Predicting boundary shear stress and sediment transport over bed forms

USGS Publications Warehouse

McLean, S.R.; Wolfe, S.R.; Nelson, J.M.

1999-01-01

To estimate bed-load sediment transport rates in flows over bed forms such as ripples and dunes, spatially averaged velocity profiles are frequently used to predict mean boundary shear stress. However, such averaging obscures the complex, nonlinear interaction of wake decay, boundary-layer development, and topographically induced acceleration downstream of flow separation and often leads to inaccurate estimates of boundary stress, particularly skin friction, which is critically important in predicting bed-load transport rates. This paper presents an alternative methodology for predicting skin friction over 2D bed forms. The approach is based on combining the equations describing the mechanics of the internal boundary layer with semiempirical structure functions to predict the velocity at the crest of a bedform, where the flow is most similar to a uniform boundary layer. Significantly, the methodology is directed toward making specific predictions only at the bed-form crest, and as a result it avoids the difficulty and questionable validity of spatial averaging. The model provides an accurate estimate of the skin friction at the crest where transport rates are highest. Simple geometric constraints can be used to derive the mean transport rates as long as bed load is dominant.To estimate bed-load sediment transport rates in flows over bed forms such as ripples and dunes, spatially averaged velocity profiles are frequently used to predict mean boundary shear stress. However, such averaging obscures the complex, nonlinear interaction of wake decay, boundary-layer development, and topographically induced acceleration downstream of flow separation and often leads to inaccurate estimates of boundary stress, particularly skin friction, which is critically important in predicting bed-load transport rates. This paper presents an alternative methodology for predicting skin friction over 2D bed forms. The approach is based on combining the equations describing the mechanics of the internal boundary layer with semiempirical structure functions to predict the velocity at the crest of a bedform, where the flow is most similar to a uniform boundary layer. Significantly, the methodology is directed toward making specific predictions only at the bed-form crest, and as a result it avoids the difficulty and questionable validity of spatial averaging. The model provides an accurate estimate of the skin friction at the crest where transport rates are highest. Simple geometric constraints can be used to derive the mean transport rates as long as bed load is dominant.

The Generation, Radiation and Prediction of Supersonic Jet Noise. Volume 1

DTIC Science & Technology

1978-10-01

standard, Gaussian correlation function model can yield a good noise spectrum prediction (at 900), but the corresponding axial source distributions do not...forms for the turbulence cross-correlation function. Good agreement was obtained between measured and calculated far- field noise spectra. However, the...complementary error function profile (3.63) was found to provide a good fit to the axial velocity distribution tor a wide range of Mach numbers in the Initial

A generalized predictive model for direct gain

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

Givoni, B.

In the correlational model for direct gain developed by the Los Alamos National Laboratory, a list of constants applicable to different types of buildings or passive solar systems was specified separately for each type. In its original form, the model was applicable only to buildings similar in their heat capacity, type of glazing, or night insulation to the types specified by the model. While maintaining the general form of the predictive equations, the new model, the predictive model for direct gain (PMDG), replaces the constants with functions dependent upon the thermal properties of the building, or the components of themore » solar system, or both. By this transformation, the LANL model for direct gain becomes a generalized one. The new model predicts the performance of buildings heated by direct gain with any heat capacity, glazing, and night insulation as functions of their thermophysical properties and climatic conditions.« less

Differential Forms: A New Tool in Economics

NASA Astrophysics Data System (ADS)

Mimkes, Jürgen

Econophysics is the transfer of methods from natural to socio-economic sciences. This concept has first been applied to finance1, but it is now also used in various applications of economics and social sciences [2,3]. The present paper focuses on problems in macro economics and growth. 1. Neoclassical theory [4, 5] neglects the “ex post” property of income and growth. Income Y(K, L) is assumed to be a function of capital and labor. But functions cannot model the “ex post” character of income. 2. Neoclassical theory is based on a Cobb Douglas function [6] with variable elasticity α, which may be fitted to economic data. But an undefined elasticity α leads to a descriptive rather than a predictive economic theory. The present paper introduces a new tool - differential forms and path dependent integrals - to macro economics. This is a solution to the problems above: 1. The integral of not exact differential forms is path dependent and can only be calculated “ex post” like income and economic growth. 2. Not exact differential forms can be made exact by an integrating factor, this leads to a new, well defined, unique production function F and a predictive economic theory.

Pyranopterin conformation defines the function of molybdenum and tungsten enzymes.

PubMed

Rothery, Richard A; Stein, Benjamin; Solomonson, Matthew; Kirk, Martin L; Weiner, Joel H

2012-09-11

We have analyzed the conformations of 319 pyranopterins in 102 protein structures of mononuclear molybdenum and tungsten enzymes. These span a continuum between geometries anticipated for quinonoid dihydro, tetrahydro, and dihydro oxidation states. We demonstrate that pyranopterin conformation is correlated with the protein folds defining the three major mononuclear molybdenum and tungsten enzyme families, and that binding-site micro-tuning controls pyranopterin oxidation state. Enzymes belonging to the bacterial dimethyl sulfoxide reductase (DMSOR) family contain a metal-bis-pyranopterin cofactor, the two pyranopterins of which have distinct conformations, with one similar to the predicted tetrahydro form, and the other similar to the predicted dihydro form. Enzymes containing a single pyranopterin belong to either the xanthine dehydrogenase (XDH) or sulfite oxidase (SUOX) families, and these have pyranopterin conformations similar to those predicted for tetrahydro and dihydro forms, respectively. This work provides keen insight into the roles of pyranopterin conformation and oxidation state in catalysis, redox potential modulation of the metal site, and catalytic function.

Predicting landslides in clearcut patches

Treesearch

Raymond M. Rice; Norman H. Pillsbury

1982-01-01

Abstract - Accelerated erosion in the form of landslides can be an undesirable consequence of clearcut logging on steep slopes. Forest managers need a method of predicting the risk of such erosion. Data collected after logging in a granitic area of northwestern California were used to develop a predictive equation. A linear discriminant function was developed that...

Mathematical beta function formulation for maxillary arch form prediction in normal occlusion population.

PubMed

Mina, Morteza; Borzabadi-Farahani, Ali; Tehranchi, Azita; Nouri, Mahtab; Younessian, Farnaz

2017-04-01

The aim of this study was to assess the dental arch curvature in subjects with normal occlusion in an Iranian population and propose a beta function formula to predict maxillary arch form using the mandibular intermolar widths (IMW) and intermolar depths (IMD). The materials used were study casts of 54 adolescents with normal occlusion and mean age of 14.1 years (25 males, 29 females, age range 12-16 years). Curve-fitting analyses were carried out and the curves passing through the facial-axis point of the canines, premolars, first molars, and the incisal edges of the anterior teeth were studied using a 3D laser scanner. Using the measured IMW and IMD of the dental arches at the maxillary and mandibular first molar region, a beta function formula proposed for predicting maxillary arch form. The accuracy of the proposed formula was assessed on 10 randomly selected dental casts. The mean (SD) of the maxillary and mandibular IMW and IMD were 57.92 (4.75), 54.19 (5.31), and 31.59 (2.90) and 28.10 (2.59) mm, respectively. There was no gender dimorphism (P > 0.05) for both variables (IMW, IMD). There was a strong positive association (n = 10, Pearson r = 0.98, P < 0.05) between the measured (actual) maxillary arch length and proposed arch length derived from generated formula. The goodness of fit (whole arch) for the proposed beta function formula, using adjusted r square measure and root mean square in 10 patients averaged 0.97 and 1.49 mm, respectively. The corresponding figures for the maxillary anterior arch (canine to canine) were 0.90 and 0.92 mm, respectively. The proposed beta function formula used for predicting maxillary arch form based on two mandibular measures (IMW, IMD) was found to have a high accuracy for maxillary arch prediction in the Iranian population and may be used as a guide to fabricate customized arch wires or as an aid in maxillary reconstructive surgery.

Decoupled form and function in disparate herbivorous dinosaur clades

NASA Astrophysics Data System (ADS)

Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

2016-05-01

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Decoupled form and function in disparate herbivorous dinosaur clades.

PubMed

Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

2016-05-20

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Dust-obscured star-forming galaxies in the early universe

NASA Astrophysics Data System (ADS)

Wilkins, Stephen M.; Feng, Yu; Di Matteo, Tiziana; Croft, Rupert; Lovell, Christopher C.; Thomas, Peter

2018-02-01

Motivated by recent observational constraints on dust reprocessed emission in star-forming galaxies at z ∼ 6 and above, we use the very large cosmological hydrodynamical simulation BLUETIDES to explore predictions for the amount of dust-obscured star formation in the early Universe (z > 8). BLUETIDES matches current observational constraints on both the UV luminosity function and galaxy stellar mass function and predicts that approximately 90 per cent of the star formation in high-mass (M* > 1010 M⊙) galaxies at z = 8 is already obscured by dust. The relationship between dust attenuation and stellar mass predicted by BLUETIDES is consistent with that observed at lower redshift. However, observations of several individual objects at z > 6 are discrepant with the predictions, though it is possible that their uncertainties may have been underestimated. We find that the predicted surface density of z ≥ 8 submm sources is below that accessible to current Herschel, SCUBA-2 and Atacama Large Millimetre Array (ALMA) submm surveys. However, as ALMA continues to accrue an additional surface area the population of z > 8 dust-obscured galaxies may become accessible in the near future.

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.

On Predicting Success in Training for Males and Females: Marine Corps Clerical Specialties and ASVAB Forms 6 and 7.

ERIC Educational Resources Information Center

Dunbar, Stephen B.; Novick, Melvin R.

The presence of differences between prediction systems for males and females is investigated through a detailed study of clerical specialties in the Marine Corps. When various aptitude composites are used to predict success of recruits in training, sizeable differences in regression functions are found between male and female groups. The paper…

Linear modeling of steady-state behavioral dynamics.

PubMed Central

Palya, William L; Walter, Donald; Kessel, Robert; Lucke, Robert

2002-01-01

The observed steady-state behavioral dynamics supported by unsignaled periods of reinforcement within repeating 2,000-s trials were modeled with a linear transfer function. These experiments employed improved schedule forms and analytical methods to improve the precision of the measured transfer function, compared to previous work. The refinements include both the use of multiple reinforcement periods that improve spectral coverage and averaging of independently determined transfer functions. A linear analysis was then used to predict behavior observed for three different test schedules. The fidelity of these predictions was determined. PMID:11831782

Understanding the relationship between duration of untreated psychosis and outcomes: A statistical perspective.

PubMed

Hannigan, Ailish; Bargary, Norma; Kinsella, Anthony; Clarke, Mary

2017-06-14

Although the relationships between duration of untreated psychosis (DUP) and outcomes are often assumed to be linear, few studies have explored the functional form of these relationships. The aim of this study is to demonstrate the potential of recent advances in curve fitting approaches (splines) to explore the form of the relationship between DUP and global assessment of functioning (GAF). Curve fitting approaches were used in models to predict change in GAF at long-term follow-up using DUP for a sample of 83 individuals with schizophrenia. The form of the relationship between DUP and GAF was non-linear. Accounting for non-linearity increased the percentage of variance in GAF explained by the model, resulting in better prediction and understanding of the relationship. The relationship between DUP and outcomes may be complex and model fit may be improved by accounting for the form of the relationship. This should be routinely assessed and new statistical approaches for non-linear relationships exploited, if appropriate. © 2017 John Wiley & Sons Australia, Ltd.

Modified Displacement Transfer Functions for Deformed Shape Predictions of Slender Curved Structures with Varying Curvatives

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2014-01-01

To eliminate the need to use finite-element modeling for structure shape predictions, a new method was invented. This method is to use the Displacement Transfer Functions to transform the measured surface strains into deflections for mapping out overall structural deformed shapes. The Displacement Transfer Functions are expressed in terms of rectilinearly distributed surface strains, and contain no material properties. This report is to apply the patented method to the shape predictions of non-symmetrically loaded slender curved structures with different curvatures up to a full circle. Because the measured surface strains are not available, finite-element analysis had to be used to analytically generate the surface strains. Previously formulated straight-beam Displacement Transfer Functions were modified by introducing the curvature-effect correction terms. Through single-point or dual-point collocations with finite-elementgenerated deflection curves, functional forms of the curvature-effect correction terms were empirically established. The resulting modified Displacement Transfer Functions can then provide quite accurate shape predictions. Also, the uniform straight-beam Displacement Transfer Function was applied to the shape predictions of a section-cut of a generic capsule (GC) outer curved sandwich wall. The resulting GC shape predictions are quite accurate in partial regions where the radius of curvature does not change sharply.

Physical Function Does Not Predict Care Assessment Need Score in Older Veterans.

PubMed

Serra, Monica C; Addison, Odessa; Giffuni, Jamie; Paden, Lydia; Morey, Miriam C; Katzel, Leslie

2017-01-01

The Veterans Health Administration's Care Assessment Need (CAN) score is a statistical model, aimed to predict high-risk patients. We were interested in determining if a relationship existed between physical function and CAN scores. Seventy-four older (71 ± 1 years) male Veterans underwent assessment of CAN score and subjective (Short Form-36 [SF-36]) and objective (self-selected walking speed, four square step test, short physical performance battery) assessment of physical function. Approximately 25% of participants self-reported limitations performing lower intensity activities, while 70% to 90% reported limitations with more strenuous activities. When compared with cut points indicative of functional limitations, 35% to 65% of participants had limitations for each of the objective measures. Any measure of subjective or objective physical function did not predict CAN score. These data indicate that the addition of a physical function assessment may complement the CAN score in the identification of high-risk patients.

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

NASA Astrophysics Data System (ADS)

Xu, Xin; Zhang, Qingsong; Muller, Richard P.; Goddard, William A.

2005-01-01

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with Re and De within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions.

A formulation of directivity for earthquake sources using isochrone theory

USGS Publications Warehouse

Spudich, Paul; Chiou, Brian S.J.; Graves, Robert; Collins, Nancy; Somerville, Paul

2004-01-01

A functional form for directivity effects can be derived from isochrone theory, in which the measure of the directivity-induced amplification of an S body wave is c, the isochrone velocity. Ground displacement of the near-, intermediate-, and far-field terms of P and S waves is linear in isochrone velocity for a finite source in a whole space. We have developed an approximation c-tilde-prime of isochrone velocity that can easily be implemented as a predictor of directivity effects in empirical ground motion prediction relations. Typically, for a given fault surface, hypocenter, and site geometry, c-tilde-prime is a simple function of the hypocentral distance, the rupture distance, the crustal shear wave speed in the seismogenic zone, and the rupture velocity. c-tilde-prime typically ranges in the interval 0.44, for rupture away from the station, to about 4, for rupture toward the station. In this version of the theory directivity is independent of period. Additionally, we have created another functional form which is c-tilde-prime modified to include the approximate radiation pattern of a finite fault having a given rake. This functional form can be used to model the spatial variations of fault-parallel and fault-normal horizontal ground motions. The strengths of this formulation are 1) the proposed functional form is based on theory, 2) the predictor is unambiguously defined for all possible site locations and source rakes, and 3) it can easily be implemented for well-studied important previous earthquakes. We compare predictions of our functional form with synthetic ground motions calculated for finite strike-slip and dip-slip faults in the magnitude range 6.5 - 7.5. In general our functional form correlates best with computed fault-normal and fault-parallel motions in the synthetic motions calculated for events with M6.5. Correlation degrades but is still useful for larger events and for the geometric average horizontal motions. We have had limited success applying it to geometrically complicated faults.

Application-driven ground motion prediction equation for seismic hazard assessments in non-cratonic moderate-seismicity areas

NASA Astrophysics Data System (ADS)

Bindi, D.; Cotton, F.; Kotha, S. R.; Bosse, C.; Stromeyer, D.; Grünthal, G.

2017-09-01

We present a ground motion prediction equation (GMPE) for probabilistic seismic hazard assessments (PSHA) in low-to-moderate seismicity areas, such as Germany. Starting from the NGA-West2 flat-file (Ancheta et al. in Earthquake Spectra 30:989-1005, 2014), we develop a model tailored to the hazard application in terms of data selection and implemented functional form. In light of such hazard application, the GMPE is derived for hypocentral distance (along with the Joyner-Boore one), selecting recordings at sites with vs30 ≥ 360 m/s, distances within 300 km, and magnitudes in the range 3 to 8 (being 7.4 the maximum magnitude for the PSHA in the target area). Moreover, the complexity of the considered functional form is reflecting the availability of information in the target area. The median predictions are compared with those from the NGA-West2 models and with one recent European model, using the Sammon's map constructed for different scenarios. Despite the simplification in the functional form, the assessed epistemic uncertainty in the GMPE median is of the order of those affecting the NGA-West2 models for the magnitude range of interest of the hazard application. On the other hand, the simplification of the functional form led to an increment of the apparent aleatory variability. In conclusion, the GMPE developed in this study is tailored to the needs for applications in low-to-moderate seismic areas and for short return periods (e.g., 475 years); its application in studies where the hazard is involving magnitudes above 7.4 and for long return periods is not advised.

Canonical microcircuits for predictive coding

PubMed Central

Bastos, Andre M.; Usrey, W. Martin; Adams, Rick A.; Mangun, George R.; Fries, Pascal; Friston, Karl J.

2013-01-01

Summary This review considers the influential notion of a canonical (cortical) microcircuit in light of recent theories about neuronal processing. Specifically, we conciliate quantitative studies of microcircuitry and the functional logic of neuronal computations. We revisit the established idea that message passing among hierarchical cortical areas implements a form of Bayesian inference – paying careful attention to the implications for intrinsic connections among neuronal populations. By deriving canonical forms for these computations, one can associate specific neuronal populations with specific computational roles. This analysis discloses a remarkable correspondence between the microcircuitry of the cortical column and the connectivity implied by predictive coding. Furthermore, it provides some intuitive insights into the functional asymmetries between feedforward and feedback connections and the characteristic frequencies over which they operate. PMID:23177956

Influence of the local-spin-density correlation functional on the stability of bcc ferromagnetic iron

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

Singh, D.; Clougherty, D.P.; MacLaren, J.M.

1991-10-01

The influence of local-spin-dependent correlation effects on the predicted stable ground-state phase of iron is reexamined with use of general-potential linearized augmented-plane-wave calculations. Differences in the form of the Vosko-Wilk-Nusair (VWN) local-spin-density functional used in previous studies are noted, since in previous studies significant additional approximations were made with respect to those of Vosko, Wilk, and Nusan (Can. J. Phys. 58, 1200 (1980)) and of MacLaren, Clougherty, and Albers (Phys. Rev. B 42, 3205 (1990)). While the results of previous linear muffin-tin orbital calculations using the VWN functional predict a bcc ferromagnetic ground state, the present calculations show that themore » VWN spin-correlation effects fail to stabilize a bcc ground state. Considerable sensitivity to the form of the spin interpolation is found.« less

Species-area relationships and extinction forecasts.

PubMed

Halley, John M; Sgardeli, Vasiliki; Monokrousos, Nikolaos

2013-05-01

The species-area relationship (SAR) predicts that smaller areas contain fewer species. This is the basis of the SAR method that has been used to forecast large numbers of species committed to extinction every year due to deforestation. The method has a number of issues that must be handled with care to avoid error. These include the functional form of the SAR, the choice of equation parameters, the sampling procedure used, extinction debt, and forest regeneration. Concerns about the accuracy of the SAR technique often cite errors not much larger than the natural scatter of the SAR itself. Such errors do not undermine the credibility of forecasts predicting large numbers of extinctions, although they may be a serious obstacle in other SAR applications. Very large errors can arise from misinterpretation of extinction debt, inappropriate functional form, and ignoring forest regeneration. Major challenges remain to understand better the relationship between sampling protocol and the functional form of SARs and the dynamics of relaxation, especially in continental areas, and to widen the testing of extinction forecasts. © 2013 New York Academy of Sciences.

Regional height-diameter equations for major tree species of southwest Oregon.

Treesearch

H. Temesgen; D.W. Hann; V.J. Monleon

2006-01-01

Selected tree height and diameter functions were evaluated for their predictive abilities for major tree species of southwest Oregon. The equations included tree diameter alone, or diameter plus alternative measures of stand density and relative position. Two of the base equations were asymptotic functions, and two were exponential functional forms. The inclusion of...

QCD evolution of the Sivers function

NASA Astrophysics Data System (ADS)

Aybat, S. M.; Collins, J. C.; Qiu, J. W.; Rogers, T. C.

2012-02-01

We extend the Collins-Soper-Sterman (CSS) formalism to apply it to the spin dependence governed by the Sivers function. We use it to give a correct numerical QCD evolution of existing fixed-scale fits of the Sivers function. With the aid of approximations useful for the nonperturbative region, we present the results as parametrizations of a Gaussian form in transverse-momentum space, rather than in the Fourier conjugate transverse coordinate space normally used in the CSS formalism. They are specifically valid at small transverse momentum. Since evolution has been applied, our results can be used to make predictions for Drell-Yan and semi-inclusive deep inelastic scattering at energies different from those where the original fits were made. Our evolved functions are of a form that they can be used in the same parton-model factorization formulas as used in the original fits, but now with a predicted scale dependence in the fit parameters. We also present a method by which our evolved functions can be corrected to allow for twist-3 contributions at large parton transverse momentum.

A study of consumers' perceptions and prediction of consumption patterns for generic health functional foods

PubMed Central

Kang, Nam E; Kim, Ju Hyeon; Lee, Yeon Kyoung; Lee, Hye Young

2011-01-01

The Korea Food and Drug Administration (KFDA) revised the Health Functional Food Act in 2008 and extended the form of health functional foods to general food types. Therefore, this study was performed to investigate consumers' perceptions of the expanded form of health functional food and to predict consumption patterns. For this study, 1,006 male and female adults aged 19 years and older were selected nationwide by multi-stage stratified random sampling and were surveyed in 1:1 interviews. The questionnaire survey was conducted by Korea Gallup. The subjects consisted of 497 (49.4%) males and 509 (50.6%) females. About 57.9% of the subjects recognized the KFDA's permission procedures for health functional foods. Regarding the health functional foods that the subjects had consumed, red ginseng products were the highest (45.3%), followed by nutritional supplements (34.9%), ginseng products (27.9%), lactobacillus-containing products (21.0%), aloe products (20.3%), and Japanese apricot extract products (18.4%). Opinions on expanding the form of health functional foods to general food types scored 4.7 points on a 7-point scale, showing positive responses. In terms of the effects of medicine-type health functional foods versus generic health functional foods, the highest response was 'same effects if the same ingredients are contained' at a rate of 34.7%. For intake frequency by food type, the response of 'daily consistent intake' was 31.7% for capsules, tablets, and pills, and 21.7% for extracts. For general food types, 'daily consistent intake' was 44.5% for rice and 22.8% for beverages, which were higher rates than those for medicine types. From the above results, consumers had positive opinions of the expansion of health functional foods to generic forms but are not expected to maintain accurate intake frequencies or amounts. Thus, continuous promotion and education are needed for proper intake of generic health functional foods. PMID:21994526

Predicting the development of interrogative forms and functions in early years: a corpus-based study of Mandarin-speaking young children.

PubMed

Li, Hui; Jing, Mengguo; Wong, Eileen Chin Mei

2017-01-01

This study examined the development of and possible predictors of interrogative forms and functions in early childhood Mandarin. All the interrogatives drawn from the Early Child Mandarin Corpus (168 children 2;6, 3;6, 4;6, and 5;6) were analyzed. The main results indicated that (i) there were significant age effects in interrogative forms and functions, with the periods between the ages of 3;6 and 4;6 and between the ages of 2;6 and 3;6 being critical in the early acquisition of interrogative forms and functions, respectively; (ii) the form-function preference was verified, with wh-questions being primarily used to seek information (RfI), and intonation/echo and rhetorical questions being used to request action (RfA); (iii) more than half (59·5%) of the Mandarin interrogatives were used for RfI, whereas only 38·9% of them were used for RfA; and (iv) age, TV viewing time, and parent-child conversation time were the significant predictors of interrogative development.

Comparing models for IMF variation across cosmological time in Milky Way-like galaxies

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Hopkins, Philip F.; Ma, Xiangcheng

2017-12-01

One of the key observations regarding the stellar initial mass function (IMF) is its near-universality in the Milky Way (MW), which provides a powerful way to constrain different star formation models that predict the IMF. However, those models are almost universally 'cloud-scale' or smaller - they take as input or simulate single molecular clouds (GMCs), clumps or cores, and predict the resulting IMF as a function of the cloud properties. Without a model for the progenitor properties of all clouds that formed the stars at different locations in the MW (including ancient stellar populations formed in high redshift, likely gas-rich dwarf progenitor galaxies that looked little like the Galaxy today), the predictions cannot be fully explored nor safely applied to 'live' cosmological calculations of the IMF in different galaxies at different cosmological times. We therefore combine a suite of high-resolution cosmological simulations (from the Feedback In Realistic Environments project), which form MW-like galaxies with reasonable star formation properties and explicitly resolve massive GMCs, with various proposed cloud-scale IMF models. We apply the models independently to every star particle formed in the simulations to synthesize the predicted IMF in the present-day galaxy. We explore models where the IMF depends on Jeans mass, sonic or 'turbulent Bonnor-Ebert' mass, fragmentation with a polytropic equation of state, or where it is self-regulated by protostellar feedback. We show that all of these models, except the feedback-regulated ones, predict far more variation (∼0.6-1 dex 1σ scatter in the IMF turnover mass) in the simulations than is observed in the MW.

Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM

PubMed Central

Petkovic, Sonja; Badelt, Stefan; Flamm, Christoph; Delcea, Mihaela

2015-01-01

Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions. PMID:25999318

Self-regulation: from goal orientation to job performance.

PubMed

Porath, Christine L; Bateman, Thomas S

2006-01-01

The authors investigated the effects on job performance of 3 forms of goal orientation and 4 self-regulation (SR) tactics. In a longitudinal field study with salespeople, learning and performance-prove goal orientation predicted subsequent sales performance, whereas performance-avoid goal orientation negatively predicted sales performance. The SR tactics functioned as mediating variables between learning and performance-prove goal orientations and performance. Social competence and proactive behavior directly and positively predicted sales performance, and emotional control negatively predicted performance. (c) 2006 APA, all rights reserved.

The incremental value of self-reported mental health measures in predicting functional outcomes of veterans.

PubMed

Eisen, Susan V; Bottonari, Kathryn A; Glickman, Mark E; Spiro, Avron; Schultz, Mark R; Herz, Lawrence; Rosenheck, Robert; Rofman, Ethan S

2011-04-01

Research on patient-centered care supports use of patient/consumer self-report measures in monitoring health outcomes. This study examined the incremental value of self-report mental health measures relative to a clinician-rated measure in predicting functional outcomes among mental health service recipients. Participants (n = 446) completed the Behavior and Symptom Identification Scale, the Brief Symptom Inventory, and the Veterans/Rand Short Form-36 at enrollment in the study (T1) and 3 months later (T2). Global Assessment of Functioning (GAF) ratings, mental health service utilization, and psychiatric diagnoses were obtained from administrative data files. Controlling for demographic and clinical variables, results indicated that improvement based on the self-report measures significantly predicted one or more functional outcomes (i.e., decreased likelihood of post-enrollment psychiatric hospitalization and increased likelihood of paid employment), above and beyond the predictive value of the GAF. Inclusion of self-report measures may be a useful addition to performance measurement efforts.

Properties of the Bayesian Knowledge Tracing Model

ERIC Educational Resources Information Center

van de Sande, Brett

2013-01-01

Bayesian Knowledge Tracing is used very widely to model student learning. It comes in two different forms: The first form is the Bayesian Knowledge Tracing "hidden Markov model" which predicts the probability of correct application of a skill as a function of the number of previous opportunities to apply that skill and the model…

Form factors and differential branching ratio of B →K μ+μ- in AdS/QCD

NASA Astrophysics Data System (ADS)

Momeni, S.; Khosravi, R.

2018-03-01

The holographic distribution amplitudes (DAs) for the K pseudoscalar meson are derived. For this aim, the light-front wave function (LFWF) of the K meson is extracted within the framework of the anti-de Sitter/quantum chromodynamics (AdS/QCD) correspondence. We consider a momentum-dependent (dynamical) helicity wave function that contains the dynamical spin effects. We use the LFWF to predict the radius and the electromagnetic form factor of the kaon and compare them with the experimental values. Then, the holographic twist-2 DA of K meson ϕK(α ,μ ) is investigated and compared with the result of the light-cone sum rules (LCSR). The transition form factors of the semileptonic B →K ℓ+ℓ- decays are derived from the holographic DAs of the kaon. With the help of these form factors, the differential branching ratio of the B →K μ+μ- on q2 is plotted. A comparison is made between our prediction in AdS/QCD and the results obtained from two models including the LCSR and the lattice QCD as well as the experimental values.

Parallel computational and experimental studies of the morphological modification of calcium carbonate by cobalt

NASA Astrophysics Data System (ADS)

Braybrook, A. L.; Heywood, B. R.; Jackson, R. A.; Pitt, K.

2002-08-01

Crystal growth can be controlled by the incorporation of dopant ions into the lattice and yet the question of how such substituents affect the morphology has not been addressed. This paper describes the forms of calcite (CaCO 3) which arise when the growth assay is doped with cobalt. Distinct and specific morphological changes are observed; the calcite crystals adopt a morphology which is dominated by the {01.1} family of faces. These experimental studies paralleled the development of computational methods for the analysis of crystal habit as a function of dopant concentration. In this case, the predicted defect morphology also argued for the dominance of the (01.1) face in the growth form. The appearance of this face was related to the preferential segregation of the dopant ions to the crystal surface. This study confirms the evolution of a robust computational model for the analysis of calcite growth forms under a range of environmental conditions and presages the use of such tools for the predictive development of crystal morphologies in those applications where chemico-physical functionality is linked closely to a specific crystallographic form.

Unfolding the laws of star formation: the density distribution of molecular clouds.

PubMed

Kainulainen, Jouni; Federrath, Christoph; Henning, Thomas

2014-04-11

The formation of stars shapes the structure and evolution of entire galaxies. The rate and efficiency of this process are affected substantially by the density structure of the individual molecular clouds in which stars form. The most fundamental measure of this structure is the probability density function of volume densities (ρ-PDF), which determines the star formation rates predicted with analytical models. This function has remained unconstrained by observations. We have developed an approach to quantify ρ-PDFs and establish their relation to star formation. The ρ-PDFs instigate a density threshold of star formation and allow us to quantify the star formation efficiency above it. The ρ-PDFs provide new constraints for star formation theories and correctly predict several key properties of the star-forming interstellar medium.

Mapping the current–current correlation function near a quantum critical point

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

Prodan, Emil, E-mail: prodan@yu.edu; Bellissard, Jean

2016-05-15

The current–current correlation function is a useful concept in the theory of electron transport in homogeneous solids. The finite-temperature conductivity tensor as well as Anderson’s localization length can be computed entirely from this correlation function. Based on the critical behavior of these two physical quantities near the plateau–insulator or plateau–plateau transitions in the integer quantum Hall effect, we derive an asymptotic formula for the current–current correlation function, which enables us to make several theoretical predictions about its generic behavior. For the disordered Hofstadter model, we employ numerical simulations to map the current–current correlation function, obtain its asymptotic form near amore » critical point and confirm the theoretical predictions.« less

Empirical calibration of the near-infrared Ca II triplet - III. Fitting functions

NASA Astrophysics Data System (ADS)

Cenarro, A. J.; Gorgas, J.; Cardiel, N.; Vazdekis, A.; Peletier, R. F.

2002-02-01

Using a near-infrared stellar library of 706 stars with a wide coverage of atmospheric parameters, we study the behaviour of the CaII triplet strength in terms of effective temperature, surface gravity and metallicity. Empirical fitting functions for recently defined line-strength indices, namely CaT*, CaT and PaT, are provided. These functions can be easily implemented into stellar population models to provide accurate predictions for integrated CaII strengths. We also present a thorough study of the various error sources and their relation to the residuals of the derived fitting functions. Finally, the derived functional forms and the behaviour of the predicted CaII are compared with those of previous works in the field.

Isotope and Chemical Methods in Support of the U.S. Geological Survey Science Strategy, 2003-2008

USGS Publications Warehouse

Rye, R.O.; Johnson, C.A.; Landis, G.P.; Hofstra, A.H.; Emsbo, P.; Stricker, C.A.; Hunt, A.G.; Rusk, B.G.

2008-01-01

Principal functions of the Mineral Resources Program are providing information to decision-makers related to mineral deposits on federal lands and predicting the environmental consequences of the mining or natural weathering of those deposits. Performing these functions requires that predictions be made of the likelihood of undiscovered deposits. The predictions are based on geologic and geoenvironmental models that are constructed for the various types of mineral deposits from detailed descriptions of actual deposits and detailed understanding of the processes that formed them. Over the past three decades the understanding of ore-forming processes has benefitted greatly from the integration of laboratory-based geochemical tools with field observations and other data sources. Under the aegis of the Evolution of Ore Deposits and Technology Transfer Project (EODTTP), a five-year effort that terminated in 2008, the Mineral Resources Program provided state-of-the-art analytical capabilities to support applications of several related geochemical tools.

Predicting functional ability in mild cognitive impairment with the Dementia Rating Scale-2.

PubMed

Greenaway, Melanie C; Duncan, Noah L; Hanna, Sherrie; Smith, Glenn E

2012-06-01

We examined the utility of cognitive evaluation to predict instrumental activities of daily living (IADLs) and decisional ability in Mild Cognitive Impairment (MCI). Sixty-seven individuals with single-domain amnestic MCI were administered the Dementia Rating Scale-2 (DRS-2) as well as the Everyday Cognition assessment form to assess functional ability. The DRS-2 Total Scores and Initiation/Perseveration and Memory subscales were found to be predictive of IADLs, with Total Scores accounting for 19% of the variance in IADL performance on average. In addition, the DRS-2 Initiation/Perseveration and Total Scores were predictive of ability to understand information, and the DRS-2 Conceptualization helped predict ability to communicate with others, both key variables in decision-making ability. These findings suggest that performance on the DRS-2, and specific subscales related to executive function and memory, is significantly related to IADLs in individuals with MCI. These cognitive measures are also associated with decision-making-related abilities in MCI.

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems.

PubMed

Xu, Xin; Zhang, Qingsong; Muller, Richard P; Goddard, William A

2005-01-01

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with R(e) and D(e) within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions. (c) 2005 American Institute of Physics.

Predicting Student Success from the "LASSI for Learning Online" (LLO)

ERIC Educational Resources Information Center

Carson, Andrew D.

2011-01-01

This study tested the degree to which subscales of the "LASSI for Learning Online" (LLO) (Weinstein & Palmer, 2006), a measure of learning strategies and study skills, predict student success in the form of passing grades, using a combination of large training (N = 4,409) and cross-validation (N = 3,203) samples. Discriminant function analysis…

Functional annotation from the genome sequence of the giant panda.

PubMed

Huo, Tong; Zhang, Yinjie; Lin, Jianping

2012-08-01

The giant panda is one of the most critically endangered species due to the fragmentation and loss of its habitat. Studying the functions of proteins in this animal, especially specific trait-related proteins, is therefore necessary to protect the species. In this work, the functions of these proteins were investigated using the genome sequence of the giant panda. Data on 21,001 proteins and their functions were stored in the Giant Panda Protein Database, in which the proteins were divided into two groups: 20,179 proteins whose functions can be predicted by GeneScan formed the known-function group, whereas 822 proteins whose functions cannot be predicted by GeneScan comprised the unknown-function group. For the known-function group, we further classified the proteins by molecular function, biological process, cellular component, and tissue specificity. For the unknown-function group, we developed a strategy in which the proteins were filtered by cross-Blast to identify panda-specific proteins under the assumption that proteins related to the panda-specific traits in the unknown-function group exist. After this filtering procedure, we identified 32 proteins (2 of which are membrane proteins) specific to the giant panda genome as compared against the dog and horse genomes. Based on their amino acid sequences, these 32 proteins were further analyzed by functional classification using SVM-Prot, motif prediction using MyHits, and interacting protein prediction using the Database of Interacting Proteins. Nineteen proteins were predicted to be zinc-binding proteins, thus affecting the activities of nucleic acids. The 32 panda-specific proteins will be further investigated by structural and functional analysis.

Automorphic Forms and Mock Modular Forms in String Theory

NASA Astrophysics Data System (ADS)

Nazaroglu, Caner

We study a variety of modular invariant objects in relation to string theory. First, we focus on Jacobi forms over generic rank lattices and Siegel forms that appear in N = 2, D = 4 compactifications of heterotic string with Wilson lines. Constraints from low energy spectrum and modularity are employed to deduce the relevant supersymmetric partition functions entirely. This procedure is applied on models that lead to Jacobi forms of index 3, 4, 5 as well as Jacobi forms over root lattices A2 and A3. These computations are then checked against an explicit orbifold model which can be Higgsed to the models under question. Models with a single Wilson line are then studied in detail with their relation to paramodular group Gammam as T-duality group made explicit. These results on the heterotic string side are then turned into predictions for geometric invariants using TypeII - Heterotic duality. Secondly, we study theta functions for indenite signature lattices of generic signature. Building on results in literature for signature (n-1,1) and (n-2,2) lattices, we work out the properties of generalized error functions which we call r-tuple error functions. We then use these functions to build such indenite theta functions and describe their modular completions.

Investigating the effects of the fixed and varying dispersion parameters of Poisson-gamma models on empirical Bayes estimates.

PubMed

Lord, Dominique; Park, Peter Young-Jin

2008-07-01

Traditionally, transportation safety analysts have used the empirical Bayes (EB) method to improve the estimate of the long-term mean of individual sites; to correct for the regression-to-the-mean (RTM) bias in before-after studies; and to identify hotspots or high risk locations. The EB method combines two different sources of information: (1) the expected number of crashes estimated via crash prediction models, and (2) the observed number of crashes at individual sites. Crash prediction models have traditionally been estimated using a negative binomial (NB) (or Poisson-gamma) modeling framework due to the over-dispersion commonly found in crash data. A weight factor is used to assign the relative influence of each source of information on the EB estimate. This factor is estimated using the mean and variance functions of the NB model. With recent trends that illustrated the dispersion parameter to be dependent upon the covariates of NB models, especially for traffic flow-only models, as well as varying as a function of different time-periods, there is a need to determine how these models may affect EB estimates. The objectives of this study are to examine how commonly used functional forms as well as fixed and time-varying dispersion parameters affect the EB estimates. To accomplish the study objectives, several traffic flow-only crash prediction models were estimated using a sample of rural three-legged intersections located in California. Two types of aggregated and time-specific models were produced: (1) the traditional NB model with a fixed dispersion parameter and (2) the generalized NB model (GNB) with a time-varying dispersion parameter, which is also dependent upon the covariates of the model. Several statistical methods were used to compare the fitting performance of the various functional forms. The results of the study show that the selection of the functional form of NB models has an important effect on EB estimates both in terms of estimated values, weight factors, and dispersion parameters. Time-specific models with a varying dispersion parameter provide better statistical performance in terms of goodness-of-fit (GOF) than aggregated multi-year models. Furthermore, the identification of hazardous sites, using the EB method, can be significantly affected when a GNB model with a time-varying dispersion parameter is used. Thus, erroneously selecting a functional form may lead to select the wrong sites for treatment. The study concludes that transportation safety analysts should not automatically use an existing functional form for modeling motor vehicle crashes without conducting rigorous analyses to estimate the most appropriate functional form linking crashes with traffic flow.

Grandparenting predicts late-life cognition: Results from the Women's Healthy Ageing Project.

PubMed

Burn, Katherine; Szoeke, Cassandra

2015-06-01

Social engagement provides dynamic stimulation for older individuals that influences cognition. Grandparenting is an increasingly popular form of childcare that provides social activity for older adults. To investigate the relationship between grandparenting, as a form of social engagement, and cognitive function in adults aged over 65, a decade after our previous work. Participants were 224 Australian women (mean age=70) from the longitudinal prospective Women's Healthy Ageing Project (WHAP). Cognitive function was assessed using a neuropsychological battery consisting of previously validated measures including the California Verbal Learning Test, Digit Span task, and Controlled Oral Word Association Test. Individual test scores were combined using factor analysis into executive function and episodic memory scores. Grandmothers minding grandchildren had higher executive function than those who were not minding grandchildren or who did not have grandchildren (p<0.05). Minding grandchildren for one day per week predicted better executive function performance than more frequent grandparenting (p<0.05), consistent with previous findings. While grandparenting is associated with better executive function overall, highly frequent grandparenting is associated with lower executive function, which may be due to demands. Social engagement comprises various aspects which need to be taken into consideration when studying cognition. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Non-B-Form DNA Is Enriched at Centromeres

PubMed Central

Henikoff, Steven

2018-01-01

Abstract Animal and plant centromeres are embedded in repetitive “satellite” DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA-binding proteins with DNA-bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B-form DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically nonessential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. This may resolve the CENP-B paradox and provide a general basis for centromere specification. PMID:29365169

Discrete coding of stimulus value, reward expectation, and reward prediction error in the dorsal striatum.

PubMed

Oyama, Kei; Tateyama, Yukina; Hernádi, István; Tobler, Philippe N; Iijima, Toshio; Tsutsui, Ken-Ichiro

2015-11-01

To investigate how the striatum integrates sensory information with reward information for behavioral guidance, we recorded single-unit activity in the dorsal striatum of head-fixed rats participating in a probabilistic Pavlovian conditioning task with auditory conditioned stimuli (CSs) in which reward probability was fixed for each CS but parametrically varied across CSs. We found that the activity of many neurons was linearly correlated with the reward probability indicated by the CSs. The recorded neurons could be classified according to their firing patterns into functional subtypes coding reward probability in different forms such as stimulus value, reward expectation, and reward prediction error. These results suggest that several functional subgroups of dorsal striatal neurons represent different kinds of information formed through extensive prior exposure to CS-reward contingencies. Copyright © 2015 the American Physiological Society.

Discrete coding of stimulus value, reward expectation, and reward prediction error in the dorsal striatum

PubMed Central

Oyama, Kei; Tateyama, Yukina; Hernádi, István; Tobler, Philippe N.; Iijima, Toshio

2015-01-01

To investigate how the striatum integrates sensory information with reward information for behavioral guidance, we recorded single-unit activity in the dorsal striatum of head-fixed rats participating in a probabilistic Pavlovian conditioning task with auditory conditioned stimuli (CSs) in which reward probability was fixed for each CS but parametrically varied across CSs. We found that the activity of many neurons was linearly correlated with the reward probability indicated by the CSs. The recorded neurons could be classified according to their firing patterns into functional subtypes coding reward probability in different forms such as stimulus value, reward expectation, and reward prediction error. These results suggest that several functional subgroups of dorsal striatal neurons represent different kinds of information formed through extensive prior exposure to CS-reward contingencies. PMID:26378201

Fitting the low-frequency Raman spectra to boson peak models: glycerol, triacetin and polystyrene

NASA Astrophysics Data System (ADS)

Kirillov, S. A.; Perova, T. S.; Faurskov Nielsen, O.; Praestgaard, E.; Rasmussen, U.; Kolomiyets, T. M.; Voyiatzis, G. A.; Anastasiadis, S. H.

1999-04-01

A computational approach was elaborated to explicitly account for the Rayleigh line wing, the Boson peak and vibrational contributions to the low-frequency Raman spectra of amorphous solids and viscous liquids. It was shown that the low-frequency Raman spectra of glycerol and polystyrene consist of the Rayleigh contribution of Lorentzian form and the Boson peak which profile follows the predictions of the theory by Martin and Brenig in the version by Malinovsky and Sokolov. In the case of triacetin, the Boson peaks decay faster in their high-frequency side than the above theory predicts. Their form can be successfully modeled with a newly introduced empirical function intermediate between the Martin-Brenig and Malinovsky-Sokolov predictions.

Connectivity precedes function in the development of the visual word form area.

PubMed

Saygin, Zeynep M; Osher, David E; Norton, Elizabeth S; Youssoufian, Deanna A; Beach, Sara D; Feather, Jenelle; Gaab, Nadine; Gabrieli, John D E; Kanwisher, Nancy

2016-09-01

What determines the cortical location at which a given functionally specific region will arise in development? We tested the hypothesis that functionally specific regions develop in their characteristic locations because of pre-existing differences in the extrinsic connectivity of that region to the rest of the brain. We exploited the visual word form area (VWFA) as a test case, scanning children with diffusion and functional imaging at age 5, before they learned to read, and at age 8, after they learned to read. We found the VWFA developed functionally in this interval and that its location in a particular child at age 8 could be predicted from that child's connectivity fingerprints (but not functional responses) at age 5. These results suggest that early connectivity instructs the functional development of the VWFA, possibly reflecting a general mechanism of cortical development.

How Prediction Errors Shape Perception, Attention, and Motivation

PubMed Central

den Ouden, Hanneke E. M.; Kok, Peter; de Lange, Floris P.

2012-01-01

Prediction errors (PE) are a central notion in theoretical models of reinforcement learning, perceptual inference, decision-making and cognition, and prediction error signals have been reported across a wide range of brain regions and experimental paradigms. Here, we will make an attempt to see the forest for the trees and consider the commonalities and differences of reported PE signals in light of recent suggestions that the computation of PE forms a fundamental mode of brain function. We discuss where different types of PE are encoded, how they are generated, and the different functional roles they fulfill. We suggest that while encoding of PE is a common computation across brain regions, the content and function of these error signals can be very different and are determined by the afferent and efferent connections within the neural circuitry in which they arise. PMID:23248610

Compact Assumption Applied to the Monopole Term of Farassat's Formulations

NASA Technical Reports Server (NTRS)

Lopes, Leonard V.

2015-01-01

Farassat's formulations provide an acoustic prediction at an observer location provided a source surface, including motion and flow conditions. This paper presents compact forms for the monopole term of several of Farassat's formulations. When the physical surface is elongated, such as the case of a high aspect ratio rotorcraft blade, compact forms can be derived which are shown to be a function of the blade cross sectional area by reducing the computation from a surface integral to a line integral. The compact forms of all formulations are applied to two example cases: a short span wing with constant airfoil cross section moving at three forward flight Mach numbers and a rotor at two advance ratios. Acoustic pressure time histories and power spectral densities of monopole noise predicted from the compact forms of all the formulations at several observer positions are shown to compare very closely to the predictions from their non-compact counterparts. A study on the influence of rotorcraft blade shape on the high frequency portion of the power spectral density shows that there is a direct correlation between the aspect ratio of the airfoil and the error incurred by using the compact form. Finally, a prediction of pressure gradient from the non-compact and compact forms of the thickness term of Formulation G1A shows that using the compact forms results in a 99.6% improvement in computation time, which will be critical when noise is incorporated into a design environment.

Associations between Macrophyte Life Forms and Environmental and Morphometric Factors in a Large Sub-tropical Floodplain

PubMed Central

Schneider, Berenice; Cunha, Eduardo R.; Marchese, Mercedes; Thomaz, Sidinei M.

2018-01-01

Macrophyte assemblages are composed of species with different life forms and various ecological functions. Our aim was to investigate the potential environmental determinants of changes in the biomass of individual life forms and of the composition of the macrophyte assemblage in terms of life forms diversity. We sampled 23 waterbodies at low and high water levels in the Middle Paraná River floodplain. Macrophyte biomass samples were collected and classified in terms of life forms. We performed a redundancy analysis using the biomass of the various life forms to assess the importance of environmental variables to the composition of macrophyte life forms. Linear regressions were applied to investigate the environmental determinants of the biomasses of individual life forms. The degree of connectivity and the combination of depth, hydrology and nitrate were the main determinants of the composition in terms of life forms. The biomass of each individual life form was explained by different combinations of environmental variables, but the connectivity was the most important one. Our study shows that groups of species with similar life forms respond to environmental factors in particular ways, which might alter the biomass composition of life forms. Given that the ecosystem functioning depends on the functional characteristics of local communities, our findings about the relation between environmental changes and the community composition in terms of life forms (or functional composition) can be a helpful tool for predicting changes on ecosystem processes (such as nutrient cycling) against possible future scenarios. PMID:29515608

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

Hill functions for stochastic gene regulatory networks from master equations with split nodes and time-scale separation

NASA Astrophysics Data System (ADS)

Lipan, Ovidiu; Ferwerda, Cameron

2018-02-01

The deterministic Hill function depends only on the average values of molecule numbers. To account for the fluctuations in the molecule numbers, the argument of the Hill function needs to contain the means, the standard deviations, and the correlations. Here we present a method that allows for stochastic Hill functions to be constructed from the dynamical evolution of stochastic biocircuits with specific topologies. These stochastic Hill functions are presented in a closed analytical form so that they can be easily incorporated in models for large genetic regulatory networks. Using a repressive biocircuit as an example, we show by Monte Carlo simulations that the traditional deterministic Hill function inaccurately predicts time of repression by an order of two magnitudes. However, the stochastic Hill function was able to capture the fluctuations and thus accurately predicted the time of repression.

Balance of baryon number in the quark coalescence model

NASA Astrophysics Data System (ADS)

Bialas, A.; Rafelski, J.

2006-02-01

The charge and baryon balance functions are studied in the coalescence hadronization mechanism of quark-gluon plasma. Assuming that in the plasma phase the qqbar pairs form uncorrelated clusters whose decay is also uncorrelated, one can understand the observed small width of the charge balance function in the Gaussian approximation. The coalescence model predicts even smaller width of the baryon-antibaryon balance function: σBBbar /σ+ - =√{ 2 / 3 }.

Research on Al-alloy sheet forming formability during warm/hot sheet hydroforming based on elliptical warm bulging test

NASA Astrophysics Data System (ADS)

Cai, Gaoshen; Wu, Chuanyu; Gao, Zepu; Lang, Lihui; Alexandrov, Sergei

2018-05-01

An elliptical warm/hot sheet bulging test under different temperatures and pressure rates was carried out to predict Al-alloy sheet forming limit during warm/hot sheet hydroforming. Using relevant formulas of ultimate strain to calculate and dispose experimental data, forming limit curves (FLCS) in tension-tension state of strain (TTSS) area are obtained. Combining with the basic experimental data obtained by uniaxial tensile test under the equivalent condition with bulging test, complete forming limit diagrams (FLDS) of Al-alloy are established. Using a quadratic polynomial curve fitting method, material constants of fitting function are calculated and a prediction model equation for sheet metal forming limit is established, by which the corresponding forming limit curves in TTSS area can be obtained. The bulging test and fitting results indicated that the sheet metal FLCS obtained were very accurate. Also, the model equation can be used to instruct warm/hot sheet bulging test.

Boundary-Layer Receptivity and Integrated Transition Prediction

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Choudhari, Meelan

2005-01-01

The adjoint parabold stability equations (PSE) formulation is used to calculate the boundary layer receptivity to localized surface roughness and suction for compressible boundary layers. Receptivity efficiency functions predicted by the adjoint PSE approach agree well with results based on other nonparallel methods including linearized Navier-Stokes equations for both Tollmien-Schlichting waves and crossflow instability in swept wing boundary layers. The receptivity efficiency function can be regarded as the Green's function to the disturbance amplitude evolution in a nonparallel (growing) boundary layer. Given the Fourier transformed geometry factor distribution along the chordwise direction, the linear disturbance amplitude evolution for a finite size, distributed nonuniformity can be computed by evaluating the integral effects of both disturbance generation and linear amplification. The synergistic approach via the linear adjoint PSE for receptivity and nonlinear PSE for disturbance evolution downstream of the leading edge forms the basis for an integrated transition prediction tool. Eventually, such physics-based, high fidelity prediction methods could simulate the transition process from the disturbance generation through the nonlinear breakdown in a holistic manner.

Investigating the Energetic Ordering of Stable and Metastable TiO 2 Polymorphs Using DFT+ U and Hybrid Functionals

DOE PAGES

Curnan, Matthew T.; Kitchin, John R.

2015-08-12

Prediction of transition metal oxide BO 2 (B = Ti, V, etc.) polymorph energetic properties is critical to tunable material design and identifying thermodynamically accessible structures. Determining procedures capable of synthesizing particular polymorphs minimally requires prior knowledge of their relative energetic favorability. Information concerning TiO 2 polymorph relative energetic favorability has been ascertained from experimental research. In this study, the consistency of first-principles predictions and experimental results involving the relative energetic ordering of stable (rutile), metastable (anatase and brookite), and unstable (columbite) TiO 2 polymorphs is assessed via density functional theory (DFT). Considering the issues involving electron–electron interaction and chargemore » delocalization in TiO 2 calculations, relative energetic ordering predictions are evaluated over trends varying Ti Hubbard U 3d or exact exchange fraction parameter values. Energetic trends formed from varying U 3d predict experimentally consistent energetic ordering over U 3d intervals when using GGA-based functionals, regardless of pseudopotential selection. Given pertinent linear response calculated Hubbard U values, these results enable TiO 2 polymorph energetic ordering prediction. Here, the hybrid functional calculations involving rutile–anatase relative energetics, though demonstrating experimentally consistent energetic ordering over exact exchange fraction ranges, are not accompanied by predicted fractions, for a first-principles methodology capable of calculating exact exchange fractions precisely predicting TiO 2 polymorph energetic ordering is not available.« less

Predicting Keto-Enol Equilibrium from Combining UV/Visible Absorption Spectroscopy with Quantum Chemical Calculations of Vibronic Structures for Many Excited States. A Case Study on Salicylideneanilines.

PubMed

Zutterman, Freddy; Louant, Orian; Mercier, Gabriel; Leyssens, Tom; Champagne, Benoît

2018-06-21

Salicylideneanilines are characterized by a tautomer equilibrium, between an enol and a keto form of different colors, at the origin of their remarkable thermochromic, solvatochromic, and photochromic properties. The enol form is usually the most stable but appropriate choice of substituents and conditions (solvent, crystal, host compound) can displace the equilibrium toward the keto form so that there is a need for fast prediction of the keto:enol abundance ratio. Here we demonstrate the reliability of a combined theoretical-experimental method, based on comparing simulated and measured UV/visible absorption spectra, to determine this keto/enol ratio. The calculations of the excitation energies, oscillator strengths, and vibronic structures of both enol and keto forms are performed for all excited states absorbing in the relevant (visible and near-UV) wavelength range at the time-dependent density functional theory level by accounting for solvent effects using the polarizable continuum model. This approach is illustrated for two salicylideneaniline derivatives, which are present, in solution, under the form of keto-enol mixtures. The results are compared to those of chemometric analysis as well as ab initio predictions of the reaction free enthalpies.

Physically-based model of soil hydraulic properties accounting for variable contact angle and its effect on hysteresis

NASA Astrophysics Data System (ADS)

Diamantopoulos, Efstathios; Durner, Wolfgang

2013-09-01

The description of soil water movement in the unsaturated zone requires the knowledge of the soil hydraulic properties, i.e. the water retention and the hydraulic conductivity function. A great amount of parameterizations for this can be found in the literature, the majority of which represent the complex pore space of soils as a bundle of cylindrical capillary tubes of various sizes. The assumption of zero contact angles between water and surface of the grains is also made. However, these assumptions limit the predictive capabilities of these models, leading often to errors in the prediction of water dynamics in soils. We present a pore-scale analysis for equilibrium liquid configuration in angular pores taking pore-scale hysteresis and the effect of contact angle into account. Furthermore, we propose a derivation of the hydraulic conductivity function, again as a function of the contact angle. An additional parameter was added to the conductivity function in order take into account effects which are not included in the analysis. Finally, we upscale our model from the pore to the sample scale by assuming a gamma statistical distribution of the pore sizes. Closed-form expressions are derived for both water retention and conductivity functions. The new model was tested against experimental data from multistep inflow/outflow (MSI/MSO) experiments for a sandy material. They were conducted using ethanol and water as the wetting liquid. Ethanol was assumed to form a zero contact angle with the soil grains. By keeping constant the parameters fitted from the ethanol MSO experiment we could predict the ethanol MSI dynamics based on our theory. Furthermore, by keeping constant the pore size distribution parameters from the ethanol experiments we could also predict very well the water dynamics for the MSO experiment. Lastly, we could predict the imbibition dynamics for the water MSI experiment by introducing a finite value of the contact angle. Most importantly, the predictions for both ethanol and water MSI/MSO dynamics were made by assuming a unique pore-size distribution.

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

PubMed

Wiebe, Nicholas J P; Meyer, Irmtraud M

2010-06-24

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment.

Linear dispersion properties of ring velocity distribution functions

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

Vandas, Marek, E-mail: marek.vandas@asu.cas.cz; Hellinger, Petr; Institute of Atmospheric Physics, AS CR, Bocni II/1401, CZ-14100 Prague

2015-06-15

Linear properties of ring velocity distribution functions are investigated. The dispersion tensor in a form similar to the case of a Maxwellian distribution function, but for a general distribution function separable in velocities, is presented. Analytical forms of the dispersion tensor are derived for two cases of ring velocity distribution functions: one obtained from physical arguments and one for the usual, ad hoc ring distribution. The analytical expressions involve generalized hypergeometric, Kampé de Fériet functions of two arguments. For a set of plasma parameters, the two ring distribution functions are compared. At the parallel propagation with respect to the ambientmore » magnetic field, the two ring distributions give the same results identical to the corresponding bi-Maxwellian distribution. At oblique propagation, the two ring distributions give similar results only for strong instabilities, whereas for weak growth rates their predictions are significantly different; the two ring distributions have different marginal stability conditions.« less

A Focus on Reward Prediction and the Lateral Habenula: Functional Alterations and the Behavioral Outcomes Induced by Drugs of Abuse.

