric cluster surveys requires a thorough understanding of the richness-mass relation of galaxy clusters. We use Monte Carlo simulations to study the impact of various sources of observational scatter on this relation. Cluster ellipticity, photometric errors, photometric redshift errors, and cluster-to-cluster variations in the properties of red-sequence galaxies contribute negligible noise. Miscentering, however, can be important, and likely contributes to the scatter in the richness-mass relation of galaxy maxBCG clusters at the low-mass end, where centering is more difficult. We also investigate the impact of projection effects under several empirically motivated assumptions about cluster environments. Using Sloan Digital Sky Survey data and the maxBCG cluster catalog, we demonstrate that variations in cluster environments can rarely (≈1%-5% of the time) result in significant richness boosts. Due to the steepness of the mass/richness function, the corresponding fraction of optically selected clusters that suffer from these projection effects is ≈5%-15%. We expect these numbers to be generic in magnitude, but a precise determination requires detailed, survey-specific modeling.

Eight-Channel AC Magnetosusceptometer of Magnetic Nanoparticles for High-Throughput and Ultra-High-Sensitivity Immunoassay

PubMed Central

Chieh, Jen-Jie; Wei, Wen-Chun; Chen, Hsin-Hsein; Lee, Yen-Fu; Lin, Feng-Chun; Chiang, Ming-Hsien; Chiu, Ming-Jang; Horng, Herng-Er; Yang, Shieh-Yueh

2018-01-01

An alternating-current magnetosusceptometer of antibody-functionalized magnetic nanoparticles (MNPs) was developed for immunomagnetic reduction (IMR). A high-sensitivity, high-critical-temperature superconducting quantum interference device was used in the magnetosusceptometer. Minute levels of biomarkers of early-stage neurodegeneration diseases were detectable in serum, but measuring each biomarker required approximately 4 h. Hence, an eight-channel platform was developed in this study to fit minimal screening requirements for Alzheimer’s disease. Two consistent results were measured for three biomarkers, namely Aβ40, Aβ42, and tau protein, per human specimen. This paper presents the instrument configuration as well as critical characteristics, such as the low noise level variations among channels, a high signal-to-noise ratio, and the coefficient of variation for the biomarkers’ IMR values. The instrument’s ultrahigh sensitivity levels for the three biomarkers and the substantially shorter total measurement time in comparison with the previous single- and four-channels platforms were also demonstrated in this study. Thus, the eight-channel instrument may serve as a powerful tool for clinical high-throughput screening of Alzheimer’s disease. PMID:29601532

Optimal design of gas adsorption refrigerators for cryogenic cooling

NASA Technical Reports Server (NTRS)

Chan, C. K.

1983-01-01

The design of gas adsorption refrigerators used for cryogenic cooling in the temperature range of 4K to 120K was examined. The functional relationships among the power requirement for the refrigerator, the system mass, the cycle time and the operating conditions were derived. It was found that the precool temperature, the temperature dependent heat capacities and thermal conductivities, and pressure and temperature variations in the compressors have important impacts on the cooling performance. Optimal designs based on a minimum power criterion were performed for four different gas adsorption refrigerators and a multistage system. It is concluded that the estimates of the power required and the system mass are within manageable limits in various spacecraft environments.

AAFE man-made noise experiment project. Volume 1: Introduction experiment definition and requirements

NASA Technical Reports Server (NTRS)

1974-01-01

An experiment was conducted to measure and map the man-made radio frequency emanations which exist at earth orbital altitudes. The major objectives of the program are to develop a complete conceptual experiment and developmental hardware for the collection and processing of data required to produce meaningful statistics on man-made noise level variations as functions of time, frequency, and geographic location. A wide dispersion measurement receiver mounted in a spacecraft operating in a specialized orbit is used to obtain the data. A summary of the experiment designs goals and constraints is provided. The recommended orbit for the spacecraft is defined. The characteristics of the receiver and the antennas are analyzed.

Genetics/Genomics Research in the Central Region

USGS Publications Warehouse

,

2006-01-01

Genetics-based research within the Biological Resources Discipline (BRD) Science Centers in the Central Region incorporates many aspects of the field of genetics. Research activities range from documenting patterns of genetic variation in order to investigate relationships among species, populations and individuals to investigating the structure, function and expression of genes and their response to environmental stressors. Research in the broad areas of genetics requires multidisciplinary expertise and specialized equipment and instrumentation. Brief summaries of the capabilities of the five BRD Centers are given below.

De Novo Chromosome Copy Number Variation in Fanconi Anemia-Associated Hematopoietic Defects

DTIC Science & Technology

2014-08-01

protein, and not FANCA , is required for the suppression of spontaneous de novo CNV. These findings support a model whereby the FANCD2 protein, possibly...cancer susceptibility gene products BRCA1 and BRCA2 function cooperatively in the FA-BRCA pathway to repair damaged DNA. Recent studies have...the FA-BRCA pathway in the suppression of spontaneous de novo CNVs Task 1. Correction of FA-A, FA-C, and FA-D2 hTERT cells with pLenti6.2/V5- FANCA

Effective Stress Law in Unconventional Reservoirs under Different Boundary Conditions

NASA Astrophysics Data System (ADS)

Saurabh, S.; Harpalani, S.

2017-12-01

Unconventional reservoirs have attracted a great deal of research interest worldwide during the past two decades. Low permeability and specialized techniques required to exploit these resources present opportunities for improvement in both production rates and ultimate recovery. Understanding subsurface stress modifications and permeability evolution are valuable when evaluating the prospects of unconventional reservoirs. These reservoir properties are functions of effective stress. As a part of this study, effective stress law, specifically the variation of anisotropic Biot's coefficient under various boundary conditions believed to exist in gas reservoirs by different researchers, has been established. Pressure-dependent-permeability (PdK) experiments were carried out on San Juan coal under different boundary conditions, that is, uniaxial strain condition and constant volume condition. Stress and strain in the vertical and horizontal directions were monitored throughout the experiment. Data collected during the experiments was used to determine the Biot's coefficient in vertical and horizontal directions under these two boundary conditions, treating coal as transversely isotropic. The variation of Biot's coefficient was found to be well correlated with the variation in coal permeability. Based on the estimated values of Biot's coefficients, a theory of variation in its value is presented for other boundary conditions. The findings of the study shed light on the inherent behavior of Biot's coefficient under different reservoir boundary conditions. This knowledge can improve the modeling work requiring estimation of effective stress in reservoirs, such as, pressure-/stress- dependent permeability. At the same time, if the effective stresses are known with more certainty by other methods, it enables assessment of the unknown reservoir boundary conditions.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

IMAGEP - A FORTRAN ALGORITHM FOR DIGITAL IMAGE PROCESSING

NASA Technical Reports Server (NTRS)

Roth, D. J.

1994-01-01

IMAGEP is a FORTRAN computer algorithm containing various image processing, analysis, and enhancement functions. It is a keyboard-driven program organized into nine subroutines. Within the subroutines are other routines, also, selected via keyboard. Some of the functions performed by IMAGEP include digitization, storage and retrieval of images; image enhancement by contrast expansion, addition and subtraction, magnification, inversion, and bit shifting; display and movement of cursor; display of grey level histogram of image; and display of the variation of grey level intensity as a function of image position. This algorithm has possible scientific, industrial, and biomedical applications in material flaw studies, steel and ore analysis, and pathology, respectively. IMAGEP is written in VAX FORTRAN for DEC VAX series computers running VMS. The program requires the use of a Grinnell 274 image processor which can be obtained from Mark McCloud Associates, Campbell, CA. An object library of the required GMR series software is included on the distribution media. IMAGEP requires 1Mb of RAM for execution. The standard distribution medium for this program is a 1600 BPI 9track magnetic tape in VAX FILES-11 format. It is also available on a TK50 tape cartridge in VAX FILES-11 format. This program was developed in 1991. DEC, VAX, VMS, and TK50 are trademarks of Digital Equipment Corporation.

Repeated pulse feeding induces functional stability in anaerobic digestion.

PubMed

De Vrieze, Jo; Verstraete, Willy; Boon, Nico

2013-07-01

Anaerobic digestion is an environmental key technology in the future bio-based economy. To achieve functional stability, a minimal microbial community diversity is required. This microbial community should also have a certain 'elasticity', i.e. the ability to rapidly adapt to suboptimal conditions or stress. In this study it was evaluated whether a higher degree of functional stability could be achieved by changing the feeding pattern, which can change the evenness, dynamics and richness of the bacterial community. The first reactor (CSTR stable ) was fed on daily basis, whereas the second reactor (CSTR dynamic ) was fed every 2 days. Average biogas production was 0.30 l CH4 l(-1) day(-1) in both reactors, although daily variation was up to four times higher in the CSTR dynamic compared with the CSTR stable during the first 50 days. Bacterial analysis revealed that this CSTR dynamic had a two times higher degree of bacterial community dynamics. The CSTR dynamic also appeared to be more tolerant to an organic shock load of 8 g COD l(-1) and ammonium levels up to 8000 mg TAN l(-1). These results suggest that the regular application of a limited pulse of organic material and/or a variation in the substrate composition might promote higher functional stability in anaerobic digestion. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microchambers with Solid-State Phosphorescent Sensor for Measuring Single Mitochondrial Respiration.

PubMed

Pham, Ted D; Wallace, Douglas C; Burke, Peter J

2016-07-09

It is now well established that, even within a single cell, multiple copies of the mitochondrial genome may be present (genetic heteroplasmy). It would be interesting to develop techniques to determine if and to what extent this genetic variation results in functional variation from one mitochondrion to the next (functional heteroplasmy). Measuring mitochondrial respiration can reveal the organelles' functional capacity for Adenosine triphosphate (ATP) production and determine mitochondrial damage that may arise from genetic or age related defects. However, available technologies require significant quantities of mitochondria. Here, we develop a technology to assay the respiration of a single mitochondrion. Our "micro-respirometer" consists of micron sized chambers etched out of borofloat glass substrates and coated with an oxygen sensitive phosphorescent dye Pt(II) meso-tetra(pentafluorophenyl)porphine (PtTFPP) mixed with polystyrene. The chambers are sealed with a polydimethylsiloxane layer coated with oxygen impermeable Viton rubber to prevent diffusion of oxygen from the environment. As the mitochondria consume oxygen in the chamber, the phosphorescence signal increases, allowing direct determination of the respiration rate. Experiments with coupled vs. uncoupled mitochondria showed a substantial difference in respiration, confirming the validity of the microchambers as single mitochondrial respirometers. This demonstration could enable future high-throughput assays of mitochondrial respiration and benefit the study of mitochondrial functional heterogeneity, and its role in health and disease.

A complete VLBI delay model for deforming radio telescopes: the Effelsberg case

NASA Astrophysics Data System (ADS)

Artz, T.; Springer, A.; Nothnagel, A.

2014-12-01

Deformations of radio telescopes used in geodetic and astrometric very long baseline interferometry (VLBI) observations belong to the class of systematic error sources which require correction in data analysis. In this paper we present a model for all path length variations in the geometrical optics of radio telescopes which are due to gravitational deformation. The Effelsberg 100 m radio telescope of the Max Planck Institute for Radio Astronomy, Bonn, Germany, has been surveyed by various terrestrial methods. Thus, all necessary information that is needed to model the path length variations is available. Additionally, a ray tracing program has been developed which uses as input the parameters of the measured deformations to produce an independent check of the theoretical model. In this program as well as in the theoretical model, the illumination function plays an important role because it serves as the weighting function for the individual path lengths depending on the distance from the optical axis. For the Effelsberg telescope, the biggest contribution to the total path length variations is the bending of the main beam located along the elevation axis which partly carries the weight of the paraboloid at its vertex. The difference in total path length is almost 100 mm when comparing observations at 90 and at 0 elevation angle. The impact of the path length corrections is validated in a global VLBI analysis. The application of the correction model leads to a change in the vertical position of mm. This is more than the maximum path length, but the effect can be explained by the shape of the correction function.

Stochastic Protein Multimerization, Cooperativity and Fitness

NASA Astrophysics Data System (ADS)

Hagner, Kyle; Setayeshgar, Sima; Lynch, Michael

Many proteins assemble into multimeric structures that can vary greatly among phylogenetic lineages. As protein-protein interactions (PPI) require productive encounters among subunits, these structural variations are related in part to variation in cellular protein abundance. The protein abundance in turn depends on the intrinsic rates of production and decay of mRNA and protein molecules, as well as rates of cell growth and division. We present a stochastic model for prediction of the multimeric state of a protein as a function of these processes and the free energy associated with binding interfaces. We demonstrate favorable agreement between the model and a wide class of proteins using E. coli proteome data. As such, this platform, which links protein abundance, PPI and quaternary structure in growing and dividing cells can be extended to evolutionary models for the emergence and diversification of multimeric proteins. We investigate cooperativity - a ubiquitous functional property of multimeric proteins - as a possible selective force driving multimerization, demonstrating a reduction in the cost of protein production relative to the overall proteome energy budget that can be tied to fitness.

Algebraic grid generation using tensor product B-splines. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Saunders, B. V.

1985-01-01

Finite difference methods are more successful if the accompanying grid has lines which are smooth and nearly orthogonal. The development of an algorithm which produces such a grid when given the boundary description. Topological considerations in structuring the grid generation mapping are discussed. The concept of the degree of a mapping and how it can be used to determine what requirements are necessary if a mapping is to produce a suitable grid is examined. The grid generation algorithm uses a mapping composed of bicubic B-splines. Boundary coefficients are chosen so that the splines produce Schoenberg's variation diminishing spline approximation to the boundary. Interior coefficients are initially chosen to give a variation diminishing approximation to the transfinite bilinear interpolant of the function mapping the boundary of the unit square onto the boundary grid. The practicality of optimizing the grid by minimizing a functional involving the Jacobian of the grid generation mapping at each interior grid point and the dot product of vectors tangent to the grid lines is investigated. Grids generated by using the algorithm are presented.

Longitudinal Distribution of the Functional Feeding Groups of Aquatic Insects in Streams of the Brazilian Cerrado Savanna.

PubMed

Brasil, L S; Juen, L; Batista, J D; Pavan, M G; Cabette, H S R

2014-10-01

We demonstrate that the distribution of the functional feeding groups of aquatic insects is related to hierarchical patch dynamics. Patches are sites with unique environmental and functional characteristics that are discontinuously distributed in time and space within a lotic system. This distribution predicts that the occurrence of species will be based predominantly on their environmental requirements. We sampled three streams within the same drainage basin in the Brazilian Cerrado savanna, focusing on waterfalls and associated habitats (upstream, downstream), representing different functional zones. We collected 2,636 specimens representing six functional feeding groups (FFGs): brushers, collector-gatherers, collector-filterers, shredders, predators, and scrapers. The frequency of occurrence of these groups varied significantly among environments. This variation appeared to be related to the distinct characteristics of the different habitat patches, which led us to infer that the hierarchical patch dynamics model can best explain the distribution of functional feeding groups in minor lotic environments, such as waterfalls.

Method and apparatus for non-invasive evaluation of diaphragmatic function

NASA Technical Reports Server (NTRS)

Yost, William T. (Inventor); Wait, Juliette L. (Inventor); Nahormek, Patricia A. (Inventor); Cantrell, John H. (Inventor); Hanna-Hawver, Pamela D. (Inventor)

1995-01-01

A method for non-invasive evaluation of diaphragmatic function in humans measures the thickness of the diaphragm in real time with an ultrasonic device, and displays the variations of diaphragm thickness versus time. Formulae are given for calculating a quantitative value for the reserve fatigue capacity of a patient's diaphragm from data obtained by measuring the time limits for maintaining a constant breathing pattern on the display at two different pressure differentials in series with the patient's airways. An apparatus for displaying the diaphragm thickness in real time is also described. The method can be used both on healthy patients and on patients with so severe breathing dysfunctions that they require breathing support from respirators.

Method and apparatus for non-invasive evaluation of diaphragmatic function

NASA Technical Reports Server (NTRS)

Yost, William T. (Inventor); Wait, Juliette L. (Inventor); Nahormek, Patricia A. (Inventor); Cantrell, John H. (Inventor); Hanna-Hawver, Pamela D. (Inventor)

1994-01-01

A method for non-invasive evaluation of diaphragmatic function in humans measures the thickness of the diaphragm in real time with an ultrasonic device, and displays the variations of diaphragm thickness versus time. Formulae are given for calculating a quantitative value for the reserve fatigue capacity of a patient's diaphragm from data obtained by measuring the time limits for maintaining a constant breathing pattern on the display at two different pressure differentials in series with the patient's airways. An apparatus for displaying the diaphragm thickness in real time is also described. The method can be used both on healthy patients and on patients with so severe breathing dysfunctions that they require breathing support from respirators.

Variation of renal function over time is associated with major bleeding in patients treated with direct oral anticoagulants for atrial fibrillation.

PubMed

Becattini, C; Giustozzi, M; Ranalli, M G; Bogliari, G; Cianella, F; Verso, M; Agnelli, G; Vedovati, M C

2018-05-01

Essential In patients on treatment with direct anticoagulants (DOACs) variation of renal function is common. The effect of variations of renal function over time on major bleeding is not well defined. Variation of renal function over time is an independent predictor of major bleeding. Identifying conditions associated with variation of renal function may increase safety of DOACs. Background Chronic kidney disease is a risk factor for major bleeding in patients with atrial fibrillation (AF) treated with warfarin. Objective To assess the effect of variations in renal function over time on the risk of major bleeding during treatment with direct oral anticoagulants (DOACs) in patients with non-valvular AF. Methods Consecutive AF patients were prospectively followed after they had received the first DOAC prescription. Estimated glomerular filtration rate (eGFR) was periodically assessed, and the incidence of major bleeding was recorded. A joint survival model was used to estimate the association between variation in eGFR and the risk of major bleeding. Results During a mean follow-up of 575 days, 44 major bleeds occurred in 449 patients (6.1% per patient-year). eGFR over time was inversely and independently associated with the risk of major bleeding; every 1 mL min -1 absolute decrease in eGFR was associated with a 2% increase in the risk of major bleeding (hazard ratio [HR] 1.02, 95% confidence interval [CI] 1.01-1.04). A similar effect of the variation in eGFR over time was observed on the risk of clinically relevant non-major bleeding (HR 1.02, 95% CI 1.01-1.03). Deterioration of renal function leading to a change in eGFR staging was associated with an increase in the risk of major bleeding (HR 2.43, 95% CI 1.33-4.45). Conclusions Variation in renal function over time is associated with the risk of major bleeding in AF patients treated with DOACs in real life. Identification of intervening clinical conditions associated with variation in renal function is essential to reduce the risk of major bleeding and to make DOAC treatment more safe. © 2018 International Society on Thrombosis and Haemostasis.

Functional diversification of hsp40: distinct j-protein functional requirements for two prions allow for chaperone-dependent prion selection.

PubMed

Harris, Julia M; Nguyen, Phil P; Patel, Milan J; Sporn, Zachary A; Hines, Justin K

2014-07-01

Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins. Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor, recognizing prion and other amyloid aggregates and enabling Ssa and Hsp104 to act in prion fragmentation. Chaperone interactions with prions, however, can be affected by variations in amyloid-core structure resulting in distinct prion variants or 'strains'. Our genetic analysis revealed that Sis1 domain requirements by distinct variants of [PSI+] are strongly dependent upon overall variant stability. Notably, multiple strong [PSI+] variants can be maintained by a minimal construct of Sis1 consisting of only the J-domain and glycine/phenylalanine-rich (G/F) region that was previously shown to be sufficient for cell viability and [RNQ+] prion propagation. In contrast, weak [PSI+] variants are lost under the same conditions but maintained by the expression of an Sis1 construct that lacks only the G/F region and cannot support [RNQ+] propagation, revealing mutually exclusive requirements for Sis1 function between these two prions. Prion loss is not due to [PSI+]-dependent toxicity or dependent upon a particular yeast genetic background. These observations necessitate that Sis1 must have at least two distinct functional roles that individual prions differentially require for propagation and which are localized to the glycine-rich domains of the Sis1. Based on these distinctions, Sis1 plasmid-shuffling in a [PSI+]/[RNQ+] strain permitted J-protein-dependent prion selection for either prion. We also found that, despite an initial report to the contrary, the human homolog of Sis1, Hdj1, is capable of [PSI+] prion propagation in place of Sis1. This conservation of function is also prion-variant dependent, indicating that only one of the two Sis1-prion functions may have been maintained in eukaryotic chaperone evolution.

Functional Diversification of Hsp40: Distinct J-Protein Functional Requirements for Two Prions Allow for Chaperone-Dependent Prion Selection

PubMed Central

Patel, Milan J.; Sporn, Zachary A.; Hines, Justin K.

2014-01-01

Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins. Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor, recognizing prion and other amyloid aggregates and enabling Ssa and Hsp104 to act in prion fragmentation. Chaperone interactions with prions, however, can be affected by variations in amyloid-core structure resulting in distinct prion variants or ‘strains’. Our genetic analysis revealed that Sis1 domain requirements by distinct variants of [PSI +] are strongly dependent upon overall variant stability. Notably, multiple strong [PSI +] variants can be maintained by a minimal construct of Sis1 consisting of only the J-domain and glycine/phenylalanine-rich (G/F) region that was previously shown to be sufficient for cell viability and [RNQ +] prion propagation. In contrast, weak [PSI +] variants are lost under the same conditions but maintained by the expression of an Sis1 construct that lacks only the G/F region and cannot support [RNQ +] propagation, revealing mutually exclusive requirements for Sis1 function between these two prions. Prion loss is not due to [PSI +]-dependent toxicity or dependent upon a particular yeast genetic background. These observations necessitate that Sis1 must have at least two distinct functional roles that individual prions differentially require for propagation and which are localized to the glycine-rich domains of the Sis1. Based on these distinctions, Sis1 plasmid-shuffling in a [PSI +]/[RNQ +] strain permitted J-protein-dependent prion selection for either prion. We also found that, despite an initial report to the contrary, the human homolog of Sis1, Hdj1, is capable of [PSI +] prion propagation in place of Sis1. This conservation of function is also prion-variant dependent, indicating that only one of the two Sis1-prion functions may have been maintained in eukaryotic chaperone evolution. PMID:25058638

Do sex, body size and reproductive condition influence the thermal preferences of a large lizard? A study in Tupinambis merianae.

PubMed

Cecchetto, Nicolas Rodolfo; Naretto, Sergio

2015-10-01

Body temperature is a key factor in physiological processes, influencing lizard performances; and life history traits are expected to generate variability of thermal preferences in different individuals. Gender, body size and reproductive condition may impose specific requirements on preferred body temperatures. If these three factors have different physiological functions and thermal requirements, then the preferred temperature may represent a compromise that optimizes these physiological functions. Therefore, the body temperatures that lizards select in a controlled environment may reflect a temperature that maximizes their physiological needs. The tegu lizard Tupinambis merianae is one of the largest lizards in South America and has wide ontogenetic variation in body size and sexual dimorphism. In the present study we evaluate intraspecific variability of thermal preferences of T. merianae. We determined the selected body temperature and the rate at which males and females attain their selected temperature, in relation to body size and reproductive condition. We also compared the behavior in the thermal gradient between males and females and between reproductive condition of individuals. Our study show that T. merianae selected body temperature within a narrow range of temperatures variation in the laboratory thermal gradient, with 36.24±1.49°C being the preferred temperature. We observed no significant differences between sex, body size and reproductive condition in thermal preferences. Accordingly, we suggest that the evaluated categories of T. merianae have similar thermal requirements. Males showed higher rates to obtain heat than females and reproductive females, higher rates than non-reproductive ones females. Moreover, males and reproductive females showed a more dynamic behavior in the thermal gradient. Therefore, even though they achieve the same selected temperature, they do it differentially. Copyright © 2015 Elsevier Ltd. All rights reserved.

Data Assimilation on a Quantum Annealing Computer: Feasibility and Scalability

NASA Astrophysics Data System (ADS)

Nearing, G. S.; Halem, M.; Chapman, D. R.; Pelissier, C. S.

2014-12-01

Data assimilation is one of the ubiquitous and computationally hard problems in the Earth Sciences. In particular, ensemble-based methods require a large number of model evaluations to estimate the prior probability density over system states, and variational methods require adjoint calculations and iteration to locate the maximum a posteriori solution in the presence of nonlinear models and observation operators. Quantum annealing computers (QAC) like the new D-Wave housed at the NASA Ames Research Center can be used for optimization and sampling, and therefore offers a new possibility for efficiently solving hard data assimilation problems. Coding on the QAC is not straightforward: a problem must be posed as a Quadratic Unconstrained Binary Optimization (QUBO) and mapped to a spherical Chimera graph. We have developed a method for compiling nonlinear 4D-Var problems on the D-Wave that consists of five steps: Emulating the nonlinear model and/or observation function using radial basis functions (RBF) or Chebyshev polynomials. Truncating a Taylor series around each RBF kernel. Reducing the Taylor polynomial to a quadratic using ancilla gadgets. Mapping the real-valued quadratic to a fixed-precision binary quadratic. Mapping the fully coupled binary quadratic to a partially coupled spherical Chimera graph using ancilla gadgets. At present the D-Wave contains 512 qbits (with 1024 and 2048 qbit machines due in the next two years); this machine size allows us to estimate only 3 state variables at each satellite overpass. However, QAC's solve optimization problems using a physical (quantum) system, and therefore do not require iterations or calculation of model adjoints. This has the potential to revolutionize our ability to efficiently perform variational data assimilation, as the size of these computers grows in the coming years.

Female reproductive success variation in a Pseudotsuga menziesii seed orchard as revealed by pedigree reconstruction from a bulk seed collection.

PubMed

El-Kassaby, Yousry A; Funda, Tomas; Lai, Ben S K

2010-01-01

The impact of female reproductive success on the mating system, gene flow, and genetic diversity of the filial generation was studied using a random sample of 801 bulk seed from a 49-clone Pseudotsuga menziesii seed orchard. We used microsatellite DNA fingerprinting and pedigree reconstruction to assign each seed's maternal and paternal parents and directly estimated clonal reproductive success, selfing rate, and the proportion of seed sired by outside pollen sources. Unlike most family array mating system and gene flow studies conducted on natural and experimental populations, which used an equal number of seeds per maternal genotype and thus generating unbiased inferences only on male reproductive success, the random sample we used was a representative of the entire seed crop; therefore, provided a unique opportunity to draw unbiased inferences on both female and male reproductive success variation. Selfing rate and the number of seed sired by outside pollen sources were found to be a function of female fertility variation. This variation also substantially and negatively affected female effective population size. Additionally, the results provided convincing evidence that the use of clone size as a proxy to fertility is questionable and requires further consideration.

Developmental trends in the interaction between auditory and linguistic processing.

PubMed

Jerger, S; Pirozzolo, F; Jerger, J; Elizondo, R; Desai, S; Wright, E; Reynosa, R

1993-09-01

The developmental course of multidimensional speech processing was examined in 80 children between 3 and 6 years of age and in 60 adults between 20 and 86 years of age. Processing interactions were assessed with a speeded classification task (Garner, 1974a), which required the subjects to attend selectively to the voice dimension while ignoring the linguistic dimension, and vice versa. The children and adults exhibited both similarities and differences in the patterns of processing dependencies. For all ages, performance for each dimension was slower in the presence of variation in the irrelevant dimension; irrelevant variation in the voice dimension disrupted performance more than irrelevant variation in the linguistic dimension. Trends in the degree of interference, on the other hand, showed significant differences between dimensions as a function of age. Whereas the degree of interference for the voice-dimension-relevant did not show significant age-related change, the degree of interference for the word-dimension-relevant declined significantly with age in a linear as well as a quadratic manner. A major age-related change in the relation between dimensions was that word processing, relative to voice-gender processing, required significantly more time in the children than in the adults. Overall, the developmental course characterizing multidimensional speech processing evidenced more pronounced change when the linguistic dimension, rather than the voice dimension, was relevant.

Single cell wound generates electric current circuit and cell membrane potential variations that requires calcium influx.

PubMed

Luxardi, Guillaume; Reid, Brian; Maillard, Pauline; Zhao, Min

2014-07-24

Breaching of the cell membrane is one of the earliest and most common causes of cell injury, tissue damage, and disease. If the compromise in cell membrane is not repaired quickly, irreversible cell damage, cell death and defective organ functions will result. It is therefore fundamentally important to efficiently repair damage to the cell membrane. While the molecular aspects of single cell wound healing are starting to be deciphered, its bio-physical counterpart has been poorly investigated. Using Xenopus laevis oocytes as a model for single cell wound healing, we describe the temporal and spatial dynamics of the wound electric current circuitry and the temporal dynamics of cell membrane potential variation. In addition, we show the role of calcium influx in controlling electric current circuitry and cell membrane potential variations. (i) Upon wounding a single cell: an inward electric current appears at the wound center while an outward electric current is observed at its sides, illustrating the wound electric current circuitry; the cell membrane is depolarized; calcium flows into the cell. (ii) During cell membrane re-sealing: the wound center current density is maintained for a few minutes before decreasing; the cell membrane gradually re-polarizes; calcium flow into the cell drops. (iii) In conclusion, calcium influx is required for the formation and maintenance of the wound electric current circuitry, for cell membrane re-polarization and for wound healing.

AN INVERSE MODELING APPROACH FOR STRESS ESTIMATION IN MITRAL VALVE ANTERIOR LEAFLET VALVULOPLASTY FOR IN-VIVO VALVULAR BIOMATERIAL ASSESSMENT

PubMed Central

Lee, Chung-Hao; Amini, Rouzbeh; Gorman, Robert C.; Gorman, Joseph H.; Sacks, Michael S.

2013-01-01

Estimation of regional tissue stresses in the functioning heart valve remains an important goal in our understanding of normal valve function and in developing novel engineered tissue strategies for valvular repair and replacement. Methods to accurately estimate regional tissue stresses are thus needed for this purpose, and in particular to develop accurate, statistically informed means to validate computational models of valve function. Moreover, there exists no currently accepted method to evaluate engineered heart valve tissues and replacement heart valve biomaterials undergoing valvular stresses in blood contact. While we have utilized mitral valve anterior leaflet valvuloplasty as an experimental approach to address this limitation, robust computational techniques to estimate implant stresses are required. In the present study, we developed a novel numerical analysis approach for estimation of the in-vivo stresses of the central region of the mitral valve anterior leaflet (MVAL) delimited by a sonocrystal transducer array. The in-vivo material properties of the MVAL were simulated using an inverse FE modeling approach based on three pseudo-hyperelastic constitutive models: the neo-Hookean, exponential-type isotropic, and full collagen-fiber mapped transversely isotropic models. A series of numerical replications with varying structural configurations were developed by incorporating measured statistical variations in MVAL local preferred fiber directions and fiber splay. These model replications were then used to investigate how known variations in the valve tissue microstructure influence the estimated ROI stresses and its variation at each time point during a cardiac cycle. Simulations were also able to include estimates of the variation in tissue stresses for an individual specimen dataset over the cardiac cycle. Of the three material models, the transversely anisotropic model produced the most accurate results, with ROI averaged stresses at the fully-loaded state of 432.6±46.5 kPa and 241.4±40.5 kPa in the radial and circumferential directions, respectively. We conclude that the present approach can provide robust instantaneous mean and variation estimates of tissue stresses of the central regions of the MVAL. PMID:24275434

A worldview of root traits: the influence of ancestry, growth form, climate and mycorrhizal association on the functional trait variation of fine-root tissues in seed plants.

PubMed

Valverde-Barrantes, Oscar J; Freschet, Grégoire T; Roumet, Catherine; Blackwood, Christopher B

2017-09-01

Fine-root traits play key roles in ecosystem processes, but the drivers of fine-root trait diversity remain poorly understood. The plant economic spectrum (PES) hypothesis predicts that leaf and root traits evolved in coordination. Mycorrhizal association type, plant growth form and climate may also affect root traits. However, the extent to which these controls are confounded with phylogenetic structuring remains unclear. Here we compiled information about root and leaf traits for > 600 species. Using phylogenetic relatedness, climatic ranges, growth form and mycorrhizal associations, we quantified the importance of these factors in the global distribution of fine-root traits. Phylogenetic structuring accounts for most of the variation for all traits excepting root tissue density, with root diameter and nitrogen concentration showing the strongest phylogenetic signal and specific root length showing intermediate values. Climate was the second most important factor, whereas mycorrhizal type had little effect. Substantial trait coordination occurred between leaves and roots, but the strength varied between growth forms and clades. Our analyses provide evidence that the integration of roots and leaves in the PES requires better accounting of the variation in traits across phylogenetic clades. Inclusion of phylogenetic information provides a powerful framework for predictions of belowground functional traits at global scales. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Human germline and pan-cancer variomes and their distinct functional profiles

PubMed Central

Pan, Yang; Karagiannis, Konstantinos; Zhang, Haichen; Dingerdissen, Hayley; Shamsaddini, Amirhossein; Wan, Quan; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations. PMID:25232094

Understanding the General Packing Rearrangements Required for Successful Template Based Modeling of Protein Structure from a CASP Experiment

PubMed Central

Day, Ryan; Joo, Hyun; Chavan, Archana; Lennox, Kristin P.; Chen, Ann; Dahl, David B.; Vannucci, Marina; Tsai, Jerry W.

2012-01-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. PMID:23266765

Ecological strategies in california chaparral: Interacting effects of soils, climate, and fire on specific leaf area

USGS Publications Warehouse

Anacker, Brian; Rajakaruna, Nishanta; Ackerly, David; Harrison, Susan; Keeley, Jon E.; Vasey, Michael

2011-01-01

Background: High values of specific leaf area (SLA) are generally associated with high maximal growth rates in resource-rich conditions, such as mesic climates and fertile soils. However, fire may complicate this relationship since its frequency varies with both climate and soil fertility, and fire frequency selects for regeneration strategies (resprouting versus seeding) that are not independent of resource-acquisition strategies. Shared ancestry is also expected to affect the distribution of resource-use and regeneration traits.Aims: We examined climate, soil, and fire as drivers of community-level variation in a key functional trait, SLA, in chaparral in California.Methods: We quantified the phylogenetic, functional, and environmental non-independence of key traits for 87 species in 115 plots.Results: Among species, SLA was higher in resprouters than seeders, although not after phylogeny correction. Among communities, mean SLA was lower in harsh interior climates, but in these climates it was higher on more fertile soils and on more recently burned sites; in mesic coastal climates, mean SLA was uniformly high despite variation in soil fertility and fire history.Conclusions: We conclude that because important correlations exist among both species traits and environmental filters, interpreting the functional and phylogenetic structure of communities may require an understanding of complex interactive effects.

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

PubMed

Day, Ryan; Joo, Hyun; Chavan, Archana C; Lennox, Kristin P; Chen, Y Ann; Dahl, David B; Vannucci, Marina; Tsai, Jerry W

2013-02-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. Copyright © 2012 Elsevier Ltd. All rights reserved.

Variational model for one-dimensional quantum magnets

NASA Astrophysics Data System (ADS)

Kudasov, Yu. B.; Kozabaranov, R. V.

2018-04-01

A new variational technique for investigation of the ground state and correlation functions in 1D quantum magnets is proposed. A spin Hamiltonian is reduced to a fermionic representation by the Jordan-Wigner transformation. The ground state is described by a new non-local trial wave function, and the total energy is calculated in an analytic form as a function of two variational parameters. This approach is demonstrated with an example of the XXZ-chain of spin-1/2 under a staggered magnetic field. Generalizations and applications of the variational technique for low-dimensional magnetic systems are discussed.

Regularization by Functions of Bounded Variation and Applications to Image Enhancement

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

Casas, E.; Kunisch, K.; Pola, C.

1999-09-15

Optimization problems regularized by bounded variation seminorms are analyzed. The optimality system is obtained and finite-dimensional approximations of bounded variation function spaces as well as of the optimization problems are studied. It is demonstrated that the choice of the vector norm in the definition of the bounded variation seminorm is of special importance for approximating subspaces consisting of piecewise constant functions. Algorithms based on a primal-dual framework that exploit the structure of these nondifferentiable optimization problems are proposed. Numerical examples are given for denoising of blocky images with very high noise.

Polarization variations in installed fibers and their influence on quantum key distribution systems.

PubMed

Ding, Yu-Yang; Chen, Hua; Wang, Shuang; He, De-Yong; Yin, Zhen-Qiang; Chen, Wei; Zhou, Zheng; Guo, Guang-Can; Han, Zheng-Fu

2017-10-30

Polarization variations in the installed fibers are complex and volatile, and would severely affect the performances of polarization-sensitive quantum key distribution (QKD) systems. Based on the recorded data about polarization variations of different installed fibers, we establish an analytical methodology to quantitatively evaluate the influence of polarization variations on polarization-sensitive QKD systems. Using the increased quantum bit error rate induced by polarization variations as a key criteria, we propose two parameters - polarization drift time and required tracking speed - to characterize polarization variations. For field buried and aerial fibers with different length, we quantitatively evaluate the influence of polarization variations, and also provide requirements and suggestions for polarization basis alignment modules of QKD systems deployed in different kind of fibers.

Lunar and Artificial Satellite Laser Ranging: The Use of Queue Scheduling and Worth Functions to Maximize Scientific Results

NASA Astrophysics Data System (ADS)

Shelus, P. J.; Ricklefs, R. L.; Wiant, J. R.; Ries, J. G.

2003-08-01

The lunar and artificial satellite laser ranging network, part of the International Laser Ranging Service, monitors a large number of targets. Many scientific disciplines are investigated using these data. These include the realization and maintenance of the International Terrestrial Reference Frame; the 3-dimensional deformation of the solid Earth; Earth orientation; variations in the topography and volume of the liquid Earth, including ocean circulation, mean sea level, ice sheet thickness, and wave heights; tidally generated variations in atmospheric mass distribution; calibration of microwave tracking techniques; picosecond global time transfer; determination of the dynamic equinox, the obliquity of the ecliptic, the precession constant and theories of nutation; gravitational and general relativistic studies, including Einstein's Equivalence Principle, the Robertson-Walker b parameter and time rate of change of the gravitational constant; lunar physics, including the dissipation of rotational energy, shape of the core-mantle boundary (Love Number k2), and free librations and their stimulating mechanisms; Solar System ties to the International Celestial Reference Frame. With shrinking resources, we must not only assess specific data requirements for each target, but also maximize the efficiency of the observing network. Several factors must be considered. First, not only does a result depend critically upon the quality and quantity of the data, it also depends upon the data distribution. Second, as technology improves, the cost of obtaining data can increase. Both require that scientific endeavor pay close attention to the manner in which the data is gathered. We examine the evolution of the laser network, using data analysis requirements and efficient network scheduling to maximize the scientific return. This requires an understanding of the observing equipment, as well as the scientific principles being studied. Queue scheduling and worth functions become important. This work is funded by: NSF AST-0204127, NASA NAG5-10195, NAS5-01096, NAG5-11464.

A spacecraft integrated power/attitude control system

NASA Technical Reports Server (NTRS)

Keckler, C. R.; Jacobs, K. L.

1974-01-01

A study to determine the viability and application of a system capable of performing the dual function of power storage/generation and attitude control has been conducted. Results from the study indicate that an integrated power/attitude control system (IPACS) can satisfy future mission requirements while providing significant savings in weight, volume, and cost over conventional systems. A failure-mode configuration of an IPACS was applied to a shuttle-launched RAM free-flyer and simulated using make-do hardware linked to a hybrid computer. Data from the simulation runs indicate that control interactions resulting from heavy power demands have minimal effect on system control effectiveness. The system was shown to be capable of meeting the stringent pointing requirements of 1 arc-second while operating under the influence of an orbital disturbance environment and during periods of momentum variations imposed by energy transfer requirements.

Variation in habitat suitability does not always relate to variation in species' plant functional traits

PubMed Central

Thuiller, Wilfried; Albert, Cécile H.; Dubuis, Anne; Randin, Christophe; Guisan, Antoine

2010-01-01

Habitat suitability models, which relate species occurrences to environmental variables, are assumed to predict suitable conditions for a given species. If these models are reliable, they should relate to change in plant growth and function. In this paper, we ask the question whether habitat suitability models are able to predict variation in plant functional traits, often assumed to be a good surrogate for a species' overall health and vigour. Using a thorough sampling design, we show a tight link between variation in plant functional traits and habitat suitability for some species, but not for others. Our contrasting results pave the way towards a better understanding of how species cope with varying habitat conditions and demonstrate that habitat suitability models can provide meaningful descriptions of the functional niche in some cases, but not in others. PMID:19793738

Temporal and spatial variations in fly ash quality

USGS Publications Warehouse

Hower, J.C.; Trimble, A.S.; Eble, C.F.

2001-01-01

Fly ash quality, both as the amount of petrographically distinguishable carbons and in chemistry, varies in both time and space. Temporal variations are a function of a number of variables. Variables can include variations in the coal blend organic petrography, mineralogy, and chemistry; variations in the pulverization of the coal, both as a function of the coal's Hardgrove grindability index and as a function of the maintenance and settings of the pulverizers; and variations in the operating conditions of the boiler, including changes in the pollution control system. Spatial variation, as an instantaneous measure of fly ash characteristics, should not involve changes in the first two sets of variables listed above. Spatial variations are a function of the gas flow within the boiler and ducts, certain flow conditions leading to a tendency for segregation of the less-dense carbons in one portion of the gas stream. Caution must be applied in sampling fly ash. Samples from a single bin, or series of bins, m ay not be representative of the whole fly ash, providing a biased view of the nature of the material. Further, it is generally not possible to be certain about variation until the analysis of the ash is complete. ?? 2001 Elsevier Science B.V. All rights reserved.

Image irradiance distribution in the 3MI wide field of view polarimeter

NASA Astrophysics Data System (ADS)

Gabrieli, Riccardo; Bartoli, Alessandro; Maiorano, Michele; Bruno, Umberto; Olivieri, Monica; Calamai, Luciano; Manolis, Ilias; Labate, Demetrio

2015-09-01

The Multi-Viewing, Multi-Channel, Multi-Polarisation Imager (3MI) is an imaging radiometer for the ESA/Eumetsat MeteOp-SG programme. Based on the heritage of the POLDER/PARASOL instrument, 3MI is designed to collect global observations of the top-of-atmosphere polarised bi-directional reflectance distribution function in 12 spectral bands, by observing the same target from multiple views using a pushbroom scanning concept. The demanding challenge of the 3MI optical design is represented by the polarisation and image irradiance fall-off (throughput uniformity) requirements. In a generic optical system, the image irradiance fall-off is a function of: target radiance distribution and polarisation, entrance pupil size and optical transmittance variations across the field of view (FOV), distortion and vignetting. In most applications these aspects can be considered as independent; however, when high image irradiance uniformity is required, they have to be considered as linked together. This is particularly true in case of a wide FOV polarimeter as 3MI is. In order to properly account for these aspects, an irradiance fall-off analytical model has been developed in the frame of 3MI Optics Pre-Development (OPD), whose aim is to mitigate any technological risks associated with the 3MI instrument development. It is shown how it is possible to control the image irradiance distribution acting on optical design parameters (e.g. distortion and entrance pupil size variation with FOV). Moreover, the impact of polarisation performances on irradiance fall-off is discussed.

Exploiting genomics and natural genetic variation to decode macrophage enhancers

PubMed Central

Romanoski, Casey E.; Link, Verena M.; Heinz, Sven; Glass, Christopher K.

2015-01-01

The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease. PMID:26298065

Fast state transfer in a Λ-system: a shortcut-to-adiabaticity approach to robust and resource optimized control

NASA Astrophysics Data System (ADS)

Mortensen, Henrik Lund; Sørensen, Jens Jakob W. H.; Mølmer, Klaus; Sherson, Jacob Friis

2018-02-01

We propose an efficient strategy to find optimal control functions for state-to-state quantum control problems. Our procedure first chooses an input state trajectory, that can realize the desired transformation by adiabatic variation of the system Hamiltonian. The shortcut-to-adiabaticity formalism then provides a control Hamiltonian that realizes the reference trajectory exactly but on a finite time scale. As the final state is achieved with certainty, we define a cost functional that incorporates the resource requirements and a perturbative expression for robustness. We optimize this functional by systematically varying the reference trajectory. We demonstrate the method by application to population transfer in a laser driven three-level Λ-system, where we find solutions that are fast and robust against perturbations while maintaining a low peak laser power.

Impact of seasonal variation on soil bacterial diversity and ecosystem functioning

NASA Astrophysics Data System (ADS)

Amoo, Adenike Eunice; Oluranti Babalola, Olubukola

2017-04-01

Soil biodiversity boosts the functioning of the ecosystem thereby contributing to the provision of various ecosystem services. Understanding the link between biodiversity and ecosystem functioning and their reaction to environmental heterogeneity can maximize the contribution of soil microbes to ecosystem services. The diversity, abundance and function of microorganisms can be altered by seasonal variation. There is a dearth of information on how soil biodiversity respond to environmental changes. The impact of seasonal variation on bacterial communities and its effects on soil functioning in four South African forests was investigated. The samples were analysed for pH, moisture content, total carbon and nitrogen, soil nitrate and extractable phosphate. High-throughput sequencing and quantitative PCR were used to determine the diversity and abundance of bacteria. Community level physiological profiles (CLPPs) were measured using the MicroResp™ method. Enzyme activities were additionally used as proxy for ecosystem functions. The functional genes for nitrification and phosphate solubilisation were also measured. Seasonal variation has strong effects on bacterial communities and consequently soil processes. A reduction in biodiversity has direct results on soil ecosystem functioning.

Decomposing functional trait associations in a Chinese subtropical forest

PubMed Central

Pei, Kequan; Kéry, Marc; Niklaus, Pascal A.; Schmid, Bernhard

2017-01-01

Functional traits, properties of organisms correlated with ecological performance, play a central role in plant community assembly and functioning. To some extents, functional traits vary in concert, reflecting fundamental ecological strategies. While “trait syndromes” characteristic of e.g. fast-growing, early-successional vs. competitive, late-successional species are recognized in principle, less is known about the environmental and genetic factors at the source of trait variation and covariation within plant communities. We studied the three leaf traits leaf half-life (LHL), leaf mass per area (LMA) and nitrogen concentration in green leaves (Ngreen) and the wood trait wood density (WD) in 294 individuals belonging to 45 tree or shrub species in a Chinese subtropical forest from September 2006 to January 2009. Using multilevel ANOVA and decomposition of sums of products, we estimated the amount of trait variation and covariation among species (mainly genetic causes), i.e. plant functional type (deciduous vs. evergreen species), growth form (tree vs. shrub species), family/genus/species differences, and within species (mainly environmental causes), i.e. individual and season. For single traits, the variation between functional types and among species within functional types was large, but only LMA and Ngreen varied significantly among families and thus showed phylogenetic signal. Trait variation among individuals within species was small, but large temporal variation due to seasonal effects was found within individuals. We did not find any trait variation related to soil conditions underneath the measured individuals. For pairs of traits, variation between functional types and among species within functional types was large, reflecting a strong evolutionary coordination of the traits, with LMA, LHL and WD being positively correlated among each other and negatively with Ngreen. This integration of traits was consistent with a putative stem-leaf economics spectrum ranging from deciduous species with thin, high-nitrogen leaves and low-density wood to evergreen species with thick, low-nitrogen leaves and dense wood and was not influenced by phylogenetic history. Trait coordination within species was weak, allowing individual trees to deviate from the interspecific trait coordination and thus respond flexibly to environmental heterogeneity. Our findings suggest that within a single woody plant community variation and covariation in functional traits allows a large number of species to co-exist and cover a broad spectrum of multivariate niche space, which in turn may increase total resource extraction by the community and community functioning. PMID:28419169

Electrical Properties and Power Considerations of a Piezoelectric Actuator

NASA Technical Reports Server (NTRS)

Jordan, T.; Ounaies, Z.; Tripp, J.; Tcheng, P.

1999-01-01

This paper assesses the electrical characteristics of piezoelectric wafers for use in aeronautical applications such as active noise control in aircraft. Determination of capacitive behavior and power consumption is necessary to optimize the system configuration and to design efficient driving electronics. Empirical relations are developed from experimental data to predict the capacitance and loss tangent of a PZT5A ceramic as nonlinear functions of both applied peak voltage and driving frequency. Power consumed by the PZT is the rate of energy required to excite the piezoelectric system along with power dissipated due to dielectric loss and mechanical and structural damping. Overall power consumption is thus quantified as a function of peak applied voltage and driving frequency. It was demonstrated that by incorporating the variation of capacitance and power loss with voltage and frequency, satisfactory estimates of power requirements can be obtained. These relations allow general guidelines in selection and application of piezoelectric actuators and driving electronics for active control applications.

Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World

PubMed Central

Haas, W. Randall; Klink, Cynthia J.; Maggard, Greg J.; Aldenderfer, Mark S.

2015-01-01

Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare—behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation. PMID:26536241

Experimental observation of the influence of furnace temperature profile on convection and segregation in the vertical Bridgman crystal growth technique

NASA Technical Reports Server (NTRS)

Neugebauer, G. T.; Wilcox, William R.

1992-01-01

Azulene-doped naphthalene was directionally solidified during the vertical Bridgman-Stockbarger technique. Doping homogeneity and convection were determined as a function of the temperature profile in the furnace and the freezing rate. Convection velocities were two orders of magnitude lower when the temperature increased with height. Rarely was the convection pattern axisymmetric, even though the temperature varied less than 0.1 K around the circumference of the growth ampoule. Correspondingly the cross sectional variation in azulene concentration tended to be asymmetric, especially when the temperature increased with height. This cross sectional variation changed dramatically along the ingot, reflecting changes in convection presumably due to the decreasing height of the melt. Although there was large scatter and irreproducibility in the cross sectional variation in doping, this variation tended to be least when the growth rate was low and the convection was vigorous. It is expected that compositional variations would also be small at high growth rates with weak convection and flat interfaces, although this was not investigated in the present experiments. Neither rotation of the ampoule nor deliberate introduction of thermal asymmetries during solidification had a significant influence on cross sectional variations in doping. It is predicted that slow directional solidification under microgravity conditions could produce greater inhomogeneities than on Earth. Combined use of microgravity and magnetic fields would be required to achieve homogeneity when it is necessary to freeze slowly in order to avoid constitutional supercooling.

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

Large Work Function Modulation of Monolayer MoS2 by Ambient Gases.

PubMed

Lee, Si Young; Kim, Un Jeong; Chung, JaeGwan; Nam, Honggi; Jeong, Hye Yun; Han, Gang Hee; Kim, Hyun; Oh, Hye Min; Lee, Hyangsook; Kim, Hyochul; Roh, Young-Geun; Kim, Jineun; Hwang, Sung Woo; Park, Yeonsang; Lee, Young Hee

2016-06-28

Although two-dimensional monolayer transition-metal dichalcogenides reveal numerous unique features that are inaccessible in bulk materials, their intrinsic properties are often obscured by environmental effects. Among them, work function, which is the energy required to extract an electron from a material to vacuum, is one critical parameter in electronic/optoelectronic devices. Here, we report a large work function modulation in MoS2 via ambient gases. The work function was measured by an in situ Kelvin probe technique and further confirmed by ultraviolet photoemission spectroscopy and theoretical calculations. A measured work function of 4.04 eV in vacuum was converted to 4.47 eV with O2 exposure, which is comparable with a large variation in graphene. The homojunction diode by partially passivating a transistor reveals an ideal junction with an ideality factor of almost one and perfect electrical reversibility. The estimated depletion width obtained from photocurrent mapping was ∼200 nm, which is much narrower than bulk semiconductors.

Two-Component Noncollinear Time-Dependent Spin Density Functional Theory for Excited State Calculations.

PubMed

Egidi, Franco; Sun, Shichao; Goings, Joshua J; Scalmani, Giovanni; Frisch, Michael J; Li, Xiaosong

2017-06-13

We present a linear response formalism for the description of the electronic excitations of a noncollinear reference defined via Kohn-Sham spin density functional methods. A set of auxiliary variables, defined using the density and noncollinear magnetization density vector, allows the generalization of spin density functional kernels commonly used in collinear DFT to noncollinear cases, including local density, GGA, meta-GGA and hybrid functionals. Working equations and derivations of functional second derivatives with respect to the noncollinear density, required in the linear response noncollinear TDDFT formalism, are presented in this work. This formalism takes all components of the spin magnetization into account independent of the type of reference state (open or closed shell). As a result, the method introduced here is able to afford a nonzero local xc torque on the spin magnetization while still satisfying the zero-torque theorem globally. The formalism is applied to a few test cases using the variational exact-two-component reference including spin-orbit coupling to illustrate the capabilities of the method.

Multicompetence and Native Speaker Variation in Clausal Packaging in Japanese

ERIC Educational Resources Information Center

Brown, Amanda; Gullberg, Marianne

2012-01-01

Native speakers show systematic variation in a range of linguistic domains as a function of a variety of sociolinguistic variables. This article addresses native language variation in the context of multicompetence, i.e. knowledge of two languages in one mind (Cook, 1991). Descriptions of motion were elicited from functionally monolingual and…

Variations in the ceramide profile in different seasons and regions of the body contribute to stratum corneum functions.

PubMed

Ishikawa, Junko; Shimotoyodome, Yoshie; Ito, Shotaro; Miyauchi, Yuki; Fujimura, Tsutomu; Kitahara, Takashi; Hase, Tadashi

2013-03-01

The objective of this study was to clarify variations of the ceramide (CER) profile in human stratum corneum (SC) in different seasons and in different regions of the body and to estimate the contributions of CERs to the SC barrier and water-holding functions. Based on the information that there are great variations of SC functions among body sites, we compared the CER profiles obtained from ten different anatomical sites in healthy Japanese males in four seasons. Not only the physiological parameters of skin but also the CER profile showed body region and seasonal variations. The total CER level, the CER composition and the C34-CER[NS] species displayed strong correlations with the values of transepidermal water loss and capacitance throughout the body. Especially in the cheek, a strong correlation between the capacitance and the CER profile was observed. There were seasonal variations of the CER profile in the lip, upper arm and palm. Our results indicate that regional and seasonal variations of the CER profile may contribute to SC functions.

Planning and response to Ebola virus disease: An integrated approach.

PubMed

Smith, Philip W; Boulter, Kathleen C; Hewlett, Angela L; Kratochvil, Christopher J; Beam, Elizabeth J; Gibbs, Shawn G; Lowe, John-Martin J; Schwedhelm, Michelle M

2015-05-01

The care of patients with Ebola virus disease (EVD) requires the application of critical care medicine principles under conditions of stringent infection control precautions. The care of patients with EVD requires a number of elements in terms of physical layout, personal protective apparel, and other equipment. Provision of care is demanding in terms of depth of staff and training. The key to safely providing such care is a system that brings many valuable skills to the table, and allows communication between these individuals. We present our approach to leadership structure and function--a variation of incident command--in providing care to 3 patients with EVD. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Isometric deformations of unstretchable material surfaces, a spatial variational treatment

NASA Astrophysics Data System (ADS)

Chen, Yi-Chao; Fosdick, Roger; Fried, Eliot

2018-07-01

The stored energy of an unstretchable material surface is assumed to depend only upon the curvature tensor. By control of its edge(s), the surface is deformed isometrically from its planar undistorted reference configuration into an equilibrium shape. That shape is to be determined from a suitably constrained variational problem as a state of relative minimal potential energy. We pose the variational problem as one of relative minimum potential energy in a spatial form, wherein the deformation of a flat, undistorted region D in E2 to its distorted form S in E3 is assumed specified. We then apply the principle that the first variation of the potential energy, expressed as a functional over S ∪ ∂S , must vanish for all admissible variations that correspond to isometric deformations from the distorted configuration S and that also contain the essence of flatness that characterizes the reference configuration D , but is not covered by the single statement that the variation of S correspond to an isometric deformation. We emphasize the commonly overlooked condition that the spatial expression of the variational problem requires an additional variational constraint of zero Gaussian curvature to ensure that variations from S that are isometric deformations also contain the notion of flatness. In this context, it is particularly revealing to observe that the two constraints produce distinct, but essential and complementary, conditions on the first variation of S. The resulting first variation integral condition, together with the constraints, may be applied, for example, to the case of a flat, undistorted, rectangular strip D that is deformed isometrically into a closed ring S by connecting its short edges and specifying that its long edges are free of loading and, therefore, subject to zero traction and couple traction. The elementary example of a closed ring without twist as a state of relative minimum potential energy is discussed in detail, and the bending of the strip by opposing specific bending moments on its short edges is treated as a particular case. Finally, the constrained variational problem, with the introduction of appropriate constraint reactions as Lagrangian multipliers to account for the requirements that the deformation from D to S is isometric and that D is flat, is formulated in the spatial form, and the associated Euler-Lagrange equations are derived. We then solve the Euler-Lagrange equations for two representative problems in which a planar undistorted rectangular material strip is isometrically deformed by applied edge tractions and couple tractions (i.e., specific edge moments) into (i) a bent and twisted circular cylindrical helical state, and (ii) a state conformal with the surface of a right circular conical form.

Taking advantage of inclination variation in resonant remote-sensing satellite orbits

NASA Astrophysics Data System (ADS)

Gopinath, N. S.; Ravindrababu, T.; Rao, S. V.; Daniel, D. A.; Goel, P. S.

2004-08-01

The inclination of remote-sensing satellites, which are generally placed in sun-synchronous orbits, varies as a function of the nominal equatorial crossing local mean solar time selected for a given mission. The Indian Remote-Sensing satellites will have an inclination reduction of about 0.034° per year and for most of the satellites, the local time chosen was around 10:30 hours at descending node. In practice, the initial inclination is biased appropriately so that the expensive out-of-plane maneuvers could be taken up after few years of mission operations, depending on the deviations permitted in the local time for a given mission. However, the scenario differs when the mission objectives require an almost exact repeat orbit of 14 or 15 per day. In such a situation, the satellite orbit, which passes through a 14th or 15th order resonance, undergoes a nearly secular increase in orbit inclination. This paper presents a detailed analysis carried out for such an orbit, based on Cowell's approach. Long-term predictions have been carried out by considering all major forces that perturbs the satellite orbit. Observed behavior of orbit, based on the daily definitive orbit determination is also presented. The variation in inclination and the cause is clearly brought out. Further, it is demonstrated that the selection of longitude for nominal ground track pattern has an impact on the inclination variation. A proposal is made to take advantage of such expected inclination variation so that initial inclination bias can be chosen appropriately. Ground track longitude can be chosen to take advantage, subject to the mission coverage requirements. The paper contains the results of an exhaustive analysis of the actually observed orbit resonance. It is felt that the work has both theoretical and operational importance for remote-sensing missions.

In situ electron microscopy four-point electromechanical characterization of freestanding metallic and semiconducting nanowires.

PubMed

Bernal, Rodrigo A; Filleter, Tobin; Connell, Justin G; Sohn, Kwonnam; Huang, Jiaxing; Lauhon, Lincoln J; Espinosa, Horacio D

2014-02-26

Electromechanical coupling is a topic of current interest in nanostructures, such as metallic and semiconducting nanowires, for a variety of electronic and energy applications. As a result, the determination of structure-property relations that dictate the electromechanical coupling requires the development of experimental tools to perform accurate metrology. Here, a novel micro-electro-mechanical system (MEMS) that allows integrated four-point, uniaxial, electromechanical measurements of freestanding nanostructures in-situ electron microscopy, is reported. Coupled mechanical and electrical measurements are carried out for penta-twinned silver nanowires, their resistance is identified as a function of strain, and it is shown that resistance variations are the result of nanowire dimensional changes. Furthermore, in situ SEM piezoresistive measurements on n-type, [111]-oriented silicon nanowires up to unprecedented levels of ∼7% strain are demonstrated. The piezoresistance coefficients are found to be similar to bulk values. For both metallic and semiconducting nanowires, variations of the contact resistance as strain is applied are observed. These variations must be considered in the interpretation of future two-point electromechanical measurements. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni.

PubMed

Sternes, Peter R; Borneman, Anthony R

2016-04-27

Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes. Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe. By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species.

Beyond directed evolution - semi-rational protein engineering and design

PubMed Central

Lutz, Stefan

2010-01-01

Over the last two decades, directed evolution has transformed the field of protein engineering. The advances in understanding protein structure and function, in no insignificant part a result of directed evolution studies, are increasingly empowering scientists and engineers to device more effective methods for manipulating and tailoring biocatalysts. Abandoning large combinatorial libraries, the focus has shifted to small, functionally-rich libraries and rational design. A critical component to the success of these emerging engineering strategies are computational tools for the evaluation of protein sequence datasets and the analysis of conformational variations of amino acids in proteins. Highlighting the opportunities and limitations of such approaches, this review focuses on recent engineering and design examples that require screening or selection of small libraries. PMID:20869867

Effort of spanwise variation of turbulence on the normal acceleration of airplanes with small span relative to turbulence scale

NASA Technical Reports Server (NTRS)

Pratt, K. G.

1975-01-01

A rigid airplane with an unswept wing is analyzed. The results show that the power spectrum, relative to that for a one-dimensional turbulence field, is significantly attenuated at the higher frequencies even for airplanes with arbitrarily small ratios of span to scale of turbulence. This attenuation is described by a simple weighting function of frequency that depends only on aspect ratio. The weighting function, together with the attenuation due to the unsteady flow of gust penetration, allows the determination of the average rate of zero crossings for airplanes having very small spans without recourse to an integral truncation which is often required in calculations based on a one-dimensional turbulence field.

Use of mixed-function oxygenases to monitor contaminant exposure in wildlife

USGS Publications Warehouse

Rattner, B.A.; Hoffman, D.J.; Marn, C.M.

1989-01-01

This overview examines the utility of mixed-function oxygenase (MFO) enzymes as a bioeffects monitor for wildlife (amphibians, reptiles, birds and mammals) in view of their widespread use as indicators of contaminant exposure in aquatic invertebrates and fish. Phylogenetic trends in MFO activity, toxicological implications of induction and the relationship between contaminant exposure and MFO activity are discussed. Field studies using avian embryos and hatchlings suggest that MFO induction has utility for documenting contaminant exposure; however, findings in adult birds and mammals are equivocal. Age, sex and season are sources of variation that require consideration when undertaking field trials. Further understanding of MFO inducibility among species and application of recently developed analytical techniques including quantification of specific cytochrome P-450 isozymes are warranted.

ANIMAL BEHAVIOR AND WELL-BEING SYMPOSIUM: Interaction between coping style/personality, stress, and welfare: Relevance for domestic farm animals.

PubMed

Koolhaas, J M; Van Reenen, C G

2016-06-01

This paper will argue that understanding animal welfare and the individual vulnerability to stress-related disease requires a fundamental understanding of functional individual variation as it occurs in nature as well as the underlying neurobiology and neuroendocrinology. Ecological studies in feral populations of mice, fish, and birds start to recognize the functional significance of phenotypes that individually differ in their behavioral and neuroendocrine response to environmental challenge. Recent studies indicate that the individual variation within a species may buffer the species for strong fluctuations in the natural habitat. Similarly, evolutionary ancient behavioral trait characteristics have now been identified in a range of domestic farm animals including cattle, pigs, and horses. Individual variation in behavior can be summarized in a 3-dimensional model with coping style, emotionality, and sociality as independent dimensions. These dimensions can be considered trait characteristics that are stable over time and across situations within the individual. This conceptual model has several consequences. First, the coping style dimension is strongly associated with differential stress vulnerability. Social stress studies show that proactive individuals are resilient under stable environmental conditions but vulnerable when outcome expectancies are violated. Reactive individuals are, in fact, rather flexible and seem to adapt more easily to a changing environment. A second consequence relates to genetics and breeding. Genetic selection for one trait usually implies selection for other traits as well. It is discussed that a more balanced breeding program that takes into account biologically functional temperamental traits will lead to more robust domestic farm animals. Finally, the relationship between temperamental traits, animal production, fitness, and welfare is discussed.

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

PubMed Central

Kutyavin, Tanya; Stamatoyannopoulos, John A.

2012-01-01

The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation. However, it is currently not possible to interpret reliably the functional consequences of genetic variation within any given transcription factor recognition sequence. To address this, we comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic variability in binding site sequences across a multi-generational pedigree. We localized and quantified CTCF occupancy by ChIP-seq in 12 related and unrelated individuals spanning three generations, followed by comprehensive targeted resequencing of the entire CTCF–binding landscape across all individuals. We identified hundreds of variants with reproducible quantitative effects on CTCF occupancy (both positive and negative). While these effects paralleled protein–DNA recognition energetics when averaged, they were extensively buffered by striking local context dependencies. In the significant majority of cases buffering was complete, resulting in silent variants spanning every position within the DNA recognition interface irrespective of level of binding energy or evolutionary constraint. The prevalence of complex partial or complete buffering effects severely constrained the ability to predict reliably the impact of variation within any given binding site instance. Surprisingly, 40% of variants that increased CTCF occupancy occurred at positions of human–chimp divergence, challenging the expectation that the vast majority of functional regulatory variants should be deleterious. Our results suggest that, even in the presence of “perfect” genetic information afforded by resequencing and parallel studies in multiple related individuals, genomic site-specific prediction of the consequences of individual variation in regulatory DNA will require systematic coupling with empirical functional genomic measurements. PMID:22457641

Thyroid Function Variations Within the Reference Range Do Not Affect Quality of Life, Mood, or Cognitive Function in Community-Dwelling Older Men.

PubMed

Samuels, Mary H; Kaimal, Rajani; Waring, Avantika; Fink, Howard A; Yaffe, Kristine; Hoffman, Andrew R; Orwoll, Eric; Bauer, Douglas

2016-09-01

Variations in thyroid function within the laboratory reference range have been associated with a number of clinical outcomes. However, quality of life, mood, and cognitive function have not been extensively studied, and it is not clear whether mild variations in thyroid function have major effects on these neurocognitive outcomes. Data were analyzed from the Osteoporotic Fractures in Men (MrOS) Study, a cohort of community-dwelling men aged 65 years and older in the United States. A total of 539 participants who were not taking thyroid medications and had age-adjusted TSH levels within the reference range underwent detailed testing of quality of life, mood, and cognitive function at baseline. The same quality of life, mood, and cognitive outcomes were measured again in 193 of the men after a mean follow-up of 6 years. Outcomes were analyzed using thyrotropin (TSH) and free thyroxine (FT4) levels as continuous independent variables, adjusting for relevant covariates. At baseline, there were no associations between TSH or FT4 levels and measures of quality of life, mood, or cognition in the 539 euthyroid men. Baseline thyroid function did not predict changes in these outcomes over a mean of 6 years in the 193 men in the longitudinal analysis. Variations in thyroid function within the age-adjusted laboratory reference range are not associated with variations in quality of life, mood, or cognitive function in community-dwelling older men.

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.

PubMed

Hautier, Yann; Isbell, Forest; Borer, Elizabeth T; Seabloom, Eric W; Harpole, W Stanley; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Adler, Peter B; Alberti, Juan; Bakker, Jonathan D; Brudvig, Lars A; Buckley, Yvonne M; Cadotte, Marc; Caldeira, Maria C; Chaneton, Enrique J; Chu, Chengjin; Daleo, Pedro; Dickman, Christopher R; Dwyer, John M; Eskelinen, Anu; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Hillebrand, Helmut; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; McCulley, Rebecca L; Morgan, John W; Pärtel, Meelis; Pascual, Jesus; Price, Jodi N; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Standish, Rachel J; Virtanen, Risto; Wardle, Glenda M; Yahdjian, Laura; Hector, Andy

2018-01-01

Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.

Partitioning of functional gene expression data using principal points.

PubMed

Kim, Jaehee; Kim, Haseong

2017-10-12

DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data since they are considered as independent realizations of a stochastic process. This process requires appropriate models to identify patterns of gene functions. The partitioning of the functional data can find homogeneous subgroups of entities for the massive genes within the inherent biological networks. Therefor it can be a useful technique for the analysis of time-course gene expression data. We propose a new self-consistent partitioning method of functional coefficients for individual expression profiles based on the orthonormal basis system. A principal points based functional partitioning method is proposed for time-course gene expression data. The method explores the relationship between genes using Legendre coefficients as principal points to extract the features of gene functions. Our proposed method provides high connectivity in connectedness after clustering for simulated data and finds a significant subsets of genes with the increased connectivity. Our approach has comparative advantages that fewer coefficients are used from the functional data and self-consistency of principal points for partitioning. As real data applications, we are able to find partitioned genes through the gene expressions found in budding yeast data and Escherichia coli data. The proposed method benefitted from the use of principal points, dimension reduction, and choice of orthogonal basis system as well as provides appropriately connected genes in the resulting subsets. We illustrate our method by applying with each set of cell-cycle-regulated time-course yeast genes and E. coli genes. The proposed method is able to identify highly connected genes and to explore the complex dynamics of biological systems in functional genomics.

Adaptation of the Carter-Tracy water influx calculation to groundwater flow simulation

USGS Publications Warehouse

Kipp, Kenneth L.

1986-01-01

The Carter-Tracy calculation for water influx is adapted to groundwater flow simulation with additional clarifying explanation not present in the original papers. The Van Everdingen and Hurst aquifer-influence functions for radial flow from an outer aquifer region are employed. This technique, based on convolution of unit-step response functions, offers a simple but approximate method for embedding an inner region of groundwater flow simulation within a much larger aquifer region where flow can be treated in an approximate fashion. The use of aquifer-influence functions in groundwater flow modeling reduces the size of the computational grid with a corresponding reduction in computer storage and execution time. The Carter-Tracy approximation to the convolution integral enables the aquifer influence function calculation to be made with an additional storage requirement of only two times the number of boundary nodes more than that required for the inner region simulation. It is a good approximation for constant flow rates but is poor for time-varying flow rates where the variation is large relative to the mean. A variety of outer aquifer region geometries, exterior boundary conditions, and flow rate versus potentiometric head relations can be used. The radial, transient-flow case presented is representative. An analytical approximation to the functions of Van Everdingen and Hurst for the dimensionless potentiometric head versus dimensionless time is given.

Understanding the cellular and molecular mechanisms of dominant and recessive inheritance in genetics course.

PubMed

Wanjin, Xing; Morigen, Morigen

2015-01-01

In Mendellian genetics, the dominance and recessiveness are used to describe the functional relationship between two alleles of one gene in a heterozygote. The allele which constitutes a phenotypical character over the other is named dominant and the one functionally masked is called recessive. The definitions thereby led to the creation of Mendel's laws on segregation and independent assortment and subsequent classic genetics. The discrimination of dominance and recessiveness originally is a requirement for Mendel's logical reasoning, but now it should be explained by cellular and molecular principles in the modern genetics. To answer the question raised by students of how the dominance and recessiveness are controlled, we reviewed the recent articles and tried to summarize the cellular and molecular basis of dominant and recessive inheritance. Clearly, understanding the essences of dominant and recessive inheritance requires us to know the dissimilarity of the alleles and their products (RNA and/or proteins), and the way of their function in cells. The alleles spatio-temporally play different roles on offering cells, tissues or organs with discernible phenotypes, namely dominant or recessive. Here, we discuss the changes of allele dominance and recessiveness at the cellular and molecular levels based on the variation of gene structure, gene regulation, function and types of gene products, in order to make students understand gene mutation and function more comprehensively and concretely.

α satellite DNA variation and function of the human centromere

PubMed Central

Sullivan, Lori L.; Chew, Kimberline

2017-01-01

ABSTRACT Genomic variation is a source of functional diversity that is typically studied in genic and non-coding regulatory regions. However, the extent of variation within noncoding portions of the human genome, particularly highly repetitive regions, and the functional consequences are not well understood. Satellite DNA, including α satellite DNA found at human centromeres, comprises up to 10% of the genome, but is difficult to study because its repetitive nature hinders contiguous sequence assemblies. We recently described variation within α satellite DNA that affects centromere function. On human chromosome 17 (HSA17), we showed that size and sequence polymorphisms within primary array D17Z1 are associated with chromosome aneuploidy and defective centromere architecture. However, HSA17 can counteract this instability by assembling the centromere at a second, “backup” array lacking variation. Here, we discuss our findings in a broader context of human centromere assembly, and highlight areas of future study to uncover links between genomic and epigenetic features of human centromeres. PMID:28406740

Effects of Surface Nonuniformities on the Mean Transverse Energy from Photocathodes

NASA Astrophysics Data System (ADS)

Karkare, Siddharth; Bazarov, Ivan

2015-08-01

The performance of photoinjectors is limited by the lowest value of the mean transverse energy of the electrons obtained from photocathodes. The factors that influence the mean transverse energy are poorly understood. In this paper, we develop models to calculate the effect of spatial work-function variations and subnanometer-scale roughness and surface defects on the mean transverse energy. We show that these can limit the lowest value of mean transverse energy achieved and that atomically perfect surfaces will be required to further reduce the mean transverse energy obtained from photocathodes.

Modeling games from the 20th century

PubMed Central

Killeen, P.R.

2008-01-01

A scientific framework is described in which scientists are cast as problem-solvers, and problems as solved when data are mapped to models. This endeavor is limited by finite attentional capacity which keeps depth of understanding complementary to breadth of vision; and which distinguishes the process of science from its products, scientists from scholars. All four aspects of explanation described by Aristotle trigger, function, substrate, and model are required for comprehension. Various modeling languages are described, ranging from set theory to calculus of variations, along with exemplary applications in behavior analysis. PMID:11369459

Variation in Sulfur and Selenium Accumulation Is Controlled by Naturally Occurring Isoforms of the Key Sulfur Assimilation Enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis Species Range1[W][OPEN

PubMed Central

Chao, Dai-Yin; Baraniecka, Patrycja; Danku, John; Koprivova, Anna; Lahner, Brett; Luo, Hongbing; Yakubova, Elena; Dilkes, Brian; Kopriva, Stanislav; Salt, David E.

2014-01-01

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored. PMID:25245030

Further Constraints on Variations in the Initial Mass Function from Low-mass X-ray Binary Populations

NASA Astrophysics Data System (ADS)

Peacock, Mark B.; Zepf, Stephen E.; Kundu, Arunav; Maccarone, Thomas J.; Lehmer, Bret D.; Maraston, Claudia; Gonzalez, Anthony H.; Eufrasio, Rafael T.; Coulter, David A.

2017-05-01

We present constraints on variations in the initial mass function (IMF) of nine local early-type galaxies based on their low-mass X-ray binary (LMXB) populations. Comprised of accreting black holes and neutron stars, these LMXBs can be used to constrain the important high-mass end of the IMF. We consider LMXB populations beyond the cores of the galaxies (>0.2R e; covering 75%-90% of their stellar light) and find no evidence for systematic variations of the IMF with velocity dispersion (σ). We reject IMFs which become increasingly bottom-heavy with σ, up to steep power laws (exponent, α > 2.8) in massive galaxies (σ > 300 {km} {{{s}}}-1), for galactocentric radii >1/4 R e. Previously proposed IMFs that become increasingly bottom-heavy with σ are consistent with these data if only the number of low-mass stars (<0.5 M ⊙) varies. We note that our results are consistent with some recent work which proposes that extreme IMFs are only present in the central regions of these galaxies. We also consider IMFs that become increasingly top-heavy with σ, resulting in significantly more LMXBs. Such a model is consistent with these observations, but additional data are required to significantly distinguish between this and an invariant IMF. For six of these galaxies, we directly compare with published “IMF mismatch” parameters from the Atlas3D survey, α dyn. We find good agreement with the LMXB population if galaxies with higher α dyn have more top-heavy IMFs—although we caution that our sample is quite small. Future LMXB observations can provide further insights into the origin of α dyn variations.

Greek classicism in living structure? Some deductive pathways in animal morphology.