PubMed

Graziane, Nicholas M; Neumann, Peter A; Dong, Yan

2018-01-01

The lateral habenula (LHb) regulates reward learning and controls the updating of reward-related information. Drugs of abuse have the capacity to hijack the cellular and neurocircuit mechanisms mediating reward learning, forming non-adaptable, compulsive behaviors geared toward obtaining illicit substances. Here, we discuss current findings demonstrating how drugs of abuse alter intrinsic and synaptic LHb neuronal function. Additionally, we discuss evidence for how drug-induced LHb alterations may affect the ability to predict reward, potentially facilitating an addiction-like state. Altogether, we combine ex vivo and in vivo results for an overview of how drugs of abuse alter LHb function and how these functional alterations affect the ability to learn and update behavioral responses to hedonic external stimuli.

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

PubMed Central

Sutphin, George L.; Mahoney, J. Matthew; Sheppard, Keith; Walton, David O.; Korstanje, Ron

2016-01-01

The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species—humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/. PMID:27812085

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

PubMed

Sutphin, George L; Mahoney, J Matthew; Sheppard, Keith; Walton, David O; Korstanje, Ron

2016-11-01

The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

Predicting the practice effects on the blood oxygenation level-dependent (BOLD) function of fMRI in a symbolic manipulation task

NASA Astrophysics Data System (ADS)

Qin, Yulin; Sohn, Myeong-Ho; Anderson, John R.; Stenger, V. Andrew; Fissell, Kate; Goode, Adam; Carter, Cameron S.

2003-04-01

Based on adaptive control of thought-rational (ACT-R), a cognitive architecture for cognitive modeling, researchers have developed an information-processing model to predict the blood oxygenation level-dependent (BOLD) response of functional MRI in symbol manipulation tasks. As an extension of this research, the current event-related functional MRI study investigates the effect of relatively extensive practice on the activation patterns of related brain regions. The task involved performing transformations on equations in an artificial algebra system. This paper shows that the base-level activation learning in the ACT-R theory can predict the change of the BOLD response in practice in a left prefrontal region reflecting retrieval of information. In contrast, practice has relatively little effect on the form of BOLD response in the parietal region reflecting imagined transformations to the equation or the motor region reflecting manual programming.

Analysis of the J /ψ →π0γ* transition form factor

NASA Astrophysics Data System (ADS)

Kubis, Bastian; Niecknig, Franz

2015-02-01

In view of the first measurement of the branching fraction for J /ψ →π0e+e- by the BESIII collaboration, we analyze what can be learned on the corresponding transition form factor using dispersion theory. We show that light-quark degrees of freedom dominate the spectral function, in particular two-pion intermediate states. Estimating the effects of multipion states as well as charmonium, we arrive at a prediction for the complete form factor that should be scrutinized experimentally in the future.

The mysterious age invariance of the planetary nebula luminosity function bright cut-off

NASA Astrophysics Data System (ADS)

Gesicki, K.; Zijlstra, A. A.; Miller Bertolami, M. M.

2018-05-01

Planetary nebulae mark the end of the active life of 90% of all stars. They trace the transition from a red giant to a degenerate white dwarf. Stellar models1,2 predicted that only stars above approximately twice the solar mass could form a bright nebula. But the ubiquitous presence of bright planetary nebulae in old stellar populations, such as elliptical galaxies, contradicts this: such high-mass stars are not present in old systems. The planetary nebula luminosity function, and especially its bright cut-off, is almost invariant between young spiral galaxies, with high-mass stars, and old elliptical galaxies, with only low-mass stars. Here, we show that new evolutionary tracks of low-mass stars are capable of explaining in a simple manner this decades-old mystery. The agreement between the observed luminosity function and computed stellar evolution validates the latest theoretical modelling. With these models, the planetary nebula luminosity function provides a powerful diagnostic to derive star formation histories of intermediate-age stars. The new models predict that the Sun at the end of its life will also form a planetary nebula, but it will be faint.

The vacuole system is a significant intracellular pathway for longitudinal solute transport in basidiomycete fungi.

PubMed

Darrah, P R; Tlalka, M; Ashford, A; Watkinson, S C; Fricker, M D

2006-07-01

Mycelial fungi have a growth form which is unique among multicellular organisms. The data presented here suggest that they have developed a unique solution to internal solute translocation involving a complex, extended vacuole. In all filamentous fungi examined, this extended vacuole forms an interconnected network, dynamically linked by tubules, which has been hypothesized to act as an internal distribution system. We have tested this hypothesis directly by quantifying solute movement within the organelle by photobleaching a fluorescent vacuolar marker. Predictive simulation models were then used to determine the transport characteristics over extended length scales. This modeling showed that the vacuolar organelle forms a functionally important, bidirectional diffusive transport pathway over distances of millimeters to centimeters. Flux through the pathway is regulated by the dynamic tubular connections involving homotypic fusion and fission. There is also a strongly predicted interaction among vacuolar organization, predicted diffusion transport distances, and the architecture of the branching colony margin.

Application of a stochastic snowmelt model for probabilistic decisionmaking

NASA Technical Reports Server (NTRS)

Mccuen, R. H.

1983-01-01

A stochastic form of the snowmelt runoff model that can be used for probabilistic decision-making was developed. The use of probabilistic streamflow predictions instead of single valued deterministic predictions leads to greater accuracy in decisions. While the accuracy of the output function is important in decisionmaking, it is also important to understand the relative importance of the coefficients. Therefore, a sensitivity analysis was made for each of the coefficients.

Utility functions predict variance and skewness risk preferences in monkeys

PubMed Central

Genest, Wilfried; Stauffer, William R.; Schultz, Wolfram

2016-01-01

Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals’ preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals’ preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys’ choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences. PMID:27402743

Utility functions predict variance and skewness risk preferences in monkeys.

PubMed

Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

2016-07-26

Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals' preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals' preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys' choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences.

Modeling the effects of AADT on predicting multiple-vehicle crashes at urban and suburban signalized intersections.

PubMed

Chen, Chen; Xie, Yuanchang

2016-06-01

Annual Average Daily Traffic (AADT) is often considered as a main covariate for predicting crash frequencies at urban and suburban intersections. A linear functional form is typically assumed for the Safety Performance Function (SPF) to describe the relationship between the natural logarithm of expected crash frequency and covariates derived from AADTs. Such a linearity assumption has been questioned by many researchers. This study applies Generalized Additive Models (GAMs) and Piecewise Linear Negative Binomial (PLNB) regression models to fit intersection crash data. Various covariates derived from minor-and major-approach AADTs are considered. Three different dependent variables are modeled, which are total multiple-vehicle crashes, rear-end crashes, and angle crashes. The modeling results suggest that a nonlinear functional form may be more appropriate. Also, the results show that it is important to take into consideration the joint safety effects of multiple covariates. Additionally, it is found that the ratio of minor to major-approach AADT has a varying impact on intersection safety and deserves further investigations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Form and Function in Human Song.

PubMed

Mehr, Samuel A; Singh, Manvir; York, Hunter; Glowacki, Luke; Krasnow, Max M

2018-02-05

Humans use music for a variety of social functions: we sing to accompany dance, to soothe babies, to heal illness, to communicate love, and so on. Across animal taxa, vocalization forms are shaped by their functions, including in humans. Here, we show that vocal music exhibits recurrent, distinct, and cross-culturally robust form-function relations that are detectable by listeners across the globe. In Experiment 1, internet users (n = 750) in 60 countries listened to brief excerpts of songs, rating each song's function on six dimensions (e.g., "used to soothe a baby"). Excerpts were drawn from a geographically stratified pseudorandom sample of dance songs, lullabies, healing songs, and love songs recorded in 86 mostly small-scale societies, including hunter-gatherers, pastoralists, and subsistence farmers. Experiment 1 and its analysis plan were pre-registered. Despite participants' unfamiliarity with the societies represented, the random sampling of each excerpt, their very short duration (14 s), and the enormous diversity of this music, the ratings demonstrated accurate and cross-culturally reliable inferences about song functions on the basis of song forms alone. In Experiment 2, internet users (n = 1,000) in the United States and India rated three contextual features (e.g., gender of singer) and seven musical features (e.g., melodic complexity) of each excerpt. The songs' contextual features were predictive of Experiment 1 function ratings, but musical features and the songs' actual functions explained unique variance in function ratings. These findings are consistent with the existence of universal links between form and function in vocal music. Copyright © 2017 Elsevier Ltd. All rights reserved.

Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

PubMed

Zeil, Catharina; Widmann, Michael; Fademrecht, Silvia; Vogel, Constantin; Pleiss, Jürgen

2016-05-01

The Lactamase Engineering Database (www.LacED.uni-stuttgart.de) was developed to facilitate the classification and analysis of TEM β-lactamases. The current version contains 474 TEM variants. Two hundred fifty-nine variants form a large scale-free network of highly connected point mutants. The network was divided into three subnetworks which were enriched by single phenotypes: one network with predominantly 2be and two networks with 2br phenotypes. Fifteen positions were found to be highly variable, contributing to the majority of the observed variants. Since it is expected that a considerable fraction of the theoretical sequence space is functional, the currently sequenced 474 variants represent only the tip of the iceberg of functional TEM β-lactamase variants which form a huge natural reservoir of highly interconnected variants. Almost 50% of the variants are part of a quartet. Thus, two single mutations that result in functional enzymes can be combined into a functional protein. Most of these quartets consist of the same phenotype, or the mutations are additive with respect to the phenotype. By predicting quartets from triplets, 3,916 unknown variants were constructed. Eighty-seven variants complement multiple quartets and therefore have a high probability of being functional. The construction of a TEM β-lactamase network and subsequent analyses by clustering and quartet prediction are valuable tools to gain new insights into the viable sequence space of TEM β-lactamases and to predict their phenotype. The highly connected sequence space of TEM β-lactamases is ideally suited to network analysis and demonstrates the strengths of network analysis over tree reconstruction methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparison between splines and fractional polynomials for multivariable model building with continuous covariates: a simulation study with continuous response.

PubMed

Binder, Harald; Sauerbrei, Willi; Royston, Patrick

2013-06-15

In observational studies, many continuous or categorical covariates may be related to an outcome. Various spline-based procedures or the multivariable fractional polynomial (MFP) procedure can be used to identify important variables and functional forms for continuous covariates. This is the main aim of an explanatory model, as opposed to a model only for prediction. The type of analysis often guides the complexity of the final model. Spline-based procedures and MFP have tuning parameters for choosing the required complexity. To compare model selection approaches, we perform a simulation study in the linear regression context based on a data structure intended to reflect realistic biomedical data. We vary the sample size, variance explained and complexity parameters for model selection. We consider 15 variables. A sample size of 200 (1000) and R(2)  = 0.2 (0.8) is the scenario with the smallest (largest) amount of information. For assessing performance, we consider prediction error, correct and incorrect inclusion of covariates, qualitative measures for judging selected functional forms and further novel criteria. From limited information, a suitable explanatory model cannot be obtained. Prediction performance from all types of models is similar. With a medium amount of information, MFP performs better than splines on several criteria. MFP better recovers simpler functions, whereas splines better recover more complex functions. For a large amount of information and no local structure, MFP and the spline procedures often select similar explanatory models. Copyright © 2012 John Wiley & Sons, Ltd.

Entropy Filtered Density Function for Large Eddy Simulation of Turbulent Reacting Flows

NASA Astrophysics Data System (ADS)

Safari, Mehdi

Analysis of local entropy generation is an effective means to optimize the performance of energy and combustion systems by minimizing the irreversibilities in transport processes. Large eddy simulation (LES) is employed to describe entropy transport and generation in turbulent reacting flows. The entropy transport equation in LES contains several unclosed terms. These are the subgrid scale (SGS) entropy flux and entropy generation caused by irreversible processes: heat conduction, mass diffusion, chemical reaction and viscous dissipation. The SGS effects are taken into account using a novel methodology based on the filtered density function (FDF). This methodology, entitled entropy FDF (En-FDF), is developed and utilized in the form of joint entropy-velocity-scalar-turbulent frequency FDF and the marginal scalar-entropy FDF, both of which contain the chemical reaction effects in a closed form. The former constitutes the most comprehensive form of the En-FDF and provides closure for all the unclosed filtered moments. This methodology is applied for LES of a turbulent shear layer involving transport of passive scalars. Predictions show favor- able agreements with the data generated by direct numerical simulation (DNS) of the same layer. The marginal En-FDF accounts for entropy generation effects as well as scalar and entropy statistics. This methodology is applied to a turbulent nonpremixed jet flame (Sandia Flame D) and predictions are validated against experimental data. In both flows, sources of irreversibility are predicted and analyzed.

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

NASA Astrophysics Data System (ADS)

Mardirossian, Narbe; Head-Gordon, Martin

2015-02-01

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 1010 choices carved out of a functional space of almost 1040 possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

A Two-Time Scale Decentralized Model Predictive Controller Based on Input and Output Model

PubMed Central

Niu, Jian; Zhao, Jun; Xu, Zuhua; Qian, Jixin

2009-01-01

A decentralized model predictive controller applicable for some systems which exhibit different dynamic characteristics in different channels was presented in this paper. These systems can be regarded as combinations of a fast model and a slow model, the response speeds of which are in two-time scale. Because most practical models used for control are obtained in the form of transfer function matrix by plant tests, a singular perturbation method was firstly used to separate the original transfer function matrix into two models in two-time scale. Then a decentralized model predictive controller was designed based on the two models derived from the original system. And the stability of the control method was proved. Simulations showed that the method was effective. PMID:19834542

Red coral extinction risk enhanced by ocean acidification

PubMed Central

Cerrano, Carlo; Cardini, Ulisse; Bianchelli, Silvia; Corinaldesi, Cinzia; Pusceddu, Antonio; Danovaro, Roberto

2013-01-01

The red coral Corallium rubrum is a habitat-forming species with a prominent and structural role in mesophotic habitats, which sustains biodiversity hotspots. This precious coral is threatened by both over-exploitation and temperature driven mass mortality events. We report here that biocalcification, growth rates and polyps' (feeding) activity of Corallium rubrum are significantly reduced at pCO2 scenarios predicted for the end of this century (0.2 pH decrease). Since C. rubrum is a long-living species (>200 years), our results suggest that ocean acidification predicted for 2100 will significantly increases the risk of extinction of present populations. Given the functional role of these corals in the mesophotic zone, we predict that ocean acidification might have cascading effects on the functioning of these habitats worldwide. PMID:23492780

A Combined Adaptive Neural Network and Nonlinear Model Predictive Control for Multirate Networked Industrial Process Control.

PubMed

Wang, Tong; Gao, Huijun; Qiu, Jianbin

2016-02-01

This paper investigates the multirate networked industrial process control problem in double-layer architecture. First, the output tracking problem for sampled-data nonlinear plant at device layer with sampling period T(d) is investigated using adaptive neural network (NN) control, and it is shown that the outputs of subsystems at device layer can track the decomposed setpoints. Then, the outputs and inputs of the device layer subsystems are sampled with sampling period T(u) at operation layer to form the index prediction, which is used to predict the overall performance index at lower frequency. Radial basis function NN is utilized as the prediction function due to its approximation ability. Then, considering the dynamics of the overall closed-loop system, nonlinear model predictive control method is proposed to guarantee the system stability and compensate the network-induced delays and packet dropouts. Finally, a continuous stirred tank reactor system is given in the simulation part to demonstrate the effectiveness of the proposed method.

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

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

Reeve, Samuel Temple; Strachan, Alejandro, E-mail: strachan@purdue.edu

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated undermore » three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.« less

Theory of Mind and Selective Attention, Response Inhibition, Cognitive Flexibility in Patients with Schizophrenia.

PubMed

Eşsizoğlu, Altan; Köşger, Ferdi; Akarsu, Ferdane Özlem; Özaydin, Özer; Güleç, Gülcan

2017-06-01

The aims of the current study are to investigate the relationship between selective attention, response inhibition, and cognitive flexibility that are among executive functions and sociocognitive and socioperceptual theory of mind (ToM) functions and also to investigate whether selective attention, response inhibition, and cognitive flexibility are predictive factors for ToM functions in patients with schizophrenia. Forty-seven patients diagnosed with schizophrenia and a control group consisting of 42 individuals were administered demographic information form, Wisconsin card sorting test (WCST), Stroop test, Eye test, Hinting test. Positive and negative syndrome scale was applied to the schizophrenia group. In comparison to the control group, the schizophrenia group performed significantly worse on Eyes test and Hinting test. Eyes Test score and age, WCST perseverative error scores were significantly negatively correlated; education and WCST categories achieved scores were significantly positively correlated in patients with schizophrenia. Age and cognitive flexibility were found to predict the Eyes test score in patients with schizophrenia. ToM functions that are important in maintaining socioperceptual functioning are closely related with cognitive flexibility, and impairment in cognitive flexibility may predict the ToM functions in patients with schizophrenia.

Predicting Diameter Distributions of Longleaf Pine Plantations: A Comparison Between Artificial Neural Networks and Other Accepted Methodologies

Treesearch

Daniel J. Leduc; Thomas G. Matney; Keith L. Belli; V. Clark Baldwin

2001-01-01

Artificial neural networks (NN) are becoming a popular estimation tool. Because they require no assumptions about the form of a fitting function, they can free the modeler from reliance on parametric approximating functions that may or may not satisfactorily fit the observed data. To date there have been few applications in forestry science, but as better NN software...

Planning versus action: Different decision-making processes predict plans to change one's diet versus actual dietary behavior.

PubMed

Kiviniemi, Marc T; Brown-Kramer, Carolyn R

2015-05-01

Most health decision-making models posit that deciding to engage in a health behavior involves forming a behavioral intention which then leads to actual behavior. However, behavioral intentions and actual behavior may not be functionally equivalent. Two studies examined whether decision-making factors predicting dietary behaviors were the same as or distinct from those predicting intentions. Actual dietary behavior was proximally predicted by affective associations with the behavior. By contrast, behavioral intentions were predicted by cognitive beliefs about behaviors, with no contribution of affective associations. This dissociation has implications for understanding individual regulation of health behaviors and for behavior change interventions. © The Author(s) 2015.

Controlled growth and form of precipitating microsculptures

NASA Astrophysics Data System (ADS)

Kaplan, C. Nadir; Noorduin, Wim L.; Li, Ling; Sadza, Roel; Folkertsma, Laura; Aizenberg, Joanna; Mahadevan, L.

2017-03-01

Controlled self-assembly of three-dimensional shapes holds great potential for fabrication of functional materials. Their practical realization requires a theoretical framework to quantify and guide the dynamic sculpting of the curved structures that often arise in accretive mineralization. Motivated by a variety of bioinspired coprecipitation patterns of carbonate and silica, we develop a geometrical theory for the kinetics of the growth front that leaves behind thin-walled complex structures. Our theory explains the range of previously observed experimental patterns and, in addition, predicts unexplored assembly pathways. This allows us to design a number of functional base shapes of optical microstructures, which we synthesize to demonstrate their light-guiding capabilities. Overall, our framework provides a way to understand and control the growth and form of functional precipitating microsculptures.

Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters.

PubMed

Mali, Gregor

2017-03-01

Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS 2 , exhibiting a modified rocksalt structure, in which S 2- anions were replaced by S 2 2- dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, 25 Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined 25 Mg NMR parameters of magnesium sulfide species.

Force Density Function Relationships in 2-D Granular Media

NASA Technical Reports Server (NTRS)

Youngquist, Robert C.; Metzger, Philip T.; Kilts, Kelly N.

2004-01-01

An integral transform relationship is developed to convert between two important probability density functions (distributions) used in the study of contact forces in granular physics. Developing this transform has now made it possible to compare and relate various theoretical approaches with one another and with the experimental data despite the fact that one may predict the Cartesian probability density and another the force magnitude probability density. Also, the transforms identify which functional forms are relevant to describe the probability density observed in nature, and so the modified Bessel function of the second kind has been identified as the relevant form for the Cartesian probability density corresponding to exponential forms in the force magnitude distribution. Furthermore, it is shown that this transform pair supplies a sufficient mathematical framework to describe the evolution of the force magnitude distribution under shearing. Apart from the choice of several coefficients, whose evolution of values must be explained in the physics, this framework successfully reproduces the features of the distribution that are taken to be an indicator of jamming and unjamming in a granular packing. Key words. Granular Physics, Probability Density Functions, Fourier Transforms

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Comparison of clinician-predicted to measured low vision outcomes.

PubMed

Chan, Tiffany L; Goldstein, Judith E; Massof, Robert W

2013-08-01

To compare low-vision rehabilitation (LVR) clinicians' predictions of the probability of success of LVR with patients' self-reported outcomes after provision of usual outpatient LVR services and to determine if patients' traits influence clinician ratings. The Activity Inventory (AI), a self-report visual function questionnaire, was administered pre-and post-LVR to 316 low-vision patients served by 28 LVR centers that participated in a collaborative observational study. The physical component of the Short Form-36, Geriatric Depression Scale, and Telephone Interview for Cognitive Status were also administered pre-LVR to measure physical capability, depression, and cognitive status. After patient evaluation, 38 LVR clinicians estimated the probability of outcome success (POS) using their own criteria. The POS ratings and change in functional ability were used to assess the effects of patients' baseline traits on predicted outcomes. A regression analysis with a hierarchical random-effects model showed no relationship between LVR physician POS estimates and AI-based outcomes. In another analysis, kappa statistics were calculated to determine the probability of agreement between POS and AI-based outcomes for different outcome criteria. Across all comparisons, none of the kappa values were significantly different from 0, which indicates that the rate of agreement is equivalent to chance. In an exploratory analysis, hierarchical mixed-effects regression models show that POS ratings are associated with information about the patient's cognitive functioning and the combination of visual acuity and functional ability, as opposed to visual acuity or functional ability alone. Clinicians' predictions of LVR outcomes seem to be influenced by knowledge of patients' cognitive functioning and the combination of visual acuity and functional ability-information clinicians acquire from the patient's history and examination. However, clinicians' predictions do not agree with observed changes in functional ability from the patient's perspective; they are no better than chance.

Materials prediction via classification learning

DOE PAGES

Balachandran, Prasanna V.; Theiler, James; Rondinelli, James M.; ...

2015-08-25

In the paradigm of materials informatics for accelerated materials discovery, the choice of feature set (i.e. attributes that capture aspects of structure, chemistry and/or bonding) is critical. Ideally, the feature sets should provide a simple physical basis for extracting major structural and chemical trends and furthermore, enable rapid predictions of new material chemistries. Orbital radii calculated from model pseudopotential fits to spectroscopic data are potential candidates to satisfy these conditions. Although these radii (and their linear combinations) have been utilized in the past, their functional forms are largely justified with heuristic arguments. Here we show that machine learning methods naturallymore » uncover the functional forms that mimic most frequently used features in the literature, thereby providing a mathematical basis for feature set construction without a priori assumptions. We apply these principles to study two broad materials classes: (i) wide band gap AB compounds and (ii) rare earth-main group RM intermetallics. The AB compounds serve as a prototypical example to demonstrate our approach, whereas the RM intermetallics show how these concepts can be used to rapidly design new ductile materials. In conclusion, our predictive models indicate that ScCo, ScIr, and YCd should be ductile, whereas each was previously proposed to be brittle.« less

Materials Prediction via Classification Learning

PubMed Central

Balachandran, Prasanna V.; Theiler, James; Rondinelli, James M.; Lookman, Turab

2015-01-01

In the paradigm of materials informatics for accelerated materials discovery, the choice of feature set (i.e. attributes that capture aspects of structure, chemistry and/or bonding) is critical. Ideally, the feature sets should provide a simple physical basis for extracting major structural and chemical trends and furthermore, enable rapid predictions of new material chemistries. Orbital radii calculated from model pseudopotential fits to spectroscopic data are potential candidates to satisfy these conditions. Although these radii (and their linear combinations) have been utilized in the past, their functional forms are largely justified with heuristic arguments. Here we show that machine learning methods naturally uncover the functional forms that mimic most frequently used features in the literature, thereby providing a mathematical basis for feature set construction without a priori assumptions. We apply these principles to study two broad materials classes: (i) wide band gap AB compounds and (ii) rare earth-main group RM intermetallics. The AB compounds serve as a prototypical example to demonstrate our approach, whereas the RM intermetallics show how these concepts can be used to rapidly design new ductile materials. Our predictive models indicate that ScCo, ScIr, and YCd should be ductile, whereas each was previously proposed to be brittle. PMID:26304800

Prediction of Heterodimeric Protein Complexes from Weighted Protein-Protein Interaction Networks Using Novel Features and Kernel Functions

PubMed Central

Ruan, Peiying; Hayashida, Morihiro; Maruyama, Osamu; Akutsu, Tatsuya

2013-01-01

Since many proteins express their functional activity by interacting with other proteins and forming protein complexes, it is very useful to identify sets of proteins that form complexes. For that purpose, many prediction methods for protein complexes from protein-protein interactions have been developed such as MCL, MCODE, RNSC, PCP, RRW, and NWE. These methods have dealt with only complexes with size of more than three because the methods often are based on some density of subgraphs. However, heterodimeric protein complexes that consist of two distinct proteins occupy a large part according to several comprehensive databases of known complexes. In this paper, we propose several feature space mappings from protein-protein interaction data, in which each interaction is weighted based on reliability. Furthermore, we make use of prior knowledge on protein domains to develop feature space mappings, domain composition kernel and its combination kernel with our proposed features. We perform ten-fold cross-validation computational experiments. These results suggest that our proposed kernel considerably outperforms the naive Bayes-based method, which is the best existing method for predicting heterodimeric protein complexes. PMID:23776458

dbSWEET: An Integrated Resource for SWEET Superfamily to Understand, Analyze and Predict the Function of Sugar Transporters in Prokaryotes and Eukaryotes.

PubMed

Gupta, Ankita; Sankararamakrishnan, Ramasubbu

2018-04-14

SWEET (Sweet Will Eventually be Exported Transporter) proteins have been recently discovered and form one of the three major families of sugar transporters. Homologs of SWEET are found in both prokaryotes and eukaryotes. Bacterial SWEET homologs have three transmembrane segments forming a triple-helical bundle and the functional form is dimers. Eukaryotic SWEETs have seven transmembrane helical segments forming two triple-helical bundles with a linker helix. Members of SWEET homologs have been shown to be involved in several important physiological processes in plants. However, not much is known regarding the biological significance of SWEET homologs in prokaryotes and in mammals. We have collected more than 2000 SWEET homologs from both prokaryotes and eukaryotes. For each homolog, we have modeled three different conformational states representing outward open, inward open and occluded states. We have provided details regarding substrate-interacting residues and residues forming the selectivity filter for each SWEET homolog. Several search and analysis options are available. The users can generate a phylogenetic tree and structure-based sequence alignment for selected set of sequences. With no metazoan SWEETs functionally characterized, the features observed in the selectivity filter residues can be used to predict the potential substrates that are likely to be transported across the metazoan SWEETs. We believe that this database will help the researchers to design mutational experiments and simulation studies that will aid to advance our understanding of the physiological role of SWEET homologs. This database is freely available to the scientific community at http://bioinfo.iitk.ac.in/bioinfo/dbSWEET/Home. Copyright © 2018 Elsevier Ltd. All rights reserved.

Study of the in-medium nucleon electromagnetic form factors using a light-front nucleon wave function combined with the quark-meson coupling model

NASA Astrophysics Data System (ADS)

de Araújo, W. R. B.; de Melo, J. P. B. C.; Tsushima, K.

2018-02-01

We study the nucleon electromagnetic (EM) form factors in symmetric nuclear matter as well as in vacuum within a light-front approach using the in-medium inputs calculated by the quark-meson coupling model. The same in-medium quark properties are used as those used for the study of in-medium pion properties. The zero of the proton EM form factor ratio in vacuum, the electric to magnetic form factor ratio μpGEp (Q2) /GMp (Q2) (Q2 = -q2 > 0 with q being the four-momentum transfer), is determined including the latest experimental data by implementing a hard constituent quark component in the nucleon wave function. A reasonable fit is achieved for the ratio μpGEp (Q2) /GMp (Q2) in vacuum, and we predict that the Q02 value to cross the zero of the ratio to be about 15 GeV2. In addition the double ratio data of the proton EM form factors in 4He and H nuclei, [GEp4He (Q2) /G4HeMp (Q2) ] / [GEp1H (Q2) /GMp1H (Q2) ], extracted by the polarized (e → ,e‧ p →) scattering experiment on 4He at JLab, are well described. We also predict that the Q02 value satisfying μpGEp (Q02) /GMp (Q0 2) = 0 in symmetric nuclear matter, shifts to a smaller value as increasing nuclear matter density, which reflects the facts that the faster falloff of GEp (Q2) as increasing Q2 and the increase of the proton mean-square charge radius. Furthermore, we calculate the neutron EM form factor double ratio in symmetric nuclear matter for 0.1

Two distinct forms of functional lateralization in the human brain

PubMed Central

Gotts, Stephen J.; Jo, Hang Joon; Wallace, Gregory L.; Saad, Ziad S.; Cox, Robert W.; Martin, Alex

2013-01-01

The hemispheric lateralization of certain faculties in the human brain has long been held to be beneficial for functioning. However, quantitative relationships between the degree of lateralization in particular brain regions and the level of functioning have yet to be established. Here we demonstrate that two distinct forms of functional lateralization are present in the left vs. the right cerebral hemisphere, with the left hemisphere showing a preference to interact more exclusively with itself, particularly for cortical regions involved in language and fine motor coordination. In contrast, right-hemisphere cortical regions involved in visuospatial and attentional processing interact in a more integrative fashion with both hemispheres. The degree of lateralization present in these distinct systems selectively predicted behavioral measures of verbal and visuospatial ability, providing direct evidence that lateralization is associated with enhanced cognitive ability. PMID:23959883

Interactions between callous unemotional behaviors and executive function in early childhood predict later socioemotional functioning

PubMed Central

Waller, Rebecca; Hyde, Luke W.; Baskin-Sommers, Arielle; Olson, Sheryl L.

2018-01-01

Callous unemotional (CU) behaviors are linked to aggression, behavior problems, and difficulties in peer relationships in children and adolescents. However, few studies have examined whether early childhood CU behaviors predict aggression or peer-rejection during late-childhood or potential moderation of this relationship by executive function. The current study examined whether the interaction of CU behaviors and executive function in early childhood predicted different forms of aggression in late-childhood, including proactive, reactive, and relational aggression, as well as how much children were liked by their peers. Data from cross-informant reports and multiple observational tasks were collected from a high-risk sample (N=240; female=118) at ages 3 and 10 years old. Parent reports of CU behaviors at age 3 predicted teacher reports of reactive, proactive, and relational aggression, as well as lower peer-liking at age 10. Moderation analysis showed that specifically at high levels of CU behaviors and low levels of observed executive function, children were reported by teachers as showing greater reactive and proactive aggression, and were less-liked by peers. Findings demonstrate that early childhood CU behaviors and executive function have unique main and interactive effects on both later aggression and lower peer-liking even when taking into account stability in behavior problems over time. By elucidating how CU behaviors and deficits in executive function potentiate each other during early childhood, we can better characterize the emergence of severe and persistent behavior and interpersonal difficulties across development. PMID:27418255

Segregation of Form, Color, Movement, and Depth: Anatomy, Physiology, and Perception

NASA Astrophysics Data System (ADS)

Livingstone, Margaret; Hubel, David

1988-05-01

Anatomical and physiological observations in monkeys indicate that the primate visual system consists of several separate and independent subdivisions that analyze different aspects of the same retinal image: cells in cortical visual areas 1 and 2 and higher visual areas are segregated into three interdigitating subdivisions that differ in their selectivity for color, stereopsis, movement, and orientation. The pathways selective for form and color seem to be derived mainly from the parvocellular geniculate subdivisions, the depth- and movement-selective components from the magnocellular. At lower levels, in the retina and in the geniculate, cells in these two subdivisions differ in their color selectivity, contrast sensitivity, temporal properties, and spatial resolution. These major differences in the properties of cells at lower levels in each of the subdivisions led to the prediction that different visual functions, such as color, depth, movement, and form perception, should exhibit corresponding differences. Human perceptual experiments are remarkably consistent with these predictions. Moreover, perceptual experiments can be designed to ask which subdivisions of the system are responsible for particular visual abilities, such as figure/ground discrimination or perception of depth from perspective or relative movement--functions that might be difficult to deduce from single-cell response properties.

Small scale clustering of late forming dark matter

NASA Astrophysics Data System (ADS)

Agarwal, S.; Corasaniti, P.-S.; Das, S.; Rasera, Y.

2015-09-01

We perform a study of the nonlinear clustering of matter in the late-forming dark matter (LFDM) scenario in which dark matter results from the transition of a nonminimally coupled scalar field from radiation to collisionless matter. A distinct feature of this model is the presence of a damped oscillatory cutoff in the linear matter power spectrum at small scales. We use a suite of high-resolution N-body simulations to study the imprints of LFDM on the nonlinear matter power spectrum, the halo mass and velocity functions and the halo density profiles. The model largely satisfies high-redshift matter power spectrum constraints from Lyman-α forest measurements, while it predicts suppressed abundance of low-mass halos (˜109- 1010 h-1 M⊙ ) at all redshifts compared to a vanilla Λ CDM model. The analysis of the LFDM halo velocity function shows a better agreement than the Λ CDM prediction with the observed abundance of low-velocity galaxies in the local volume. Halos with mass M ≳1011 h-1 M⊙ show minor departures of the density profiles from Λ CDM expectations, while smaller-mass halos are less dense, consistent with the fact that they form later than their Λ CDM counterparts.

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

PubMed

Korb, Oliver; Stützle, Thomas; Exner, Thomas E

2009-01-01

In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

The auditory brain-stem response to complex sounds: a potential biomarker for guiding treatment of psychosis.

PubMed

Tarasenko, Melissa A; Swerdlow, Neal R; Makeig, Scott; Braff, David L; Light, Gregory A

2014-01-01

Cognitive deficits limit psychosocial functioning in schizophrenia. For many patients, cognitive remediation approaches have yielded encouraging results. Nevertheless, therapeutic response is variable, and outcome studies consistently identify individuals who respond minimally to these interventions. Biomarkers that can assist in identifying patients likely to benefit from particular forms of cognitive remediation are needed. Here, we describe an event-related potential (ERP) biomarker - the auditory brain-stem response (ABR) to complex sounds (cABR) - that appears to be particularly well-suited for predicting response to at least one form of cognitive remediation that targets auditory information processing. Uniquely, the cABR quantifies the fidelity of sound encoded at the level of the brainstem and midbrain. This ERP biomarker has revealed auditory processing abnormalities in various neurodevelopmental disorders, correlates with functioning across several cognitive domains, and appears to be responsive to targeted auditory training. We present preliminary cABR data from 18 schizophrenia patients and propose further investigation of this biomarker for predicting and tracking response to cognitive interventions.

Topological self-organization and prediction learning support both action and lexical chains in the brain.

PubMed

Chersi, Fabian; Ferro, Marcello; Pezzulo, Giovanni; Pirrelli, Vito

2014-07-01

A growing body of evidence in cognitive psychology and neuroscience suggests a deep interconnection between sensory-motor and language systems in the brain. Based on recent neurophysiological findings on the anatomo-functional organization of the fronto-parietal network, we present a computational model showing that language processing may have reused or co-developed organizing principles, functionality, and learning mechanisms typical of premotor circuit. The proposed model combines principles of Hebbian topological self-organization and prediction learning. Trained on sequences of either motor or linguistic units, the network develops independent neuronal chains, formed by dedicated nodes encoding only context-specific stimuli. Moreover, neurons responding to the same stimulus or class of stimuli tend to cluster together to form topologically connected areas similar to those observed in the brain cortex. Simulations support a unitary explanatory framework reconciling neurophysiological motor data with established behavioral evidence on lexical acquisition, access, and recall. Copyright © 2014 Cognitive Science Society, Inc.

Anisotropic yield function capable of predicting eight ears

NASA Astrophysics Data System (ADS)

Yoon, J. H.; Cazacu, O.

2011-08-01

Deep drawing of a cylindrical cup from a rolled sheet is one of the typical forming operations where the effect of this anisotropy is most evident. Indeed, it is well documented in the literature that the number of ears and the shape of the earing pattern correlate with the r-values profile. For the strongly textured aluminum alloy AA 5042 (Numisheet Benchmark 2011), the experimental r-value distribution has two minima between the rolling and transverse direction data provided for this show that the r-value along the transverse direction (TD) is five times larger than the value corresponding to the rolling direction. Therefore, it is expected that there are more that the earing profile has more than four ears. The main objective of this paper is to assess whether a new form of CPB06ex2 yield function (Plunkett et al. (2008)) tailored for metals with no tension-compression asymmetry is capable of predicting more than four ears for this material.

Atomic and molecular far-infrared lines from high redshift galaxies

NASA Astrophysics Data System (ADS)

Vallini, L.

2015-03-01

The advent of Atacama Large Millimeter-submillimeter Array (ALMA), with its unprecedented sensitivity, makes it possible the detection of far-infrared (FIR) metal cooling and molecular lines from the first galaxies that formed after the Big Bang. These lines represent a powerful tool to shed light on the physical properties of the interstellar medium (ISM) in high-redshift sources. In what follows we show the potential of a physically motivated theoretical approach that we developed to predict the ISM properties of high redshift galaxies. The model allows to infer, as a function of the metallicity, the luminosities of various FIR lines observable with ALMA. It is based on high resolution cosmological simulations of star-forming galaxies at the end of the Epoch of Reionization (z˜eq6) , further implemented with sub-grid physics describing the cooling and the heating processes that take place in the neutral diffuse ISM. Finally we show how a different approach based on semi-analytical calculations can allow to predict the CO flux function at z>6.

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking.

PubMed

Ballester, Pedro J; Mitchell, John B O

2010-05-01

Accurately predicting the binding affinities of large sets of diverse protein-ligand complexes is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for analysing the outputs of molecular docking, which in turn is an important technique for drug discovery, chemical biology and structural biology. Each scoring function assumes a predetermined theory-inspired functional form for the relationship between the variables that characterize the complex, which also include parameters fitted to experimental or simulation data and its predicted binding affinity. The inherent problem of this rigid approach is that it leads to poor predictivity for those complexes that do not conform to the modelling assumptions. Moreover, resampling strategies, such as cross-validation or bootstrapping, are still not systematically used to guard against the overfitting of calibration data in parameter estimation for scoring functions. We propose a novel scoring function (RF-Score) that circumvents the need for problematic modelling assumptions via non-parametric machine learning. In particular, Random Forest was used to implicitly capture binding effects that are hard to model explicitly. RF-Score is compared with the state of the art on the demanding PDBbind benchmark. Results show that RF-Score is a very competitive scoring function. Importantly, RF-Score's performance was shown to improve dramatically with training set size and hence the future availability of more high-quality structural and interaction data is expected to lead to improved versions of RF-Score. pedro.ballester@ebi.ac.uk; jbom@st-andrews.ac.uk Supplementary data are available at Bioinformatics online.

Forms Of Memory For Representation Of Visual Objects

DTIC Science & Technology

1991-02-14

description system that functions independently of the episodic memory system that is damaged in amnesia and supports explicit remembering. Miscellaneous...well as semantic and functional information about an object, are preserved in the episodic system. 4. Priming and recognition of depth-cued, 3D objects A...requirement should serve to enhance an object’s distinctiveness in episodic memory . We also predicted robust priming for symmetric objects; this is because

Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

PubMed

Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David

2016-12-12

For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Receptive Field Vectors of Genetically-Identified Retinal Ganglion Cells Reveal Cell-Type-Dependent Visual Functions

PubMed Central

Katz, Matthew L.; Viney, Tim J.; Nikolic, Konstantin

2016-01-01

Sensory stimuli are encoded by diverse kinds of neurons but the identities of the recorded neurons that are studied are often unknown. We explored in detail the firing patterns of eight previously defined genetically-identified retinal ganglion cell (RGC) types from a single transgenic mouse line. We first introduce a new technique of deriving receptive field vectors (RFVs) which utilises a modified form of mutual information (“Quadratic Mutual Information”). We analysed the firing patterns of RGCs during presentation of short duration (~10 second) complex visual scenes (natural movies). We probed the high dimensional space formed by the visual input for a much smaller dimensional subspace of RFVs that give the most information about the response of each cell. The new technique is very efficient and fast and the derivation of novel types of RFVs formed by the natural scene visual input was possible even with limited numbers of spikes per cell. This approach enabled us to estimate the 'visual memory' of each cell type and the corresponding receptive field area by calculating Mutual Information as a function of the number of frames and radius. Finally, we made predictions of biologically relevant functions based on the RFVs of each cell type. RGC class analysis was complemented with results for the cells’ response to simple visual input in the form of black and white spot stimulation, and their classification on several key physiological metrics. Thus RFVs lead to predictions of biological roles based on limited data and facilitate analysis of sensory-evoked spiking data from defined cell types. PMID:26845435

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

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

Mardirossian, Narbe; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

2015-02-21

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10{sup 10} choices carved out of a functional space of almost 10{sup 40} possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based onmore » a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.« less

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2015-02-20

We present a meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional. The functional form is selected from more than 10 10 choices carved out of a functional space of almost 10 40 possibilities. This raw data comes from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filteredmore » based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.« less

Plasma Theory and Simulation Group Annual Progress Report for 1991

DTIC Science & Technology

1991-12-31

beam formation analitically : i) the resistance of the (low-density) to the final, high-density cylindrical wall can be approximated by the regime...model is developed that predicts the ion angular distribution function in a highly collisional sheath. In a previous study2, the normal ion velocity...gets a linear dispersion relation of the form W2 = k 2 (T + Ti/m. + m,), (40) which predicts ion acoustic waves. These waves have the highest frequency

In-vivo detectability index: development and validation of an automated methodology

NASA Astrophysics Data System (ADS)

Smith, Taylor Brunton; Solomon, Justin; Samei, Ehsan

2017-03-01

The purpose of this study was to develop and validate a method to estimate patient-specific detectability indices directly from patients' CT images (i.e., "in vivo"). The method works by automatically extracting noise (NPS) and resolution (MTF) properties from each patient's CT series based on previously validated techniques. Patient images are thresholded into skin-air interfaces to form edge-spread functions, which are further binned, differentiated, and Fourier transformed to form the MTF. The NPS is likewise estimated from uniform areas of the image. These are combined with assumed task functions (reference function: 10 mm disk lesion with contrast of -15 HU) to compute detectability indices for a non-prewhitening matched filter model observer predicting observer performance. The results were compared to those from a previous human detection study on 105 subtle, hypo-attenuating liver lesions, using a two-alternative-forcedchoice (2AFC) method, over 6 dose levels using 16 readers. The in vivo detectability indices estimated for all patient images were compared to binary 2AFC outcomes with a generalized linear mixed-effects statistical model (Probit link function, linear terms only, no interactions, random term for readers). The model showed that the in vivo detectability indices were strongly predictive of 2AFC outcomes (P < 0.05). A linear comparison between the human detection accuracy and model-predicted detection accuracy (for like conditions) resulted in Pearson and Spearman correlations coefficients of 0.86 and 0.87, respectively. These data provide evidence that the in vivo detectability index could potentially be used to automatically estimate and track image quality in a clinical operation.

Testing the Self-Consistency of the Excursion Set Approach to Predicting the Dark Matter Halo Mass Function

NASA Astrophysics Data System (ADS)

Achitouv, I.; Rasera, Y.; Sheth, R. K.; Corasaniti, P. S.

2013-12-01

The excursion set approach provides a framework for predicting how the abundance of dark matter halos depends on the initial conditions. A key ingredient of this formalism is the specification of a critical overdensity threshold (barrier) which protohalos must exceed if they are to form virialized halos at a later time. However, to make its predictions, the excursion set approach explicitly averages over all positions in the initial field, rather than the special ones around which halos form, so it is not clear that the barrier has physical motivation or meaning. In this Letter we show that once the statistical assumptions which underlie the excursion set approach are considered a drifting diffusing barrier model does provide a good self-consistent description both of halo abundance as well as of the initial overdensities of the protohalo patches.

A comparison of simple global kinetic models for coal devolatilization with the CPD model

DOE PAGES

Richards, Andrew P.; Fletcher, Thomas H.

2016-08-01

Simulations of coal combustors and gasifiers generally cannot incorporate the complexities of advanced pyrolysis models, and hence there is interest in evaluating simpler models over ranges of temperature and heating rate that are applicable to the furnace of interest. In this paper, six different simple model forms are compared to predictions made by the Chemical Percolation Devolatilization (CPD) model. The model forms included three modified one-step models, a simple two-step model, and two new modified two-step models. These simple model forms were compared over a wide range of heating rates (5 × 10 3 to 10 6 K/s) at finalmore » temperatures up to 1600 K. Comparisons were made of total volatiles yield as a function of temperature, as well as the ultimate volatiles yield. Advantages and disadvantages for each simple model form are discussed. In conclusion, a modified two-step model with distributed activation energies seems to give the best agreement with CPD model predictions (with the fewest tunable parameters).« less

Estimation of Quasi-Stiffness and Propulsive Work of the Human Ankle in the Stance Phase of Walking

PubMed Central

Shamaei, Kamran; Sawicki, Gregory S.; Dollar, Aaron M.

2013-01-01

Characterizing the quasi-stiffness and work of lower extremity joints is critical for evaluating human locomotion and designing assistive devices such as prostheses and orthoses intended to emulate the biological behavior of human legs. This work aims to establish statistical models that allow us to predict the ankle quasi-stiffness and net mechanical work for adults walking on level ground. During the stance phase of walking, the ankle joint propels the body through three distinctive phases of nearly constant stiffness known as the quasi-stiffness of each phase. Using a generic equation for the ankle moment obtained through an inverse dynamics analysis, we identify key independent parameters needed to predict ankle quasi-stiffness and propulsive work and also the functional form of each correlation. These parameters include gait speed, ankle excursion, and subject height and weight. Based on the identified form of the correlation and key variables, we applied linear regression on experimental walking data for 216 gait trials across 26 subjects (speeds from 0.75–2.63 m/s) to obtain statistical models of varying complexity. The most general forms of the statistical models include all the key parameters and have an R2 of 75% to 81% in the prediction of the ankle quasi-stiffnesses and propulsive work. The most specific models include only subject height and weight and could predict the ankle quasi-stiffnesses and work for optimal walking speed with average error of 13% to 30%. We discuss how these models provide a useful framework and foundation for designing subject- and gait-specific prosthetic and exoskeletal devices designed to emulate biological ankle function during level ground walking. PMID:23555839

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Biocrust-forming mosses mitigate the negative impacts of increasing aridity on ecosystem multifunctionality in drylands.

PubMed

Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Bowker, Matthew A; Ochoa, Victoria; Gozalo, Beatriz; Berdugo, Miguel; Val, James; Singh, Brajesh K

2016-03-01

The increase in aridity predicted with climate change will have a negative impact on the multiple functions and services (multifunctionality) provided by dryland ecosystems worldwide. In these ecosystems, soil communities dominated by mosses, lichens and cyanobacteria (biocrusts) play a key role in supporting multifunctionality. However, whether biocrusts can buffer the negative impacts of aridity on important biogeochemical processes controlling carbon (C), nitrogen (N), and phosphorus (P) pools and fluxes remains largely unknown. Here, we conducted an empirical study, using samples from three continents (North America, Europe and Australia), to evaluate how the increase in aridity predicted by climate change will alter the capacity of biocrust-forming mosses to modulate multiple ecosystem processes related to C, N and P cycles. Compared with soil surfaces lacking biocrusts, biocrust-forming mosses enhanced multiple functions related to C, N and P cycling and storage in semiarid and arid, but not in humid and dry-subhumid, environments. Most importantly, we found that the relative positive effects of biocrust-forming mosses on multifunctionality compared with bare soil increased with increasing aridity. These results were mediated by plant cover and the positive effects exerted by biocrust-forming mosses on the abundance of soil bacteria and fungi. Our findings provide strong evidence that the maintenance of biocrusts is crucial to buffer negative effects of climate change on multifunctionality in global drylands. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Evaluation of Short-Term Bioassays to Predict Functional Impairment. Selected Short-Term Cardiovascular Toxicity Tests.

DTIC Science & Technology

1980-10-01

for many cultures at one time (Acosta, 1979). When Nitro Blue tetrazolium (NBT) and phenazine methosulphate react with succinate dehydrogenase...microscopically-observable for- mazan granules are formed. When the structural integrity of the mitochondrial membranes is maintained, NBT and phenazine

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Song, Jiangning; Burrage, Kevin; Yuan, Zheng; Huber, Thomas

2006-03-09

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Predicting the Retention Behavior of Specific O-Linked Glycopeptides.

PubMed

Badgett, Majors J; Boyes, Barry; Orlando, Ron

2017-09-01

O -Linked glycosylation is a common post-translational modification that can alter the overall structure, polarity, and function of proteins. Reverse-phase (RP) chromatography is the most common chromatographic approach to analyze O -glycosylated peptides and their unmodified counterparts, even though this approach often does not provide adequate separation of these two species. Hydrophilic interaction liquid chromatography (HILIC) can be a solution to this problem, as the polar glycan interacts with the polar stationary phase and potentially offers the ability to resolve the peptide from its modified form(s). In this paper, HILIC is used to separate peptides with O - N -acetylgalactosamine ( O -GalNAc), O - N -acetylglucosamine ( O -GlcNAc), and O -fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications.

Predicting the Retention Behavior of Specific O-Linked Glycopeptides

PubMed Central

Badgett, Majors J.; Boyes, Barry; Orlando, Ron

2017-01-01

O-Linked glycosylation is a common post-translational modification that can alter the overall structure, polarity, and function of proteins. Reverse-phase (RP) chromatography is the most common chromatographic approach to analyze O-glycosylated peptides and their unmodified counterparts, even though this approach often does not provide adequate separation of these two species. Hydrophilic interaction liquid chromatography (HILIC) can be a solution to this problem, as the polar glycan interacts with the polar stationary phase and potentially offers the ability to resolve the peptide from its modified form(s). In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. PMID:28785176

Predicting Changes in Macrophyte Community Structure from Functional Traits in a Freshwater Lake: A Test of Maximum Entropy Model

PubMed Central

Fu, Hui; Zhong, Jiayou; Yuan, Guixiang; Guo, Chunjing; Lou, Qian; Zhang, Wei; Xu, Jun; Ni, Leyi; Xie, Ping; Cao, Te

2015-01-01

Trait-based approaches have been widely applied to investigate how community dynamics respond to environmental gradients. In this study, we applied a series of maximum entropy (maxent) models incorporating functional traits to unravel the processes governing macrophyte community structure along water depth gradient in a freshwater lake. We sampled 42 plots and 1513 individual plants, and measured 16 functional traits and abundance of 17 macrophyte species. Study results showed that maxent model can be highly robust (99.8%) in predicting the species relative abundance of macrophytes with observed community-weighted mean (CWM) traits as the constraints, while relative low (about 30%) with CWM traits fitted from water depth gradient as the constraints. The measured traits showed notably distinct importance in predicting species abundances, with lowest for perennial growth form and highest for leaf dry mass content. For tuber and leaf nitrogen content, there were significant shifts in their effects on species relative abundance from positive in shallow water to negative in deep water. This result suggests that macrophyte species with tuber organ and greater leaf nitrogen content would become more abundant in shallow water, but would become less abundant in deep water. Our study highlights how functional traits distributed across gradients provide a robust path towards predictive community ecology. PMID:26167856

On the luminosity function, lifetimes, and origin of blue stragglers in globular clusters

NASA Technical Reports Server (NTRS)

Bailyn, Charles D.; Pinsonneault, Marc H.

1995-01-01

We compute theoretical evolutionary tracks of blue stragglers created by mergers. Two formation scenarios are considered: mergers of primordial binaries, and stellar collisions. These two scenarios predict strikingly different luminosity functions, which are potentially distinguishable observationally. Tabulated theoretical luminosity functions and lifetimes are presented for blue stragglers formed under a variety of input conditions. We compare our results with observations of the blue straggler sequences in 47 Tucanae and M3. In the case of 47 Tuc, the luminosity function and the formation rate are compatible with the hypothesis that the blue stragglers formed through the collision of single stars. Mergers of primordial binaries are only marginally cosistent with the data, and a significant enhancement of the collision cross section by binary-single-star encounters appears to be ruled out. In the case of M3, we find that the innermost blue stragglers have a luminosity function significantly different from that of the outer stragglers, thus confirming earlier suggestions that there are two distinct populations of blue stragglers in this cluster. The inner stragglers are preferentially brighter and bluer, as would be expected if they were made by collisions, but there are so many of them that the collision rate would need to be enhanced by interactions involving wide binaries. The luminosity function of the outer stragglers is almost identical to the predictions of mergers from primordial binaries and is inconsistent with the collision hypothesis.

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.

Prediction of Turbulence-Generated Noise in Unheated Jets. Part 1; JeNo Technical Manual (Version 1.0)

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Bridges, James; Georgiadis, Nicholas

2005-01-01

The model-based approach, used by the JeNo code to predict jet noise spectral directivity, is described. A linearized form of Lilley's equation governs the non-causal Green s function of interest, with the non-linear terms on the right hand side identified as the source. A Reynolds-averaged Navier-Stokes (RANS) solution yields the required mean flow for the solution of the propagation Green s function in a locally parallel flow. The RANS solution also produces time- and length-scales needed to model the non-compact source, the turbulent velocity correlation tensor, with exponential temporal and spatial functions. It is shown that while an exact non-causal Green s function accurately predicts the observed shift in the location of the spectrum peak with angle as well as the angularity of sound at low to moderate Mach numbers, the polar directivity of radiated sound is not entirely captured by this Green s function at high subsonic and supersonic acoustic Mach numbers. Results presented for unheated jets in the Mach number range of 0.51 to 1.8 suggest that near the peak radiation angle of high-speed jets, a different source/Green s function convolution integral may be required in order to capture the peak observed directivity of jet noise. A sample Mach 0.90 heated jet is also discussed that highlights the requirements for a comprehensive jet noise prediction model.

Towards a Functionally-Formed Air Traffic System-of-Systems

NASA Technical Reports Server (NTRS)

Conway, Sheila R.; Consiglio, Maria C.

2005-01-01

Incremental improvements to the national aviation infrastructure have not resulted in sufficient increases in capacity and flexibility to meet emerging demand. Unfortunately, revolutionary changes capable of substantial and rapid increases in capacity have proven elusive. Moreover, significant changes have been difficult to implement, and the operational consequences of such change, difficult to predict due to the system s complexity. Some research suggests redistributing air traffic control functions through the system, but this work has largely been dismissed out of hand, accused of being impractical. However, the case for functionally-based reorganization of form can be made from a theoretical, systems perspective. This paper investigates Air Traffic Management functions and their intrinsic biases towards centralized/distributed operations, grounded in systems engineering and information technology theories. Application of these concepts to a small airport operations design is discussed. From this groundwork, a robust, scalable system transformation plan may be made in light of uncertain demand.

Predicting Psychosocial Maladjustment in Emerging Adulthood From High School Experiences of Peer Victimization.

PubMed

Buchanan, Carie M; McDougall, Patricia

2018-01-01

The aim of the present study was to compare recollections of sexual, physical, verbal, social, and cyber peer victimization experienced in high school in terms of depressed affect, self-esteem, and loneliness experienced in university. In all, 247 university students (70 males and 177 females; M = 20.62, SD = 2.54) completed online measures assessing retrospective accounts of their experiences of different forms of peer victimization during high school (i.e., sexual, physical, verbal, social, and cyber) and their current psychosocial adjustment (i.e., self-esteem, depressed affect, and loneliness). Three separate hierarchical multiple regressions were conducted to determine whether different indices of negative psychosocial adjustment are more strongly predicted by experiencing sexual or nonsexual forms of peer victimization. Although many university students recalled experiencing sexual peer victimization in high school at least once at an even higher percentage than verbal and social forms of peer victimization, the results of the present study suggest that social peer victimization in high school predicts higher levels of depressed affect and loneliness in university students than sexual peer victimization experienced in high school. Surprisingly, the young adults reporting higher levels of cyber peer victimization in high school were less lonely in university. Although the hypothesized relationships between each form of peer victimization and specific indices of psychosocial functioning were not consistently supported, these findings suggest that the form of peer victimization matters and may be differentially associated with well-being in emerging adulthood. It is important that future research explores how individual characteristics may further predict varied experiences of peer victimization and the long-term impact of those experiences.

A nonlinear macromodel of the bipolar integrated circuit operational amplifier for electromagnetic interference analysis

NASA Astrophysics Data System (ADS)

Chen, G. K. C.