PubMed

Zweers, G A

1985-01-01

Classical temples in ancient Greece show two deterministic illusionistic principles of architecture, which govern their functional design: geometric proportionalism and a set of illusion-strengthening rules in the proportionalism's "stochastic margin". Animal morphology, in its mechanistic-deductive revival, applies just one architectural principle, which is not always satisfactory. Whether a "Greek Classical" situation occurs in the architecture of living structure is to be investigated by extreme testing with deductive methods. Three deductive methods for explanation of living structure in animal morphology are proposed: the parts, the compromise, and the transformation deduction. The methods are based upon the systems concept for an organism, the flow chart for a functionalistic picture, and the network chart for a structuralistic picture, whereas the "optimal design" serves as the architectural principle for living structure. These methods show clearly the high explanatory power of deductive methods in morphology, but they also make one open end most explicit: neutral issues do exist. Full explanation of living structure asks for three entries: functional design within architectural and transformational constraints. The transformational constraint brings necessarily in a stochastic component: an at random variation being a sort of "free management space". This variation must be a variation from the deterministic principle of the optimal design, since any transformation requires space for plasticity in structure and action, and flexibility in role fulfilling. Nevertheless, finally the question comes up whether for animal structure a similar situation exists as in Greek Classical temples. This means that the at random variation, that is found when the optimal design is used to explain structure, comprises apart from a stochastic part also real deviations being yet another deterministic part. This deterministic part could be a set of rules that governs actualization in the "free management space".

Probing Mantle Heterogeneity Across Spatial Scales

NASA Astrophysics Data System (ADS)

Hariharan, A.; Moulik, P.; Lekic, V.

2017-12-01

Inferences of mantle heterogeneity in terms of temperature, composition, grain size, melt and crystal structure may vary across local, regional and global scales. Probing these scale-dependent effects require quantitative comparisons and reconciliation of tomographic models that vary in their regional scope, parameterization, regularization and observational constraints. While a range of techniques like radial correlation functions and spherical harmonic analyses have revealed global features like the dominance of long-wavelength variations in mantle heterogeneity, they have limited applicability for specific regions of interest like subduction zones and continental cratons. Moreover, issues like discrepant 1-D reference Earth models and related baseline corrections have impeded the reconciliation of heterogeneity between various regional and global models. We implement a new wavelet-based approach that allows for structure to be filtered simultaneously in both the spectral and spatial domain, allowing us to characterize heterogeneity on a range of scales and in different geographical regions. Our algorithm extends a recent method that expanded lateral variations into the wavelet domain constructed on a cubed sphere. The isolation of reference velocities in the wavelet scaling function facilitates comparisons between models constructed with arbitrary 1-D reference Earth models. The wavelet transformation allows us to quantify the scale-dependent consistency between tomographic models in a region of interest and investigate the fits to data afforded by heterogeneity at various dominant wavelengths. We find substantial and spatially varying differences in the spectrum of heterogeneity between two representative global Vp models constructed using different data and methodologies. Applying the orthonormality of the wavelet expansion, we isolate detailed variations in velocity from models and evaluate additional fits to data afforded by adding such complexities to long-wavelength variations. Our method provides a way to probe and evaluate localized features in a multi-scale description of mantle heterogeneity.

Evolutionary constraints or opportunities?

PubMed

Sharov, Alexei A

2014-09-01

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). Published by Elsevier Ireland Ltd.

Genetic Variation in the Vesicular Monoamine Transporter: Preliminary associations with Cognitive Outcomes after Severe Traumatic Brain Injury

PubMed Central

Markos, Steven; Failla, Michelle D.; Ritter, Anne C; Dixon, C. Edward; Conley, Yvette P.; Ricker, Joseph H; Arenth, Patricia M.; Juengst, Shannon B.; Wagner, Amy K.

2015-01-01

Introduction Traumatic brain injury (TBI) frequently results in impaired cognition, a function that can be modulated by monoaminergic signaling. Genetic variation among monoaminergic genes may affect post-TBI cognitive performance. The vesicular monoamine transporter 2 (VMAT2) gene may be a novel source of genetic variation important for cognitive outcomes post-TBI given VMAT2’s role in monoaminergic neurotransmission. Objective Evaluate associations between VMAT2 variability and cognitive outcomes post-TBI. Methods We evaluated 136 white adults with severe TBI for variation in VMAT2 using a tagging single nucleotide polymorphism (tSNP) approach (rs363223, rs363226, rs363251, and rs363341). We show genetic variation interacts with assessed cognitive impairment [cognitive composite T-scores (Comp-Cog)] to influence functional cognition [Functional Independence Measure Cognitive subscale (FIM-Cog)] 6 and 12 months post-injury. Results Multivariate analyses at 6-months post-injury showed rs363226 genotype was associated with Comp-Cog (p=0.040) and interacted with Comp-Cog to influence functional cognition (p<0.001). G-homozygotes had the largest cognitive impairment, and their cognitive impairment had the greatest adverse effect on functional cognition. Discussion We provide the first evidence that genetic variation within VMAT2 is associated with cognitive outcomes following TBI. Further work is needed to validate this finding and elucidate mechanisms by which genetic variation affects monoaminergic signaling, mediating differences in cognitive outcomes. PMID:26828714

Convolving optically addressed VLSI liquid crystal SLM

NASA Astrophysics Data System (ADS)

Jared, David A.; Stirk, Charles W.

1994-03-01

We designed, fabricated, and tested an optically addressed spatial light modulator (SLM) that performs a 3 X 3 kernel image convolution using ferroelectric liquid crystal on VLSI technology. The chip contains a 16 X 16 array of current-mirror-based convolvers with a fixed kernel for finding edges. The pixels are located on 75 micron centers, and the modulators are 20 microns on a side. The array successfully enhanced edges in illumination patterns. We developed a high-level simulation tool (CON) for analyzing the performance of convolving SLM designs. CON has a graphical interface and simulates SLM functions using SPICE-like device models. The user specifies the pixel function along with the device parameters and nonuniformities. We discovered through analysis, simulation and experiment that the operation of current-mirror-based convolver pixels is degraded at low light levels by the variation of transistor threshold voltages inherent to CMOS chips. To function acceptable, the test SLM required the input image to have an minimum irradiance of 10 (mu) W/cm2. The minimum required irradiance can be further reduced by adding a photodarlington near the photodetector or by increasing the size of the transistors used to calculate the convolution.

Trends in stratospheric ozone profiles using functional mixed models

NASA Astrophysics Data System (ADS)

Park, A.; Guillas, S.; Petropavlovskikh, I.

2013-11-01

This paper is devoted to the modeling of altitude-dependent patterns of ozone variations over time. Umkehr ozone profiles (quarter of Umkehr layer) from 1978 to 2011 are investigated at two locations: Boulder (USA) and Arosa (Switzerland). The study consists of two statistical stages. First we approximate ozone profiles employing an appropriate basis. To capture primary modes of ozone variations without losing essential information, a functional principal component analysis is performed. It penalizes roughness of the function and smooths excessive variations in the shape of the ozone profiles. As a result, data-driven basis functions (empirical basis functions) are obtained. The coefficients (principal component scores) corresponding to the empirical basis functions represent dominant temporal evolution in the shape of ozone profiles. We use those time series coefficients in the second statistical step to reveal the important sources of the patterns and variations in the profiles. We estimate the effects of covariates - month, year (trend), quasi-biennial oscillation, the solar cycle, the Arctic oscillation, the El Niño/Southern Oscillation cycle and the Eliassen-Palm flux - on the principal component scores of ozone profiles using additive mixed effects models. The effects are represented as smooth functions and the smooth functions are estimated by penalized regression splines. We also impose a heteroscedastic error structure that reflects the observed seasonality in the errors. The more complex error structure enables us to provide more accurate estimates of influences and trends, together with enhanced uncertainty quantification. Also, we are able to capture fine variations in the time evolution of the profiles, such as the semi-annual oscillation. We conclude by showing the trends by altitude over Boulder and Arosa, as well as for total column ozone. There are great variations in the trends across altitudes, which highlights the benefits of modeling ozone profiles.

Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin

PubMed Central

Natarajan, Chandrasekhar; Hoffmann, Federico G.; Lanier, Hayley C.; Wolf, Cole J.; Cheviron, Zachary A.; Spangler, Matthew L.; Weber, Roy E.; Fago, Angela; Storz, Jay F.

2015-01-01

Major challenges for illuminating the genetic basis of phenotypic evolution are to identify causative mutations, to quantify their functional effects, to trace their origins as new or preexisting variants, and to assess the manner in which segregating variation is transduced into species differences. Here, we report an experimental analysis of genetic variation in hemoglobin (Hb) function within and among species of Peromyscus mice that are native to different elevations. A multilocus survey of sequence variation in the duplicated HBA and HBB genes in Peromyscus maniculatus revealed that function-altering amino acid variants are widely shared among geographically disparate populations from different elevations, and numerous amino acid polymorphisms are also shared with closely related species. Variation in Hb-O2 affinity within and among populations of P. maniculatus is attributable to numerous amino acid mutations that have individually small effects. One especially surprising feature of the Hb polymorphism in P. maniculatus is that an appreciable fraction of functional standing variation in the two transcriptionally active HBA paralogs is attributable to recurrent gene conversion from a tandemly linked HBA pseudogene. Moreover, transpecific polymorphism in the duplicated HBA genes is not solely attributable to incomplete lineage sorting or introgressive hybridization; instead, it is mainly attributable to recurrent interparalog gene conversion that has occurred independently in different species. Partly as a result of concerted evolution between tandemly duplicated globin genes, the same amino acid changes that contribute to variation in Hb function within P. maniculatus also contribute to divergence in Hb function among different species of Peromyscus. In the case of function-altering Hb mutations in Peromyscus, there is no qualitative or quantitative distinction between segregating variants within species and fixed differences between species. PMID:25556236

A common-path optical coherence tomography based electrode for structural imaging of nerves and recording of action potentials

NASA Astrophysics Data System (ADS)

Islam, M. Shahidul; Haque, Md. Rezuanul; Oh, Christian M.; Wang, Yan; Park, B. Hyle

2013-03-01

Current technologies for monitoring neural activity either use different variety of electrodes (electrical recording) or require contrast agents introduced exogenously or through genetic modification (optical imaging). Here we demonstrate an optical method for non-contact and contrast agent free detection of nerve activity using phase-resolved optical coherence tomography (pr-OCT). A common-path variation of the pr-OCT is recently implemented and the developed system demonstrated the capability to detect rapid transient structural changes that accompany neural spike propagation. No averaging over multiple trials was required, indicating its capability of single-shot detection of individual impulses from functionally stimulated Limulus optic nerve. The strength of this OCT-based optical electrode is that it is a contactless method and does not require any exogenous contrast agent. With further improvements in accuracy and sensitivity, this optical electrode will play a complementary role to the existing recording technologies in future.

Sources of Variation in Sweat Chloride Measurements in Cystic Fibrosis.

PubMed

Collaco, Joseph M; Blackman, Scott M; Raraigh, Karen S; Corvol, Harriet; Rommens, Johanna M; Pace, Rhonda G; Boelle, Pierre-Yves; McGready, John; Sosnay, Patrick R; Strug, Lisa J; Knowles, Michael R; Cutting, Garry R

2016-12-01

Expanding the use of cystic fibrosis transmembrane conductance regulator (CFTR) potentiators and correctors for the treatment of cystic fibrosis (CF) requires precise and accurate biomarkers. Sweat chloride concentration provides an in vivo assessment of CFTR function, but it is unknown the degree to which CFTR mutations account for sweat chloride variation. To estimate potential sources of variation for sweat chloride measurements, including demographic factors, testing variability, recording biases, and CFTR genotype itself. A total of 2,639 sweat chloride measurements were obtained in 1,761 twins/siblings from the CF Twin-Sibling Study, French CF Modifier Gene Study, and Canadian Consortium for Genetic Studies. Variance component estimation was performed by nested mixed modeling. Across the tested CF population as a whole, CFTR gene mutations were found to be the primary determinant of sweat chloride variability (56.1% of variation) with contributions from variation over time (e.g., factors related to testing on different days; 13.8%), environmental factors (e.g., climate, family diet; 13.5%), other residual factors (e.g., test variability; 9.9%), and unique individual factors (e.g., modifier genes, unique exposures; 6.8%) (likelihood ratio test, P < 0.001). Twin analysis suggested that modifier genes did not play a significant role because the heritability estimate was negligible (H 2  = 0; 95% confidence interval, 0.0-0.35). For an individual with CF, variation in sweat chloride was primarily caused by variation over time (58.1%) with the remainder attributable to residual/random factors (41.9%). Variation in the CFTR gene is the predominant cause of sweat chloride variation; most of the non-CFTR variation is caused by testing variability and unique environmental factors. If test precision and accuracy can be improved, sweat chloride measurement could be a valuable biomarker for assessing response to therapies directed at mutant CFTR.

Sources of Variation in Sweat Chloride Measurements in Cystic Fibrosis

PubMed Central

Blackman, Scott M.; Raraigh, Karen S.; Corvol, Harriet; Rommens, Johanna M.; Pace, Rhonda G.; Boelle, Pierre-Yves; McGready, John; Sosnay, Patrick R.; Strug, Lisa J.; Knowles, Michael R.; Cutting, Garry R.

2016-01-01

Rationale: Expanding the use of cystic fibrosis transmembrane conductance regulator (CFTR) potentiators and correctors for the treatment of cystic fibrosis (CF) requires precise and accurate biomarkers. Sweat chloride concentration provides an in vivo assessment of CFTR function, but it is unknown the degree to which CFTR mutations account for sweat chloride variation. Objectives: To estimate potential sources of variation for sweat chloride measurements, including demographic factors, testing variability, recording biases, and CFTR genotype itself. Methods: A total of 2,639 sweat chloride measurements were obtained in 1,761 twins/siblings from the CF Twin-Sibling Study, French CF Modifier Gene Study, and Canadian Consortium for Genetic Studies. Variance component estimation was performed by nested mixed modeling. Measurements and Main Results: Across the tested CF population as a whole, CFTR gene mutations were found to be the primary determinant of sweat chloride variability (56.1% of variation) with contributions from variation over time (e.g., factors related to testing on different days; 13.8%), environmental factors (e.g., climate, family diet; 13.5%), other residual factors (e.g., test variability; 9.9%), and unique individual factors (e.g., modifier genes, unique exposures; 6.8%) (likelihood ratio test, P < 0.001). Twin analysis suggested that modifier genes did not play a significant role because the heritability estimate was negligible (H2 = 0; 95% confidence interval, 0.0–0.35). For an individual with CF, variation in sweat chloride was primarily caused by variation over time (58.1%) with the remainder attributable to residual/random factors (41.9%). Conclusions: Variation in the CFTR gene is the predominant cause of sweat chloride variation; most of the non-CFTR variation is caused by testing variability and unique environmental factors. If test precision and accuracy can be improved, sweat chloride measurement could be a valuable biomarker for assessing response to therapies directed at mutant CFTR. PMID:27258095

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

Balian, R., E-mail: roger.balian@cea.fr; Vénéroni, M.

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces themore » original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie–Poisson structure. At second order, the variational expression for two-time correlation functions separates–as does its exact counterpart–the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.« less

Global meta-analysis of leaf area index in wetlands indicates uncertainties in understanding of their ecosystem function

NASA Astrophysics Data System (ADS)

Dronova, I.; Taddeo, S.; Foster, K.

2017-12-01

Projecting ecosystem responses to global change relies on the accurate understanding of properties governing their functions in different environments. An important variable in models of ecosystem function is canopy leaf area index (LAI; leaf area per unit ground area) declared as one of the Essential Climate Variables in the Global Climate Observing System and extensively measured in terrestrial landscapes. However, wetlands have been largely under-represented in these efforts, which globally limits understanding of their contribution to carbon sequestration, climate regulation and resilience to natural and anthropogenic disturbances. This study provides a global synthesis of >350 wetland-specific LAI observations from 182 studies and compares LAI among wetland ecosystem and vegetation types, biomes and measurement approaches. Results indicate that most wetland types and even individual locations show a substantial local dispersion of LAI values (average coefficient of variation 65%) due to heterogeneity of environmental properties and vegetation composition. Such variation indicates that mean LAI values may not sufficiently represent complex wetland environments, and the use of this index in ecosystem function models needs to incorporate within-site variation in canopy properties. Mean LAI did not significantly differ between direct and indirect measurement methods on a pooled global sample; however, within some of the specific biomes and wetland types significant contrasts between these approaches were detected. These contrasts highlight unique aspects of wetland vegetation physiology and canopy structure affecting measurement principles that need to be considered in generalizing canopy properties in ecosystem models. Finally, efforts to assess wetland LAI using remote sensing strongly indicate the promise of this technology for cost-effective regional-scale modeling of canopy properties similar to terrestrial systems. However, such efforts urgently require more rigorous corrections for three-dimensional contributions of non-canopy material and non-vegetated surfaces to wetland canopy reflectance.

Estimation of environmental flow incorporating water quality and hypothetical climate change scenarios.

PubMed

Walling, Bendangtola; Chaudhary, Shushobhit; Dhanya, C T; Kumar, Arun

2017-05-01

Environmental flows (Eflow, hereafter) are the flows to be maintained in the river for its healthy functioning and the sustenance and protection of aquatic ecosystems. Estimation of Eflow in any river stretch demands consideration of various factors such as flow regime, ecosystem, and health of river. However, most of the Eflow estimation studies have neglected the water quality factor. This study urges the need to consider water quality criterion in the estimation of Eflow and proposes a framework for estimating Eflow incorporating water quality variations under present and hypothetical future scenarios of climate change and pollution load. The proposed framework is applied on the polluted stretch of Yamuna River passing through Delhi, India. Required Eflow at various locations along the stretch are determined by considering possible variations in future water quantity and quality. Eflow values satisfying minimum quality requirements for different river water usage classes (classes A, B, C, and D as specified by the Central Pollution Control Board, India) are found to be between 700 and 800 m 3 /s. The estimated Eflow values may aid policymakers to derive upstream storage-release policies or effluent restrictions. Generalized nature of this framework will help its implementation on any river systems.

Statistics, Uncertainty, and Transmitted Variation

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

Wendelberger, Joanne Roth

2014-11-05

The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

Spectral and geometrical variation of the bidirectional reflectance distribution function of diffuse reflectance standards.

PubMed

Ferrero, Alejandro; Rabal, Ana María; Campos, Joaquín; Pons, Alicia; Hernanz, María Luisa

2012-12-20

A study on the variation of the spectral bidirectional reflectance distribution function (BRDF) of four diffuse reflectance standards (matte ceramic, BaSO(4), Spectralon, and white Russian opal glass) is accomplished through this work. Spectral BRDF measurements were carried out and, using principal components analysis, its spectral and geometrical variation respect to a reference geometry was assessed from the experimental data. Several descriptors were defined in order to compare the spectral BRDF variation of the four materials.

ALDH1A2 (RALDH2) genetic variation in human congenital heart disease

PubMed Central

2009-01-01

Background Signaling by the vitamin A-derived morphogen retinoic acid (RA) is required at multiple steps of cardiac development. Since conversion of retinaldehyde to RA by retinaldehyde dehydrogenase type II (ALDH1A2, a.k.a RALDH2) is critical for cardiac development, we screened patients with congenital heart disease (CHDs) for genetic variation at the ALDH1A2 locus. Methods One-hundred and thirty-three CHD patients were screened for genetic variation at the ALDH1A2 locus through bi-directional sequencing. In addition, six SNPs (rs2704188, rs1441815, rs3784259, rs1530293, rs1899430) at the same locus were studied using a TDT-based association approach in 101 CHD trios. Observed mutations were modeled through molecular mechanics (MM) simulations using the AMBER 9 package, Sander and Pmemd programs. Sequence conservation of observed mutations was evaluated through phylogenetic tree construction from ungapped alignments containing ALDH8 s, ALDH1Ls, ALDH1 s and ALDH2 s. Trees were generated by the Neighbor Joining method. Variations potentially affecting splicing mechanisms were cloned and functional assays were designed to test splicing alterations using the pSPL3 splicing assay. Results We describe in Tetralogy of Fallot (TOF) the mutations Ala151Ser and Ile157Thr that change non-polar to polar residues at exon 4. Exon 4 encodes part of the highly-conserved tetramerization domain, a structural motif required for ALDH oligomerization. Molecular mechanics simulation studies of the two mutations indicate that they hinder tetramerization. We determined that the SNP rs16939660, previously associated with spina bifida and observed in patients with TOF, does not affect splicing. Moreover, association studies performed with classical models and with the transmission disequilibrium test (TDT) design using single marker genotype, or haplotype information do not show differences between cases and controls. Conclusion In summary, our screen indicates that ALDH1A2 genetic variation is present in TOF patients, suggesting a possible causal role for this gene in rare cases of human CHD, but does not support the hypothesis that variation at the ALDH1A2 locus is a significant modifier of the risk for CHD in humans. PMID:19886994

WE-G-18C-05: Characterization of Cross-Vendor, Cross-Field Strength MR Image Intensity Variations

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

Paulson, E; Prah, D

2014-06-15

Purpose: Variations in MR image intensity and image intensity nonuniformity (IINU) can challenge the accuracy of intensity-based image segmentation and registration algorithms commonly applied in radiotherapy. The goal of this work was to characterize MR image intensity variations across scanner vendors and field strengths commonly used in radiotherapy. Methods: ACR-MRI phantom images were acquired at 1.5T and 3.0T on GE (450w and 750, 23.1), Siemens (Espree and Verio, VB17B), and Philips (Ingenia, 4.1.3) scanners using commercial spin-echo sequences with matched parameters (TE/TR: 20/500 ms, rBW: 62.5 kHz, TH/skip: 5/5mm). Two radiofrequency (RF) coil combinations were used for each scanner: bodymore » coil alone, and combined body and phased-array head coils. Vendorspecific B1- corrections (PURE/Pre-Scan Normalize/CLEAR) were applied in all head coil cases. Images were transferred offline, corrected for IINU using the MNI N3 algorithm, and normalized. Coefficients of variation (CV=σ/μ) and peak image uniformity (PIU = 1−(Smax−Smin)/(Smax+Smin)) estimates were calculated for one homogeneous phantom slice. Kruskal-Wallis and Wilcoxon matched-pairs tests compared mean MR signal intensities and differences between original and N3 image CV and PIU. Results: Wide variations in both MR image intensity and IINU were observed across scanner vendors, field strengths, and RF coil configurations. Applying the MNI N3 correction for IINU resulted in significant improvements in both CV and PIU (p=0.0115, p=0.0235). However, wide variations in overall image intensity persisted, requiring image normalization to improve consistency across vendors, field strengths, and RF coils. These results indicate that B1- correction routines alone may be insufficient in compensating for IINU and image scaling, warranting additional corrections prior to use of MR images in radiotherapy. Conclusions: MR image intensities and IINU vary as a function of scanner vendor, field strength, and RF coil configuration. A two-step strategy consisting of MNI N3 correction followed by normalization was required to improve MR image consistency. Funding provided by Advancing a Healthier Wisconsin.« less

A rodent model for the study of invariant visual object recognition

PubMed Central

Zoccolan, Davide; Oertelt, Nadja; DiCarlo, James J.; Cox, David D.

2009-01-01

The human visual system is able to recognize objects despite tremendous variation in their appearance on the retina resulting from variation in view, size, lighting, etc. This ability—known as “invariant” object recognition—is central to visual perception, yet its computational underpinnings are poorly understood. Traditionally, nonhuman primates have been the animal model-of-choice for investigating the neuronal substrates of invariant recognition, because their visual systems closely mirror our own. Meanwhile, simpler and more accessible animal models such as rodents have been largely overlooked as possible models of higher-level visual functions, because their brains are often assumed to lack advanced visual processing machinery. As a result, little is known about rodents' ability to process complex visual stimuli in the face of real-world image variation. In the present work, we show that rats possess more advanced visual abilities than previously appreciated. Specifically, we trained pigmented rats to perform a visual task that required them to recognize objects despite substantial variation in their appearance, due to changes in size, view, and lighting. Critically, rats were able to spontaneously generalize to previously unseen transformations of learned objects. These results provide the first systematic evidence for invariant object recognition in rats and argue for an increased focus on rodents as models for studying high-level visual processing. PMID:19429704

Individual diet variation in a marine fish assemblage: Optimal Foraging Theory, Niche Variation Hypothesis and functional identity

NASA Astrophysics Data System (ADS)

Cachera, M.; Ernande, B.; Villanueva, M. C.; Lefebvre, S.

2017-02-01

Individual diet variation (i.e. diet variation among individuals) impacts intra- and inter-specific interactions. Investigating its sources and relationship with species trophic niche organization is important for understanding community structure and dynamics. Individual diet variation may increase with intra-specific phenotypic (or "individual state") variation and habitat variability, according to Optimal Foraging Theory (OFT), and with species trophic niche width, according to the Niche Variation Hypothesis (NVH). OFT proposes "proximate sources" of individual diet variation such as variations in habitat or size whereas NVH relies on "ultimate sources" related to the competitive balance between intra- and inter-specific competitions. The latter implies as a corollary that species trophic niche overlap, taken as inter-specific competition measure, decreases as species niche width and individual niche variation increase. We tested the complementary predictions of OFT and NVH in a marine fish assemblage using stomach content data and associated trophic niche metrics. The NVH predictions were tested between species of the assemblage and decomposed into a between- and a within-functional group component to assess the potential influence of species' ecological function. For most species, individual diet variation and niche overlap were consistently larger than expected. Individual diet variation increased with intra-specific variability in individual state and habitat, as expected from OFT. It also increased with species niche width but in compliance with the null expectation, thus not supporting the NVH. In contrast, species niche overlap increased significantly less than null expectation with both species niche width and individual diet variation, supporting NVH corollary. The between- and within-functional group components of the NVH relationships were consistent with those between species at the assemblage level. Changing the number of prey categories used to describe diet (from 16 to 41) did not change the results qualitatively. These results suggest that, besides proximate sources, intra-specific competition favors higher individual diet variation than expected while inter-specific competition limits the increase of individual diet variation and of species niche overlap with species niche expansion. This reveals partial trophic resource partitioning between species. Various niche metrics used in combination allow inferring competition effects on trophic niches' organization within communities.

Relationships of vascular function with measures of ambulatory blood pressure variation.

PubMed

Hodgson, Jonathan M; Woodman, Richard J; Croft, Kevin D; Ward, Natalie C; Bondonno, Catherine P; Puddey, Ian B; Lukoshkova, Elena V; Head, Geoffrey A

2014-03-01

Characteristics of short-term blood pressure (BP) variation may influence cardiovascular disease risk via effects on vascular function. In a cross-sectional study of a group of treated hypertensive and untreated largely normotensive subjects we investigated the relationships of measures of short-term BP variation with brachial artery vasodilator function. A total of 163 treated hypertensive (n = 91) and untreated largely normotensive (n = 72) men and women were recruited from the general population. Measures of systolic and diastolic BP variation were calculated from 24 h ambulatory BP assessments and included: (i) rate of measurement-to-measurement BP variation (SBP-var and DBP-var); and (ii) day-to-night BP dip (SBP-dip and DBP dip). Endothelium-dependent vasodilation was assessed as flow-mediated dilation (FMD) and endothelium-independent vasodilation was assessed in response to glyceryl trinitrate (GTN). Relationships were explored using univariate and multivariate linear regression. The relationships of brachial artery vasodilator function with BP variation were not significantly different between treated hypertensive and untreated subjects, therefore these groups were combined for analysis. In univariate analysis, higher SBP-var (P < 0.001) and lower DBP-dip (P = 0.004) were associated with lower FMD; and higher SBP-var (P = 0.002) and lower SBP-dip (P = 0.003) and DBP-dip (P = 0.001) were associated with lower GTN-mediated dilation. In multivariate analysis, lower SBP-dip (P = 0.007) and DBP-dip (P = 0.03) were independently associated with lower GTN response. Our results indicate that a lower day-to-night BP dip is independently associated with impaired smooth muscle cell function. Although rate of BP variation was associated with measures of endothelial and smooth muscle cell function, relationships were attenuated after accounting for age and BP. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

PubMed

Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg, Jason; Ng, Cherie T; Krogan, Nevan; Sharan, Roded; Ideker, Trey

2016-02-24

Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by the Gene Ontology or a complementary ontology inferred directly from previously published datasets. Guided by the ontology's hierarchical structure, we organize genotype data into an "ontotype," that is, a hierarchy of perturbations representing the effects of genetic variation at multiple cellular scales. The ontotype is then interpreted using logical rules generated by machine learning to predict phenotype. This approach substantially outperforms previous, non-hierarchical methods for translating yeast genotype to cell growth phenotype, and it accurately predicts the growth outcomes of two new screens of 2,503 double gene knockouts impacting DNA repair or nuclear lumen. Ontotypes also generalize to larger knockout combinations, setting the stage for interpreting the complex genetics of disease.

STEM-EDX tomography of bimetallic nanoparticles: A methodological investigation

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

Slater, Thomas J. A.; Janssen, Arne; Camargo, Pedro H. C.

This paper presents an investigation of the limitations and optimization of energy dispersive X-ray (EDX) tomography within the scanning transmission electron microscope, focussing on application of the technique to characterising the 3D elemental distribution of bimetallic AgAu nanoparticles. The detector collection efficiency when using a standard tomography holder is characterised using a tomographic data set from a single nanoparticle and compared to a standard low background double tilt holder. Optical depth profiling is used to investigate the angles and origin of detector shadowing as a function of specimen field of view. A novel time-varied acquisition scheme is described to compensatemore » for variations in the intensity of spectrum images at each sample tilt. Lastly, the ability of EDX spectrum images to satisfy the projection requirement for nanoparticle samples is discussed, with consideration of the effect of absorption and shadowing variations« less

STEM-EDX tomography of bimetallic nanoparticles: A methodological investigation

DOE PAGES

Slater, Thomas J. A.; Janssen, Arne; Camargo, Pedro H. C.; ...

2015-10-22

This paper presents an investigation of the limitations and optimization of energy dispersive X-ray (EDX) tomography within the scanning transmission electron microscope, focussing on application of the technique to characterising the 3D elemental distribution of bimetallic AgAu nanoparticles. The detector collection efficiency when using a standard tomography holder is characterised using a tomographic data set from a single nanoparticle and compared to a standard low background double tilt holder. Optical depth profiling is used to investigate the angles and origin of detector shadowing as a function of specimen field of view. A novel time-varied acquisition scheme is described to compensatemore » for variations in the intensity of spectrum images at each sample tilt. Lastly, the ability of EDX spectrum images to satisfy the projection requirement for nanoparticle samples is discussed, with consideration of the effect of absorption and shadowing variations« less

Parameter selection in limited data cone-beam CT reconstruction using edge-preserving total variation algorithms

NASA Astrophysics Data System (ADS)

Lohvithee, Manasavee; Biguri, Ander; Soleimani, Manuchehr

2017-12-01

There are a number of powerful total variation (TV) regularization methods that have great promise in limited data cone-beam CT reconstruction with an enhancement of image quality. These promising TV methods require careful selection of the image reconstruction parameters, for which there are no well-established criteria. This paper presents a comprehensive evaluation of parameter selection in a number of major TV-based reconstruction algorithms. An appropriate way of selecting the values for each individual parameter has been suggested. Finally, a new adaptive-weighted projection-controlled steepest descent (AwPCSD) algorithm is presented, which implements the edge-preserving function for CBCT reconstruction with limited data. The proposed algorithm shows significant robustness compared to three other existing algorithms: ASD-POCS, AwASD-POCS and PCSD. The proposed AwPCSD algorithm is able to preserve the edges of the reconstructed images better with fewer sensitive parameters to tune.

Two dimensional radial gas flows in atmospheric pressure plasma-enhanced chemical vapor deposition

NASA Astrophysics Data System (ADS)

Kim, Gwihyun; Park, Seran; Shin, Hyunsu; Song, Seungho; Oh, Hoon-Jung; Ko, Dae Hong; Choi, Jung-Il; Baik, Seung Jae

2017-12-01

Atmospheric pressure (AP) operation of plasma-enhanced chemical vapor deposition (PECVD) is one of promising concepts for high quality and low cost processing. Atmospheric plasma discharge requires narrow gap configuration, which causes an inherent feature of AP PECVD. Two dimensional radial gas flows in AP PECVD induces radial variation of mass-transport and that of substrate temperature. The opposite trend of these variations would be the key consideration in the development of uniform deposition process. Another inherent feature of AP PECVD is confined plasma discharge, from which volume power density concept is derived as a key parameter for the control of deposition rate. We investigated deposition rate as a function of volume power density, gas flux, source gas partial pressure, hydrogen partial pressure, plasma source frequency, and substrate temperature; and derived a design guideline of deposition tool and process development in terms of deposition rate and uniformity.

"Genetically Engineered" Nanoelectronics

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Salazar-Lazaro, Carlos H.; Stoica, Adrian; Cwik, Thomas

2000-01-01

The quantum mechanical functionality of nanoelectronic devices such as resonant tunneling diodes (RTDs), quantum well infrared-photodetectors (QWIPs), quantum well lasers, and heterostructure field effect transistors (HFETs) is enabled by material variations on an atomic scale. The design and optimization of such devices requires a fundamental understanding of electron transport in such dimensions. The Nanoelectronic Modeling Tool (NEMO) is a general-purpose quantum device design and analysis tool based on a fundamental non-equilibrium electron transport theory. NEW was combined with a parallelized genetic algorithm package (PGAPACK) to evolve structural and material parameters to match a desired set of experimental data. A numerical experiment that evolves structural variations such as layer widths and doping concentrations is performed to analyze an experimental current voltage characteristic. The genetic algorithm is found to drive the NEMO simulation parameters close to the experimentally prescribed layer thicknesses and doping profiles. With such a quantitative agreement between theory and experiment design synthesis can be performed.

Methods of determining complete sensor requirements for autonomous mobility

NASA Technical Reports Server (NTRS)

Curtis, Steven A. (Inventor)

2012-01-01

A method of determining complete sensor requirements for autonomous mobility of an autonomous system includes computing a time variation of each behavior of a set of behaviors of the autonomous system, determining mobility sensitivity to each behavior of the autonomous system, and computing a change in mobility based upon the mobility sensitivity to each behavior and the time variation of each behavior. The method further includes determining the complete sensor requirements of the autonomous system through analysis of the relative magnitude of the change in mobility, the mobility sensitivity to each behavior, and the time variation of each behavior, wherein the relative magnitude of the change in mobility, the mobility sensitivity to each behavior, and the time variation of each behavior are characteristic of the stability of the autonomous system.

Laser-induced retinal injury thresholds: variation with retinal irradiated area

NASA Astrophysics Data System (ADS)

Lund, David J.; Schulmeister, Karl; Seiser, Bernhard; Edthofer, Florian

2005-04-01

The retinal injury threshold for exposure to a laser source varies as a function of the irradiated area on the retina. Currently accepted guidelines for the safe use of lasers provide that the MPE will increase as the diameter of the irradiated area for retinal diameters between 25 mm and 1700 mm, based on the ED50 data available in the late 1970s. Recent studies by Zuclich and Lund produced data showing that the ED50 for ns-duration exposures at 532 nm and ms duration exposures at 590 nm varied as the square of the diameter of the irradiated area on the retina. This paper will discuss efforts to resolve the disagreement between the new data and the earlier data though an analysis of all accessible data relating the retinal injury threshold to the diameter of the incident beam on the retina and through simulations using computer models of laser-induced injury. The results show that the retinal radiant exposure required to produce retinal injury is a function of both exposure duration and retinal irradiance diameter and that the current guidelines for irradiance diameter dependence do not accurately reflect the variation of the threshold data.

Changes in tundra pond limnology: re-sampling Alaskan ponds after 40 years.

PubMed

Lougheed, Vanessa L; Butler, Malcolm G; McEwen, Daniel C; Hobbie, John E

2011-09-01

The arctic tundra ponds at the International Biological Program (IBP) site in Barrow, AK, were studied extensively in the 1970s; however, very little aquatic research has been conducted there for over three decades. Due to the rapid climate changes already occurring in northern Alaska, identifying any changes in the ponds' structure and function over the past 30-40 years can help identify any potential climate-related impacts. Current research on the IBP ponds has revealed significant changes in the physical, chemical, and biological characteristics of these ponds over time. These changes include increased water temperatures, increased water column nutrient concentrations, the presence of at least one new chironomid species, and increased macrophyte cover. However, we have also observed significant annual variation in many measured variables and caution that this variation must be taken into account when attempting to make statements about longer-term change. The Barrow IBP tundra ponds represent one of the very few locations in the Arctic where long-term data are available on freshwater ecosystem structure and function. Continued monitoring and protection of these invaluable sites is required to help understand the implications of climate change on freshwater ecosystems in the Arctic.

A crustal seismic velocity model for the UK, Ireland and surrounding seas

USGS Publications Warehouse

Kelly, A.; England, R.W.; Maguire, Peter K.H.

2007-01-01

A regional model of the 3-D variation in seismic P-wave velocity structure in the crust of NW Europe has been compiled from wide-angle reflection/refraction profiles. Along each 2-D profile a velocity-depth function has been digitised at 5 km intervals. These 1-D velocity functions were mapped into three dimensions using ordinary kriging with weights determined to minimise the difference between digitised and interpolated values. An analysis of variograms of the digitised data suggested a radial isotropic weighting scheme was most appropriate. Horizontal dimensions of the model cells are optimised at 40 ?? 40 km and the vertical dimension at 1 km. The resulting model provides a higher resolution image of the 3-D variation in seismic velocity structure of the UK, Ireland and surrounding areas than existing models. The construction of the model through kriging allows the uncertainty in the velocity structure to be assessed. This uncertainty indicates the high density of data required to confidently interpolate the crustal velocity structure, and shows that for this region the velocity is poorly constrained for large areas away from the input data. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

Simple Penalties on Maximum-Likelihood Estimates of Genetic Parameters to Reduce Sampling Variation

PubMed Central

Meyer, Karin

2016-01-01

Multivariate estimates of genetic parameters are subject to substantial sampling variation, especially for smaller data sets and more than a few traits. A simple modification of standard, maximum-likelihood procedures for multivariate analyses to estimate genetic covariances is described, which can improve estimates by substantially reducing their sampling variances. This is achieved by maximizing the likelihood subject to a penalty. Borrowing from Bayesian principles, we propose a mild, default penalty—derived assuming a Beta distribution of scale-free functions of the covariance components to be estimated—rather than laboriously attempting to determine the stringency of penalization from the data. An extensive simulation study is presented, demonstrating that such penalties can yield very worthwhile reductions in loss, i.e., the difference from population values, for a wide range of scenarios and without distorting estimates of phenotypic covariances. Moreover, mild default penalties tend not to increase loss in difficult cases and, on average, achieve reductions in loss of similar magnitude to computationally demanding schemes to optimize the degree of penalization. Pertinent details required for the adaptation of standard algorithms to locate the maximum of the likelihood function are outlined. PMID:27317681

Parallel algorithm of real-time infrared image restoration based on total variation theory

NASA Astrophysics Data System (ADS)

Zhu, Ran; Li, Miao; Long, Yunli; Zeng, Yaoyuan; An, Wei

2015-10-01

Image restoration is a necessary preprocessing step for infrared remote sensing applications. Traditional methods allow us to remove the noise but penalize too much the gradients corresponding to edges. Image restoration techniques based on variational approaches can solve this over-smoothing problem for the merits of their well-defined mathematical modeling of the restore procedure. The total variation (TV) of infrared image is introduced as a L1 regularization term added to the objective energy functional. It converts the restoration process to an optimization problem of functional involving a fidelity term to the image data plus a regularization term. Infrared image restoration technology with TV-L1 model exploits the remote sensing data obtained sufficiently and preserves information at edges caused by clouds. Numerical implementation algorithm is presented in detail. Analysis indicates that the structure of this algorithm can be easily implemented in parallelization. Therefore a parallel implementation of the TV-L1 filter based on multicore architecture with shared memory is proposed for infrared real-time remote sensing systems. Massive computation of image data is performed in parallel by cooperating threads running simultaneously on multiple cores. Several groups of synthetic infrared image data are used to validate the feasibility and effectiveness of the proposed parallel algorithm. Quantitative analysis of measuring the restored image quality compared to input image is presented. Experiment results show that the TV-L1 filter can restore the varying background image reasonably, and that its performance can achieve the requirement of real-time image processing.

Molecular and functional characterization of cry1Ac transgenic pea lines.

PubMed

Teressa Negawo, Alemayehu; Baranek, Linda; Jacobsen, Hans-Jörg; Hassan, Fathi

2016-10-01

Transgenic pea lines transformed with the cry1Ac gene were characterized at molecular (PCR, RT-PCR, qRT-PCR and immunostrip assay) and functional levels (leaf paint and insect feeding bioassays). The results showed the presence, expression, inheritance and functionality of the introduced transgene at different progeny levels. Variation in the expression of the cry1Ac gene was observed among the different transgenic lines. In the insect bioassay studies using the larvae of Heliothis virescens, both larval survival and plant damage were highly affected on the different transgenic plants. Up to 100 % larval mortality was observed on the transgenic plants compared to 17.42 % on control plants. Most of the challenged transgenic plants showed very negligible to substantially reduced feeding damage indicating the insect resistance of the developed transgenic lines. Further analysis under field condition will be required to select promising lines for future uses.

Molecular and functional characterization of cry1Ac transgenic pea lines

PubMed Central

Teressa Negawo, Alemayehu; Baranek, Linda; Jacobsen, Hans-Jörg; Hassan, Fathi

2016-01-01

ABSTRACT Transgenic pea lines transformed with the cry1Ac gene were characterized at molecular (PCR, RT-PCR, qRT-PCR and immunostrip assay) and functional levels (leaf paint and insect feeding bioassays). The results showed the presence, expression, inheritance and functionality of the introduced transgene at different progeny levels. Variation in the expression of the cry1Ac gene was observed among the different transgenic lines. In the insect bioassay studies using the larvae of Heliothis virescens, both larval survival and plant damage were highly affected on the different transgenic plants. Up to 100 % larval mortality was observed on the transgenic plants compared to 17.42 % on control plants. Most of the challenged transgenic plants showed very negligible to substantially reduced feeding damage indicating the insect resistance of the developed transgenic lines. Further analysis under field condition will be required to select promising lines for future uses. PMID:27764552

A new approach to global control of redundant manipulators

NASA Technical Reports Server (NTRS)

Seraji, Homayoun

1989-01-01

A new and simple approach to configuration control of redundant manipulators is presented. In this approach, the redundancy is utilized to control the manipulator configuration directly in task space, where the task will be performed. A number of kinematic functions are defined to reflect the desirable configuration that will be achieved for a given end-effector position. The user-defined kinematic functions and the end-effector Cartesian coordinates are combined to form a set of task-related configuration variables as generalized coordinates for the manipulator. An adaptive scheme is then utilized to globally control the configuration variables so as to achieve tracking of some desired reference trajectories. This accomplishes the basic task of desired end-effector motion, while utilizing the redundancy to achieve any additional task through the desired time variation of the kinematic functions. The control law is simple and computationally very fast, and does not require the complex manipulator dynamic model.

Ephemeral penalty functions for contact-impact dynamics

NASA Technical Reports Server (NTRS)

De La Fuente, Horacio M.; Felippa, Carlos A.

1991-01-01

The use of penalty functions to treat a class of structural contact-impact problems is investigated, with emphasis on ones in which the impact phenomena are primarily nondestructive in nature and in which only the gross characterization of the response is required. The dynamic equations of motion are integrated by the difference method. The penalty is represented as an ephemeral fictitious nonlinear spring that is inserted on anticipation of contact. The magnitude and variation of the penalty force is determined through energy balancing considerations. The 'bell shape' of the penalty force function for positive gap was found to be satisfactory, as it depends on only two parameters that can be directly assigned the physical meaning of force and distance. The determination of force law parameters by energy balance worked well. The incorporation of restitution coefficients by the area balancing method yielded excellent results, and no substantial modifications are anticipated. Extensional penalty springs are obviously sufficient for the simple examples treated.

Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

PubMed Central

Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

2014-01-01

Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such natural and interpretable isotopic biomarkers promises interesting applications in nutrition and health. PMID:25275306

Variational Problems with Long-Range Interaction

NASA Astrophysics Data System (ADS)

Soave, Nicola; Tavares, Hugo; Terracini, Susanna; Zilio, Alessandro

2018-06-01

We consider a class of variational problems for densities that repel each other at a distance. Typical examples are given by the Dirichlet functional and the Rayleigh functional D(u) = \\sum_{i=1}^k \\int_{Ω} |\

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors.

PubMed

Kim, Hee Ryung; Duc, Nguyen Minh; Chung, Ka Young

2018-03-01

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Metabolic fate of polyphenols in the human superorganism

PubMed Central

van Duynhoven, John; Vaughan, Elaine E.; Jacobs, Doris M.; Kemperman, Robèr A.; van Velzen, Ewoud J. J.; Gross, Gabriele; Roger, Laure C.; Possemiers, Sam; Smilde, Age K.; Doré, Joël; Westerhuis, Johan A.; Van de Wiele, Tom

2011-01-01

Dietary polyphenols are components of many foods such as tea, fruit, and vegetables and are associated with several beneficial health effects although, so far, largely based on epidemiological studies. The intact forms of complex dietary polyphenols have limited bioavailability, with low circulating levels in plasma. A major part of the polyphenols persists in the colon, where the resident microbiota produce metabolites that can undergo further metabolism upon entering systemic circulation. Unraveling the complex metabolic fate of polyphenols in this human superorganism requires joint deployment of in vitro and humanized mouse models and human intervention trials. Within these systems, the variation in diversity and functionality of the colonic microbiota can increasingly be captured by rapidly developing microbiomics and metabolomics technologies. Furthermore, metabolomics is coming to grips with the large biological variation superimposed on relatively subtle effects of dietary interventions. In particular when metabolomics is deployed in conjunction with a longitudinal study design, quantitative nutrikinetic signatures can be obtained. These signatures can be used to define nutritional phenotypes with different kinetic characteristics for the bioconversion capacity for polyphenols. Bottom-up as well as top-down approaches need to be pursued to link gut microbial diversity to functionality in nutritional phenotypes and, ultimately, to bioactivity of polyphenols. This approach will pave the way for personalization of nutrition based on gut microbial functionality of individuals or populations. PMID:20615997

Plant community diversity influences allocation to direct chemical defence in Plantago lanceolata.

PubMed

Mraja, Anne; Unsicker, Sybille B; Reichelt, Michael; Gershenzon, Jonathan; Roscher, Christiane

2011-01-01

Forecasting the consequences of accelerating rates of changes in biodiversity for ecosystem functioning requires a mechanistic understanding of the relationships between the structure of biological communities and variation in plant functional characteristics. So far, experimental data of how plant species diversity influences the investment of individual plants in direct chemical defences against herbivores and pathogens is lacking. We used Plantago lanceolata as a model species in experimental grasslands differing in species richness and composition (Jena Experiment) to investigate foliar concentrations of the iridoid glycosides (IG), catalpol and its biosynthetic precursor aucubin. Total IG and aucubin concentrations decreased, while catalpol concentrations increased with increasing plant diversity in terms of species or functional group richness. Negative plant diversity effects on total IG and aucubin concentrations correlated with increasing specific leaf area of P. lanceolata, suggesting that greater allocation to light acquisition reduced the investment into these carbon-based defence components. In contrast, increasing leaf nitrogen concentrations best explained increasing concentrations of the biosynthetically more advanced IG, catalpol. Observed levels of leaf damage explained a significant proportion of variation in total IG and aucubin concentrations, but did not account for variance in catalpol concentrations. Our results clearly show that plants growing in communities of varying species richness and composition differ in their defensive chemistry, which may modulate plant susceptibility to enemy attack and consequently their interactions with higher trophic level organisms.

Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus

PubMed Central

Huang, Pengyun; Lin, Fucheng

2014-01-01

Because of great challenges and workload in deleting genes on a large scale, the functions of most genes in pathogenic fungi are still unclear. In this study, we developed a high-throughput gene knockout system using a novel yeast-Escherichia-Agrobacterium shuttle vector, pKO1B, in the rice blast fungus Magnaporthe oryzae. Using this method, we deleted 104 fungal-specific Zn2Cys6 transcription factor (TF) genes in M. oryzae. We then analyzed the phenotypes of these mutants with regard to growth, asexual and infection-related development, pathogenesis, and 9 abiotic stresses. The resulting data provide new insights into how this rice pathogen of global significance regulates important traits in the infection cycle through Zn2Cys6TF genes. A large variation in biological functions of Zn2Cys6TF genes was observed under the conditions tested. Sixty-one of 104 Zn2Cys6 TF genes were found to be required for fungal development. In-depth analysis of TF genes revealed that TF genes involved in pathogenicity frequently tend to function in multiple development stages, and disclosed many highly conserved but unidentified functional TF genes of importance in the fungal kingdom. We further found that the virulence-required TF genes GPF1 and CNF2 have similar regulation mechanisms in the gene expression involved in pathogenicity. These experimental validations clearly demonstrated the value of a high-throughput gene knockout system in understanding the biological functions of genes on a genome scale in fungi, and provided a solid foundation for elucidating the gene expression network that regulates the development and pathogenicity of M. oryzae. PMID:25299517

Variation of yield loci in finite element analysis by considering texture evolution for AA5042 aluminum sheets

NASA Astrophysics Data System (ADS)

Yoon, Jonghun; Kim, Kyungjin; Yoon, Jeong Whan

2013-12-01

Yield function has various material parameters that describe how materials respond plastically in given conditions. However, a significant number of mechanical tests are required to identify the many material parameters for yield function. In this study, an effective method using crystal plasticity through a virtual experiment is introduced to develop the anisotropic yield function for AA5042. The crystal plasticity approach was used to predict the anisotropic response of the material in order to consider a number of stress or strain modes that would not otherwise be evident through mechanical testing. A rate-independent crystal plasticity model based on a smooth single crystal yield surface, which removes the innate ambiguity problem within the rate-independent model and Taylor model for polycrystalline deformation behavior were employed to predict the material's response in the balanced biaxial stress, pure shear, and plane strain states to identify the parameters for the anisotropic yield function of AA5042.

Valid approximation of spatially distributed grain size distributions - A priori information encoded to a feedforward network

NASA Astrophysics Data System (ADS)

Berthold, T.; Milbradt, P.; Berkhahn, V.

2018-04-01

This paper presents a model for the approximation of multiple, spatially distributed grain size distributions based on a feedforward neural network. Since a classical feedforward network does not guarantee to produce valid cumulative distribution functions, a priori information is incor porated into the model by applying weight and architecture constraints. The model is derived in two steps. First, a model is presented that is able to produce a valid distribution function for a single sediment sample. Although initially developed for sediment samples, the model is not limited in its application; it can also be used to approximate any other multimodal continuous distribution function. In the second part, the network is extended in order to capture the spatial variation of the sediment samples that have been obtained from 48 locations in the investigation area. Results show that the model provides an adequate approximation of grain size distributions, satisfying the requirements of a cumulative distribution function.

Functional Architecture of the Retina: Development and Disease

PubMed Central

Hoon, Mrinalini; Okawa, Haruhisa; Santina, Luca Della; Wong, Rachel O.L.

2014-01-01

Structure and function are highly correlated in the vertebrate retina, a sensory tissue that is organized into cell layers with microcircuits working in parallel and together to encode visual information. All vertebrate retinas share a fundamental plan, comprising five major neuronal cell classes with cell body distributions and connectivity arranged in stereotypic patterns. Conserved features in retinal design have enabled detailed analysis and comparisons of structure, connectivity and function across species. Each species, however, can adopt structural and/or functional retinal specializations, implementing variations to the basic design in order to satisfy unique requirements in visual function. Recent advances in molecular tools, imaging and electrophysiological approaches have greatly facilitated identification of the cellular and molecular mechanisms that establish the fundamental organization of the retina and the specializations of its microcircuits during development. Here, we review advances in our understanding of how these mechanisms act to shape structure and function at the single cell level, to coordinate the assembly of cell populations, and to define their specific circuitry. We also highlight how structure is rearranged and function is disrupted in disease, and discuss current approaches to re-establish the intricate functional architecture of the retina. PMID:24984227

Functional architecture of the retina: development and disease.

PubMed

Hoon, Mrinalini; Okawa, Haruhisa; Della Santina, Luca; Wong, Rachel O L

2014-09-01

Structure and function are highly correlated in the vertebrate retina, a sensory tissue that is organized into cell layers with microcircuits working in parallel and together to encode visual information. All vertebrate retinas share a fundamental plan, comprising five major neuronal cell classes with cell body distributions and connectivity arranged in stereotypic patterns. Conserved features in retinal design have enabled detailed analysis and comparisons of structure, connectivity and function across species. Each species, however, can adopt structural and/or functional retinal specializations, implementing variations to the basic design in order to satisfy unique requirements in visual function. Recent advances in molecular tools, imaging and electrophysiological approaches have greatly facilitated identification of the cellular and molecular mechanisms that establish the fundamental organization of the retina and the specializations of its microcircuits during development. Here, we review advances in our understanding of how these mechanisms act to shape structure and function at the single cell level, to coordinate the assembly of cell populations, and to define their specific circuitry. We also highlight how structure is rearranged and function is disrupted in disease, and discuss current approaches to re-establish the intricate functional architecture of the retina. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolutionary constraints or opportunities?

PubMed

Sharov, Alexei A

2014-04-22

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). Copyright © 2014. Published by Elsevier Ireland Ltd.

Regulation of circadian blood pressure: from mice to astronauts.

PubMed

Agarwal, Rajiv

2010-01-01

Circadian variation is commonly seen in healthy people; aberration in these biological rhythms is an early sign of disease. Impaired circadian variation of blood pressure (BP) has been shown to be associated with greater target organ damage and with an elevated risk of cardiovascular events independent of the BP load. The purpose of this review is to examine the physiology of circadian BP variation and propose a tripartite model that explains the regulation of circadian BP. The time-keeper in mammals resides centrally in the suprachiasmatic nucleus. Apart from this central clock, molecular clocks exist in most peripheral tissues including vascular tissue and the kidney. These molecular clocks regulate sodium balance, sympathetic function and vascular tone. A physiological model is proposed that integrates our understanding of molecular clocks in mice with the circadian BP variation among humans. The master regulator in this proposed model is the sleep-activity cycle. The equivalents of peripheral clocks are endothelial and adrenergic functions. Thus, in the proposed model, the variation in circadian BP is dependent upon three major factors: physical activity, autonomic function, and sodium sensitivity. The integrated consideration of physical activity, autonomic function, and sodium sensitivity appears to explain the physiology of circadian BP variation and the pathophysiology of disrupted BP rhythms in various conditions and disease states. Our understanding of molecular clocks in mice may help to explain the provenance of blunted circadian BP variation even among astronauts.

Anatomic variations in vascular and collecting systems of kidneys from deceased donors.

PubMed

Costa, H C; Moreira, R J; Fukunaga, P; Fernandes, R C; Boni, R C; Matos, A C

2011-01-01

Nephroureterectomy for transplantation has increased owing to the greater number of deceased donors. Anatomic variations may complicate the procedure or, if unrecognized, compromise the viability of kidneys for transplantation. We reviewed 254 surgical descriptions of nephroureterectomy specimens from January 2008 to December 2009. All organs collected according by standard techniques were evaluated for age, cause of death, renal function, frequency of injury during the procedure, as well as variations in the vascular and collecting systems. The mean donor age was 42 years (range, 2-74). The mean serum creatinine was 1.2 mg/dL (range, 1.0-7.0). The causes of death were cerebrovascular cause (stroke; n = 130), traumatic brain injury (n = 81) or other cause (n = 43). Among the anatomic variations: 8.6% (n = 22) were right arterial anatomical variations: 19 cases with 2 arteries and 3 cases with 3 arteries. In 25 cases (9.8%) the identified variation was the left artery: 2 arteries (n = 23), 3 arteries (n = 1) and 4 arteries (n = 1). We observed 9.8% on right side and 1.5% on left side venous anatomic variations, including 24 cases with 2 veins on the right side and 4 cases with 2 veins on the left side. Three cases of a retroaortic left renal vein and 1 case of a retro necklace vein (anterior and posterior to the aorta). Two cases of ureteral duplication were noted on the left and 1 on the right kidney. There were 3 horseshoe and 1 pelvic kidney. In 7.5% of cases, an injury to the graft included ureteral (n = 3), arterial (n = 10), or venous (n = 6). The most common anatomic variation was arterial (17.8%). Duplication of the renal vein was more frequent on the right. The high incidences of anatomic variations require more attention in the dissection of the renal hilum to avoid an injury that may compromise the graft. Copyright © 2011 Elsevier Inc. All rights reserved.

How to normalize metatranscriptomic count data for differential expression analysis.

PubMed

Klingenberg, Heiner; Meinicke, Peter

2017-01-01

Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ widely. Our studies indicate that in real data applications performed with global scaling it might be impossible to distinguish between differential expression in terms of transcriptomic changes and differential composition in terms of changing taxonomic proportions. As in transcriptomics, a proper normalization of count data is also essential for differential expression analysis in metatranscriptomics. Our model implies a taxon-specific scaling of counts for normalization of the data. The application of taxon-specific scaling consequently removes taxonomic composition variations from functional profiles and therefore provides a clear interpretation of the observed functional differences.

Evaluation of an Integrated Framework for Biodiversity with a New Metric for Functional Dispersion

PubMed Central

Presley, Steven J.; Scheiner, Samuel M.; Willig, Michael R.

2014-01-01

Growing interest in understanding ecological patterns from phylogenetic and functional perspectives has driven the development of metrics that capture variation in evolutionary histories or ecological functions of species. Recently, an integrated framework based on Hill numbers was developed that measures three dimensions of biodiversity based on abundance, phylogeny and function of species. This framework is highly flexible, allowing comparison of those diversity dimensions, including different aspects of a single dimension and their integration into a single measure. The behavior of those metrics with regard to variation in data structure has not been explored in detail, yet is critical for ensuring an appropriate match between the concept and its measurement. We evaluated how each metric responds to particular data structures and developed a new metric for functional biodiversity. The phylogenetic metric is sensitive to variation in the topology of phylogenetic trees, including variation in the relative lengths of basal, internal and terminal branches. In contrast, the functional metric exhibited multiple shortcomings: (1) species that are functionally redundant contribute nothing to functional diversity and (2) a single highly distinct species causes functional diversity to approach the minimum possible value. We introduced an alternative, improved metric based on functional dispersion that solves both of these problems. In addition, the new metric exhibited more desirable behavior when based on multiple traits. PMID:25148103

An empirical method to correct for temperature-dependent variations in the overlap function of CHM15k ceilometers

NASA Astrophysics Data System (ADS)

Hervo, Maxime; Poltera, Yann; Haefele, Alexander

2016-07-01

Imperfections in a lidar's overlap function lead to artefacts in the background, range and overlap-corrected lidar signals. These artefacts can erroneously be interpreted as an aerosol gradient or, in extreme cases, as a cloud base leading to false cloud detection. A correct specification of the overlap function is hence crucial in the use of automatic elastic lidars (ceilometers) for the detection of the planetary boundary layer or of low cloud. In this study, an algorithm is presented to correct such artefacts. It is based on the assumption of a homogeneous boundary layer and a correct specification of the overlap function down to a minimum range, which must be situated within the boundary layer. The strength of the algorithm lies in a sophisticated quality-check scheme which allows the reliable identification of favourable atmospheric conditions. The algorithm was applied to 2 years of data from a CHM15k ceilometer from the company Lufft. Backscatter signals corrected for background, range and overlap were compared using the overlap function provided by the manufacturer and the one corrected with the presented algorithm. Differences between corrected and uncorrected signals reached up to 45 % in the first 300 m above ground. The amplitude of the correction turned out to be temperature dependent and was larger for higher temperatures. A linear model of the correction as a function of the instrument's internal temperature was derived from the experimental data. Case studies and a statistical analysis of the strongest gradient derived from corrected signals reveal that the temperature model is capable of a high-quality correction of overlap artefacts, in particular those due to diurnal variations. The presented correction method has the potential to significantly improve the detection of the boundary layer with gradient-based methods because it removes false candidates and hence simplifies the attribution of the detected gradients to the planetary boundary layer. A particularly significant benefit can be expected for the detection of shallow stable layers typical of night-time situations. The algorithm is completely automatic and does not require any on-site intervention but requires the definition of an adequate instrument-specific configuration. It is therefore suited for use in large ceilometer networks.

27 CFR 18.14 - Emergency variations from requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Emergency variations from requirements. 18.14 Section 18.14 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Administrative...

27 CFR 18.14 - Emergency variations from requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Emergency variations from requirements. 18.14 Section 18.14 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Administrative...

27 CFR 18.14 - Emergency variations from requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Emergency variations from requirements. 18.14 Section 18.14 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Administrative...

27 CFR 18.14 - Emergency variations from requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Emergency variations from requirements. 18.14 Section 18.14 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Administrative...

27 CFR 18.14 - Emergency variations from requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Emergency variations from requirements. 18.14 Section 18.14 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Administrative...

A guide to large-scale RNA sample preparation.

PubMed

Baronti, Lorenzo; Karlsson, Hampus; Marušič, Maja; Petzold, Katja

2018-05-01

RNA is becoming more important as an increasing number of functions, both regulatory and enzymatic, are being discovered on a daily basis. As the RNA boom has just begun, most techniques are still in development and changes occur frequently. To understand RNA functions, revealing the structure of RNA is of utmost importance, which requires sample preparation. We review the latest methods to produce and purify a variation of RNA molecules for different purposes with the main focus on structural biology and biophysics. We present a guide aimed at identifying the most suitable method for your RNA and your biological question and highlighting the advantages of different methods. Graphical abstract In this review we present different methods for large-scale production and purification of RNAs for structural and biophysical studies.

Allometric variation among juvenile, adult male and female eastern bearded dragons Pogona barbata (Cuvier, 1829), with comments on the behavioural implications.

PubMed

Wotherspoon, Danny; Burgin, Shelley

2011-02-01

The functional significance of allometric change in reptiles has received limited attention and the reason for such changes has been regarded as 'obscure'. In this paper we report data on the Australian Pogona barbata, the eastern bearded dragon, from across their range and review changes in allometric growth among juveniles, and adult males and females and consider the functional relevance of these changes. There were significant differences in the population for mass, tail length, tail width, rear leg length and jaw length. These differences were consistent with differences required in locomotor performance and thus habitat use, together with access to different preferred dietary components. Crown Copyright © 2011. Published by Elsevier GmbH. All rights reserved.

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.

PubMed

Ryan, Michael C; Cleland, James; Kim, RyangGuk; Wong, Wing Chung; Weinstein, John N

2012-09-15

SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. mryan@insilico.us.com Supplementary data are available at Bioinformatics online.

Structural characteristics of novel symmetrical diaryl derivatives with nitrogenated functions. Requirements for cytotoxic activity.

PubMed

Font, María; Ardaiz, Elena; Cordeu, Lucia; Cubedo, Elena; García-Foncillas, Jesús; Sanmartin, Carmen; Palop, Juan-Antonio

2006-03-15

In an attempt to discover the essential features that would allow us to explain the differences in cytotoxic activity shown by a series of symmetrical diaryl derivatives with nitrogenated functions, we have studied by molecular modelling techniques the variation in Log P and conformational behaviour, in terms of structural modifications. The Log P data--although they provide few clues concerning the observed variability in activity--suggest that an initial separation of active and inactive compounds is possible based on this parameter. The subsequent study of the conformational behaviour of the compounds, selected according to their Log P values, showed that the active compounds preferentially display an extended conformation and inactive ones are associated with a certain type of folding, with a triangular-type conformation adopted in these cases.

Protein function in precision medicine: deep understanding with machine learning.

PubMed

Rost, Burkhard; Radivojac, Predrag; Bromberg, Yana

2016-08-01

Precision medicine and personalized health efforts propose leveraging complex molecular, medical and family history, along with other types of personal data toward better life. We argue that this ambitious objective will require advanced and specialized machine learning solutions. Simply skimming some low-hanging results off the data wealth might have limited potential. Instead, we need to better understand all parts of the system to define medically relevant causes and effects: how do particular sequence variants affect particular proteins and pathways? How do these effects, in turn, cause the health or disease-related phenotype? Toward this end, deeper understanding will not simply diffuse from deeper machine learning, but from more explicit focus on understanding protein function, context-specific protein interaction networks, and impact of variation on both. © 2016 Federation of European Biochemical Societies.

Endocrine mechanisms, behavioral phenotypes and plasticity: known relationships and open questions.

PubMed

Hau, Michaela; Goymann, Wolfgang

2015-01-01

Behavior of wild vertebrate individuals can vary in response to environmental or social factors. Such within-individual behavioral variation is often mediated by hormonal mechanisms. Hormones also serve as a basis for among-individual variations in behavior including animal personalities and the degree of responsiveness to environmental and social stimuli. How do relationships between hormones and behavioral traits evolve to produce such behavioral diversity within and among individuals? Answering questions about evolutionary processes generating among-individual variation requires characterizing how specific hormones are related to variation in specific behavioral traits, whether observed hormonal variation is related to individual fitness and, whether hormonal traits are consistent (repeatable) aspects of an individual's phenotype. With respect to within-individual variation, we need to improve our insight into the nature of the quantitative relationships between hormones and the traits they regulate, which in turn will determine how they may mediate behavioral plasticity of individuals. To address these questions, we review the actions of two steroid hormones, corticosterone and testosterone, in mediating changes in vertebrate behavior, focusing primarily on birds. In the first part, we concentrate on among-individual variation and present examples for how variation in corticosterone concentrations can relate to behaviors such as exploration of novel environments and parental care. We then review studies on correlations between corticosterone variation and fitness, and on the repeatability over time of corticosterone concentrations. At the end of this section, we suggest that further progress in our understanding of evolutionary patterns in the hormonal regulation of behavior may require, as one major tool, reaction norm approaches to characterize hormonal phenotypes as well as their responses to environments. In the second part, we discuss types of quantitative relationships between hormones and behavioral traits within individuals, using testosterone as an example. We review conceptual models for testosterone-behavior relationships and discuss the relevance of these models for within-individual plasticity in behavior. Next, we discuss approaches for testing the nature of quantitative relationships between testosterone and behavior, concluding that again reaction norm approaches might be a fruitful way forward. We propose that an integration of new tools, especially of reaction norm approaches into the field of behavioral endocrinology will allow us to make significant progress in our understanding of the mechanisms, the functional implications and the evolution of hormone-behavior relationships that mediate variation both within and among individuals. This knowledge will be crucial in light of already ongoing habitat alterations due to global change, as it will allow us to evaluate the mechanisms as well as the capacity of wild populations to adjust hormonally-mediated behaviors to altered environmental conditions.

Robust Multivariable Optimization and Performance Simulation for ASIC Design

NASA Technical Reports Server (NTRS)

DuMonthier, Jeffrey; Suarez, George

2013-01-01

Application-specific-integrated-circuit (ASIC) design for space applications involves multiple challenges of maximizing performance, minimizing power, and ensuring reliable operation in extreme environments. This is a complex multidimensional optimization problem, which must be solved early in the development cycle of a system due to the time required for testing and qualification severely limiting opportunities to modify and iterate. Manual design techniques, which generally involve simulation at one or a small number of corners with a very limited set of simultaneously variable parameters in order to make the problem tractable, are inefficient and not guaranteed to achieve the best possible results within the performance envelope defined by the process and environmental requirements. What is required is a means to automate design parameter variation, allow the designer to specify operational constraints and performance goals, and to analyze the results in a way that facilitates identifying the tradeoffs defining the performance envelope over the full set of process and environmental corner cases. The system developed by the Mixed Signal ASIC Group (MSAG) at the Goddard Space Flight Center is implemented as a framework of software modules, templates, and function libraries. It integrates CAD tools and a mathematical computing environment, and can be customized for new circuit designs with only a modest amount of effort as most common tasks are already encapsulated. Customization is required for simulation test benches to determine performance metrics and for cost function computation.

Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding apparatus.

PubMed

Hu, Yinan; Albertson, R Craig

2014-06-10

Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression--the opercular four-bar linkage apparatus--among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches.

Evidence of Dynamic Crustal Deformation in Tohoku, Japan, From Time-Varying Receiver Functions

NASA Astrophysics Data System (ADS)

Porritt, R. W.; Yoshioka, S.

2017-10-01

Temporal variation of crustal structure is key to our understanding of Earth processes on human timescales. Often, we expect that the most significant structural variations are caused by strong ground shaking associated with large earthquakes, and recent studies seem to confirm this. Here we test the possibility of using P receiver functions (PRF) to isolate structural variations over time. Synthetic receiver function tests indicate that structural variation could produce PRF changes on the same order of magnitude as random noise or contamination by local earthquakes. Nonetheless, we find significant variability in observed receiver functions over time at several stations located in northeastern Honshu. Immediately following the Tohoku-oki earthquake, we observe high PRF variation clustering spatially, especially in two regions near the beginning and end of the rupture plane. Due to the depth sensitivity of PRF and the timescales over which this variability is observed, we infer this effect is primarily due to fluid migration in volcanic regions and shear stress/strength reorganization. While the noise levels in PRF are high for this type of analysis, by sampling small data sets, the computational cost is lower than other methods, such as ambient noise, thereby making PRF a useful tool for estimating temporal variations in crustal structure.

Abundant raw material for cis-regulatory evolution in humans

NASA Technical Reports Server (NTRS)

Rockman, Matthew V.; Wray, Gregory A.

2002-01-01

Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

Nonlinear Network Description for Many-Body Quantum Systems in Continuous Space

NASA Astrophysics Data System (ADS)

Ruggeri, Michele; Moroni, Saverio; Holzmann, Markus

2018-05-01

We show that the recently introduced iterative backflow wave function can be interpreted as a general neural network in continuum space with nonlinear functions in the hidden units. Using this wave function in variational Monte Carlo simulations of liquid 4He in two and three dimensions, we typically find a tenfold increase in accuracy over currently used wave functions. Furthermore, subsequent stages of the iteration procedure define a set of increasingly good wave functions, each with its own variational energy and variance of the local energy: extrapolation to zero variance gives energies in close agreement with the exact values. For two dimensional 4He, we also show that the iterative backflow wave function can describe both the liquid and the solid phase with the same functional form—a feature shared with the shadow wave function, but now joined by much higher accuracy. We also achieve significant progress for liquid 3He in three dimensions, improving previous variational and fixed-node energies.

Genetic variation for agronomic and fiber quality traits in a population derived from high-quality cotton germplasm

USDA-ARS?s Scientific Manuscript database

Genetic improvement of fiber quality is necessary to meet the requirements of processors and users of cotton fiber. To foster genetic improvement of cotton fiber quality, adequate genetic variation for the quantitatively inherited physical properties of cotton is required. Additionally, knowledge of...

27 CFR 19.667 - Emergency variations from requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Emergency variations from requirements. 19.667 Section 19.667 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Distilled Spirits for Fuel Use...

27 CFR 19.904 - Emergency variations from requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Emergency variations from requirements. 19.904 Section 19.904 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Distilled Spirits For Fuel Use § 19...

27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Alternate methods or procedures; and emergency variations from requirements. 22.22 Section 22.22 Alcohol, Tobacco Products and... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures...

27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Alternate methods or procedures; and emergency variations from requirements. 22.22 Section 22.22 Alcohol, Tobacco Products and... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures...

27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Alternate methods or procedures; and emergency variations from requirements. 22.22 Section 22.22 Alcohol, Tobacco Products and... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures...

27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Alternate methods or procedures; and emergency variations from requirements. 22.22 Section 22.22 Alcohol, Tobacco Products and... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures...

27 CFR 22.22 - Alternate methods or procedures; and emergency variations from requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Alternate methods or procedures; and emergency variations from requirements. 22.22 Section 22.22 Alcohol, Tobacco Products and... OF TAX-FREE ALCOHOL Administrative Provisions Authorities § 22.22 Alternate methods or procedures...

Functional relevance of water and glycerol channels in Saccharomyces cerevisiae.

PubMed

Sabir, Farzana; Loureiro-Dias, Maria C; Soveral, Graça; Prista, Catarina

2017-05-01

Our understanding of the functional relevance of orthodox aquaporins and aquaglyceroporins in Saccharomyces cerevisiae is essentially based on phenotypic variations obtained by expression/overexpression/deletion of these major intrinsic proteins in selected strains. These water/glycerol channels are considered crucial during various life-cycle phases, such as sporulation and mating and in some life processes such as rapid freeze-thaw tolerance, osmoregulation and phenomena associated with cell surface. Despite their putative functional roles not only as channels but also as sensors, their underlying mechanisms and their regulation are still poorly understood. In the present review, we summarize and discuss the physiological relevance of S. cerevisiae aquaporins (Aqy1 and Aqy2) and aquaglyceroporins (Fps1 and Yfl054c). In particular, the fact that most S. cerevisiae laboratory strains harbor genes coding for non-functional aquaporins, while wild and industrial strains possess at least one functional aquaporin, suggests that aquaporin activity is required for cell survival under more harsh conditions. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variation in Differential and Total Cross Sections Due to Different Radial Wave Functions

ERIC Educational Resources Information Center

Williamson, W., Jr.; Greene, T.

1976-01-01

Three sets of analytical wave functions are used to calculate the Na (3s---3p) transition differential and total electron excitation cross sections by Born approximations. Results show expected large variations in values. (Author/CP)

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

PubMed Central

2012-01-01

Background Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice. PMID:22921105

Model parameters for representative wetland plant functional groups

USGS Publications Warehouse

Williams, Amber S.; Kiniry, James R.; Mushet, David M.; Smith, Loren M.; McMurry, Scott T.; Attebury, Kelly; Lang, Megan; McCarty, Gregory W.; Shaffer, Jill A.; Effland, William R.; Johnson, Mari-Vaughn V.

2017-01-01

Wetlands provide a wide variety of ecosystem services including water quality remediation, biodiversity refugia, groundwater recharge, and floodwater storage. Realistic estimation of ecosystem service benefits associated with wetlands requires reasonable simulation of the hydrology of each site and realistic simulation of the upland and wetland plant growth cycles. Objectives of this study were to quantify leaf area index (LAI), light extinction coefficient (k), and plant nitrogen (N), phosphorus (P), and potassium (K) concentrations in natural stands of representative plant species for some major plant functional groups in the United States. Functional groups in this study were based on these parameters and plant growth types to enable process-based modeling. We collected data at four locations representing some of the main wetland regions of the United States. At each site, we collected on-the-ground measurements of fraction of light intercepted, LAI, and dry matter within the 2013–2015 growing seasons. Maximum LAI and k variables showed noticeable variations among sites and years, while overall averages and functional group averages give useful estimates for multisite simulation modeling. Variation within each species gives an indication of what can be expected in such natural ecosystems. For P and K, the concentrations from highest to lowest were spikerush (Eleocharis macrostachya), reed canary grass (Phalaris arundinacea), smartweed (Polygonum spp.), cattail (Typha spp.), and hardstem bulrush (Schoenoplectus acutus). Spikerush had the highest N concentration, followed by smartweed, bulrush, reed canary grass, and then cattail. These parameters will be useful for the actual wetland species measured and for the wetland plant functional groups they represent. These parameters and the associated process-based models offer promise as valuable tools for evaluating environmental benefits of wetlands and for evaluating impacts of various agronomic practices in adjacent areas as they affect wetlands.