1981-06-01

A nonlinear macromodel for the bipolar transistor integrated circuit operational amplifier is derived from the macromodel proposed by Boyle. The nonlinear macromodel contains only two nonlinear transistors in the input stage in a differential amplifier configuration. Parasitic capacitance effects are represented by capacitors placed at the collectors and emitters of the input transistors. The nonlinear macromodel is effective in predicting the second order intermodulation effect of operational amplifiers in a unity gain buffer amplifier configuration. The nonlinear analysis computer program NCAP is used for the analysis. Accurate prediction of demodulation of amplitude modulated RF signals with RF carrier frequencies in the 0.05 to 100 MHz range is achieved. The macromodel predicted results, presented in the form of second order nonlinear transfer function, come to within 6 dB of the full model predictions for the 741 type of operational amplifiers for values of the second order transfer function greater than -40 dB.

Gaussian functional regression for output prediction: Model assimilation and experimental design

NASA Astrophysics Data System (ADS)

Nguyen, N. C.; Peraire, J.

2016-03-01

In this paper, we introduce a Gaussian functional regression (GFR) technique that integrates multi-fidelity models with model reduction to efficiently predict the input-output relationship of a high-fidelity model. The GFR method combines the high-fidelity model with a low-fidelity model to provide an estimate of the output of the high-fidelity model in the form of a posterior distribution that can characterize uncertainty in the prediction. A reduced basis approximation is constructed upon the low-fidelity model and incorporated into the GFR method to yield an inexpensive posterior distribution of the output estimate. As this posterior distribution depends crucially on a set of training inputs at which the high-fidelity models are simulated, we develop a greedy sampling algorithm to select the training inputs. Our approach results in an output prediction model that inherits the fidelity of the high-fidelity model and has the computational complexity of the reduced basis approximation. Numerical results are presented to demonstrate the proposed approach.

The ORF1 Protein Encoded by LINE-1: Structure and Function During L1 Retrotransposition

PubMed Central

Martin, Sandra L.

2006-01-01

LINE-1, or L1 is an autonomous non-LTR retrotransposon in mammals. Retrotransposition requires the function of the two, L1-encoded polypeptides, ORF1p and ORF2p. Early recognition of regions of homology between the predicted amino acid sequence of ORF2 and known endonuclease and reverse transcriptase enzymes led to testable hypotheses regarding the function of ORF2p in retrotransposition. As predicted, ORF2p has been demonstrated to have both endonuclease and reverse transcriptase activities. In contrast, no homologs of known function have contributed to our understanding of the function of ORF1p during retrotransposition. Nevertheless, significant advances have been made such that we now know that ORF1p is a high affinity RNA binding protein that forms a ribonucleoprotein particle together with L1 RNA. Furthermore, ORF1p is a nucleic acid chaperone and this nucleic acid chaperone activity is required for L1 retrotransposition. PMID:16877816

Does adolescent risk taking imply weak executive function? A prospective study of relations between working memory performance, impulsivity, and risk taking in early adolescence.

PubMed

Romer, Daniel; Betancourt, Laura M; Brodsky, Nancy L; Giannetta, Joan M; Yang, Wei; Hurt, Hallam

2011-09-01

Studies of brain development suggest that the increase in risk taking observed during adolescence may be due to insufficient prefrontal executive function compared to a more rapidly developing subcortical motivation system. We examined executive function as assessed by working memory ability in a community sample of youth (n = 387, ages 10 to 12 at baseline) in three annual assessments to determine its relation to two forms of impulsivity (sensation seeking and acting without thinking) and a wide range of risk and externalizing behavior. Using structural equation modeling, we tested a model in which differential activation of the dorsal and ventral striatum produces imbalance in the function of these brain regions. For youth high in sensation seeking, both regions were predicted to develop with age. However, for youth high in the tendency to act without thinking, the ventral striatum was expected to dominate. The model predicted that working memory ability would exhibit (1) early weakness in youth high in acting without thinking but (2) growing strength in those high in sensation seeking. In addition, it predicted that (3) acting without thinking would be more strongly related to risk and externalizing behavior than sensation seeking. Finally, it predicted that (4) controlling for acting without thinking, sensation seeking would predict later increases in risky and externalizing behavior. All four of these predictions were confirmed. The results indicate that the rise in sensation seeking that occurs during adolescence is not accompanied by a deficit in executive function and therefore requires different intervention strategies from those for youth whose impulsivity is characterized by early signs of acting without thinking. © 2011 Blackwell Publishing Ltd.

High-energy gamma-ray and neutrino production in star-forming galaxies across cosmic time: Difficulties in explaining the IceCube data

NASA Astrophysics Data System (ADS)

Sudoh, Takahiro; Totani, Tomonori; Kawanaka, Norita

2018-06-01

We present new theoretical modeling to predict the luminosity and spectrum of gamma-ray and neutrino emission of a star-forming galaxy, from the star formation rate (ψ), gas mass (Mgas), stellar mass, and disk size, taking into account production, propagation, and interactions of cosmic rays. The model reproduces the observed gamma-ray luminosities of nearby galaxies detected by Fermi better than the simple power-law models as a function of ψ or ψMgas. This model is then used to predict the cosmic background flux of gamma-rays and neutrinos from star-forming galaxies, by using a semi-analytical model of cosmological galaxy formation that reproduces many observed quantities of local and high-redshift galaxies. Calibration of the model using gamma-ray luminosities of nearby galaxies allows us to make a more reliable prediction than previous studies. In our baseline model, star-forming galaxies produce about 20% of the isotropic gamma-ray background unresolved by Fermi, and only 0.5% of IceCube neutrinos. Even with an extreme model assuming a hard injection cosmic-ray spectral index of 2.0 for all galaxies, at most 22% of IceCube neutrinos can be accounted for. These results indicate that it is difficult to explain most of the IceCube neutrinos by star-forming galaxies, without violating the gamma-ray constraints from nearby galaxies.

High-energy gamma-ray and neutrino production in star-forming galaxies across cosmic time: Difficulties in explaining the IceCube data

NASA Astrophysics Data System (ADS)

Sudoh, Takahiro; Totani, Tomonori; Kawanaka, Norita

2018-04-01

We present new theoretical modeling to predict the luminosity and spectrum of gamma-ray and neutrino emission of a star-forming galaxy, from the star formation rate (ψ), gas mass (Mgas), stellar mass, and disk size, taking into account production, propagation, and interactions of cosmic rays. The model reproduces the observed gamma-ray luminosities of nearby galaxies detected by Fermi better than the simple power-law models as a function of ψ or ψMgas. This model is then used to predict the cosmic background flux of gamma-rays and neutrinos from star-forming galaxies, by using a semi-analytical model of cosmological galaxy formation that reproduces many observed quantities of local and high-redshift galaxies. Calibration of the model using gamma-ray luminosities of nearby galaxies allows us to make a more reliable prediction than previous studies. In our baseline model, star-forming galaxies produce about 20% of the isotropic gamma-ray background unresolved by Fermi, and only 0.5% of IceCube neutrinos. Even with an extreme model assuming a hard injection cosmic-ray spectral index of 2.0 for all galaxies, at most 22% of IceCube neutrinos can be accounted for. These results indicate that it is difficult to explain most of the IceCube neutrinos by star-forming galaxies, without violating the gamma-ray constraints from nearby galaxies.

An integrated computational approach can classify VHL missense mutations according to risk of clear cell renal carcinoma

PubMed Central

Gossage, Lucy; Pires, Douglas E. V.; Olivera-Nappa, Álvaro; Asenjo, Juan; Bycroft, Mark; Blundell, Tom L.; Eisen, Tim

2014-01-01

Mutations in the von Hippel–Lindau (VHL) gene are pathogenic in VHL disease, congenital polycythaemia and clear cell renal carcinoma (ccRCC). pVHL forms a ternary complex with elongin C and elongin B, critical for pVHL stability and function, which interacts with Cullin-2 and RING-box protein 1 to target hypoxia-inducible factor for polyubiquitination and proteasomal degradation. We describe a comprehensive database of missense VHL mutations linked to experimental and clinical data. We use predictions from in silico tools to link the functional effects of missense VHL mutations to phenotype. The risk of ccRCC in VHL disease is linked to the degree of destabilization resulting from missense mutations. An optimized binary classification system (symphony), which integrates predictions from five in silico methods, can predict the risk of ccRCC associated with VHL missense mutations with high sensitivity and specificity. We use symphony to generate predictions for risk of ccRCC for all possible VHL missense mutations and present these predictions, in association with clinical and experimental data, in a publically available, searchable web server. PMID:24969085

What's So Bad about Being Wet All Over: Investigating Leaf Surface Wetness.

ERIC Educational Resources Information Center

Brewer, Carol A.

1996-01-01

Presents investigations of leaf surface wetness that provide ideal opportunities for students to explore the relationships between leaf form and function, to study surface conditions of leaves and plant physiology, and to make predictions about plant adaptation in different environments. Describes simple procedures for exploring questions related…

Suppression or activation of immune responses by predicted secreted proteins of the soybean rust pathogen Phakopsora pachyrhizi

USDA-ARS?s Scientific Manuscript database

Rust fungi, such as Phakopsora pachyrhizi, are major threats to crop production. They form specialized haustoria that are intimately associated with plant cells. These haustoria have roles in acquiring nutrients and secreting effector proteins that manipulate host immune systems. Functional characte...

The Norwegian Computerized Adaptive Test of Personality Disorder-Static Form (CAT-PD-SF): Reliability, Factor Structure, and Relationships With Personality Functioning.

PubMed

Thimm, Jens C

2017-12-01

The Computerized Adaptive Test of Personality Disorder-Static Form (CAT-PD-SF) is a self-report inventory developed to assess pathological personality traits. The current study explored the reliability and higher order factor structure of the Norwegian version of the CAT-PD-SF and the relationships between the CAT-PD traits and domains of personality functioning in an undergraduate student sample ( N = 375). In addition to the CAT-PD-SF, the short form of the Severity Indices of Personality Problems and the Brief Symptom Inventory were administered. The results showed that the Norwegian CAT-PD-SF has good score reliability. Factor analysis of the CAT-PD-SF scales indicated five superordinate factors that correspond to the trait domains of the alternative DSM-5 model for personality disorders. The CAT-PD traits were highly predictive of impaired personality functioning after controlling for psychological distress. It is concluded that the CAT-PD-SF is a promising tool for the assessment of personality disorder traits.

Amplitude modulation detection by human listeners in sound fields.

PubMed

Zahorik, Pavel; Kim, Duck O; Kuwada, Shigeyuki; Anderson, Paul W; Brandewie, Eugene; Srinivasan, Nirmal

2011-10-01

The temporal modulation transfer function (TMTF) approach allows techniques from linear systems analysis to be used to predict how the auditory system will respond to arbitrary patterns of amplitude modulation (AM). Although this approach forms the basis for a standard method of predicting speech intelligibility based on estimates of the acoustical modulation transfer function (MTF) between source and receiver, human sensitivity to AM as characterized by the TMTF has not been extensively studied under realistic listening conditions, such as in reverberant sound fields. Here, TMTFs (octave bands from 2 - 512 Hz) were obtained in 3 listening conditions simulated using virtual auditory space techniques: diotic, anechoic sound field, reverberant room sound field. TMTFs were then related to acoustical MTFs estimated using two different methods in each of the listening conditions. Both diotic and anechoic data were found to be in good agreement with classic results, but AM thresholds in the reverberant room were lower than predictions based on acoustical MTFs. This result suggests that simple linear systems techniques may not be appropriate for predicting TMTFs from acoustical MTFs in reverberant sound fields, and may be suggestive of mechanisms that functionally enhance modulation during reverberant listening.

The effects of glutamine/asparagine content on aggregation and heterologous prion induction by yeast prion-like domains.

PubMed

Shattuck, Jenifer E; Waechter, Aubrey C; Ross, Eric D

2017-07-04

Prion-like domains are low complexity, intrinsically disordered domains that compositionally resemble yeast prion domains. Many prion-like domains are involved in the formation of either functional or pathogenic protein aggregates. These aggregates range from highly dynamic liquid droplets to highly ordered detergent-insoluble amyloid-like aggregates. To better understand the amino acid sequence features that promote conversion to stable, detergent-insoluble aggregates, we used the prediction algorithm PAPA to identify predicted aggregation-prone prion-like domains with a range of compositions. While almost all of the predicted aggregation-prone domains formed foci when expressed in cells, the ability to form the detergent-insoluble aggregates was highly correlated with glutamine/asparagine (Q/N) content, suggesting that high Q/N content may specifically promote conversion to the amyloid state in vivo. We then used this data set to examine cross-seeding between prion-like proteins. The prion protein Sup35 requires the presence of a second prion, [PIN + ], to efficiently form prions, but this requirement can be circumvented by the expression of various Q/N-rich protein fragments. Interestingly, almost all of the Q/N-rich domains that formed SDS-insoluble aggregates were able to promote prion formation by Sup35, highlighting the highly promiscuous nature of these interactions.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Simplified combustion noise theory yielding a prediction of fluctuating pressure level

NASA Technical Reports Server (NTRS)

Huff, R. G.

1984-01-01

The first order equations for the conservation of mass and momentum in differential form are combined for an ideal gas to yield a single second order partial differential equation in one dimension and time. Small perturbation analysis is applied. A Fourier transformation is performed that results in a second order, constant coefficient, nonhomogeneous equation. The driving function is taken to be the source of combustion noise. A simplified model describing the energy addition via the combustion process gives the required source information for substitution in the driving function. This enables the particular integral solution of the nonhomogeneous equation to be found. This solution multiplied by the acoustic pressure efficiency predicts the acoustic pressure spectrum measured in turbine engine combustors. The prediction was compared with the overall sound pressure levels measured in a CF6-50 turbofan engine combustor and found to be in excellent agreement.

The vibrational spectrum of H2O3: An ab initio investigation

NASA Technical Reports Server (NTRS)

Jackels, Charles F.

1991-01-01

Theoretically determined frequencies and absorption intensities are reported for the vibrational spectrum of the covalent HOOOH and hydrogen bonded HO---HOO intermediates that may form in the reaction of the hydroxyl and hydroperoxyl radicals. Basis sets of DZP quality, augmented by diffuse and second sets of polarization functions have been used with CASSCF wave functions. The calculated harmonic vibrational frequencies of HOOOH have been corrected with empirical factors and presented in the form of a 'stick' spectrum. The oxygen backbone vibrations, predicted to occur at 519, 760, and 870 cm(exp -1), are well separated from most interferences, and may be the most useful for the species' identification. In the case of the hydrogen bonded isomer, emphasis has been placed upon prediction of the shifts in the intramolecular vibrational frequencies that take place upon formation of the complex. In particular, the HO stretch and HOO bend of HO2 are predicted to have shifts of -59 and 53 cm(exp -1), respectively, which should facilitate their identification. It is also noted that the antisymmetric stretching frequency of the oxygen backbone in HOOOH exhibits a strong sensitivity to the degree of electron correlation, such as has been previously observed for the same mode in ozone.

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML)

PubMed Central

Lechevalier, D.; Ak, R.; Ferguson, M.; Law, K. H.; Lee, Y.-T. T.; Rachuri, S.

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain. PMID:29202125

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML).

PubMed

Park, J; Lechevalier, D; Ak, R; Ferguson, M; Law, K H; Lee, Y-T T; Rachuri, S

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain.

Plane-Wave Implementation and Performance of à-la-Carte Coulomb-Attenuated Exchange-Correlation Functionals for Predicting Optical Excitation Energies in Some Notorious Cases.

PubMed

Bircher, Martin P; Rothlisberger, Ursula

2018-06-12

Linear-response time-dependent density functional theory (LR-TD-DFT) has become a valuable tool in the calculation of excited states of molecules of various sizes. However, standard generalized-gradient approximation and hybrid exchange-correlation (xc) functionals often fail to correctly predict charge-transfer (CT) excitations with low orbital overlap, thus limiting the scope of the method. The Coulomb-attenuation method (CAM) in the form of the CAM-B3LYP functional has been shown to reliably remedy this problem in many CT systems, making accurate predictions possible. However, in spite of a rather consistent performance across different orbital overlap regimes, some pitfalls remain. Here, we present a fully flexible and adaptable implementation of the CAM for Γ-point calculations within the plane-wave pseudopotential molecular dynamics package CPMD and explore how customized xc functionals can improve the optical spectra of some notorious cases. We find that results obtained using plane waves agree well with those from all-electron calculations employing atom-centered bases, and that it is possible to construct a new Coulomb-attenuated xc functional based on simple considerations. We show that such a functional is able to outperform CAM-B3LYP in some cases, while retaining similar accuracy in systems where CAM-B3LYP performs well.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

PubMed

Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G

2013-07-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

PubMed Central

Paraskevopoulou, Maria D.; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S.; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A.G.

2013-01-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA–gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines. PMID:23680784

What's Next: Recruitment of a Grounded Predictive Body Model for Planning a Robot's Actions.

PubMed

Schilling, Malte; Cruse, Holk

2012-01-01

Even comparatively simple, reactive systems are able to control complex motor tasks, such as hexapod walking on unpredictable substrate. The capability of such a controller can be improved by introducing internal models of the body and of parts of the environment. Such internal models can be applied as inverse models, as forward models or to solve the problem of sensor fusion. Usually, separate models are used for these functions. Furthermore, separate models are used to solve different tasks. Here we concentrate on internal models of the body as the brain considers its own body the most important part of the world. The model proposed is formed by a recurrent neural network with the property of pattern completion. The model shows a hierarchical structure but nonetheless comprises a holistic system. One and the same model can be used as a forward model, as an inverse model, for sensor fusion, and, with a simple expansion, as a model to internally simulate (new) behaviors to be used for prediction. The model embraces the geometrical constraints of a complex body with many redundant degrees of freedom, and allows finding geometrically possible solutions. To control behavior such as walking, climbing, or reaching, this body model is complemented by a number of simple reactive procedures together forming a procedural memory. In this article, we illustrate the functioning of this network. To this end we present examples for solutions of the forward function and the inverse function, and explain how the complete network might be used for predictive purposes. The model is assumed to be "innate," so learning the parameters of the model is not (yet) considered.

A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

PubMed Central

Tsolis, Antonios C.; Papandreou, Nikos C.; Iconomidou, Vassiliki A.; Hamodrakas, Stavros J.

2013-01-01

The purpose of this work was to construct a consensus prediction algorithm of ‘aggregation-prone’ peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/‘aggregation-prone’ peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins). PMID:23326595

Reactant conversion in homogeneous turbulence: Mathematical modeling, computational validations and practical applications

NASA Technical Reports Server (NTRS)

Madnia, C. K.; Frankel, S. H.; Givi, P.

1992-01-01

Closed form analytical expressions are obtained for predicting the limited rate of reactant conversion in a binary reaction of the type F + rO yields (1 + r) Product in unpremixed homogeneous turbulence. These relations are obtained by means of a single point Probability Density Function (PDF) method based on the Amplitude Mapping Closure. It is demonstrated that with this model, the maximum rate of the reactants' decay can be conveniently expressed in terms of definite integrals of the Parabolic Cylinder Functions. For the cases with complete initial segregation, it is shown that the results agree very closely with those predicted by employing a Beta density of the first kind for an appropriately defined Shvab-Zeldovich scalar variable. With this assumption, the final results can also be expressed in terms of closed form analytical expressions which are based on the Incomplete Beta Functions. With both models, the dependence of the results on the stoichiometric coefficient and the equivalence ratio can be expressed in an explicit manner. For a stoichiometric mixture, the analytical results simplify significantly. In the mapping closure, these results are expressed in terms of simple trigonometric functions. For the Beta density model, they are in the form of Gamma Functions. In all the cases considered, the results are shown to agree well with data generated by Direct Numerical Simulations (DNS). Due to the simplicity of these expressions and because of nice mathematical features of the Parabolic Cylinder and the Incomplete Beta Functions, these models are recommended for estimating the limiting rate of reactant conversion in homogeneous reacting flows. These results also provide useful insights in assessing the extent of validity of turbulence closures in the modeling of unpremixed reacting flows. Some discussions are provided on the extension of the model for treating more complicated reacting systems including realistic kinetics schemes and multi-scalar mixing with finite rate chemical reactions in more complex configurations.

Spectral simplicity of apparent complexity. I. The nondiagonalizable metadynamics of prediction

NASA Astrophysics Data System (ADS)

Riechers, Paul M.; Crutchfield, James P.

2018-03-01

Virtually all questions that one can ask about the behavioral and structural complexity of a stochastic process reduce to a linear algebraic framing of a time evolution governed by an appropriate hidden-Markov process generator. Each type of question—correlation, predictability, predictive cost, observer synchronization, and the like—induces a distinct generator class. Answers are then functions of the class-appropriate transition dynamic. Unfortunately, these dynamics are generically nonnormal, nondiagonalizable, singular, and so on. Tractably analyzing these dynamics relies on adapting the recently introduced meromorphic functional calculus, which specifies the spectral decomposition of functions of nondiagonalizable linear operators, even when the function poles and zeros coincide with the operator's spectrum. Along the way, we establish special properties of the spectral projection operators that demonstrate how they capture the organization of subprocesses within a complex system. Circumventing the spurious infinities of alternative calculi, this leads in the sequel, Part II [P. M. Riechers and J. P. Crutchfield, Chaos 28, 033116 (2018)], to the first closed-form expressions for complexity measures, couched either in terms of the Drazin inverse (negative-one power of a singular operator) or the eigenvalues and projection operators of the appropriate transition dynamic.

Prediction of spectral acceleration response ordinates based on PGA attenuation

USGS Publications Warehouse

Graizer, V.; Kalkan, E.

2009-01-01

Developed herein is a new peak ground acceleration (PGA)-based predictive model for 5% damped pseudospectral acceleration (SA) ordinates of free-field horizontal component of ground motion from shallow-crustal earthquakes. The predictive model of ground motion spectral shape (i.e., normalized spectrum) is generated as a continuous function of few parameters. The proposed model eliminates the classical exhausted matrix of estimator coefficients, and provides significant ease in its implementation. It is structured on the Next Generation Attenuation (NGA) database with a number of additions from recent Californian events including 2003 San Simeon and 2004 Parkfield earthquakes. A unique feature of the model is its new functional form explicitly integrating PGA as a scaling factor. The spectral shape model is parameterized within an approximation function using moment magnitude, closest distance to the fault (fault distance) and VS30 (average shear-wave velocity in the upper 30 m) as independent variables. Mean values of its estimator coefficients were computed by fitting an approximation function to spectral shape of each record using robust nonlinear optimization. Proposed spectral shape model is independent of the PGA attenuation, allowing utilization of various PGA attenuation relations to estimate the response spectrum of earthquake recordings.

Predictability and Quantification of Complex Groundwater Table Dynamics Driven by Irregular Surface Water Fluctuations

NASA Astrophysics Data System (ADS)

Xin, Pei; Wang, Shen S. J.; Shen, Chengji; Zhang, Zeyu; Lu, Chunhui; Li, Ling

2018-03-01

Shallow groundwater interacts strongly with surface water across a quarter of global land area, affecting significantly the terrestrial eco-hydrology and biogeochemistry. We examined groundwater behavior subjected to unimodal impulse and irregular surface water fluctuations, combining physical experiments, numerical simulations, and functional data analysis. Both the experiments and numerical simulations demonstrated a damped and delayed response of groundwater table to surface water fluctuations. To quantify this hysteretic shallow groundwater behavior, we developed a regression model with the Gamma distribution functions adopted to account for the dependence of groundwater behavior on antecedent surface water conditions. The regression model fits and predicts well the groundwater table oscillations resulting from propagation of irregular surface water fluctuations in both laboratory and large-scale aquifers. The coefficients of the Gamma distribution function vary spatially, reflecting the hysteresis effect associated with increased amplitude damping and delay as the fluctuation propagates. The regression model, in a relatively simple functional form, has demonstrated its capacity of reproducing high-order nonlinear effects that underpin the surface water and groundwater interactions. The finding has important implications for understanding and predicting shallow groundwater behavior and associated biogeochemical processes, and will contribute broadly to studies of groundwater-dependent ecology and biogeochemistry.

The energetics of heterogeneous deformation in open-cell elastic foams

NASA Astrophysics Data System (ADS)

Gioia, Gustavo; Cuitino, Alberto

2002-03-01

We study the energetics of a model of elastic foams to show that the stretch heterogeneity observed in experiments stems from the lack of convexity of the governing energy functional. The predicted stretch distributions correspond to stratified mixtures of two configurational phases of the foam. Stretching occurs in the form of a phase transition, by growth of one of the phases at the expense of the other. We also compare the predicted mechanical response with experimental data for foams of different densities. Lastly, we perform displacement field measurements using the digital image correlation technique, and find the results to be in agreement with our predictions.

Numerical evaluation of longitudinal motions of Wigley hulls advancing in waves by using Bessho form translating-pulsating source Green'S function

NASA Astrophysics Data System (ADS)

Xiao, Wenbin; Dong, Wencai

2016-06-01

In the framework of 3D potential flow theory, Bessho form translating-pulsating source Green's function in frequency domain is chosen as the integral kernel in this study and hybrid source-and-dipole distribution model of the boundary element method is applied to directly solve the velocity potential for advancing ship in regular waves. Numerical characteristics of the Green function show that the contribution of local-flow components to velocity potential is concentrated at the nearby source point area and the wave component dominates the magnitude of velocity potential in the far field. Two kinds of mathematical models, with or without local-flow components taken into account, are adopted to numerically calculate the longitudinal motions of Wigley hulls, which demonstrates the applicability of translating-pulsating source Green's function method for various ship forms. In addition, the mesh analysis of discrete surface is carried out from the perspective of ship-form characteristics. The study shows that the longitudinal motion results by the simplified model are somewhat greater than the experimental data in the resonant zone, and the model can be used as an effective tool to predict ship seakeeping properties. However, translating-pulsating source Green function method is only appropriate for the qualitative analysis of motion response in waves if the ship geometrical shape fails to satisfy the slender-body assumption.

Functional recovery patterns in seriously injured automotive crash victims.

PubMed

McMurry, Timothy L; Poplin, Gerald S; Crandall, Jeff

2016-09-01

The functional capacity index (FCI) is designed to predict functional loss 12 months post-injury for each injury in the 2008 Abbreviated Injury Scale (AIS) manual on a scale from 0 (death) to 100 (full recovery), but FCI has never been validated. This study compared FCI predicted loss with patient-reported 12-month outcomes as measured through the Short Form 36 (SF-36) health assessment survey. Using follow-up data collected on 2,858 adult car crash occupants in the Crash Injury Research and Engineering Network (CIREN) database, we compared FCI predicted outcomes to occupants' Physical Component Summary (PCS) scores, which are weighted averages of the SF-36 items addressing physical function. Our analyses included descriptive statistics, plots of typical recovery patterns, and a mixed effects regression model that describes PCS as a function of FCI, demographics, comorbidities, and injury pattern while also adjusting for the occupants' pre-crash physical capabilities. We further examined injuries in patients who report a significant drop in PCS 12 months post-crash despite being predicted to fully recover. At baseline, the CIREN population exhibited PCS scores similar to the overall population (mean = 51.1, SD = 10.3). Twelve months post-crash, occupants with predicted impairment (FCI < 100) report a substantial decrease in physical function, and those who were predicted to fully recover still report some, albeit less, impairment. In the multivariate mixed-effects regression model, FCI is a strongly significant (P-value <.0001) predictor of PCS, with each 1-point drop in FCI predicting a 0.27-point drop in PCS. Maximum AIS severities in the head, spine, and lower extremity body regions were also significantly associated with PCS (P-values <.05). Among occupants who were expected to fully recover but who report a significant drop in PCS at 12 months, spinal fractures without cord involvement account for 5 of the 10 most common AIS 2+ injuries. FCI was associated with 12-month outcomes but may not adequately describe the recovery from some head, spine, and lower extremity injuries. Some occupants who were expected to recover still report functional loss 12 months post-injury.

Examining the Construct Validity of the MMPI-2-RF Interpersonal Functioning Scales Using the Computerized Adaptive Test of Personality Disorder as a Comparative Framework.

PubMed

Franz, Annabel O; Harrop, Tiffany M; McCord, David M

2017-01-01

This study aimed to examine the construct validity of the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF) interpersonal functioning scales (Ben-Porath & Tellegen, 2008/2011 ) using as a criterion measure the Computerized Adaptive Test of Personality Disorder-Static Form (CAT-PD-SF; Simms et al., 2011 ). Participants were college students (n = 98) recruited through the university subject pool. A series of a priori hypotheses were developed for each of the 6 interpersonal functioning scales of the MMPI-2-RF, expressed as predicted correlations with construct-relevant CAT-PD-SF scales. Of the 27 specific predictions, 21 were supported by substantial (≥ |.30|) correlations. The MMPI-2-RF Family Problems scale (FML) demonstrated the strongest correlations with CAT-PD-SF scales Anhedonia and Mistrust; Cynicism (RC3) was most highly correlated with Mistrust and Norm Violation; Interpersonal Passivity (IPP) was most highly correlated with Domineering and Rudeness; Social Avoidance (SAV) was most highly correlated with Social Withdrawal and Anhedonia; Shyness (SHY) was most highly correlated with Social Withdrawal and Anxioiusness; and Disaffiliativeness (DSF) was most highly correlated with Emotional Detachment and Mistrust. Results are largely consistent with hypotheses suggesting support for both models of constructs relevant to interpersonal functioning. Future research designed to more precisely differentiate Social Avoidance (SAV) and Shyness (SHY) is suggested.

Comparison of Physician-Predicted to Measured Low Vision Outcomes

PubMed Central

Chan, Tiffany L.; Goldstein, Judith E.; Massof, Robert W.

2013-01-01

Purpose To compare low vision rehabilitation (LVR) physicians’ predictions of the probability of success of LVR to patients’ self-reported outcomes after provision of usual outpatient LVR services; and to determine if patients’ traits influence physician ratings. Methods The Activity Inventory (AI), a self-report visual function questionnaire, was administered pre and post-LVR to 316 low vision patients served by 28 LVR centers that participated in a collaborative observational study. The physical component of the Short Form-36, Geriatric Depression Scale, and Telephone Interview for Cognitive Status were also administered pre-LVR to measure physical capability, depression and cognitive status. Following patient evaluation, 38 LVR physicians estimated the probability of outcome success (POS), using their own criteria. The POS ratings and change in functional ability were used to assess the effects of patients’ baseline traits on predicted outcomes. Results A regression analysis with a hierarchical random effects model showed no relationship between LVR physician POS estimates and AI-based outcomes. In another analysis, Kappa statistics were calculated to determine the probability of agreement between POS and AI-based outcomes for different outcome criteria. Across all comparisons, none of the kappa values were significantly different from 0, which indicates the rate of agreement is equivalent to chance. In an exploratory analysis, hierarchical mixed effects regression models show that POS ratings are associated with information about the patient’s cognitive functioning and the combination of visual acuity and functional ability, as opposed to visual acuity or functional ability alone. Conclusions Physicians’ predictions of LVR outcomes appear to be influenced by knowledge of patients’ cognitive functioning and the combination of visual acuity and functional ability - information physicians acquire from the patient’s history and examination. However, physicians’ predictions do not agree with observed changes in functional ability from the patient’s perspective; they are no better than chance. PMID:23873036

Semileptonic decays of B and D mesons in the light-front formalism

NASA Astrophysics Data System (ADS)

Jaus, W.

1990-06-01

The light-front formalism is used to present a relativistic calculation of form factors for semileptonic D and B decays in the constituent quark model. The quark-antiquark wave functions of the mesons can be obtained, in principle, from an analysis of the meson spectrum, but are approximated in this work by harmonic-oscillator wave functions. The predictions of the model are consistent with the experimental data for B decays. The Kobayashi-Maskawa (KM) matrix element ||Vcs|| is determined by a comparison of the experimental and theoretical rates for D0-->K-e+ν, and is consistent with a unitary KM matrix for three families. The predictions for D-->K* transitions are in conflict with the data.

Degradome Products of the Matricellular Protein CCN1 as Modulators of Pathological Angiogenesis in the Retina*

PubMed Central

Choi, Jinok; Lin, Ann; Shrier, Eric; Lau, Lester F.; Grant, Maria B.; Chaqour, Brahim

2013-01-01

CCN1 is a matricellular protein involved in normal vascular development and tissue repair. CCN1 exhibits cell- and context-dependent activities that are reflective of its tetramodular structure phylogenetically linked to four domains found in various matrix proteins. Here, we show that vitreal fluids from patients with proliferative diabetic retinopathy (PDR) were enriched with a two-module form of CCN1 comprising completely or partially the insulin-like growth factor-binding protein (IGFBP) and von Willebrand factor type C (vWC) domains. The two- and three-module forms comprising, in addition to IGFBP and vWC, the thrombospondin type 1 (TSP1) repeats are CCN1 degradome products by matrix metalloproteinase-2 and -14. The functional significance of CCN1 and its truncated variants was determined in the mouse model of oxygen-induced retinopathy, which simulates neovascular growth associated with PDR and assesses treatment outcomes. In this model, lentivirus-mediated expression of either CCN1 or the IGFBP-vWC-TSP1 form reduced ischemia-induced neovascularization, whereas ectopic expression of the IGFBP-vWC variant exacerbated pathological angiogenesis. The IGFBP-vWC form has potent proangiogenic properties promoting retinal endothelial cell growth, migration, and three-dimensional tubular structure formation, whereas the IGFBP-vWC-TSP1 variant suppressed cell growth and angiogenic gene expression. Both IGFBP-vWC and IGFBP-vWC-TSP1 forms exhibited predictable variations of their domain folding that enhanced their functional potential. These data provide new insights into the formation and activities of CCN1-truncated variants and raise the predictive value of the form containing completely or partially the IGFBP and vWC domains as a surrogate marker of CCN1 activity in PDR distinguishing pathological from physiological angiogenesis. PMID:23798676

Reading the Road Signs: The Utility of the MMPI-2 Restructured Form Validity Scales in Prediction of Premature Termination.

PubMed

Anestis, Joye C; Finn, Jacob A; Gottfried, Emily; Arbisi, Paul A; Joiner, Thomas E

2015-06-01

This study examined the utility of the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF) Validity Scales in prediction of premature termination in a sample of 511 individuals seeking services from a university-based psychology clinic. Higher scores on True Response Inconsistency-Revised and Infrequent Psychopathology Responses increased the risk of premature termination, whereas higher scores on Adjustment Validity lowered the risk of premature termination. Additionally, when compared with individuals who did not prematurely terminate, individuals who prematurely terminated treatment had lower Global Assessment of Functioning scores at both intake and termination and made fewer improvements. Implications of these findings for the use of the MMPI-2-RF Validity Scales in promoting treatment compliance are discussed. © The Author(s) 2014.

Multidimensional Sexual Perfectionism and Female Sexual Function: A Longitudinal Investigation.

PubMed

Stoeber, Joachim; Harvey, Laura N

2016-11-01

Research on multidimensional sexual perfectionism differentiates four forms: self-oriented, partner-oriented, partner-prescribed, and socially prescribed. Self-oriented sexual perfectionism reflects perfectionistic standards people apply to themselves as sexual partners; partner-oriented sexual perfectionism reflects perfectionistic standards people apply to their sexual partner; partner-prescribed sexual perfectionism reflects people's beliefs that their sexual partner imposes perfectionistic standards on them; and socially prescribed sexual perfectionism reflects people's beliefs that society imposes such standards on them. Previous studies found partner-prescribed and socially prescribed sexual perfectionism to be maladaptive forms of sexual perfectionism associated with a negative sexual self-concept and problematic sexual behaviors, but only examined cross-sectional relationships. The present article presents the first longitudinal study examining whether multidimensional sexual perfectionism predicts changes in sexual self-concept and sexual function over time. A total of 366 women aged 17-69 years completed measures of multidimensional sexual perfectionism, sexual esteem, sexual anxiety, sexual problem self-blame, and sexual function (cross-sectional data). Three to six months later, 164 of the women completed the same measures again (longitudinal data). Across analyses, partner-prescribed sexual perfectionism emerged as the most maladaptive form of sexual perfectionism. In the cross-sectional data, partner-prescribed sexual perfectionism showed positive relationships with sexual anxiety, sexual problem self-blame, and intercourse pain, and negative relationships with sexual esteem, desire, arousal, lubrication, and orgasmic function. In the longitudinal data, partner-prescribed sexual perfectionism predicted increases in sexual anxiety and decreases in sexual esteem, arousal, and lubrication over time. The findings suggest that partner-prescribed sexual perfectionism contributes to women's negative sexual self-concept and female sexual dysfunction.

Effect of Evolutionary Anisotropy on Earing Prediction in Cylindrical Cup Drawing

NASA Astrophysics Data System (ADS)

Choi, H. J.; Lee, K. J.; Choi, Y.; Bae, G.; Ahn, D.-C.; Lee, M.-G.

2017-05-01

The formability of sheet metals is associated with their planar anisotropy, and finite element simulations have been applied to the sheet metal-forming process by describing the anisotropic behaviors using yield functions and hardening models. In this study, the evaluation of anisotropic constitutive models was performed based on the non-uniform height profile or earing in circular cylindrical cup drawing. Two yield functions, a quadratic Hill1948 and a non-quadratic Yld2000-2d model, were used under non-associated and associated flow rules, respectively, to simultaneously capture directional differences in yield stress and r value. The effect of the evolution of anisotropy on the earing prediction was also investigated by employing simplified equivalent plastic strain rate-dependent anisotropic coefficients. The computational results were in good agreement with experiments when the proper choice of the yield function and flow rule, which predicts the planar anisotropy, was made. Moreover, the accuracy of the earing profile could be significantly enhanced if the evolution of anisotropy between uniaxial and biaxial stress states was additionally considered.

Controlling the Surface Chemistry of Graphite by Engineered Self-Assembled Peptides

PubMed Central

Khatayevich, Dmitriy; So, Christopher R.; Hayamizu, Yuhei; Gresswell, Carolyn; Sarikaya, Mehmet

2012-01-01

The systematic control over surface chemistry is a long-standing challenge in biomedical and nanotechnological applications for graphitic materials. As a novel approach, we utilize graphite-binding dodecapeptides that self-assemble into dense domains to form monolayer thick long-range ordered films on graphite. Specifically, the peptides are rationally designed through their amino acid sequences to predictably display hydrophilic and hydrophobic characteristics while maintaining their self-assembly capabilities on the solid substrate. The peptides are observed to maintain a high tolerance for sequence modification, allowing the control over surface chemistry via their amino acid sequence. Furthermore, through a single step co-assembly of two different designed peptides, we predictably and precisely tune the wettability of the resulting functionalized graphite surfaces from 44 to 83 degrees. The modular molecular structures and predictable behavior of short peptides demonstrated here give rise to a novel platform for functionalizing graphitic materials that offers numerous advantages, including non-invasive modification of the substrate, bio-compatible processing in an aqueous environment, and simple fusion with other functional biological molecules. PMID:22428620

Adaptation, acclimation, and assembly: How optimality principles govern the scaling of form, function, and diversity of ecosystem function in the light of climate change.

NASA Astrophysics Data System (ADS)

Enquist, B. J.

2016-12-01

The link between variation in species-specific traits - due to acclimation, adaptation, and how ecological communities assemble in time and space - and larger scale ecosystem processes is an important focus for global change research. Understanding such linkages requires synthesis of evolutionary, biogeograpahic, and biogeochemical approaches. Recent observations reveal several paradoxical patterns across ecosystems. Optimality principles provide a novel framework for generating numerous predictions for how ecosystems have and will reorganize and respond to climate change. Tropical elevation gradients are natural laboratories to assess how changing climate can ramify to influence tropical forest diversity and ecosystem functioning. We tested several new predictions from trait- and metabolic scaling theories by assessing the covariation between climate, traits, biomass and gross and net primary productivity (GPP and NPP) across tropical forest plots spanning elevation gradients. We measured multiple leaf physiological, morphological, and stoichiometric traits linked to variation in tree growth. Consistent with theory, observed decreases in NPP and GPP with temperature were best predicted by forest biomass, and scaled allometrically as predicted by theory but the effect of temperature was much less, characterized by a kinetic response much lower ( 0.1eV) than predicted ( 0.65eV). This is likely due to an observed exponential increase in the mean community leaf P:N ratio and photosynthetic nutrient use efficiency with decreases in temperature. Our results are consistent with predictions from Trait Driver Theory, where adaptive/acclamatory shifts in plant traits compensate for the kinetic effects of temperature on tree growth. Further, most of the traits measured showed significantly skewed trait distributions consistent with recent observations that observed shifts in species composition. The development of trait-based scaling theory provides a robust basis to predict how shifts in climate have and will influence functional composition and ecosystem functioning. Together, these results highlight the potential critical importance optimality principles for understanding the role of the biosphere within the integrated earth system.

The Identities Hidden in the Matching Laws, and Their Uses

ERIC Educational Resources Information Center

Thorne, David R.

2010-01-01

Various theoretical equations have been proposed to predict response rate as a function of the rate of reinforcement. If both the rate and probability of reinforcement are considered, a simple identity, defining equation, or "law" holds. This identity places algebraic constraints on the allowable forms of our mathematical models and can help…

Physical health-related quality of life predicts stroke in the EPIC-Norfolk.

PubMed

Myint, P K; Surtees, P G; Wainwright, N W J; Luben, R N; Welch, A A; Bingham, S A; Wareham, N J; Khaw, K-T

2007-12-11

To examine the relationship between Short Form (SF)-36 physical functional health-related quality of life and incident stroke. A total of 13,615 men and women participating in the European Prospective Investigation into Cancer-Norfolk who were free of stroke, myocardial infarction, and cancer at baseline were included in the study. Participants completed a health and lifestyle questionnaire and attended a health examination during 1993 to 1997. Self-reported physical functional health was assessed using physical component summary scores of SF-36 18 months later. Stroke incidence was ascertained by death certification and hospital record linkage up to 2005. There were 244 incident strokes (total person years = 99,191). People who reported better physical functional health had significantly lower risk of incident stroke. Using Cox proportional hazard models adjusting for age, sex, body mass index, systolic blood pressure, cholesterol, smoking, diabetes, physical activity, social class, alcohol consumption, and respiratory function, men and women who were in the top quartile of SF-36 physical component summary scores had half the risk of stroke (RR = 0.50 [0.31, 0.78]) compared to the people in the bottom quartile. The relationships remained unchanged after excluding strokes occurring within the first 2 years of follow-up. Physical functional health-related quality of life measured as Short Form-36 predicts subsequent stroke risk independently of known risk factors in a general population. Poor physical functional health may indicate a high-risk population for stroke who may benefit most from targeted preventive interventions such as management of known risk factors.

Does the evolution of the radio luminosity function of star-forming galaxies match that of the star formation rate function?

NASA Astrophysics Data System (ADS)

Bonato, Matteo; Negrello, Mattia; Mancuso, Claudia; De Zotti, Gianfranco; Ciliegi, Paolo; Cai, Zhen-Yi; Lapi, Andrea; Massardi, Marcella; Bonaldi, Anna; Sajina, Anna; Smolčić, Vernesa; Schinnerer, Eva

2017-08-01

The assessment of the relationship between radio continuum luminosity and star formation rate (SFR) is of crucial importance to make reliable predictions for the forthcoming ultra-deep radio surveys and to allow a full exploitation of their results to measure the cosmic star formation history. We have addressed this issue by matching recent accurate determinations of the SFR function up to high redshifts with literature estimates of the 1.4 GHz luminosity functions of star-forming galaxies (SFGs). This was done considering two options, proposed in the literature, for the relationship between the synchrotron emission (Lsynch), that dominates at 1.4 GHz, and the SFR: a linear relation with a decline of the Lsynch/SFR ratio at low luminosities or a mildly non-linear relation at all luminosities. In both cases, we get good agreement with the observed radio luminosity functions but, in the non-linear case, the deviation from linearity must be small. The luminosity function data are consistent with a moderate increase of the Lsynch/SFR ratio with increasing redshift, indicated by other data sets, although a constant ratio cannot be ruled out. A stronger indication of such increase is provided by recent deep 1.4-GHz counts, down to μJy levels. This is in contradiction with models predicting a decrease of that ratio due to inverse Compton cooling of relativistic electrons at high redshifts. Synchrotron losses appear to dominate up to z ≃ 5. We have also updated the Massardi et al. evolutionary model for radio loud AGNs.

The Auditory Brain-Stem Response to Complex Sounds: A Potential Biomarker for Guiding Treatment of Psychosis

PubMed Central

Tarasenko, Melissa A.; Swerdlow, Neal R.; Makeig, Scott; Braff, David L.; Light, Gregory A.

2014-01-01

Cognitive deficits limit psychosocial functioning in schizophrenia. For many patients, cognitive remediation approaches have yielded encouraging results. Nevertheless, therapeutic response is variable, and outcome studies consistently identify individuals who respond minimally to these interventions. Biomarkers that can assist in identifying patients likely to benefit from particular forms of cognitive remediation are needed. Here, we describe an event-related potential (ERP) biomarker – the auditory brain-stem response (ABR) to complex sounds (cABR) – that appears to be particularly well-suited for predicting response to at least one form of cognitive remediation that targets auditory information processing. Uniquely, the cABR quantifies the fidelity of sound encoded at the level of the brainstem and midbrain. This ERP biomarker has revealed auditory processing abnormalities in various neurodevelopmental disorders, correlates with functioning across several cognitive domains, and appears to be responsive to targeted auditory training. We present preliminary cABR data from 18 schizophrenia patients and propose further investigation of this biomarker for predicting and tracking response to cognitive interventions. PMID:25352811

Controlling Release Kinetics of PLG Microspheres Using a Manufacturing Technique

NASA Astrophysics Data System (ADS)

Berchane, Nader

2005-11-01

Controlled drug delivery offers numerous advantages compared with conventional free dosage forms, in particular: improved efficacy and patient compliance. Emulsification is a widely used technique to entrap drugs in biodegradable microspheres for controlled drug delivery. The size of the formed microspheres has a significant influence on drug release kinetics. Despite the advantages of controlled drug delivery, previous attempts to achieve predetermined release rates have seen limited success. This study develops a tool to tailor desired release kinetics by combining microsphere batches of specified mean diameter and size distribution. A fluid mechanics based correlation that predicts the average size of Poly(Lactide-co-Glycolide) [PLG] microspheres from the manufacturing technique, is constructed and validated by comparison with experimental results. The microspheres produced are accurately represented by the Rosin-Rammler mathematical distribution function. A mathematical model is formulated that incorporates the microsphere distribution function to predict the release kinetics from mono-dispersed and poly-dispersed populations. Through this mathematical model, different release kinetics can be achieved by combining different sized populations in different ratios. The resulting design tool should prove useful for the pharmaceutical industry to achieve designer release kinetics.

Combined effect of polarity and pH on the chromatographic behavior of some angiotensin II receptor antagonists and optimization of their determination in pharmaceutical dosage forms.

PubMed

Demiralay, Ebru Cubuk; Cubuk, Burcu; Ozkan, Sibel A; Alsancak, Guleren

2010-11-02

In the present study, the combined effect of mobile phase polarity and pH on retention behavior of some ARA-IIs (irbesartan, losartan, valsartan and telmisartan) is investigated. The linear relationships established between retention factors of the species and the polarity parameter of the mobile phase has proved to predict accurately retention in LC as a function of the acetonitrile content (50%, 55%, 60%, v/v). The suggested model uses the pH value in the acetonitrile-water mixture as mobile phase instead of pH value in water and takes into account the effect of activity coefficients. Moreover, correlation between retention and the mobile phase pH can be established allowing prediction of the retention behavior as a function of the mobile phase pH. The model can be used to estimate the pKa in an acetonitrile percentage between 50% and 60%, at 30 degrees C. The developed method was successfully applied to both the simultaneous separation of these drug-active compounds and individual determination in their commercial pharmaceutical dosage forms.

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

Interactions between Callous Unemotional Behaviors and Executive Function in Early Childhood Predict later Aggression and Lower Peer-liking in Late-childhood.

PubMed

Waller, Rebecca; Hyde, Luke W; Baskin-Sommers, Arielle R; Olson, Sheryl L

2017-04-01

Callous unemotional (CU) behaviors are linked to aggression, behavior problems, and difficulties in peer relationships in children and adolescents. However, few studies have examined whether early childhood CU behaviors predict aggression or peer-rejection during late-childhood or potential moderation of this relationship by executive function. The current study examined whether the interaction of CU behaviors and executive function in early childhood predicted different forms of aggression in late-childhood, including proactive, reactive, and relational aggression, as well as how much children were liked by their peers. Data from cross-informant reports and multiple observational tasks were collected from a high-risk sample (N = 240; female = 118) at ages 3 and 10 years old. Parent reports of CU behaviors at age 3 predicted teacher reports of reactive, proactive, and relational aggression, as well as lower peer-liking at age 10. Moderation analysis showed that specifically at high levels of CU behaviors and low levels of observed executive function, children were reported by teachers as showing greater reactive and proactive aggression, and were less-liked by peers. Findings demonstrate that early childhood CU behaviors and executive function have unique main and interactive effects on both later aggression and lower peer-liking even when taking into account stability in behavior problems over time. By elucidating how CU behaviors and deficits in executive function potentiate each other during early childhood, we can better characterize the emergence of severe and persistent behavior and interpersonal difficulties across development.

Longitudinal Effects of Latino Parent Cultural Stress, Depressive Symptoms, and Family Functioning on Youth Emotional Well-Being and Health Risk Behaviors.

PubMed

Lorenzo-Blanco, Elma I; Meca, Alan; Unger, Jennifer B; Romero, Andrea; Szapocznik, José; Piña-Watson, Brandy; Cano, Miguel Ángel; Zamboanga, Byron L; Baezconde-Garbanati, Lourdes; Des Rosiers, Sabrina E; Soto, Daniel W; Villamar, Juan A; Lizzi, Karina M; Pattarroyo, Monica; Schwartz, Seth J

2017-12-01

U.S. Latino parents can face cultural stressors in the form of acculturative stress, perceived discrimination, and a negative context of reception. It stands to reason that these cultural stressors may negatively impact Latino youth's emotional well-being and health risk behaviors by increasing parents' depressive symptoms and compromising the overall functioning of the family. To test this possibility, we analyzed data from a six-wave longitudinal study with 302 recently immigrated (<5 years in the United States) Latino parents (74% mothers, M age  = 41.09 years) and their adolescent children (47% female, M age  = 14.51 years). Results of a cross-lagged analysis indicated that parent cultural stress predicted greater parent depressive symptoms (and not vice versa). Both parent cultural stress and depressive symptoms, in turn, predicted lower parent-reported family functioning, which mediated the links from parent cultural stress and depressive symptoms to youth alcohol and cigarette use. Parent cultural stress also predicted lower youth-reported family functioning, which mediated the link from parent cultural stress to youth self-esteem. Finally, mediation analyses indicated that parent cultural stress predicted youth alcohol use by a way of parent depressive symptoms and parent-reported family functioning. Our findings point to parent depressive symptoms and family functioning as key mediators in the links from parent cultural stress to youth emotional well-being and health risk behaviors. We discuss implications for research and preventive interventions. © 2016 Family Process Institute.

Rough-to-smooth transition of an equilibrium neutral constant stress layer

NASA Technical Reports Server (NTRS)

Logan, E., Jr.; Fichtl, G. H.

1975-01-01

Purpose of research on rough-to-smooth transition of an equilibrium neutral constant stress layer is to develop a model for low-level atmospheric flow over terrains of abruptly changing roughness, such as those occurring near the windward end of a landing strip, and to use the model to derive functions which define the extent of the region affected by the roughness change and allow adequate prediction of wind and shear stress profiles at all points within the region. A model consisting of two bounding logarithmic layers and an intermediate velocity defect layer is assumed, and dimensionless velocity and stress distribution functions which meet all boundary and matching conditions are hypothesized. The functions are used in an asymptotic form of the equation of motion to derive a relation which governs the growth of the internal boundary layer. The growth relation is used to predict variation of surface shear stress.

Expanded explorations into the optimization of an energy function for protein design

PubMed Central

Huang, Yao-ming; Bystroff, Christopher

2014-01-01

Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here we present new insights towards the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross-terms correct for the observed non-additivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at ACM-BCB, Orlando FL , October 2012. PMID:24384706

Fundamental gaps with approximate density functionals: The derivative discontinuity revealed from ensemble considerations

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

Kraisler, Eli; Kronik, Leeor

2014-05-14

The fundamental gap is a central quantity in the electronic structure of matter. Unfortunately, the fundamental gap is not generally equal to the Kohn-Sham gap of density functional theory (DFT), even in principle. The two gaps differ precisely by the derivative discontinuity, namely, an abrupt change in slope of the exchange-correlation energy as a function of electron number, expected across an integer-electron point. Popular approximate functionals are thought to be devoid of a derivative discontinuity, strongly compromising their performance for prediction of spectroscopic properties. Here we show that, in fact, all exchange-correlation functionals possess a derivative discontinuity, which arises naturallymore » from the application of ensemble considerations within DFT, without any empiricism. This derivative discontinuity can be expressed in closed form using only quantities obtained in the course of a standard DFT calculation of the neutral system. For small, finite systems, addition of this derivative discontinuity indeed results in a greatly improved prediction for the fundamental gap, even when based on the most simple approximate exchange-correlation density functional – the local density approximation (LDA). For solids, the same scheme is exact in principle, but when applied to LDA it results in a vanishing derivative discontinuity correction. This failure is shown to be directly related to the failure of LDA in predicting fundamental gaps from total energy differences in extended systems.« less

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

DOE PAGES

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.; ...

2016-09-20

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Microbial genome analysis: the COG approach.

PubMed

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Formulation and process considerations affecting the stability of solid dosage forms formulated with methacrylate copolymers.

PubMed

Petereit, H U; Weisbrod, W

1999-01-01

General considerations concerning the stability of coated dosage forms are discussed, in order to avoid predictable interactions which may cause long-term stability problems. As polymers themselves maintain a high chemical stability and a low reactivity, instability phenomena mainly have to be explained by interactions of low molecular weight substances or physical changes. Possible interactions of functional groups can be predicted easily and insulating subcoates are proper countermeasures. Impurities, remaining in the polymeric material from the manufacturing process, may accelerate the hydrolysis of sensitive drugs. Instabilities of coated dosage forms are mainly based on physical interactions, caused by improper formulations of coating suspensions (i.e. plasticizers or pigments) or the film coating process. Residual moisture or solvents, probably enclosed in the core and migrating over time, may increase the permeability of coatings, due to plasticizing effects. The functionality of coatings from aqueous dispersions is linked to coalescence of latex particles. Thus any incomplete film formation, caused by too high or too low coating temperatures, may result in high permeable coatings. During storage, preferably under stress conditions this process will continue and thus change the release profile. Therefore bed temperatures of 10-20 degrees C above MFT must ensure the formation of homogeneous polymer layers during the coating process. Stability test procedures and packaging materials also need to be adapted to the physicochemical properties of the dosage form, in order to get meaningful results in stability tests.

Prefrontal-Hippocampal-Fusiform Activity During Encoding Predicts Intraindividual Differences in Free Recall Ability: An Event-Related Functional-Anatomic MRI Study

PubMed Central

Dickerson, B.C.; Miller, S.L.; Greve, D.N.; Dale, A.M.; Albert, M.S.; Schacter, D.L.; Sperling, R.A.

2009-01-01

The ability to spontaneously recall recently learned information is a fundamental mnemonic activity of daily life, but has received little study using functional neuroimaging. We developed a functional MRI (fMRI) paradigm to study regional brain activity during encoding that predicts free recall. In this event-related fMRI study, ten lists of fourteen pictures of common objects were shown to healthy young individuals and regional brain activity during encoding was analyzed based on subsequent free recall performance. Free recall of items was predicted by activity during encoding in hippocampal, fusiform, and inferior prefrontal cortical regions. Within-subject variance in free recall performance for the ten lists was predicted by a linear combination of condition-specific inferior prefrontal, hippocampal, and fusiform activity. Recall performance was better for lists in which pre-frontal activity was greater for all items of the list and hippocampal and fusi-form activity were greater specifically for items that were recalled from the list. Thus, the activity of medial temporal, fusiform, and prefrontal brain regions during the learning of new information is important for the subsequent free recall of this information. These fronto-temporal brain regions act together as a large-scale memory-related network, the components of which make distinct yet interacting contributions during encoding that predict subsequent successful free recall performance. PMID:17604356

Elevated Peak Postoperative B-type Natriuretic Peptide Predicts Decreased Longer-Term Physical Function after Primary Coronary Artery Bypass Graft Surgery

PubMed Central

Fox, Amanda A.; Marcantonio, Edward R.; Collard, Charles D.; Thoma, Mathis; Perry, Tjorvi E.; Shernan, Stanton K.; Muehlschlegel, Jochen D.; Body, Simon C.