Couple of the Variational Iteration Method and Fractional-Order Legendre Functions Method for Fractional Differential Equations

PubMed Central

Song, Junqiang; Leng, Hongze; Lu, Fengshun

2014-01-01

We present a new numerical method to get the approximate solutions of fractional differential equations. A new operational matrix of integration for fractional-order Legendre functions (FLFs) is first derived. Then a modified variational iteration formula which can avoid “noise terms” is constructed. Finally a numerical method based on variational iteration method (VIM) and FLFs is developed for fractional differential equations (FDEs). Block-pulse functions (BPFs) are used to calculate the FLFs coefficient matrices of the nonlinear terms. Five examples are discussed to demonstrate the validity and applicability of the technique. PMID:24511303

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods.

PubMed

Buckley, Mike

2016-03-24

Collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. It has been widely investigated scientifically, not only as a biomedical material for regenerative medicine, but also for its role as a food source for both humans and livestock. Due to the long-term stability of collagen, as well as its abundance in bone, it has been proposed as a source of biomarkers for species identification not only for heat- and pressure-rendered animal feed but also in ancient archaeological and palaeontological specimens, typically carried out by peptide mass fingerprinting (PMF) as well as in-depth liquid chromatography (LC)-based tandem mass spectrometric methods. Through the analysis of the three most common domesticates species, cow, sheep, and pig, this research investigates the advantages of each approach over the other, investigating sites of sequence variation with known functional properties of the collagen molecule. Results indicate that the previously identified species biomarkers through PMF analysis are not among the most variable type 1 collagen peptides present in these tissues, the latter of which can be detected by LC-based methods. However, it is clear that the highly repetitive sequence motif of collagen throughout the molecule, combined with the variability of the sites and relative abundance levels of hydroxylation, can result in high scoring false positive peptide matches using these LC-based methods. Additionally, the greater alpha 2(I) chain sequence variation, in comparison to the alpha 1(I) chain, did not appear to be specific to any particular functional properties, implying that intra-chain functional constraints on sequence variation are not as great as inter-chain constraints. However, although some of the most variable peptides were only observed in LC-based methods, until the range of publicly available collagen sequences improves, the simplicity of the PMF approach and suitable range of peptide sequence variation observed makes it the ideal method for initial taxonomic identification prior to further analysis by LC-based methods only when required.

Evidence for a Constant Initial Mass Function in Early-type Galaxies Based on Their X-Ray Binary Populations

NASA Astrophysics Data System (ADS)

Peacock, Mark B.; Zepf, Stephen E.; Maccarone, Thomas J.; Kundu, Arunav; Gonzalez, Anthony H.; Lehmer, Bret D.; Maraston, Claudia

2014-04-01

A number of recent studies have proposed that the stellar initial mass function (IMF) of early type galaxies varies systematically as a function of galaxy mass, with higher mass galaxies having bottom-heavy IMFs. These bottom-heavy IMFs have more low-mass stars relative to the number of high mass stars, and therefore naturally result in proportionally fewer neutron stars (NSs) and black holes (BHs). In this paper, we specifically predict the variation in the number of BHs and NSs based on the power-law IMF variation required to reproduce the observed mass-to-light ratio trends with galaxy mass. We then test whether such variations are observed by studying the field low-mass X-ray binary (LMXB) populations of nearby early-type galaxies. In these binaries, an NS or BH accretes matter from a low-mass donor star. Their number is therefore expected to scale with the number of BHs and NSs present in a galaxy. We find that the number of LMXBs per K-band light is similar among the galaxies in our sample. These data therefore demonstrate the uniformity of the slope of the IMF from massive stars down to those now dominating the K-band light and are consistent with an invariant IMF. Our results are inconsistent with an IMF which varies from a Kroupa/Chabrier like IMF for low-mass galaxies to a steep power-law IMF (with slope x = 2.8) for high mass galaxies. We discuss how these observations constrain the possible forms of the IMF variations and how future Chandra observations can enable sharper tests of the IMF. Based in part on observations made with the NASA/ESA Hubble Space Telescope, and obtained from the Hubble Legacy Archive, which is a collaboration between the Space Telescope Science Institute (STScI/NASA), the Space Telescope European Coordinating Facility (ST-ECF/ESA) and the Canadian Astronomy Data Centre (CADC/NRC/CSA). The scientific results reported in this article are based in part on data obtained from the Chandra Data Archive and observations made by the Chandra X-ray Observatory and published previously in cited articles.

Testing simulations of intra- and inter-annual variation in the plant production response to elevated CO(2) against measurements from an 11-year FACE experiment on grazed pasture.

PubMed

Li, Frank Yonghong; Newton, Paul C D; Lieffering, Mark

2014-01-01

Ecosystem models play a crucial role in understanding and evaluating the combined impacts of rising atmospheric CO2 concentration and changing climate on terrestrial ecosystems. However, we are not aware of any studies where the capacity of models to simulate intra- and inter-annual variation in responses to elevated CO2 has been tested against long-term experimental data. Here we tested how well the ecosystem model APSIM/AgPasture was able to simulate the results from a free air carbon dioxide enrichment (FACE) experiment on grazed pasture. At this FACE site, during 11 years of CO2 enrichment, a wide range in annual plant production response to CO2 (-6 to +28%) was observed. As well as running the full model, which includes three plant CO2 response functions (plant photosynthesis, nitrogen (N) demand and stomatal conductance), we also tested the influence of these three functions on model predictions. Model/data comparisons showed that: (i) overall the model over-predicted the mean annual plant production response to CO2 (18.5% cf 13.1%) largely because years with small or negative responses to CO2 were not well simulated; (ii) in general seasonal and inter-annual variation in plant production responses to elevated CO2 were well represented by the model; (iii) the observed CO2 enhancement in overall mean legume content was well simulated but year-to-year variation in legume content was poorly captured by the model; (iv) the best fit of the model to the data required all three CO2 response functions to be invoked; (v) using actual legume content and reduced N fixation rate under elevated CO2 in the model provided the best fit to the experimental data. We conclude that in temperate grasslands the N dynamics (particularly the legume content and N fixation activity) play a critical role in pasture production responses to elevated CO2 , and are processes for model improvement. © 2013 John Wiley & Sons Ltd.

Massive-scale gene co-expression network construction and robustness testing using random matrix theory.

PubMed

Gibson, Scott M; Ficklin, Stephen P; Isaacson, Sven; Luo, Feng; Feltus, Frank A; Smith, Melissa C

2013-01-01

The study of gene relationships and their effect on biological function and phenotype is a focal point in systems biology. Gene co-expression networks built using microarray expression profiles are one technique for discovering and interpreting gene relationships. A knowledge-independent thresholding technique, such as Random Matrix Theory (RMT), is useful for identifying meaningful relationships. Highly connected genes in the thresholded network are then grouped into modules that provide insight into their collective functionality. While it has been shown that co-expression networks are biologically relevant, it has not been determined to what extent any given network is functionally robust given perturbations in the input sample set. For such a test, hundreds of networks are needed and hence a tool to rapidly construct these networks. To examine functional robustness of networks with varying input, we enhanced an existing RMT implementation for improved scalability and tested functional robustness of human (Homo sapiens), rice (Oryza sativa) and budding yeast (Saccharomyces cerevisiae). We demonstrate dramatic decrease in network construction time and computational requirements and show that despite some variation in global properties between networks, functional similarity remains high. Moreover, the biological function captured by co-expression networks thresholded by RMT is highly robust.

Method and apparatus for configuration control of redundant robots

NASA Technical Reports Server (NTRS)

Seraji, Homayoun (Inventor)

1991-01-01

A method and apparatus to control a robot or manipulator configuration over the entire motion based on augmentation of the manipulator forward kinematics is disclosed. A set of kinematic functions is defined in Cartesian or joint space to reflect the desirable configuration that will be achieved in addition to the specified end-effector motion. The user-defined kinematic functions and the end-effector Cartesian coordinates are combined to form a set of task-related configuration variables as generalized coordinates for the manipulator. A task-based adaptive scheme is then utilized to directly control the configuration variables so as to achieve tracking of some desired reference trajectories throughout the robot motion. This accomplishes the basic task of desired end-effector motion, while utilizing the redundancy to achieve any additional task through the desired time variation of the kinematic functions. The present invention can also be used for optimization of any kinematic objective function, or for satisfaction of a set of kinematic inequality constraints, as in an obstacle avoidance problem. In contrast to pseudoinverse-based methods, the configuration control scheme ensures cyclic motion of the manipulator, which is an essential requirement for repetitive operations. The control law is simple and computationally very fast, and does not require either the complex manipulator dynamic model or the complicated inverse kinematic transformation. The configuration control scheme can alternatively be implemented in joint space.

System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.

PubMed

Gresham, David; Boer, Viktor M; Caudy, Amy; Ziv, Naomi; Brandt, Nathan J; Storey, John D; Botstein, David

2011-01-01

An essential property of all cells is the ability to exit from active cell division and persist in a quiescent state. For single-celled microbes this primarily occurs in response to nutrient deprivation. We studied the genetic requirements for survival of Saccharomyces cerevisiae when starved for either of two nutrients: phosphate or leucine. We measured the survival of nearly all nonessential haploid null yeast mutants in mixed populations using a quantitative sequencing method that estimates the abundance of each mutant on the basis of frequency of unique molecular barcodes. Starvation for phosphate results in a population half-life of 337 hr whereas starvation for leucine results in a half-life of 27.7 hr. To measure survival of individual mutants in each population we developed a statistical framework that accounts for the multiple sources of experimental variation. From the identities of the genes in which mutations strongly affect survival, we identify genetic evidence for several cellular processes affecting survival during nutrient starvation, including autophagy, chromatin remodeling, mRNA processing, and cytoskeleton function. In addition, we found evidence that mitochondrial and peroxisome function is required for survival. Our experimental and analytical methods represent an efficient and quantitative approach to characterizing genetic functions and networks with unprecedented resolution and identified genotype-by-environment interactions that have important implications for interpretation of studies of aging and quiescence in yeast.

Variational bounds on the temperature distribution

NASA Astrophysics Data System (ADS)

Kalikstein, Kalman; Spruch, Larry; Baider, Alberto

1984-02-01

Upper and lower stationary or variational bounds are obtained for functions which satisfy parabolic linear differential equations. (The error in the bound, that is, the difference between the bound on the function and the function itself, is of second order in the error in the input function, and the error is of known sign.) The method is applicable to a range of functions associated with equalization processes, including heat conduction, mass diffusion, electric conduction, fluid friction, the slowing down of neutrons, and certain limiting forms of the random walk problem, under conditions which are not unduly restrictive: in heat conduction, for example, we do not allow the thermal coefficients or the boundary conditions to depend upon the temperature, but the thermal coefficients can be functions of space and time and the geometry is unrestricted. The variational bounds follow from a maximum principle obeyed by the solutions of these equations.

Functional anatomy of complement factor H.

PubMed

Makou, Elisavet; Herbert, Andrew P; Barlow, Paul N

2013-06-11

Factor H (FH) is a soluble regulator of the proteolytic cascade at the core of the evolutionarily ancient vertebrate complement system. Although FH consists of a single chain of similar protein modules, it has a demanding job description. Its chief role is to prevent complement-mediated injury to healthy host cells and tissues. This entails recognition of molecular patterns on host surfaces combined with control of one of nature's most dangerous examples of a positive-feedback loop. In this way, FH modulates, where and when needed, an amplification process that otherwise exponentially escalates the production of the pro-inflammatory, pro-phagocytic, and pro-cytolytic cleavage products of complement proteins C3 and C5. Mutations and single-nucleotide polymorphisms in the FH gene and autoantibodies against FH predispose individuals to diseases, including age-related macular degeneration, dense-deposit disease, and atypical hemolytic uremic syndrome. Moreover, deletions or variations of genes for FH-related proteins also influence the risk of disease. Numerous pathogens hijack FH and use it for self-defense. As reviewed herein, a molecular understanding of FH function is emerging. While its functional oligomeric status remains uncertain, progress has been achieved in characterizing its three-dimensional architecture and, to a lesser extent, its intermodular flexibility. Models are proposed, based on the reconciliation of older data with a wealth of recent evidence, in which a latent circulating form of FH is activated by its principal target, C3b tethered to a self-surface. Such models suggest hypotheses linking sequence variations to pathophysiology, but improved, more quantitative, functional assays and rigorous data analysis are required to test these ideas.

Autophonic Loudness of Singers in Simulated Room Acoustic Environments.

PubMed

Yadav, Manuj; Cabrera, Densil

2017-05-01

This paper aims to study the effect of room acoustics and phonemes on the perception of loudness of one's own voice (autophonic loudness) for a group of trained singers. For a set of five phonemes, 20 singers vocalized over several autophonic loudness ratios, while maintaining pitch constancy over extreme voice levels, within five simulated rooms. There were statistically significant differences in the slope of the autophonic loudness function (logarithm of autophonic loudness as a function of voice sound pressure level) for the five phonemes, with slopes ranging from 1.3 (/a:/) to 2.0 (/z/). There was no significant variation in the autophonic loudness function slopes with variations in room acoustics. The autophonic room response, which represents a systematic decrease in voice levels with increasing levels of room reflections, was also studied, with some evidence found in support. Overall, the average slope of the autophonic room response for the three corner vowels (/a:/, /i:/, and /u:/) was -1.4 for medium autophonic loudness. The findings relating to the slope of the autophonic loudness function are in agreement with the findings of previous studies where the sensorimotor mechanisms in regulating voice were shown to be more important in the perception of autophonic loudness than hearing of room acoustics. However, the role of room acoustics, in terms of the autophonic room response, is shown to be more complicated, requiring further inquiry. Overall, it is shown that autophonic loudness grows at more than twice the rate of loudness growth for sounds created outside the human body. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Water-vapor pressure control in a volume

NASA Technical Reports Server (NTRS)

Scialdone, J. J.

1978-01-01

The variation with time of the partial pressure of water in a volume that has openings to the outside environment and includes vapor sources was evaluated as a function of the purging flow and its vapor content. Experimental tests to estimate the diffusion of ambient humidity through openings and to validate calculated results were included. The purging flows required to produce and maintain a certain humidity in shipping containers, storage rooms, and clean rooms can be estimated with the relationship developed here. These purging flows are necessary to prevent the contamination, degradation, and other effects of water vapor on the systems inside these volumes.

Analysis of the Quality of Parabolic Flight

NASA Technical Reports Server (NTRS)

Lambot, Thomas; Ord, Stephan F.

2016-01-01

Parabolic flights allow researchers to conduct several 20 second micro-gravity experiments in the course of a single day. However, the measurement can have large variations over the course of a single parabola, requiring the knowledge of the actual flight environment as a function of time. The NASA Flight Opportunities program (FO) reviewed the acceleration data of over 400 parabolic flights and investigated the quality of micro-gravity for scientific purposes. It was discovered that a parabolic flight can be segmented into multiple parts of different quality and duration, a fact to be aware of when planning an experiment.

Posterior shoulder instability in the athletic population: Variations in assessment, clinical outcomes, and return to sport.

PubMed

DeLong, Jeffrey M; Bradley, James P

2015-12-18

Posterior instability of the shoulder is becoming an increasingly recognized shoulder injury in the athletic population. Diagnostic elements, such as etiology, directionality, and degree of instability are essential factors to assess in the unstable athletic shoulder. Concomitant injuries and associated pathologic lesions continue to be a significant challenge in the surgical management of posterior shoulder instability. Return to sport and previous level of play is ultimately the goal for every committed athlete and surgeon, thus subpopulations of athletes should be recognized as distinct entities requiring unique diagnostic, functional outcome measures, and surgical approaches.

Apollo experience report: Command and service module communications subsystem

NASA Technical Reports Server (NTRS)

Lattier, E. E., Jr.

1974-01-01

The development of spacecraft communications hardware from design to operation is described. Programs, requirements, specifications, and design approaches for a variety of functions (such as voice, telemetry, television, and antennas) are reviewed. Equipment environmental problems such as vibration, extreme temperature variation, and zero gravity are discussed. A review of the development of managerial techniques used in refining the roles of prime and subcontractors is included. The hardware test program is described in detail as it progressed from breadboard design to manned flight system evaluations. Finally, a series of actions is recommended to managers of similar projects to facilitate administration.

[Perioperative management of Parkinson's disease].

PubMed

Mariscal, A; Medrano, I Hernández; Cánovas, A Alonso; Lobo, E; Loinaz, C; Vela, L; Espiga, P García-Ruiz; Castrillo, J C Martínez

2012-01-01

One of the particular characteristics of Parkinson's disease (PD) is the wide clinical variation as regards the treatment that can be found in the same patient. This occurs with specific treatment for PD, as well as with other drug groups that can make motor function worse. For this reason, the perioperative management of PD requires experience and above all appropriate planning. In this article, the peculiarities of PD and its treatment are reviewed, and a strategy is set out for the perioperative management of these patients. Copyright © 2010 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

Reducing Bolt Preload Variation with Angle-of-Twist Bolt Loading

NASA Technical Reports Server (NTRS)

Thompson, Bryce; Nayate, Pramod; Smith, Doug; McCool, Alex (Technical Monitor)

2001-01-01

Critical high-pressure sealing joints on the Space Shuttle reusable solid rocket motor require precise control of bolt preload to ensure proper joint function. As the reusable solid rocket motor experiences rapid internal pressurization, correct bolt preloads maintain the sealing capability and structural integrity of the hardware. The angle-of-twist process provides the right combination of preload accuracy, reliability, process control, and assembly-friendly design. It improves significantly over previous methods. The sophisticated angle-of-twist process controls have yielded answers to all discrepancies encountered while the simplicity of the root process has assured joint preload reliability.

Use of constrained optimization in the conceptual design of a medium-range subsonic transport

NASA Technical Reports Server (NTRS)

Sliwa, S. M.

1980-01-01

Constrained parameter optimization was used to perform the optimal conceptual design of a medium range transport configuration. The impact of choosing a given performance index was studied, and the required income for a 15 percent return on investment was proposed as a figure of merit. A number of design constants and constraint functions were systematically varied to document the sensitivities of the optimal design to a variety of economic and technological assumptions. A comparison was made for each of the parameter variations between the baseline configuration and the optimally redesigned configuration.

Noncontact Atomic Force Microscopy: An Emerging Tool for Fundamental Catalysis Research.

PubMed

Altman, Eric I; Baykara, Mehmet Z; Schwarz, Udo D

2015-09-15

Although atomic force microscopy (AFM) was rapidly adopted as a routine surface imaging apparatus after its introduction in 1986, it has not been widely used in catalysis research. The reason is that common AFM operating modes do not provide the atomic resolution required to follow catalytic processes; rather the more complex noncontact (NC) mode is needed. Thus, scanning tunneling microscopy has been the principal tool for atomic scale catalysis research. In this Account, recent developments in NC-AFM will be presented that offer significant advantages for gaining a complete atomic level view of catalysis. The main advantage of NC-AFM is that the image contrast is due to the very short-range chemical forces that are of interest in catalysis. This motivated our development of 3D-AFM, a method that yields quantitative atomic resolution images of the potential energy surfaces that govern how molecules approach, stick, diffuse, and rebound from surfaces. A variation of 3D-AFM allows the determination of forces required to push atoms and molecules on surfaces, from which diffusion barriers and variations in adsorption strength may be obtained. Pushing molecules towards each other provides access to intermolecular interaction between reaction partners. Following reaction, NC-AFM with CO-terminated tips yields textbook images of intramolecular structure that can be used to identify reaction intermediates and products. Because NC-AFM and STM contrast mechanisms are distinct, combining the two methods can produce unique insight. It is demonstrated for surface-oxidized Cu(100) that simultaneous 3D-AFM/STM yields resolution of both the Cu and O atoms. Moreover, atomic defects in the Cu sublattice lead to variations in the reactivity of the neighboring O atoms. It is shown that NC-AFM also allows a straightforward imaging of work function variations which has been used to identify defect charge states on catalytic surfaces and to map charge transfer within an individual molecule. These advances highlight the potential for NC-AFM-based methods to become the cornerstone upon which a quantitative atomic scale view of each step of a catalytic process may be gained. Realizing this potential will rely on two breakthroughs: (1) development of robust methods for tip functionalization and (2) simplification of NC-AFM instrumentation and control schemes. Quartz force sensors may offer paths forward in both cases. They allow any material with an atomic asperity to be used as a tip, opening the door to a wide range of surface functionalization chemistry. In addition, they do not suffer from the instabilities that motivated the initial adoption of complex control strategies that are still used today.

UK Renal Registry 16th annual report: chapter 14 2012 multisite dialysis access audit in England, Northern Ireland and Wales and 2011 PD one year follow-up: national and centre-specific analyses.

PubMed

Briggs, Victoria; Pitcher, David; Shaw, Catriona; Fluck, Richard; Wilkie, Martin

2013-01-01

Dialysis access should be timely, minimise complications and maintain functionality. Good functional access is required for renal replacement therapy (RRT) to be successful. The aim of the combined vascular and peritoneal dialysis access audit was to examine practice patterns with respect to dialysis access and highlight variations in practice between renal centres. The UK Renal Registry collected centre-specific information on vascular and peritoneal access outcome measures including patient demographics, dialysis access type (at start of dialysis and three months after start of dialysis), surgical assessment and access functionality. The combined access audit covered incident haemodialysis (HD) and peritoneal dialysis (PD) patients in 2012 from England, Northern Ireland and Wales. Centres who had reported data on incident PD patients for the previous audit in 2011 were additionally asked to provide one year follow up data for this group. Fifty-one centres in England, Wales and Northern Ireland (representing 82% of all centres) returned data on first access from 3,720 incident HD patients and 1,018 incident PD patients. A strong relationship was seen between surgical assessment and the likelihood of starting HD with an arteriovenous fistula (AVF). Type of first access was related to the length of time known to renal services with higher numbers of AVFs and PD catheters used in patients known to renal services for at least one year. Three month and one year outcomes of HD and PD access were poorly reported. This audit provides information on important patient related outcome measures with the potential to lead to an improvement in access provision. This represents an important advance, however data collection remains suboptimal. There is wide practice variation across the England, Wales and Northern Ireland in provision of both HD and PD access which requires further exploration. © 2014 S. Karger AG, Basel.

Azimuthal Dependence of the Ground Motion Variability from Scenario Modeling of the 2014 Mw6.0 South Napa, California, Earthquake Using an Advanced Kinematic Source Model

NASA Astrophysics Data System (ADS)

Gallovič, F.

2017-09-01

Strong ground motion simulations require physically plausible earthquake source model. Here, I present the application of such a kinematic model introduced originally by Ruiz et al. (Geophys J Int 186:226-244, 2011). The model is constructed to inherently provide synthetics with the desired omega-squared spectral decay in the full frequency range. The source is composed of randomly distributed overlapping subsources with fractal number-size distribution. The position of the subsources can be constrained by prior knowledge of major asperities (stemming, e.g., from slip inversions), or can be completely random. From earthquake physics point of view, the model includes positive correlation between slip and rise time as found in dynamic source simulations. Rupture velocity and rise time follows local S-wave velocity profile, so that the rupture slows down and rise times increase close to the surface, avoiding unrealistically strong ground motions. Rupture velocity can also have random variations, which result in irregular rupture front while satisfying the causality principle. This advanced kinematic broadband source model is freely available and can be easily incorporated into any numerical wave propagation code, as the source is described by spatially distributed slip rate functions, not requiring any stochastic Green's functions. The source model has been previously validated against the observed data due to the very shallow unilateral 2014 Mw6 South Napa, California, earthquake; the model reproduces well the observed data including the near-fault directivity (Seism Res Lett 87:2-14, 2016). The performance of the source model is shown here on the scenario simulations for the same event. In particular, synthetics are compared with existing ground motion prediction equations (GMPEs), emphasizing the azimuthal dependence of the between-event ground motion variability. I propose a simple model reproducing the azimuthal variations of the between-event ground motion variability, providing an insight into possible refinement of GMPEs' functional forms.

Identification and characterization of a locus which regulates multiple functions in Pseudomonas tolaasii, the cause of brown blotch disease of Agaricus bisporus.

PubMed Central

Grewal, S I; Han, B; Johnstone, K

1995-01-01

Pseudomonas tolaasii, the causal agent of brown blotch disease of Agaricus bisporus, spontaneously gives rise to morphologically distinct stable sectors, referred to as the phenotypic variant form, at the margins of the wild-type colonies. The phenotypic variant form is nonpathogenic and differs from the wild type in a range of biochemical and physiological characteristics. A genomic cosmid clone (pSISG29) from a wild-type P. tolaasii library was shown to be capable of restoring a range of characteristics of the phenotypic variant to those of the wild-type form, when present in trans. Subcloning and saturation mutagenesis analysis with Tn5lacZ localized a 3.0-kb region from pSISG29, designated the pheN locus, required for complementation of the phenotypic variant to the wild-type form. Marker exchange of the Tn5lacZ-mutagenized copy of the pheN locus into the wild-type strain demonstrated that a functional copy of the pheN gene is required to maintain the wild-type pathogenic phenotype and that loss of the pheN gene or its function results in conversion of the wild-type form to the phenotypic variant form. The pheN locus contained a 2,727-bp open reading frame encoding an 83-kDa protein. The predicted amino acid sequence of the PheN protein showed homology to the sensor and regulator domains of the conserved family of two component bacterial sensor regulator proteins. Southern hybridization analysis of pheN genes from the wild type and the phenotypic variant form revealed that DNA rearrangement occurs within the pheN locus during phenotypic variation. Analysis of pheN expression with a pheN::lacZ fusion demonstrated that expression is regulated by environmental factors. These results are related to a model for control for phenotypic variation in P. tolaasii. PMID:7642492

FUNCTIONAL IMPLICATION OF MAJOR HISTOCOMPATIBILITY (MH) VARIATION USING AN ESTUARINE FISH POPULATION

EPA Science Inventory

Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under ...

Application of variational principles and adjoint integrating factors for constructing numerical GFD models

NASA Astrophysics Data System (ADS)

Penenko, Vladimir; Tsvetova, Elena; Penenko, Alexey

2015-04-01

The proposed method is considered on an example of hydrothermodynamics and atmospheric chemistry models [1,2]. In the development of the existing methods for constructing numerical schemes possessing the properties of total approximation for operators of multiscale process models, we have developed a new variational technique, which uses the concept of adjoint integrating factors. The technique is as follows. First, a basic functional of the variational principle (the integral identity that unites the model equations, initial and boundary conditions) is transformed using Lagrange's identity and the second Green's formula. As a result, the action of the operators of main problem in the space of state functions is transferred to the adjoint operators defined in the space of sufficiently smooth adjoint functions. By the choice of adjoint functions the order of the derivatives becomes lower by one than those in the original equations. We obtain a set of new balance relationships that take into account the sources and boundary conditions. Next, we introduce the decomposition of the model domain into a set of finite volumes. For multi-dimensional non-stationary problems, this technique is applied in the framework of the variational principle and schemes of decomposition and splitting on the set of physical processes for each coordinate directions successively at each time step. For each direction within the finite volume, the analytical solutions of one-dimensional homogeneous adjoint equations are constructed. In this case, the solutions of adjoint equations serve as integrating factors. The results are the hybrid discrete-analytical schemes. They have the properties of stability, approximation and unconditional monotony for convection-diffusion operators. These schemes are discrete in time and analytic in the spatial variables. They are exact in case of piecewise-constant coefficients within the finite volume and along the coordinate lines of the grid area in each direction on a time step. In each direction, they have tridiagonal structure. They are solved by the sweep method. An important advantage of the discrete-analytical schemes is that the values of derivatives at the boundaries of finite volume are calculated together with the values of the unknown functions. This technique is particularly attractive for problems with dominant convection, as it does not require artificial monotonization and limiters. The same idea of integrating factors is applied in temporal dimension to the stiff systems of equations describing chemical transformation models [2]. The proposed method is applicable for the problems involving convection-diffusion-reaction operators. The work has been partially supported by the Presidium of RAS under Program 43, and by the RFBR grants 14-01-00125 and 14-01-31482. References: 1. V.V. Penenko, E.A. Tsvetova, A.V. Penenko. Variational approach and Euler's integrating factors for environmental studies// Computers and Mathematics with Applications, (2014) V.67, Issue 12, P. 2240-2256. 2. V.V.Penenko, E.A.Tsvetova. Variational methods of constructing monotone approximations for atmospheric chemistry models // Numerical analysis and applications, 2013, V. 6, Issue 3, pp 210-220.

Genomics of lactation: role of nutrigenomics and nutrigenetics in the fatty acid composition of human milk.

PubMed

Sosa-Castillo, Elizabeth; Rodríguez-Cruz, Maricela; Moltó-Puigmartí, Carolina

2017-08-01

Human milk covers the infant's nutrient requirements during the first 6 months of life. The composition of human milk progressively changes during lactation and it is influenced by maternal nutritional factors. Nowadays, it is well known that nutrients have the ability to interact with genes and modulate molecular mechanisms impacting physiological functions. This has led to a growing interest among researchers in exploring nutrition at a molecular level and to the development of two fields of study: nutrigenomics, which evaluates the influence of nutrients on gene expression, and nutrigenetics, which evaluates the heterogeneous individual response to nutrients due to genetic variation. Fatty acids are one of the nutrients most studied in relation to lactation given their biologically important roles during early postnatal life. Fatty acids modulate transcription factors involved in the regulation of lipid metabolism, which in turn causes a variation in the proportion of lipids in milk. This review focuses on understanding, on the one hand, the gene transcription mechanisms activated by maternal dietary fatty acids and, on the other hand, the interaction between dietary fatty acids and genetic variation in genes involved in lipid metabolism. Both of these mechanisms affect the fatty acid composition of human milk.

Impact of IgG Fc-Oligosaccharides on Recombinant Monoclonal Antibody Structure, Stability, Safety, and Efficacy.

PubMed

Liu, Hongcheng; Nowak, Christine; Andrien, Bruce; Shao, Mei; Ponniah, Gomathinayagam; Neill, Alyssa

2017-09-01

Glycosylation of the conserved asparagine residue in the CH2 domain is the most common posttranslational modification of recombinant monoclonal antibodies. Ideally, a consistent oligosaccharide profile should be maintained from early clinical material to commercial material for the development of recombinant monoclonal therapeutics, though variation in the profile is a typical result of process changes. The risk of oligosaccharide variation posed to further development is required to be thoroughly evaluated based on its impact on antibody structure, stability, efficacy and safety. The variation should be controlled within a range so that there is no detrimental impact on safety and efficacy and thus allowing the use of early phase safety and efficacy data to support project advancement to later phase. This review article focuses on the current scientific understanding of the commonly observed oligosaccharides found in recombinant monoclonal antibodies and their impact on structure, stability and biological functions, which are the basis to evaluate safety and efficacy. It also provides a brief discussion on critical quality attribute (CQA) assessment with regard to oligosaccharides based on the mechanism of action (MOA). © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1173-1181, 2017. © 2017 American Institute of Chemical Engineers.

Variational Methods in Sensitivity Analysis and Optimization for Aerodynamic Applications

NASA Technical Reports Server (NTRS)

Ibrahim, A. H.; Hou, G. J.-W.; Tiwari, S. N. (Principal Investigator)

1996-01-01

Variational methods (VM) sensitivity analysis, which is the continuous alternative to the discrete sensitivity analysis, is employed to derive the costate (adjoint) equations, the transversality conditions, and the functional sensitivity derivatives. In the derivation of the sensitivity equations, the variational methods use the generalized calculus of variations, in which the variable boundary is considered as the design function. The converged solution of the state equations together with the converged solution of the costate equations are integrated along the domain boundary to uniquely determine the functional sensitivity derivatives with respect to the design function. The determination of the sensitivity derivatives of the performance index or functional entails the coupled solutions of the state and costate equations. As the stable and converged numerical solution of the costate equations with their boundary conditions are a priori unknown, numerical stability analysis is performed on both the state and costate equations. Thereafter, based on the amplification factors obtained by solving the generalized eigenvalue equations, the stability behavior of the costate equations is discussed and compared with the state (Euler) equations. The stability analysis of the costate equations suggests that the converged and stable solution of the costate equation is possible only if the computational domain of the costate equations is transformed to take into account the reverse flow nature of the costate equations. The application of the variational methods to aerodynamic shape optimization problems is demonstrated for internal flow problems at supersonic Mach number range. The study shows, that while maintaining the accuracy of the functional sensitivity derivatives within the reasonable range for engineering prediction purposes, the variational methods show a substantial gain in computational efficiency, i.e., computer time and memory, when compared with the finite difference sensitivity analysis.

On the sensitivity of annual streamflow to air temperature

USGS Publications Warehouse

Milly, Paul C.D.; Kam, Jonghun; Dunne, Krista A.

2018-01-01

Although interannual streamflow variability is primarily a result of precipitation variability, temperature also plays a role. The relative weakness of the temperature effect at the annual time scale hinders understanding, but may belie substantial importance on climatic time scales. Here we develop and evaluate a simple theory relating variations of streamflow and evapotranspiration (E) to those of precipitation (P) and temperature. The theory is based on extensions of the Budyko water‐balance hypothesis, the Priestley‐Taylor theory for potential evapotranspiration ( ), and a linear model of interannual basin storage. The theory implies that the temperature affects streamflow by modifying evapotranspiration through a Clausius‐Clapeyron‐like relation and through the sensitivity of net radiation to temperature. We apply and test (1) a previously introduced “strong” extension of the Budyko hypothesis, which requires that the function linking temporal variations of the evapotranspiration ratio (E/P) and the index of dryness ( /P) at an annual time scale is identical to that linking interbasin variations of the corresponding long‐term means, and (2) a “weak” extension, which requires only that the annual evapotranspiration ratio depends uniquely on the annual index of dryness, and that the form of that dependence need not be known a priori nor be identical across basins. In application of the weak extension, the readily observed sensitivity of streamflow to precipitation contains crucial information about the sensitivity to potential evapotranspiration and, thence, to temperature. Implementation of the strong extension is problematic, whereas the weak extension appears to capture essential controls of the temperature effect efficiently.

Context specificity of inhibitory control in dogs

PubMed Central

MacLean, Evan L.; Hare, Brian A.

2014-01-01

Across three experiments, we explored whether a dog's capacity for inhibitory control is stable or variable across decision-making contexts. In the social task, dogs were first exposed to the reputations of a stingy experimenter that never shared food and a generous experimenter who always shared food. In subsequent test trials, dogs were required to avoid approaching the stingy experimenter when this individual offered (but withheld) a higher-value reward than the generous experimenter did. In the A-not-B task, dogs were required to inhibit searching for food in a previously rewarded location after witnessing the food being moved from this location to a novel hiding place. In the cylinder task, dogs were required to resist approaching visible food directly (because it was behind a transparent barrier), in favor of a detour reaching response. Overall, dogs exhibited inhibitory control in all three tasks. However, individual scores were not correlated between tasks, suggesting that context has a large effect on dogs' behavior. This result mirrors studies of humans, which have highlighted intra-individual variation in inhibitory control as a function of the decision-making context. Lastly, we observed a correlation between a subject's age and performance on the cylinder task, corroborating previous observations of age-related decline in dogs' executive function. PMID:23584618

Environmental Drivers of Benthic Flux Variation and Ecosystem Functioning in Salish Sea and Northeast Pacific Sediments.

PubMed

Belley, Rénald; Snelgrove, Paul V R; Archambault, Philippe; Juniper, S Kim

2016-01-01

The upwelling of deep waters from the oxygen minimum zone in the Northeast Pacific from the continental slope to the shelf and into the Salish Sea during spring and summer offers a unique opportunity to study ecosystem functioning in the form of benthic fluxes along natural gradients. Using the ROV ROPOS we collected sediment cores from 10 sites in May and July 2011, and September 2013 to perform shipboard incubations and flux measurements. Specifically, we measured benthic fluxes of oxygen and nutrients to evaluate potential environmental drivers of benthic flux variation and ecosystem functioning along natural gradients of temperature and bottom water dissolved oxygen concentrations. The range of temperature and dissolved oxygen encountered across our study sites allowed us to apply a suite of multivariate analyses rarely used in flux studies to identify bottom water temperature as the primary environmental driver of benthic flux variation and organic matter remineralization. Redundancy analysis revealed that bottom water characteristics (temperature and dissolved oxygen), quality of organic matter (chl a:phaeo and C:N ratios) and sediment characteristics (mean grain size and porosity) explained 51.5% of benthic flux variation. Multivariate analyses identified significant spatial and temporal variation in benthic fluxes, demonstrating key differences between the Northeast Pacific and Salish Sea. Moreover, Northeast Pacific slope fluxes were generally lower than shelf fluxes. Spatial and temporal variation in benthic fluxes in the Salish Sea were driven primarily by differences in temperature and quality of organic matter on the seafloor following phytoplankton blooms. These results demonstrate the utility of multivariate approaches in differentiating among potential drivers of seafloor ecosystem functioning, and indicate that current and future predictive models of organic matter remineralization and ecosystem functioning of soft-muddy shelf and slope seafloor habitats should consider bottom water temperature variation. Bottom temperature has important implications for estimates of seasonal and spatial benthic flux variation, benthic-pelagic coupling, and impacts of predicted ocean warming at high latitudes.

Variation and Defect Tolerance for Nano Crossbars

NASA Astrophysics Data System (ADS)

Tunc, Cihan

With the extreme shrinking in CMOS technology, quantum effects and manufacturing issues are getting more crucial. Hence, additional shrinking in CMOS feature size seems becoming more challenging, difficult, and costly. On the other hand, emerging nanotechnology has attracted many researchers since additional scaling down has been demonstrated by manufacturing nanowires, Carbon nanotubes as well as molecular switches using bottom-up manufacturing techniques. In addition to the progress in manufacturing, developments in architecture show that emerging nanoelectronic devices will be promising for the future system designs. Using nano crossbars, which are composed of two sets of perpendicular nanowires with programmable intersections, it is possible to implement logic functions. In addition, nano crossbars present some important features as regularity, reprogrammability, and interchangeability. Combining these features, researchers have presented different effective architectures. Although bottom-up nanofabrication can greatly reduce manufacturing costs, due to low controllability in the manufacturing process, some critical issues occur. Bottom- up nanofabrication process results in high variation compared to conventional top- down lithography used in CMOS technology. In addition, an increased failure rate is expected. Variation and defect tolerance methods used for conventional CMOS technology seem inadequate for adapting to emerging nano technology because the variation and the defect rate for emerging nano technology is much more than current CMOS technology. Therefore, variations and defect tolerance methods for emerging nano technology are necessary for a successful transition. In this work, in order to tolerate variations for crossbars, we introduce a framework that is established based on reprogrammability and interchangeability features of nano crossbars. This framework is shown to be applicable for both FET-based and diode-based nano crossbars. We present a characterization testing method which requires minimal number of test vectors. We formulate the variation optimization problem using Simulated Annealing with different optimization goals. Furthermore, we extend the framework for defect tolerance. Experimental results and comparison of proposed framework with exhaustive methods confirm its effectiveness for both variation and defect tolerance.

Geographical variation in parasitism shapes larval immune function in a phytophagous insect

NASA Astrophysics Data System (ADS)

Vogelweith, Fanny; Dourneau, Morgane; Thiéry, Denis; Moret, Yannick; Moreau, Jérôme

2013-12-01

Two of the central goals of immunoecology are to understand natural variation in the immune system among populations and to identify those selection pressures that shape immune traits. Maintenance of the immune system can be costly, and both food quality and parasitism selection pressure are factors potentially driving immunocompetence. In tritrophic interactions involving phytophagous insects, host plants, and natural enemies, the immunocompetence of phytophagous insects is constrained by selective forces from both the host plants and the natural enemies. Here, we assessed the roles of host plants and natural enemies as selective pressures on immune variation among natural populations of Lobesia botrana. Our results showed marked geographical variation in immune defenses and parasitism among different natural populations. Larval immune functions were dependent of the host plant quality and were positively correlated to parasitism, suggesting that parasitoids select for greater investment into immunity in moth. Furthermore, investment in immune defense was negatively correlated with body size, suggesting that it is metabolically expensive. The findings emphasize the roles of host plants and parasitoids as selective forces shaping host immune functions in natural conditions. We argue that kinds of study are central to understanding natural variations in immune functions, and the selective forces beyond.

An Analysis of State Autism Educational Assessment Practices and Requirements

ERIC Educational Resources Information Center

Barton, Erin E.; Harris, Bryn; Leech, Nancy; Stiff, Lillian; Choi, Gounah; Joel, Tiffany

2016-01-01

States differ in the procedures and criteria used to identify ASD. These differences are likely to impact the prevalence and age of identification for children with ASD. The purpose of the current study was to examine the specific state variations in ASD identification and eligibility criteria requirements. We examined variations by state in…

Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb.

PubMed

Medrano, Mónica; Herrera, Carlos M; Bazaga, Pilar

2014-10-01

The ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation-sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker-trait association analyses for 20 whole-plant, leaf and regenerative functional traits in a large sample of wild-growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south-eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between-site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity. © 2014 John Wiley & Sons Ltd.

The dopamine D2 receptor antagonist sulpiride modulates striatal BOLD signal during the manipulation of information in working memory.

PubMed

Dodds, Chris M; Clark, Luke; Dove, Anja; Regenthal, Ralf; Baumann, Frank; Bullmore, Ed; Robbins, Trevor W; Müller, Ulrich

2009-11-01

Dopamine (DA) plays an important role in working memory. However, the precise functions supported by different DA receptor subtypes in different neural regions remain unclear. The present study used pharmacological, event-related fMRI to test the hypothesis that striatal dopamine is important for the manipulation of information in working memory. Twenty healthy human subjects were scanned twice, once after placebo and once after sulpiride 400 mg, a selective DA D2 receptor antagonist, while performing a verbal working memory task requiring different levels of manipulation. Whilst there was no overall effect of sulpiride on task-dependent activation, individual variation in sulpiride plasma levels predicted the effect of working memory manipulation on activation in the putamen, suggesting a dose-dependent effect of DA antagonism on a striatally based manipulation process. These effects occurred in the context of a drug-induced improvement in performance on trials requiring the manipulation of information in working memory but not on simple retrieval trials. No significant drug effects were observed in the prefrontal cortex. These results support models of dopamine function that posit a 'gating' function for dopamine D2 receptors in the striatum, which enables the flexible updating and manipulation of information in working memory.

Distinguishing between evidence and its explanations in the steering of atomic clocks

NASA Astrophysics Data System (ADS)

Myers, John M.; Hadi Madjid, F.

2014-11-01

Quantum theory reflects within itself a separation of evidence from explanations. This separation leads to a known proof that: (1) no wave function can be determined uniquely by evidence, and (2) any chosen wave function requires a guess reaching beyond logic to things unforeseeable. Chosen wave functions are encoded into computer-mediated feedback essential to atomic clocks, including clocks that step computers through their phases of computation and clocks in space vehicles that supply evidence of signal propagation explained by hypotheses of spacetimes with metric tensor fields. The propagation of logical symbols from one computer to another requires a shared rhythm-like a bucket brigade. Here we show how hypothesized metric tensors, dependent on guesswork, take part in the logical synchronization by which clocks are steered in rate and position toward aiming points that satisfy phase constraints, thereby linking the physics of signal propagation with the sharing of logical symbols among computers. Recognizing the dependence of the phasing of symbol arrivals on guesses about signal propagation transports logical synchronization from the engineering of digital communications to a discipline essential to physics. Within this discipline we begin to explore questions invisible under any concept of time that fails to acknowledge unforeseeable events. In particular, variation of spacetime curvature is shown to limit the bit rate of logical communication.

Global trends

NASA Technical Reports Server (NTRS)

Megie, G.; Chanin, M.-L.; Ehhalt, D.; Fraser, P.; Frederick, J. F.; Gille, J. C.; Mccormick, M. P.; Schoebert, M.; Bishop, L.; Bojkov, R. D.

1990-01-01

Measuring trends in ozone, and most other geophysical variables, requires that a small systematic change with time be determined from signals that have large periodic and aperiodic variations. Their time scales range from the day-to-day changes due to atmospheric motions through seasonal and annual variations to 11 year cycles resulting from changes in the sun UV output. Because of the magnitude of all of these variations is not well known and highly variable, it is necessary to measure over more than one period of the variations to remove their effects. This means that at least 2 or more times the 11 year sunspot cycle. Thus, the first requirement is for a long term data record. The second related requirement is that the record be consistent. A third requirement is for reasonable global sampling, to ensure that the effects are representative of the entire Earth. The various observational methods relevant to trend detection are reviewed to characterize their quality and time and space coverage. Available data are then examined for long term trends or recent changes in ozone total content and vertical distribution, as well as related parameters such as stratospheric temperature, source gases and aerosols.

Normal Genetic Variation, Cognition, and Aging

PubMed Central

Greenwood, P. M.; Parasuraman, Raja

2005-01-01

This article reviews the modulation of cognitive function by normal genetic variation. Although the heritability of “g” is well established, the genes that modulate specific cognitive functions are largely unidentified. Application of the allelic association approach to individual differences in cognition has begun to reveal the effects of single nucleotide polymorphisms on specific and general cognitive functions. This article proposes a framework for relating genotype to cognitive phenotype by considering the effect of genetic variation on the protein product of specific genes within the context of the neural basis of particular cognitive domains. Specificity of effects is considered, from genes controlling part of one receptor type to genes controlling agents of neuronal repair, and evidence is reviewed of cognitive modulation by polymorphisms in dopaminergic and cholinergic receptor genes, dopaminergic enzyme genes, and neurotrophic genes. Although allelic variation in certain genes can be reliably linked to cognition—specifically to components of attention, working memory, and executive function in healthy adults—the specificity, generality, and replicability of the effects are not fully known. PMID:15006290

The uncertainty in the radon hazard classification of areas as a function of the number of measurements.

PubMed

Friedmann, H; Baumgartner, A; Gruber, V; Kaineder, H; Maringer, F J; Ringer, W; Seidel, C

2017-07-01

The administration in many countries demands a classification of areas concerning their radon risk taking into account the requirements of the EU Basic Safety Standards. The wide variation of indoor radon concentrations in an area which is caused by different house construction, different living style and different geological situations introduces large uncertainties for any classification scheme. Therefore, it is of importance to estimate the size of the experimental coefficient of variation (relative standard deviation) of the parameter which is used to classify an area. Besides the time period of measurement it is the number of measurements which strongly influences this uncertainty and it is important to find a compromise between the economic possibilities and the needed confidence level. Some countries do not use pure measurement results for the classification of areas but use derived quantities, usually called radon potential, which should reduce the influence of house construction, living style etc. and should rather represent the geological situation of an area. Here, radon indoor measurements in nearly all homes in three municipalities and its conversion into a radon potential were used to determine the uncertainty of the mean radon potential of an area as a function of the number of investigated homes. It could be shown that the coefficient of variation scales like 1/√n with n the number of measured dwellings. The question how to deal with uncertainties when using a classification scheme for the radon risk is discussed and a general procedure is proposed. Copyright © 2016 Elsevier Ltd. All rights reserved.

There is more to pollinator-mediated selection than pollen limitation.

PubMed

Sletvold, Nina; Agren, Jon

2014-07-01

Spatial variation in pollinator-mediated selection (Δβpoll ) is a major driver of floral diversification, but we lack a quantitative understanding of its link to pollen limitation (PL) and net selection on floral traits. For 2-5 years, we quantified Δβpoll on floral traits in two populations each of two orchid species differing in PL. In both species, spatiotemporal variation in Δβpoll explained much of the variation in net selection. Selection was consistently stronger and the proportion that was pollinator-mediated was higher in the severely pollen-limited deceptive species than in the rewarding species. Within species, variation in PL could not explain variation in Δβpoll for any trait, indicating that factors influencing the functional relationship between trait variation and pollination success govern a major part of the observed variation in Δβpoll . Separating the effects of variation in mean interaction intensity and in the functional significance of traits will be necessary to understand spatiotemporal variation in selection exerted by the biotic environment. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Noise in neonatal intensive care units (NICUs) and its effect on high risk newborns

NASA Astrophysics Data System (ADS)

Lasky, Robert E.; Williams, Amber L.; van Drongelen, Wim; Gray, Lincoln C.

2005-09-01

We conducted sound surveys in a large state of the art NICU with six separate rooms devoted to the sickest babies requiring the most intensive care (Level III) and six rooms devoted to babies requiring special but less intensive care (Level II). Each room was capable of caring for up to 8 babies. Additionally, there were 8 individual Isolation rooms. We used Larson Davis Spark squflg 703+ dosimeters to record 21 week long sound surveys, seven in each type of room. The American Academy of Pediatrics (1997) has recommended that sound levels in NICUs should never exceed 45 dB(A). That recommendation was exceeded 73.6% of the time in Level II, 92.1% of the time in Isolation, and 96.6% of the time in Level III. Sound levels were lowest in the Level II rooms especially for the softest sounds recorded (L90 and L70). Level III rooms were noisiest except for the noisiest decile of sound (L10). Isolation rooms were noisiest at the highest sound levels (probably because of their reverberant construction materials and enclosed space). Autocorrelation functions were calculated identifying periodic components in all three rooms at about 12 and 24 hrs. Periodic variations were very small compared to random sound variations.

The Faber–Jackson relation and Fundamental Plane from halo abundance matching

DOE PAGES

Desmond, Harry; Wechsler, Risa H.

2016-11-02

The Fundamental Plane (FP) describes the relation between the stellar mass, size, and velocity dispersion of elliptical galaxies; the Faber–Jackson relation (FJR) is its projection on to {mass, velocity} space. In this work, we re-deploy and expand the framework of Desmond & Wechsler to ask whether abundance matching-based Λ-cold dark matter models which have shown success in matching the spatial distribution of galaxies are also capable of explaining key properties of the FJR and FP, including their scatter. Within our framework, agreement with the normalization of the FJR requires haloes to expand in response to disc formation. We find thatmore » the tilt of the FP may be explained by a combination of the observed non-homology in galaxy structure and the variation in mass-to-light ratio produced by abundance matching with a universal initial mass function, provided that the anisotropy of stellar motions is taken into account. However, the predicted scatter around the FP is considerably increased by situating galaxies in cosmologically motivated haloes due to the variations in halo properties at fixed stellar mass and appears to exceed that of the data. Finally, this implies that additional correlations between galaxy and halo variables may be required to fully reconcile these models with elliptical galaxy scaling relations.« less

Natural Variation in the Thermotolerance of Neural Function and Behavior due to a cGMP-Dependent Protein Kinase

PubMed Central

Dawson-Scully, Ken; Armstrong, Gary A.B.; Kent, Clement; Robertson, R. Meldrum; Sokolowski, Marla B.

2007-01-01

Although it is acknowledged that genetic variation contributes to individual differences in thermotolerance, the specific genes and pathways involved and how they are modulated by the environment remain poorly understood. We link natural variation in the thermotolerance of neural function and behavior in Drosophila melanogaster to the foraging gene (for, which encodes a cGMP-dependent protein kinase (PKG)) as well as to its downstream target, protein phosphatase 2A (PP2A). Genetic and pharmacological manipulations revealed that reduced PKG (or PP2A) activity caused increased thermotolerance of synaptic transmission at the larval neuromuscular junction. Like synaptic transmission, feeding movements were preserved at higher temperatures in larvae with lower PKG levels. In a comparative assay, pharmacological manipulations altering thermotolerance in a central circuit of Locusta migratoria demonstrated conservation of this neuroprotective pathway. In this circuit, either the inhibition of PKG or PP2A induced robust thermotolerance of neural function. We suggest that PKG and therefore the polymorphism associated with the allelic variation in for may provide populations with natural variation in heat stress tolerance. for's function in behavior is conserved across most organisms, including ants, bees, nematodes, and mammals. PKG's role in thermotolerance may also apply to these and other species. Natural variation in thermotolerance arising from genes involved in the PKG pathway could impact the evolution of thermotolerance in natural populations. PMID:17712421

To what extent is altitudinal variation of functional traits driven by genetic adaptation in European oak and beech?

PubMed

Bresson, Caroline C; Vitasse, Yann; Kremer, Antoine; Delzon, Sylvain

2011-11-01

The phenotypic responses of functional traits in natural populations are driven by genetic diversity and phenotypic plasticity. These two mechanisms enable trees to cope with rapid climate change. We studied two European temperate tree species (sessile oak and European beech), focusing on (i) in situ variations of leaf functional traits (morphological and physiological) along two altitudinal gradients and (ii) the extent to which these variations were under environmental and/or genetic control using a common garden experiment. For all traits, altitudinal trends tended to be highly consistent between species and transects. For both species, leaf mass per area displayed a positive linear correlation with altitude, whereas leaf size was negatively correlated with altitude. We also observed a significant increase in leaf physiological performance with increasing altitude: populations at high altitudes had higher maximum rates of assimilation, stomatal conductance and leaf nitrogen content than those at low altitudes. In the common garden experiment, genetic differentiation between populations accounted for 0-28% of total phenotypic variation. However, only two traits (leaf mass per area and nitrogen content) exhibited a significant cline. The combination of in situ and common garden experiments used here made it possible to demonstrate, for both species, a weaker effect of genetic variation than of variations in natural conditions, suggesting a strong effect of the environment on leaf functional traits. Finally, we demonstrated that intrapopulation variability was systematically higher than interpopulation variability, whatever the functional trait considered, indicating a high potential capacity to adapt to climate change.

Functional-diversity indices can be driven by methodological choices and species richness.

PubMed

Poos, Mark S; Walker, Steven C; Jackson, Donald A

2009-02-01

Functional diversity is an important concept in community ecology because it captures information on functional traits absent in measures of species diversity. One popular method of measuring functional diversity is the dendrogram-based method, FD. To calculate FD, a variety of methodological choices are required, and it has been debated about whether biological conclusions are sensitive to such choices. We studied the probability that conclusions regarding FD were sensitive, and that patterns in sensitivity were related to alpha and beta components of species richness. We developed a randomization procedure that iteratively calculated FD by assigning species into two assemblages and calculating the probability that the community with higher FD varied across methods. We found evidence of sensitivity in all five communities we examined, ranging from a probability of sensitivity of 0 (no sensitivity) to 0.976 (almost completely sensitive). Variations in these probabilities were driven by differences in alpha diversity between assemblages and not by beta diversity. Importantly, FD was most sensitive when it was most useful (i.e., when differences in alpha diversity were low). We demonstrate that trends in functional-diversity analyses can be largely driven by methodological choices or species richness, rather than functional trait information alone.

Decorrelation scales for Arctic Ocean hydrography - Part I: Amerasian Basin

NASA Astrophysics Data System (ADS)

Sumata, Hiroshi; Kauker, Frank; Karcher, Michael; Rabe, Benjamin; Timmermans, Mary-Louise; Behrendt, Axel; Gerdes, Rüdiger; Schauer, Ursula; Shimada, Koji; Cho, Kyoung-Ho; Kikuchi, Takashi

2018-03-01

Any use of observational data for data assimilation requires adequate information of their representativeness in space and time. This is particularly important for sparse, non-synoptic data, which comprise the bulk of oceanic in situ observations in the Arctic. To quantify spatial and temporal scales of temperature and salinity variations, we estimate the autocorrelation function and associated decorrelation scales for the Amerasian Basin of the Arctic Ocean. For this purpose, we compile historical measurements from 1980 to 2015. Assuming spatial and temporal homogeneity of the decorrelation scale in the basin interior (abyssal plain area), we calculate autocorrelations as a function of spatial distance and temporal lag. The examination of the functional form of autocorrelation in each depth range reveals that the autocorrelation is well described by a Gaussian function in space and time. We derive decorrelation scales of 150-200 km in space and 100-300 days in time. These scales are directly applicable to quantify the representation error, which is essential for use of ocean in situ measurements in data assimilation. We also describe how the estimated autocorrelation function and decorrelation scale should be applied for cost function calculation in a data assimilation system.

Variations in grain-scale sediment structure and entrainment force in a gravel-bed channel as a function of fine sediment content and morphological location

NASA Astrophysics Data System (ADS)

Voepel, Hal; Ahmed, Sharif; Hodge, Rebecca; Leyland, Julian; Sear, David

2017-04-01

One of the major causes of uncertainty in estimates of bedload transport rates in gravel-bed rivers is a lack of understanding of grain-scale sediment structure, and the impact that this structure has on the force required to entrain sediment. There are at least two factors that standard entrainment models do not consider. The first is the way in which the spatial arrangement and orientation of grains and the resultant forces varies throughout a channel and over time, ways that have yet to be fully quantified. The second is that sediment entrainment is a 3D process, yet calculations of entrainment thresholds for sediment grains are typically based on 2D diagrams where we calculate static moments of force vectors about a pivot angle, represented as a single point rather than as a more realistic axis of rotation. Our research addresses these limitations by quantifying variations in 3D sediment structure and entrainment force requirements across two key parameters: morphological location within a riffle-pool sequence (reflecting variation in hydraulic conditions), and the fine sediment content of the gravel-bed (sand and clay). We report results from a series of flume experiments in which we water-worked a gravel-bed with a riffle-pool morphology containing varying amounts of fine sediment. After each experimental run intact samples of the bed at different locations were extracted and the internal structure of the bed was measured using non-destructive, micro-focus X-ray computed tomography (CT) imaging. The CT images were processed to measure the properties of individual grains, including volume, center of mass, dimension, and contact points. From these data we were able to quantify the sediment structure and entrainment force requirements through measurement of 3D metrics including grain pivot angles, grain exposure and protrusion. Comparison of the metrics across different morphological locations and fine sediment content demonstrates how these factors affect the bed structure and entrainment force requirement. These results have implications for the development of sediment entrainment models for gravel-bed rivers. Keywords: fluvial sediment, geomorphology, entrainment models, X-ray computed tomography, 3D imaging, vector mechanics

Robust dynamic inversion controller design and analysis (using the X-38 vehicle as a case study)

NASA Astrophysics Data System (ADS)

Ito, Daigoro

A new way to approach robust Dynamic Inversion controller synthesis is addressed in this paper. A Linear Quadratic Gaussian outer-loop controller improves the robustness of a Dynamic Inversion inner-loop controller in the presence of uncertainties. Desired dynamics are given by the dynamic compensator, which shapes the loop. The selected dynamics are based on both performance and stability robustness requirements. These requirements are straightforwardly formulated as frequency-dependent singular value bounds during synthesis of the controller. Performance and robustness of the designed controller is tested using a worst case time domain quadratic index, which is a simple but effective way to measure robustness due to parameter variation. Using this approach, a lateral-directional controller for the X-38 vehicle is designed and its robustness to parameter variations and disturbances is analyzed. It is found that if full state measurements are available, the performance of the designed lateral-directional control system, measured by the chosen cost function, improves by approximately a factor of four. Also, it is found that the designed system is stable up to a parametric variation of 1.65 standard deviation with the set of uncertainty considered. The system robustness is determined to be highly sensitive to the dihedral derivative and the roll damping coefficients. The controller analysis is extended to the nonlinear system where both control input displacements and rates are bounded. In this case, the considered nonlinear system is stable up to 48.1° in bank angle and 1.59° in sideslip angle variations, indicating it is more sensitive to variations in sideslip angle than in bank angle. This nonlinear approach is further extended for the actuator failure mode analysis. The results suggest that the designed system maintains a high level of stability in the event of aileron failure. However, only 35% or less of the original stability range is maintained for the rudder failure case. Overall, this combination of controller synthesis and robustness criteria compares well with the mu-synthesis technique. It also is readily accessible to the practicing engineer, in terms of understanding and use.

Built-in self-test (BIST) techniques for millimeter wave CMOS transceivers

NASA Astrophysics Data System (ADS)

Mahzabeen, Tabassum

The seamless integration of complementary metal oxide semiconductor (CMOS) transceivers with a digital CMOS process enhances on-chip testability, thus reducing production and testing costs. Built in self testability also improves yield by offering on-chip compensation. This work focuses on built in self test techniques for CMOS based millimeter wave (mm-wave) transceivers. Built-in-self-test (BIST) using the loopback method is one cost-effective method for testing these transceivers. Since the loopback switch is always present during the normal operation of the transceiver, the requirement of the switch is different than for a conventional switch. The switch needs to have high isolation and high impedance during its OFF period. Two 80 GHz single pole single throw (SPST) switches have been designed, fabricated in standard CMOS process, and measured to connect the loopback path for BIST applications. The loopback switches in this work provide the required criteria for loopback BIST. A stand alone 80 GHz low noise amplifier (LNA) and the same LNA integrated with one of the loopback switches have been fabricated, and measured to observe the difference in performance when the loopback switch is present. Besides the loopback switch, substrate leakage also forms a path between the transmitter and receiver. Substrate leakage has been characterized as a function of distance between the transmitter and receiver for consideration in using the BIST method. A BIST algorithm has been developed to estimate the process variation in device sizes by probing a low frequency ring oscillator to estimate the device variation and map this variation to the 80 GHz LNA. Probing a low frequency circuit is cheaper compared to the probing of a millimeter wave circuit and reduces the testing costs. The performance of the LNA degrades due to variation in device size. Once the shift in the device size is being estimated (from the ring oscillator's shifted frequency), the LNA's performance can be recovered using several methods; for example, using tunable transmission line lengths in the amplifier or using a variable supply voltage. This concept of estimating process variation has been demonstrated in Agilent Design System (ADS).

Inelastic scattering with Chebyshev polynomials and preconditioned conjugate gradient minimization.

PubMed

Temel, Burcin; Mills, Greg; Metiu, Horia

2008-03-27

We describe and test an implementation, using a basis set of Chebyshev polynomials, of a variational method for solving scattering problems in quantum mechanics. This minimum error method (MEM) determines the wave function Psi by minimizing the least-squares error in the function (H Psi - E Psi), where E is the desired scattering energy. We compare the MEM to an alternative, the Kohn variational principle (KVP), by solving the Secrest-Johnson model of two-dimensional inelastic scattering, which has been studied previously using the KVP and for which other numerical solutions are available. We use a conjugate gradient (CG) method to minimize the error, and by preconditioning the CG search, we are able to greatly reduce the number of iterations necessary; the method is thus faster and more stable than a matrix inversion, as is required in the KVP. Also, we avoid errors due to scattering off of the boundaries, which presents substantial problems for other methods, by matching the wave function in the interaction region to the correct asymptotic states at the specified energy; the use of Chebyshev polynomials allows this boundary condition to be implemented accurately. The use of Chebyshev polynomials allows for a rapid and accurate evaluation of the kinetic energy. This basis set is as efficient as plane waves but does not impose an artificial periodicity on the system. There are problems in surface science and molecular electronics which cannot be solved if periodicity is imposed, and the Chebyshev basis set is a good alternative in such situations.

Global Characterization of Tropospheric Noise for InSAR Analysis Using MODIS Data

NASA Astrophysics Data System (ADS)

Yun, S.; Hensley, S.; Chaubell, M.; Fielding, E. J.; Pan, L.; Rosen, P. A.

2013-12-01

Radio wave's differential phase delay variation through the troposphere is one of the largest error sources in Interferometric Synthetic Aperture Radar (InSAR) measurements, and water vapor variability in the troposphere is known to be the dominant factor. We use the precipitable water vapor products from NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) sensors mounted on Terra and Aqua satellites to produce tropospheric noise maps of InSAR. Then we extract a small set of characteristic parameters of its power spectral density curve and 1-D covariance function, and calculate the structure function to estimate the expected tropospheric noise level as a function of distance. The results serve two purposes: 1) to provide guidance on the expected covariance matrix for geophysical modeling, 2) to provide quantitative basis of the measurement requirements for the planned US L-band SAR mission. We build over a decade span (2000-2013) of a lookup table of the parameters derived from 2-by-2 degree tiles at 1-by-1 degree posting of global coverage, representing 10 days of each season in each year. The MODIS data were retrieved from OSCAR (Online Services for Correcting Atmosphere in Radar) server. MODIS images with 5 percent or more cloud cover were discarded. Cloud mask and sensor scanning artifacts were removed with interpolation and spectral filtering, respectively. We also mitigate topography dependent stratified tropospheric delay variation using the European Centre for Medium-Range Weather Forecasts (ECMWF) and Shuttle Radar Topography Mission Digital Elevation Models (SRTM DEMs).

A Two-Dimensional Variational Analysis Method for NSCAT Ambiguity Removal: Methodology, Sensitivity, and Tuning

NASA Technical Reports Server (NTRS)

Hoffman, R. N.; Leidner, S. M.; Henderson, J. M.; Atlas, R.; Ardizzone, J. V.; Bloom, S. C.; Atlas, Robert (Technical Monitor)

2001-01-01

In this study, we apply a two-dimensional variational analysis method (2d-VAR) to select a wind solution from NASA Scatterometer (NSCAT) ambiguous winds. 2d-VAR determines a "best" gridded surface wind analysis by minimizing a cost function. The cost function measures the misfit to the observations, the background, and the filtering and dynamical constraints. The ambiguity closest in direction to the minimizing analysis is selected. 2d-VAR method, sensitivity and numerical behavior are described. 2d-VAR is compared to statistical interpolation (OI) by examining the response of both systems to a single ship observation and to a swath of unique scatterometer winds. 2d-VAR is used with both NSCAT ambiguities and NSCAT backscatter values. Results are roughly comparable. When the background field is poor, 2d-VAR ambiguity removal often selects low probability ambiguities. To avoid this behavior, an initial 2d-VAR analysis, using only the two most likely ambiguities, provides the first guess for an analysis using all the ambiguities or the backscatter data. 2d-VAR and median filter selected ambiguities usually agree. Both methods require horizontal consistency, so disagreements occur in clumps, or as linear features. In these cases, 2d-VAR ambiguities are often more meteorologically reasonable and more consistent with satellite imagery.

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

DOE PAGES

Chua, Xin-Yi; Buckingham, Lawrence; Hogan, James M.; ...

2015-06-01

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond thosemore » of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.« less

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

PubMed

Kimura, Yasumasa; Soma, Takahiro; Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J L; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.

Mitochondrial-Nuclear Epistasis: Implications for Human Aging and Longevity

PubMed Central

Tranah, Gregory

2010-01-01

There is substantial evidence that mitochondria are involved in the aging process. Mitochondrial function requires the coordinated expression of hundreds of nuclear genes and a few dozen mitochondrial genes, many of which have been associated with either extended or shortened life span. Impaired mitochondrial function resulting from mtDNA and nuclear DNA variation is likely to contribute to an imbalance in cellular energy homeostasis, increased vulnerability to oxidative stress, and an increased rate of cellular senescence and aging. The complex genetic architecture of mitochondria suggests that there may be an equally complex set of gene interactions (epistases) involving genetic variation in the nuclear and mitochondrial genomes. Results from Drosophila suggest that the effects of mtDNA haplotypes on longevity vary among different nuclear allelic backgrounds, which could account for the inconsistent associations that have been observed between mitochondrial DNA (mtDNA) haplogroups and survival in humans. A diversity of pathways may influence the way mitochondria and nuclear – mitochondrial interactions modulate longevity, including: oxidative phosphorylation; mitochondrial uncoupling; antioxidant defenses; mitochondrial fission and fusion; and sirtuin regulation of mitochondrial genes. We hypothesize that aging and longevity, as complex traits having a significant genetic component, are likely to be controlled by nuclear gene variants interacting with both inherited and somatic mtDNA variability. PMID:20601194

Short communication: Genetic variation of saturated fatty acids in Holsteins in the Walloon region of Belgium.

PubMed

Arnould, V M-R; Hammami, H; Soyeurt, H; Gengler, N

2010-09-01

Random regression test-day models using Legendre polynomials are commonly used for the estimation of genetic parameters and genetic evaluation for test-day milk production traits. However, some researchers have reported that these models present some undesirable properties such as the overestimation of variances at the edges of lactation. Describing genetic variation of saturated fatty acids expressed in milk fat might require the testing of different models. Therefore, 3 different functions were used and compared to take into account the lactation curve: (1) Legendre polynomials with the same order as currently applied for genetic model for production traits; 2) linear splines with 10 knots; and 3) linear splines with the same 10 knots reduced to 3 parameters. The criteria used were Akaike's information and Bayesian information criteria, percentage square biases, and log-likelihood function. These criteria indentified Legendre polynomials and linear splines with 10 knots reduced to 3 parameters models as the most useful. Reducing more complex models using eigenvalues seemed appealing because the resulting models are less time demanding and can reduce convergence difficulties, because convergence properties also seemed to be improved. Finally, the results showed that the reduced spline model was very similar to the Legendre polynomials model. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

PubMed Central

Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J. L.; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download. PMID:26863543

A simple-harmonic model for depicting the annual cycle of seasonal temperatures of streams

USGS Publications Warehouse

Steele, Timothy Doak

1978-01-01

Due to economic or operational constraints, stream-temperature records cannot always be collected at all sites where information is desired or at frequencies dictated by continuous or near-continuous surveillance requirements. For streams where only periodic measurements are made during the year, and that are not appreciably affected by regulation or by thermal loading , a simple harmonic function may adequately depict the annual seasonal cycle of stream temperature at any given site. Resultant harmonic coefficients obtained from available stream-temperature records may be used in the following ways: (1) To interpolate between discrete measurements by solving the harmonic function at specified times, thereby filling in estimates of stream-temperature values; (2) to characterize areal or regional patterns of natural stream-temperature values; (2) to characterize areal or regional patterns of natural stream-temperature conditions; and (3) to detect and to assess any significant at a site brought about by streamflow regulation or basin development. Moreover, less-than-daily or sampling frequencies at a given site may give estimates of annual variation of stream temperatures that are statistically comparable to estimates obtained from a daily or continuous sampling scheme. The latter procedure may result in potential savings of resources in network operations, with negligible loss in information on annual stream-temperature variations. (Woodard -USGS)

Application of toxicogenomic profiling to evaluate effects of benzene and formaldehyde: from yeast to human

PubMed Central

McHale, Cliona M.; Smith, Martyn T.; Zhang, Luoping

2014-01-01

Genetic variation underlies a significant proportion of the individual variation in human susceptibility to toxicants. The primary current approaches to identify gene–environment (GxE) associations, genome-wide association studies (GWAS) and candidate gene association studies, require large exposed and control populations and an understanding of toxicity genes and pathways, respectively. This limits their application in the study of GxE associations for the leukemogens benzene and formaldehyde, whose toxicity has long been a focus of our research. As an alternative approach, we applied innovative in vitro functional genomics testing systems, including unbiased functional screening assays in yeast and a near-haploid human bone marrow cell line (KBM7). Through comparative genomic and computational analyses of the resulting data, we have identified human genes and pathways that may modulate susceptibility to benzene and formaldehyde. We have validated the roles of several genes in mammalian cell models. In populations occupationally exposed to low levels of benzene, we applied peripheral blood mononuclear cell transcriptomics and chromosome-wide aneuploidy studies (CWAS) in lymphocytes. In this review of the literature, we describe our comprehensive toxicogenomic approach and the potential mechanisms of toxicity and susceptibility genes identified for benzene and formaldehyde, as well as related studies conducted by other researchers. PMID:24571325

Reduced levels of Cacna1c attenuate mesolimbic dopamine system function.

PubMed

Terrillion, C E; Dao, D T; Cachope, R; Lobo, M K; Puche, A C; Cheer, J F; Gould, T D

2017-06-01

Genetic variation in CACNA1C, which codes for the L-type calcium channel (LTCC) Ca v 1.2, is associated with clinical diagnoses of bipolar disorder, depression and schizophrenia. Dysregulation of the mesolimbic-dopamine (ML-DA) system is linked to these syndromes and LTCCs are required for normal DAergic neurotransmission between the ventral tegmental area (VTA) and nucleus accumbens (NAc). It is unclear, however, how variations in CACNA1C genotype, and potential subsequent changes in expression levels in these regions, modify risk. Using constitutive and conditional knockout mice, and treatment with the LTCC antagonist nimodipine, we examined the role of Cacna1c in DA-mediated behaviors elicited by psychomotor stimulants. Using fast-scan cyclic voltammetry, DA release and reuptake in the NAc were measured. We find that subsecond DA release in Cacna1c haploinsufficient mice lacks normal sensitivity to inhibition of the DA transporter (DAT). Constitutive haploinsufficiency of Cacna1c led to attenuation of hyperlocomotion following acute administration of stimulants specific to DAT, and locomotor sensitization of these mice to the DAT antagonist GBR12909 did not reach the same level as wild-type mice. The maintenance of sensitization to GBR12909 was attenuated by administration of nimodipine. Sensitization to GBR12909 was attenuated in mice with reduced Cacna1c selectively in the VTA but not in the NAc. Our findings show that Cacna1c is crucial for normal behavioral responses to DA stimulants and that its activity in the VTA is required for behavioral sensitization. Cacna1c likely exerts these effects through modifications to presynaptic ML-DA system function. © 2017 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Combining various space geodetic techniques for regional modeling of ionospheric electron density over Iran

NASA Astrophysics Data System (ADS)

Zare, Saeed; Alizadeh, M. Mahdi; Schuh, Harald

2017-04-01

Ionosphere is a layer of the upper atmosphere, between the thermosphere and the exosphere, distinguished because it is ionized by solar radiation. As an important part of human living environment, ionosphere affects our modern society in many ways. International broadcasters use this medium to reflect radio signals back toward the Earth. Ionosphere provides long range capabilities for commercial ship-to-shore communications, for trans-oceanic aircraft links, and for military communication and surveillance systems. Space geodetic techniques have turned into a capable tool for studying the ionosphere in the last decades. Up to now, two dimensional (2-D) models of vertical TEC (VTEC) have been widely developed and used by different communities; however, due to the fact that these models provide information about the integral of the whole electron content along the vertical or slant ray path, these maps are not useful when information about the ionosphere at different altitude is required. The aim of this study is to develop three dimensional (3-D) regional model of electron density by using combination of various space geodetic techniques. B-Spline basis functions are used for longitude and latitude variations of the electron density and Chapman profile function for altitude variations. The National Cartographic Center of Iran (NCC) has established a network of one hundred GPS stations: The Iranian Permanent GPS Network for Geodynamics (IPGN). The main task of the GPS stations is to collect and store raw GPS data and send it to Tehran processing center on a daily basis for final processing. The required data for our investigation are ground based measurements of permanent GPS stations over Iran and radio occultation data from Formosat-3/Cosmic for region of interest. We expect to increase accuracy and reliability of final model by integrating different observation techniques.

Managing Complex IT Security Processes with Value Based Measures

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

Abercrombie, Robert K; Sheldon, Frederick T; Mili, Ali

2009-01-01

Current trends indicate that IT security measures will need to greatly expand to counter the ever increasingly sophisticated, well-funded and/or economically motivated threat space. Traditional risk management approaches provide an effective method for guiding courses of action for assessment, and mitigation investments. However, such approaches no matter how popular demand very detailed knowledge about the IT security domain and the enterprise/cyber architectural context. Typically, the critical nature and/or high stakes require careful consideration and adaptation of a balanced approach that provides reliable and consistent methods for rating vulnerabilities. As reported in earlier works, the Cyberspace Security Econometrics System provides amore » comprehensive measure of reliability, security and safety of a system that accounts for the criticality of each requirement as a function of one or more stakeholders interests in that requirement. This paper advocates a dependability measure that acknowledges the aggregate structure of complex system specifications, and accounts for variations by stakeholder, by specification components, and by verification and validation impact.« less

Our contaminated atmosphere: The danger of climate change, phases 1 and 2. [effect of atmospheric particulate matter on surface temperature and earth's radiation budget

NASA Technical Reports Server (NTRS)

Cimorelli, A. J.; House, F. B.

1974-01-01

The effects of increased concentrations of atmospheric particulate matter on average surface temperature and on the components of the earth's radiation budget are studied. An atmospheric model which couples particulate loading to surface temperature and to changes in the earth's radiation budget was used. A determination of the feasibility of using satellites to monitor the effect of increased atmospheric particulate concentrations is performed. It was found that: (1) a change in man-made particulate loading of a factor of 4 is sufficient to initiate an ice age; (2) variations in the global and hemispheric weighted averages of surface temperature, reflected radiant fluz and emitted radiant flux are nonlinear functions of particulate loading; and (3) a black satellite sphere meets the requirement of night time measurement sensitivity, but not the required day time sensitivity. A nonblack, spherical radiometer whose external optical properties are sensitive to either the reflected radiant fluz or the emitted radiant flux meets the observational sensitivity requirements.