2011-01-01

Background Elevated peak postoperative B-type natriuretic peptide (BNP) is associated with increased major adverse cardiovascular events and all-cause mortality after coronary artery bypass graft (CABG) surgery. Whether elevated postoperative BNP predicts worse post-discharge physical function (PF) is unknown. We hypothesized that peak postoperative BNP associates with PF assessed up to 2 years after CABG surgery, even after adjusting for clinical risk factors including preoperative PF. Methods This two institution prospective cohort study included patients undergoing primary CABG surgery with cardiopulmonary bypass. Short Form-36 questionnaires were administered to subjects preoperatively and 6 months, 1 and 2 years postoperatively. Short Form-36 PF domain scores were calculated using the Short Form-36 norm based scoring algorithm. Plasma BNP concentrations measured preoperatively and on postoperative days 1–5 were log10 transformed before analysis. To determine whether peak postoperative BNP independently predicts PF scores 6 months through 2 years after CABG surgery, multivariable longitudinal regression analysis of the postoperative PF scores was performed, adjusting for important clinical risk factors. Results 845 subjects (mean age±SD: 65±10 years) were analyzed. Peak postoperative BNP was significantly associated with postoperative PF (effect estimate for log10 peak BNP = −7.66 PF score points; 95% CI = −9.68, −5.64; P=<0.0001). After multivariable adjustments, peak postoperative BNP remained independently associated with postoperative PF (effect estimate for log10 peak BNP =−3.06 PF score points; 95% CI = −5.15, −0.97; P=0.004). Conclusions Elevated peak postoperative BNP independently associates with worse longer-term physical function after primary CABG surgery. Future studies are needed to determine whether medical management targeted towards reducing elevated postoperative BNP can improve PF after CABG surgery. PMID:21427536

Forms of non-suicidal self-injury as a function of trait aggression.

PubMed

Kleiman, Evan M; Ammerman, Brooke A; Kulper, Daniel A; Uyeji, Lauren L; Jenkins, Abigail L; McCloskey, Michael S

2015-05-01

To date, the considerable body of research on predictors of non-suicidal self-injury (NSSI) has conceptualized NSSI as a unitary construct despite the fact that NSSI can exist in many forms (e.g., hitting, cutting, burning). The goal of the present study is to examine differential prediction of forms of NSSI. Specifically, we examined trait aggression as a predictor of more aggressive forms of NSSI (i.e., hitting). We hypothesized that higher trait aggression would differentiate those who engaged in hitting forms of NSSI from those who did not, whereas other factors (i.e., emotion regulation and trait anger) would serve as a non-specific predictor of NSSI. We also hypothesized that higher trait aggression would be related to lifetime frequency of hitting NSSI, but not other forms of NSSI, whereas emotion regulation and anger would act as predictors of other forms of NSSI. To test these hypotheses, a large sample of young adults completed measures of trait aggression, trait anger, emotion regulation, and NSSI behaviors. Results were generally in line with our hypotheses. Higher levels of trait aggression differentiated those who engaged in hitting NSSI from those who did not and was also associated with greater frequency of hitting NSSI. These results imply that different factors predict different forms of NSSI and that NSSI may be best examined as a multi-faceted construct. Copyright © 2015 Elsevier Inc. All rights reserved.

A Comparison of QSAR Based Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected Traditional Chemical Warfare Agents and Simulants

DTIC Science & Technology

2014-07-01

Labs uses parameterized Hammett -type equations to describe 1500 possible combinations of more than 650 ionizable functional groups. The change in...of the form ⋯ , ⋯ Equation (1) where Ypred is the predicted property, c0 is a constant, c1 to cn are coefficients from the...regression to the training set of measurements, X1 to Xn represent molecular or fragment or field-based descriptors, and the final term in Equation 1

The basis function approach for modeling autocorrelation in ecological data

USGS Publications Warehouse

Hefley, Trevor J.; Broms, Kristin M.; Brost, Brian M.; Buderman, Frances E.; Kay, Shannon L.; Scharf, Henry; Tipton, John; Williams, Perry J.; Hooten, Mevin B.

2017-01-01

Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data.

Application of a New Resource-Constrained Triage Method to Military-Age Victims

DTIC Science & Technology

2009-12-01

evidence based, does not consider resources, and has been shown to be scientifically and opera- tionally flawed.’ General P . K. Carlton, former USAF Surgeon...metric that can be used to predict sur- vival probability) P ^ (t) = the survival probability of victims with original SCORE s treated in time period t. n...function coefficients were derived on the design set, and validated on the test set. The logistic function has the form: P ^ - 1/(1 + e"), where P ^ is

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

PubMed

Fekete, Attila; Komáromi, István

2016-12-07

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Processing Speed Predicts Behavioral Treatment Outcomes in Children with Attention-Deficit/Hyperactivity Disorder Predominantly Inattentive Type.

PubMed

Adalio, Christopher J; Owens, Elizabeth B; McBurnett, Keith; Hinshaw, Stephen P; Pfiffner, Linda J

2018-05-01

Neuropsychological functioning underlies behavioral symptoms of attention-deficit/hyperactivity disorder (ADHD). Children with all forms of ADHD are vulnerable to working memory deficits and children presenting with the inattentive form of ADHD (ADHD-I) appear particularly vulnerable to processing speed deficits. As ADHD-I is the most common form of ADHD presented by children in community settings, it is important to consider how treatment interventions for children with ADHD-I may be affected by deficits in processing speed and working memory. We utilize data collected from 199 children with ADHD-I, aged 7 to 11 years, who participated in a randomized clinical trial of a psychosocial-behavioral intervention. Our aims are first to determine whether processing speed or working memory predict treatment outcomes in ADHD-I symptom severity, and second whether they moderate treatment effects on ADHD-I symptom severity. Results of linear regression analyses reveal that baseline processing speed significantly predicts posttreatment ADHD-I symptom severity when controlling for baseline ADHD-I symptom severity, such that better processing speed is associated with greater symptom improvement. However, predictive effects of working memory and moderation effects of both working memory and processing speed are not supported in the present study. We discuss study limitations and implications of the relation between processing speed and treatment benefits from psychosocial treatments for children with ADHD-I.

Geostatistical Interpolation of Particle-Size Curves in Heterogeneous Aquifers

NASA Astrophysics Data System (ADS)

Guadagnini, A.; Menafoglio, A.; Secchi, P.

2013-12-01

We address the problem of predicting the spatial field of particle-size curves (PSCs) from measurements associated with soil samples collected at a discrete set of locations within an aquifer system. Proper estimates of the full PSC are relevant to applications related to groundwater hydrology, soil science and geochemistry and aimed at modeling physical and chemical processes occurring in heterogeneous earth systems. Hence, we focus on providing kriging estimates of the entire PSC at unsampled locations. To this end, we treat particle-size curves as cumulative distribution functions, model their densities as functional compositional data and analyze them by embedding these into the Hilbert space of compositional functions endowed with the Aitchison geometry. On this basis, we develop a new geostatistical methodology for the analysis of spatially dependent functional compositional data. Our functional compositional kriging (FCK) approach allows providing predictions at unsampled location of the entire particle-size curve, together with a quantification of the associated uncertainty, by fully exploiting both the functional form of the data and their compositional nature. This is a key advantage of our approach with respect to traditional methodologies, which treat only a set of selected features (e.g., quantiles) of PSCs. Embedding the full PSC into a geostatistical analysis enables one to provide a complete characterization of the spatial distribution of lithotypes in a reservoir, eventually leading to improved predictions of soil hydraulic attributes through pedotransfer functions as well as of soil geochemical parameters which are relevant in sorption/desorption and cation exchange processes. We test our new method on PSCs sampled along a borehole located within an alluvial aquifer near the city of Tuebingen, Germany. The quality of FCK predictions is assessed through leave-one-out cross-validation. A comparison between hydraulic conductivity estimates obtained via FCK approach and those predicted by classical kriging of effective particle diameters (i.e., quantiles of the PSCs) is finally performed.

Perturbative corrections to B → D form factors in QCD

NASA Astrophysics Data System (ADS)

Wang, Yu-Ming; Wei, Yan-Bing; Shen, Yue-Long; Lü, Cai-Dian

2017-06-01

We compute perturbative QCD corrections to B → D form factors at leading power in Λ/ m b , at large hadronic recoil, from the light-cone sum rules (LCSR) with B-meson distribution amplitudes in HQET. QCD factorization for the vacuum-to- B-meson correlation function with an interpolating current for the D-meson is demonstrated explicitly at one loop with the power counting scheme {m}_c˜ O(√{Λ {m}_b}) . The jet functions encoding information of the hard-collinear dynamics in the above-mentioned correlation function are complicated by the appearance of an additional hard-collinear scale m c , compared to the counterparts entering the factorization formula of the vacuum-to- B-meson correction function for the construction of B → π from factors. Inspecting the next-to-leading-logarithmic sum rules for the form factors of B → Dℓν indicates that perturbative corrections to the hard-collinear functions are more profound than that for the hard functions, with the default theory inputs, in the physical kinematic region. We further compute the subleading power correction induced by the three-particle quark-gluon distribution amplitudes of the B-meson at tree level employing the background gluon field approach. The LCSR predictions for the semileptonic B → Dℓν form factors are then extrapolated to the entire kinematic region with the z-series parametrization. Phenomenological implications of our determinations for the form factors f BD +,0 ( q 2) are explored by investigating the (differential) branching fractions and the R( D) ratio of B → Dℓν and by determining the CKM matrix element |V cb | from the total decay rate of B → Dμν μ .

Hadronic Form Factors in Asymptotically Free Field Theories

DOE R&D Accomplishments Database

Gross, D. J.; Treiman, S. B.

1974-01-01

The breakdown of Bjorken scaling in asymptotically free gauge theories of the strong interactions is explored for its implications on the large q{sup 2} behavior of nucleon form factors. Duality arguments of Bloom and Gilman suggest a connection between the form factors and the threshold properties of the deep inelastic structure functions. The latter are addressed directly in an analysis of asymptotically free theories; and through the duality connection we are then led to statements about the form factors. For very large q{sup 2} the form factors are predicted to fall faster than any inverse power of q{sup 2}. For the more modest range of q{sup 2} reached in existing experiments the agreement with data is fairly good, though this may well be fortuitous. Extrapolations beyond this range are presented.

Resolving phase stability in the Ti-O binary with first-principles statistical mechanics methods

NASA Astrophysics Data System (ADS)

Gunda, N. S. Harsha; Puchala, Brian; Van der Ven, Anton

2018-03-01

The Ti-O system consists of a multitude of stable and metastable oxides that are used in wide ranging applications. In this work we investigate phase stability in the Ti-O binary from first principles. We perform a systematic search for ground state structures as a function of oxygen concentration by considering oxygen-vacancy and/or titanium-vacancy orderings over four parent crystal structures: (i) hcp Ti, (ii) ω -Ti, (iii) rocksalt, and (iv) hcp oxygen containing interstitial titanium. We explore phase stability at finite temperature using cluster expansion Hamiltonians and Monte Carlo simulations. The calculations predict a high oxygen solubility in hcp Ti and the stability of suboxide phases that undergo order-disorder transitions upon heating. Vacancy ordered rocksalt phases are also predicted at low temperature that disorder to form an extended solid solution at high temperatures. Predicted stable and metastable phase diagrams are qualitatively consistent with experimental observations, however, important discrepancies are revealed between first-principles density functional theory predictions of phase stability and the current understanding of phase stability in this system.

Beta Dips in the Gaia Era: Simulation Predictions of the Galactic Velocity Anisotropy Parameter (β)

NASA Astrophysics Data System (ADS)

Loebman, Sarah; Valluri, Monica; Hattori, Kohei; Debattista, Victor P.; Bell, Eric F.; Stinson, Greg; Christensen, Charlotte; Brooks, Alyson; Quinn, Thomas R.; Governato, Fabio

2017-01-01

Milky Way (MW) science has entered a new era with the advent of Gaia. Combined with spectroscopic survey data, we have newfound access to full 6D phase space information for halo stars. Such data provides an invaluable opportunity to assess kinematic trends as a function of radius and confront simulations with these observations to draw insight about our merger history. I will discuss predictions for the velocity anisotropy parameter, β, drawn from three suites of state-of-the-art cosmological N-body and N-body+SPH MW-like simulations. On average, all three suites predict a monotonically increasing value of β that is radially biased, and beyond 10 kpc, β > 0.5. I will also discuss β as a function of time for individual simulated galaxies. I will highlight when "dips" in β form, the severity (the rarity of β < 0), origin (in situ versus accreted halo), and persistence of these dips. Thereby, I present a cohesive set of predictions of β from simulations for comparison to forthcoming observations.

Calculation and validation of heat transfer coefficient for warm forming operations

NASA Astrophysics Data System (ADS)

Omer, Kaab; Butcher, Clifford; Worswick, Michael

2017-10-01

In an effort to reduce the weight of their products, the automotive industry is exploring various hot forming and warm forming technologies. One critical aspect in these technologies is understanding and quantifying the heat transfer between the blank and the tooling. The purpose of the current study is twofold. First, an experimental procedure to obtain the heat transfer coefficient (HTC) as a function of pressure for the purposes of a metal forming simulation is devised. The experimental approach was used in conjunction with finite element models to obtain HTC values as a function of die pressure. The materials that were characterized were AA5182-O and AA7075-T6. Both the heating operation and warm forming deep draw were modelled using the LS-DYNA commercial finite element code. Temperature-time measurements were obtained from both applications. The results of the finite element model showed that the experimentally derived HTC values were able to predict the temperature-time history to within a 2% of the measured response. It is intended that the HTC values presented herein can be used in warm forming models in order to accurately capture the heat transfer characteristics of the operation.

Functional formation of domain V of the poliovirus noncoding region: significance of unpaired bases.

PubMed

Rowe, A; Burlison, J; Macadam, A J; Minor, P D

2001-10-10

Previously we have shown that polioviruses with mutations that disrupt the predicted secondary structure of the 5' noncoding region of domain V are temperature sensitive for growth. Non-temperature-sensitive revertant viruses had mutations that re-formed secondary structure by a direct back mutation of changes in the opposite strand. We mutated unpaired regions and selected revertants of viruses with single base deletions, where no obvious back mutation was available in order to gain information on secondary structure. Results indicated that conservation of length of a three base loop between two double-stranded stems was essential for a functional domain V to form. The requirement for the unpaired "hinge" base at 484 which is implicated in the attenuation of Sabin 2 was also confirmed. Results also underline the necessity for functional folding over local secondary structure stability. Copyright 2001 Academic Press.

Linking density functional and mode coupling models for supercooled liquids

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

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P.

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicitymore » transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.« less

Determining the functional form of density dependence: deductive approaches for consumer-resource systems having a single resource.

PubMed

Abrams, Peter A

2009-09-01

Consumer-resource models are used to deduce the functional form of density dependence in the consumer population. A general approach to determining the form of consumer density dependence is proposed; this involves determining the equilibrium (or average) population size for a series of different harvest rates. The relationship between a consumer's mortality and its equilibrium population size is explored for several one-consumer/one-resource models. The shape of density dependence in the resource and the shape of the numerical and functional responses all tend to be "inherited" by the consumer's density dependence. Consumer-resource models suggest that density dependence will very often have both concave and convex segments, something that is impossible under the commonly used theta-logistic model. A range of consumer-resource models predicts that consumer population size often declines at a decelerating rate with mortality at low mortality rates, is insensitive to or increases with mortality over a wide range of intermediate mortalities, and declines at a rapidly accelerating rate with increased mortality when mortality is high. This has important implications for management and conservation of natural populations.

Axon and dendrite geography predict the specificity of synaptic connections in a functioning spinal cord network.

PubMed

Li, Wen-Chang; Cooke, Tom; Sautois, Bart; Soffe, Stephen R; Borisyuk, Roman; Roberts, Alan

2007-09-10

How specific are the synaptic connections formed as neuronal networks develop and can simple rules account for the formation of functioning circuits? These questions are assessed in the spinal circuits controlling swimming in hatchling frog tadpoles. This is possible because detailed information is now available on the identity and synaptic connections of the main types of neuron. The probabilities of synapses between 7 types of identified spinal neuron were measured directly by making electrical recordings from 500 pairs of neurons. For the same neuron types, the dorso-ventral distributions of axons and dendrites were measured and then used to calculate the probabilities that axons would encounter particular dendrites and so potentially form synaptic connections. Surprisingly, synapses were found between all types of neuron but contact probabilities could be predicted simply by the anatomical overlap of their axons and dendrites. These results suggested that synapse formation may not require axons to recognise specific, correct dendrites. To test the plausibility of simpler hypotheses, we first made computational models that were able to generate longitudinal axon growth paths and reproduce the axon distribution patterns and synaptic contact probabilities found in the spinal cord. To test if probabilistic rules could produce functioning spinal networks, we then made realistic computational models of spinal cord neurons, giving them established cell-specific properties and connecting them into networks using the contact probabilities we had determined. A majority of these networks produced robust swimming activity. Simple factors such as morphogen gradients controlling dorso-ventral soma, dendrite and axon positions may sufficiently constrain the synaptic connections made between different types of neuron as the spinal cord first develops and allow functional networks to form. Our analysis implies that detailed cellular recognition between spinal neuron types may not be necessary for the reliable formation of functional networks to generate early behaviour like swimming.

Solar-cell interconnect design for terrestrial photovoltaic modules

NASA Technical Reports Server (NTRS)

Mon, G. R.; Moore, D. M.; Ross, R. G., Jr.

1984-01-01

Useful solar cell interconnect reliability design and life prediction algorithms are presented, together with experimental data indicating that the classical strain cycle (fatigue) curve for the interconnect material does not account for the statistical scatter that is required in reliability predictions. This shortcoming is presently addressed by fitting a functional form to experimental cumulative interconnect failure rate data, which thereby yields statistical fatigue curves enabling not only the prediction of cumulative interconnect failures during the design life of an array field, but also the quantitative interpretation of data from accelerated thermal cycling tests. Optimal interconnect cost reliability design algorithms are also derived which may allow the minimization of energy cost over the design life of the array field.

Solar-cell interconnect design for terrestrial photovoltaic modules

NASA Astrophysics Data System (ADS)

Mon, G. R.; Moore, D. M.; Ross, R. G., Jr.

1984-11-01

Useful solar cell interconnect reliability design and life prediction algorithms are presented, together with experimental data indicating that the classical strain cycle (fatigue) curve for the interconnect material does not account for the statistical scatter that is required in reliability predictions. This shortcoming is presently addressed by fitting a functional form to experimental cumulative interconnect failure rate data, which thereby yields statistical fatigue curves enabling not only the prediction of cumulative interconnect failures during the design life of an array field, but also the quantitative interpretation of data from accelerated thermal cycling tests. Optimal interconnect cost reliability design algorithms are also derived which may allow the minimization of energy cost over the design life of the array field.

A comparison of two modeling approaches for evaluating wildlife--habitat relationships

Treesearch

Ryan A. Long; Jonathan D. Muir; Janet L. Rachlow; John G. Kie

2009-01-01

Studies of resource selection form the basis for much of our understanding of wildlife habitat requirements, and resource selection functions (RSFs), which predict relative probability of use, have been proposed as a unifying concept for analysis and interpretation of wildlife habitat data. Logistic regression that contrasts used and available or unused resource units...

Effects of Family Functioning and Parenting Style on Early Entrants' Academic Performance and Program Completion

ERIC Educational Resources Information Center

Huey, Erron L.; Sayler, Michael F.; Rinn, Anne N.

2013-01-01

The purpose of the current study was to examine the predictive nature of parenting style and overall family environment on the academic performance and program completion of early college entrants. Furthermore, gender and family form were examined as possible moderators to these relationships. A total of 88 early college entrants participated in…

Do Allegations of Emotional Maltreatment Predict Developmental Outcomes beyond that of Other Forms of Maltreatment?

ERIC Educational Resources Information Center

Schneider, M.W.; Ross, A.; Graham, J.C.; Zielinski, A.

2005-01-01

Objectives:: To understand the features of child abuse/neglect (CA/N) allegations in cases with emotional maltreatment (EMT) allegations, as well as the features of the EMT allegations themselves, and to describe any associations of EMT with distinct impairments of children's behavior, emotion and functioning. Method:: The sample consisted of 806…

Hydraulic integration and shrub growth form linked across continental aridity gradients

Treesearch

H. Jochen Schenk; Christine M. Goedhart; Marisa Nordenstahl; Hugo I. Martinez Cabrera; Cynthia S. Jones

2008-01-01

Both engineered hydraulic systems and plant hydraulic systems are protected against failure by resistance, reparability, and redundancy. A basic rule of reliability engineering is that the level of independent redundancy should increase with increasing risk of fatal system failure. Here we show that hydraulic systems of plants function as predicted by this engineering...

Predicting Body Fat Using Data on the BMI

ERIC Educational Resources Information Center

Mills, Terence C.

2005-01-01

A data set contained in the "Journal of Statistical Education's" data archive provides a way of exploring regression analysis at a variety of teaching levels. An appropriate functional form for the relationship between percentage body fat and the BMI is shown to be the semi-logarithmic, with variation in the BMI accounting for a little over half…

Stellar mass and velocity functions of galaxies. Backward evolution and the fate of Milky Way siblings

NASA Astrophysics Data System (ADS)

Boissier, S.; Buat, V.; Ilbert, O.

2010-11-01

Context. In recent years, stellar mass functions of both star-forming and quiescent galaxies have been observed at different redshifts in various fields. In addition, star formation rate (SFR) distributions (e.g. in the form of far infrared luminosity functions) were also obtained. Taken together, they offer complementary pieces of information concerning the evolution of galaxies. Aims: We attempt in this paper to check the consistency of the observed stellar mass functions, SFR functions, and the cosmic SFR density with simple backward evolutionary models. Methods: Starting from observed stellar mass functions for star-forming galaxies, we use backwards models to predict the evolution of a number of quantities, such as the SFR function, the cosmic SFR density and the velocity function. Because the velocity is a parameter attached to a galaxy during its history (contrary to the stellar mass), this approach allows us to quantify the number density evolution of galaxies of a given velocity, e.g. of the Milky Way siblings. Results: Observations suggest that the stellar mass function of star-forming galaxies is constant between redshift 0 and 1. To reproduce this result, we must quench star formation in a number of star-forming galaxies. The stellar mass function of these “quenched” galaxies is consistent with available data concerning the increase in the population of quiescent galaxies in the same redshift interval. The stellar mass function of quiescent galaxies is then mainly determined by the distribution of active galaxies that must stop star formation, with a modest mass redistribution during mergers. The cosmic SFR density and the evolution of the SFR functions are recovered relatively well, although they provide some clues to a minor evolution of the stellar mass function of star forming galaxies at the lowest redshifts. We thus consider that we have obtained in a simple way a relatively consistent picture of the evolution of galaxies at intermediate redshifts. If this picture is correct, 50% of the Milky-Way sisters (galaxies with the same velocity as our Galaxy, i.e. 220 km s-1) have quenched their star formation since redshift 1 (and an even higher fraction for higher velocities). We discuss the processes that might be responsible for this transformation.

Measuring self-esteem in context: the importance of stability of self-esteem in psychological functioning.

PubMed

Kernis, Michael H

2005-12-01

In this article, I report on a research program that has focused on the joint roles of stability and level of self-esteem in various aspects of psychological functioning. Stability of self-esteem refers to the magnitude of short-term fluctuations that people experience in their current, contextually based feelings of self-worth. In contrast, level of self-esteem refers to representations of people's general, or typical, feelings of self-worth. A considerable amount of research reveals that self-esteem stability has predictive value beyond the predictive value of self-esteem level. Moreover, considering self-esteem stability provides one way to distinguish fragile from secure forms of high self-esteem. Results from a number of studies are presented and theoretical implications are discussed.

Method and system for monitoring and displaying engine performance parameters

NASA Technical Reports Server (NTRS)

Abbott, Terence S. (Inventor); Person, Lee H., Jr. (Inventor)

1988-01-01

The invention is believed a major improvement that will have a broad application in governmental and commercial aviation. It provides a dynamic method and system for monitoring and simultaneously displaying in easily scanned form the available, predicted, and actual thrust of a jet aircraft engine under actual operating conditions. The available and predicted thrusts are based on the performance of a functional model of the aircraft engine under the same operating conditions. Other critical performance parameters of the aircraft engine and functional model are generated and compared, the differences in value being simultaneously displayed in conjunction with the displayed thrust values. Thus, the displayed information permits the pilot to make power adjustments directly while keeping him aware of total performance at a glance of a single display panel.

New predictive model for microsurgical outcome of intracranial arteriovenous malformations: study protocol.

PubMed

Tong, Xianzeng; Wu, Jun; Cao, Yong; Zhao, Yuanli; Wang, Shuo

2017-01-27

Although microsurgical resection is currently the first-line treatment modality for arteriovenous malformations (AVMs), microsurgery of these lesions is complicated due to the fact that they are very heterogeneous vascular anomalies. The Spetzler-Martin grading system and the supplementary grading system have demonstrated excellent performances in predicting the risk of AVM surgery. However, there are currently no predictive models based on multimodal MRI techniques. The purpose of this study is to propose a predictive model based on multimodal MRI techniques to assess the microsurgical risk of intracranial AVMs. The study consists of 2 parts: the first part is to conduct a single-centre retrospective analysis of 201 eligible patients to create a predictive model of AVM surgery based on multimodal functional MRIs (fMRIs); the second part is to validate the efficacy of the predictive model in a prospective multicentre cohort study of 400 eligible patients. Patient characteristics, AVM features and multimodal fMRI data will be collected. The functional status at pretreatment and 6 months after surgery will be analysed using the modified Rankin Scale (mRS) score. The patients in each part of this study will be dichotomised into 2 groups: those with improved or unchanged functional status (a decreased or unchanged mRS 6 months after surgery) and those with worsened functional status (an increased mRS). The first part will determine the risk factors of worsened functional status after surgery and create a predictive model. The second part will validate the predictive model and then a new AVM grading system will be proposed. The study protocol and informed consent form have been reviewed and approved by the Institutional Review Board of Beijing Tiantan Hospital Affiliated to Capital Medical University (KY2016-031-01). The results of this study will be disseminated through printed media. NCT02868008. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Unusual structures of MgF5- superhalogen anion

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Skurski, Piotr

2007-05-01

The vertical electron detachment energies (VDE) of three MgF5- anions were calculated at the outer valence Green function level with the 6-311 + G(3df) basis sets. This species was found to form unusual geometrical structures each of which corresponds to an anionic state exhibiting superhalogen nature. The global minimum structure was described as a system in which two central magnesium atoms are linked via symmetrical triangle formed by three fluorine atoms. Extremely large electron binding energies of these anions (exceeding 8.5 eV in all cases) were predicted and discussed.

New ligand-based approach for the discovery of antitrypanosomal compounds.

PubMed

Vega, María Celeste; Montero-Torres, Alina; Marrero-Ponce, Yovani; Rolón, Miriam; Gómez-Barrio, Alicia; Escario, José Antonio; Arán, Vicente J; Nogal, Juan José; Meneses-Marcel, Alfredo; Torrens, Francisco

2006-04-01

The antitrypanosomal activity of 10 already synthesized compounds was in silico predicted as well as in vitro and in vivo explored against Trypanosoma cruzi. For the computational study, an approach based on non-stochastic linear fingerprints to the identification of potential antichagasic compounds is introduced. Molecular structures of 66 organic compounds, 28 with antitrypanosomal activity and 38 having other clinical uses, were parameterized by means of the TOMOCOMD-CARDD software. A linear classification function was derived allowing the discrimination between active and inactive compounds with a confidence of 95%. As predicted, seven compounds showed antitrypanosomal activity (%AE>70) against epimastigotic forms of T. cruzi at a concentration of 100mug/mL. After an unspecific cytotoxic assay, three compounds were evaluated against amastigote forms of the parasite. An in vivo test was carried out for one of the studied compounds.

Designer's unified cost model

NASA Technical Reports Server (NTRS)

Freeman, William T.; Ilcewicz, L. B.; Swanson, G. D.; Gutowski, T.

1992-01-01

A conceptual and preliminary designers' cost prediction model has been initiated. The model will provide a technically sound method for evaluating the relative cost of different composite structural designs, fabrication processes, and assembly methods that can be compared to equivalent metallic parts or assemblies. The feasibility of developing cost prediction software in a modular form for interfacing with state of the art preliminary design tools and computer aided design programs is being evaluated. The goal of this task is to establish theoretical cost functions that relate geometric design features to summed material cost and labor content in terms of process mechanics and physics. The output of the designers' present analytical tools will be input for the designers' cost prediction model to provide the designer with a data base and deterministic cost methodology that allows one to trade and synthesize designs with both cost and weight as objective functions for optimization. The approach, goals, plans, and progress is presented for development of COSTADE (Cost Optimization Software for Transport Aircraft Design Evaluation).

Predictive coding accelerates word recognition and learning in the early stages of language development.

PubMed

Ylinen, Sari; Bosseler, Alexis; Junttila, Katja; Huotilainen, Minna

2017-11-01

The ability to predict future events in the environment and learn from them is a fundamental component of adaptive behavior across species. Here we propose that inferring predictions facilitates speech processing and word learning in the early stages of language development. Twelve- and 24-month olds' electrophysiological brain responses to heard syllables are faster and more robust when the preceding word context predicts the ending of a familiar word. For unfamiliar, novel word forms, however, word-expectancy violation generates a prediction error response, the strength of which significantly correlates with children's vocabulary scores at 12 months. These results suggest that predictive coding may accelerate word recognition and support early learning of novel words, including not only the learning of heard word forms but also their mapping to meanings. Prediction error may mediate learning via attention, since infants' attention allocation to the entire learning situation in natural environments could account for the link between prediction error and the understanding of word meanings. On the whole, the present results on predictive coding support the view that principles of brain function reported across domains in humans and non-human animals apply to language and its development in the infant brain. A video abstract of this article can be viewed at: http://hy.fi/unitube/video/e1cbb495-41d8-462e-8660-0864a1abd02c. [Correction added on 27 January 2017, after first online publication: The video abstract link was added.]. © 2016 John Wiley & Sons Ltd.

Human neural stem cell-derived cultures in three-dimensional substrates form spontaneously functional neuronal networks.

PubMed

Smith, Imogen; Silveirinha, Vasco; Stein, Jason L; de la Torre-Ubieta, Luis; Farrimond, Jonathan A; Williamson, Elizabeth M; Whalley, Benjamin J

2017-04-01

Differentiated human neural stem cells were cultured in an inert three-dimensional (3D) scaffold and, unlike two-dimensional (2D) but otherwise comparable monolayer cultures, formed spontaneously active, functional neuronal networks that responded reproducibly and predictably to conventional pharmacological treatments to reveal functional, glutamatergic synapses. Immunocytochemical and electron microscopy analysis revealed a neuronal and glial population, where markers of neuronal maturity were observed in the former. Oligonucleotide microarray analysis revealed substantial differences in gene expression conferred by culturing in a 3D vs a 2D environment. Notable and numerous differences were seen in genes coding for neuronal function, the extracellular matrix and cytoskeleton. In addition to producing functional networks, differentiated human neural stem cells grown in inert scaffolds offer several significant advantages over conventional 2D monolayers. These advantages include cost savings and improved physiological relevance, which make them better suited for use in the pharmacological and toxicological assays required for development of stem cell-based treatments and the reduction of animal use in medical research. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Renormalization group analysis of the 2000-2002 anti-bubble in the US S&P500 index: explanation of the hierarchy of five crashes and prediction

NASA Astrophysics Data System (ADS)

Zhou, Wei-Xing; Sornette, Didier

2003-12-01

We propose a straightforward extension of our previously proposed log-periodic power-law model of the “anti-bubble” regime of the USA stock market since the summer of 2000, in terms of the renormalization group framework to model critical points. Using a previous work by Gluzman and Sornette (Phys. Rev. E 65 (2003) 036142) on the classification of the class of Weierstrass-like functions, we show that the five crashes that occurred since August 2000 can be accurately modeled by this approach, in a fully consistent way with no additional parameters. Our theory suggests an overall consistent organization of the investors forming a collective network which interact to form the pessimistic bearish “anti-bubble” regime with intermittent acceleration of the positive feedbacks of pessimistic sentiment leading to these crashes. We develop retrospective predictions, that confirm the existence of significant arbitrage opportunities for a trader using our model. Finally, we offer a prediction for the unknown future of the US S&P500 index extending over 2003 and 2004, that refines the previous prediction of Sornette and Zhou (Quant. Finance 2 (2002) 468).

Prediction of Mechanical Properties of Polymers With Various Force Fields

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

PubMed Central

Severing, Edouard I.; van Dijk, Aalt D. J.; Morabito, Giuseppa; Busscher-Lange, Jacqueline; Immink, Richard G. H.; van Ham, Roeland C. H. J.

2012-01-01

Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1–3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins. PMID:22295091

Estimation and Application of Ecological Memory Functions in Time and Space

NASA Astrophysics Data System (ADS)

Itter, M.; Finley, A. O.; Dawson, A.

2017-12-01

A common goal in quantitative ecology is the estimation or prediction of ecological processes as a function of explanatory variables (or covariates). Frequently, the ecological process of interest and associated covariates vary in time, space, or both. Theory indicates many ecological processes exhibit memory to local, past conditions. Despite such theoretical understanding, few methods exist to integrate observations from the recent past or within a local neighborhood as drivers of these processes. We build upon recent methodological advances in ecology and spatial statistics to develop a Bayesian hierarchical framework to estimate so-called ecological memory functions; that is, weight-generating functions that specify the relative importance of local, past covariate observations to ecological processes. Memory functions are estimated using a set of basis functions in time and/or space, allowing for flexible ecological memory based on a reduced set of parameters. Ecological memory functions are entirely data driven under the Bayesian hierarchical framework—no a priori assumptions are made regarding functional forms. Memory function uncertainty follows directly from posterior distributions for model parameters allowing for tractable propagation of error to predictions of ecological processes. We apply the model framework to simulated spatio-temporal datasets generated using memory functions of varying complexity. The framework is also applied to estimate the ecological memory of annual boreal forest growth to local, past water availability. Consistent with ecological understanding of boreal forest growth dynamics, memory to past water availability peaks in the year previous to growth and slowly decays to zero in five to eight years. The Bayesian hierarchical framework has applicability to a broad range of ecosystems and processes allowing for increased understanding of ecosystem responses to local and past conditions and improved prediction of ecological processes.

Cognition Predicts Quality of Life Among Patients With End-Stage Liver Disease.

PubMed

Paulson, Daniel; Shah, Mona; Miller-Matero, Lisa Renee; Eshelman, Anne; Abouljoud, Marwan

2016-01-01

Impaired cognitive functioning and poor quality of life (QoL) are both common among patients with end-stage liver disease; however, it is unclear how these are related. This study examines how specific cognitive domains predict QoL among liver transplant candidates by replicating Stewart and colleagues' (2010) 3-factor model of cognitive functioning, and determining how variability in these cognitive domains predicts mental health and physical QoL. The sample included 246 patients with end-stage liver disease who were candidates for liver transplant at a large, Midwestern health care center. Measures, including the Repeatable Battery for the Assessment of Neuropsychological Status, Trail Making Test, Shipley Institute of Living Scale, Short-Form Health Survey-36 Version 2, and Hospital Anxiety and Depression Scale, comprised latent variables representing global intellectual functioning, psychomotor speed, and learning and memory functioning. Confirmatory factor analysis results indicate that the 3-factor solution model comprised of global intellectual functioning, psychomotor speed, and learning and memory functioning fit the data well. Addition of physical and mental health QoL latent factors resulted in a structural model also with good fit. Results related physical QoL to global intellectual functioning, and mental health QoL to global intellectual functioning and psychomotor functioning. Findings elucidate a relationship between cognition and QoL and support the use of routine neuropsychological screening with end-stage liver disease patients, specifically examining the cognitive domains of global intellectual, psychomotor, and learning and memory functioning. Subsequently, screening results may inform implementation of targeted interventions to improve QoL. Copyright © 2016 The Academy of Psychosomatic Medicine. Published by Elsevier Inc. All rights reserved.

Retooling Predictive Relations for non-volatile PM by Comparison to Measurements

NASA Astrophysics Data System (ADS)

Vander Wal, R. L.; Abrahamson, J. P.

2015-12-01

Non-volatile particulate matter (nvPM) emissions from jet aircraft at cruise altitude are of particular interest for climate and atmospheric processes but are difficult to measure and are normally approximated. To provide such inventory estimates the present approach is to use measured, ground-based values with scaling to cruise (engine operating) conditions. Several points are raised by this approach. First is what ground based values to use. Empirical and semi-empirical approaches, such as the revised first order approximation (FOA3) and formation-oxidation (FOX) methods, each with embedded assumptions are available to calculate a ground-based black carbon concentration, CBC. Second is the scaling relation that can depend upon the ratios of fuel-air equivalence, pressure, and combustor flame temperature. We are using measured ground-based values to evaluate the accuracy of present methods towards developing alternative methods for CBCby smoke number or via a semi-empirical kinetic method for the specific engine, CFM56-2C, representative of a rich-dome style combustor, and as one of the most prevalent engine families in commercial use. Applying scaling relations to measured ground based values and comparison to measurements at cruise evaluates the accuracy of current scaling formalism. In partnership with GE Aviation, performing engine cycle deck calculations enables critical comparison between estimated or predicted thermodynamic parameters and true (engine) operational values for the CFM56-2C engine. Such specific comparisons allow tracing differences between predictive estimates for, and measurements of nvPM to their origin - as either divergence of input parameters or in the functional form of the predictive relations. Such insights will lead to development of new predictive tools for jet aircraft nvPM emissions. Such validated relations can then be extended to alternative fuels with confidence in operational thermodynamic values and functional form. Comparisons will then be made between these new predictive relationships and measurements of nvPM from alternative fuels using ground and cruise data - as collected during NASA-led AAFEX and ACCESS field campaigns, respectively.

Predictive motor control of sensory dynamics in Auditory Active Sensing

PubMed Central

Morillon, Benjamin; Hackett, Troy A.; Kajikawa, Yoshinao; Schroeder, Charles E.

2016-01-01

Neuronal oscillations present potential physiological substrates for brain operations that require temporal prediction. We review this idea in the context of auditory perception. Using speech as an exemplar, we illustrate how hierarchically organized oscillations can be used to parse and encode complex input streams. We then consider the motor system as a major source of rhythms (temporal priors) in auditory processing, that act in concert with attention to sharpen sensory representations and link them across areas. We discuss the anatomo-functional pathways that could mediate this audio-motor interaction, and notably the potential role of the somatosensory cortex. Finally, we reposition temporal predictions in the context of internal models, discussing how they interact with feature-based or spatial predictions. We argue that complementary predictions interact synergistically according to the organizational principles of each sensory system, forming multidimensional filters crucial to perception. PMID:25594376

Equilibration and aging of dense soft-sphere glass-forming liquids

NASA Astrophysics Data System (ADS)

Sánchez-Díaz, Luis Enrique; Ramírez-González, Pedro; Medina-Noyola, Magdaleno

2013-05-01

The recently developed nonequilibrium extension of the self-consistent generalized Langevin equation theory of irreversible relaxation [Ramírez-González and Medina-Noyola, Phys. Rev. E10.1103/PhysRevE.82.061503 82, 061503 (2010); Ramírez-González and Medina-Noyola, Phys. Rev. E10.1103/PhysRevE.82.061504 82, 061504 (2010)] is applied to the description of the irreversible process of equilibration and aging of a glass-forming soft-sphere liquid that follows a sudden temperature quench, within the constraint that the local mean particle density remains uniform and constant. For these particular conditions, this theory describes the nonequilibrium evolution of the static structure factor S(k;t) and of the dynamic properties, such as the self-intermediate scattering function FS(k,τ;t), where τ is the correlation delay time and t is the evolution or waiting time after the quench. Specific predictions are presented for the deepest quench (to zero temperature). The predicted evolution of the α-relaxation time τα(t) as a function of t allows us to define the equilibration time teq(ϕ), as the time after which τα(t) has attained its equilibrium value ταeq(ϕ). It is predicted that both, teq(ϕ) and ταeq(ϕ), diverge as ϕ→ϕ(a), where ϕ(a) is the hard-sphere dynamic-arrest volume fraction ϕ(a)(≈0.582), thus suggesting that the measurement of equilibrium properties at and above ϕ(a) is experimentally impossible. The theory also predicts that for fixed finite waiting times t, the plot of τα(t;ϕ) as a function of ϕ exhibits two regimes, corresponding to samples that have fully equilibrated within this waiting time (ϕ≤ϕ(c)(t)), and to samples for which equilibration is not yet complete (ϕ≥ϕ(c)(t)). The crossover volume fraction ϕ(c)(t) increases with t but saturates to the value ϕ(a).

Predicting protein complex geometries with a neural network.

PubMed

Chae, Myong-Ho; Krull, Florian; Lorenzen, Stephan; Knapp, Ernst-Walter

2010-03-01

A major challenge of the protein docking problem is to define scoring functions that can distinguish near-native protein complex geometries from a large number of non-native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom-pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near-native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge-based energy functions for scoring. We show that a distance-dependent atom pair potential performs much better than a simple atom-pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge-based scoring functions such as ZDOCK 3.0, ZRANK, ITScore-PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network-based scoring function achieves a reasonable performance in rigid-body unbound docking of proteins. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

PubMed Central

Bryan, Kenneth; Cunningham, Pádraig

2008-01-01

Background Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of providing a more accurate model of the natural gene functional classes. This approach also has the potential to aid functional annotation of unclassified open reading frames (ORFs). Until now this aspect of biclustering has been under-explored. In this work we illustrate how bicluster analysis may be extended into a 'semi-supervised' ORF annotation approach referred to as BALBOA. Results The efficacy of the BALBOA ORF classification technique is first assessed via cross validation and compared to a multi-class k-Nearest Neighbour (kNN) benchmark across three independent gene expression datasets. BALBOA is then used to assign putative functional annotations to unclassified yeast ORFs. These predictions are evaluated using existing experimental and protein sequence information. Lastly, we employ a related semi-supervised method to predict the presence of novel functional modules within yeast. Conclusion In this paper we demonstrate how unsupervised classification methods, such as bicluster analysis, may be extended using of available annotations to form semi-supervised approaches within the gene expression analysis domain. We show that such methods have the potential to improve upon supervised approaches and shed new light on the functions of unclassified ORFs and their co-regulation. PMID:18831786

Towards programmable plant genetic circuits.

PubMed

Medford, June I; Prasad, Ashok

2016-07-01

Synthetic biology enables the construction of genetic circuits with predictable gene functions in plants. Detailed quantitative descriptions of the transfer function or input-output function for genetic parts (promoters, 5' and 3' untranslated regions, etc.) are collected. These data are then used in computational simulations to determine their robustness and desired properties, thereby enabling the best components to be selected for experimental testing in plants. In addition, the process forms an iterative workflow which allows vast improvement to validated elements with sub-optimal function. These processes enable computational functions such as digital logic in living plants and follow the pathway of technological advances which took us from vacuum tubes to cell phones. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

The basis function approach for modeling autocorrelation in ecological data.

PubMed

Hefley, Trevor J; Broms, Kristin M; Brost, Brian M; Buderman, Frances E; Kay, Shannon L; Scharf, Henry R; Tipton, John R; Williams, Perry J; Hooten, Mevin B

2017-03-01

Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data. © 2016 by the Ecological Society of America.

The four-loop six-gluon NMHV ratio function

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N=4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q¯ differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result againstmore » multi-Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. As a result, we also provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

The four-loop six-gluon NMHV ratio function

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

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N = 4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q - differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We testmore » the result against multi- Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We also study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. Furthermore, we provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

PREFACE: Protein protein interactions: principles and predictions

NASA Astrophysics Data System (ADS)

Nussinov, Ruth; Tsai, Chung-Jung

2005-06-01

Proteins are the `workhorses' of the cell. Their roles span functions as diverse as being molecular machines and signalling. They carry out catalytic reactions, transport, form viral capsids, traverse membranes and form regulated channels, transmit information from DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to do this is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Their identification is at the heart of functional genomics; their prediction is crucial for drug discovery. Knowledge of the pathway, its topology, length, and dynamics may provide useful information for forecasting side effects. The goal of predicting protein-protein interactions is daunting. Some associations are obligatory, others are continuously forming and dissociating. In principle, from the physical standpoint, any two proteins can interact, but under what conditions and at which strength? The principles of protein-protein interactions are general: the non-covalent interactions of two proteins are largely the outcome of the hydrophobic effect, which drives the interactions. In addition, hydrogen bonds and electrostatic interactions play important roles. Thus, many of the interactions observed in vitro are the outcome of experimental overexpression. Protein disorder is important in protein-protein association. It has been estimated that a large fraction of cellular proteins are `natively disordered', i.e., unstable in solution. The disordered state has a significant residual structure. In this state, a protein exists in an ensemble of rapidly interconverting conformers. They play roles in cell-cycle control, signal transduction, transcriptional and translational regulation, and in large macromolecular complexes. It has been suggested that natively disordered proteins are more `adaptive', and thus advantageous in regulation and in binding diverse ligands. Alternatively, since the native conformation is still likely to be the most abundant within the ensemble, disordered proteins, which typically have larger interface to size ratios, lead to smaller protein, genome and cell sizes, and thus are functionally advantageous. To be able to predict protein-protein interactions, we need to discern various aspects of their associations: from their shape complementarity to the organization and relative contributions of the different physical components to their stability. They involve the static and the dynamic. Proteins interact through their surfaces. Thus, to analyze their interactions, we typically study residues (or atoms) which are in contact across the two-chain interface. In addition, we often inspect the residues in their vicinity, exploring their supporting matrix. The hope is that through the understanding of the principles and mechanisms of the interactions, we shall eventually be able to solve the protein-protein interaction puzzle.

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

PubMed

Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

2016-01-04

The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Extension of Ko Straight-Beam Displacement Theory to Deformed Shape Predictions of Slender Curved Structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2011-01-01

The Ko displacement theory originally developed for shape predictions of straight beams is extended to shape predictions of curved beams. The surface strains needed for shape predictions were analytically generated from finite-element nodal stress outputs. With the aid of finite-element displacement outputs, mathematical functional forms for curvature-effect correction terms are established and incorporated into straight-beam deflection equations for shape predictions of both cantilever and two-point supported curved beams. The newly established deflection equations for cantilever curved beams could provide quite accurate shape predictions for different cantilever curved beams, including the quarter-circle cantilever beam. Furthermore, the newly formulated deflection equations for two-point supported curved beams could provide accurate shape predictions for a range of two-point supported curved beams, including the full-circular ring. Accuracy of the newly developed curved-beam deflection equations is validated through shape prediction analysis of curved beams embedded in the windward shallow spherical shell of a generic crew exploration vehicle. A single-point collocation method for optimization of shape predictions is discussed in detail

Quark-hadron duality and parity violating asymmetry of electroweak reactions in the {delta} region

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

Matsui, K.; Sato, T.; Lee, T.-S.H.

2005-08-01

A dynamical model [T. Sato and T.-S. H. Lee, Phys. Rev. C 54, 2660 (1996); 63, 055201 (2001); T. Sato, D. Uno, and T.-S. H. Lee, ibid. 67, 065201 (2003)] of electroweak pion production reactions in the {delta}(1232) region has been extended to include the neutral current contributions for examining the local quark-hadron duality in neutrino-induced reactions and for investigating how the axial N-{delta} form factor can be determined by the parity violating asymmetry of N(e{sup {yields}},e{sup '}) reactions. We first show that the recent data of (e,e{sup '}) structure functions F{sub 1} and F{sub 2}, which exhibit the quark-hadronmore » duality, are in good agreement with our predictions. For possible future experimental tests, we then predict that the structure functions F{sub 1},F{sub 2}, and F{sub 3} for ({nu},e) and ({nu},{nu}{sup '}) processes also show the similar quark-hadron duality. The spin-dependent structure functions g{sub 1} and g{sub 2} of (e,e{sup '}) have also been calculated from our model. It is found that the local quark-hadron duality is not seen in the calculated g{sub 1} and g{sub 2}, while our results for g{sub 1} and some polarization observables associated with the exclusive p(e{sup {yields}},e{sup '}{pi}) and p{sup {yields}}(e{sup {yields}},e{sup '}{pi}) reactions are in reasonably good agreement with the recent data. In the study of parity violating asymmetry A of N(e{sup {yields}},e{sup '}) reactions, the relative importance between the nonresonant mechanisms and the {delta} excitation is investigated by taking into account the unitarity condition. Predictions are made for using the data of A to test the axial N-{delta} form factors determined previously in the studies of N({nu}{sub {mu}},{mu}{sup -}{pi}) reactions. The predicted asymmetry A are also compared with the parton model predictions for future experimental investigations of quark-hadron duality.« less

Tree height estimation in redwood/Douglas-fir stands in Mendocino County

Treesearch

Helge Eng

2012-01-01

In this study, height-diameter equations were developed for managed stands of coastal redwood/Douglas-fir stands in Mendocino County. Equations were developed by species to predict tree height as a function of diameter as well as other factors that are known to potentially explain tree height, including site class and live crown ratio. Two equation forms were compared...

A Height–Diameter Curve for Longleaf Pine Plantations in the Gulf Coastal Plain

Treesearch

Daniel Leduc; Jeffery Goelz

2009-01-01

Tree height is a critical component of a complete growth-and-yield model because it is one of the primary components used in volume calculation. To develop an equation to predict total height from dbh for longleaf pine (Pinus palustris Mill.) plantations in the West Gulf region, many different sigmoidal curve forms, weighting functions, and ways of...

The AFIS tree growth model for updating annual forest inventories in Minnesota

Treesearch

Margaret R. Holdaway

2000-01-01

As the Forest Service moves towards annual inventories, states may use model predictions of growth to update unmeasured plots. A tree growth model (AFIS) based on the scaled Weibull function and using the average-adjusted model form is presented. Annual diameter growth for four species was modeled using undisturbed plots from Minnesota's Aspen-Birch and Northern...

Comparison of Attachment theory and Cognitive-Motivational Structure theory.

PubMed

Malerstein, A J

2005-01-01

Attachment theory and Cognitive-Motivational Structure (CMS) are similar in most respects. They differ primarily in their proposal of when, during development, one's sense of the self and of the outside world are formed. I propose that the theories supplement each other after about age seven years--when Attachment theory's predictions of social function become unreliable, CMS theory comes into play.

Nonvolatile memories using deep traps formed in HfO2 by Nb ion implantation

NASA Astrophysics Data System (ADS)

Choul Kim, Min; Oh Kim, Chang; Taek Oh, Houng; Choi, Suk-Ho; Belay, K.; Elliman, R. G.; Russo, S. P.

2011-03-01

We report nonvolatile memories (NVMs) based on deep-energy trap levels formed in HfO2 by metal ion implantation. A comparison of Nb- and Ta-implanted samples shows that suitable charge-trapping centers are formed in Nb-implanted samples, but not in Ta-implanted samples. This is consistent with density-functional theory calculations which predict that only Nb will form deep-energy levels in the bandgap of HfO2. Photocurrent spectroscopy exhibits characteristics consistent with one of the trap levels predicted in these calculations. Nb-implanted samples showing memory windows in capacitance-voltage (V) curves always exhibit current (I) peaks in I-V curves, indicating that NVM effects result from deep traps in HfO2. In contrast, Ta-implanted samples show dielectric breakdowns during the I-V sweeps between 5 and 11 V, consistent with the fact that no trap levels are present. For a sample implanted with a fluence of 1013 Nb cm-2, the charge losses after 104 s are ˜9.8 and ˜25.5% at room temperature (RT) and 85°C, respectively, and the expected charge loss after 10 years is ˜34% at RT, very promising for commercial NVMs.

Bending analysis of embedded nanoplates based on the integral formulation of Eringen's nonlocal theory using the finite element method

NASA Astrophysics Data System (ADS)

Ansari, R.; Torabi, J.; Norouzzadeh, A.

2018-04-01

Due to the capability of Eringen's nonlocal elasticity theory to capture the small length scale effect, it is widely used to study the mechanical behaviors of nanostructures. Previous studies have indicated that in some cases, the differential form of this theory cannot correctly predict the behavior of structure, and the integral form should be employed to avoid obtaining inconsistent results. The present study deals with the bending analysis of nanoplates resting on elastic foundation based on the integral formulation of Eringen's nonlocal theory. Since the formulation is presented in a general form, arbitrary kernel functions can be used. The first order shear deformation plate theory is considered to model the nanoplates, and the governing equations for both integral and differential forms are presented. Finally, the finite element method is applied to solve the problem. Selected results are given to investigate the effects of elastic foundation and to compare the predictions of integral nonlocal model with those of its differential nonlocal and local counterparts. It is found that by the use of proposed integral formulation of Eringen's nonlocal model, the paradox observed for the cantilever nanoplate is resolved.

Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

PubMed Central

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J. Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V.; Craig, Timothy K.; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C.; van Raaij, Mark J.; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-01-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, over 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this paper, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict trans-membrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin IL-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fibre protein gp17 from bacteriophage T7; the Bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. PMID:24318984

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

Experiments on the Motion of Drops on a Horizontal Solid Surface due to a Wettability Gradient

NASA Technical Reports Server (NTRS)

Moumen, Nadjoua; Subramanian, R, Shankar; MLaughlin, john B.

2006-01-01

Results from experiments performed on the motion of drops of tetraethylene glycol in a wettability gradient present on a silicon surface are reported and compared with predictions from a recently developed theoretical model. The gradient in wettability was formed by exposing strips cut from a silicon wafer to decyltrichlorosiland vapors. Video images of the drops captured during the experiments were subsequently analyzed for drop size and velocity as functions of position along the gradient. In separate experiments on the same strips, the static contact angle formed by small drops was measured and used to obtain the local wettability gradient to which a drop is subjected. The velocity of the drops was found to be a strong function of position along the gradient. A quasi-steady theoretical model that balances the local hydrodynamic resistance with the local driving force generally describes the observations; possible reasons for the remaining discrepancies are discussed. It is shown that a model in which the driving force is reduced to accomodate the hysteresis effect inferred from the data is able to remove most of the discrepancy between the observed and predicted velocities.

Effect of the determination method of the material parameters on the accuracy of the hole expansion simulation for cold rolled steel sheet

NASA Astrophysics Data System (ADS)

Nakano, Hayato; Hakoyama, Tomoyuki; Kuwabara, Toshihiko

2017-10-01

Hole expansion forming of a cold rolled steel sheet is investigated both experimentally and analytically to clarify the effects of material models on the predictive accuracy of finite element analyses (FEA). The multiaxial plastic deformation behavior of a cold rolled steel sheet with a thickness of 1.2 mm was measured using a servo-controlled multiaxial tube expansion testing machine for the range of strain from initial yield to fracture. Tubular specimens were fabricated from the sheet sample by roller bending and laser welding. Many linear stress paths in the first quadrant of stress space were applied to the tubular specimens to measure the contours of plastic work in stress space up to a reference plastic strain of 0.24 along with the directions of plastic strain rates. The anisotropic parameters and exponent of the Yld2000-2d yield function (Barlat et al., 2003) were optimized to approximate the contours of plastic work and the directions of plastic strain rates. The hole expansion forming simulations were performed using the different model identifications based on the Yld2000-2d yield function. It is concluded that the yield function best capturing both the plastic work contours and the directions of plastic strain rates leads to the most accurate predicted FEA.

Phthalo-carbonitride: an ab initio prediction of a stable two-dimensional material

NASA Astrophysics Data System (ADS)

Tsetseris, Leonidas

2016-06-01

Using density-functional theory calculations, we identify a stable two-dimensional carbonitride polymorph which resembles the core of phthalocyanine molecules. This so-called phthalo-carbonitride is found to be the lowest-energy polymer made of tetracyanoethylene molecules. It is a two-dimensional metal in its pristine form. Functionalization of the phthalo-cores with copper or iron atoms retains the metallic character of the material, but also adds magnetization to the system. Based on these properties and the established use of phthalocyanine molecules in various applications, the growth of phthalo-carbonitride sheets can add another multi-functional building block to the research and technology of two-dimensional materials.

A Co-operative Regulation of Neuronal Excitability by UNC-7 Innexin and NCA/NALCN Leak Channel

PubMed Central

2011-01-01

Gap junctions mediate the electrical coupling and intercellular communication between neighboring cells. Some gap junction proteins, namely connexins and pannexins in vertebrates, and innexins in invertebrates, may also function as hemichannels. A conserved NCA/Dmα1U/NALCN family cation leak channel regulates the excitability and activity of vertebrate and invertebrate neurons. In the present study, we describe a genetic and functional interaction between the innexin UNC-7 and the cation leak channel NCA in Caenorhabditis elegans neurons. While the loss of the neuronal NCA channel function leads to a reduced evoked postsynaptic current at neuromuscular junctions, a simultaneous loss of the UNC-7 function restores the evoked response. The expression of UNC-7 in neurons reverts the effect of the unc-7 mutation; moreover, the expression of UNC-7 mutant proteins that are predicted to be unable to form gap junctions also reverts this effect, suggesting that UNC-7 innexin regulates neuronal activity, in part, through gap junction-independent functions. We propose that, in addition to gap junction-mediated functions, UNC-7 innexin may also form hemichannels to regulate C. elegans' neuronal activity cooperatively with the NCA family leak channels. PMID:21489288

Phosphorus allotropes: Stability of black versus red phosphorus re-examined by means of the van der Waals inclusive density functional method

NASA Astrophysics Data System (ADS)

Aykol, Muratahan; Doak, Jeff W.; Wolverton, C.