Numerical investigation of the hydrodynamics of carangiform swimming in the transitional and inertial flow regimes.

PubMed

Borazjani, Iman; Sotiropoulos, Fotis

2008-05-01

We employ numerical simulation to investigate the hydrodynamics of carangiform locomotion as the relative magnitude of viscous and inertial forces, i.e. the Reynolds number (Re), and the tail-beat frequency, i.e. the Strouhal number (St), are systematically varied. The model fish is a three-dimensional (3D) mackerel-like flexible body undulating with prescribed experimental kinematics of carangiform type. Simulations are carried out for three Re spanning the transitional and inertial flow regimes, Re=300 and 4000 (viscous flow), and infinity (inviscid flow). For each Re there is a critical Strouhal number, St*, at which the net mean force becomes zero, making constant-speed self-propulsion possible. St* is a decreasing function of Re and approaches the range of St at which most carangiform swimmers swim in nature (St approximately 0.25) only as Re approaches infinity. The propulsive efficiency at St* is an increasing function of Re while the power required for swimming is decreasing with Re. For all Re, however, the swimming power is shown to be significantly greater than that required to tow the rigid body at the same speed. We also show that the variation of the total drag and its viscous and form components with St depend on the Re. For Re=300, body undulations increase the drag over the rigid body level, while significant drag reduction is observed for Re=4000. This difference is shown to be due to the fact that at sufficiently high Re the drag force variation with St is dominated by its form component variation, which is reduced by undulatory swimming for St>0.2. Finally, our simulations clarify the 3D structure of various wake patterns observed in experiments--single and double row vortices--and suggest that the wake structure depends primarily on the St. Our numerical findings help elucidate the results of previous experiments with live fish, underscore the importance of scale (Re) effects on the hydrodynamic performance of carangiform swimming, and help explain why in nature this mode of swimming is typically preferred by fast swimmers.

Synthesis: Intertwining product and process

NASA Technical Reports Server (NTRS)

Weiss, David M.

1990-01-01

Synthesis is a proposed systematic process for rapidly creating different members of a program family. Family members are described by variations in their requirements. Requirements variations are mapped to variations on a standard design to generate production quality code and documentation. The approach is made feasible by using principles underlying design for change. Synthesis incorporates ideas from rapid prototyping, application generators, and domain analysis. The goals of Synthesis and the Synthesis process are discussed. The technology needed and the feasibility of the approach are also briefly discussed. The status of current efforts to implement Synthesis methodologies is presented.

Absolute dose calibration of an X-ray system and dead time investigations of photon-counting techniques

NASA Astrophysics Data System (ADS)

Carpentieri, C.; Schwarz, C.; Ludwig, J.; Ashfaq, A.; Fiederle, M.

2002-07-01

High precision concerning the dose calibration of X-ray sources is required when counting and integrating methods are compared. The dose calibration for a dental X-ray tube was executed with special dose calibration equipment (dosimeter) as function of exposure time and rate. Results were compared with a benchmark spectrum and agree within ±1.5%. Dead time investigations with the Medipix1 photon-counting chip (PCC) have been performed by rate variations. Two different types of dead time, paralysable and non-paralysable will be discussed. The dead time depends on settings of the front-end electronics and is a function of signal height, which might lead to systematic defects of systems. Dead time losses in excess of 30% have been found for the PCC at 200 kHz absorbed photons per pixel.

A vector autopilot system. [aircraft attitude determination with three-axis magnetometer

NASA Technical Reports Server (NTRS)

Pietila, R.; Dunn, W. R., Jr.

1976-01-01

Current technology has evolved low cost, highly reliable solid state vector magnetometers with excellent angular resolution. This paper discusses the role of a three-axis magnetometer as a new instrument for aircraft attitude determination. Using flight data acquired by an instrumented aircraft, attitude is calculated using the earth's magnetic field vector and compared to measured attitudes. The magnetic field alone is not adequate to resolve all attitude variations and the need for a second reference angle or vector is discussed. A system combining the functions of heading determination and attitude measurement is presented to show that both functions can be implemented with essentially the same component count required to measure heading alone. It is concluded that with the correlation achieved in calculated and measured attitude there is a potential application of vector magnetometry in attitude measurement systems.

Canonical fluid thermodynamics

NASA Technical Reports Server (NTRS)

Schmid, L. A.

1972-01-01

The space-time integral of the thermodynamic pressure plays the role of the thermodynamic potential for compressible, adiabatic flow in the sense that the pressure integral for stable flow is less than for all slightly different flows. This stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and the temperature, which are the arguments of the pressure function, to be generalized velocities, that is, the proper-time derivatives of scalar spare-time functions which are generalized coordinates in the canonical formalism. In a fluid context, proper-time differentiation must be expressed in terms of three independent quantities that specify the fluid velocity. This can be done in several ways, all of which lead to different variants (canonical transformations) of the same constraint-free action integral whose Euler-Lagrange equations are just the well-known equations of motion for adiabatic compressible flow.

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

PubMed Central

Ryan, Michael C.; Cleland, James; Kim, RyangGuk; Wong, Wing Chung; Weinstein, John N.

2012-01-01

Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. Availability and implementation: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. Contact: mryan@insilico.us.com Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22820202

Current challenges in genome annotation through structural biology and bioinformatics.

PubMed

Furnham, Nicholas; de Beer, Tjaart A P; Thornton, Janet M

2012-10-01

With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry. Copyright © 2012. Published by Elsevier Ltd.

Mitochondrial respiratory efficiency is positively correlated with human sperm motility.

PubMed

Ferramosca, Alessandra; Provenzano, Sara Pinto; Coppola, Lamberto; Zara, Vincenzo

2012-04-01

To correlate sperm mitochondrial respiratory efficiency with variations in sperm motility and with sperm morphologic anomalies. Sperm mitochondrial respiratory activity was evaluated with a polarographic assay of oxygen consumption carried out in hypotonically-treated sperm cells. A possible relationship among sperm mitochondrial respiratory efficiency, sperm motility, and morphologic anomalies was investigated. Mitochondrial respiratory efficiency was positively correlated with sperm motility and negatively correlated with the percentage of immotile spermatozoa. Moreover, midpiece defects impaired mitochondrial functionality. Our data indicate that an increase in sperm motility requires a parallel increase in mitochondrial respiratory capacity, thereby supporting the fundamental role played by mitochondrial oxidative phosphorylation in sperm motility of normozoospermic subjects. These results are of physiopathological relevance because they suggest that disturbances of sperm mitochondrial function and of energy production could be responsible for asthenozoospermia. Copyright © 2012 Elsevier Inc. All rights reserved.

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

Berry, Ryan S.; Adolf, Douglas Brian; Stavig, Mark Edwin

Variations in the neutron generator encapsulation process can affect functionality. However, instead of following the historical path in which the effects of process variations are assessed directly through functional tests, this study examines how material properties key to generator functionality correlate with process variations. The results of this type of investigation will be applicable to all generators and can provide insight on the most profitable paths to process and material improvements. Surprisingly, the results at this point imply that the process is quite robust, and many of the current process tolerances are perhaps overly restrictive. The good news lies inmore » the fact that our current process ensures reproducible material properties. The bad new lies in the fact that it would be difficult to solve functional problems by changes in the process.« less

Ecological and evolutionary consequences of tri-trophic interactions: Spatial variation and effects of plant density.

PubMed

Abdala-Roberts, Luis; Parra-Tabla, Víctor; Moreira, Xoaquín; Ramos-Zapata, José

2017-02-01

The factors driving variation in species interactions are often unknown, and few studies have made a link between changes in interactions and the strength of selection. We report on spatial variation in functional responses by a seed predator (SP) and its parasitic wasps associated with the herb Ruellia nudiflora . We assessed the influence of plant density on consumer responses and determined whether density effects and spatial variation in functional responses altered natural selection by these consumers on the plant. We established common gardens at two sites in Yucatan, Mexico, and planted R. nudiflora at two densities in each garden. We recorded fruit output and SP and parasitoid attack; calculated relative fitness (seed number) under scenarios of three trophic levels (accounting for SP and parasitoid effects), two trophic levels (accounting for SP but not parasitoid effects), and one trophic level (no consumer effects); and compared selection strength on fruit number under these scenarios across sites and densities. There was spatial variation in SP recruitment, whereby the SP functional response was negatively density-dependent at one site but density-independent at the other; parasitoid responses were density-independent and invariant across sites. Site variation in SP attack led, in turn, to differences in SP selection on fruit output, and parasitoids did not alter SP selection. There were no significant effects of density at either site. Our results provide a link between consumer functional responses and consumer selection on plants, which deepens our understanding of geographic variation in the evolutionary outcomes of multitrophic interactions. © 2017 Botanical Society of America.

Functional and morphological correlates of mandibular symphyseal form in a living human sample.

PubMed

Holton, Nathan E; Franciscus, Robert G; Ravosa, Matthew J; Southard, Thomas E

2014-03-01

Variation in recent human mandibular form is often thought to reflect differences in masticatory behavior associated with variation in food preparation and subsistence strategies. Nevertheless, while mandibular variation in some human comparisons appear to reflect differences in functional loading, other comparisons indicate that this relationship is not universal. This suggests that morphological variation in the mandible is influenced by other factors that may obscure the effects of loading on mandibular form. It is likely that highly strained mandibular regions, including the corpus, are influenced by well-established patterns of lower facial skeletal integration. As such, it is unclear to what degree mandibular form reflects localized stresses incurred during mastication vs. a larger set of correlated features that may influence bone distribution patterns. In this study, we examine the relationship between mandibular symphyseal bone distribution (i.e., second moments of area, cortical bone area) and masticatory force production (i.e., in vivo maximal bite force magnitude and estimated symphyseal bending forces) along with lower facial shape variation in a sample of n = 20 living human male subjects. Our results indicate that while some aspects of symphyseal form (e.g., wishboning resistance) are significantly correlated with estimates of symphyseal bending force magnitude, others (i.e., vertical bending resistance) are more closely tied to variation in lower facial shape. This suggests that while the symphysis reflects variation in some variables related to functional loading, the complex and multifactorial influences on symphyseal form underscores the importance of exercising caution when inferring function from the mandible especially in narrow taxonomic comparisons. Copyright © 2013 Wiley Periodicals, Inc.

Combining Formal and Functional Approaches to Topic Structure

ERIC Educational Resources Information Center

Zellers, Margaret; Post, Brechtje

2012-01-01

Fragmentation between formal and functional approaches to prosodic variation is an ongoing problem in linguistic research. In particular, the frameworks of the Phonetics of Talk-in-Interaction (PTI) and Empirical Phonology (EP) take very different theoretical and methodological approaches to this kind of variation. We argue that it is fruitful to…

Variation of parameters using Battin's universal functions

NASA Astrophysics Data System (ADS)

Burton, James R., III; Melton, Robert G.

This paper presents a variation of parameters analysis, suitable for use in situations involving small perturbations to the two-body problem, using Battin's universal functions. Unlike the universal variable formulation, this approach avoids the need to switch among different functional representations if the orbit transitions from elliptical, through parabolic, to hyperbolic state, making it attractive for use in simulating low-thrust trajectories ascending to escape or capturing into orbit.

Quantifying the thermal heat requirement of Brassica in assessing biophysical parameters under semi-arid microenvironments

NASA Astrophysics Data System (ADS)

Adak, Tarun; Chakravarty, N. V. K.

2010-07-01

Evaluation of the thermal heat requirement of Brassica spp. across agro-ecological regions is required in order to understand the further effects of climate change. Spatio-temporal changes in hydrothermal regimes are likely to affect the physiological growth pattern of the crop, which in turn will affect economic yields and crop quality. Such information is helpful in developing crop simulation models to describe the differential thermal regimes that prevail at different phenophases of the crop. Thus, the current lack of quantitative information on the thermal heat requirement of Brassica crops under debranched microenvironments prompted the present study, which set out to examine the response of biophysical parameters [leaf area index (LAI), dry biomass production, seed yield and oil content] to modified microenvironments. Following 2 years of field experiments on Typic Ustocrepts soils under semi-arid climatic conditions, it was concluded that the Brassica crop is significantly responsive to microenvironment modification. A highly significant and curvilinear relationship was observed between LAI and dry biomass production with accumulated heat units, with thermal accumulation explaining ≥80% of the variation in LAI and dry biomass production. It was further observed that the economic seed yield and oil content, which are a function of the prevailing weather conditions, were significantly responsive to the heat units accumulated from sowing to 50% physiological maturity. Linear regression analysis showed that growing degree days (GDD) could indicate 60-70% variation in seed yield and oil content, probably because of the significant response to differential thermal microenvironments. The present study illustrates the statistically strong and significant response of biophysical parameters of Brassica spp. to microenvironment modification in semi-arid regions of northern India.

Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation

PubMed Central

Chatterjee, Aniruddha; Stockwell, Peter A.; Rodger, Euan J.; Duncan, Elizabeth J.; Parry, Matthew F.; Weeks, Robert J.; Morison, Ian M.

2015-01-01

The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript. PMID:26612583

An improved optical flow tracking technique for real-time MR-guided beam therapies in moving organs

NASA Astrophysics Data System (ADS)

Zachiu, C.; Papadakis, N.; Ries, M.; Moonen, C.; de Senneville, B. Denis

2015-12-01

Magnetic resonance (MR) guided high intensity focused ultrasound and external beam radiotherapy interventions, which we shall refer to as beam therapies/interventions, are promising techniques for the non-invasive ablation of tumours in abdominal organs. However, therapeutic energy delivery in these areas becomes challenging due to the continuous displacement of the organs with respiration. Previous studies have addressed this problem by coupling high-framerate MR-imaging with a tracking technique based on the algorithm proposed by Horn and Schunck (H and S), which was chosen due to its fast convergence rate and highly parallelisable numerical scheme. Such characteristics were shown to be indispensable for the real-time guidance of beam therapies. In its original form, however, the algorithm is sensitive to local grey-level intensity variations not attributed to motion such as those that occur, for example, in the proximity of pulsating arteries. In this study, an improved motion estimation strategy which reduces the impact of such effects is proposed. Displacements are estimated through the minimisation of a variation of the H and S functional for which the quadratic data fidelity term was replaced with a term based on the linear L1norm, resulting in what we have called an L2-L1 functional. The proposed method was tested in the livers and kidneys of two healthy volunteers under free-breathing conditions, on a data set comprising 3000 images equally divided between the volunteers. The results show that, compared to the existing approaches, our method demonstrates a greater robustness to local grey-level intensity variations introduced by arterial pulsations. Additionally, the computational time required by our implementation make it compatible with the work-flow of real-time MR-guided beam interventions. To the best of our knowledge this study was the first to analyse the behaviour of an L1-based optical flow functional in an applicative context: real-time MR-guidance of beam therapies in moving organs.

Repeatability of dose painting by numbers treatment planning in prostate cancer radiotherapy based on multiparametric magnetic resonance imaging

NASA Astrophysics Data System (ADS)

van Schie, Marcel A.; Steenbergen, Peter; Viet Dinh, Cuong; Ghobadi, Ghazaleh; van Houdt, Petra J.; Pos, Floris J.; Heijmink, Stijn W. T. J. P.; van der Poel, Henk G.; Renisch, Steffen; Vik, Torbjørn; van der Heide, Uulke A.

2017-07-01

Dose painting by numbers (DPBN) refers to a voxel-wise prescription of radiation dose modelled from functional image characteristics, in contrast to dose painting by contours which requires delineations to define the target for dose escalation. The direct relation between functional imaging characteristics and DPBN implies that random variations in images may propagate into the dose distribution. The stability of MR-only prostate cancer treatment planning based on DPBN with respect to these variations is as yet unknown. We conducted a test-retest study to investigate the stability of DPBN for prostate cancer in a semi-automated MR-only treatment planning workflow. Twelve patients received a multiparametric MRI on two separate days prior to prostatectomy. The tumor probability (TP) within the prostate was derived from image features with a logistic regression model. Dose mapping functions were applied to acquire a DPBN prescription map that served to generate an intensity modulated radiation therapy (IMRT) treatment plan. Dose calculations were done on a pseudo-CT derived from the MRI. The TP and DPBN map and the IMRT dose distribution were compared between both MRI sessions, using the intraclass correlation coefficient (ICC) to quantify repeatability of the planning pipeline. The quality of each treatment plan was measured with a quality factor (QF). Median ICC values for the TP and DPBN map and the IMRT dose distribution were 0.82, 0.82 and 0.88, respectively, for linear dose mapping and 0.82, 0.84 and 0.94 for square root dose mapping. A median QF of 3.4% was found among all treatment plans. We demonstrated the stability of DPBN radiotherapy treatment planning in prostate cancer, with excellent overall repeatability and acceptable treatment plan quality. Using validated tumor probability modelling and simple dose mapping techniques it was shown that despite day-to-day variations in imaging data still consistent treatment plans were obtained.

Parietal structure and function explain human variation in working memory biases of visual attention.

PubMed

Soto, David; Rotshtein, Pia; Kanai, Ryota

2014-04-01

Recent research indicates that human attention appears inadvertently biased by items that match the contents of working memory (WM). WM-biases can lead to attentional costs when the memory content matches goal-irrelevant items and to attentional benefits when it matches the sought target. Here we used functional and structural MRI data to determine the neural basis of human variation in WM biases. We asked whether human variation in WM-benefits and WM-costs merely reflects the process of attentional capture by the contents of WM or whether variation in WM biases may be associated with distinct forms of cognitive control over internal WM signals based on selection goals. Human ability to use WM contents to facilitate selection was positively correlated with gray matter volume in the left superior posterior parietal cortex (PPC), while the ability to overcome interference by WM-matching distracters was associated with the left inferior PPC in the anterior IPS. Functional activity in the left PPC, measured by functional MRI, also predicted the magnitude of WM-costs on selection. Both structure and function of left PPC mediate the expression of WM biases in human visual attention. Copyright © 2013 Elsevier Inc. All rights reserved.

Probing the pH sensitivity of R-phycoerythrin: investigations of active conformational and functional variation.

PubMed

Liu, Lu-Ning; Su, Hai-Nan; Yan, Shi-Gan; Shao, Si-Mi; Xie, Bin-Bin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2009-07-01

Crystal structures of phycobiliproteins have provided valuable information regarding the conformations and amino acid organizations of peptides and chromophores, and enable us to investigate their structural and functional relationships with respect to environmental variations. In this work, we explored the pH-induced conformational and functional dynamics of R-phycoerythrin (R-PE) by means of absorption, fluorescence and circular dichroism spectra, together with analysis of its crystal structure. R-PE presents stronger functional stability in the pH range of 3.5-10 compared to the structural stability. Beyond this range, pronounced functional and structural changes occur. Crystal structure analysis shows that the tertiary structure of R-PE is fixed by several key anchoring points of the protein. With this specific association, the fundamental structure of R-PE is stabilized to present physiological spectroscopic properties, while local variations in protein peptides are also allowed in response to environmental disturbances. The functional stability and relative structural sensitivity of R-PE allow environmental adaptation.

On the formulation of a minimal uncertainty model for robust control with structured uncertainty

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Chang, B.-C.; Fischl, Robert

1991-01-01

In the design and analysis of robust control systems for uncertain plants, representing the system transfer matrix in the form of what has come to be termed an M-delta model has become widely accepted and applied in the robust control literature. The M represents a transfer function matrix M(s) of the nominal closed loop system, and the delta represents an uncertainty matrix acting on M(s). The nominal closed loop system M(s) results from closing the feedback control system, K(s), around a nominal plant interconnection structure P(s). The uncertainty can arise from various sources, such as structured uncertainty from parameter variations or multiple unsaturated uncertainties from unmodeled dynamics and other neglected phenomena. In general, delta is a block diagonal matrix, but for real parameter variations delta is a diagonal matrix of real elements. Conceptually, the M-delta structure can always be formed for any linear interconnection of inputs, outputs, transfer functions, parameter variations, and perturbations. However, very little of the currently available literature addresses computational methods for obtaining this structure, and none of this literature addresses a general methodology for obtaining a minimal M-delta model for a wide class of uncertainty, where the term minimal refers to the dimension of the delta matrix. Since having a minimally dimensioned delta matrix would improve the efficiency of structured singular value (or multivariable stability margin) computations, a method of obtaining a minimal M-delta would be useful. Hence, a method of obtaining the interconnection system P(s) is required. A generalized procedure for obtaining a minimal P-delta structure for systems with real parameter variations is presented. Using this model, the minimal M-delta model can then be easily obtained by closing the feedback loop. The procedure involves representing the system in a cascade-form state-space realization, determining the minimal uncertainty matrix, delta, and constructing the state-space representation of P(s). Three examples are presented to illustrate the procedure.

Anomalous droughts, not invasion, decrease persistence of native fishes in a desert river.

PubMed

Ruhí, Albert; Holmes, Elizabeth E; Rinne, John N; Sabo, John L

2015-04-01

Changing climate extremes and invasion by non-native species are two of the most prominent threats to native faunas. Predicting the relationships between global change and native faunas requires a quantitative toolkit that effectively links the timing and magnitude of extreme events to variation in species abundances. Here, we examine how discharge anomalies--unexpected floods and droughts--determine covariation in abundance of native and non-native fish species in a highly variable desert river in Arizona. We quantified stochastic variation in discharge using Fourier analyses on >15,000 daily observations. We subsequently coupled maximum annual spectral anomalies with a 15-year time series of fish abundances (1994-2008), using Multivariate Autoregressive State-Space (MARSS) models. Abiotic drivers (discharge anomalies) were paramount in determining long-term fish abundances, whereas biotic drivers (species interactions) played only a secondary role. As predicted, anomalous droughts reduced the abundances of native species, while floods increased them. However, in contrast to previous studies, we observed that the non-native assemblage was surprisingly unresponsive to extreme events. Biological trait analyses showed that functional uniqueness was higher in native than in non-native fishes. We also found that discharge anomalies influenced diversity patterns at the meta-community level, with nestedness increasing after anomalous droughts due to the differential impairment of native species. Overall, our results advance the notion that discharge variation is key in determining community trajectories in the long term, predicting the persistence of native fauna even in the face of invasion. We suggest this variation, rather than biotic interactions, may commonly underlie covariation between native and non-native faunas, especially in highly variable environments. If droughts become increasingly severe due to climate change, and floods increasingly muted due to regulation, fish assemblages in desert rivers may become taxonomically and functionally impoverished and dominated by non-native taxa. © 2014 John Wiley & Sons Ltd.

Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome

PubMed Central

2012-01-01

Background Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea. Results We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana. Conclusions We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is not syntenic with A. thaliana FRI due to an ancient recombination event. This has complicated previous association analyses of FRI with variation in life history strategy in the Brassica genus. PMID:22333192

New Insights on the Structure of the Cascadia Subduction Zone from Amphibious Seismic Data

NASA Astrophysics Data System (ADS)

Janiszewski, Helen Anne

A new onshore-offshore seismic dataset from the Cascadia subduction zone was used to characterize mantle lithosphere structure from the ridge to the volcanic arc, and plate interface structure offshore within the seismogenic zone. The Cascadia Initiative (CI) covered the Juan de Fuca plate offshore the northwest coast of the United States with an ocean bottom seismometer (OBS) array for four years; this was complemented by a simultaneous onshore seismic array. Teleseismic data recorded by this array allows the unprecedented imaging of an entire tectonic plate from its creation at the ridge through subduction initiation and back beyond the volcanic arc along the entire strike of the Cascadia subduction zone. Higher frequency active source seismic data also provides constraints on the crustal structure along the plate interface offshore. Two seismic datasets were used to image the plate interface structure along a line extending 100 km offshore central Washington. These are wide-angle reflections from ship-to-shore seismic data from the Ridge-To-Trench seismic cruise and receiver functions calculated from a densely spaced CI OBS focus array in a similar region. Active source seismic observations are consistent with reflections from the plate interface offshore indicating the presence of a P-wave velocity discontinuity. Until recently, there has been limited success in using the receiver function technique on OBS data. I avoid these traditional challenges by using OBS constructed with shielding deployed in shallow water on the continental shelf. These data have quieter horizontals and avoid water- and sediment-multiple contamination at the examined frequencies. The receiver functions are consistently modeled with a velocity structure that has a low velocity zone (LVZ) with elevated P to S-wave velocity ratios at the plate interface. A similar LVZ structure has been observed onshore and interpreted as a combination of elevated pore-fluid pressures or metasediments. This new offshore result indicates that the structure may persist updip indicating the plate interface may be weak. To focus more broadly on the entire subduction system, I calculate phase velocities from teleseismic Rayleigh waves from 20-100 s period across the entire onshore-offshore array. The shear-wave velocity model calculated from these data can provide constrains on the thermal structure of the lithosphere both prior to and during subduction of the Juan de Fuca plate. Using OBS data in this period band requires removal of tilt and compliance noise, two types of water-induced noise that affect long period data. To facilitate these corrections on large seismic arrays such as the CI, an automated quality control routine was developed for selecting noise windows for the calculation of the required transfer functions. These corrections typically involve either averaging out transient signals, which requires the assumption of stationarity of the noise over the long periods of time, or laborious hand selection of noise segments. This new method calculates transfer functions based on daily time series that exclude transient signals, but allows for the investigation of long-term variation over the course of an instrument's deployment. I interpret these new shoreline-crossing phase velocity maps in terms of the tectonics associated with the Cascadia subduction system. Major findings include that oceanic plate cooling models do not explain the velocities observed beneath the Juan de Fuca plate, that slow velocities in the forearc appear to be more prevalent in areas modeled to have experienced high slip in past Cascadia megathrust earthquakes, and along strike variations in phase velocity reflect variations in arc structure and backarc tectonics.

Genetics of Taste Receptors

PubMed Central

Bachmanov, Alexander A.; Bosak, Natalia P.; Lin, Cailu; Matsumoto, Ichiro; Ohmoto, Makoto; Reed, Danielle R.; Nelson, Theodore M.

2016-01-01

Taste receptors function as one of the interfaces between internal and external milieus. Taste receptors for sweet and umami (T1R [taste receptor, type 1]), bitter (T2R [taste receptor, type 2]), and salty (ENaC [epithelial sodium channel]) have been discovered in the recent years, but transduction mechanisms of sour taste and ENaC-independent salt taste are still poorly understood. In addition to these five main taste qualities, the taste system detects such noncanonical “tastes” as water, fat, and complex carbohydrates, but their reception mechanisms require further research. Variations in taste receptor genes between and within vertebrate species contribute to individual and species differences in taste-related behaviors. These variations are shaped by evolutionary forces and reflect species adaptations to their chemical environments and feeding ecology. Principles of drug discovery can be applied to taste receptors as targets in order to develop novel taste compounds to satisfy demand in better artificial sweeteners, enhancers of sugar and sodium taste, and blockers of bitterness of food ingredients and oral medications. PMID:23886383

A mathematical representation of an advanced helicopter for piloted simulator investigations of control system and display variations

NASA Technical Reports Server (NTRS)

Aiken, E. W.

1980-01-01

A mathematical model of an advanced helicopter is described. The model is suitable for use in control/display research involving piloted simulation. The general design approach for the six degree of freedom equations of motion is to use the full set of nonlinear gravitational and inertial terms of the equations and to express the aerodynamic forces and moments as the reference values and first order terms of a Taylor series expansion about a reference trajectory defined as a function of longitudinal airspeed. Provisions for several different specific and generic flight control systems are included in the model. The logic required to drive various flight control and weapon delivery symbols on a pilot's electronic display is also provided. Finally, the model includes a simplified representation of low altitude wind and turbulence effects. This model was used in a piloted simulator investigation of the effects of control system and display variations for an attack helicopter mission.

This is SPIRAL-TAP: Sparse Poisson Intensity Reconstruction ALgorithms--theory and practice.

PubMed

Harmany, Zachary T; Marcia, Roummel F; Willett, Rebecca M

2012-03-01

Observations in many applications consist of counts of discrete events, such as photons hitting a detector, which cannot be effectively modeled using an additive bounded or Gaussian noise model, and instead require a Poisson noise model. As a result, accurate reconstruction of a spatially or temporally distributed phenomenon (f*) from Poisson data (y) cannot be effectively accomplished by minimizing a conventional penalized least-squares objective function. The problem addressed in this paper is the estimation of f* from y in an inverse problem setting, where the number of unknowns may potentially be larger than the number of observations and f* admits sparse approximation. The optimization formulation considered in this paper uses a penalized negative Poisson log-likelihood objective function with nonnegativity constraints (since Poisson intensities are naturally nonnegative). In particular, the proposed approach incorporates key ideas of using separable quadratic approximations to the objective function at each iteration and penalization terms related to l1 norms of coefficient vectors, total variation seminorms, and partition-based multiscale estimation methods.

Density-Functional Theory with Optimized Effective Potential and Self-Interaction Correction for the Double Ionization of He and Be Atoms

NASA Astrophysics Data System (ADS)

Heslar, John; Telnov, Dmitry; Chu, Shih-I.

2012-06-01

We present a self-interaction-free (SIC) time-dependent density-functional theory (TDDFT) for the treatment of double ionization processes of many-electron systems. The method is based on the Krieger-Li-Iafrate (KLI) treatment of the optimized effective potential (OEP) theory and the incorporation of an explicit self-interaction correction (SIC) term. In the framework of the time-dependent density functional theory, we have performed 3D calculations of double ionization of He and Be atoms by strong near-infrared laser fields. We make use of the exchange-correlation potential with the integer discontinuity which improves the description of the double ionization process. We found that proper description of the double ionization requires the TDDFT exchange-correlation potential with the discontinuity with respect to the variation of the spin particle numbers (SPN) only. The results for the intensity-dependent probabilities of single and double ionization are presented and reproduce the famous ``knee'' structure.

Analogy of transistor function with modulating photonic band gap in electromagnetically induced grating

PubMed Central

Wang, Zhiguo; Ullah, Zakir; Gao, Mengqin; Zhang, Dan; Zhang, Yiqi; Gao, Hong; Zhang, Yanpeng

2015-01-01

Optical transistor is a device used to amplify and switch optical signals. Many researchers focus on replacing current computer components with optical equivalents, resulting in an optical digital computer system processing binary data. Electronic transistor is the fundamental building block of modern electronic devices. To replace electronic components with optical ones, an equivalent optical transistor is required. Here we compare the behavior of an optical transistor with the reflection from a photonic band gap structure in an electromagnetically induced transparency medium. A control signal is used to modulate the photonic band gap structure. Power variation of the control signal is used to provide an analogy between the reflection behavior caused by modulating the photonic band gap structure and the shifting of Q-point (Operation point) as well as amplification function of optical transistor. By means of the control signal, the switching function of optical transistor has also been realized. Such experimental schemes could have potential applications in making optical diode and optical transistor used in quantum information processing. PMID:26349444

Survey Of High Speed Test Techniques

NASA Astrophysics Data System (ADS)

Gheewala, Tushar

1988-02-01

The emerging technologies for the characterization and production testing of high-speed devices and integrated circuits are reviewed. The continuing progress in the field of semiconductor technologies will, in the near future, demand test techniques to test 10ps to lOOps gate delays, 10 GHz to 100 GHz analog functions and 10,000 to 100,000 gates on a single chip. Clearly, no single test technique would provide a cost-effective answer to all the above demands. A divide-and-conquer approach based on a judicial selection of parametric, functional and high-speed tests will be required. In addition, design-for-test methods need to be pursued which will include on-chip test electronics as well as circuit techniques that minimize the circuit performance sensitivity to allowable process variations. The electron and laser beam based test technologies look very promising and may provide the much needed solutions to not only the high-speed test problem but also to the need for high levels of fault coverage during functional testing.

Analogy of transistor function with modulating photonic band gap in electromagnetically induced grating

NASA Astrophysics Data System (ADS)

Wang, Zhiguo; Ullah, Zakir; Gao, Mengqin; Zhang, Dan; Zhang, Yiqi; Gao, Hong; Zhang, Yanpeng

2015-09-01

Optical transistor is a device used to amplify and switch optical signals. Many researchers focus on replacing current computer components with optical equivalents, resulting in an optical digital computer system processing binary data. Electronic transistor is the fundamental building block of modern electronic devices. To replace electronic components with optical ones, an equivalent optical transistor is required. Here we compare the behavior of an optical transistor with the reflection from a photonic band gap structure in an electromagnetically induced transparency medium. A control signal is used to modulate the photonic band gap structure. Power variation of the control signal is used to provide an analogy between the reflection behavior caused by modulating the photonic band gap structure and the shifting of Q-point (Operation point) as well as amplification function of optical transistor. By means of the control signal, the switching function of optical transistor has also been realized. Such experimental schemes could have potential applications in making optical diode and optical transistor used in quantum information processing.

The electrical conductivity of the Earth's upper mantle as estimated from satellite measured magnetic field variations. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Didwall, E. M.

1981-01-01

Low latitude magnetic field variations (magnetic storms) caused by large fluctuations in the equatorial ring current were derived from magnetic field magnitude data obtained by OGO 2, 4, and 6 satellites over an almost 5 year period. Analysis procedures consisted of (1) separating the disturbance field into internal and external parts relative to the surface of the Earth; (2) estimating the response function which related to the internally generated magnetic field variations to the external variations due to the ring current; and (3) interpreting the estimated response function using theoretical response functions for known conductivity profiles. Special consideration is given to possible ocean effects. A temperature profile is proposed using conductivity temperature data for single crystal olivine. The resulting temperature profile is reasonable for depths below 150-200 km, but is too high for shallower depths. Apparently, conductivity is not controlled solely by olivine at shallow depths.

Variational Approach to Enhanced Sampling and Free Energy Calculations

NASA Astrophysics Data System (ADS)

Valsson, Omar; Parrinello, Michele

2014-08-01

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

Neighbourhood green space, physical function and participation in physical activities among elderly men: the Caerphilly Prospective study

PubMed Central

2014-01-01

Background The built environment in which older people live plays an important role in promoting or inhibiting physical activity. Most work on this complex relationship between physical activity and the environment has excluded people with reduced physical function or ignored the difference between groups with different levels of physical function. This study aims to explore the role of neighbourhood green space in determining levels of participation in physical activity among elderly men with different levels of lower extremity physical function. Method Using data collected from the Caerphilly Prospective Study (CaPS) and green space data collected from high resolution Landmap true colour aerial photography, we first investigated the effect of the quantity of neighbourhood green space and the variation in neighbourhood vegetation on participation in physical activity for 1,010 men aged 66 and over in Caerphilly county borough, Wales, UK. Second, we explored whether neighbourhood green space affects groups with different levels of lower extremity physical function in different ways. Results Increasing percentage of green space within a 400 meters radius buffer around the home was significantly associated with more participation in physical activity after adjusting for lower extremity physical function, psychological distress, general health, car ownership, age group, marital status, social class, education level and other environmental factors (OR = 1.21, 95% CI 1.05, 1.41). A statistically significant interaction between the variation in neighbourhood vegetation and lower extremity physical function was observed (OR = 1.92, 95% CI 1.12, 3.28). Conclusion Elderly men living in neighbourhoods with more green space have higher levels of participation in regular physical activity. The association between variation in neighbourhood vegetation and regular physical activity varied according to lower extremity physical function. Subjects reporting poor lower extremity physical function living in neighbourhoods with more homogeneous vegetation (i.e. low variation) were more likely to participate in regular physical activity than those living in neighbourhoods with less homogeneous vegetation (i.e. high variation). Good lower extremity physical function reduced the adverse effect of high variation vegetation on participation in regular physical activity. This provides a basis for the future development of novel interventions that aim to increase levels of physical activity in later life, and has implications for planning policy to design, preserve, facilitate and encourage the use of green space near home. PMID:24646136

Neighbourhood green space, physical function and participation in physical activities among elderly men: the Caerphilly Prospective study.

PubMed

Gong, Yi; Gallacher, John; Palmer, Stephen; Fone, David

2014-03-19

The built environment in which older people live plays an important role in promoting or inhibiting physical activity. Most work on this complex relationship between physical activity and the environment has excluded people with reduced physical function or ignored the difference between groups with different levels of physical function. This study aims to explore the role of neighbourhood green space in determining levels of participation in physical activity among elderly men with different levels of lower extremity physical function. Using data collected from the Caerphilly Prospective Study (CaPS) and green space data collected from high resolution Landmap true colour aerial photography, we first investigated the effect of the quantity of neighbourhood green space and the variation in neighbourhood vegetation on participation in physical activity for 1,010 men aged 66 and over in Caerphilly county borough, Wales, UK. Second, we explored whether neighbourhood green space affects groups with different levels of lower extremity physical function in different ways. Increasing percentage of green space within a 400 meters radius buffer around the home was significantly associated with more participation in physical activity after adjusting for lower extremity physical function, psychological distress, general health, car ownership, age group, marital status, social class, education level and other environmental factors (OR = 1.21, 95% CI 1.05, 1.41). A statistically significant interaction between the variation in neighbourhood vegetation and lower extremity physical function was observed (OR = 1.92, 95% CI 1.12, 3.28). Elderly men living in neighbourhoods with more green space have higher levels of participation in regular physical activity. The association between variation in neighbourhood vegetation and regular physical activity varied according to lower extremity physical function. Subjects reporting poor lower extremity physical function living in neighbourhoods with more homogeneous vegetation (i.e. low variation) were more likely to participate in regular physical activity than those living in neighbourhoods with less homogeneous vegetation (i.e. high variation). Good lower extremity physical function reduced the adverse effect of high variation vegetation on participation in regular physical activity. This provides a basis for the future development of novel interventions that aim to increase levels of physical activity in later life, and has implications for planning policy to design, preserve, facilitate and encourage the use of green space near home.

Land-use intensification effects on functional properties in tropical plant communities.