2017-06-01

We evaluate the energetic stabilities of white, red, and black allotropes of phosphorus using density functional theory (DFT) and hybrid functional methods, van der Waals (vdW) corrections (DFT+vdW and hybrid+vdW), vdW density functionals, and random phase approximation (RPA). We find that stability of black phosphorus over red-V (i.e., the violet form) is not ubiquitous among these methods, and the calculated enthalpies for the reaction phosphorus (red-V)→phosphorus (black) are scattered between -20 and 40 meV/atom. With local density and generalized gradient approximations, and hybrid functionals, mean absolute errors (MAEs) in densities of P allotropes relative to experiments are found to be around 10%-25%, whereas with vdW-inclusive methods, MAEs in densities drop below ˜5 %. While the inconsistency among the density functional methods could not shed light on the stability puzzle of black versus red phosphorus, comparison of their accuracy in predicting densities and the supplementary RPA results on relative stabilities indicate that opposite to the common belief, black and red phosphorus are almost degenerate, or the red-V (violet) form of phosphorus might even be the ground state.

Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes.

PubMed

Engqvist, Martin K M

2016-01-01

The biology of living organisms is determined by the action and interaction of a large number of individual gene products, each with specific functions. Discovering and annotating the function of gene products is key to our understanding of these organisms. Controlled experiments and bioinformatic predictions both contribute to functional gene annotation. For most species it is difficult to gain an overview of what portion of gene annotations are based on experiments and what portion represent predictions. Here, I survey the current state of experimental knowledge of enzymes and metabolism in Arabidopsis thaliana as well as eleven economically important crops and forestry trees - with a particular focus on reactions involving organic acids in central metabolism. I illustrate the limited availability of experimental data for functional annotation of enzymes in most of these species. Many enzymes involved in metabolism of citrate, malate, fumarate, lactate, and glycolate in crops and forestry trees have not been characterized. Furthermore, enzymes involved in key biosynthetic pathways which shape important traits in crops and forestry trees have not been characterized. I argue for the development of novel high-throughput platforms with which limited functional characterization of gene products can be performed quickly and relatively cheaply. I refer to this approach as systems-level experimental characterization. The data collected from such platforms would form a layer intermediate between bioinformatic gene function predictions and in-depth experimental studies of these functions. Such a data layer would greatly aid in the pursuit of understanding a multiplicity of biological processes in living organisms.

The formation and analysis of a 5 deg equal area block terrestrial gravity field

NASA Technical Reports Server (NTRS)

Rapp, R. H.

1972-01-01

A set of 23,355 1 degree x 1 degree mean free air anomalies were used to predict a set of 5 degree equal area anomalies and their standard errors. Using the 1 degree data incorporating geophysically predicted values of ACIC, 1283 5 degree blocks were computed. Excluding the geophysically predicted anomalies 1249 blocks were computed. The 1 degree data were also used to compute covariance functions and the equatorial gravity and flattening implied by this data. The predicted anomalies were supplemented by model anomalies to form a complete 1654 global anomaly field. These data were used in a weighted least squares to determine potential coefficients to degree 15, and in a summation type formulation to determine potential coefficients to degree 25. These potential coefficients sets are compared to recent satellite determinations.

Predicting the tensile strength of A UD basalt/ epoxy composite used for the confinement of concrete structures

NASA Astrophysics Data System (ADS)

Ciniņa, I.; Zīle, O.; Andersons, J.

2013-01-01

The principal aim of the present research was to predict the strength of UD basalt fiber/epoxy matrix composites in tension along the reinforcement direction. Tension tests on single basalt fibers were performed to determine the functional form of their strength distribution and to evaluate the parameters of the distribution. Also, microbond tests were carried out to assess the interfacial shear strength of the fibers and polymer matrix. UD composite specimens were produced and tested for the longitudinal tensile strength. The predicted strength of the composite was found to exceed the experimental values by ca. 20%, which can be explained by imperfections in the fiber alignment, impregnation, and adhesion in the composite specimens.

A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

PubMed

Han, Dianwei; Tang, Guiliang; Zhang, Jun

2013-01-01

The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs.

Pathways, Contributors, and Correlates of Functional Limitation across Specialties: Workshop Summary.

PubMed

Kritchevsky, Stephen B; Forman, Daniel E; Callahan, Kathryn; Ely, E Wesley; High, Kevin P; McFarland, Frances; Pérez-Stable, Eliseo J; Schmader, Kenneth; Studenski, Stephanie; Williams, John; Zieman, Susan; Guralnik, Jack M

2018-04-25

Traditional clinical care models focus on the measurement and normalization of individual organ systems and de-emphasize aspects of health related to the integration of physiologic systems. Measures of physical, cognitive and sensory, and psychosocial or emotional function predict important health outcomes like death and disability independently from the severity of a specific disease, cumulative co-morbidity, or disease severity measures. A growing number of clinical scientists in several subspecialties are exploring the utility of functional assessment to predict complication risk, indicate stress resistance, inform disease screening approaches and risk factor interpretation, and evaluate care. Because a substantial number of older adults in the community have some form of functional limitation, integrating functional assessment into clinical medicine could have a large impact. Although interest in functional implications for health and disease management is growing, the science underlying functional capacity, functional limitation, physical frailty, and functional metrics is often siloed among different clinicians and researchers, with fragmented concepts and methods. On August 25-26, 2016, participants at a trans-disciplinary workshop, supported by the National Institute on Aging and the John A. Hartford Foundation, explored what is known about the pathways, contributors, and correlates of physical, cognitive and sensory functional measures across conditions and disease states; considered social determinants and health disparities; identified knowledge gaps, and suggested priorities for future research. This paper summarizes those discussions.

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A Density Functional Theory Study of New Boron Nanotubes

NASA Astrophysics Data System (ADS)

Chen, Zhao-Hua; Xie, Zun

2017-11-01

Using first-principles calculations, a series of new boron nanotubes (BNTs), which show various electronic properties, were theoretically predicted. Stable nanotubes with various chiral vectors and diameters can be formed by rolling up the boron sheet with relative stability [H. Tang and S. I. Beigi, Phys. Rev. B 82, 115412 (2010).]. By increasing the diameter for BNT, the stability is enhanced. The calculated density of states and band structures demonstrate that all the predicted BNTs are metallic, regardless of their diameter and chirality. The multicentre chemical bonds of the relatively stable boron sheet and BNTs are analysed using the deformation electron density. Within our study, the BNTs all have metallic conductive characteristics, in addition to having a low effective quality and high carrier concentration, which are very good nanoconductive material properties and could be combined to form high-power electrodes for lithium-ion batteries such as those used in many modern electronics.

A kinematic hardening constitutive model for the uniaxial cyclic stress-strain response of magnesium sheet alloys at room temperature

NASA Astrophysics Data System (ADS)

He, Zhitao; Chen, Wufan; Wang, Fenghua; Feng, Miaolin

2017-11-01

A kinematic hardening constitutive model is presented, in which a modified form of von Mises yield function is adopted, and the initial asymmetric tension and compression yield stresses of magnesium (Mg) alloys at room temperature (RT) are considered. The hardening behavior was classified into slip, twinning, and untwinning deformation modes, and these were described by two forms of back stress to capture the mechanical response of Mg sheet alloys under cyclic loading tests at RT. Experimental values were obtained for AZ31B-O and AZ31B sheet alloys under both tension-compression-tension (T-C-T) and compression-tension (C-T) loadings to calibrate the parameters of back stresses in the proposed model. The predicted parameters of back stresses in the twinning and untwinning modes were expressed as a cubic polynomial. The predicted curves based on these parameters showed good agreement with the tests.

Potential implementation of reservoir computing models based on magnetic skyrmions

NASA Astrophysics Data System (ADS)

Bourianoff, George; Pinna, Daniele; Sitte, Matthias; Everschor-Sitte, Karin

2018-05-01

Reservoir Computing is a type of recursive neural network commonly used for recognizing and predicting spatio-temporal events relying on a complex hierarchy of nested feedback loops to generate a memory functionality. The Reservoir Computing paradigm does not require any knowledge of the reservoir topology or node weights for training purposes and can therefore utilize naturally existing networks formed by a wide variety of physical processes. Most efforts to implement reservoir computing prior to this have focused on utilizing memristor techniques to implement recursive neural networks. This paper examines the potential of magnetic skyrmion fabrics and the complex current patterns which form in them as an attractive physical instantiation for Reservoir Computing. We argue that their nonlinear dynamical interplay resulting from anisotropic magnetoresistance and spin-torque effects allows for an effective and energy efficient nonlinear processing of spatial temporal events with the aim of event recognition and prediction.

The spike trains of inhibited pacemaker neurons seen through the magnifying glass of nonlinear analyses.

PubMed

Segundo, J P; Sugihara, G; Dixon, P; Stiber, M; Bersier, L F

1998-12-01

This communication describes the new information that may be obtained by applying nonlinear analytical techniques to neurobiological time-series. Specifically, we consider the sequence of interspike intervals Ti (the "timing") of trains recorded from synaptically inhibited crayfish pacemaker neurons. As reported earlier, different postsynaptic spike train forms (sets of timings with shared properties) are generated by varying the average rate and/or pattern (implying interval dispersions and sequences) of presynaptic spike trains. When the presynaptic train is Poisson (independent exponentially distributed intervals), the form is "Poisson-driven" (unperturbed and lengthened intervals succeed each other irregularly). When presynaptic trains are pacemaker (intervals practically equal), forms are either "p:q locked" (intervals repeat periodically), "intermittent" (mostly almost locked but disrupted irregularly), "phase walk throughs" (intermittencies with briefer regular portions), or "messy" (difficult to predict or describe succinctly). Messy trains are either "erratic" (some intervals natural and others lengthened irregularly) or "stammerings" (intervals are integral multiples of presynaptic intervals). The individual spike train forms were analysed using attractor reconstruction methods based on the lagged coordinates provided by successive intervals from the time-series Ti. Numerous models were evaluated in terms of their predictive performance by a trial-and-error procedure: the most successful model was taken as best reflecting the true nature of the system's attractor. Each form was characterized in terms of its dimensionality, nonlinearity and predictability. (1) The dimensionality of the underlying dynamical attractor was estimated by the minimum number of variables (coordinates Ti) required to model acceptably the system's dynamics, i.e. by the system's degrees of freedom. Each model tested was based on a different number of Ti; the smallest number whose predictions were judged successful provided the best integer approximation of the attractor's true dimension (not necessarily an integer). Dimensionalities from three to five provided acceptable fits. (2) The degree of nonlinearity was estimated by: (i) comparing the correlations between experimental results and data from linear and nonlinear models, and (ii) tuning model nonlinearity via a distance-weighting function and identifying the either local or global neighborhood size. Lockings were compatible with linear models and stammerings were marginal; nonlinear models were best for Poisson-driven, intermittent and erratic forms. (3) Finally, prediction accuracy was plotted against increasingly long sequences of intervals forecast: the accuracies for Poisson-driven, locked and stammering forms were invariant, revealing irregularities due to uncorrelated noise, but those of intermittent and messy erratic forms decayed rapidly, indicating an underlying deterministic process. The excellent reconstructions possible for messy erratic and for some intermittent forms are especially significant because of their relatively low dimensionality (around 4), high degree of nonlinearity and prediction decay with time. This is characteristic of chaotic systems, and provides evidence that nonlinear couplings between relatively few variables are the major source of the apparent complexity seen in these cases. This demonstration of different dimensions, degrees of nonlinearity and predictabilities provides rigorous support for the categorization of different synaptically driven discharge forms proposed earlier on the basis of more heuristic criteria. This has significant implications. (1) It demonstrates that heterogeneous postsynaptic forms can indeed be induced by manipulating a few presynaptic variables. (2) Each presynaptic timing induces a form with characteristic dimensionality, thus breaking up the preparation into subsystems such that the physical variables in each operate as one

A Comparison of Descriptive and Functional Analyses of Inappropriate Mealtime Behavior.

PubMed

Borrero, Carrie S W; England, Jennie D; Sarcia, Ben; Woods, Julia N

2016-12-01

In recent years, rather than being used to assess the potential function of a response, descriptive assessment methods have been applied to evaluate potential consequences or contingencies for problem behavior (Borrero, Woods, Borrero, Masler, & Lesser in Journal of Applied Behavior Analysis, 43 , 71-88. doi: 10.1901/jaba.2010.43-71, 2010) or to assist with designing baseline conditions to approximate caregiver behavior (Casey et al. in Behavior Modification, 33 , 537-558. doi: 10.1177/0145445509341457, 2009). It has been shown that descriptive assessments of some forms of problem behavior (e.g., self-injury, aggression) are not good indicators of behavioral function and should not be used exclusively when conducting functional behavior assessments (Thompson & Iwata in Journal of Applied Behavior Analysis, 40 , 333-338. doi: 10.1901/jaba.2007.56.06/epdf, 2007). However, the extent to which descriptive assessments of inappropriate mealtime behavior can predict behavioral function is not yet clear. We conducted descriptive assessments of inappropriate mealtime behavior and compared the results to functional analyses for ten children with severe food refusal. Results showed that, for 71 % of participants, the descriptive and functional analyses matched. These results suggest that the correspondence between descriptive and functional analyses, at least for inappropriate mealtime behavior, may be higher than that for other forms of problem behavior.

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

PubMed Central

Pedersen, Jakob Skou; Bejerano, Gill; Siepel, Adam; Rosenbloom, Kate; Lindblad-Toh, Kerstin; Lander, Eric S; Kent, Jim; Miller, Webb; Haussler, David

2006-01-01

The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3′UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization. PMID:16628248

Evaluating predictive modeling’s potential to improve teleretinal screening participation in urban safety net clinics

PubMed Central

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Introduction Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Methods Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. Results The predictive models were modestly predictive with the best model having an AUC of 0.71. Discussion Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics. PMID:23920536

Evaluating predictive modeling's potential to improve teleretinal screening participation in urban safety net clinics.

PubMed

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. The predictive models were modestly predictive with the best model having an AUC of 0.71. Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics.

Prediction of Breakthrough Curves for Conservative and Reactive Transport from the Structural Parameters of Highly Heterogeneous Media

NASA Astrophysics Data System (ADS)

Hansen, S. K.; Haslauer, C. P.; Cirpka, O. A.; Vesselinov, V. V.

2016-12-01

It is desirable to predict the shape of breakthrough curves downgradient of a solute source from subsurface structural parameters (as in the small-perturbation macrodispersion theory) both for realistically heterogeneous fields, and at early time, before any sort of Fickian model is applicable. Using a combination of a priori knowledge, large-scale Monte Carlo simulation, and regression techniques, we have developed closed-form predictive expressions for pre- and post-Fickian flux-weighted solute breakthrough curves as a function of distance from the source (in integral scales) and variance of the log hydraulic conductivity field. Using the ensemble of Monte Carlo realizations, we have simultaneously computed error envelopes for the estimated flux-weighted breakthrough, and for the divergence of point breakthrough curves from the flux-weighted average, as functions of the predictive parameters. We have also obtained implied late-time macrodispersion coefficients for highly heterogeneous environments from the breakthrough statistics. This analysis is relevant for the modelling of reactive as well as conservative transport, since for many kinetic sorption and decay reactions, Laplace-domain modification of the breakthrough curve for conservative solute produces the correct curve for the reactive system.

Past makes future: role of pFC in prediction.

PubMed

Fuster, Joaquín M; Bressler, Steven L

2015-04-01

The pFC enables the essential human capacities for predicting future events and preadapting to them. These capacities rest on both the structure and dynamics of the human pFC. Structurally, pFC, together with posterior association cortex, is at the highest hierarchical level of cortical organization, harboring neural networks that represent complex goal-directed actions. Dynamically, pFC is at the highest level of the perception-action cycle, the circular processing loop through the cortex that interfaces the organism with the environment in the pursuit of goals. In its predictive and preadaptive roles, pFC supports cognitive functions that are critical for the temporal organization of future behavior, including planning, attentional set, working memory, decision-making, and error monitoring. These functions have a common future perspective and are dynamically intertwined in goal-directed action. They all utilize the same neural infrastructure: a vast array of widely distributed, overlapping, and interactive cortical networks of personal memory and semantic knowledge, named cognits, which are formed by synaptic reinforcement in learning and memory acquisition. From this cortex-wide reservoir of memory and knowledge, pFC generates purposeful, goal-directed actions that are preadapted to predicted future events.

Gender differences in the content of cognitive distraction during sex.

PubMed

Meana, Marta; Nunnink, Sarah E

2006-02-01

This study compared 220 college men and 237 college women on two types of self-reported cognitive distraction during sex, performance- and appearance-based. Affect, psychological distress, sexual knowledge, attitudes, fantasies, experiences, body image, satisfaction, and sexual function were assessed with the Derogatis Sexual Functioning Inventory and the Sexual History Form to determine associations with distraction. Between-gender analyses revealed that women reported higher levels of overall and appearance-based distraction than did men, but similar levels of performance-based distraction. Within-gender analyses revealed that women reported as much of one type of distraction as the other, while men reported more performance- than appearance-based distraction. In women, appearance-based distraction was predicted by negative body image, psychological distress, and not being in a relationship, while performance-based distraction was predicted by negative body image, psychological distress, and sexual dissatisfaction. In men, appearance-based distraction was predicted by negative body image, sexual dissatisfaction and not being in a relationship, while performance-based distraction was predicted by negative body image and sexual dissatisfaction. Investigating the content of cognitive distraction may be useful in understanding gender differences in sexual experience and in refining cognitive components of sex therapy.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

PubMed

Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

2013-04-02

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

Blade Tip Rubbing Stress Prediction

NASA Technical Reports Server (NTRS)

Davis, Gary A.; Clough, Ray C.

1991-01-01

An analytical model was constructed to predict the magnitude of stresses produced by rubbing a turbine blade against its tip seal. This model used a linearized approach to the problem, after a parametric study, found that the nonlinear effects were of insignificant magnitude. The important input parameters to the model were: the arc through which rubbing occurs, the turbine rotor speed, normal force exerted on the blade, and the rubbing coefficient of friction. Since it is not possible to exactly specify some of these parameters, values were entered into the model which bracket likely values. The form of the forcing function was another variable which was impossible to specify precisely, but the assumption of a half-sine wave with a period equal to the duration of the rub was taken as a realistic assumption. The analytical model predicted resonances between harmonics of the forcing function decomposition and known harmonics of the blade. Thus, it seemed probable that blade tip rubbing could be at least a contributor to the blade-cracking phenomenon. A full-scale, full-speed test conducted on the space shuttle main engine high pressure fuel turbopump Whirligig tester was conducted at speeds between 33,000 and 28,000 RPM to confirm analytical predictions.

Peer socialization of masculinity and femininity: differential effects of overt and relational forms of peer victimization.

PubMed

Ewing Lee, Elizabeth A; Troop-Gordon, Wendy

2011-06-01

Although peer influence has been implicated in recent theories of gender socialization, few investigations have tested whether children's gendered behaviours change over time as a function of peer experiences and whether some peer experiences may exacerbate, rather than dampen, gender non-conformity. Accordingly, the current study examined prospective links between specific forms of peer victimization and children's adherence to traditional gender roles. Peer reports of victimization and self-reports of engagement in stereotypically masculine and feminine activities were collected from 199 children (104 girls; 95 boys) in the Fall and Spring of their fifth-grade year. Multi-group path analysis was used to explore the relations between forms of victimization and masculinity and femininity for girls and boys. For girls, peer victimization predicted withdrawal from both feminine and masculine behaviours. For boys, physical, verbal, and general victimization predicted lower levels of feminine behaviours, but social exclusion forecast heightened engagement in traditionally feminine activities. These findings underscore how social experiences can amplify, as well as reduce, gender non-conformity.

A theoretical approach to evaluate the release rate of acetaminophen from erosive wax matrix dosage forms.

PubMed

Agata, Yasuyoshi; Iwao, Yasunori; Shiino, Kai; Miyagishima, Atsuo; Itai, Shigeru

2011-07-29

To predict drug dissolution and understand the mechanisms of drug release from wax matrix dosage forms containing glyceryl monostearate (GM; a wax base), aminoalkyl methacrylate copolymer E (AMCE; a pH-dependent functional polymer), and acetaminophen (APAP; a model drug), we tried to derive a novel mathematical model with respect to erosion and diffusion theory. Our model exhibited good agreement with the whole set of experimentally obtained values pertaining to APAP release at pH 4.0 and pH 6.5. In addition, this model revealed that the eroding speed of wax matrices was strongly influenced by the loading content of AMCE, but not that of APAP, and that the diffusion coefficient increased as APAP loading decreased and AMCE loading increased, thus directly defining the physicochemical properties of erosion and diffusion. Therefore, this model might prove a useful equation for the precise prediction of dissolution and for understanding the mechanisms of drug release from wax matrix dosage forms. Copyright © 2011 Elsevier B.V. All rights reserved.

Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property

PubMed Central

Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

Given a regulatory pathway system consisting of a set of proteins, can we predict which pathway class it belongs to? Such a problem is closely related to the biological function of the pathway in cells and hence is quite fundamental and essential in systems biology and proteomics. This is also an extremely difficult and challenging problem due to its complexity. To address this problem, a novel approach was developed that can be used to predict query pathways among the following six functional categories: (i) “Metabolism”, (ii) “Genetic Information Processing”, (iii) “Environmental Information Processing”, (iv) “Cellular Processes”, (v) “Organismal Systems”, and (vi) “Human Diseases”. The prediction method was established trough the following procedures: (i) according to the general form of pseudo amino acid composition (PseAAC), each of the pathways concerned is formulated as a 5570-D (dimensional) vector; (ii) each of components in the 5570-D vector was derived by a series of feature extractions from the pathway system according to its graphic property, biochemical and physicochemical property, as well as functional property; (iii) the minimum redundancy maximum relevance (mRMR) method was adopted to operate the prediction. A cross-validation by the jackknife test on a benchmark dataset consisting of 146 regulatory pathways indicated that an overall success rate of 78.8% was achieved by our method in identifying query pathways among the above six classes, indicating the outcome is quite promising and encouraging. To the best of our knowledge, the current study represents the first effort in attempting to identity the type of a pathway system or its biological function. It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area. PMID:21980418

Influence of family environment on long-term psychosocial functioning of adolescents with juvenile fibromyalgia.

PubMed

Sil, Soumitri; Lynch-Jordan, Anne; Ting, Tracy V; Peugh, James; Noll, Jennie; Kashikar-Zuck, Susmita

2013-06-01

Little is known about the impact of family environment on the long-term adjustment of patients with juvenile-onset fibromyalgia (JFM). Our objective was to evaluate whether family environment in early adolescence predicted later physical functioning and depressive symptoms of adolescents with JFM as they transitioned to early adulthood in the context of a controlled long-term followup study. Participants consisted of 39 youth (mean age 18.7 years) with JFM and 38 healthy matched controls who completed web-based surveys about their health status (Short Form 36 health survey) and depressive symptoms (Beck Depression Inventory II) ~4 years after a home-based, in-person assessment of child and family functioning. During the initial assessment, parents of the participants (94% mothers) completed the Family Environment Scale and adolescents (mean age 14.8 years) completed self-report questionnaires about pain (visual analog scale) and depressive symptoms (Children's Depression Inventory). The results indicated that family environment during early adolescence significantly predicted greater depressive symptoms in early adulthood for both the JFM group and the healthy controls. In particular, a controlling family environment (use of rules to control the family and allowing little independence) during early adolescence was the driving factor in predicting poorer long-term emotional functioning for patients with JFM. Family environment did not significantly predict longer-term physical impairment for either group. Adolescents with JFM from controlling family environments are at an increased risk for poorer emotional functioning in early adulthood. Behavioral and family interventions should foster independent coping among adolescents with JFM and greater parenting flexibility to enhance successful long-term coping. Copyright © 2013 by the American College of Rheumatology.

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

PubMed Central

Firth, Andrew E; Atkins, John F

2009-01-01

Japanese encephalitis, West Nile, Usutu and Murray Valley encephalitis viruses form a tight subgroup within the larger Flavivirus genus. These viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. Such peaks are generally indicative of functionally important non-coding sequence elements. The second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. Since cleavage at the NS1-NS2A boundary is known to require synthesis of NS2A in cis, the resulting transframe fusion protein is predicted to be NS1-NS2AN-term-FOO. We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'. PMID:19196463

Relationship between fear of falling and outcomes of an inpatient geriatric rehabilitation population--fear of the fear of falling.

PubMed

Denkinger, Michael D; Igl, Wilmar; Lukas, Albert; Bader, Anne; Bailer, Stefanie; Franke, Sebastian; Denkinger, Claudia M; Nikolaus, Thorsten; Jamour, Michael

2010-04-01

To examine the effects of various risk factors on three functional outcomes during rehabilitation. Geriatric inpatient rehabilitation unit. Observational longitudinal study. One hundred sixty-one geriatric rehabilitation inpatients (men, women), mean age 82, who were capable of walking at baseline. Functional status was assessed weekly between admission and discharge and at a follow-up 4 months later at home using the function component of the Short Form-Late Life Function and Disability Instrument, the Barthel Index, and Habitual Gait Speed. Various risk factors, such as falls-related self-efficacy (Falls Efficacy Scale-International), were measured. Associations between predictors and functional status at discharge and follow-up were analyzed using linear regression models and bivariate plots. Fear of falling predicted functioning across all outcomes except for habitual gait speed at discharge and follow-up. Visual comparison of functional trajectories between subgroups confirmed these findings, with different levels of fear of falling across time in linear plots. Thus, superior ability of this measure to discriminate between functional status at baseline across all outcomes and to discriminate between functional change especially with regard to the performance-based outcome was demonstrated. Falls-related self-efficacy is the only parameter that significantly predicts rehabilitation outcome at discharge and follow-up across all outcomes. Therefore, it should be routinely assessed in future studies in (geriatric) rehabilitation and considered to be an important treatment goal.

Physical function and independence 1 year after myocardial infarction: observations from the Translational Research Investigating Underlying disparities in recovery from acute Myocardial infarction: Patients' Health status registry.

PubMed

Dodson, John A; Arnold, Suzanne V; Reid, Kimberly J; Gill, Thomas M; Rich, Michael W; Masoudi, Frederick A; Spertus, John A; Krumholz, Harlan M; Alexander, Karen P

2012-05-01

Acute myocardial infarction (AMI) may contribute to health status declines including "independence loss" and "physical function decline." Despite the importance of these outcomes for prognosis and quality of life, their incidence and predictors have not been well described. We studied 2,002 patients with AMI enrolled across 24 sites in the TRIUMPH registry who completed assessments of independence and physical function at the time of AMI and 1 year later. Independence was evaluated by the EuroQol-5D (mobility, self-care, and usual activities), and physical function was assessed with the Short Form-12 physical component score. Declines in ≥1 level on EuroQol-5D and >5 points in PCS were considered clinically significant changes. Hierarchical, multivariable, modified Poisson regression models accounting for within-site variability were used to identify predictors of independence loss and physical function decline. One-year post AMI, 43.0% of patients experienced health status declines: 12.8% independence loss alone, 15.2% physical function decline alone, and 15.0% both. After adjustment, variables that predicted independence loss included female sex, nonwhite race, unmarried status, uninsured status, end-stage renal disease, and depression. Variables that predicted physical function decline were uninsured status, lack of cardiac rehabilitation referral, and absence of pre-AMI angina. Age was not predictive of either outcome after adjustment. >40% of patients experience independence loss or physical function decline 1 year after AMI. These changes are distinct but can occur simultaneously. Although some risk factors are not modifiable, others suggest potential targets for strategies to preserve patients' health status. Copyright © 2012 Mosby, Inc. All rights reserved.

Deformation properties of lead isotopes

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

Tolokonnikov, S. V.; Borzov, I. N.; Lutostansky, Yu. S.

2016-01-15

The deformation properties of a long lead isotopic chain up to the neutron drip line are analyzed on the basis of the energy density functional (EDF) in the FaNDF{sup 0} Fayans form. The question of whether the ground state of neutron-deficient lead isotopes can have a stable deformation is studied in detail. The prediction of this deformation is contained in the results obtained on the basis of the HFB-17 and HFB-27 Skyrme EDF versions and reported on Internet. The present analysis reveals that this is at odds with experimental data on charge radii and magnetic moments of odd lead isotopes.more » The Fayans EDF version predicts a spherical ground state for all light lead isotopes, but some of them (for example, {sup 180}Pb and {sup 184}Pb) prove to be very soft—that is, close to the point of a phase transition to a deformed state. Also, the results obtained in our present study are compared with the predictions of some other Skyrme EDF versions, including SKM*, SLy4, SLy6, and UNE1. By and large, their predictions are closer to the results arising upon the application of the Fayans functional. For example, the SLy4 functional predicts, in just the same way as the FaNDF{sup 0} functional, a spherical shape for all nuclei of this region. The remaining three Skyrme EDF versions lead to a deformation of some light lead isotopes, but their number is substantially smaller than that in the case of the HFB-17 and HFB-27 functionals. Moreover, the respective deformation energy is substantially lower, which gives grounds to hope for the restoration of a spherical shape upon going beyond the mean-field approximation, which we use here. Also, the deformation properties of neutron-rich lead isotopes are studied up to the neutron drip line. Here, the results obtained with the FaNDF{sup 0} functional are compared with the predictions of the HFB-17, HFB-27, SKM*, and SLy4 Skyrme EDF versions. All of the EDF versions considered here predict the existence of a region where neutron-rich lead isotopes undergo deformations, but the size of this region is substantially different for the different functionals being considered. Once again, it is maximal for the HFB-17 and HFB-27 functionals, is substantially narrower for the FaNDF{sup 0} functional, and is still narrower for the SKM* and SLy4 functionals. The two-neutron drip line proved to be A{sub drip}{sup 2n} = 266 for all of the EDF versions considered here, with the exception of SKM*, for which it is shifted to A{sub drip}{sup 2n}(SKM*) = 272.« less

dPotFit: A computer program to fit diatomic molecule spectral data to potential energy functions

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.

2017-01-01

This paper describes program dPotFit, which performs least-squares fits of diatomic molecule spectroscopic data consisting of any combination of microwave, infrared or electronic vibrational bands, fluorescence series, and tunneling predissociation level widths, involving one or more electronic states and one or more isotopologs, and for appropriate systems, second virial coefficient data, to determine analytic potential energy functions defining the observed levels and other properties of each state. Four families of analytical potential functions are available for fitting in the current version of dPotFit: the Expanded Morse Oscillator (EMO) function, the Morse/Long-Range (MLR) function, the Double-Exponential/Long-Range (DELR) function, and the 'Generalized Potential Energy Function' (GPEF) of Šurkus, which incorporates a variety of polynomial functional forms. In addition, dPotFit allows sets of experimental data to be tested against predictions generated from three other families of analytic functions, namely, the 'Hannover Polynomial' (or "X-expansion") function, and the 'Tang-Toennies' and Scoles-Aziz 'HFD', exponential-plus-van der Waals functions, and from interpolation-smoothed pointwise potential energies, such as those obtained from ab initio or RKR calculations. dPotFit also allows the fits to determine atomic-mass-dependent Born-Oppenheimer breakdown functions, and singlet-state Λ-doubling, or 2Σ splitting radial strength functions for one or more electronic states. dPotFit always reports both the 95% confidence limit uncertainty and the "sensitivity" of each fitted parameter; the latter indicates the number of significant digits that must be retained when rounding fitted parameters, in order to ensure that predictions remain in full agreement with experiment. It will also, if requested, apply a "sequential rounding and refitting" procedure to yield a final parameter set defined by a minimum number of significant digits, while ensuring no significant loss of accuracy in the predictions yielded by those parameters.

Quantifying wall turbulence via a symmetry approach: A Lie group theory

NASA Astrophysics Data System (ADS)

She, Zhen-Su; Chen, Xi; Hussain, Fazle

2017-11-01

We present a symmetry-based approach which yields analytic expressions for the mean velocity and kinetic energy profiles from a Lie-group analysis. After verifying the dilation-group invariance of the Reynolds averaged Navier-Stokes equation in the presence of a wall, we select a stress and energy length function as similarity variables which are assumed to have a simple dilation-invariant form. Three kinds of (local) invariant forms of the length functions are postulated, a combination of which yields a multi-layer formula giving its distribution in the entire flow region normal to the wall. The mean velocity profile is then predicted using the mean momentum equation, which yields, in particular, analytic expressions for the (universal) wall function and separate wake functions for pipe and channel - which are validated by data from direct numerical simulations (DNS). Future applications to a variety of wall flows such as flows around flat plate or airfoil, in a Rayleigh-Benard cell or Taylor-Couette system, etc., are discussed, for which the dilation group invariance is valid in the wall-normal direction.

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

PubMed

Taylor, James; Tyekucheva, Svitlana; King, David C; Hardison, Ross C; Miller, Webb; Chiaromonte, Francesca

2006-12-01

Genomic sequence signals - such as base composition, presence of particular motifs, or evolutionary constraint - have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy ( approximately 94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).

A new water retention and hydraulic conductivity model accounting for contact angle

NASA Astrophysics Data System (ADS)

Diamantopoulos, Efstathios; Durner, Wolfgang

2013-04-01

The description of soil water transport in the unsaturated zone requires the knowledge of the soil hydraulic properties, i.e. the water retention and the hydraulic conductivity function. A great amount of parameterizations for this can be found in the literature, the majority of which represent the complex pore space of soils as a bundle of cylindrical capillary tubes of various sizes. The assumption of zero contact angles between water and surface of the grains is also made. However, these assumptions limit the predictive capabilities of these models, leading often to enormous errors in the prediction of water dynamics in soils. We present a pore scale analysis for equilibrium liquid configurations (retention) in angular pores taking the effect of contact angle into account. Furthermore, we propose an alternative derivation of the hydraulic conductivity function, again as a function of the contact angle, assuming flow perpendicular to pore cross sections. Finally, we upscale our model from the pore to the sample scale by assuming a gamma statistical distribution of the pore sizes. Closed form expressions are derived for both sample water retention and conductivity functions. The new model was tested against experimental data from multistep inflow/outflow (MSI/MSO) experiments for a sandy material. They were conducted using ethanol and water as the wetting liquid. Ethanol was assumed to form a zero contact angle with the soil grains. The proposed model described both imbibition and drainage of water and ethanol very well. Lastly, the consideration of the contact angle allowed the description of the observed hysteresis.

Short forms of the Social Interaction Anxiety Scale and the Social Phobia Scale.

PubMed

Fergus, Thomas A; Valentiner, David P; McGrath, Patrick B; Gier-Lonsway, Stephanie L; Kim, Hyun-Soo

2012-01-01

Mattick and Clarke's (1998) Social Interaction Anxiety Scale (SIAS) and Social Phobia Scale (SPS) are commonly used self-report measures that assess 2 dimensions of social anxiety. Given the need for short, readable measures, this research proposes short forms of both scales. Item-level analyses of readability characteristics of the SIAS and SPS items led to the selection of 6 items from each scale for use in the short forms. The SIAS and SPS short forms had reading levels at approximately the 6th and 5th grade level, respectively. Results using nonclinical (Study 1: N = 469) and clinical (Study 2: N = 145) samples identified these short forms as being factorially sound, possessing adequate internal consistency, and having strong convergence with their full-length counterparts. Moreover, these short forms showed convergence with other measures of social anxiety, showed divergence from measures assessing related constructs, and predicted concurrent interpersonal functioning. Recommendations for the use of these short forms are discussed.

Development of an Environmental Fate Simulator for New and Proposed Military Unique Munition Compounds

DTIC Science & Technology

2015-05-07

i.e., methylenedintramine) is susceptible to further biodegradation resulting in the formation of N20 and CO2. Developing the capability to predict...ensuring complete biodegradation of the munition compound into harmless products. Methylenedinitramine from RDX degradation can form from either...anaerobic biodegradation . Furthermore, only those transformation processes that are currently supported by reaction libraries will be functional

Relating Worry and Executive Functioning During Childhood: The Moderating Role of Age.

PubMed

Geronimi, Elena M C; Patterson, Heather L; Woodruff-Borden, Janet

2016-06-01

The associations between worry and executive functioning across development have not been previously explored. Examining the interrelationships between these variables in childhood may further elucidate the cognitive nature of worry as well as its developmental course. Hypotheses predicted that difficulties with executive functioning would correlate with child worry; based on extant literature, age-related hypotheses were proposed for particular aspects of executive functioning. Children (N = 130) participated in the present study. Difficulties with executive functioning and child worry were assessed. Results demonstrated that each executive functioning subscale correlated with worry. The relations between worry and several facets of executive functioning were no longer significant at older ages, while the relations between worry and the facets of inhibition, shifting, and emotional control did not demonstrate age-related interaction effects. Overall, the findings suggest that worry is associated with executive functioning at young ages and that this association takes distinct forms during different childhood stages.

The structure and health correlates of trait repetitive thought in older adults.

PubMed

Segerstrom, Suzanne C; Roach, Abbey R; Evans, Daniel R; Schipper, Lindsey J; Darville, Audrey K

2010-09-01

Repetitive thought (RT) involves frequent or prolonged thoughts about oneself and one's world, encompassing discrete forms such as trait worry, rumination, processing, and reminiscing. These forms of RT can be described using 3 basic, underlying qualities: total propensity for RT of all types, valence (positive vs. negative content), and purpose (searching or uncertainty vs. solving or certainty). The adaptiveness of discrete forms with regard to health is likely to be related to these qualities, particularly valence and total propensity. The present study confirmed the model and identified the relationship of these qualities of RT to subjective psychological, physical, and cognitive health in older adults aged 60-94 (N = 179). As predicted, more negatively valenced trait RT was associated with worse psychological, physical, and cognitive health. More total propensity for RT was associated only with worse psychological health. Searching purpose was associated only with worse cognitive health. In turn, negatively valenced RT was predicted by poorer executive functions, suggesting that such functions may be important for directing this quality of RT. The valence of older adults' RT is important insofar as it may contribute to their sense of good or ill health. However, the propensity for all kinds of RT to associate with poorer psychological health may reflect the co-occurrence of negative and positive RT, such as rumination and emotional processing. Although RT has not been extensively investigated in older adults, it appears to play an important role in their subjective health. (c) 2010 APA, all rights reserved.

Intraoperative linguistic performance during awake brain surgery predicts postoperative linguistic deficits.

PubMed

Chang, Wei-Han; Pei, Yu-Cheng; Wei, Kuo-Chen; Chao, Yi-Ping; Chen, Mei-Hui; Yeh, Heng-An; Jaw, Fu-Shan; Chen, Pin-Yuan

2018-04-10

Awake craniotomy pursues a balance between extensive tumor resection and preservation of postoperative language function. A dilemma exists in patients whose tumor resection is restricted due to signs of language impairment observed during awake craniotomy. In order to determine the degree to which recovery of language function caused by tumor resection can be achieved by spontaneous neuroplasticity, the change in postoperative language function was compared to quantified intraoperative linguistic performance. The modified, short-form Boston Diagnostic Aphasia Examination (sfBDAE) was used to assess pre- and postoperative language functions; visual object naming (DO 80) and semantic-association (Pyramid and Palm Tree Test, PPTT) tests assessed intraoperative linguistic performance. DO 80 and PPTT were performed alternatively during subcortical functional monitoring while performing tumor resection and sfBDAE was assessed 1-week postoperatively. Most patients with observed language impairment during awake surgery showed improved language function postoperatively. Both intraoperative DO 80 and PPTT showed significant correlation to postoperative sfBDAE domain scores (p < 0.05), with a higher correlation observed with PPTT. A linear regression model showed that only PPTT predicted the postoperative sfBDAE domain scores with the adjusted R 2 ranging from 0.51 to 0.89 (all p < 0.01). Receiver operating characteristic analysis showed a cutoff value of PPTT that yielded a sensitivity of 80% and specificity of 100%. PPTT may be a feasible tool for intraoperative linguistic evaluation that can predict postoperative language outcomes. Further studies are needed to determine the extent of tumor resection that optimizes the postoperative language following neuroplasticity.

Issues associated with the use of Yoshida nonlinear isotropic/kinematic hardening material model in Advanced High Strength Steels

NASA Astrophysics Data System (ADS)

Shi, Ming F.; Zhang, Li; Zhu, Xinhai

2016-08-01

The Yoshida nonlinear isotropic/kinematic hardening material model is often selected in forming simulations where an accurate springback prediction is required. Many successful application cases in the industrial scale automotive components using advanced high strength steels (AHSS) have been reported to give better springback predictions. Several issues have been raised recently in the use of the model for higher strength AHSS including the use of two C vs. one C material parameters in the Armstrong and Frederick model (AF model), the original Yoshida model vs. Original Yoshida model with modified hardening law, and constant Young's Modulus vs. decayed Young's Modulus as a function of plastic strain. In this paper, an industrial scale automotive component using 980 MPa strength materials is selected to study the effect of two C and one C material parameters in the AF model on both forming and springback prediction using the Yoshida model with and without the modified hardening law. The effect of decayed Young's Modulus on the springback prediction for AHSS is also evaluated. In addition, the limitations of the material parameters determined from tension and compression tests without multiple cycle tests are also discussed for components undergoing several bending and unbending deformations.

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

2016-09-01

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

Modeling of Turbulence Generated Noise in Jets

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Bridges, James

2004-01-01

A numerically calculated Green's function is used to predict jet noise spectrum and its far-field directivity. A linearized form of Lilley's equation governs the non-causal Green s function of interest, with the non-linear terms on the right hand side identified as the source. In this paper, contributions from the so-called self- and shear-noise source terms will be discussed. A Reynolds-averaged Navier-Stokes solution yields the required mean flow as well as time- and length scales of a noise-generating turbulent eddy. A non-compact source, with exponential temporal and spatial functions, is used to describe the turbulence velocity correlation tensors. It is shown that while an exact non-causal Green's function accurately predicts the observed shift in the location of the spectrum peak with angle as well as the angularity of sound at moderate Mach numbers, at high subsonic and supersonic acoustic Mach numbers the polar directivity of radiated sound is not entirely captured by this Green's function. Results presented for Mach 0.5 and 0.9 isothermal jets, as well as a Mach 0.8 hot jet conclude that near the peak radiation angle a different source/Green's function convolution integral may be required in order to capture the peak observed directivity of jet noise.

Long-term effects of psychosocial work stress in midlife on health functioning after labor market exit--results from the GAZEL study.

PubMed

Wahrendorf, Morten; Sembajwe, Grace; Zins, Marie; Berkman, Lisa; Goldberg, Marcel; Siegrist, Johannes

2012-07-01

To study long-term effects of psychosocial work stress in mid-life on health functioning after labor market exit using two established work stress models. In the frame of the prospective French Gazel cohort study, data on psychosocial work stress were assessed using the full questionnaires measuring the demand-control-support model (in 1997 and 1999) and the effort-reward imbalance model (in 1998). In 2007, health functioning was assessed, using the Short Form 36 mental and physical component scores. Multivariate regressions were calculated to predict health functioning in 2007, controlling for age, gender, social position, and baseline self-perceived health. Consistent effects of both work stress models and their single components on mental and physical health functioning during retirement were observed. Effects remained significant after adjustment including baseline self-perceived health. Whereas the predictive power of both work stress models was similar in the case of the physical composite score, in the case of the mental health score, values of model fit were slightly higher for the effort-reward imbalance model (R(2): 0.13) compared with the demand-control model (R²: 0.11). Findings underline the importance of working conditions in midlife not only for health in midlife but also for health functioning after labor market exit.

Quantifying uncertainty in partially specified biological models: how can optimal control theory help us?

PubMed

Adamson, M W; Morozov, A Y; Kuzenkov, O A

2016-09-01

Mathematical models in biology are highly simplified representations of a complex underlying reality and there is always a high degree of uncertainty with regards to model function specification. This uncertainty becomes critical for models in which the use of different functions fitting the same dataset can yield substantially different predictions-a property known as structural sensitivity. Thus, even if the model is purely deterministic, then the uncertainty in the model functions carries through into uncertainty in model predictions, and new frameworks are required to tackle this fundamental problem. Here, we consider a framework that uses partially specified models in which some functions are not represented by a specific form. The main idea is to project infinite dimensional function space into a low-dimensional space taking into account biological constraints. The key question of how to carry out this projection has so far remained a serious mathematical challenge and hindered the use of partially specified models. Here, we propose and demonstrate a potentially powerful technique to perform such a projection by using optimal control theory to construct functions with the specified global properties. This approach opens up the prospect of a flexible and easy to use method to fulfil uncertainty analysis of biological models.

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

PubMed

Haider, Kamran; Huggins, David J

2013-10-28

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.

Predictive Suppression of Cortical Excitability and Its Deficit in Schizophrenia

PubMed Central

Schroeder, Charles E.; Leitman, David I.

2013-01-01

Recent neuroscience advances suggest that when interacting with our environment, along with previous experience, we use contextual cues and regularities to form predictions that guide our perceptions and actions. The goal of such active “predictive sensing” is to selectively enhance the processing and representation of behaviorally relevant information in an efficient manner. Since a hallmark of schizophrenia is impaired information selection, we tested whether this deficiency stems from dysfunctional predictive sensing by measuring the degree to which neuronal activity predicts relevant events. In healthy subjects, we established that these mechanisms are engaged in an effort-dependent manner and that, based on a correspondence between human scalp and intracranial nonhuman primate recordings, their main role is a predictive suppression of excitability in task-irrelevant regions. In contrast, schizophrenia patients displayed a reduced alignment of neuronal activity to attended stimuli, which correlated with their behavioral performance deficits and clinical symptoms. These results support the relevance of predictive sensing for normal and aberrant brain function, and highlight the importance of neuronal mechanisms that mold internal ongoing neuronal activity to model key features of the external environment. PMID:23843536

Predictive Coding Strategies for Developmental Neurorobotics

PubMed Central

Park, Jun-Cheol; Lim, Jae Hyun; Choi, Hansol; Kim, Dae-Shik

2012-01-01

In recent years, predictive coding strategies have been proposed as a possible means by which the brain might make sense of the truly overwhelming amount of sensory data available to the brain at any given moment of time. Instead of the raw data, the brain is hypothesized to guide its actions by assigning causal beliefs to the observed error between what it expects to happen and what actually happens. In this paper, we present a variety of developmental neurorobotics experiments in which minimalist prediction error-based encoding strategies are utilize to elucidate the emergence of infant-like behavior in humanoid robotic platforms. Our approaches will be first naively Piagian, then move onto more Vygotskian ideas. More specifically, we will investigate how simple forms of infant learning, such as motor sequence generation, object permanence, and imitation learning may arise if minimizing prediction errors are used as objective functions. PMID:22586416

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.

PubMed

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-02-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. Copyright © 2013 The Authors. Wiley Periodicals, Inc.

Acoustics Research of Propulsion Systems

NASA Technical Reports Server (NTRS)

Gao, Ximing; Houston, Janice D.

2014-01-01

The liftoff phase induces some of the highest acoustic loading over a broad frequency for a launch vehicle. These external acoustic environments are used in the prediction of the internal vibration responses of the vehicle and components. Thus, predicting these liftoff acoustic environments is critical to the design requirements of any launch vehicle but there are challenges. Present liftoff vehicle acoustic environment prediction methods utilize stationary data from previously conducted hold-down tests; i.e. static firings conducted in the 1960's, to generate 1/3 octave band Sound Pressure Level (SPL) spectra. These data sets are used to predict the liftoff acoustic environments for launch vehicles. To facilitate the accuracy and quality of acoustic loading, predictions at liftoff for future launch vehicles such as the Space Launch System (SLS), non-stationary flight data from the Ares I-X were processed in PC-Signal in two forms which included a simulated hold-down phase and the entire launch phase. In conjunction, the Prediction of Acoustic Vehicle Environments (PAVE) program was developed in MATLAB to allow for efficient predictions of sound pressure levels (SPLs) as a function of station number along the vehicle using semiempirical methods. This consisted, initially, of generating the Dimensionless Spectrum Function (DSF) and Dimensionless Source Location (DSL) curves from the Ares I-X flight data. These are then used in the MATLAB program to generate the 1/3 octave band SPL spectra. Concluding results show major differences in SPLs between the hold-down test data and the processed Ares IX flight data making the Ares I-X flight data more practical for future vehicle acoustic environment predictions.

Thermodynamic properties and crystallization kinetics at high liquid undercooling

NASA Technical Reports Server (NTRS)

Fecht, Hans J.

1990-01-01

The heat capacities of liquid and crystalline Au-Pb-Sb alloys in the glass-forming composition range were measured with droplet emulsion and bulk samples. Based on the measured C(sub p) data, the entropy, enthalpy, and Gibbs free energy functions of the eutectic, solid mixture, and undercooled liquid were determined as a function of undercooling and compared with theoretical predictions. The results indicate an isentropic temperature at 313 + or - 5 K, which agrees well with experimental data for the glass transition. A kinetics analysis of the nucleation undercooling response suggests that the proper choice for the Gibbs free energy change during crystallization is most important in analyzing the nucleation kinetics. By classical nucleation theory, the prefactors obtained, based on a variety of theoretical predictions for the driving force, can differ by six orders of magnitude. If the nucleation rates are extrapolated to high undercooling, the extrapolations based on measured heat capacity data show agreement, whereas the predicted nucleation rates are inconsistent with results from drop tower experiments. The implications for microg experiments are discussed.

Designers' unified cost model

NASA Technical Reports Server (NTRS)

Freeman, W.; Ilcewicz, L.; Swanson, G.; Gutowski, T.

1992-01-01

The Structures Technology Program Office (STPO) at NASA LaRC has initiated development of a conceptual and preliminary designers' cost prediction model. The model will provide a technically sound method for evaluating the relative cost of different composite structural designs, fabrication processes, and assembly methods that can be compared to equivalent metallic parts or assemblies. The feasibility of developing cost prediction software in a modular form for interfacing with state-of-the-art preliminary design tools and computer aided design programs is being evaluated. The goal of this task is to establish theoretical cost functions that relate geometric design features to summed material cost and labor content in terms of process mechanics and physics. The output of the designers' present analytical tools will be input for the designers' cost prediction model to provide the designer with a database and deterministic cost methodology that allows one to trade and synthesize designs with both cost and weight as objective functions for optimization. This paper presents the team members, approach, goals, plans, and progress to date for development of COSTADE (Cost Optimization Software for Transport Aircraft Design Evaluation).

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

SINGLE NEURON ACTIVITY AND THETA MODULATION IN POSTRHINAL CORTEX DURING VISUAL OBJECT DISCRIMINATION

PubMed Central

Furtak, Sharon C.; Ahmed, Omar J.; Burwell, Rebecca D.

2012-01-01

Postrhinal cortex, the rodent homolog of the primate parahippocampal cortex, processes spatial and contextual information. Our hypothesis of postrhinal function is that it serves to encode context, in part, by forming representations that link objects to places. We recorded postrhinal neuronal activity and local field potentials (LFPs) in rats trained on a two-choice, visual discrimination task. As predicted, a large proportion of postrhinal neurons signaled object-location conjunctions. In addition, postrhinal LFPs exhibited strong oscillatory rhythms in the theta band, and many postrhinal neurons were phase locked to theta. Although correlated with running speed, theta power was lower than predicted by speed alone immediately before and after choice. However, theta power was significantly increased following incorrect decisions, suggesting a role in signaling error. These findings provide evidence that postrhinal cortex encodes representations that link objects to places and suggest that postrhinal theta modulation extends to cognitive as well as spatial functions. PMID:23217745

Investigation of chaos and its control in a Duffing-type nano beam model

NASA Astrophysics Data System (ADS)

Jha, Abhishek Kumar; Dasgupta, Sovan Sundar

2018-04-01

The prediction of chaos of a nano beam with harmonic excitation is investigated. Using the Galerkin method the nonlinear lumped model of a clamped-clamped nano beam with nonlinear cubic stiffness is obtained. This is a Duffing system with hardening type of nonlinearity. Based on the energy function and the phase portrait of the system, the resonator dynamics is categorized into four situations in which Using Malnikov function, an analytical criterion for homoclinic intersection in the form of inequality is written in terms of the system parameters. A numerical study including largest lyapunov exponent, Poincare diagram and phase portrait confirm the analytical prediction of chaos and effect of forcing amplitude. Subsequently, a linear velocity feedback controller is introduced into the system to successfully control the chaotic motion of the system at a faster rate at larger value of gain parameter.

A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects

PubMed Central

Gloss, Andrew D.; Groen, Simon C.; Whiteman, Noah K.

2017-01-01

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales—from variation within populations to divergence among populations—to form a comprehensive view of adaptation in herbivorous insects. PMID:28736510

Coiling of viscous jets

NASA Astrophysics Data System (ADS)

Ribe, Neil M.

2004-11-01

A stream of viscous fluid falling from a sufficient height onto a surface forms a series of regular coils. I use a numerical model for a deformable fluid thread to predict the coiling frequency as a function of the thread's radius, the flow rate, the fall height, and the fluid viscosity. Three distinct modes of coiling can occur: viscous (e.g. toothpaste), gravitational (honey falling from a moderate height) and inertial (honey falling from a great height). When inertia is significant, three states of steady coiling with different frequencies can exist over a range of fall heights. The numerically predicted coiling frequencies agree well with experimental measurements in the inertial coiling regime.

Theoretical prediction of novel ultrafine nanowires formed by Si12C12 cage-like clusters

NASA Astrophysics Data System (ADS)

Yong, Yongliang; Song, Bin; He, Pimo

2014-02-01

Using density functional theory calculations, we predict that novel SiC ultrafine nanowires can be produced via the coalescence of stable Si12C12 clusters. For the isolated Si12C12 clusters, we find that the cage-like structure with a distinct segregation between Si and C atoms is energetically more favourable than the fullerene-like structure with alternating Si-C bonds. Via the coalescence of Si12C12 clusters, three novel stable nanowires have been characterised. The band structure reveals that these nanowires are semiconductors with narrow gap, indicating that they may be used as infrared detectors and thermoelectrics.

Separated kaon electroproduction cross section and the kaon form factor from 6 GeV JLab data

DOE PAGES

Carmignotto, M.; Ali, S.; Aniol, K.; ...

2018-02-28

The 1H(e,e 'K +)Λ reaction was studied as a function of the Mandelstam variable -t using data from the E01-004 (FPI-2) and E93-018 experiments that were carried out in Hall C at the 6 GeV Jefferson Laboratory. The cross section was fully separated into longitudinal and transverse components, and two interference terms at four-momentum transfers Q 2 of 1.00, 1.36, and 2.07 GeV 2. The kaon form factor was extracted from the longitudinal cross section using the Regge model by Vanderhaeghen et al. [Phys. Rev. C 57, 1454 (1998)]. Here, the results establish the method, previously used successfully for pionmore » analyses, for extracting the kaon form factor. Data from 12 GeV Jefferson Laboratory experiments are expected to have sufficient precision to distinguish between theoretical predictions, for example, recent perturbative QCD calculations with modern parton distribution amplitudes. The leading-twist behavior for light mesons is predicted to set in for values of Q 2 between 5 and 10 GeV 2, which makes data in the few-GeV regime particularly interesting. Finally, the Q 2 dependence at fixed x and -t of the longitudinal cross section that we extracted seems consistent with the QCD factorization prediction within the experimental uncertainty.« less

Separated kaon electroproduction cross section and the kaon form factor from 6 GeV JLab data

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

Carmignotto, M.; Ali, S.; Aniol, K.

The 1H(e,e 'K +)Λ reaction was studied as a function of the Mandelstam variable -t using data from the E01-004 (FPI-2) and E93-018 experiments that were carried out in Hall C at the 6 GeV Jefferson Laboratory. The cross section was fully separated into longitudinal and transverse components, and two interference terms at four-momentum transfers Q 2 of 1.00, 1.36, and 2.07 GeV 2. The kaon form factor was extracted from the longitudinal cross section using the Regge model by Vanderhaeghen et al. [Phys. Rev. C 57, 1454 (1998)]. Here, the results establish the method, previously used successfully for pionmore » analyses, for extracting the kaon form factor. Data from 12 GeV Jefferson Laboratory experiments are expected to have sufficient precision to distinguish between theoretical predictions, for example, recent perturbative QCD calculations with modern parton distribution amplitudes. The leading-twist behavior for light mesons is predicted to set in for values of Q 2 between 5 and 10 GeV 2, which makes data in the few-GeV regime particularly interesting. Finally, the Q 2 dependence at fixed x and -t of the longitudinal cross section that we extracted seems consistent with the QCD factorization prediction within the experimental uncertainty.« less

Separated kaon electroproduction cross section and the kaon form factor from 6 GeV JLab data

NASA Astrophysics Data System (ADS)

Carmignotto, M.; Ali, S.; Aniol, K.; Arrington, J.; Barrett, B.; Beise, E. J.; Blok, H. P.; Boeglin, W.; Brash, E. J.; Breuer, H.; Chang, C. C.; Christy, M. E.; Dittmann, A.; Ent, R.; Fenker, H.; Gaskell, D.; Gibson, E.; Holt, R. J.; Horn, T.; Huber, G. M.; Jin, S.; Jones, M. K.; Keppel, C. E.; Kim, W.; King, P. M.; Kovaltchouk, V.; Liu, J.; Lolos, G. J.; Mack, D. J.; Margaziotis, D. J.; Markowitz, P.; Matsumura, A.; Meekins, D.; Miyoshi, T.; Mkrtchyan, H.; Niculescu, G.; Niculescu, I.; Okayasu, Y.; Pegg, I. L.; Pentchev, L.; Perdrisat, C.; Potterveld, D.; Punjabi, V.; Reimer, P. E.; Reinhold, J.; Roche, J.; Sarty, A.; Smith, G. R.; Tadevosyan, V.; Tang, L. G.; Trotta, R.; Tvaskis, V.; Vargas, A.; Vidakovic, S.; Volmer, J.; Vulcan, W.; Warren, G.; Wood, S. A.; Xu, C.; Zheng, X.; JLAB FPI-2; E93-018 Collaboration

2018-02-01

The 1H(e ,e'K+ )Λ reaction was studied as a function of the Mandelstam variable -t using data from the E01-004 (FPI-2) and E93-018 experiments that were carried out in Hall C at the 6 GeV Jefferson Laboratory. The cross section was fully separated into longitudinal and transverse components, and two interference terms at four-momentum transfers Q2 of 1.00, 1.36, and 2.07 GeV2. The kaon form factor was extracted from the longitudinal cross section using the Regge model by Vanderhaeghen et al. [Phys. Rev. C 57, 1454 (1998), 10.1103/PhysRevC.57.1454]. The results establish the method, previously used successfully for pion analyses, for extracting the kaon form factor. Data from 12 GeV Jefferson Laboratory experiments are expected to have sufficient precision to distinguish between theoretical predictions, for example, recent perturbative QCD calculations with modern parton distribution amplitudes. The leading-twist behavior for light mesons is predicted to set in for values of Q2 between 5 and 10 GeV2, which makes data in the few-GeV regime particularly interesting. The Q2 dependence at fixed x and -t of the longitudinal cross section that we extracted seems consistent with the QCD factorization prediction within the experimental uncertainty.

Late Stage Azidation of Complex Molecules

PubMed Central

2016-01-01

Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

[The application of gene expression programming in the diagnosis of heart disease].

PubMed

Dai, Wenbin; Zhang, Yuntao; Gao, Xingyu

2009-02-01

GEP (Gene expression programming) is a new genetic algorithm, and it has been proved to be excellent in function finding. In this paper, for the purpose of setting up a diagnostic model, GEP is used to deal with the data of heart disease. Eight variables, Sex, Chest pain, Blood pressure, Angina, Peak, Slope, Colored vessels and Thal, are picked out of thirteen variables to form a classified function. This function is used to predict a forecasting set of 100 samples, and the accuracy is 87%. Other algorithms such as SVM (Support vector machine) are applied to the same data and the forecasting results show that GEP is better than other algorithms.

The Separation and Quantitation of Peptides with and without Oxidation of Methionine and Deamidation of Asparagine Using Hydrophilic Interaction Liquid Chromatography with Mass Spectrometry (HILIC-MS)

NASA Astrophysics Data System (ADS)

Badgett, Majors J.; Boyes, Barry; Orlando, Ron

2017-05-01

Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein's function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts. Furthermore, coefficients describing the extent of the hydrophilicity of these modifications have been derived and were incorporated into a previously made peptide retention prediction model that is capable of predicting the retention times of peptides with and without these modifications.

The Separation and Quantitation of Peptides with and without Oxidation of Methionine and Deamidation of Asparagine Using Hydrophilic Interaction Liquid Chromatography with Mass Spectrometry (HILIC-MS).

PubMed

Badgett, Majors J; Boyes, Barry; Orlando, Ron

2017-05-01

Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein's function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts. Furthermore, coefficients describing the extent of the hydrophilicity of these modifications have been derived and were incorporated into a previously made peptide retention prediction model that is capable of predicting the retention times of peptides with and without these modifications. Graphical Abstract ᅟ.

From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties.

PubMed

Xu, Xin; Goddard, William A

2004-03-02

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

NASA Astrophysics Data System (ADS)

Xu, Xin; Goddard, William A., III

2004-03-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

PubMed Central

Xu, Xin; Goddard, William A.

2004-01-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee–Yang–Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA. PMID:14981235

Functional Performances on Admission Predict In-Hospital Falls, Injurious Falls, and Fractures in Older Patients: A Prospective Study.

PubMed

Hars, Mélany; Audet, Marie-Claude; Herrmann, François; De Chassey, Jean; Rizzoli, René; Reny, Jean-Luc; Gold, Gabriel; Ferrari, Serge; Trombetti, Andrea

2018-05-01

Falls are common among older inpatients and remain a great challenge for hospitals. Despite the relevance of physical impairments to falls, the prognostic value of performance-based functional measures for in-hospital falls and injurious falls remains unknown. This study aimed to determine the predictive ability and accuracy of various functional tests administered at or close to admission in a geriatric hospital to identify in-hospital fallers and injurious fallers. In this prospective study, conducted in a geriatric hospital in Geneva, Switzerland, 807 inpatients (mean age 85.0 years) were subjected to a battery of functional tests administered by physiotherapists within 3 days (interquartile range 1 to 6) of admission, including Short Physical Performance Battery (SPPB), simplified Tinetti, and Timed Up and Go tests. Patients were prospectively followed up for falls and injurious falls until discharge using mandatory standardized incident report forms and electronic patients' records. During a median length of hospital stay of 23 days (interquartile range 14 to 36), 329 falls occurred in 189 (23.4%) patients, including 161 injurious falls of which 24 were serious. In-hospital fallers displayed significantly poorer functional performances at admission on all tests compared with non-fallers (p < 0.001 for all). In multivariate analysis controlling for age, sex, previous falls, and fall as cause of admission, poorer functional performances on all functional tests predicted in-hospital falls and injurious falls (p < 0.001 for all). The SPPB only significantly predicted serious injurious falls (adjusted odds ratio [OR] = 0.76; 95% confidence interval [CI] 0.60-0.96) and fractures (adjusted OR = 0.76; 95% CI 0.59-0.98). In conclusion, poor functional performances, as assessed by SPPB, are independent predictors of in-hospital falls, injurious falls, and fractures in patients admitted to a geriatric hospital. These findings should help to design preventive strategies for in-hospital falls and support the adoption of objective performance-based functional measures into routine hospital practice. © 2018 American Society for Bone and Mineral Research. © 2018 American Society for Bone and Mineral Research.

Inconsistent Responding in a Criminal Forensic Setting: An Evaluation of the VRIN-r and TRIN-r Scales of the MMPI-2-RF.

PubMed

Gu, Wen; Reddy, Hima B; Green, Debbie; Belfi, Brian; Einzig, Shanah

2017-01-01

Criminal forensic evaluations are complicated by the risk that examinees will respond in an unreliable manner. Unreliable responding could occur due to lack of personal investment in the evaluation, severe mental illness, and low cognitive abilities. In this study, 31% of Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF; Ben-Porath & Tellegen, 2008/2011) profiles were invalid due to random or fixed-responding (T score ≥ 80 on the VRIN-r or TRIN-r scales) in a sample of pretrial criminal defendants evaluated in the context of treatment for competency restoration. Hierarchical regression models showed that symptom exaggeration variables, as measured by inconsistently reported psychiatric symptoms, contributed over and above education and intellectual functioning in their prediction of both random responding and fixed responding. Psychopathology variables, as measured by mood disturbance, better predicted fixed responding after controlling for estimates of cognitive abilities, but did not improve the prediction for random responding. These findings suggest that random responding and fixed responding are not only affected by education and intellectual functioning, but also by intentional exaggeration and aspects of psychopathology. Measures of intellectual functioning and effort and response style should be considered for administration in conjunction with self-report personality measures to rule out rival hypotheses of invalid profiles.

Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red

NASA Astrophysics Data System (ADS)

Zuehlsdorff, T. J.; Haynes, P. D.; Payne, M. C.; Hine, N. D. M.

2017-03-01

The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.

Structure and function of transmembrane segment XII in osmosensor and osmoprotectant transporter ProP of Escherichia coli.

PubMed

Liu, Feng; Culham, Doreen E; Vernikovska, Yaroslava I; Keates, Robert A B; Boggs, Joan M; Wood, Janet M

2007-05-15

Escherichia coli transporter ProP acts as both an osmosensor and an osmoregulator. As medium osmolality rises, ProP is activated and mediates H+-coupled uptake of osmolytes like proline. A homology model of ProP with 12-transmembrane (TM) helices and cytoplasmic termini was created, and the protein's topology was substantiated experimentally. Residues 468-497, at the end of the C-terminal domain and linked to TM XII, form an intermolecular, homodimeric alpha-helical coiled-coil that tunes the transporter's response to osmolality. We aim to further define the structure and function of ProP residues Q415-E440, predicted to include TM XII. Each residue was replaced with cysteine (Cys) in a histidine-tagged, Cys-less ProP variant (ProP*). Cys at positions 415-418 and 438-440 were most reactive with Oregon Green Maleimide (OGM), suggesting that residues 419 through 437 are in the membrane. Except for V429-I433, reactivity of those Cys varied with helical periodicity. Cys predicted to face the interior of ProP were more reactive than Cys predicted to face the lipid. The former may be exposed to hydrated polar residues in the protein interior, particularly on the periplasmic side. Intermolecular cross-links formed when ProP* variants with Cys at positions 419, 420, 422, and 439 were treated with DTME. Thus TM XII can participate, along its entire length, in the dimer interface of ProP. Cys substitution E440C rendered ProP* inactive. All other variants retained more than 30% of the proline uptake activity of ProP* at high osmolality. Most variants with Cys substitutions in the periplasmic half of TM XII activated at lower osmolalities than ProP*. Variants with Cys substitutions on one face of the cytoplasmic half of TM XII required a higher osmolality to activate. They included elements of a GXXXG motif that are predicted to form the interface of TM XII with TM VII. These studies define the position of ProP TM XII within the membrane, further support the predicted structure of ProP, reveal the dimerization interface, and show that the structure of TM XII influences the osmolality at which ProP activates.

Fatigue life prediction in bending from axial fatigue information

NASA Technical Reports Server (NTRS)

Manson, S. S.; Muralidharan, U.

1982-01-01

Bending fatigue in the low cyclic life range differs from axial fatigue due to the plastic flow which alters the linear stress-strain relation normally used to determine the nominal stresses. An approach is presented to take into account the plastic flow in calculating nominal bending stress (S sub bending) based on true surface stress. These functions are derived in closed form for rectangular and circular cross sections. The nominal bending stress and the axial fatigue stress are plotted as a function of life (N sub S) and these curves are shown for several materials of engineering interest.

Algorithm for Lossless Compression of Calibrated Hyperspectral Imagery

NASA Technical Reports Server (NTRS)

Kiely, Aaron B.; Klimesh, Matthew A.

2010-01-01

A two-stage predictive method was developed for lossless compression of calibrated hyperspectral imagery. The first prediction stage uses a conventional linear predictor intended to exploit spatial and/or spectral dependencies in the data. The compressor tabulates counts of the past values of the difference between this initial prediction and the actual sample value. To form the ultimate predicted value, in the second stage, these counts are combined with an adaptively updated weight function intended to capture information about data regularities introduced by the calibration process. Finally, prediction residuals are losslessly encoded using adaptive arithmetic coding. Algorithms of this type are commonly tested on a readily available collection of images from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) hyperspectral imager. On the standard calibrated AVIRIS hyperspectral images that are most widely used for compression benchmarking, the new compressor provides more than 0.5 bits/sample improvement over the previous best compression results. The algorithm has been implemented in Mathematica. The compression algorithm was demonstrated as beneficial on 12-bit calibrated AVIRIS images.

Prediction of primary somatosensory neuron activity during active tactile exploration

PubMed Central

Campagner, Dario; Evans, Mathew Hywel; Bale, Michael Ross; Erskine, Andrew; Petersen, Rasmus Strange

2016-01-01

Primary sensory neurons form the interface between world and brain. Their function is well-understood during passive stimulation but, under natural behaving conditions, sense organs are under active, motor control. In an attempt to predict primary neuron firing under natural conditions of sensorimotor integration, we recorded from primary mechanosensory neurons of awake, head-fixed mice as they explored a pole with their whiskers, and simultaneously measured both whisker motion and forces with high-speed videography. Using Generalised Linear Models, we found that primary neuron responses were poorly predicted by whisker angle, but well-predicted by rotational forces acting on the whisker: both during touch and free-air whisker motion. These results are in apparent contrast to previous studies of passive stimulation, but could be reconciled by differences in the kinematics-force relationship between active and passive conditions. Thus, simple statistical models can predict rich neural activity elicited by natural, exploratory behaviour involving active movement of sense organs. DOI: http://dx.doi.org/10.7554/eLife.10696.001 PMID:26880559

Galaxy Evolution in the Radio Band: The Role of Star-forming Galaxies and Active Galactic Nuclei

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

Mancuso, C.; Prandoni, I.; Lapi, A.

We investigate the astrophysics of radio-emitting star-forming galaxies and active galactic nuclei (AGNs) and elucidate their statistical properties in the radio band, including luminosity functions, redshift distributions, and number counts at sub-mJy flux levels, which will be crucially probed by next-generation radio continuum surveys. Specifically, we exploit the model-independent approach by Mancuso et al. to compute the star formation rate functions, the AGN duty cycles, and the conditional probability of a star-forming galaxy to host an AGN with given bolometric luminosity. Coupling these ingredients with the radio emission properties associated with star formation and nuclear activity, we compute relevant statisticsmore » at different radio frequencies and disentangle the relative contribution of star-forming galaxies and AGNs in different radio luminosity, radio flux, and redshift ranges. Finally, we highlight that radio-emitting star-forming galaxies and AGNs are expected to host supermassive black holes accreting with different Eddington ratio distributions and to occupy different loci in the galaxy main-sequence diagrams. These specific predictions are consistent with current data sets but need to be tested with larger statistics via future radio data with multiband coverage on wide areas, as will become routinely achievable with the advent of the Square Kilometre Array and its precursors.« less

On a new functional form for the dispersive flux in porous media

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

Tompson, A.F.B.

A recently developed second-order model for local dispersive transport in porous media has been simplified to yield a new, closed-form relationship for the dispersive flux. In situations characterized by negligible velocity gradients, the flux can generally be represented as a convolution or memory integral over time of previous concentration gradients. The strength of this memory is controlled by an exponential weighting factor related to the magnitudes of the velocity and local molecular diffusive flux. The form of this result is consistent with other models of diffusive and dispersive transport phenomena over various spatial scales. In circumstances where the memory strengthmore » is small, the integral can be simplified and cast in the form of a standard Fickian relationship with apparent time-dependent dispersivity functions that grow to finite, asymptotic values. This specific formulation can be manipulated to yield a one-equation transport balance law in the form of a telegraph equation. Nonphysical effects, such as spurious upstream dispersion and instantaneous propagation of mass to extremely distant points predicted with a Fickian law, are reduced or eliminated. Although the importance of the new result in transport simulations will depend on the spatial and temporal scales of interest, it should provide some insight in the interpretation and design of new experiments.« less

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

PubMed

Ołdziej, S; Czaplewski, C; Liwo, A; Chinchio, M; Nanias, M; Vila, J A; Khalili, M; Arnautova, Y A; Jagielska, A; Makowski, M; Schafroth, H D; Kaźmierkiewicz, R; Ripoll, D R; Pillardy, J; Saunders, J A; Kang, Y K; Gibson, K D; Scheraga, H A

2005-05-24

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.

A review of the revised Functional Capacity Index as a predictor of 12 month outcomes following injury.

PubMed

Palmer, Cameron S; Cameron, Peter A; Gabbe, Belinda J

2017-03-01

The measurement of functional outcomes following severe trauma has been widely recognised as a priority for countries with developed trauma systems. In this respect, the Functional Capacity Index (FCI), a multi-attribute index which has been incorporated into the most recent Abbreviated Injury Scale (AIS) dictionary, is potentially attractive as it offers 12-month functional outcome predictions for patients captured by existing AIS-coded datasets. This review paper outlines the development, construction and validation of the predictive form of the FCI (termed the pFCI), the modifications made which produced the currently available 'revised' pFCI, and the extent to which the revised pFCI has been validated and used. The original pFCI performed poorly in validation studies. The revised pFCI does not address many of the identified limitations of the original version, and despite the ready availability of a truncated version in the AIS dictionary, it has only been used in a handful of studies since its introduction several years ago. Additionally, there is little evidence for its validity. It is suggested that the pFCI should be better validated, whether in the narrow population group of young, healthy individuals for which it was developed, or in the wider population of severely injured patients. Methods for accounting for the presence of multiple injures (of which two have currently been used) should also be evaluated. Many factors other than anatomical injury are known to affect functional outcomes following trauma. However, it is intuitive that any model which attempts to predict the ongoing morbidity burden in a trauma population should consider the effects of the injuries sustained. Although the revised pFCI potentially offers a low-cost assessment of likely functional limitations resulting from anatomical injury, it must be more rigorously evaluated before more comprehensive predictive tools can be developed from it. Copyright © 2017 Elsevier Ltd. All rights reserved.

Competition from below for light and nutrients shifts productivity among tropical species.

PubMed

Ewel, John J; Mazzarino, María Julia

2008-12-02

Chance events such as seed dispersal determine the potential composition of plant communities, but the eventual assemblage is determined in large part by subsequent interactions among species. Postcolonization sorting also affects the ultimate composition of communities assembled by people for restoration, horticulture, or conservation. Thus, knowledge of the mechanisms controlling interspecific interactions in plant communities is important for explaining patterns observed in nature and predicting success or failure of utilitarian combinations. Relationships among species, especially those from studies of biological diversity and ecosystem functioning, are largely based on studies of short-lived, temperate-zone plants. Extrapolation to perennial plants in the humid tropics is risky because functional relationships among large-stature species change with time. Shifts in competitive relationships among 3 life forms--trees, palms, and perennial herbs--occurred during 13 yr in experimental tropical ecosystems. In 2 cases the novel competitive mechanism responsible for the shift was reduction in crown volume, and therefore light-capturing capability, of overtopping deciduous trees by intrusive growth from below a palm. In a third case, complementary resource use developed between 2 evergreen life forms (overstory tree and palm), probably because of differential nutrient acquisition. Species-level traits and adequate time for shifts in interspecific relationships to emerge are crucial for predicting community trajectories.

Multiscale asymmetric orthogonal wavelet kernel for linear programming support vector learning and nonlinear dynamic systems identification.

PubMed

Lu, Zhao; Sun, Jing; Butts, Kenneth

2014-05-01

Support vector regression for approximating nonlinear dynamic systems is more delicate than the approximation of indicator functions in support vector classification, particularly for systems that involve multitudes of time scales in their sampled data. The kernel used for support vector learning determines the class of functions from which a support vector machine can draw its solution, and the choice of kernel significantly influences the performance of a support vector machine. In this paper, to bridge the gap between wavelet multiresolution analysis and kernel learning, the closed-form orthogonal wavelet is exploited to construct new multiscale asymmetric orthogonal wavelet kernels for linear programming support vector learning. The closed-form multiscale orthogonal wavelet kernel provides a systematic framework to implement multiscale kernel learning via dyadic dilations and also enables us to represent complex nonlinear dynamics effectively. To demonstrate the superiority of the proposed multiscale wavelet kernel in identifying complex nonlinear dynamic systems, two case studies are presented that aim at building parallel models on benchmark datasets. The development of parallel models that address the long-term/mid-term prediction issue is more intricate and challenging than the identification of series-parallel models where only one-step ahead prediction is required. Simulation results illustrate the effectiveness of the proposed multiscale kernel learning.

Trade-off between reservoir yield and evaporation losses as a function of lake morphology in semi-arid Brazil.

PubMed

Campos, José N B; Lima, Iran E; Studart, Ticiana M C; Nascimento, Luiz S V

2016-05-31

This study investigates the relationships between yield and evaporation as a function of lake morphology in semi-arid Brazil. First, a new methodology was proposed to classify the morphology of 40 reservoirs in the Ceará State, with storage capacities ranging from approximately 5 to 4500 hm3. Then, Monte Carlo simulations were conducted to study the effect of reservoir morphology (including real and simplified conical forms) on the water storage process at different reliability levels. The reservoirs were categorized as convex (60.0%), slightly convex (27.5%) or linear (12.5%). When the conical approximation was used instead of the real lake form, a trade-off occurred between reservoir yield and evaporation losses, with different trends for the convex, slightly convex and linear reservoirs. Using the conical approximation, the water yield prediction errors reached approximately 5% of the mean annual inflow, which is negligible for large reservoirs. However, for smaller reservoirs, this error became important. Therefore, this paper presents a new procedure for correcting the yield-evaporation relationships that were obtained by assuming a conical approximation rather than the real reservoir morphology. The combination of this correction with the Regulation Triangle Diagram is useful for rapidly and objectively predicting reservoir yield and evaporation losses in semi-arid environments.

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.

PubMed

Rajeev, Lara; Luning, Eric G; Dehal, Paramvir S; Price, Morgan N; Arkin, Adam P; Mukhopadhyay, Aindrila

2011-10-12

Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.

Computational-based structural, functional and phylogenetic analysis of Enterobacter phytases.

PubMed

Pramanik, Krishnendu; Kundu, Shreyasi; Banerjee, Sandipan; Ghosh, Pallab Kumar; Maiti, Tushar Kanti

2018-06-01

Myo-inositol hexakisphosphate phosphohydrolases (i.e., phytases) are known to be a very important enzyme responsible for solubilization of insoluble phosphates. In the present study, Enterobacter phytases have characterized by different phylogenetic, structural and functional parameters using some standard bio-computational tools. Results showed that majority of the Enterobacter phytases are acidic in nature as most of the isoelectric points were under 7.0. The aliphatic indices predicted for the selected proteins were below 40 indicating their thermostable nature. The average molecular weight of the proteins was 48 kDa. The lower values of GRAVY of the said proteins implied that they have better interactions with water. Secondary structure prediction revealed that alpha-helical content was highest among the other forms such as sheets, coils, etc. Moreover, the predicted 3D structure of Enterobacter phytases divulged that the proteins consisted of four monomeric polypeptide chains i.e., it was a tetrameric protein. The predicted tertiary model of E. aerogenes (A0A0M3HCJ2) was deposited in Protein Model Database (Acc. No.: PM0080561) for further utilization after a thorough quality check from QMEAN and SAVES server. Functional analysis supported their classification as histidine acid phosphatases. Besides, multiple sequence alignment revealed that "DG-DP-LG" was the most highly conserved residues within the Enterobacter phytases. Thus, the present study will be useful in selecting suitable phytase-producing microbe exclusively for using in the animal food industry as a food additive.

A domain-centric solution to functional genomics via dcGO Predictor

PubMed Central

2013-01-01

Background Computational/manual annotations of protein functions are one of the first routes to making sense of a newly sequenced genome. Protein domain predictions form an essential part of this annotation process. This is due to the natural modularity of proteins with domains as structural, evolutionary and functional units. Sometimes two, three, or more adjacent domains (called supra-domains) are the operational unit responsible for a function, e.g. via a binding site at the interface. These supra-domains have contributed to functional diversification in higher organisms. Traditionally functional ontologies have been applied to individual proteins, rather than families of related domains and supra-domains. We expect, however, to some extent functional signals can be carried by protein domains and supra-domains, and consequently used in function prediction and functional genomics. Results Here we present a domain-centric Gene Ontology (dcGO) perspective. We generalize a framework for automatically inferring ontological terms associated with domains and supra-domains from full-length sequence annotations. This general framework has been applied specifically to primary protein-level annotations from UniProtKB-GOA, generating GO term associations with SCOP domains and supra-domains. The resulting 'dcGO Predictor', can be used to provide functional annotation to protein sequences. The functional annotation of sequences in the Critical Assessment of Function Annotation (CAFA) has been used as a valuable opportunity to validate our method and to be assessed by the community. The functional annotation of all completely sequenced genomes has demonstrated the potential for domain-centric GO enrichment analysis to yield functional insights into newly sequenced or yet-to-be-annotated genomes. This generalized framework we have presented has also been applied to other domain classifications such as InterPro and Pfam, and other ontologies such as mammalian phenotype and disease ontology. The dcGO and its predictor are available at http://supfam.org/SUPERFAMILY/dcGO including an enrichment analysis tool. Conclusions As functional units, domains offer a unique perspective on function prediction regardless of whether proteins are multi-domain or single-domain. The 'dcGO Predictor' holds great promise for contributing to a domain-centric functional understanding of genomes in the next generation sequencing era. PMID:23514627

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.

PubMed

Hansen, Jens; Meretzky, David; Woldesenbet, Simeneh; Stolovitzky, Gustavo; Iyengar, Ravi

2017-12-18

Whole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific manner to give rise to whole cell function. We sought to determine if capturing such relationships enables us to describe the emergence of whole cell functions from interacting SCPs. We developed the Molecular Biology of the Cell Ontology based on standard cell biology and biochemistry textbooks and review articles. Currently, our ontology contains 5,384 genes, 753 SCPs and 19,180 expertly curated gene-SCP associations. Our algorithm to populate the SCPs with genes enables extension of the ontology on demand and the adaption of the ontology to the continuously growing cell biological knowledge. Since whole cell responses most often arise from the coordinated activity of multiple SCPs, we developed a dynamic enrichment algorithm that flexibly predicts SCP-SCP relationships beyond the current taxonomy. This algorithm enables us to identify interactions between SCPs as a basis for higher order function in a context dependent manner, allowing us to provide a detailed description of how SCPs together can give rise to whole cell functions. We conclude that this ontology can, from omics data sets, enable the development of detailed SCP networks for predictive modeling of emergent whole cell functions.

Hydraulic trade-offs and space filling enable better predictions of vascular structure and function in plants

PubMed Central

Savage, V. M.; Bentley, L. P.; Enquist, B. J.; Sperry, J. S.; Smith, D. D.; Reich, P. B.; von Allmen, E. I.

2010-01-01

Plant vascular networks are central to botanical form, function, and diversity. Here, we develop a theory for plant network scaling that is based on optimal space filling by the vascular system along with trade-offs between hydraulic safety and efficiency. Including these evolutionary drivers leads to predictions for sap flow, the taper of the radii of xylem conduits from trunk to terminal twig, and how the frequency of xylem conduits varies with conduit radius. To test our predictions, we use comprehensive empirical measurements of maple, oak, and pine trees and complementary literature data that we obtained for a wide range of tree species. This robust intra- and interspecific assessment of our botanical network model indicates that the central tendency of observed scaling properties supports our predictions much better than the West, Brown, and Enquist (WBE) or pipe models. Consequently, our model is a more accurate description of vascular architecture than what is given by existing network models and should be used as a baseline to understand and to predict the scaling of individual plants to whole forests. In addition, our model is flexible enough to allow the quantification of species variation around rules for network design. These results suggest that the evolutionary drivers that we propose have been fundamental in determining how physiological processes scale within and across plant species. PMID:21149696

Hydraulic trade-offs and space filling enable better predictions of vascular structure and function in plants.

PubMed

Savage, V M; Bentley, L P; Enquist, B J; Sperry, J S; Smith, D D; Reich, P B; von Allmen, E I

2010-12-28

Plant vascular networks are central to botanical form, function, and diversity. Here, we develop a theory for plant network scaling that is based on optimal space filling by the vascular system along with trade-offs between hydraulic safety and efficiency. Including these evolutionary drivers leads to predictions for sap flow, the taper of the radii of xylem conduits from trunk to terminal twig, and how the frequency of xylem conduits varies with conduit radius. To test our predictions, we use comprehensive empirical measurements of maple, oak, and pine trees and complementary literature data that we obtained for a wide range of tree species. This robust intra- and interspecific assessment of our botanical network model indicates that the central tendency of observed scaling properties supports our predictions much better than the West, Brown, and Enquist (WBE) or pipe models. Consequently, our model is a more accurate description of vascular architecture than what is given by existing network models and should be used as a baseline to understand and to predict the scaling of individual plants to whole forests. In addition, our model is flexible enough to allow the quantification of species variation around rules for network design. These results suggest that the evolutionary drivers that we propose have been fundamental in determining how physiological processes scale within and across plant species.

Phase separation and the formation of cellular bodies

NASA Astrophysics Data System (ADS)

Xu, Bin; Broedersz, Chase P.; Meir, Yigal; Wingreen, Ned S.

Cellular bodies in eukaryotic cells spontaneously assemble to form cellular compartments. Among other functions, these bodies carry out essential biochemical reactions. Cellular bodies form micron-sized structures, which, unlike canonical cell organelles, are not surrounded by membranes. A recent in vitro experiment has shown that phase separation of polymers in solution can explain the formation of cellular bodies. We constructed a lattice-polymer model to capture the essential mechanism leading to this phase separation. We used both analytical and numerical tools to predict the phase diagram of a system of two interacting polymers, including the concentration of each polymer type in the condensed and dilute phase.

Analysis of delamination related fracture processes in composites

NASA Technical Reports Server (NTRS)

Armanios, Erian A.

1992-01-01

An anisotropic thin walled closed section beam theory was developed based on an asymptotical analysis of the shell energy functional. The displacement field is not assumed a priori and emerges as a result of the analysis. In addition to the classical out-of-plane torsional warping, two new contributions are identified namely, axial strain and bending warping. A comparison of the derived governing equations confirms the theory developed by Reissner and Tsai. Also, explicit closed form expressions for the beam stiffness coefficients, the stress and displacement fields are provided. The predictions of the present theory were validated by comparison with finite element simulation, other closed form analyses and test data.

From crater functions to partial differential equations: a new approach to ion bombardment induced nonequilibrium pattern formation.

PubMed

Norris, Scott A; Brenner, Michael P; Aziz, Michael J

2009-06-03

We develop a methodology for deriving continuum partial differential equations for the evolution of large-scale surface morphology directly from molecular dynamics simulations of the craters formed from individual ion impacts. Our formalism relies on the separation between the length scale of ion impact and the characteristic scale of pattern formation, and expresses the surface evolution in terms of the moments of the crater function. We demonstrate that the formalism reproduces the classical Bradley-Harper results, as well as ballistic atomic drift, under the appropriate simplifying assumptions. Given an actual set of converged molecular dynamics moments and their derivatives with respect to the incidence angle, our approach can be applied directly to predict the presence and absence of surface morphological instabilities. This analysis represents the first work systematically connecting molecular dynamics simulations of ion bombardment to partial differential equations that govern topographic pattern-forming instabilities.

Spiral Form of the Human Cochlea Results from Spatial Constraints.

PubMed

Pietsch, M; Aguirre Dávila, L; Erfurt, P; Avci, E; Lenarz, T; Kral, A

2017-08-08

The human inner ear has an intricate spiral shape often compared to shells of mollusks, particularly to the nautilus shell. It has inspired many functional hearing theories. The reasons for this complex geometry remain unresolved. We digitized 138 human cochleae at microscopic resolution and observed an astonishing interindividual variability in the shape. A 3D analytical cochlear model was developed that fits the analyzed data with high precision. The cochlear geometry neither matched a proposed function, namely sound focusing similar to a whispering gallery, nor did it have the form of a nautilus. Instead, the innate cochlear blueprint and its actual ontogenetic variants were determined by spatial constraints and resulted from an efficient packing of the cochlear duct within the petrous bone. The analytical model predicts well the individual 3D cochlear geometry from few clinical measures and represents a clinical tool for an individualized approach to neurosensory restoration with cochlear implants.

Corneal changes induced by laser ablation: study of the visual-quality evolution by a customized eye model

NASA Astrophysics Data System (ADS)

Ortiz, D.; Anera, R. G.; Saiz, J. M.; Jiménez, J. R.; Moreno, F.; Jiménez Del Barco, L.; González, F.

2006-11-01

This study focuses on the changes induced in both the asphericity and homogeneity of the cornea for a group of myopic eyes undergoing LASIK surgery. Eyes were characterized by a Kooijman-based customized eye model in which changes were introduced in the form of Gaussian-distributed refractive-index variations of given correlation length for the inhomogeneities and in the form of an expression, based on the modified Munnerlyn's paraxial formula, for the post-LASIK asphericity. Visual quality was evaluated in terms of the Modulation Transfer Function and the Point-Spread Function. The results show that, on average, the evolution of visual acuity is consistent with the change in corneal asphericity, while the evolution of contrast sensitivity requires a loss in corneal homogeneity in order to be explained. By including both effects in the model, the overall model performance in predicting visual quality is improved.

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles.

PubMed

Dedrick, Rebekah M; Marinelli, Laura J; Newton, Gerald L; Pogliano, Kit; Pogliano, Joseph; Hatfull, Graham F

2013-05-01

Bacteriophages represent a majority of all life forms, and the vast, dynamic population with early origins is reflected in their enormous genetic diversity. A large number of bacteriophage genomes have been sequenced. They are replete with novel genes without known relatives. We know little about their functions, which genes are required for lytic growth, and how they are expressed. Furthermore, the diversity is such that even genes with required functions - such as virion proteins and repressors - cannot always be recognized. Here we describe a functional genomic dissection of mycobacteriophage Giles, in which the virion proteins are identified, genes required for lytic growth are determined, the repressor is identified, and the transcription patterns determined. We find that although all of the predicted phage genes are expressed either in lysogeny or in lytic growth, 45% of the predicted genes are non-essential for lytic growth. We also describe genes required for DNA replication, show that recombination is required for lytic growth, and that Giles encodes a novel repressor. RNAseq analysis reveals abundant expression of a small non-coding RNA in a lysogen and in late lytic growth, although it is non-essential for lytic growth and does not alter lysogeny. © 2013 Blackwell Publishing Ltd.

Systematic study on the TD-DFT calculated electronic circular dichroism spectra of chiral aromatic nitro compounds: A comparison of B3LYP and CAM-B3LYP.

PubMed

Komjáti, Balázs; Urai, Ákos; Hosztafi, Sándor; Kökösi, József; Kováts, Benjámin; Nagy, József; Horváth, Péter

2016-02-15

B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

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

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less

Point-to-point migration functions and gravity model renormalization: approaches to aggregation in spatial interaction modeling.

PubMed

Slater, P B

1985-08-01

Two distinct approaches to assessing the effect of geographic scale on spatial interactions are modeled. In the first, the question of whether a distance deterrence function, which explains interactions for one system of zones, can also succeed on a more aggregate scale, is examined. Only the two-parameter function for which it is found that distances between macrozones are weighted averaged of distances between component zones is satisfactory in this regard. Estimation of continuous (point-to-point) functions--in the form of quadrivariate cubic polynomials--for US interstate migration streams, is then undertaken. Upon numerical integration, these higher order surfaces yield predictions of interzonal and intrazonal movements at any scale of interest. Test of spatial stationarity, isotropy, and symmetry of interstate migration are conducted in this framework.

Neural activity during affect labeling predicts expressive writing effects on well-being: GLM and SVM approaches

PubMed Central

Memarian, Negar; Torre, Jared B.; Haltom, Kate E.; Stanton, Annette L.

2017-01-01

Abstract Affect labeling (putting feelings into words) is a form of incidental emotion regulation that could underpin some benefits of expressive writing (i.e. writing about negative experiences). Here, we show that neural responses during affect labeling predicted changes in psychological and physical well-being outcome measures 3 months later. Furthermore, neural activity of specific frontal regions and amygdala predicted those outcomes as a function of expressive writing. Using supervised learning (support vector machines regression), improvements in four measures of psychological and physical health (physical symptoms, depression, anxiety and life satisfaction) after an expressive writing intervention were predicted with an average of 0.85% prediction error [root mean square error (RMSE) %]. The predictions were significantly more accurate with machine learning than with the conventional generalized linear model method (average RMSE: 1.3%). Consistent with affect labeling research, right ventrolateral prefrontal cortex (RVLPFC) and amygdalae were top predictors of improvement in the four outcomes. Moreover, RVLPFC and left amygdala predicted benefits due to expressive writing in satisfaction with life and depression outcome measures, respectively. This study demonstrates the substantial merit of supervised machine learning for real-world outcome prediction in social and affective neuroscience. PMID:28992270

Workplace harassment/abuse and alcohol-related outcomes: the mediating role of psychological distress.

PubMed

Richman, Judith A; Shinsako, Stephanie A; Rospenda, Kathleen M; Flaherty, Joseph A; Freels, Sally

2002-07-01

This article embraces a tension-reduction or self-medication perspective on alcohol use and misuse. It empirically addresses the role that psychological distress plays in mediating the relationships between harassing and abusive interpersonal experiences in the workplace and altered alcohol use and misuse. A mail survey was completed by 2,038 university employees (1,098 women and 940 men) at two points in time. Specific hypotheses were tested involving (1) the extent to which the onset and chronicity of harassment and abuse predicted varied Wave-2 drinking outcomes, (2) the extent to which the onset and chronicity of harassment and abuse predicted three forms of Wave-2 psychological distress, (3) the associations between Wave-2 psychological distress and drinking outcomes and (4) the extent to which the associations between harassment/abuse and drinking outcomes disappeared when the salient forms of symptomatic distress functioned as control variables. The data showed that harassment and abuse predicted drinking outcomes and psychological distress, and that the associations between harassment/abuse and drinking outcomes were partially mediated by distress. The findings lend support to the tension-reduction perspective and have important implications for intervention and prevention involving workplace harassment and abuse.

Electrophysiological correlates of forming memories for faces, names, and face-name associations.

PubMed

Guo, Chunyan; Voss, Joel L; Paller, Ken A

2005-02-01

The ability to put a name to a face is a vital aspect of human interaction, but many people find this extremely difficult, especially after being introduced to someone for the first time. Creating enduring associations between arbitrary stimuli in this manner is also a prime example of what patients with amnesia find most difficult. To help develop a better understanding of this type of memory, we sought to obtain measures of the neural events responsible for successfully forming a new face-name association. We used event-related potentials (ERPs) extracted from high-density scalp EEG recordings in order to compare (1) memory for faces, (2) memory for names, and (3) memory for face-name associations. Each visual face appeared simultaneously with a unique spoken name. Signals observed 200-800 ms after the onset of face-name pairs predicted subsequent memory for faces, names, or face-name associations. Difference potentials observed as a function of subsequent memory performance were not identical for these three memory tests, nor were potentials predicting associative memory equivalent to the sum of potentials predicting item memory, suggesting that different neural events at the time of encoding are relevant for these distinct aspects of remembering people.

A general one-dimension nonlinear magneto-elastic coupled constitutive model for magnetostrictive materials

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

Zhang, Da-Guang; Li, Meng-Han; Zhou, Hao-Miao, E-mail: zhouhm@cjlu.edu.cn

2015-10-15

For magnetostrictive rods under combined axial pre-stress and magnetic field, a general one-dimension nonlinear magneto-elastic coupled constitutive model was built in this paper. First, the elastic Gibbs free energy was expanded into polynomial, and the relationship between stress and strain and the relationship between magnetization and magnetic field with the polynomial form were obtained with the help of thermodynamic relations. Then according to microscopic magneto-elastic coupling mechanism and some physical facts of magnetostrictive materials, a nonlinear magneto-elastic constitutive with concise form was obtained when the relations of nonlinear strain and magnetization in the polynomial constitutive were instead with transcendental functions.more » The comparisons between the prediction and the experimental data of different magnetostrictive materials, such as Terfenol-D, Metglas and Ni showed that the predicted magnetostrictive strain and magnetization curves were consistent with experimental results under different pre-stresses whether in the region of low and moderate field or high field. Moreover, the model can fully reflect the nonlinear magneto-mechanical coupling characteristics between magnetic, magnetostriction and elasticity, and it can effectively predict the changes of material parameters with pre-stress and bias field, which is useful in practical applications.« less

Cosmic reionization on computers: The faint end of the galaxy luminosity function

DOE PAGES

Gnedin, Nickolay Y.

2016-07-01

Using numerical cosmological simulations completed under the “Cosmic Reionization On Computers” project, I explore theoretical predictions for the faint end of the galaxy UV luminosity functions atmore » $$z\\gtrsim 6$$. A commonly used Schechter function approximation with the magnitude cut at $${M}_{{\\rm{cut}}}\\sim -13$$ provides a reasonable fit to the actual luminosity function of simulated galaxies. When the Schechter functional form is forced on the luminosity functions from the simulations, the magnitude cut $${M}_{{\\rm{cut}}}$$ is found to vary between -12 and -14 with a mild redshift dependence. Here, an analytical model of reionization from Madau et al., as used by Robertson et al., provides a good description of the simulated results, which can be improved even further by adding two physically motivated modifications to the original Madau et al. equation.« less

New Mathematical Functions for Vacuum System Analysis

NASA Technical Reports Server (NTRS)

Woronowicz, Michael S.

2017-01-01

A new bivariate function has been found that provides solutions of integrals having the form u (sup minus eta) e (sup u) du which arise when developing predictions for the behavior of pressure within a rigid volume under high vacuum conditions in the presence of venting as well as sources characterized by power law transient decay over the range [0,1] for eta and for u greater than or equal to 0. A few properties of the new function are explored in this work. For instance the eta equals 1/2 case reproduces the Dawson function. In addition, a slight variation of the solution technique reproduces the exponential integral for eta equals 1. The technique used to generate these functions leads to an approach for solving a more general class of nonlinear ordinary differential equations, with the potential for identifying other new functions that solve other integrals.

Cosmic reionization on computers: The faint end of the galaxy luminosity function

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

Gnedin, Nickolay Y.

Using numerical cosmological simulations completed under the “Cosmic Reionization On Computers” project, I explore theoretical predictions for the faint end of the galaxy UV luminosity functions atmore » $$z\\gtrsim 6$$. A commonly used Schechter function approximation with the magnitude cut at $${M}_{{\\rm{cut}}}\\sim -13$$ provides a reasonable fit to the actual luminosity function of simulated galaxies. When the Schechter functional form is forced on the luminosity functions from the simulations, the magnitude cut $${M}_{{\\rm{cut}}}$$ is found to vary between -12 and -14 with a mild redshift dependence. Here, an analytical model of reionization from Madau et al., as used by Robertson et al., provides a good description of the simulated results, which can be improved even further by adding two physically motivated modifications to the original Madau et al. equation.« less

Predictions for boson-jet observables and fragmentation function ratios from a hybrid strong/weak coupling model for jet quenching

DOE PAGES

Casalderrey-Solana, Jorge; Gulhan, Doga Can; Milhano, José Guilherme; ...

2016-03-09

We have previously introduced a hybrid strong/weak coupling model for jet quenching in heavy ion collisions in which we describe the production and fragmentation of jets at weak coupling, using Pythia, and describe the rate at which each parton in the jet shower loses energy as it propagates through the strongly coupled plasma, dE/dx, using an expression computed holographically at strong coupling. The model has a single free parameter that we fit to a single experimental measurement. We then confront our model with experimental data on many other jet observables, focusing in this paper on boson-jet observables, finding that itmore » provides a good description of present jet data. Next, we provide the predictions of our hybrid model for many measurements to come, including those for inclusive jet, dijet, photon-jet and Z-jet observables in heavy ion collisions with energy √s = 5 : 02 ATeV coming soon at the LHC. As the statistical uncertainties on near-future measurements of photon-jet observables are expected to be much smaller than those in present data, with about an order of magnitude more photon-jet events expected, predictions for these observables are particularly important. We find that most of our pre- and post-dictions do not depend sensitively on the form we choose for the rate of energy loss dE/dx of the partons in the shower. This gives our predictions considerable robustness. To better discriminate between possible forms for the rate of energy loss, though, we must turn to intrajet observables. Here, we focus on ratios of fragmentation functions. Finally, we close with a suggestion for a particular ratio, between the fragmentation functions of inclusive and associated jets with the same kinematics in the same collisions, which is particularly sensitive to the x- and E-dependence of dE/dx, and hence may be used to learn which mechanism of parton energy loss best describes the quenching of jets.« less

Prediction of Soil Deformation in Tunnelling Using Artificial Neural Networks.

PubMed

Lai, Jinxing; Qiu, Junling; Feng, Zhihua; Chen, Jianxun; Fan, Haobo

2016-01-01

In the past few decades, as a new tool for analysis of the tough geotechnical problems, artificial neural networks (ANNs) have been successfully applied to address a number of engineering problems, including deformation due to tunnelling in various types of rock mass. Unlike the classical regression methods in which a certain form for the approximation function must be presumed, ANNs do not require the complex constitutive models. Additionally, it is traced that the ANN prediction system is one of the most effective ways to predict the rock mass deformation. Furthermore, it could be envisaged that ANNs would be more feasible for the dynamic prediction of displacements in tunnelling in the future, especially if ANN models are combined with other research methods. In this paper, we summarized the state-of-the-art and future research challenges of ANNs on the tunnel deformation prediction. And the application cases as well as the improvement of ANN models were also presented. The presented ANN models can serve as a benchmark for effective prediction of the tunnel deformation with characters of nonlinearity, high parallelism, fault tolerance, learning, and generalization capability.

Prediction of Soil Deformation in Tunnelling Using Artificial Neural Networks

PubMed Central

Lai, Jinxing

2016-01-01

In the past few decades, as a new tool for analysis of the tough geotechnical problems, artificial neural networks (ANNs) have been successfully applied to address a number of engineering problems, including deformation due to tunnelling in various types of rock mass. Unlike the classical regression methods in which a certain form for the approximation function must be presumed, ANNs do not require the complex constitutive models. Additionally, it is traced that the ANN prediction system is one of the most effective ways to predict the rock mass deformation. Furthermore, it could be envisaged that ANNs would be more feasible for the dynamic prediction of displacements in tunnelling in the future, especially if ANN models are combined with other research methods. In this paper, we summarized the state-of-the-art and future research challenges of ANNs on the tunnel deformation prediction. And the application cases as well as the improvement of ANN models were also presented. The presented ANN models can serve as a benchmark for effective prediction of the tunnel deformation with characters of nonlinearity, high parallelism, fault tolerance, learning, and generalization capability. PMID:26819587

Prediction of metabolites of epoxidation reaction in MetaTox.

PubMed

Rudik, A V; Dmitriev, A V; Bezhentsev, V M; Lagunin, A A; Filimonov, D A; Poroikov, V V

2017-10-01

Biotransformation is a process of the chemical modifications which may lead to the reactive metabolites, in particular the epoxides. Epoxide reactive metabolites may cause the toxic effects. The prediction of such metabolites is important for drug development and ecotoxicology studies. Epoxides are formed by some oxidation reactions, usually catalysed by cytochromes P450, and represent a large class of three-membered cyclic ethers. Identification of molecules, which may be epoxidized, and indication of the specific location of epoxide functional group (which is called SOE - site of epoxidation) are important for prediction of epoxide metabolites. Datasets from 355 molecules and 615 reactions were created for training and validation. The prediction of SOE is based on a combination of LMNA (Labelled Multilevel Neighbourhood of Atom) descriptors and Bayesian-like algorithm implemented in PASS software and MetaTox web-service. The average invariant accuracy of prediction (AUC) calculated in leave-one-out and 20-fold cross-validation procedures is 0.9. Prediction of epoxide formation based on the created SAR model is included as the component of MetaTox web-service ( http://www.way2drug.com/mg ).

Linearized blade row compression component model. Stability and frequency response analysis of a J85-3 compressor

NASA Technical Reports Server (NTRS)

Tesch, W. A.; Moszee, R. H.; Steenken, W. G.

1976-01-01

NASA developed stability and frequency response analysis techniques were applied to a dynamic blade row compression component stability model to provide a more economic approach to surge line and frequency response determination than that provided by time-dependent methods. This blade row model was linearized and the Jacobian matrix was formed. The clean-inlet-flow stability characteristics of the compressors of two J85-13 engines were predicted by applying the alternate Routh-Hurwitz stability criterion to the Jacobian matrix. The predicted surge line agreed with the clean-inlet-flow surge line predicted by the time-dependent method to a high degree except for one engine at 94% corrected speed. No satisfactory explanation of this discrepancy was found. The frequency response of the linearized system was determined by evaluating its Laplace transfer function. The results of the linearized-frequency-response analysis agree with the time-dependent results when the time-dependent inlet total-pressure and exit-flow function amplitude boundary conditions are less than 1 percent and 3 percent, respectively. The stability analysis technique was extended to a two-sector parallel compressor model with and without interstage crossflow and predictions were carried out for total-pressure distortion extents of 180 deg, 90 deg, 60 deg, and 30 deg.

Equilibrium Propagation: Bridging the Gap between Energy-Based Models and Backpropagation

PubMed Central

Scellier, Benjamin; Bengio, Yoshua

2017-01-01

We introduce Equilibrium Propagation, a learning framework for energy-based models. It involves only one kind of neural computation, performed in both the first phase (when the prediction is made) and the second phase of training (after the target or prediction error is revealed). Although this algorithm computes the gradient of an objective function just like Backpropagation, it does not need a special computation or circuit for the second phase, where errors are implicitly propagated. Equilibrium Propagation shares similarities with Contrastive Hebbian Learning and Contrastive Divergence while solving the theoretical issues of both algorithms: our algorithm computes the gradient of a well-defined objective function. Because the objective function is defined in terms of local perturbations, the second phase of Equilibrium Propagation corresponds to only nudging the prediction (fixed point or stationary distribution) toward a configuration that reduces prediction error. In the case of a recurrent multi-layer supervised network, the output units are slightly nudged toward their target in the second phase, and the perturbation introduced at the output layer propagates backward in the hidden layers. We show that the signal “back-propagated” during this second phase corresponds to the propagation of error derivatives and encodes the gradient of the objective function, when the synaptic update corresponds to a standard form of spike-timing dependent plasticity. This work makes it more plausible that a mechanism similar to Backpropagation could be implemented by brains, since leaky integrator neural computation performs both inference and error back-propagation in our model. The only local difference between the two phases is whether synaptic changes are allowed or not. We also show experimentally that multi-layer recurrently connected networks with 1, 2, and 3 hidden layers can be trained by Equilibrium Propagation on the permutation-invariant MNIST task. PMID:28522969

A generalized functional response for predators that switch between multiple prey species.

PubMed

van Leeuwen, E; Brännström, Å; Jansen, V A A; Dieckmann, U; Rossberg, A G

2013-07-07

We develop a theory for the food intake of a predator that can switch between multiple prey species. The theory addresses empirical observations of prey switching and is based on the behavioural assumption that a predator tends to continue feeding on prey that are similar to the prey it has consumed last, in terms of, e.g., their morphology, defences, location, habitat choice, or behaviour. From a predator's dietary history and the assumed similarity relationship among prey species, we derive a general closed-form multi-species functional response for describing predators switching between multiple prey species. Our theory includes the Holling type II functional response as a special case and makes consistent predictions when populations of equivalent prey are aggregated or split. An analysis of the derived functional response enables us to highlight the following five main findings. (1) Prey switching leads to an approximate power-law relationship between ratios of prey abundance and prey intake, consistent with experimental data. (2) In agreement with empirical observations, the theory predicts an upper limit of 2 for the exponent of such power laws. (3) Our theory predicts deviations from power-law switching at very low and very high prey-abundance ratios. (4) The theory can predict the diet composition of a predator feeding on multiple prey species from diet observations for predators feeding only on pairs of prey species. (5) Predators foraging on more prey species will show less pronounced prey switching than predators foraging on fewer prey species, thus providing a natural explanation for the known difficulties of observing prey switching in the field. Copyright © 2013 Elsevier Ltd. All rights reserved.

Body composition and lung function in cystic fibrosis and their association with adiposity and normal-weight obesity.

PubMed

Alvarez, Jessica A; Ziegler, Thomas R; Millson, Erin C; Stecenko, Arlene A

2016-04-01

This study aimed to evaluate the relationship between lung function and body composition in cystic fibrosis (CF) and examine the presence of normal-weight obesity (NWO), a high body fat percentage with a normal body mass index (BMI), in this population. In a pilot, cross-sectional study, 32 subjects with CF and a reference group of 20 adults without CF underwent body composition analysis with air displacement plethysmography. NWO was defined as a BMI <25 kg/m(2) and body fat >30% (for women) or >23% (for men). Lung function in subjects with CF was determined by the percentage of predicted forced expiratory volume in 1 s (FEV1% predicted). Despite lower BMI and fat-free mass index (P < 0.01), fat mass index and percent body fat did not differ between subjects with CF and the reference group. Among subjects with CF, FEV1% predicted was positively associated with fat-free mass index (β = 6.31 ± 2.93, P = 0.04) and inversely associated with fat mass index (β = -6.44 ± 2.93, P = 0.04), after adjusting for age, sex, and BMI. Ten subjects with CF (31%) had NWO, which corresponded with lower fat-free mass index and FEV1% predicted compared with overweight subjects (P = 0.006 and 0.004, respectively). Excess adiposity, particularly in the form of NWO, was inversely associated with lung function in CF. Larger prospective studies should be undertaken to confirm these findings and determine the long-term metabolic and clinical consequences of excess adiposity in CF. As the lifespan of individuals with CF increases, nutrition screening protocols, which primarily rely on BMI, may require reassessment. Copyright © 2016 Elsevier Inc. All rights reserved.

Hot Spots in a Network of Functional Sites

PubMed Central

Ozbek, Pemra; Soner, Seren; Haliloglu, Turkan

2013-01-01

It is of significant interest to understand how proteins interact, which holds the key phenomenon in biological functions. Using dynamic fluctuations in high frequency modes, we show that the Gaussian Network Model (GNM) predicts hot spot residues with success rates ranging between S 8–58%, C 84–95%, P 5–19% and A 81–92% on unbound structures and S 8–51%, C 97–99%, P 14–50%, A 94–97% on complex structures for sensitivity, specificity, precision and accuracy, respectively. High specificity and accuracy rates with a single property on unbound protein structures suggest that hot spots are predefined in the dynamics of unbound structures and forming the binding core of interfaces, whereas the prediction of other functional residues with similar dynamic behavior explains the lower precision values. The latter is demonstrated with the case studies; ubiquitin, hen egg-white lysozyme and M2 proton channel. The dynamic fluctuations suggest a pseudo network of residues with high frequency fluctuations, which could be plausible for the mechanism of biological interactions and allosteric regulation. PMID:24023934

Analysis of the transfer function for layered piezoelectric ultrasonic sensors

NASA Astrophysics Data System (ADS)

Gutiérrrez-Reyes, E.; García-Segundo, C.; García-Valenzuela, A.; Reyes-Ramírez, B.; Gutiérrez-Juárez, G.; Guadarrama-Santana, A.

2017-06-01

We model theoretically the voltage response to an acoustic pulse of a multilayer system forming a low noise capacitive sensor including a Polyvinylidene Fluoride piezoelectric film. First we model a generic piezoelectric detector consisting of a piezoelectric film between two metallic electrodes that are the responsible to convert the acoustic signal into a voltage signal. Then we calculate the pressure-to-voltage transfer function for a N-layer piezo-electric capacitor detector, allowing to study the effects of the electrode and protective layers thickness in typical layered piezoelectric sensors. The derived transfer function, when multiplied by the Fourier transform of the incident acoustic pulse, gives the voltage electric response in the frequency domain. An important concern regarding the transfer function is that it may have zeros at specific frequencies, and thus inverting the voltage Fourier transform of the pulse to recover the pressure signal in the time domain is not always, in principle, possible. Our formulas can be used to predict the existence and locations of such zeroes. We illustrate the use of the transfer function by predicting the electric signal generated at a multilayer piezoelectric sensor to an ultrasonic pulse generated photoacoustically by a laser pulse at a three media system with impedance mismatch. This theoretical calculations are compared with our own experimental measurements.

Surface energetics and protein-protein interactions: analysis and mechanistic implications

PubMed Central

Peri, Claudio; Morra, Giulia; Colombo, Giorgio

2016-01-01

Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks located on the surface of proteins, isolated and in complex with their respective partners. Interestingly, the analysis of individual proteins identifies patches of surface residues that, when mapped on the structure of their respective complexes, reveal regions of residue-pair couplings that extend across the binding interfaces, forming continuous motifs. An enhanced effect is visible across the proteins of the dataset forming larger quaternary assemblies. The method indicates the presence of energetic signatures in the isolated proteins that are retained in the bound form, which we hypothesize to determine binding orientation upon complex formation. We propose our method, BLUEPRINT, as a complement to different approaches ranging from the ab-initio characterization of PPIs, to protein-protein docking algorithms, for the physico-chemical and functional investigation of protein-protein interactions. PMID:27050828

Current Understanding of Usher Syndrome Type II

PubMed Central

Yang, Jun; Wang, Le; Song, Hongman; Sokolov, Maxim

2012-01-01

Usher syndrome is the most common deafness-blindness caused by genetic mutations. To date, three genes have been identified underlying the most prevalent form of Usher syndrome, the type II form (USH2). The proteins encoded by these genes are demonstrated to form a complex in vivo. This complex is localized mainly at the periciliary membrane complex in photoreceptors and the ankle-link of the stereocilia in hair cells. Many proteins have been found to interact with USH2 proteins in vitro, suggesting that they are potential additional components of this USH2 complex and that the genes encoding these proteins may be the candidate USH2 genes. However, further investigations are critical to establish their existence in the USH2 complex in vivo. Based on the predicted functional domains in USH2 proteins, their cellular localizations in photoreceptors and hair cells, the observed phenotypes in USH2 mutant mice, and the known knowledge about diseases similar to USH2, putative biological functions of the USH2 complex have been proposed. Finally, therapeutic approaches for this group of diseases are now being actively explored. PMID:22201796

Towards force spectroscopy of single tip-link bonds

NASA Astrophysics Data System (ADS)

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.; Corey, David P.