PubMed

Carreño-Rocabado, Geovana; Peña-Claros, Marielos; Bongers, Frans; Díaz, Sandra; Quetier, Fabien; Chuviña, José; Poorter, Lourens

2016-01-01

There is consensus that plant diversity and ecosystem processes are negatively affected by land-use intensification (LUI), but, at the same time, there is empirical evidence that a large heterogeneity can be found in the responses. This heterogeneity is especially poorly understood in tropical ecosystems. We evaluated changes in community functional properties across five common land-use types in the wet tropics with different land-use intensity: mature forest, logged forest, secondary forest, agricultural land, and pastureland, located in the lowlands of Bolivia. For the dominant plant species, we measured 12 functional response traits related to their life history, acquisition and conservation of resources, plant domestication, and breeding. We used three single-trait metrics to describe community functional properties: community abundance-weighted mean (CWM) traits values, coefficient of variation, and kurtosis of distribution. The CWM of all 12 traits clearly responded to LUI. Overall, we found that an increase in LUI resulted in communities dominated by plants with acquisitive leaf trait values. However, contrary to our expectations, secondary forests had more conservative trait values (i.e., lower specific leaf area) than mature and logged forest, probably because they were dominated by palm species. Functional variation peaked at intermediate land-use intensity (high coefficient of variation and low kurtosis), which included secondary forest but, unexpectedly, also agricultural land, which is an intensely managed system. The high functional variation of these systems is due to a combination of how response traits (and species) are filtered out by biophysical filters and how management practices introduced a range of exotic species and their trait values into the local species pool. Our results showed that, at local scales and depending on prevailing environmental and management practices, LUI does not necessarily result in communities with more acquisitive trait values or with less functional variation. Instead of the widely expected negative impacts of LUI on plant diversity, we found varying responses of functional variation, with possible repercussions on many ecosystem services. These findings provide a background for actively mitigating negative effects of LUI while meeting the needs of local communities that rely mainly on provisioning ecosystem services for their livelihoods.

Immunological discrimination of Atlantic striped bass stocks

USGS Publications Warehouse

Schill, W.B.; Dorazio, R.M.

1990-01-01

Stocks of Atlantic striped bass Morone saxatilis that were assumed to be geographically isolated during spawning showed strong antigenic differences in blood serum albumin. A discriminant function was estimated from the immunologic responses of northern (Canadian and Hudson River) and southern (Chesapeake Bay and Roanoke River) stocks to two reference antisera. The function correctly classified 92% of the northern and 95% of the southern fish in the training set. Cross-validation revealed similar percentages of correct classification for fish that were of known origin but not used to estimate the discriminant function. Monte Carlo experiments were used to evaluate the ability of the discriminant function to predict the relative contribution of northern fish in samples of various size and stock composition. Averages of predicted proportions of northern fish in the samples agreed well with actual proportions. Coefficients of variation (100 × SD/mean) in the predicted proportions ranged from 1.5 to 36% for samples of 50–400 fish that contained at least 10% northern stock. In samples that contained only 2% northern stock, however, at least 1,600 fish were required to achieve similar levels of precision.

Effect of species, pretreatments, and drying methods on the functional and pasting properties of high-quality yam flour.

PubMed

Wahab, Bashirat A; Adebowale, Abdul-Rasaq A; Sanni, Silifat A; Sobukola, Olajide P; Obadina, Adewale O; Kajihausa, Olatundun E; Adegunwa, Mojisola O; Sanni, Lateef O; Tomlins, Keith

2016-01-01

The study investigated the functional properties of HQYF (high-quality yam flour) from tubers of four dioscorea species. The tubers were processed into HQYF using two pretreatments (potassium metabisulphite: 0.28%, 15 min; blanching: 70°C, 15 min) and drying methods (cabinet: 60°C, 48 h; sun drying: 3 days). Significant differences (P < 0.05) were observed in pasting characteristics of flours among the four species. The drying method significantly affected only the peak viscosity. The interactive effect of species, pretreatment, and drying methods on the functional properties was significant (P < 0.05) except for emulsification capacity, angle of repose, and least gelation concentration. The significant variation observed in most of the functional properties of the HQYF could contribute significantly to breeding programs of the yam species for diverse food applications. The pastes of flour from Dioscorea dumetorum pretreated with potassium metabisulphite and dried under a cabinet dryer were stable compared to other samples, hence will have better applications in products requiring lower retrogradation during freeze/thaw cycles.

The Metals in the Biological Periodic System of the Elements: Concepts and Conjectures

PubMed Central

Maret, Wolfgang

2016-01-01

A significant number of chemical elements are either essential for life with known functions, or present in organisms with poorly defined functional outcomes. We do not know all the essential elements with certainty and we know even less about the functions of apparently non-essential elements. In this article, I discuss a basis for a biological periodic system of the elements and that biochemistry should include the elements that are traditionally part of inorganic chemistry and not only those that are in the purview of organic chemistry. A biological periodic system of the elements needs to specify what “essential” means and to which biological species it refers. It represents a snapshot of our present knowledge and is expected to undergo further modifications in the future. An integrated approach of biometal sciences called metallomics is required to understand the interactions of metal ions, the biological functions that their chemical structures acquire in the biological system, and how their usage is fine-tuned in biological species and in populations of species with genetic variations (the variome). PMID:26742035

Selecting Magnet Laminations Recipes Using the Meth-od of Sim-u-la-ted Annealing

NASA Astrophysics Data System (ADS)

Russell, A. D.; Baiod, R.; Brown, B. C.; Harding, D. J.; Martin, P. S.

1997-05-01

The Fermilab Main Injector project is building 344 dipoles using more than 7000 tons of steel. Budget and logistical constraints required that steel production, lamination stamping and magnet fabrication proceed in parallel. There were significant run-to-run variations in the magnetic properties of the steel (Martin, P.S., et al., Variations in the Steel Properties and the Excitation Characteristics of FMI Dipoles, this conference). The large lamination size (>0.5 m coil opening) resulted in variations of gap height due to differences in stress relief in the steel after stamping. To minimize magnet-to-magnet strength and field shape variations the laminations were shuffled based on the available magnetic and mechanical data and assigned to magnets using a computer program based on the method of simulated annealing. The lamination sets selected by the program have produced magnets which easily satisfy the design requirements. Variations of the average magnet gap are an order of magnitude smaller than the variations in lamination gaps. This paper discusses observed gap variations, the program structure and the strength uniformity results.

Evolutionary Perspective on Collective Decision Making

NASA Astrophysics Data System (ADS)

Farrell, Dene; Sayama, Hiroki; Dionne, Shelley D.; Yammarino, Francis J.; Wilson, David Sloan

Team decision making dynamics are investigated from a novel perspective by shifting agency from decision makers to representations of potential solutions. We provide a new way to navigate social dynamics of collective decision making by interpreting decision makers as constituents of an evolutionary environment of an ecology of evolving solutions. We demonstrate distinct patterns of evolution with respect to three forms of variation: (1) Results with random variations in utility functions of individuals indicate that groups demonstrating minimal internal variation produce higher true utility values of group solutions and display better convergence; (2) analysis of variations in behavioral patterns within a group shows that a proper balance between selective and creative evolutionary forces is crucial to producing adaptive solutions; and (3) biased variations of the utility functions diminish the range of variation for potential solution utility, leaving only the differential of convergence performance static. We generally find that group cohesion (low random variation within a group) and composition (appropriate variation of behavioral patterns within a group) are necessary for a successful navigation of the solution space, but performance in both cases is susceptible to group level biases.

Spatiotemporal variations in litter mass and their relationships with climate in temperate grassland: A case study from Xilingol grassland, Inner Mongolia (China)

NASA Astrophysics Data System (ADS)

Ren, Hongrui; Zhang, Bei

2018-02-01

Clarifying spatiotemporal variations of litter mass and their relationships with climate factors will advance our understanding of ecosystem structure and functioning in grasslands. Our objective is to investigate the spatiotemporal variations of litter mass in the growing season and their relationships with precipitation and temperature in the Xilingol grassland using MOD09A1 data. With widely used STI (simple tillage index), we firstly estimated the litter mass of Xilingol grassland in the growing season from 2000 to 2014. Then we investigated the variations of litter mass in the growing season at regional and site scales. We further explored the spatiotemporal relationships between litter mass and precipitation and temperature at both scales. The litter mass increased with increasing mean annual precipitation and decreasing mean annual temperature at regional scale. The variations of litter mass at given sites followed quadratic function curves in the growing season, and litter mass generally attained maximums between August 1 and September 1. Positive spatial relationship was observed between litter mass variations and precipitation, and negative spatial relationship was found between litter mass variations and temperature in the growing season. There was no significant relationship between inter-annual variations of litter mass and precipitation and temperature at given sites. Results illustrate that precipitation and temperature are important drivers in shaping ecosystem functioning as reflected in litter mass at regional scale in the Xilingol grassland. Our findings also suggest the action of distinct mechanism in controlling litter mass variations at regional and sites scales.

[Symptom variations in ADHD: importance of context, development and comorbidity].

PubMed

Purper-Ouakil, D; Wohl, M; Michel, G; Mouren, M C; Gorwood, P

2004-01-01

Attention-deficit hyperactivity (ADHD) is a common disorder in school-aged children and is associated with significant impairment in social and academic functioning. Its recognition is based on congruent information from different sources, because most ADHD children and adolescents are not completely aware of impairments caused by inattention and/or hyperactivity/impulsivity. Fluctuations in symptom expression may complicate the diagnosis: during clinical examination or tests sessions, ADHD symptoms may be less severe than usual or completely absent. This review examines variations in ADHD symptoms due to environmental context, internal state, circadian factors, development, psychiatric comorbidity and discusses their clinical relevance. Generally, ADHD symptoms are pervasive and identified in different areas of functioning. Despite their chronicity, they show a relative context-dependency. An unfamiliar environment or situation may lessen symptoms. The same happens in dual relations or in calm settings, when the child receives attention and positive reinforcement from the adult. On the contrary, the classroom situation with its high stimulation level (noise, visual distractors, large class size) is likely to reveal or accentuate instability, impulsivity and inattention. Independently from objective symptom fluctuations, the impact of ADHD symptoms, and their consequences on self-esteem may also vary with the degree of environmental mismatch. Recent research in experimental psychology also draws attention to the motivational state of ADHD children: preference for immediate gratification and delay aversion may explain why most of them show satisfactory attentional capacities in certain activities (for instance video games or TV), while showing impairment in school work or in other effortful tasks. The diagnosis of the full ADHD syndrome requires significant impact on functioning in at least two areas. Some children with "situational" ADHD are impaired either in school setting or exclusively at home. Manuzza et al. report long-term outcome of "situational" versus "pervasive" ADHD. School-ADHD, in opposition to home-ADHD shows similarities with the full blown syndrome, as regards proportion of anti-social personality disorder, psycho-social functioning and academic/professional achievements. Moderate seasonal variations have also been identified with less ADHD symptoms in August. This result is likely to reflect a better fit between individual characteristics and environmental demands during school holidays rather than neurobiological changes, as there are no convincing arguments for seasonal fluctuations of serotoninergic tone in ADHD. Another cause for variations in ADHD symptom expression may be the co-occurrence of a mood disorder. Relationships between early-onset mania and ADHD are discussed. The appropriate definition of prepubertal mania is still in debate; its recognition is hindered by symptom overlap and high level of comorbid conditions. Chronic emotional dysregulation with irritability and frequent temper tantrums, sometimes viewed as characteristics of early-onset mania, might reflect a--possibly severe--sub-type of ADHD rather than a prodrome of bipolarity. A marked cyclicity of symptoms, with periodic accentuation of ADHD and mood symptoms, requires careful monitoring and systematic analysis of comorbid conditions. Clarification of the complex interrelations between ADHD and bipolar disorder will be obtained from long-term studies.

Advances in the indirect, descriptive, and experimental approaches to the functional analysis of problem behavior.

PubMed

Wightman, Jade; Julio, Flávia; Virués-Ortega, Javier

2014-05-01

Experimental functional analysis is an assessment methodology to identify the environmental factors that maintain problem behavior in individuals with developmental disabilities and in other populations. Functional analysis provides the basis for the development of reinforcement-based approaches to treatment. This article reviews the procedures, validity, and clinical implementation of the methodological variations of functional analysis and function-based interventions. We present six variations of functional analysis methodology in addition to the typical functional analysis: brief functional analysis, single-function tests, latency-based functional analysis, functional analysis of precursors, and trial-based functional analysis. We also present the three general categories of function-based interventions: extinction, antecedent manipulation, and differential reinforcement. Functional analysis methodology is a valid and efficient approach to the assessment of problem behavior and the selection of treatment strategies.

How to calculate H3 better.

PubMed

Pavanello, Michele; Tung, Wei-Cheng; Adamowicz, Ludwik

2009-11-14

Efficient optimization of the basis set is key to achieving a very high accuracy in variational calculations of molecular systems employing basis functions that are explicitly dependent on the interelectron distances. In this work we present a method for a systematic enlargement of basis sets of explicitly correlated functions based on the iterative-complement-interaction approach developed by Nakatsuji [Phys. Rev. Lett. 93, 030403 (2004)]. We illustrate the performance of the method in the variational calculations of H(3) where we use explicitly correlated Gaussian functions with shifted centers. The total variational energy (-1.674 547 421 Hartree) and the binding energy (-15.74 cm(-1)) obtained in the calculation with 1000 Gaussians are the most accurate results to date.

The eigenfrequency spectrum of linear magnetohydrodynamic perturbations in stationary equilibria: A variational principle

NASA Astrophysics Data System (ADS)

Andries, Jesse

2010-11-01

The frequencies of the normal modes of oscillation of linear magnetohydrodynamic perturbations of a stationary equilibrium are related to the stationary points of a quadratic functional over the Hilbert space of Lagrangian displacement vectors, which is subject to a constraint. In the absence of a background flow (or of a uniform flow), the relation reduces to the well-known Rayleigh-Ritz variational principle. In contrast to the existing variational principles for perturbations of stationary equilibria, the present treatment does neither impose additional symmetry restrictions on the equilibrium, nor does it involve the generalization to bilinear functionals instead of quadratic forms. This allows a more natural interpretation of the quadratic forms as energy functionals.

Energyscapes and prey fields shape a North Atlantic seabird wintering hotspot under climate change

PubMed Central

Fort, J.; Mathewson, P. D.; Speirs, D. C.; Perret, S.; Porter, W. P.; Wilson, R. J.

2018-01-01

There is an urgent need for a better understanding of animal migratory ecology under the influence of climate change. Most current analyses require long-term monitoring of populations on the move, and shorter-term approaches are needed. Here, we analysed the ecological drivers of seabird migration within the framework of the energyscape concept, which we defined as the variations in the energy requirements of an organism across geographical space as a function of environmental conditions. We compared the winter location of seabirds with their modelled energy requirements and prey fields throughout the North Atlantic. Across six winters, we tracked the migration of 94 little auks (Alle alle), a key sentinel Arctic species, between their East Greenland breeding site and wintering areas off Newfoundland. Winter energyscapes were modelled with Niche Mapper™, a mechanistic tool which takes into account local climate and bird ecophysiology. Subsequently, we used a resource selection function to explain seabird distributions through modelled energyscapes and winter surface distribution of one of their main prey, Calanus finmarchicus. Finally, future energyscapes were calculated according to IPCC climate change scenarios. We found that little auks targeted areas with high prey densities and moderately elevated energyscapes. Predicted energyscapes for 2050 and 2095 showed a decrease in winter energy requirements under the high emission scenario, which may be beneficial if prey availability is maintained. Overall, our study demonstrates the great potential of the energyscape concept for the study of animal spatial ecology, in particular in the context of global change. PMID:29410875

Humeral torsion revisited: a functional and ontogenetic model for populational variation.

PubMed

Cowgill, Libby W

2007-12-01

Anthropological interest in humeral torsion has a long history, and several functional explanations for observed variation in the orientation of the humeral head have been proposed. Recent clinical studies have revived this topic by linking patterns of humeral torsion to habitual activities such as overhand throwing. However, the precise functional implications and ontogenetic history of humeral torsion remain unclear. This study examines the ontogeny of humeral torsion in a large sample of primarily immature remains from six different skeletal collections (n = 407). The results of this research confirm that humeral torsion displays consistent developmental variation within all populations of growing children; neonates display relatively posteriorly oriented humeral heads, and the level of torsion declines steadily into adulthood. As in adults, variation in the angle of humeral torsion in immature individuals varies by population, and these differences arise early in development. However, when examined in the context of the developing muscles of the shoulder complex, it becomes apparent that variation in the angle of humeral torsion is not necessarily related to specific habitual activities. Variability in this feature is more likely caused by a generalized functional imbalance between muscles of medial and lateral rotation that can be produced by a wide variety of upper limb activity patterns during growth. (c) 2007 Wiley-Liss, Inc.

A functional variation in the hypocretin neuropeptide precursor gene may be associated with obstructive sleep apnea syndrome in Japan.

PubMed

Ahmed, Wael A; Tsutsumi, Makiko; Nakata, Seiichi; Mori, Terumi; Nishimura, Yoichi; Fujisawa, Toshiyuki; Kato, Ichiro; Nakashima, Mayuki; Kurahashi, Hiroki; Suzuki, Kenji

2012-04-01

To evaluate the association of hypocretin neuropeptide precursor gene (HCRT) variations with obstructive sleep apnea syndrome (OSAS) in a cohort of Japanese patients and to further evaluate whether the significant HCRT variations have potential functional consequences on HCRT expression. Case-control genetic association study. We studied the genetic variations within the HCRT gene. The study population consisted of 100 OSAS patients and 100 control subjects. The HCRT gene was amplified by polymerase chain reaction in all study subjects followed by direct sequencing and analysis of sequencing data. Two genetic variations within the HCRT intron, IVS1+16T>C (rs9902709) and IVS1-69G>C, were identified with significant differences between patients and controls (P < .05). A reporter gene assay using HeLa cells showed that the construct containing the C allele of the rs9902709 variation had significantly higher luciferase activity compared with the construct containing the T allele (P = .002). Furthermore, enzyme immunoassay revealed that subjects with T/C and C/C genotypes for rs9902709 had 1.4-fold and 1.5-fold increases in sera levels of orexin-A, respectively. Our genetic association study, followed by functional and quantitative phenotyping assays, demonstrated a functional locus within the HCRT gene, which may act to increase HCRT expression and lead to a protective effect against the development of OSAS. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

Alarm signals of the great gerbil: Acoustic variation by predator context, sex, age, individual, and family group

NASA Astrophysics Data System (ADS)

Randall, Jan A.; McCowan, Brenda; Collins, Kellie C.; Hooper, Stacie L.; Rogovin, Konstantin

2005-10-01

The great gerbil, Rhombomys opinus, is a highly social rodent that usually lives in family groups consisting of related females, their offspring, and an adult male. The gerbils emit alarm vocalizations in the presence of diverse predators with different hunting tactics. Alarm calls were recorded in response to three predators, a monitor lizard, hunting dog, and human, to determine whether the most common call type, the rhythmic call, is functionally referential with regard to type of predator. Results show variation in the alarm calls of both adults and subadults with the type of predator. Discriminant function analysis classified an average of 70% of calls to predator type. Call variation, however, was not limited to the predator context, because signal structure also differed by sex, age, individual callers, and family groups. These variations illustrate the flexibility of the rhythmic alarm call of the great gerbil and how it might have multiple functions and communicate in multiple contexts. Three alarm calls, variation in the rhythmic call, and vibrational signals generated from foot-drumming provide the gerbils with a varied and multi-channel acoustic repertoire.

A note on anomalous band-gap variations in semiconductors with temperature

NASA Astrophysics Data System (ADS)

Chakraborty, P. K.; Mondal, B. N.

2018-03-01

An attempt is made to theoretically study the band-gap variations (ΔEg) in semiconductors with temperature following the works, did by Fan and O'Donnell et al. based on thermodynamic functions. The semiconductor band-gap reflects the bonding energy. An increase in temperature changes the chemical bondings, and electrons are promoted from valence band to conduction band. In their analyses, they made several approximations with respect to temperature and other fitting parameters leading to real values of band-gap variations with linear temperature dependences. In the present communication, we have tried to re-analyse the works, specially did by Fan, and derived an analytical model for ΔEg(T). Because, it was based on the second-order perturbation technique of thermodynamic functions. Our analyses are made without any approximations with respect to temperatures and other fitting parameters mentioned in the text, leading to a complex functions followed by an oscillating nature of the variations of ΔEg. In support of the existence of the oscillating energy band-gap variations with temperature in a semiconductor, possible physical explanations are provided to justify the experimental observation for various materials.

Short-Term Variations in Response Distribution to Cortical Stimulation

ERIC Educational Resources Information Center

Lesser, Ronald P.; Lee, Hyang Woon; Webber, W. R. S.; Prince, Barry; Crone, Nathan E.; Miglioretti, Diana L.

2008-01-01

Patterns of responses in the cerebral cortex can vary, and are influenced by pre-existing cortical function, but it is not known how rapidly these variations can occur in humans. We investigated how rapidly response patterns to electrical stimulation can vary in intact human brain. We also investigated whether the type of functional change…

Conceptual Variation in the Depiction of Gene Function in Upper Secondary School Textbooks

ERIC Educational Resources Information Center

Gericke, Niklas Markus; Hagberg, Mariana

2010-01-01

This paper explores conceptual variation in the depiction of gene function in upper secondary school textbooks. Historically, concepts in genetics have developed in various scientific frameworks, which has led to a level of incommensurability as concepts have changed over time within their respective frameworks. Since students may have…

Effect of spanwise variations in gust intensity on the lift due to atmospheric turbulence

NASA Technical Reports Server (NTRS)

Diederich, Franklin W; Drischler, Joseph A

1957-01-01

The effect of spanwise variations in gust intensity on the power spectrum directly due to atmospheric turbulence is calculated for several analytic approximations to the correlation function or power spectra of atmospheric turbulence, for several spanwise weighing functions (span loadings), and for various angles of sweepback.

Variations in clinical nurse leaders' confidence with performing the core role functions.

PubMed

Gilmartin, Mattia J

2014-01-01

Clinical nurse leader (CNL) practice, by definition, requires individuals to make career transitions. CNLs must adjust to their new work role and responsibilities and doing so also entails individual adjustment. Prior work has not examined the role of individual-level factors in effective CNL role transition. This study contributes to CNL implementation efforts by developing understanding of personal and contextual factors that explain variation in individuals' levels of self-confidence with performing the key functions of the CNL role. Data were gathered using a cross-sectional survey from a national sample of registered nurses (RNs) certified as CNLs. Respondents' perceptions of their confidence in performing CNL role competencies were measured with the Clinical Nurse Leader Self-Efficacy Scale (CNLSES; Gilmartin MJ, Nokes, K. (in press). The Clinical Nurse Leader Self Efficacy Scale: Results of a pilot study. Nursing Economic$). The CNLSES is a 35-item state-specific self-efficacy scale with established measurement properties that assesses nurses' perceptions of their ability to function effectively as a CNL. Demographic data were also collected. Data were analyzed using a general linear regression model. One hundred forty-seven certified CNLs participated in the survey. Results indicate that respondents vary in their confidence with performing the nine role competencies associated with CNL practice. Results from regression analyses also show that respondents' confidence in their abilities to carry out the core functions associated with the CNL role varied significantly across geographic region, organizational type, and by CNL graduate program model. The results of this study show important differences in CNLs' levels of self-confidence with the core competencies of their role. As a result, it may be important to develop targeted career transition interventions to gain the full benefit of CNL practice. Copyright © 2014 Elsevier Inc. All rights reserved.

Calm Multi-Baryon Operators

NASA Astrophysics Data System (ADS)

Berkowitz, Evan; Nicholson, Amy; Chang, Chia Cheng; Rinaldi, Enrico; Clark, M. A.; Joó, Bálint; Kurth, Thorsten; Vranas, Pavlos; Walker-Loud, André

2018-03-01

There are many outstanding problems in nuclear physics which require input and guidance from lattice QCD calculations of few baryons systems. However, these calculations suffer from an exponentially bad signal-to-noise problem which has prevented a controlled extrapolation to the physical point. The variational method has been applied very successfully to two-meson systems, allowing for the extraction of the two-meson states very early in Euclidean time through the use of improved single hadron operators. The sheer numerical cost of using the same techniques in two-baryon systems has so far been prohibitive. We present an alternate strategy which offers some of the same advantages as the variational method while being significantly less numerically expensive. We first use the Matrix Prony method to form an optimal linear combination of single baryon interpolating fields generated from the same source and different sink interpolating fields. Very early in Euclidean time this optimal linear combination is numerically free of excited state contamination, so we coin it a calm baryon. This calm baryon operator is then used in the construction of the two-baryon correlation functions. To test this method, we perform calculations on the WM/JLab iso-clover gauge configurations at the SU(3) flavor symmetric point with mπ 800 MeV — the same configurations we have previously used for the calculation of two-nucleon correlation functions. We observe the calm baryon significantly removes the excited state contamination from the two-nucleon correlation function to as early a time as the single-nucleon is improved, provided non-local (displaced nucleon) sources are used. For the local two-nucleon correlation function (where both nucleons are created from the same space-time location) there is still improvement, but there is significant excited state contamination in the region the single calm baryon displays no excited state contamination.

Teamwork and delegation in medical homes: primary care staff perspectives in the Veterans Health Administration.

PubMed

True, Gala; Stewart, Greg L; Lampman, Michelle; Pelak, Mary; Solimeo, Samantha L

2014-07-01

The patient-centered medical home (PCMH) relies on a team approach to patient care. For organizations engaged in transitioning to a PCMH model, identifying and providing the resources needed to promote team functioning is essential. To describe team-level resources required to support PCMH team functioning within the Veterans Health Administration (VHA), and provide insight into how the presence or absence of these resources facilitates or impedes within-team delegation. Semi-structured interviews with members of pilot teams engaged in PCMH implementation in 77 primary care clinics serving over 300,000 patients across two VHA regions covering the Mid-Atlantic and Midwest United States. A purposive sample of 101 core members of pilot teams, including 32 primary care providers, 42 registered nurse care managers, 15 clinical associates, and 12 clerical associates. Investigators from two evaluation sites interviewed frontline primary care staff separately, and then collaborated on joint analysis of parallel data to develop a broad, comprehensive understanding of global themes impacting team functioning and within-team delegation. We describe four themes key to understanding how resources at the team level supported ability of primary care staff to work as effective, engaged teams. Team-based task delegation was facilitated by demarcated boundaries and collective identity; shared goals and sense of purpose; mature and open communication characterized by psychological safety; and ongoing, intentional role negotiation. Our findings provide a framework for organizations to identify assets already in place to support team functioning, as well as areas in need of improvement. For teams struggling to make practice changes, our results indicate key areas where they may benefit from future support. In addition, this research sheds light on how variation in medical home implementation and outcomes may be associated with variation in team-based task delegation.

A view of annual water quality cycle and inter-annual variations in agricultural headwater catchment (Kervidy-Naizin, France)

NASA Astrophysics Data System (ADS)

Aubert, A.; Gascuel-odoux, C.; Merot, P.; Grimaldi, C.; Gruau, G.; Ruiz, L.

2011-12-01

Climatic conditions impact biotransformation and transfer of solutes. Therefore, they modify solute emissions in streams. Studying these modifications requires long term and detailed monitoring of both internal processes and river loads, which are rarely combined. The Kervidy-Naizin catchment, implemented in 1993, is part of the French network of catchment for environmental research (SOERE RBV, focused on the Critical Zone). It is an intensive agricultural catchment located in a temperate climate in Western France (Brittany) (Molenat et al., 2008; Morel et al., 2009). It presents shallow aquifers due to impervious bedrock. Both hydrology and water chemistry are monitored with a daily time step since 2000-01, as well as possible explanatory data (land use, meteorology, etc.). Concentrations in major anions in this catchment are extremely high, which make people call it a "saturated" catchment. We identified annual patterns for chloride, sulphate, dissolved organic and inorganic carbon and nitrate concentration variations. First, we considered the complete set of concentration data as function of the time. From that, we foresaw 3 cyclic temporal patterns. Then, from representing the concentrations as function of meteorological parameters, intra-annual hysteretic variations and their inter-annual variations were clearly identified. Our driving question is to know if and how climatic conditions are responsible for variations of the patterns in and between years. In winter, i.e. rainy and cold period, rainfall is closely linked to discharge because of a direct recharge to the shallow groundwater. Reversely, in transition periods (spring and fall) and hot periods, both rainfall and temperature influences discharge in relation to their range of variations. Moreover, biological processes, driven by temperature and wetness, also act during these periods. On the whole, we can emphasize the specificity of water chemistry patterns for each element. Noticeable differences between hot and cold years and between wet and dry years can mainly be observed during spring and autumn period, i.e. when combining variations of rainfall and temperature. Further jointed statistical analyses between water chemistry and meteorology have to be carried on. References Molenat, J., Gascuel-Odoux, C., Ruiz, L., and Gruau, G. (2008). Role of water table dynamics on stream nitrate export and concentration. in agricultural headwater catchment (France). Journal of Hydrology 348, 363-378. Morel, B., Durand, P., Jaffrezic, A., Gruau, G., and Molenat, J. (2009). Sources of dissolved organic carbon during stormflow in a headwater agricultural catchment. Hydrological Processes 23, 2888-2901.

A Framework for Robust Multivariable Optimization of Integrated Circuits in Space Applications

NASA Technical Reports Server (NTRS)

DuMonthier, Jeffrey; Suarez, George

2013-01-01

Application Specific Integrated Circuit (ASIC) design for space applications involves multiple challenges of maximizing performance, minimizing power and ensuring reliable operation in extreme environments. This is a complex multidimensional optimization problem which must be solved early in the development cycle of a system due to the time required for testing and qualification severely limiting opportunities to modify and iterate. Manual design techniques which generally involve simulation at one or a small number of corners with a very limited set of simultaneously variable parameters in order to make the problem tractable are inefficient and not guaranteed to achieve the best possible results within the performance envelope defined by the process and environmental requirements. What is required is a means to automate design parameter variation, allow the designer to specify operational constraints and performance goals, and to analyze the results in a way which facilitates identifying the tradeoffs defining the performance envelope over the full set of process and environmental corner cases. The system developed by the Mixed Signal ASIC Group (MSAG) at the Goddard Space Flight Center is implemented as framework of software modules, templates and function libraries. It integrates CAD tools and a mathematical computing environment, and can be customized for new circuit designs with only a modest amount of effort as most common tasks are already encapsulated. Customization is required for simulation test benches to determine performance metrics and for cost function computation. Templates provide a starting point for both while toolbox functions minimize the code required. Once a test bench has been coded to optimize a particular circuit, it is also used to verify the final design. The combination of test bench and cost function can then serve as a template for similar circuits or be re-used to migrate the design to different processes by re-running it with the new process specific device models. The system has been used in the design of time to digital converters for laser ranging and time-of-flight mass spectrometry to optimize analog, mixed signal and digital circuits such as charge sensitive amplifiers, comparators, delay elements, radiation tolerant dual interlocked (DICE) flip-flops and two of three voter gates.

Climate, soil and plant functional types as drivers of global fine-root trait variation

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

Freschet, Grégoire T.; Valverde-Barrantes, Oscar J.; Tucker, Caroline M.

Ecosystem functioning relies heavily on below-ground processes, which are largely regulated by plant fine-roots and their functional traits. However, our knowledge of fine-root trait distribution relies to date on local- and regional-scale studies with limited numbers of species, growth forms and environmental variation. We compiled a world-wide fine-root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine-root trait variation. Most particularly, we tested the competing hypothesesmore » that fine-root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness. We demonstrate that: (i) Climate conditions promoting soil fertility relate negatively to fine-root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine-root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (ii) Soil bulk density strongly influences species fine-root morphology, by favouring thicker, denser fine-roots; (iii) Fine-roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N 2-fixing capacity positively relates to root nitrogen; and (iv) Plants growing in pots have higher SRL than those grown in the field. Synthesis. This study reveals both the large variation in fine-root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine-root trait variation. High trait variation occurred at local scales, suggesting that wide-ranging below-ground resource economics strategies are viable within most climatic areas and soil conditions.« less

Climate, soil and plant functional types as drivers of global fine-root trait variation

DOE PAGES

Freschet, Grégoire T.; Valverde-Barrantes, Oscar J.; Tucker, Caroline M.; ...

2017-03-08

Ecosystem functioning relies heavily on below-ground processes, which are largely regulated by plant fine-roots and their functional traits. However, our knowledge of fine-root trait distribution relies to date on local- and regional-scale studies with limited numbers of species, growth forms and environmental variation. We compiled a world-wide fine-root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine-root trait variation. Most particularly, we tested the competing hypothesesmore » that fine-root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness. We demonstrate that: (i) Climate conditions promoting soil fertility relate negatively to fine-root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine-root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (ii) Soil bulk density strongly influences species fine-root morphology, by favouring thicker, denser fine-roots; (iii) Fine-roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N 2-fixing capacity positively relates to root nitrogen; and (iv) Plants growing in pots have higher SRL than those grown in the field. Synthesis. This study reveals both the large variation in fine-root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine-root trait variation. High trait variation occurred at local scales, suggesting that wide-ranging below-ground resource economics strategies are viable within most climatic areas and soil conditions.« less

Approximating the Helium Wavefunction in Positronium-Helium Scattering

NASA Technical Reports Server (NTRS)

DiRienzi, Joseph; Drachman, Richard J.

2003-01-01

In the Kohn variational treatment of the positronium- hydrogen scattering problem the scattering wave function is approximated by an expansion in some appropriate basis set, but the target and projectile wave functions are known exactly. In the positronium-helium case, however, a difficulty immediately arises in that the wave function of the helium target atom is not known exactly, and there are several ways to deal with the associated eigenvalue in formulating the variational scattering equations to be solved. In this work we will use the Kohn variational principle in the static exchange approximation to d e t e e the zero-energy scattering length for the Ps-He system, using a suite of approximate target functions. The results we obtain will be compared with each other and with corresponding values found by other approximation techniques.

TDIGG - TWO-DIMENSIONAL, INTERACTIVE GRID GENERATION CODE

NASA Technical Reports Server (NTRS)

Vu, B. T.

1994-01-01

TDIGG is a fast and versatile program for generating two-dimensional computational grids for use with finite-difference flow-solvers. Both algebraic and elliptic grid generation systems are included. The method for grid generation by algebraic transformation is based on an interpolation algorithm and the elliptic grid generation is established by solving the partial differential equation (PDE). Non-uniform grid distributions are carried out using a hyperbolic tangent stretching function. For algebraic grid systems, interpolations in one direction (univariate) and two directions (bivariate) are considered. These interpolations are associated with linear or cubic Lagrangian/Hermite/Bezier polynomial functions. The algebraic grids can subsequently be smoothed using an elliptic solver. For elliptic grid systems, the PDE can be in the form of Laplace (zero forcing function) or Poisson. The forcing functions in the Poisson equation come from the boundary or the entire domain of the initial algebraic grids. A graphics interface procedure using the Silicon Graphics (GL) Library is included to allow users to visualize the grid variations at each iteration. This will allow users to interactively modify the grid to match their applications. TDIGG is written in FORTRAN 77 for Silicon Graphics IRIS series computers running IRIX. This package requires either MIT's X Window System, Version 11 Revision 4 or SGI (Motif) Window System. A sample executable is provided on the distribution medium. It requires 148K of RAM for execution. The standard distribution medium is a .25 inch streaming magnetic IRIX tape cartridge in UNIX tar format. This program was developed in 1992.

49 CFR 195.104 - Variations in pressure.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Variations in pressure. 195.104 Section 195.104... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Design Requirements § 195.104 Variations in pressure. If, within a pipeline system, two or more...

49 CFR 195.104 - Variations in pressure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Variations in pressure. 195.104 Section 195.104... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Design Requirements § 195.104 Variations in pressure. If, within a pipeline system, two or more...

49 CFR 195.104 - Variations in pressure.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Variations in pressure. 195.104 Section 195.104... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Design Requirements § 195.104 Variations in pressure. If, within a pipeline system, two or more...

49 CFR 195.104 - Variations in pressure.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Variations in pressure. 195.104 Section 195.104... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Design Requirements § 195.104 Variations in pressure. If, within a pipeline system, two or more...

49 CFR 195.104 - Variations in pressure.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Variations in pressure. 195.104 Section 195.104... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF HAZARDOUS LIQUIDS BY PIPELINE Design Requirements § 195.104 Variations in pressure. If, within a pipeline system, two or more...

Thermo-Elastic Triangular Sandwich Element for the Complete Stress Field Based on a Single-Layer Theory

NASA Technical Reports Server (NTRS)

Das, M.; Barut, A.; Madenci, E.; Ambur, D. R.

2004-01-01

This study presents a new triangular finite element for modeling thick sandwich panels, subjected to thermo-mechanical loading, based on a {3,2}-order single-layer plate theory. A hybrid energy functional is employed in the derivation of the element because of a C interelement continuity requirement. The single-layer theory is based on five weighted-average field variables arising from the cubic and quadratic representations of the in-plane and transverse displacement fields, respectively. The variations of temperature and distributed loading acting on the top and bottom surfaces are non-uniform. The temperature varies linearly through the thickness.

SAR calibration technology review

NASA Technical Reports Server (NTRS)

Walker, J. L.; Larson, R. W.

1981-01-01

Synthetic Aperture Radar (SAR) calibration technology including a general description of the primary calibration techniques and some of the factors which affect the performance of calibrated SAR systems are reviewed. The use of reference reflectors for measurement of the total system transfer function along with an on-board calibration signal generator for monitoring the temporal variations of the receiver to processor output is a practical approach for SAR calibration. However, preliminary error analysis and previous experimental measurements indicate that reflectivity measurement accuracies of better than 3 dB will be difficult to achieve. This is not adequate for many applications and, therefore, improved end-to-end SAR calibration techniques are required.