2015-12-01

Inner-ear mechanotransduction relies on tip links, fine protein filaments made of cadherin-23 and protocadherin-15 that convey tension to mechanosensitive channels at the tips of hair-cell stereocilia. The tip-link cadherins are thought to form a heterotetrameric complex, with two cadherin-23 molecules forming the upper part of the filament and two protocadherin-15 molecules forming the lower end. The interaction between cadherin-23 and protocadherin-15 is mediated by their N-terminal tips. Missense mutations that modify the interaction interface impair binding and lead to deafness. Molecular dynamics simulations predict that the tip-link bond is mechanically strong enough to withstand forces in hair cells, but its experimentally determined strength is unknown. We have developed molecular tools to facilitate single-molecule force spectroscopy on the tip link bond. Self-assembling DNA nanoswitches are functionalized with the interacting tips of cadherin-23 and protocadherin-15 using the enzyme sortase under conditions that preserve protein function. These tip link nanoswitches are designed to provide a signature force-extension profile. This molecular signature should allow us to identify single-molecule rupture events in pulling experiments.

Theory of structure formation in snowfields motivated by penitentes, suncups, and dirt cones.

PubMed

Betterton, M D

2001-05-01

Penitentes and suncups are structures formed as snow melts, typically high in the mountains. When the snow is dirty, dirt cones and other structures can form instead. Building on previous field observations and experiments, this paper presents a theory of ablation morphologies, and the role of surface dirt in determining the structures formed. The glaciological literature indicates that sunlight, heating from air, and dirt all play a role in the formation of structure on an ablating snow surface. The present paper formulates a minimal model for the formation of ablation morphologies as a function of measurable parameters and considers the linear stability of this model. The dependence of ablation morphologies on weather conditions and initial dirt thickness is studied, focusing on the initial growth of perturbations away from a flat surface. We derive a single-parameter expression for the melting rate as a function of dirt thickness, which agrees well with a set of measurements by Driedger. An interesting result is the prediction of a dirt-induced traveling instability for a range of parameters.

A theoretical study on pure bending of hexagonal close-packed metal sheet

NASA Astrophysics Data System (ADS)

Mehrabi, Hamed; Yang, Chunhui

2018-05-01

Hexagonal close-packed (HCP) metals have quite different mechanical behaviours in comparison to conventional cubic metals such as steels and aluminum alloys [1, 2]. They exhibit a significant tension-compression asymmetry in initial yielding and subsequent plastic hardening. The reason for this unique behaviour can be attributed to their limited symmetric crystal structure, which leads to twining deformation [3-5]. This unique behaviour strongly influences sheet metal forming of such metals, especially for roll forming, in which the bending is dominant. Hence, it is crucial to represent constitutive relations of HCP metals for accurate estimation of bending moment-curvature behaviours. In this paper, an analytical model for asymmetric elastoplastic pure bending with an application of Cazacu-Barlat asymmetric yield function [6] is presented. This yield function considers the asymmetrical tension-compression behaviour of HCP metals by using second and third invariants of the stress deviator tensor and a specified constant, which can be expressed in terms of uniaxial yield stresses in tension and compression. As a case study, the analytical model is applied to predict the moment-curvature behaviours of AZ31B magnesium alloy sheets under uniaxial loading condition. Furthermore, the analytical model is implemented as a user-defined material through the UMAT interface in Abaqus [7, 8] for conducting pure bending simulations. The results show that the analytical model can reasonably capture the asymmetric tension-compression behaviour of the magnesium alloy. The predicted moment-curvature behaviour has good agreement with the experimental results. Furthermore, numerical results show a better accuracy by the application of the Cazacu-Barlat yield function than those using the von-Mises yield function, which are more conservative than analytical results.

Global Organization of a Positive-strand RNA Virus Genome

PubMed Central

Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew

2013-01-01

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context. PMID:23717202

Disease Prediction based on Functional Connectomes using a Scalable and Spatially-Informed Support Vector Machine

PubMed Central

Watanabe, Takanori; Kessler, Daniel; Scott, Clayton; Angstadt, Michael; Sripada, Chandra

2014-01-01

Substantial evidence indicates that major psychiatric disorders are associated with distributed neural dysconnectivity, leading to strong interest in using neuroimaging methods to accurately predict disorder status. In this work, we are specifically interested in a multivariate approach that uses features derived from whole-brain resting state functional connectomes. However, functional connectomes reside in a high dimensional space, which complicates model interpretation and introduces numerous statistical and computational challenges. Traditional feature selection techniques are used to reduce data dimensionality, but are blind to the spatial structure of the connectomes. We propose a regularization framework where the 6-D structure of the functional connectome (defined by pairs of points in 3-D space) is explicitly taken into account via the fused Lasso or the GraphNet regularizer. Our method only restricts the loss function to be convex and margin-based, allowing non-differentiable loss functions such as the hinge-loss to be used. Using the fused Lasso or GraphNet regularizer with the hinge-loss leads to a structured sparse support vector machine (SVM) with embedded feature selection. We introduce a novel efficient optimization algorithm based on the augmented Lagrangian and the classical alternating direction method, which can solve both fused Lasso and GraphNet regularized SVM with very little modification. We also demonstrate that the inner subproblems of the algorithm can be solved efficiently in analytic form by coupling the variable splitting strategy with a data augmentation scheme. Experiments on simulated data and resting state scans from a large schizophrenia dataset show that our proposed approach can identify predictive regions that are spatially contiguous in the 6-D “connectome space,” offering an additional layer of interpretability that could provide new insights about various disease processes. PMID:24704268

The composition of engineered cartilage at the time of implantation determines the likelihood of regenerating tissue with a normal collagen architecture.

PubMed

Nagel, Thomas; Kelly, Daniel J

2013-04-01

The biomechanical functionality of articular cartilage is derived from both its biochemical composition and the architecture of the collagen network. Failure to replicate this normal Benninghoff architecture in regenerating articular cartilage may in turn predispose the tissue to failure. In this article, the influence of the maturity (or functionality) of a tissue-engineered construct at the time of implantation into a tibial chondral defect on the likelihood of recapitulating a normal Benninghoff architecture was investigated using a computational model featuring a collagen remodeling algorithm. Such a normal tissue architecture was predicted to form in the intact tibial plateau due to the interplay between the depth-dependent extracellular matrix properties, foremost swelling pressures, and external mechanical loading. In the presence of even small empty defects in the articular surface, the collagen architecture in the surrounding cartilage was predicted to deviate significantly from the native state, indicating a possible predisposition for osteoarthritic changes. These negative alterations were alleviated by the implantation of tissue-engineered cartilage, where a mature implant was predicted to result in the formation of a more native-like collagen architecture than immature implants. The results of this study highlight the importance of cartilage graft functionality to maintain and/or re-establish joint function and suggest that engineering a tissue with a native depth-dependent composition may facilitate the establishment of a normal Benninghoff collagen architecture after implantation into load-bearing defects.

Mapping structural landmarks, ligand binding sites and missense mutations to the collagen IV heterotrimers predicts major functional domains, novel interactions and variation in phenotypes in inherited diseases affecting basement membranes

PubMed Central

Des Parkin, J.; San Antonio, James D.; Pedchenko, Vadim; Hudson, Billy; Jensen, Shane T.; Savige, Judy

2016-01-01

Collagen IV is the major protein found in basement membranes. It comprises 3 heterotrimers (α1α1α2, α3α4α5, and α5α5α6) that form distinct networks, and are responsible for membrane strength and integrity. We constructed linear maps of the collagen IV heterotrimers (‘interactomes’) that indicated major structural landmarks, known and predicted ligand-binding sites, and missense mutations, in order to identify functional and disease-associated domains, potential interactions between ligands, and genotype-phenotype relationships. The maps documented more than 30 known ligand-binding sites as well as motifs for integrins, heparin, von Willebrand factor (VWF), decorin and bone morphogenetic protein (BMP). They predicted functional domains for angiogenesis and haemostasis, and disease domains for autoimmunity, tumor growth and inhibition, infection and glycation. Cooperative ligand interactions were indicated by binding site proximity, for example, between integrins, matrix metalloproteinases and heparin. The maps indicated that mutations affecting major ligand-binding sites, for example for Von Hippel Lindau (VHL) protein in the α1 chain or integrins in the α5 chain, resulted in distinctive phenotypes (Hereditary Angiopathy, Nephropathy, Aneurysms and muscle Cramps (HANAC) syndrome, and early onset Alport syndrome respectively). These maps further our understanding of basement membrane biology and disease, and suggest novel membrane interactions, functions, and therapeutic targets. PMID:21280145

[A Structural Equation Model on Family Strength of Married Working Women].

PubMed

Hong, Yeong Seon; Han, Kuem Sun

2015-12-01

The purpose of this study was to identify the effect of predictive factors related to family strength and develop a structural equation model that explains family strength among married working women. A hypothesized model was developed based on literature reviews and predictors of family strength by Yoo. This constructed model was built of an eight pathway form. Two exogenous variables included in this model were ego-resilience and family support. Three endogenous variables included in this model were functional couple communication, family stress and family strength. Data were collected using a self-report questionnaire from 319 married working women who were 30~40 of age and lived in cities of Chungnam province in Korea. Data were analyzed with PASW/WIN 18.0 and AMOS 18.0 programs. Family support had a positive direct, indirect and total effect on family strength. Family stress had a negative direct, indirect and total effect on family strength. Functional couple communication had a positive direct and total effect on family strength. These predictive variables of family strength explained 61.8% of model. The results of the study show a structural equation model for family strength of married working women and that predicting factors for family strength are family support, family stress, and functional couple communication. To improve family strength of married working women, the results of this study suggest nursing access and mediative programs to improve family support and functional couple communication, and reduce family stress.

The impact of female reproductive function on outcomes after traumatic brain injury.

PubMed

Ripley, David L; Harrison-Felix, Cindy; Sendroy-Terrill, Melissa; Cusick, Christopher P; Dannels-McClure, Amy; Morey, Clare

2008-06-01

To determine the impact of traumatic brain injury (TBI) on female menstrual and reproductive functioning and to examine the relationships between severity of injury, duration of amenorrhea, and TBI outcomes. Retrospective cohort survey. Telephone interview. Women (N=30; age range, 18-45y), between 1 and 3 years postinjury, who had completed inpatient rehabilitation for TBI. Not applicable. Data collected included menstrual and reproductive functioning pre- and postinjury, demographic, and injury characteristics. Outcome measures included the Glasgow Outcome Scale-Extended (GOS-E), the Mayo-Portland Adaptability Inventory-4 (MPAI-4), and the Medical Outcome Study 12-Item Short-Form Health Survey, Version 2 (SF-12v2). The median duration of amenorrhea was 61 days (range, 20-344d). Many subjects' menstrual function changed after TBI, reporting a significant increase in skipped menses postinjury (P<.001) and a trend toward more painful menses (P=.061). More severe TBI, as measured by the duration of posttraumatic amnesia, was significantly predictive of a longer duration of amenorrhea (P=.004). Subjects with a shorter duration of amenorrhea scored significantly better on the SF-12 physical component subscale (P=.004), the GOS-E (P=.05), and the MPAI-4 participation subscale (P=.05) after controlling for age, injury severity, and time postinjury. The severity of TBI was predictive of duration of amenorrhea and a shorter duration of amenorrhea was predictive of better ratings of global outcome, community participation, and health-related quality of life postinjury.

Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory.

PubMed

Chen, Mingchen; Zheng, Weihua; Wolynes, Peter G

2016-05-03

Aplysia cytoplasmic polyadenylation element binding (CPEB) protein, a translational regulator that recruits mRNAs and facilitates translation, has been shown to be a key component in the formation of long-term memory. Experimental data show that CPEB exists in at least a low-molecular weight coiled-coil oligomeric form and an amyloid fiber form involving the Q-rich domain (CPEB-Q). Using a coarse-grained energy landscape model, we predict the structures of the low-molecular weight oligomeric form and the dynamics of their transitions to the β-form. Up to the decamer, the oligomeric structures are predicted to be coiled coils. Free energy profiles confirm that the coiled coil is the most stable form for dimers and trimers. The structural transition from α to β is shown to be concentration dependent, with the transition barrier decreasing with increased concentration. We observe that a mechanical pulling force can facilitate the α-helix to β-sheet (α-to-β) transition by lowering the free energy barrier between the two forms. Interactome analysis of the CPEB protein suggests that its interactions with the cytoskeleton could provide the necessary mechanical force. We propose that, by exerting mechanical forces on CPEB oligomers, an active cytoskeleton can facilitate fiber formation. This mechanical catalysis makes possible a positive feedback loop that would help localize the formation of CPEB fibers to active synapse areas and mark those synapses for forming a long-term memory after the prion form is established. The functional role of the CPEB helical oligomers in this mechanism carries with it implications for targeting such species in neurodegenerative diseases.

Chemical modelling of glycolaldehyde and ethylene glycol in star-forming regions

NASA Astrophysics Data System (ADS)

Coutens, A.; Viti, S.; Rawlings, J. M. C.; Beltrán, M. T.; Holdship, J.; Jiménez-Serra, I.; Quénard, D.; Rivilla, V. M.

2018-04-01

Glycolaldehyde (HOCH2CHO) and ethylene glycol ((CH2OH)2) are two complex organic molecules detected in the hot cores and hot corinos of several star-forming regions. The ethylene glycol/glycolaldehyde abundance ratio seems to show an increase with the source luminosity. In the literature, several surface-chemistry formation mechanisms have been proposed for these two species. With the UCLCHEM chemical code, we explored the different scenarios and compared the predictions for a range of sources of different luminosities with the observations. None of the scenarios reproduce perfectly the trend. A better agreement is, however, found for a formation through recombination of two HCO radicals followed by successive hydrogenations. The reaction between HCO and CH2OH could also contribute to the formation of glycolaldehyde in addition to the hydrogenation pathway. The predictions are improved when a trend of decreasing H2 density within the core region with T≥100 K as a function of luminosity is included in the model. Destruction reactions of complex organic molecules in the gas phase would also need to be investigated, since they can affect the abundance ratios once the species have desorbed in the warm inner regions of the star-forming regions.

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

John F. Schabron; A. Troy Pauli; Joseph F. Rovani Jr.

The dispersed particle solution model of petroleum residua structure was used to develop predictors for pyrolytic coke formation. Coking Indexes were developed in prior years that measure how near a pyrolysis system is to coke formation during the coke formation induction period. These have been demonstrated to be universally applicable for residua regardless of the source of the material. Coking onset is coincidental with the destruction of the ordered structure and the formation of a multiphase system. The amount of coke initially formed appears to be a function of the free solvent volume of the original residua. In the currentmore » work, three-dimensional coke make predictability maps were developed at 400 C, 450 C, and 500 C (752 F, 842 F, and 932 F). These relate residence time and free solvent volume to the amount of coke formed at a particular pyrolysis temperature. Activation energies for two apparent types of zero-order coke formation reactions were estimated. The results provide a new tool for ranking residua, gauging proximity to coke formation, and predicting initial coke make tendencies.« less

Statistical Tools And Artificial Intelligence Approaches To Predict Fracture In Bulk Forming Processes

NASA Astrophysics Data System (ADS)

Di Lorenzo, R.; Ingarao, G.; Fonti, V.

2007-05-01

The crucial task in the prevention of ductile fracture is the availability of a tool for the prediction of such defect occurrence. The technical literature presents a wide investigation on this topic and many contributions have been given by many authors following different approaches. The main class of approaches regards the development of fracture criteria: generally, such criteria are expressed by determining a critical value of a damage function which depends on stress and strain paths: ductile fracture is assumed to occur when such critical value is reached during the analysed process. There is a relevant drawback related to the utilization of ductile fracture criteria; in fact each criterion usually has good performances in the prediction of fracture for particular stress - strain paths, i.e. it works very well for certain processes but may provide no good results for other processes. On the other hand, the approaches based on damage mechanics formulation are very effective from a theoretical point of view but they are very complex and their proper calibration is quite difficult. In this paper, two different approaches are investigated to predict fracture occurrence in cold forming operations. The final aim of the proposed method is the achievement of a tool which has a general reliability i.e. it is able to predict fracture for different forming processes. The proposed approach represents a step forward within a research project focused on the utilization of innovative predictive tools for ductile fracture. The paper presents a comparison between an artificial neural network design procedure and an approach based on statistical tools; both the approaches were aimed to predict fracture occurrence/absence basing on a set of stress and strain paths data. The proposed approach is based on the utilization of experimental data available, for a given material, on fracture occurrence in different processes. More in detail, the approach consists in the analysis of experimental tests in which fracture occurs followed by the numerical simulations of such processes in order to track the stress-strain paths in the workpiece region where fracture is expected. Such data are utilized to build up a proper data set which was utilized both to train an artificial neural network and to perform a statistical analysis aimed to predict fracture occurrence. The developed statistical tool is properly designed and optimized and is able to recognize the fracture occurrence. The reliability and predictive capability of the statistical method were compared with the ones obtained from an artificial neural network developed to predict fracture occurrence. Moreover, the approach is validated also in forming processes characterized by a complex fracture mechanics.

Predicting weak lensing statistics from halo mass reconstructions - Final Paper

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

Everett, Spencer

2015-08-20

As dark matter does not absorb or emit light, its distribution in the universe must be inferred through indirect effects such as the gravitational lensing of distant galaxies. While most sources are only weakly lensed, the systematic alignment of background galaxies around a foreground lens can constrain the mass of the lens which is largely in the form of dark matter. In this paper, I have implemented a framework to reconstruct all of the mass along lines of sight using a best-case dark matter halo model in which the halo mass is known. This framework is then used to makemore » predictions of the weak lensing of 3,240 generated source galaxies through a 324 arcmin² field of the Millennium Simulation. The lensed source ellipticities are characterized by the ellipticity-ellipticity and galaxy-mass correlation functions and compared to the same statistic for the intrinsic and ray-traced ellipticities. In the ellipticity-ellipticity correlation function, I and that the framework systematically under predicts the shear power by an average factor of 2.2 and fails to capture correlation from dark matter structure at scales larger than 1 arcminute. The model predicted galaxy-mass correlation function is in agreement with the ray-traced statistic from scales 0.2 to 0.7 arcminutes, but systematically underpredicts shear power at scales larger than 0.7 arcminutes by an average factor of 1.2. Optimization of the framework code has reduced the mean CPU time per lensing prediction by 70% to 24 ± 5 ms. Physical and computational shortcomings of the framework are discussed, as well as potential improvements for upcoming work.« less

Reference Values for Spirometry Derived Using Lambda, Mu, Sigma (LMS) Method in Korean Adults: in Comparison with Previous References.

PubMed

Jo, Bum Seak; Myong, Jun Pyo; Rhee, Chin Kook; Yoon, Hyoung Kyu; Koo, Jung Wan; Kim, Hyoung Ryoul

2018-01-15

The present study aimed to update the prediction equations for spirometry and their lower limits of normal (LLN) by using the lambda, mu, sigma (LMS) method and to compare the outcomes with the values of previous spirometric reference equations. Spirometric data of 10,249 healthy non-smokers (8,776 females) were extracted from the fourth and fifth versions of the Korea National Health and Nutrition Examination Survey (KNHANES IV, 2007-2009; V, 2010-2012). Reference equations were derived using the LMS method which allows modeling skewness (lambda [L]), mean (mu [M]), and coefficient of variation (sigma [S]). The outcome equations were compared with previous reference values. Prediction equations were presented in the following form: predicted value = e{a + b × ln(height) + c × ln(age) + M - spline}. The new predicted values for spirometry and their LLN derived using the LMS method were shown to more accurately reflect transitions in pulmonary function in young adults than previous prediction equations derived using conventional regression analysis in 2013. There were partial discrepancies between the new reference values and the reference values from the Global Lung Function Initiative in 2012. The results should be interpreted with caution for young adults and elderly males, particularly in terms of the LLN for forced expiratory volume in one second/forced vital capacity in elderly males. Serial spirometry follow-up, together with correlations with other clinical findings, should be emphasized in evaluating the pulmonary function of individuals. Future studies are needed to improve the accuracy of reference data and to develop continuous reference values for spirometry across all ages. © 2018 The Korean Academy of Medical Sciences.

Artificial neural network with backpropagation learning to predict mean monthly total ozone in Arosa, Switzerland

NASA Astrophysics Data System (ADS)

Chattopadhyay, Surajit; Bandyopadhyay, Goutami

2007-01-01

Present study deals with the mean monthly total ozone time series over Arosa, Switzerland. The study period is 1932-1971. First of all, the total ozone time series has been identified as a complex system and then Artificial Neural Networks models in the form of Multilayer Perceptron with back propagation learning have been developed. The models are Single-hidden-layer and Two-hidden-layer Perceptrons with sigmoid activation function. After sequential learning with learning rate 0.9 the peak total ozone period (February-May) concentrations of mean monthly total ozone have been predicted by the two neural net models. After training and validation, both of the models are found skillful. But, Two-hidden-layer Perceptron is found to be more adroit in predicting the mean monthly total ozone concentrations over the aforesaid period.

On Predicting Form and Meaning in a Second Language

ERIC Educational Resources Information Center

Ito, Aine; Martin, Andrea E.; Nieuwland, Mante S.

2017-01-01

We used event-related potentials (ERP) to investigate whether Spanish-English bilinguals preactivate form and meaning of predictable words. Participants read high-cloze sentence contexts (e.g., "The student is going to the library to borrow a..."), followed by the predictable word ("book"), a word that was form-related…

Prediction of the turbulent wake with second-order closure

NASA Technical Reports Server (NTRS)

Taulbee, D. B.; Lumley, J. L.

1981-01-01

A turbulence was envisioned whose energy containing scales would be Gaussian in the absence of inhomogeneity, gravity, etc. An equation was constructed for a function equivalent to the probability density, the second moment of which corresponded to the accepted modeled form of the Reynolds stress equation. The third moment equations obtained from this were simplified by the assumption of weak inhomogeneity. Calculations are presented with this model as well as interpretations of the results.

Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource.

PubMed

Yao, Heng; Wang, Xiaoxuan; Chen, Pengcheng; Hai, Ling; Jin, Kang; Yao, Lixia; Mao, Chuanzao; Chen, Xin

2018-05-01

An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest versions of the Predicted Arabidopsis Interactome Resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes [DEGs]) in Arabidopsis ( Arabidopsis thaliana ) with respect to its functional impact for biological processes. PAIR version 5.0 integrates functional association data between genes in multiple forms and infers 335,301 putative functional interactions. GSLA relies on this high-confidence inferred functional association network to expand our perception of the functional impacts of an observed transcriptomic change. GSLA then interprets the biological significance of the observed DEGs using established biological concepts (annotation terms), describing not only the DEGs themselves but also their potential functional impacts. This unique analytical capability can help researchers gain deeper insights into their experimental results and highlight prospective directions for further investigation. We demonstrate the utility of GSLA with two case studies in which GSLA uncovered how molecular events may have caused physiological changes through their collective functional influence on biological processes. Furthermore, we showed that typical annotation-enrichment tools were unable to produce similar insights to PAIR/GSLA. The PAIR version 5.0-inferred interactome and GSLA Web tool both can be accessed at http://public.synergylab.cn/pair/. © 2018 American Society of Plant Biologists. All Rights Reserved.

Theoretical predictions of latitude dependencies in the solar wind

NASA Technical Reports Server (NTRS)

Winge, C. R., Jr.; Coleman, P. J., Jr.

1974-01-01

Results are presented which were obtained with the Winge-Coleman model for theoretical predictions of latitudinal dependencies in the solar wind. A first-order expansion is described which allows analysis of first-order latitudinal variations in the coronal boundary conditions and results in a second-order partial differential equation for the perturbation stream function. Latitudinal dependencies are analytically separated out in the form of Legendre polynomials and their derivative, and are reduced to the solution of radial differential equations. This analysis is shown to supply an estimate of how large the coronal variation in latitude must be to produce an 11 km/sec/deg gradient in the radial velocity of the solar wind, assuming steady-state processes.

Isolated rotor noise due to inlet distortion or turbulence

NASA Technical Reports Server (NTRS)

Mani, R.

1974-01-01

Theoretical formulation, analysis, and results are presented that are necessary to analyze quadrupole noise generated from a loaded, subsonic rotor because of its interaction with an inflow distortion or inlet turbulence. The ratio of quadrupole to dipole noise is largely a function of the axial Mach number, wheel tip Mach number, rotor solidity, and total pressure ratio across the rotor. It is relatively independent of the specific form of the inflow distortion or inlet turbulence. Comparisons with experimental data only succeed in predicting gross levels at a given speed and fail to predict the variation of noise at fixed speed with flow and pressure ratio. Likely sources of this discrepancy are discussed.

Computer modeling of a two-junction, monolithic cascade solar cell

NASA Technical Reports Server (NTRS)

Lamorte, M. F.; Abbott, D.

1979-01-01

The theory and design criteria for monolithic, two-junction cascade solar cells are described. The departure from the conventional solar cell analytical method and the reasons for using the integral form of the continuity equations are briefly discussed. The results of design optimization are presented. The energy conversion efficiency that is predicted for the optimized structure is greater than 30% at 300 K, AMO and one sun. The analytical method predicts device performance characteristics as a function of temperature. The range is restricted to 300 to 600 K. While the analysis is capable of determining most of the physical processes occurring in each of the individual layers, only the more significant device performance characteristics are presented.

Model for small arms fire muzzle blast wave propagation in air

NASA Astrophysics Data System (ADS)

Aguilar, Juan R.; Desai, Sachi V.

2011-11-01

Accurate modeling of small firearms muzzle blast wave propagation in the far field is critical to predict sound pressure levels, impulse durations and rise times, as functions of propagation distance. Such a task being relevant to a number of military applications including the determination of human response to blast noise, gunfire detection and localization, and gun suppressor design. Herein, a time domain model to predict small arms fire muzzle blast wave propagation is introduced. The model implements a Friedlander wave with finite rise time which diverges spherically from the gun muzzle. Additionally, the effects in blast wave form of thermoviscous and molecular relaxational processes, which are associated with atmospheric absorption of sound were also incorporated in the model. Atmospheric absorption of blast waves is implemented using a time domain recursive formula obtained from numerical integration of corresponding differential equations using a Crank-Nicholson finite difference scheme. Theoretical predictions from our model were compared to previously recorded real world data of muzzle blast wave signatures obtained by shooting a set different sniper weapons of varying calibers. Recordings containing gunfire acoustical signatures were taken at distances between 100 and 600 meters from the gun muzzle. Results shows that predicted blast wave slope and exponential decay agrees well with measured data. Analysis also reveals the persistency of an oscillatory phenomenon after blast overpressure in the recorded wave forms.

Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era

PubMed Central

Kallianpur, Asha R.; Wang, Quan; Jia, Peilin; Hulgan, Todd; Zhao, Zhongming; Letendre, Scott L.; Ellis, Ronald J.; Heaton, Robert K.; Franklin, Donald R.; Barnholtz-Sloan, Jill; Collier, Ann C.; Marra, Christina M.; Clifford, David B.; Gelman, Benjamin B.; McArthur, Justin C.; Morgello, Susan; Simpson, David M.; McCutchan, J. A.; Grant, Igor

2016-01-01

Background. Anemia has been linked to adverse human immunodeficiency virus (HIV) outcomes, including dementia, in the era before highly active antiretroviral therapy (HAART). Milder forms of HIV-associated neurocognitive disorder (HAND) remain common in HIV-infected persons, despite HAART, but whether anemia predicts HAND in the HAART era is unknown. Methods. We evaluated time-dependent associations of anemia and cross-sectional associations of red blood cell indices with neurocognitive impairment in a multicenter, HAART-era HIV cohort study (N = 1261), adjusting for potential confounders, including age, nadir CD4+ T-cell count, zidovudine use, and comorbid conditions. Subjects underwent comprehensive neuropsychiatric and neuromedical assessments. Results. HAND, defined according to standardized criteria, occurred in 595 subjects (47%) at entry. Mean corpuscular volume and mean corpuscular hemoglobin were positively associated with the global deficit score, a continuous measure of neurocognitive impairment (both P < .01), as well as with all HAND, milder forms of HAND, and HIV-associated dementia in multivariable analyses (all P < .05). Anemia independently predicted development of HAND during a median follow-up of 72 months (adjusted hazard ratio, 1.55; P < .01). Conclusions. Anemia and red blood cell indices predict HAND in the HAART era and may contribute to risk assessment. Future studies should address whether treating anemia may help to prevent HAND or improve cognitive function in HIV-infected persons. PMID:26690344

Female-directed violence as a form of sexual coercion in humans (Homo sapiens).

PubMed

Barbaro, Nicole; Shackelford, Todd K

2016-11-01

Male-perpetrated female-directed violence (FDV) may be associated with greater sexual access to a female. Accordingly, FDV is expected to be associated with greater copulation frequency. Research on nonhuman primates affirms this hypothesis, but no previous research has investigated this relationship in humans (Homo sapiens). The current research tests the hypothesis that FDV is associated with in-pair copulation frequency and, thus, may function as a form of sexual coercion. It was predicted that men who perpetrate FDV will secure more in-pair copulations than men who do not perpetrate violence (Prediction 1a), and that average monthly rates of FDV would positively correlate with in-pair copulation frequency (Prediction 1b). Male participants (n = 355) completed a survey, reporting limited demographic information (e.g., age, relationship length), in-pair copulation frequency, and history of physical violence perpetration. As predicted, violent men secured more in-pair copulations, on average, than nonviolent men, and monthly rates of violence positively correlated with in-pair copulation frequency. In humans, as in nonhuman primates, FDV by males may facilitate greater sexual access to a female. We discuss the implications of the current research for an evolutionary perspective on partner violence, and draw on research on nonhuman primates to highlight profitable avenues of research on FDV in humans. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Reasoning, learning, and creativity: frontal lobe function and human decision-making.

PubMed

Collins, Anne; Koechlin, Etienne

2012-01-01

The frontal lobes subserve decision-making and executive control--that is, the selection and coordination of goal-directed behaviors. Current models of frontal executive function, however, do not explain human decision-making in everyday environments featuring uncertain, changing, and especially open-ended situations. Here, we propose a computational model of human executive function that clarifies this issue. Using behavioral experiments, we show that unlike others, the proposed model predicts human decisions and their variations across individuals in naturalistic situations. The model reveals that for driving action, the human frontal function monitors up to three/four concurrent behavioral strategies and infers online their ability to predict action outcomes: whenever one appears more reliable than unreliable, this strategy is chosen to guide the selection and learning of actions that maximize rewards. Otherwise, a new behavioral strategy is tentatively formed, partly from those stored in long-term memory, then probed, and if competitive confirmed to subsequently drive action. Thus, the human executive function has a monitoring capacity limited to three or four behavioral strategies. This limitation is compensated by the binary structure of executive control that in ambiguous and unknown situations promotes the exploration and creation of new behavioral strategies. The results support a model of human frontal function that integrates reasoning, learning, and creative abilities in the service of decision-making and adaptive behavior.

Long-term Effects of Psychosocial Work Stress in Midlife on Health Functioning After Labor Market Exit—Results From the GAZEL Study

PubMed Central

Sembajwe, Grace; Zins, Marie; Berkman, Lisa; Goldberg, Marcel; Siegrist, Johannes

2012-01-01

Objectives. To study long-term effects of psychosocial work stress in mid-life on health functioning after labor market exit using two established work stress models. Methods. In the frame of the prospective French Gazel cohort study, data on psychosocial work stress were assessed using the full questionnaires measuring the demand-control-support model (in 1997 and 1999) and the effort–reward imbalance model (in 1998). In 2007, health functioning was assessed, using the Short Form 36 mental and physical component scores. Multivariate regressions were calculated to predict health functioning in 2007, controlling for age, gender, social position, and baseline self-perceived health. Results. Consistent effects of both work stress models and their single components on mental and physical health functioning during retirement were observed. Effects remained significant after adjustment including baseline self-perceived health. Whereas the predictive power of both work stress models was similar in the case of the physical composite score, in the case of the mental health score, values of model fit were slightly higher for the effort–reward imbalance model (R²: 0.13) compared with the demand-control model (R²: 0.11). Conclusions. Findings underline the importance of working conditions in midlife not only for health in midlife but also for health functioning after labor market exit. PMID:22546992

Reasoning, Learning, and Creativity: Frontal Lobe Function and Human Decision-Making

PubMed Central

Collins, Anne; Koechlin, Etienne

2012-01-01

The frontal lobes subserve decision-making and executive control—that is, the selection and coordination of goal-directed behaviors. Current models of frontal executive function, however, do not explain human decision-making in everyday environments featuring uncertain, changing, and especially open-ended situations. Here, we propose a computational model of human executive function that clarifies this issue. Using behavioral experiments, we show that unlike others, the proposed model predicts human decisions and their variations across individuals in naturalistic situations. The model reveals that for driving action, the human frontal function monitors up to three/four concurrent behavioral strategies and infers online their ability to predict action outcomes: whenever one appears more reliable than unreliable, this strategy is chosen to guide the selection and learning of actions that maximize rewards. Otherwise, a new behavioral strategy is tentatively formed, partly from those stored in long-term memory, then probed, and if competitive confirmed to subsequently drive action. Thus, the human executive function has a monitoring capacity limited to three or four behavioral strategies. This limitation is compensated by the binary structure of executive control that in ambiguous and unknown situations promotes the exploration and creation of new behavioral strategies. The results support a model of human frontal function that integrates reasoning, learning, and creative abilities in the service of decision-making and adaptive behavior. PMID:22479152

Density functional theory studies on the electronic, structural, phonon dynamical and thermo-stability properties of bicarbonates MHCO3, M = Li, Na, K

NASA Astrophysics Data System (ADS)

Duan, Yuhua; Zhang, Bo; Sorescu, Dan C.; Johnson, J. Karl; Majzoub, Eric H.; Luebke, David R.

2012-08-01

The structural, electronic, phonon dispersion and thermodynamic properties of MHCO3 (M = Li, Na, K) solids were investigated using density functional theory. The calculated bulk properties for both their ambient and the high-pressure phases are in good agreement with available experimental measurements. Solid phase LiHCO3 has not yet been observed experimentally. We have predicted several possible crystal structures for LiHCO3 using crystallographic database searching and prototype electrostatic ground state modeling. Our total energy and phonon free energy (FPH) calculations predict that LiHCO3 will be stable under suitable conditions of temperature and partial pressures of CO2 and H2O. Our calculations indicate that the {{HCO}}_{3}^{-} groups in LiHCO3 and NaHCO3 form an infinite chain structure through O⋯H⋯O hydrogen bonds. In contrast, the {{HCO}}_{3}^{-} anions form dimers, ({{HCO}}_{3}^{-})_{2}, connected through double hydrogen bonds in all phases of KHCO3. Based on density functional perturbation theory, the Born effective charge tensor of each atom type was obtained for all phases of the bicarbonates. Their phonon dispersions with the longitudinal optical-transverse optical splitting were also investigated. Based on lattice phonon dynamics study, the infrared spectra and the thermodynamic properties of these bicarbonates were obtained. Over the temperature range 0-900 K, the FPH and the entropies (S) of MHCO3 (M =Li, Na, K) systems vary as FPH(LiHCO3) > FPH(NaHCO3) > FPH(KHCO3) and S(KHCO3) > S(NaHCO3) > S(LiHCO3), respectively, in agreement with the available experimental data. Analysis of the predicted thermodynamics of the CO2 capture reactions indicates that the carbonate/bicarbonate transition reactions for Na and K could be used for CO2 capture technology, in agreement with experiments.

Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm

PubMed Central

Palamara, Gian Marco; Childs, Dylan Z; Clements, Christopher F; Petchey, Owen L; Plebani, Marco; Smith, Matthew J

2014-01-01

Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important implications in understanding and predicting the effects of temperature on the dynamics of populations. PMID:25558365

Affixation in semantic space: Modeling morpheme meanings with compositional distributional semantics.

PubMed

Marelli, Marco; Baroni, Marco

2015-07-01

The present work proposes a computational model of morpheme combination at the meaning level. The model moves from the tenets of distributional semantics, and assumes that word meanings can be effectively represented by vectors recording their co-occurrence with other words in a large text corpus. Given this assumption, affixes are modeled as functions (matrices) mapping stems onto derived forms. Derived-form meanings can be thought of as the result of a combinatorial procedure that transforms the stem vector on the basis of the affix matrix (e.g., the meaning of nameless is obtained by multiplying the vector of name with the matrix of -less). We show that this architecture accounts for the remarkable human capacity of generating new words that denote novel meanings, correctly predicting semantic intuitions about novel derived forms. Moreover, the proposed compositional approach, once paired with a whole-word route, provides a new interpretative framework for semantic transparency, which is here partially explained in terms of ease of the combinatorial procedure and strength of the transformation brought about by the affix. Model-based predictions are in line with the modulation of semantic transparency on explicit intuitions about existing words, response times in lexical decision, and morphological priming. In conclusion, we introduce a computational model to account for morpheme combination at the meaning level. The model is data-driven, theoretically sound, and empirically supported, and it makes predictions that open new research avenues in the domain of semantic processing. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Coagulation monitoring based on blood elastic measurement using optical coherence tomography

NASA Astrophysics Data System (ADS)

Xu, Xiangqun; Zhu, Jiang; Chen, Zhongping

2017-02-01

Blood coagulation monitoring is important to diagnose hematological diseases and cardiovascular diseases and to predict the risk of bleeding and excessive clotting. In this study, we developed a system to dynamically monitor blood coagulation and quantitatively determine the coagulation function by blood elastic measurement. When blood forms a clot from a liquid, ultrasonic force induces a shear wave, which is detected by optical coherence tomography (OCT). The coagulation of porcine whole blood recalcified by calcium chloride is assessed using the metrics of reaction time, clot formation kinetics and maximum shear modulus. The OCE system can noninvasively monitor the blood coagulation and quantitatively determine the coagulation function.

Kinetic energy partition method applied to ground state helium-like atoms.

PubMed

Chen, Yu-Hsin; Chao, Sheng D

2017-03-28

We have used the recently developed kinetic energy partition (KEP) method to solve the quantum eigenvalue problems for helium-like atoms and obtain precise ground state energies and wave-functions. The key to treating properly the electron-electron (repulsive) Coulomb potential energies for the KEP method to be applied is to introduce a "negative mass" term into the partitioned kinetic energy. A Hartree-like product wave-function from the subsystem wave-functions is used to form the initial trial function, and the variational search for the optimized adiabatic parameters leads to a precise ground state energy. This new approach sheds new light on the all-important problem of solving many-electron Schrödinger equations and hopefully opens a new way to predictive quantum chemistry. The results presented here give very promising evidence that an effective one-electron model can be used to represent a many-electron system, in the spirit of density functional theory.

Different forms of effective connectivity in primate frontotemporal pathways.

PubMed

Petkov, Christopher I; Kikuchi, Yukiko; Milne, Alice E; Mishkin, Mortimer; Rauschecker, Josef P; Logothetis, Nikos K

2015-01-23

It is generally held that non-primary sensory regions of the brain have a strong impact on frontal cortex. However, the effective connectivity of pathways to frontal cortex is poorly understood. Here we microstimulate sites in the superior temporal and ventral frontal cortex of monkeys and use functional magnetic resonance imaging to evaluate the functional activity resulting from the stimulation of interconnected regions. Surprisingly, we find that, although certain earlier stages of auditory cortical processing can strongly activate frontal cortex, downstream auditory regions, such as voice-sensitive cortex, appear to functionally engage primarily an ipsilateral temporal lobe network. Stimulating other sites within this activated temporal lobe network shows strong activation of frontal cortex. The results indicate that the relative stage of sensory processing does not predict the level of functional access to the frontal lobes. Rather, certain brain regions engage local networks, only parts of which have a strong functional impact on frontal cortex.

Different forms of effective connectivity in primate frontotemporal pathways

PubMed Central

Petkov, Christopher I.; Kikuchi, Yukiko; Milne, Alice E.; Mishkin, Mortimer; Rauschecker, Josef P.; Logothetis, Nikos K.

2015-01-01

It is generally held that non-primary sensory regions of the brain have a strong impact on frontal cortex. However, the effective connectivity of pathways to frontal cortex is poorly understood. Here we microstimulate sites in the superior temporal and ventral frontal cortex of monkeys and use functional magnetic resonance imaging to evaluate the functional activity resulting from the stimulation of interconnected regions. Surprisingly, we find that, although certain earlier stages of auditory cortical processing can strongly activate frontal cortex, downstream auditory regions, such as voice-sensitive cortex, appear to functionally engage primarily an ipsilateral temporal lobe network. Stimulating other sites within this activated temporal lobe network shows strong activation of frontal cortex. The results indicate that the relative stage of sensory processing does not predict the level of functional access to the frontal lobes. Rather, certain brain regions engage local networks, only parts of which have a strong functional impact on frontal cortex. PMID:25613079

Distinct hippocampal functional networks revealed by tractography-based parcellation.

PubMed

Adnan, Areeba; Barnett, Alexander; Moayedi, Massieh; McCormick, Cornelia; Cohn, Melanie; McAndrews, Mary Pat

2016-07-01

Recent research suggests the anterior and posterior hippocampus form part of two distinct functional neural networks. Here we investigate the structural underpinnings of this functional connectivity difference using diffusion-weighted imaging-based parcellation. Using this technique, we substantiated that the hippocampus can be parcellated into distinct anterior and posterior segments. These structurally defined segments did indeed show different patterns of resting state functional connectivity, in that the anterior segment showed greater connectivity with temporal and orbitofrontal cortex, whereas the posterior segment was more highly connected to medial and lateral parietal cortex. Furthermore, we showed that the posterior hippocampal connectivity to memory processing regions, including the dorsolateral prefrontal cortex, parahippocampal, inferior temporal and fusiform gyri and the precuneus, predicted interindividual relational memory performance. These findings provide important support for the integration of structural and functional connectivity in understanding the brain networks underlying episodic memory.

Predicting overlapping protein complexes from weighted protein interaction graphs by gradually expanding dense neighborhoods.

PubMed

Dimitrakopoulos, Christos; Theofilatos, Konstantinos; Pegkas, Andreas; Likothanassis, Spiros; Mavroudi, Seferina

2016-07-01

Proteins are vital biological molecules driving many fundamental cellular processes. They rarely act alone, but form interacting groups called protein complexes. The study of protein complexes is a key goal in systems biology. Recently, large protein-protein interaction (PPI) datasets have been published and a plethora of computational methods that provide new ideas for the prediction of protein complexes have been implemented. However, most of the methods suffer from two major limitations: First, they do not account for proteins participating in multiple functions and second, they are unable to handle weighted PPI graphs. Moreover, the problem remains open as existing algorithms and tools are insufficient in terms of predictive metrics. In the present paper, we propose gradually expanding neighborhoods with adjustment (GENA), a new algorithm that gradually expands neighborhoods in a graph starting from highly informative "seed" nodes. GENA considers proteins as multifunctional molecules allowing them to participate in more than one protein complex. In addition, GENA accepts weighted PPI graphs by using a weighted evaluation function for each cluster. In experiments with datasets from Saccharomyces cerevisiae and human, GENA outperformed Markov clustering, restricted neighborhood search and clustering with overlapping neighborhood expansion, three state-of-the-art methods for computationally predicting protein complexes. Seven PPI networks and seven evaluation datasets were used in total. GENA outperformed existing methods in 16 out of 18 experiments achieving an average improvement of 5.5% when the maximum matching ratio metric was used. Our method was able to discover functionally homogeneous protein clusters and uncover important network modules in a Parkinson expression dataset. When used on the human networks, around 47% of the detected clusters were enriched in gene ontology (GO) terms with depth higher than five in the GO hierarchy. In the present manuscript, we introduce a new method for the computational prediction of protein complexes by making the realistic assumption that proteins participate in multiple protein complexes and cellular functions. Our method can detect accurate and functionally homogeneous clusters. Copyright © 2016 Elsevier B.V. All rights reserved.

Predicting galaxy star formation rates via the co-evolution of galaxies and haloes

NASA Astrophysics Data System (ADS)

Watson, Douglas F.; Hearin, Andrew P.; Berlind, Andreas A.; Becker, Matthew R.; Behroozi, Peter S.; Skibba, Ramin A.; Reyes, Reinabelle; Zentner, Andrew R.; van den Bosch, Frank C.

2015-01-01

In this paper, we test the age matching hypothesis that the star formation rate (SFR) of a galaxy of fixed stellar mass is determined by its dark matter halo formation history, e.g. more quiescent galaxies reside in older haloes. We present new Sloan Digital Sky Survey measurements of the galaxy two-point correlation function and galaxy-galaxy lensing as a function of stellar mass and SFR, separated into quenched and star-forming galaxy samples to test this simple model. We find that our age matching model is in excellent agreement with these new measurements. We also find that our model is able to predict: (1) the relative SFRs of central and satellite galaxies, (2) the SFR dependence of the radial distribution of satellite galaxy populations within galaxy groups, rich groups, and clusters and their surrounding larger scale environments, and (3) the interesting feature that the satellite quenched fraction as a function of projected radial distance from the central galaxy exhibits an ˜r-.15 slope, independent of environment. These accurate predictions are intriguing given that we do not explicitly model satellite-specific processes after infall, and that in our model the virial radius does not mark a special transition region in the evolution of a satellite. The success of the model suggests that present-day galaxy SFR is strongly correlated with halo mass assembly history.

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (<10 ps), but the effects on slow chemistry and the free energy surface are not well-known. We present a force matching approach to increase the accuracy of DFTB predictions for free energy surfaces. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials without a priori knowledge of transition states. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT results for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Electromyography of the buccal musculature of octopus (Octopus bimaculoides): a test of the function of the muscle articulation in support and movement.

PubMed

Uyeno, Theodore A; Kier, William M

2007-01-01

The buccal mass musculature of the octopus (Octopus bimaculoides) was studied with electromyography to test the predictions of a previous morphological study in which we suggested that the muscles of the buccal mass serve as both the effectors of movement and as the joint itself, forming a new category of flexible joint termed a ;muscle articulation'. The predictions of muscle function were tested by correlating muscle electrical activity in isolated buccal masses with spontaneous beak movements. Bipolar electromyography electrodes were implanted in the various beak muscles and beak position was recorded simultaneously with an electronic movement monitor (N=14). The results are consistent with the hypothesis that the lateral mandibular muscles produce opening movements of the beaks and provide the first definitive explanation of the opening mechanism. The results are also consistent with the hypothesis that the superior mandibular muscle functions primarily in closing. Co-contraction of the lateral mandibular muscles and the superior mandibular muscles was also observed, suggesting that these muscles may also stabilize the beaks during movement or provide a means of controlling the location of the pivot between the beaks. This study provides an important first test of the predictions of the role of the complex musculature found in muscle articulations such as the cephalopod buccal mass.

Image classification at low light levels

NASA Astrophysics Data System (ADS)

Wernick, Miles N.; Morris, G. Michael

1986-12-01

An imaging photon-counting detector is used to achieve automatic sorting of two image classes. The classification decision is formed on the basis of the cross correlation between a photon-limited input image and a reference function stored in computer memory. Expressions for the statistical parameters of the low-light-level correlation signal are given and are verified experimentally. To obtain a correlation-based system for two-class sorting, it is necessary to construct a reference function that produces useful information for class discrimination. An expression for such a reference function is derived using maximum-likelihood decision theory. Theoretically predicted results are used to compare on the basis of performance the maximum-likelihood reference function with Fukunaga-Koontz basis vectors and average filters. For each method, good class discrimination is found to result in milliseconds from a sparse sampling of the input image.

Modeling personnel turnover in the parametric organization

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1991-01-01

A model is developed for simulating the dynamics of a newly formed organization, credible during all phases of organizational development. The model development process is broken down into the activities of determining the tasks required for parametric cost analysis (PCA), determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the model, implementing the model, and testing it. The model, parameterized by the likelihood of job function transition, has demonstrated by the capability to represent the transition of personnel across functional boundaries within a parametric organization using a linear dynamical system, and the ability to predict required staffing profiles to meet functional needs at the desired time. The model can be extended by revisions of the state and transition structure to provide refinements in functional definition for the parametric and extended organization.

A Comparative Study of Some Dynamic Stall Models

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Kaza, K. R. V.

1987-01-01

Three semi-empirical aerodynamic stall models are compared with respect to their lift and moment hysteresis loop prediction, limit cycle behavior, easy implementation, and feasibility in developing the parameters required for stall flutter prediction of advanced turbines. For the comparison of aeroelastic response prediction including stall, a typical section model and a plate structural model are considered. The response analysis includes both plunging and pitching motions of the blades. In model A, a correction to the angle of attack is applied when the angle of attack exceeds the static stall angle. In model B, a synthesis procedure is used for angles of attack above static stall angles and the time history effects are accounted through the Wagner function. In both models the life and moment coefficients for angle of attack below stall are obtained from tabular data for a given Mach number and angle of attack. In model C, referred to an the ONERA model, the life and moment coefficients are given in the form of two differential equations, one for angles below stall, and the other for angles above stall. The parameters of those equations are nonlinear functions of the angle of attack.

Chemoselective Aliphatic C–H Bond Oxidation Enabled by Polarity Reversal

PubMed Central

2017-01-01

Methods for selective oxidation of aliphatic C–H bonds are called on to revolutionize organic synthesis by providing novel and more efficient paths. Realization of this goal requires the discovery of mechanisms that can alter in a predictable manner the innate reactivity of these bonds. Ideally, these mechanisms need to make oxidation of aliphatic C–H bonds, which are recognized as relatively inert, compatible with the presence of electron rich functional groups that are highly susceptible to oxidation. Furthermore, predictable modification of the relative reactivity of different C–H bonds within a molecule would enable rapid diversification of the resulting oxidation products. Herein we show that by engaging in hydrogen bonding, fluorinated alcohols exert a polarity reversal on electron rich functional groups, directing iron and manganese catalyzed oxidation toward a priori stronger and unactivated C–H bonds. As a result, selective hydroxylation of methylenic sites in hydrocarbons and remote aliphatic C–H oxidation of otherwise sensitive alcohol, ether, amide, and amine substrates is achieved employing aqueous hydrogen peroxide as oxidant. Oxidations occur in a predictable manner, with outstanding levels of product chemoselectivity, preserving the first-formed hydroxylation product, thus representing an extremely valuable tool for synthetic planning and development. PMID:29296677

Higher order alchemical derivatives from coupled perturbed self-consistent field theory.

PubMed

Lesiuk, Michał; Balawender, Robert; Zachara, Janusz

2012-01-21

We present an analytical approach to treat higher order derivatives of Hartree-Fock (HF) and Kohn-Sham (KS) density functional theory energy in the Born-Oppenheimer approximation with respect to the nuclear charge distribution (so-called alchemical derivatives). Modified coupled perturbed self-consistent field theory is used to calculate molecular systems response to the applied perturbation. Working equations for the second and the third derivatives of HF/KS energy are derived. Similarly, analytical forms of the first and second derivatives of orbital energies are reported. The second derivative of Kohn-Sham energy and up to the third derivative of Hartree-Fock energy with respect to the nuclear charge distribution were calculated. Some issues of practical calculations, in particular the dependence of the basis set and Becke weighting functions on the perturbation, are considered. For selected series of isoelectronic molecules values of available alchemical derivatives were computed and Taylor series expansion was used to predict energies of the "surrounding" molecules. Predicted values of energies are in unexpectedly good agreement with the ones computed using HF/KS methods. Presented method allows one to predict orbital energies with the error less than 1% or even smaller for valence orbitals. © 2012 American Institute of Physics

Chemoselective Aliphatic C-H Bond Oxidation Enabled by Polarity Reversal.

PubMed

Dantignana, Valeria; Milan, Michela; Cussó, Olaf; Company, Anna; Bietti, Massimo; Costas, Miquel

2017-12-27

Methods for selective oxidation of aliphatic C-H bonds are called on to revolutionize organic synthesis by providing novel and more efficient paths. Realization of this goal requires the discovery of mechanisms that can alter in a predictable manner the innate reactivity of these bonds. Ideally, these mechanisms need to make oxidation of aliphatic C-H bonds, which are recognized as relatively inert, compatible with the presence of electron rich functional groups that are highly susceptible to oxidation. Furthermore, predictable modification of the relative reactivity of different C-H bonds within a molecule would enable rapid diversification of the resulting oxidation products. Herein we show that by engaging in hydrogen bonding, fluorinated alcohols exert a polarity reversal on electron rich functional groups, directing iron and manganese catalyzed oxidation toward a priori stronger and unactivated C-H bonds. As a result, selective hydroxylation of methylenic sites in hydrocarbons and remote aliphatic C-H oxidation of otherwise sensitive alcohol, ether, amide, and amine substrates is achieved employing aqueous hydrogen peroxide as oxidant. Oxidations occur in a predictable manner, with outstanding levels of product chemoselectivity, preserving the first-formed hydroxylation product, thus representing an extremely valuable tool for synthetic planning and development.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

PubMed Central

2011-01-01

Background Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. Results We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. Conclusions The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms. PMID:21992415

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

Saikatendu, Kumar Singh; Zhang, Xuejun; Kinch, Lisa

The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. The structure of SA1388 has been solved to 2.0{angstrom} resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals.more » It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric 'lids' formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric 'lids' that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.« less

The global prevalence of HFE and non-HFE hemochromatosis estimated from analysis of next-generation sequencing data.

PubMed

Wallace, Daniel F; Subramaniam, V Nathan

2016-06-01

The prevalence of HFE-related hereditary hemochromatosis (HH) among European populations has been well studied. There are no prevalence data for atypical forms of HH caused by mutations in HFE2, HAMP, TFR2, or SLC40A1. The purpose of this study was to estimate the population prevalence of these non-HFE forms of HH. A list of HH pathogenic variants in publically available next-generation sequence (NGS) databases was compiled and allele frequencies were determined. Of 161 variants previously associated with HH, 43 were represented among the NGS data sets; an additional 40 unreported functional variants also were identified. The predicted prevalence of HFE HH and the p.Cys282Tyr mutation closely matched previous estimates from similar populations. Of the non-HFE forms of iron overload, TFR2-, HFE2-, and HAMP-related forms are predicted to be rare, with pathogenic allele frequencies in the range of 0.00007 to 0.0005. Significantly, SLC40A1 variants that have been previously associated with autosomal-dominant ferroportin disease were identified in several populations (pathogenic allele frequency 0.0004), being most prevalent among Africans. We have, for the first time, estimated the population prevalence of non-HFE HH. This methodology could be applied to estimate the population prevalence of a wide variety of genetic disorders.Genet Med 18 6, 618-626.

The expanding universe of thiolated gold nanoclusters and beyond.

PubMed

Jiang, De-en

2013-08-21

Thiolated gold nanoclusters form a universe of their own. Researchers in this field are constantly pushing the boundary of this universe by identifying new compositions and in a few "lucky" cases, solving their structures. Such solved structures, even if there are only few, provide important hints for predicting the many identified compositions that are yet to be crystallized or structure determined. Structure prediction is the most pressing issue for a computational chemist in this field. The success of the density functional theory method in gauging the energetic ordering of isomers for thiolated gold clusters has been truly remarkable, but to predict the most stable structure for a given composition remains a great challenge. In this feature article from a computational chemist's point of view, the author shows how one understands and predicts structures for thiolated gold nanoclusters based on his old and new results. To further entertain the reader, the author also offers several "imaginative" structures, claims, and challenges for this field.

Predictive modeling of crystal accumulation in high-level waste glass melters processing radioactive waste

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

Matyáš, Josef; Gervasio, Vivianaluxa; Sannoh, Sulaiman E.

The effectiveness of HLW vitrification is limited by precipitation/accumulation of spinel crystals [(Fe, Ni, Mn, Zn)(Fe, Cr)2O4] in the glass discharge riser of Joule-heated ceramic melters during idling. These crystals do not affect glass durability; however, if accumulated in thick layer, they can clog the melter and prevent discharge of molten glass into canisters. To address this problem, an empirical model was developed that can predict thicknesses of accumulated layers as a function of glass composition. This model predicts well the accumulation of single crystals and/or small-scale agglomerates, but, excessive agglomeration observed in high-Ni-Fe glass resulted in an under-prediction ofmore » accumulated layers, which gradually worsen over time as an increased number of agglomerates formed. Accumulation rate of ~53.8 ± 3.7 µm/h determined for this glass will result in ~26 mm thick layer in 20 days of melter idling.« less

Conservation of hot regions in protein-protein interaction in evolution.

PubMed

Hu, Jing; Li, Jiarui; Chen, Nansheng; Zhang, Xiaolong

2016-11-01

The hot regions of protein-protein interactions refer to the active area which formed by those most important residues to protein combination process. With the research development on protein interactions, lots of predicted hot regions can be discovered efficiently by intelligent computing methods, while performing biology experiments to verify each every prediction is hardly to be done due to the time-cost and the complexity of the experiment. This study based on the research of hot spot residue conservations, the proposed method is used to verify authenticity of predicted hot regions that using machine learning algorithm combined with protein's biological features and sequence conservation, though multiple sequence alignment, module substitute matrix and sequence similarity to create conservation scoring algorithm, and then using threshold module to verify the conservation tendency of hot regions in evolution. This research work gives an effective method to verify predicted hot regions in protein-protein interactions, which also provides a useful way to deeply investigate the functional activities of protein hot regions. Copyright © 2016. Published by Elsevier Inc.

Sharply curved turn around duct flow predictions using spectral partitioning of the turbulent kinetic energy and a pressure modified wall law

NASA Technical Reports Server (NTRS)

Santi, L. Michael

1986-01-01

Computational predictions of turbulent flow in sharply curved 180 degree turn around ducts are presented. The CNS2D computer code is used to solve the equations of motion for two-dimensional incompressible flows transformed to a nonorthogonal body-fitted coordinate system. This procedure incorporates the pressure velocity correction algorithm SIMPLE-C to iteratively solve a discretized form of the transformed equations. A multiple scale turbulence model based on simplified spectral partitioning is employed to obtain closure. Flow field predictions utilizing the multiple scale model are compared to features predicted by the traditional single scale k-epsilon model. Tuning parameter sensitivities of the multiple scale model applied to turn around duct flows are also determined. In addition, a wall function approach based on a wall law suitable for incompressible turbulent boundary layers under strong adverse pressure gradients is tested. Turn around duct flow characteristics utilizing this modified wall law are presented and compared to results based on a standard wall treatment.

Satellite freeze forecast system: Executive summary

NASA Technical Reports Server (NTRS)

Martsolf, J. D. (Principal Investigator)

1983-01-01

A satellite-based temperature monitoring and prediction system consisting of a computer controlled acquisition, processing, and display system and the ten automated weather stations called by that computer was developed and transferred to the national weather service. This satellite freeze forecasting system (SFFS) acquires satellite data from either one of two sources, surface data from 10 sites, displays the observed data in the form of color-coded thermal maps and in tables of automated weather station temperatures, computes predicted thermal maps when requested and displays such maps either automatically or manually, archives the data acquired, and makes comparisons with historical data. Except for the last function, SFFS handles these tasks in a highly automated fashion if the user so directs. The predicted thermal maps are the result of two models, one a physical energy budget of the soil and atmosphere interface and the other a statistical relationship between the sites at which the physical model predicts temperatures and each of the pixels of the satellite thermal map.

Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction

PubMed Central

Hu, Jianfei; Neiswinger, Johnathan; Zhang, Jin; Zhu, Heng; Qian, Jiang

2015-01-01

Scaffold proteins play a crucial role in facilitating signal transduction in eukaryotes by bringing together multiple signaling components. In this study, we performed a systematic analysis of scaffold proteins in signal transduction by integrating protein-protein interaction and kinase-substrate relationship networks. We predicted 212 scaffold proteins that are involved in 605 distinct signaling pathways. The computational prediction was validated using a protein microarray-based approach. The predicted scaffold proteins showed several interesting characteristics, as we expected from the functionality of scaffold proteins. We found that the scaffold proteins are likely to interact with each other, which is consistent with previous finding that scaffold proteins tend to form homodimers and heterodimers. Interestingly, a single scaffold protein can be involved in multiple signaling pathways by interacting with other scaffold protein partners. Furthermore, we propose two possible regulatory mechanisms by which the activity of scaffold proteins is coordinated with their associated pathways through phosphorylation process. PMID:26393507

Dimerization of a flocculent protein from Moringa oleifera: experimental evidence and in silico interpretation.

PubMed

Pavankumar, Asalapuram R; Kayathri, Rajarathinam; Murugan, Natarajan A; Zhang, Qiong; Srivastava, Vaibhav; Okoli, Chuka; Bulone, Vincent; Rajarao, Gunaratna K; Ågren, Hans

2014-01-01

Many proteins exist in dimeric and other oligomeric forms to gain stability and functional advantages. In this study, the dimerization property of a coagulant protein (MO2.1) from Moringa oleifera seeds was addressed through laboratory experiments, protein-protein docking studies and binding free energy calculations. The structure of MO2.1 was predicted by homology modelling, while binding free energy and residues-distance profile analyses provided insight into the energetics and structural factors for dimer formation. Since the coagulation activities of the monomeric and dimeric forms of MO2.1 were comparable, it was concluded that oligomerization does not affect the biological activity of the protein.

Transmembrane helix M6 in sarco(endo)plasmic reticulum Ca(2+)-ATPase forms a functional interaction site with phospholamban. Evidence for physical interactions at other sites.

PubMed

Asahi, M; Kimura, Y; Kurzydlowski, K; Tada, M; MacLennan, D H

1999-11-12

In an earlier study (Kimura, Y., Kurzydlowski, K., Tada, M., and MacLennan, D. H. (1997) J. Biol. Chem. 272, 15061-15064), mutation of amino acids on one face of the phospholamban (PLN) transmembrane helix led to loss of PLN inhibition of sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) molecules. This helical face was proposed to form a site of PLN interaction with a transmembrane helix in SERCA molecules. To determine whether predicted transmembrane helices M4, M5, M6, or M8 in SERCA1a interact with PLN, SERCA1a mutants were co-expressed with wild-type PLN and effects on Ca(2+) dependence of Ca(2+) transport were measured. Wild-type inhibitory interactions shifted apparent Ca(2+) affinity of SERCA1a by an average of -0.34 pCa units, but four of the seven mutations in M4 led to a more inhibitory shift in apparent Ca(2+) affinity, averaging -0.53 pCa units. Seven mutations in M5 led to an average shift of -0.32 pCa units and seven mutations in M8 led to an average shift of -0.30 pCa units. Among 11 mutations in M6, 1, Q791A, increased the inhibitory shift (-0.59 pCa units) and 5, V795A (-0.11), L802A (-0.07), L802V (-0.04), T805A (-0.11), and F809A (-0.12), reduced the inhibitory shift, consistent with the view that Val(795), Leu(802), Thr(805), and Phe(809), located on one face of a predicted M6 helix, form a site in SERCA1a for interaction with PLN. Those mutations in M4, M6, or M8 of SERCA1a that enhanced PLN inhibitory function did not enhance PLN physical association with SERCA1a, but mutants V795A and L802A in M6, which decreased PLN inhibitory function, decreased physical association, as measured by co-immunoprecipitation. In related studies, those PLN mutants that gained inhibitory function also increased levels of co-immunoprecipitation of wild-type SERCA1a and those that lost inhibitory function also reduced association, correlating functional interaction sites with physical interaction sites. Thus, both functional and physical data confirm that PLN interacts with M6 SERCA1a.

Density dependence of the nuclear energy-density functional

NASA Astrophysics Data System (ADS)

Papakonstantinou, Panagiota; Park, Tae-Sun; Lim, Yeunhwan; Hyun, Chang Ho

2018-01-01

Background: The explicit density dependence in the coupling coefficients entering the nonrelativistic nuclear energy-density functional (EDF) is understood to encode effects of three-nucleon forces and dynamical correlations. The necessity for the density-dependent coupling coefficients to assume the form of a preferably small fractional power of the density ρ is empirical and the power is often chosen arbitrarily. Consequently, precision-oriented parametrizations risk overfitting in the regime of saturation and extrapolations in dilute or dense matter may lose predictive power. Purpose: Beginning with the observation that the Fermi momentum kF, i.e., the cubic root of the density, is a key variable in the description of Fermi systems, we first wish to examine if a power hierarchy in a kF expansion can be inferred from the properties of homogeneous matter in a domain of densities, which is relevant for nuclear structure and neutron stars. For subsequent applications we want to determine a functional that is of good quality but not overtrained. Method: For the EDF, we fit systematically polynomial and other functions of ρ1 /3 to existing microscopic, variational calculations of the energy of symmetric and pure neutron matter (pseudodata) and analyze the behavior of the fits. We select a form and a set of parameters, which we found robust, and examine the parameters' naturalness and the quality of resulting extrapolations. Results: A statistical analysis confirms that low-order terms such as ρ1 /3 and ρ2 /3 are the most relevant ones in the nuclear EDF beyond lowest order. It also hints at a different power hierarchy for symmetric vs. pure neutron matter, supporting the need for more than one density-dependent term in nonrelativistic EDFs. The functional we propose easily accommodates known or adopted properties of nuclear matter near saturation. More importantly, upon extrapolation to dilute or asymmetric matter, it reproduces a range of existing microscopic results, to which it has not been fitted. It also predicts a neutron-star mass-radius relation consistent with observations. The coefficients display naturalness. Conclusions: Having been already determined for homogeneous matter, a functional of the present form can be mapped onto extended Skyrme-type functionals in a straightforward manner, as we outline here, for applications to finite nuclei. At the same time, the statistical analysis can be extended to higher orders and for different microscopic (ab initio) calculations with sufficient pseudodata points and for polarized matter.

Quality of Life and Bronchial Hyper-Responsiveness in Subjects With Bronchiectasis: Validation of the Seattle Obstructive Lung Disease Questionnaire in Bronchiectasis.

PubMed

Bulcun, Emel; Arslan, Mesut; Ekici, Aydanur; Ekici, Mehmet

2015-11-01

Bronchiectasis can adversely affect quality of life. However, the tests examining quality of life in bronchiectasis are not sufficient. We examined the validity of a measure designed for COPD, the Seattle Obstructive Lung Disease Questionnaire (SOLQ), in bronchiectasis. In addition, we aimed to compare the quality of life of subjects with bronchiectasis and bronchial hyper-responsiveness with that of those without to identify the effective factors. We studied 78 subjects with clinically stable bronchiectasis and 41 healthy controls matched for age and sex. Subjects were assessed by the SOLQ. A detailed history, physical examination, the Medical Outcomes Study 36-Item Short Form questionnaire, the Hospital Anxiety and Depression Scale, and spirometric measurements were obtained. Cronbach α coefficients, which reflected internal consistency, were >0.70 for all SOLQ components except for treatment satisfaction. SOLQ component scores correlated with all of the component scores of the Medical Outcomes Study 36-Item Short Form questionnaire and the Hospital Anxiety and Depression Scale, confirming their concurrent validity. All SOLQ scores correlated positively with percent-of-predicted FEV1, whereas the physical function, treatment satisfaction, and emotional function correlated negatively with the exacerbation frequency in Pearson analysis. Emotional and physical functions were positively associated with percent-of-predicted FEV1 in linear regression analysis. Compared with subjects without bronchial hyper-responsiveness, those with bronchial hyper-responsiveness had lower FEV1/FVC and more exacerbations/y. Compared with bronchiectasis subjects without bronchial hyper-responsiveness, those with bronchial hyper-responsiveness had significantly lower SOLQ, physical function, and coping skills scores but not emotional function and treatment satisfaction. The SOLQ is a valid instrument for determining quality of life in subjects with bronchiectasis. Subjects with bronchiectasis and bronchial hyper-responsiveness had a poorer quality of life, lower baseline spirometric values, and more frequent exacerbations, suggesting more severe disease. Copyright © 2015 by Daedalus Enterprises.

Complement Factor B Mutations in Atypical Hemolytic Uremic Syndrome—Disease-Relevant or Benign?

PubMed Central

Marinozzi, Maria Chiara; Vergoz, Laura; Rybkine, Tania; Ngo, Stephanie; Bettoni, Serena; Pashov, Anastas; Cayla, Mathieu; Tabarin, Fanny; Jablonski, Mathieu; Hue, Christophe; Smith, Richard J.; Noris, Marina; Halbwachs-Mecarelli, Lise; Donadelli, Roberta; Fremeaux-Bacchi, Veronique

2014-01-01

Atypical hemolytic uremic syndrome (aHUS) is a genetic ultrarare renal disease associated with overactivation of the alternative pathway of complement. Four gain-of-function mutations that form a hyperactive or deregulated C3 convertase have been identified in Factor B (FB) ligand binding sites. Here, we studied the functional consequences of 10 FB genetic changes recently identified from different aHUS cohorts. Using several tests for alternative C3 and C5 convertase formation and regulation, we identified two gain-of-function and potentially disease-relevant mutations that formed either an overactive convertase (M433I) or a convertase resistant to decay by FH (K298Q). One mutation (R178Q) produced a partially cleaved protein with no ligand binding or functional activity. Seven genetic changes led to near-normal or only slightly reduced ligand binding and functional activity compared with the most common polymorphism at position 7, R7. Notably, none of the algorithms used to predict the disease relevance of FB mutations agreed completely with the experimental data, suggesting that in silico approaches should be undertaken with caution. These data, combined with previously published results, suggest that 9 of 15 FB genetic changes identified in patients with aHUS are unrelated to disease pathogenesis. This study highlights that functional assessment of identified nucleotide changes in FB is mandatory to confirm disease association. PMID:24652797

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations

PubMed Central

Esteve-Altava, Borja; Rasskin-Gutman, Diego

2014-01-01

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non-facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton. PMID:24975579

Analytical steady-state solutions for water-limited cropping systems using saline irrigation water

NASA Astrophysics Data System (ADS)

Skaggs, T. H.; Anderson, R. G.; Corwin, D. L.; Suarez, D. L.

2014-12-01

Due to the diminishing availability of good quality water for irrigation, it is increasingly important that irrigation and salinity management tools be able to target submaximal crop yields and support the use of marginal quality waters. In this work, we present a steady-state irrigated systems modeling framework that accounts for reduced plant water uptake due to root zone salinity. Two explicit, closed-form analytical solutions for the root zone solute concentration profile are obtained, corresponding to two alternative functional forms of the uptake reduction function. The solutions express a general relationship between irrigation water salinity, irrigation rate, crop salt tolerance, crop transpiration, and (using standard approximations) crop yield. Example applications are illustrated, including the calculation of irrigation requirements for obtaining targeted submaximal yields, and the generation of crop-water production functions for varying irrigation waters, irrigation rates, and crops. Model predictions are shown to be mostly consistent with existing models and available experimental data. Yet the new solutions possess advantages over available alternatives, including: (i) the solutions were derived from a complete physical-mathematical description of the system, rather than based on an ad hoc formulation; (ii) the analytical solutions are explicit and can be evaluated without iterative techniques; (iii) the solutions permit consideration of two common functional forms of salinity induced reductions in crop water uptake, rather than being tied to one particular representation; and (iv) the utilized modeling framework is compatible with leading transient-state numerical models.

Brain Network Modularity Predicts Exercise-Related Executive Function Gains in Older Adults

PubMed Central

Baniqued, Pauline L.; Gallen, Courtney L.; Voss, Michelle W.; Burzynska, Agnieszka Z.; Wong, Chelsea N.; Cooke, Gillian E.; Duffy, Kristin; Fanning, Jason; Ehlers, Diane K.; Salerno, Elizabeth A.; Aguiñaga, Susan; McAuley, Edward; Kramer, Arthur F.; D'Esposito, Mark

2018-01-01

Recent work suggests that the brain can be conceptualized as a network comprised of groups of sub-networks or modules. The extent of segregation between modules can be quantified with a modularity metric, where networks with high modularity have dense connections within modules and sparser connections between modules. Previous work has shown that higher modularity predicts greater improvements after cognitive training in patients with traumatic brain injury and in healthy older and young adults. It is not known, however, whether modularity can also predict cognitive gains after a physical exercise intervention. Here, we quantified modularity in older adults (N = 128, mean age = 64.74) who underwent one of the following interventions for 6 months (NCT01472744 on ClinicalTrials.gov): (1) aerobic exercise in the form of brisk walking (Walk), (2) aerobic exercise in the form of brisk walking plus nutritional supplement (Walk+), (3) stretching, strengthening and stability (SSS), or (4) dance instruction. After the intervention, the Walk, Walk+ and SSS groups showed gains in cardiorespiratory fitness (CRF), with larger effects in both walking groups compared to the SSS and Dance groups. The Walk, Walk+ and SSS groups also improved in executive function (EF) as measured by reasoning, working memory, and task-switching tests. In the Walk, Walk+, and SSS groups that improved in EF, higher baseline modularity was positively related to EF gains, even after controlling for age, in-scanner motion and baseline EF. No relationship between modularity and EF gains was observed in the Dance group, which did not show training-related gains in CRF or EF control. These results are consistent with previous studies demonstrating that individuals with a more modular brain network organization are more responsive to cognitive training. These findings suggest that the predictive power of modularity may be generalizable across interventions aimed to enhance aspects of cognition and that, especially in low-performing individuals, global network properties can capture individual differences in neuroplasticity. PMID:29354050

Lumbar Muscle Cross-Sectional Areas Do Not Predict Clinical Outcomes in Adults With Spinal Stenosis: A Longitudinal Study.

PubMed

Gellhorn, Alfred C; Suri, Pradeep; Rundell, Sean D; Olafsen, Nathan; Carlson, M Jake; Johnson, Steve; Fry, Adrielle; Annaswamy, Thiru M; Gilligan, Christopher; Comstock, Bryan; Heagerty, Patrick; Friedly, Janna; Jarvik, Jeffrey G

2017-06-01

Minimal longitudinal data exist regarding the role of lumbar musculature in predicting back pain and function. In cross-sectional study designs, there is often atrophy of the segmental multifidus muscle in subjects with low back pain compared with matched controls. However, the cross-sectional design of these studies prevents drawing conclusions regarding whether lumbar muscle characteristics predict or modify future back pain or function. The primary objective of this study is to determine whether the cross-sectional area (CSA) of lumbar muscles predict functional status or back pain at 6- or 12-month follow-up in older adults with spinal degeneration. The secondary objective is to evaluate whether these muscle characteristics improve outcome prediction above and beyond the prognostic information conferred by demographic and psychosocial variables. Secondary analysis of a randomized controlled trial. A total of 209 adults aged 50 years and older with clinical and radiographic spinal stenosis from the Lumbar Epidural steroid injection for Spinal Stenosis (LESS) trial. Using baseline magnetic resonance images, we calculated CSAs of the lumbar multifidus, psoas, and quadratus lumborum muscles using a standardized protocol by manually tracing the borders of each of the muscles. The relationship between lumbar muscle CSAs and baseline measures was assessed with Pearson or Spearman correlation coefficients. The relationship between lumbar muscle characteristics and 6- and 12-month Roland Morris Disability Questionnaire (RDQ) and back pain Numeric Rating Scale (NRS) responses was further evaluated with multivariate linear regression. A hierarchical approach to the regression was performed: a basic model with factors of conceptual importance including age, gender, BMI, and baseline RDQ score formed the first step. The second and third steps evaluated whether psychosocial variables or muscle measures conferred additional prognostic information to the basic model. Function as measured by the RDQ and back pain as measured by the NRS at 6- and 12-month follow-up. Lumbar muscle CSA was not a significant predictor of 6- or 12-month RDQ or pain score in multivariate analyses. Cross-sectional areas of lumbar muscles do not predict function or pain at medium- and long-term follow-up in adults with lumbar spinal stenosis. III. Copyright © 2017 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

FGF and TGFβ signaling link form and function during jaw development and evolution.

PubMed

Woronowicz, Katherine C; Gline, Stephanie E; Herfat, Safa T; Fields, Aaron J; Schneider, Richard A

2018-05-16

How does form arise during development and change during evolution? How does form relate to function, and what enables embryonic structures to presage their later use in adults? To address these questions, we leverage the distinct functional morphology of the jaw in duck, chick, and quail. In connection with their specialized mode of feeding, duck develop a secondary cartilage at the tendon insertion of their jaw adductor muscle on the mandible. An equivalent cartilage is absent in chick and quail. We hypothesize that species-specific jaw architecture and mechanical forces promote secondary cartilage in duck through the differential regulation of FGF and TGFβ signaling. First, we perform transplants between chick and duck embryos and demonstrate that the ability of neural crest mesenchyme (NCM) to direct the species-specific insertion of muscle and the formation of secondary cartilage depends upon the amount and spatial distribution of NCM-derived connective tissues. Second, we quantify motility and build finite element models of the jaw complex in duck and quail, which reveals a link between species-specific jaw architecture and the predicted mechanical force environment. Third, we investigate the extent to which mechanical load mediates FGF and TGFβ signaling in the duck jaw adductor insertion, and discover that both pathways are mechano-responsive and required for secondary cartilage formation. Additionally, we find that FGF and TGFβ signaling can also induce secondary cartilage in the absence of mechanical force or in the adductor insertion of quail embryos. Thus, our results provide novel insights on molecular, cellular, and biomechanical mechanisms that couple musculoskeletal form and function during development and evolution. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Prediction of HR/BP response to the spontaneous breathing trial by fluctuation dissipation theory

NASA Astrophysics Data System (ADS)

Chen, Man

2014-03-01

We applied the non-equilibrium fluctuation dissipation theorem to predict how critically-ill patients respond to treatment, based on both heart rate data and blood pressure data collected by standard hospital monitoring devices. The non-equilibrium fluctuation dissipation theorem relates the response of a system to a perturbation to the fluctuations in the stationary state of the system. It is shown that the response of patients to a standard procedure performed on patients, the spontaneous breathing trial (SBT), can be predicted by the non-equilibrium fluctuation dissipation approach. We classify patients into different groups according to the patients' characteristics. For each patient group, we extend the fluctuation dissipation theorem to predict interactions between blood pressure and beat-to-beat dynamics of heart rate in response to a perturbation (SBT), We also extract the form of the perturbation function directly from the physiological data, which may help to reduce the prediction error. We note this method is not limited to the analysis of the heart rate dynamics, but also can be applied to analyze the response of other physiological signals to other clinical interventions.

Enhancing membrane protein subcellular localization prediction by parallel fusion of multi-view features.

PubMed

Yu, Dongjun; Wu, Xiaowei; Shen, Hongbin; Yang, Jian; Tang, Zhenmin; Qi, Yong; Yang, Jingyu

2012-12-01

Membrane proteins are encoded by ~ 30% in the genome and function importantly in the living organisms. Previous studies have revealed that membrane proteins' structures and functions show obvious cell organelle-specific properties. Hence, it is highly desired to predict membrane protein's subcellular location from the primary sequence considering the extreme difficulties of membrane protein wet-lab studies. Although many models have been developed for predicting protein subcellular locations, only a few are specific to membrane proteins. Existing prediction approaches were constructed based on statistical machine learning algorithms with serial combination of multi-view features, i.e., different feature vectors are simply serially combined to form a super feature vector. However, such simple combination of features will simultaneously increase the information redundancy that could, in turn, deteriorate the final prediction accuracy. That's why it was often found that prediction success rates in the serial super space were even lower than those in a single-view space. The purpose of this paper is investigation of a proper method for fusing multiple multi-view protein sequential features for subcellular location predictions. Instead of serial strategy, we propose a novel parallel framework for fusing multiple membrane protein multi-view attributes that will represent protein samples in complex spaces. We also proposed generalized principle component analysis (GPCA) for feature reduction purpose in the complex geometry. All the experimental results through different machine learning algorithms on benchmark membrane protein subcellular localization datasets demonstrate that the newly proposed parallel strategy outperforms the traditional serial approach. We also demonstrate the efficacy of the parallel strategy on a soluble protein subcellular localization dataset indicating the parallel technique is flexible to suite for other computational biology problems. The software and datasets are available at: http://www.csbio.sjtu.edu.cn/bioinf/mpsp.

Automated diagnoses of attention deficit hyperactive disorder using magnetic resonance imaging.

PubMed

Eloyan, Ani; Muschelli, John; Nebel, Mary Beth; Liu, Han; Han, Fang; Zhao, Tuo; Barber, Anita D; Joel, Suresh; Pekar, James J; Mostofsky, Stewart H; Caffo, Brian

2012-01-01

Successful automated diagnoses of attention deficit hyperactive disorder (ADHD) using imaging and functional biomarkers would have fundamental consequences on the public health impact of the disease. In this work, we show results on the predictability of ADHD using imaging biomarkers and discuss the scientific and diagnostic impacts of the research. We created a prediction model using the landmark ADHD 200 data set focusing on resting state functional connectivity (rs-fc) and structural brain imaging. We predicted ADHD status and subtype, obtained by behavioral examination, using imaging data, intelligence quotients and other covariates. The novel contributions of this manuscript include a thorough exploration of prediction and image feature extraction methodology on this form of data, including the use of singular value decompositions (SVDs), CUR decompositions, random forest, gradient boosting, bagging, voxel-based morphometry, and support vector machines as well as important insights into the value, and potentially lack thereof, of imaging biomarkers of disease. The key results include the CUR-based decomposition of the rs-fc-fMRI along with gradient boosting and the prediction algorithm based on a motor network parcellation and random forest algorithm. We conjecture that the CUR decomposition is largely diagnosing common population directions of head motion. Of note, a byproduct of this research is a potential automated method for detecting subtle in-scanner motion. The final prediction algorithm, a weighted combination of several algorithms, had an external test set specificity of 94% with sensitivity of 21%. The most promising imaging biomarker was a correlation graph from a motor network parcellation. In summary, we have undertaken a large-scale statistical exploratory prediction exercise on the unique ADHD 200 data set. The exercise produced several potential leads for future scientific exploration of the neurological basis of ADHD.

Automated diagnoses of attention deficit hyperactive disorder using magnetic resonance imaging

PubMed Central

Eloyan, Ani; Muschelli, John; Nebel, Mary Beth; Liu, Han; Han, Fang; Zhao, Tuo; Barber, Anita D.; Joel, Suresh; Pekar, James J.; Mostofsky, Stewart H.; Caffo, Brian

2012-01-01

Successful automated diagnoses of attention deficit hyperactive disorder (ADHD) using imaging and functional biomarkers would have fundamental consequences on the public health impact of the disease. In this work, we show results on the predictability of ADHD using imaging biomarkers and discuss the scientific and diagnostic impacts of the research. We created a prediction model using the landmark ADHD 200 data set focusing on resting state functional connectivity (rs-fc) and structural brain imaging. We predicted ADHD status and subtype, obtained by behavioral examination, using imaging data, intelligence quotients and other covariates. The novel contributions of this manuscript include a thorough exploration of prediction and image feature extraction methodology on this form of data, including the use of singular value decompositions (SVDs), CUR decompositions, random forest, gradient boosting, bagging, voxel-based morphometry, and support vector machines as well as important insights into the value, and potentially lack thereof, of imaging biomarkers of disease. The key results include the CUR-based decomposition of the rs-fc-fMRI along with gradient boosting and the prediction algorithm based on a motor network parcellation and random forest algorithm. We conjecture that the CUR decomposition is largely diagnosing common population directions of head motion. Of note, a byproduct of this research is a potential automated method for detecting subtle in-scanner motion. The final prediction algorithm, a weighted combination of several algorithms, had an external test set specificity of 94% with sensitivity of 21%. The most promising imaging biomarker was a correlation graph from a motor network parcellation. In summary, we have undertaken a large-scale statistical exploratory prediction exercise on the unique ADHD 200 data set. The exercise produced several potential leads for future scientific exploration of the neurological basis of ADHD. PMID:22969709

Predicting complex traits using a diffusion kernel on genetic markers with an application to dairy cattle and wheat data

PubMed Central

2013-01-01

Background Arguably, genotypes and phenotypes may be linked in functional forms that are not well addressed by the linear additive models that are standard in quantitative genetics. Therefore, developing statistical learning models for predicting phenotypic values from all available molecular information that are capable of capturing complex genetic network architectures is of great importance. Bayesian kernel ridge regression is a non-parametric prediction model proposed for this purpose. Its essence is to create a spatial distance-based relationship matrix called a kernel. Although the set of all single nucleotide polymorphism genotype configurations on which a model is built is finite, past research has mainly used a Gaussian kernel. Results We sought to investigate the performance of a diffusion kernel, which was specifically developed to model discrete marker inputs, using Holstein cattle and wheat data. This kernel can be viewed as a discretization of the Gaussian kernel. The predictive ability of the diffusion kernel was similar to that of non-spatial distance-based additive genomic relationship kernels in the Holstein data, but outperformed the latter in the wheat data. However, the difference in performance between the diffusion and Gaussian kernels was negligible. Conclusions It is concluded that the ability of a diffusion kernel to capture the total genetic variance is not better than that of a Gaussian kernel, at least for these data. Although the diffusion kernel as a choice of basis function may have potential for use in whole-genome prediction, our results imply that embedding genetic markers into a non-Euclidean metric space has very small impact on prediction. Our results suggest that use of the black box Gaussian kernel is justified, given its connection to the diffusion kernel and its similar predictive performance. PMID:23763755

Dielectric and Radiative Properties of Sea Foam at Microwave Frequencies: Conceptual Understanding of Foam Emissivity

DTIC Science & Technology

2012-04-27

papers. Anguelova [ 24 ] analyzed the available information to determine suitable formula to predict the complex permittivity of sea foam εf. Anguelova...active whitecaps. Whitecaps in their decaying phase are thinner and dimmer and are referred to as residual whitecaps. Anguelova [ 24 ] gives an extended...considered [ 24 ]. It was shown that various functional forms could represent the shape of the void fraction profile in the foam depth [25]. A review of

Photonics of 2D gold nanolayers on sapphire surface

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

Muslimov, A. E., E-mail: amuslimov@mail.ru; Butashin, A. V.; Nabatov, B. V.

Gold layers with thicknesses of up to several nanometers, including ordered and disordered 2D nanostructures of gold particles, have been formed on sapphire substrates; their morphology is described; and optical investigations are carried out. The possibility of increasing the accuracy of predicting the optical properties of gold layers and 2D nanostructures using quantum-mechanical models based on functional density theory calculation techniques is considered. The application potential of the obtained materials in photonics is estimated.

Method to Predict Tempering of Steels Under Non-isothermal Conditions

NASA Astrophysics Data System (ADS)

Poirier, D. R.; Kohli, A.

2017-05-01

A common way of representing the tempering responses of steels is with a "tempering parameter" that includes the effect of temperature and time on hardness after hardening. Such functions, usually in graphical form, are available for many steels and have been applied for isothermal tempering. In this article, we demonstrate that the method can be extended to non-isothermal conditions. Controlled heating experiments were done on three grades in order to verify the method.

Antihydrogen from positronium impact with cold antiprotons: a Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cassidy, D. B.; Merrison, J. P.; Charlton, M.; Mitroy, J.; Ryzhikh, G.

1999-04-01

A Monte Carlo simulation of the reaction to form antihydrogen by positronium impact upon antiprotons has been undertaken. Total and differential cross sections have been utilized as inputs to the simulation which models the conditions foreseen in planned antihydrogen formation experiments using positrons and antiprotons held in Penning traps. Thus, predictions of antihydrogen production rates, angular distributions and the variation of the mean antihydrogen temperature as a function of incident positronium kinetic energy have been produced.

Fold Prediction of VP24 Protein of Ebola and Marburg Viruses using de novo Fragment Assembly

DTIC Science & Technology

2009-05-15

Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M., 1998. All-atom empirical potential for molecular modeling and dynamics studies of...aqueous forms that may be related to its role as a matrix protein. Specifically, the molecular weight of VP24 oligomers was determined using differ...dielectric electrostatic function. Next, the PARAM22 plus generalized Born molecular volume solvation (GBMV2) (Lee et al., 2003) energy (including a 15

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

Kittell, David Erik; Yarrington, Cole Davis

Here, a physically-based form of the Mie–Grüneisen equation of state (EOS) is derived for calculating 1d planar shock temperatures, as well as hot spot temperature distributions from heterogeneous impact simulations. This form utilises a multi-term Einstein oscillator model for specific heat, and is completely algebraic in terms of temperature, volume, an integrating factor, and the cold curve energy. Moreover, any empirical relation for the reference pressure and energy may be substituted into the equations via the use of a generalised reference function. The complete EOS is then applied to calculations of the Hugoniot temperature and simulation of hydrodynamic pore collapsemore » using data for the secondary explosive, hexanitrostilbene (HNS). From these results, it is shown that the choice of EOS is even more significant for determining hot spot temperature distributions than planar shock states. The complete EOS is also compared to an alternative derivation assuming that specific heat is a function of temperature alone, i.e. cv(T). Temperature discrepancies on the order of 100–600 K were observed corresponding to the shock pressures required to initiate HNS (near 10 GPa). Overall, the results of this work will improve confidence in temperature predictions. By adopting this EOS, future work may be able to assign physical meaning to other thermally sensitive constitutive model parameters necessary to predict the shock initiation and detonation of heterogeneous explosives.« less

A Model of Reduced Kinetics for Alkane Oxidation Using Constituents and Species for N-Heptane

NASA Technical Reports Server (NTRS)

Harstad, Kenneth G.; Bellan, Josette

2011-01-01

The reduction of elementary or skeletal oxidation kinetics to a subgroup of tractable reactions for inclusion in turbulent combustion codes has been the subject of numerous studies. The skeletal mechanism is obtained from the elementary mechanism by removing from it reactions that are considered negligible for the intent of the specific study considered. As of now, there are many chemical reduction methodologies. A methodology for deriving a reduced kinetic mechanism for alkane oxidation is described and applied to n-heptane. The model is based on partitioning the species of the skeletal kinetic mechanism into lights, defined as those having a carbon number smaller than 3, and heavies, which are the complement of the species ensemble. For modeling purposes, the heavy species are mathematically decomposed into constituents, which are similar but not identical to groups in the group additivity theory. From analysis of the LLNL (Lawrence Livermore National Laboratory) skeletal mechanism in conjunction with CHEMKIN II, it is shown that a similarity variable can be formed such that the appropriately non-dimensionalized global constituent molar density exhibits a self-similar behavior over a very wide range of equivalence ratios, initial pressures and initial temperatures that is of interest for predicting n-heptane oxidation. Furthermore, the oxygen and water molar densities are shown to display a quasi-linear behavior with respect to the similarity variable. The light species ensemble is partitioned into quasi-steady and unsteady species. The reduced model is based on concepts consistent with those of Large Eddy Simulation (LES) in which functional forms are used to replace the small scales eliminated through filtering of the governing equations; in LES, these small scales are unimportant as far as the overwhelming part of dynamic energy is concerned. Here, the scales thought unimportant for recovering the thermodynamic energy are removed. The concept is tested by using tabular information from the LLNL skeletal mechanism in conjunction with CHEMKIN II utilized as surrogate ideal functions replacing the necessary functional forms. The test reveals that the similarity concept is indeed justified and that the combustion temperature is well predicted, but that the ignition time is over-predicted, a fact traced to neglecting a detailed description of the processes leading to the heavies chemical decomposition. To palliate this deficiency, functional modeling is incorporated into this conceptual reduction in addition to the modeling the evolution of the global constituent molar density, the enthalpy evolution of the heavies, the contribution to the reaction rate of the unsteady lights from other light species and from the heavies, the molar density evolution of oxygen and water, and the mole fractions of the quasisteady light species. The model is compact in that there are only nine species-related progress variables. Results are presented showing the performance of the model for predicting the temperature and species evolution. The model reproduces the ignition time over a wide range of equivalence ratios, initial pressure, and initial temperature.

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

PubMed Central

Diament, Alon; Tuller, Tamir

2015-01-01

The study of the 3D architecture of chromosomes has been advancing rapidly in recent years. While a number of methods for 3D reconstruction of genomic models based on Hi-C data were proposed, most of the analyses in the field have been performed on different 3D representation forms (such as graphs). Here, we reproduce most of the previous results on the 3D genomic organization of the eukaryote Saccharomyces cerevisiae using analysis of 3D reconstructions. We show that many of these results can be reproduced in sparse reconstructions, generated from a small fraction of the experimental data (5% of the data), and study the properties of such models. Finally, we propose for the first time a novel approach for improving the accuracy of 3D reconstructions by introducing additional predicted physical interactions to the model, based on orthologous interactions in an evolutionary-related organism and based on predicted functional interactions between genes. We demonstrate that this approach indeed leads to the reconstruction of improved models. PMID:26000633

Time-dependent Fracture Behaviour of Polyampholyte Hydrogels

NASA Astrophysics Data System (ADS)

Sun, Tao Lin; Luo, Feng; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

Recently, we report that polyampholytes, polymers bearing randomly dispersed cationic and anionic repeat groups, form tough and self-healing hydrogels with excellent multiple mechanical functions. The randomness makes ionic bonds with a wide distribution of strength, via inter and intra chain complexation. As the breaking and reforming of ionic bonds are time dependent, the hydrogels exhibit rate dependent mechanical behaviour. We systematically studied the tearing energy by tearing test with various tearing velocity under different temperature, and the linear viscoelastic behaviour over a wide range of frequency and temperature. Results have shown that the tearing energy markedly increase with the crack velocity and decrease with the measured temperature. In accordance with the prediction of Williams, Landel, and Ferry (WLF) rate-temperature equivalence, a master curve of tearing energy dependence of crack velocity can be well constructed using the same shift factor from the linear viscoelastic data. The scaling relation of tearing energy as a function of crack velocity can be predicted well by the rheological data according to the developed linear fracture mechanics.

Visual Functioning and Health-related Quality-of-Life are Compromised in Patients with Uveitis.

PubMed

Hui, Michelle M; Wakefield, Denis; Patel, Ilesh; Cvejic, Erin; McCluskey, Peter J; Chang, John H

2017-08-01

To assess the vision-related (VR) and health-related (HR) quality-of-life (QoL) of patients with uveitis. In total, 60 patients with uveitis, 81 patients with diabetic retinopathy (DR), and 70 healthy subjects completed the National Eye Institute Visual Functioning Questionnaire and the Medical Outcome Study 36-Item Short Form. Patients with uveitis reported lower HR- and VR-QoL than healthy subjects (p<0.05) and lower VR-QoL (p<0.001) than patients with DR. For patients with uveitis, multiple linear regression analyses indicated that lower HR-QoL scores were predicted by younger age (p<0.01), while lower VR-QoL scores were predicted by poorer visual acuity (p<0.001), ocular comorbidities (p<0.05), and female sex (p<0.05). Patients with uveitis have significantly poorer VR- and HR-QoL than healthy control subjects. Uveitis has a more debilitating impact on VR-QoL than DR.

Redefining plant functional types for forests based on plant traits

NASA Astrophysics Data System (ADS)

Wei, L.; Xu, C.; Christoffersen, B. O.; McDowell, N. G.; Zhou, H.

2016-12-01

Our ability to predict forest mortality is limited by the simple plant functional types (PFTs) in current generations of Earth System models (ESMs). For example, forests were formerly separated into PFTs only based on leaf form and phenology across different regions (arctic, temperate, and tropic areas) in the Community Earth System Model (CESM). This definition of PFTs ignored the large variation in vulnerability of species to drought and shade tolerance within each PFT. We redefined the PFTs for global forests based on plant traits including phenology, wood density, leaf mass per area, xylem-specific conductivity, and xylem pressure at 50% loss of conductivity. Species with similar survival strategies were grouped into the same PFT. New PFTs highlighted variation in vulnerability and physiological adaptation to drought and shade. New PFTs were better clustered than old ones in the two-dimensional plane of the first two principle components in a principle component analysis. We expect that the new PFTs will strengthen ESMs' ability on predicting drought-induced mortality in the future.

Prediction of the electronic structures, thermodynamic and mechanical properties in manganese doped magnesium-based alloys and their saturated hydrides based on density functional theory

NASA Astrophysics Data System (ADS)

Zhang, Ziying; Zhang, Huizhen; Zhao, Hui; Yu, Zhishui; He, Liang; Li, Jin

2015-04-01

The crystal structures, electronic structures, thermodynamic and mechanical properties of Mg2Ni alloy and its saturated hydride with different Mn-doping contents are investigated using first-principles density functional theory. The lattice parameters for the Mn-doped Mg2Ni alloys and their saturated hydrides decreased with an increasing Mn-doping content because of the smaller atomic size of Mn compared with that of Mg. Analysis of the formation enthalpies and electronic structures reveal that the partial substitution of Mg with Mn reduces the stability of Mg2Ni alloy and its saturated hydride. The calculated elastic constants indicate that, although the partial substitution of Mg with Mn lowers the toughness of the hexagonal Mg2Ni alloy, the charge/discharge cycles are elevated when the Mn-doping content is high enough to form the predicted intermetallic compound Mg3MnNi2.

Glass shell manufacturing in space

NASA Technical Reports Server (NTRS)

Downs, R. L.; Ebner, M. A.; Nolen, R. L., Jr.

1981-01-01

Highly-uniform, hollow glass spheres (shells), which are used for inertial confinement fusion targets, were formed from metal-organic gel powder feedstock in a vertical furnace. As a result of the rapid pyrolysis caused by the furnace, the gel is transformed to a shell in five distinct stages: (a) surface closure of the porous gel; (b) generation of a closed-cell foam structure in the gel; (c) spheridization of the gel and further expansion of the foam; (d) coalescence of the closed-cell foam to a single-void shell; and (e) fining of the glass shell. The heat transfer from the furnace to the falling gel particle was modeled to determine the effective heating rate of the gel. The model predicts the temperature history for a particle as a function of mass, dimensions, specific heat, and absorptance as well as furnace temperature profile and thermal conductivity of the furnace gas. A model was developed that predicts the gravity-induced degradation of shell concentricity in falling molten shells as a function of shell characteristics and time.

Structure Shapes Dynamics and Directionality in Diverse Brain Networks: Mathematical Principles and Empirical Confirmation in Three Species

NASA Astrophysics Data System (ADS)

Moon, Joon-Young; Kim, Junhyeok; Ko, Tae-Wook; Kim, Minkyung; Iturria-Medina, Yasser; Choi, Jee-Hyun; Lee, Joseph; Mashour, George A.; Lee, Uncheol

2017-04-01

Identifying how spatially distributed information becomes integrated in the brain is essential to understanding higher cognitive functions. Previous computational and empirical studies suggest a significant influence of brain network structure on brain network function. However, there have been few analytical approaches to explain the role of network structure in shaping regional activities and directionality patterns. In this study, analytical methods are applied to a coupled oscillator model implemented in inhomogeneous networks. We first derive a mathematical principle that explains the emergence of directionality from the underlying brain network structure. We then apply the analytical methods to the anatomical brain networks of human, macaque, and mouse, successfully predicting simulation and empirical electroencephalographic data. The results demonstrate that the global directionality patterns in resting state brain networks can be predicted solely by their unique network structures. This study forms a foundation for a more comprehensive understanding of how neural information is directed and integrated in complex brain networks.

Modelling the spreading rate of controlled communicable epidemics through an entropy-based thermodynamic model

NASA Astrophysics Data System (ADS)

Wang, WenBin; Wu, ZiNiu; Wang, ChunFeng; Hu, RuiFeng

2013-11-01

A model based on a thermodynamic approach is proposed for predicting the dynamics of communicable epidemics assumed to be governed by controlling efforts of multiple scales so that an entropy is associated with the system. All the epidemic details are factored into a single and time-dependent coefficient, the functional form of this coefficient is found through four constraints, including notably the existence of an inflexion point and a maximum. The model is solved to give a log-normal distribution for the spread rate, for which a Shannon entropy can be defined. The only parameter, that characterizes the width of the distribution function, is uniquely determined through maximizing the rate of entropy production. This entropy-based thermodynamic (EBT) model predicts the number of hospitalized cases with a reasonable accuracy for SARS in the year 2003. This EBT model can be of use for potential epidemics such as avian influenza and H7N9 in China.

Relationship-contingent self-esteem and the ups and downs of romantic relationships.

PubMed

Knee, C Raymond; Canevello, Amy; Bush, Amber L; Cook, Astrid

2008-09-01

Relationship-contingent self-esteem (RCSE) emerges from perspectives on authenticity, need fulfillment, and relationship functioning and is an unhealthy form of self-esteem that depends on one's relationship. Four studies provided evidence of convergent, discriminant, incremental, and predictive validity for RCSE. Study 1 tested associations between RCSE and several conceptually related and unrelated constructs in multiple samples. In Study 2, the authors employed an event-contingent diary procedure to examine reports of self-esteem as a function of everyday relationship events. The association between event valence and changes in self-esteem became stronger with RCSE, and this interaction remained controlling for several parallel interactions by other constructs. Study 3 employed an interval-contingent diary procedure and found support for a mediation model in which the moderating role of RCSE largely occurred through momentary emotions, which in turn predicted momentary self-esteem. Study 4 sampled couples and found that partners who were both higher in RCSE felt more committed but not more satisfied or close.

Troublesome toxins: Time to re-think plant-herbivore interactions in vertebrate ecology

USGS Publications Warehouse

Swihart, R.K.; DeAngelis, D.L.; Feng, Z.; Bryant, J.P.

2009-01-01

Earlier models of plant-herbivore interactions relied on forms of functional response that related rates of ingestion by herbivores to mechanical or physical attributes such as bite size and rate. These models fail to predict a growing number of findings that implicate chemical toxins as important determinants of plant-herbivore dynamics. Specifically, considerable evidence suggests that toxins set upper limits on food intake for many species of herbivorous vertebrates. Herbivores feeding on toxin-containing plants must avoid saturating their detoxification systems, which often occurs before ingestion rates are limited by mechanical handling of food items. In light of the importance of plant toxins, a new approach is needed to link herbivores to their food base. We discuss necessary features of such an approach, note recent advances in herbivore functional response models that incorporate effects of plant toxins, and mention predictions that are consistent with observations in natural systems. Future ecological studies will need to address explicitly the importance of plant toxins in shaping plant and herbivore communities.

Infant Hand Preference and the Development of Cognitive Abilities

PubMed Central

Michel, George F.; Campbell, Julie M.; Marcinowski, Emily C.; Nelson, Eliza L.; Babik, Iryna

2016-01-01

Hand preference develops in the first two postnatal years with nearly half of infants exhibiting a consistent early preference for acquiring objects. Others exhibit a more variable developmental trajectory but by the end of their second postnatal year, most exhibit a consistent hand preference for role-differentiated bimanual manipulation. According to some forms of embodiment theory, these differences in hand use patterns should influence the way children interact with their environments, which, in turn, should affect the structure and function of brain development. Such early differences in brain development should result in different trajectories of psychological development. We present evidence that children with consistent early hand preferences exhibit advanced patterns of cognitive development as compared to children who develop a hand preference later. Differences in the developmental trajectory of hand preference are predictive of developmental differences in language, object management skills, and tool-use skills. As predicted by Casasanto’s body-specificity hypothesis, infants with different hand preferences proceed along different developmental pathways of cognitive functioning. PMID:27047431

Computational discovery of small open reading frames in Bacillus lehensis

NASA Astrophysics Data System (ADS)

Zainuddin, Nurhafizhoh; Illias, Rosli Md.; Mahadi, Nor Muhammad; Firdaus-Raih, Mohd

2015-09-01

Bacillus lehensis is a Gram-positive and endospore-forming alkalitolerant bacterial strain. In recent years there has been increasing interest in alkaliphilic bacteria and their ability to grow under extreme conditions as well as their ability to serve various important functions in industrial biology especially enzyme production. Small open reading frames (sORFs) have emerged as important regulators in various biological roles such as tumor progression, hormone signalling and stress response. Over the past decade, many biocomputational tools have been developed to predict genes in bacterial genomes. In this study, three softwares were used to predict sORF (≤ 80 aa) in B. lehensis by using whole genome sequence. We used comparative analysis to identify the sORFs in B. lehensis that conserved across all other bacterial genomes. We extended the analysis by doing the homology analysis against protein database. This study established the sORFs in B. lehensis that are conserved across bacteria which might has important biological function which still remain elusive in biological field.

The perspective of prostate cancer patients and patients' partners on the psychological burden of androgen deprivation and the dyadic adjustment of prostate cancer couples.

PubMed

Hamilton, Lisa Dawn; Van Dam, Dexter; Wassersug, Richard J

2016-07-01

Prostate cancer and its treatments, particularly androgen deprivation therapy (ADT), affect both patients and partners. This study assessed how prostate cancer treatment type, patient mood, and sexual function related to dyadic adjustment from patient and partner perspectives. Men with prostate cancer (n = 206) and partners of men with prostate cancer (n = 66) completed an online survey assessing the patients' mood (profile of mood states short form), their dyadic adjustment (dyadic adjustment scale), and sexual function (expanded prostate cancer index composite). Analyses of covariance found that men on ADT reported better dyadic adjustment compared with men not on ADT. Erectile dysfunction was high for all patients, but a multivariate analysis of variance found that those on ADT experienced greater bother at loss of sexual function than patients not on ADT, suggesting that loss of libido when on ADT does not mitigate the psychological distress associated with loss of erections. In a multiple linear regression, patients' mood predicted their dyadic adjustment, such that worse mood was related to worse dyadic adjustment. However, more bother with patients' overall sexual function predicted lower relationship scores for the patients, while the patients' lack of sexual desire predicted lower dyadic adjustment for partners. Both patients and partners are impacted by the prostate cancer treatment effects on patients' psychological and sexual function. Our data help clarify the way that prostate cancer treatments can affect relationships and that loss of libido on ADT does not attenuate distress about erectile dysfunction. Understanding these changes may help patients and partners maintain a co-supportive relationship. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Neural activity during affect labeling predicts expressive writing effects on well-being: GLM and SVM approaches.

PubMed

Memarian, Negar; Torre, Jared B; Haltom, Kate E; Stanton, Annette L; Lieberman, Matthew D

2017-09-01

Affect labeling (putting feelings into words) is a form of incidental emotion regulation that could underpin some benefits of expressive writing (i.e. writing about negative experiences). Here, we show that neural responses during affect labeling predicted changes in psychological and physical well-being outcome measures 3 months later. Furthermore, neural activity of specific frontal regions and amygdala predicted those outcomes as a function of expressive writing. Using supervised learning (support vector machines regression), improvements in four measures of psychological and physical health (physical symptoms, depression, anxiety and life satisfaction) after an expressive writing intervention were predicted with an average of 0.85% prediction error [root mean square error (RMSE) %]. The predictions were significantly more accurate with machine learning than with the conventional generalized linear model method (average RMSE: 1.3%). Consistent with affect labeling research, right ventrolateral prefrontal cortex (RVLPFC) and amygdalae were top predictors of improvement in the four outcomes. Moreover, RVLPFC and left amygdala predicted benefits due to expressive writing in satisfaction with life and depression outcome measures, respectively. This study demonstrates the substantial merit of supervised machine learning for real-world outcome prediction in social and affective neuroscience. © The Author (2017). Published by Oxford University Press.

Responses to single photons in visual cells of Limulus

PubMed Central

Borsellino, A.; Fuortes, M. G. F.

1968-01-01

1. A system proposed in a previous article as a model of responses of visual cells has been analysed with the purpose of predicting the features of responses to single absorbed photons. 2. As a result of this analysis, the stochastic variability of responses has been expressed as a function of the amplification of the system. 3. The theoretical predictions have been compared to the results obtained by recording electrical responses of visual cells of Limulus to flashes delivering only few photons. 4. Experimental responses to single photons have been tentatively identified and it was shown that the stochastic variability of these responses is similar to that predicted for a model with a multiplication factor of at least twenty-five. 5. These results lead to the conclusion that the processes responsible for visual responses incorporate some form of amplification. This conclusion may prove useful for identifying the physical mechanisms underlying the transducer action of visual cells. PMID:5664231

Constructing and predicting solitary pattern solutions for nonlinear time-fractional dispersive partial differential equations

NASA Astrophysics Data System (ADS)

Arqub, Omar Abu; El-Ajou, Ahmad; Momani, Shaher

2015-07-01

Building fractional mathematical models for specific phenomena and developing numerical or analytical solutions for these fractional mathematical models are crucial issues in mathematics, physics, and engineering. In this work, a new analytical technique for constructing and predicting solitary pattern solutions of time-fractional dispersive partial differential equations is proposed based on the generalized Taylor series formula and residual error function. The new approach provides solutions in the form of a rapidly convergent series with easily computable components using symbolic computation software. For method evaluation and validation, the proposed technique was applied to three different models and compared with some of the well-known methods. The resultant simulations clearly demonstrate the superiority and potentiality of the proposed technique in terms of the quality performance and accuracy of substructure preservation in the construct, as well as the prediction of solitary pattern solutions for time-fractional dispersive partial differential equations.

Method of empirical dependences in estimation and prediction of activity of creatine kinase isoenzymes in cerebral ischemia

NASA Astrophysics Data System (ADS)

Sergeeva, Tatiana F.; Moshkova, Albina N.; Erlykina, Elena I.; Khvatova, Elena M.

2016-04-01

Creatine kinase is a key enzyme of energy metabolism in the brain. There are known cytoplasmic and mitochondrial creatine kinase isoenzymes. Mitochondrial creatine kinase exists as a mixture of two oligomeric forms - dimer and octamer. The aim of investigation was to study catalytic properties of cytoplasmic and mitochondrial creatine kinase and using of the method of empirical dependences for the possible prediction of the activity of these enzymes in cerebral ischemia. Ischemia was revealed to be accompanied with the changes of the activity of creatine kinase isoenzymes and oligomeric state of mitochondrial isoform. There were made the models of multiple regression that permit to study the activity of creatine kinase system in cerebral ischemia using a calculating method. Therefore, the mathematical method of empirical dependences can be applied for estimation and prediction of the functional state of the brain by the activity of creatine kinase isoenzymes in cerebral ischemia.

Predicting effects of structural stress in a genome-reduced model bacterial metabolism

NASA Astrophysics Data System (ADS)

Güell, Oriol; Sagués, Francesc; Serrano, M. Ángeles

2012-08-01

Mycoplasma pneumoniae is a human pathogen recently proposed as a genome-reduced model for bacterial systems biology. Here, we study the response of its metabolic network to different forms of structural stress, including removal of individual and pairs of reactions and knockout of genes and clusters of co-expressed genes. Our results reveal a network architecture as robust as that of other model bacteria regarding multiple failures, although less robust against individual reaction inactivation. Interestingly, metabolite motifs associated to reactions can predict the propagation of inactivation cascades and damage amplification effects arising in double knockouts. We also detect a significant correlation between gene essentiality and damages produced by single gene knockouts, and find that genes controlling high-damage reactions tend to be expressed independently of each other, a functional switch mechanism that, simultaneously, acts as a genetic firewall to protect metabolism. Prediction of failure propagation is crucial for metabolic engineering or disease treatment.

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.

PubMed

Saidi, Rabie; Boudellioua, Imane; Martin, Maria J; Solovyev, Victor

2017-01-01

It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

Acid–base chemical reaction model for nucleation rates in the polluted atmospheric boundary layer

PubMed Central

Chen, Modi; Titcombe, Mari; Jiang, Jingkun; Jen, Coty; Kuang, Chongai; Fischer, Marc L.; Eisele, Fred L.; Siepmann, J. Ilja; Hanson, David R.; Zhao, Jun; McMurry, Peter H.

2012-01-01

Climate models show that particles formed by nucleation can affect cloud cover and, therefore, the earth's radiation budget. Measurements worldwide show that nucleation rates in the atmospheric boundary layer are positively correlated with concentrations of sulfuric acid vapor. However, current nucleation theories do not correctly predict either the observed nucleation rates or their functional dependence on sulfuric acid concentrations. This paper develops an alternative approach for modeling nucleation rates, based on a sequence of acid–base reactions. The model uses empirical estimates of sulfuric acid evaporation rates obtained from new measurements of neutral molecular clusters. The model predicts that nucleation rates equal the sulfuric acid vapor collision rate times a prefactor that is less than unity and that depends on the concentrations of basic gaseous compounds and preexisting particles. Predicted nucleation rates and their dependence on sulfuric acid vapor concentrations are in reasonable agreement with measurements from Mexico City and Atlanta. PMID:23091030

On the importance of cotranscriptional RNA structure formation

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Meyer, Irmtraud M.

2013-01-01

The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation. PMID:24131802

Acid-base chemical reaction model for nucleation rates in the polluted atmospheric boundary layer.

PubMed

Chen, Modi; Titcombe, Mari; Jiang, Jingkun; Jen, Coty; Kuang, Chongai; Fischer, Marc L; Eisele, Fred L; Siepmann, J Ilja; Hanson, David R; Zhao, Jun; McMurry, Peter H

2012-11-13

Climate models show that particles formed by nucleation can affect cloud cover and, therefore, the earth's radiation budget. Measurements worldwide show that nucleation rates in the atmospheric boundary layer are positively correlated with concentrations of sulfuric acid vapor. However, current nucleation theories do not correctly predict either the observed nucleation rates or their functional dependence on sulfuric acid concentrations. This paper develops an alternative approach for modeling nucleation rates, based on a sequence of acid-base reactions. The model uses empirical estimates of sulfuric acid evaporation rates obtained from new measurements of neutral molecular clusters. The model predicts that nucleation rates equal the sulfuric acid vapor collision rate times a prefactor that is less than unity and that depends on the concentrations of basic gaseous compounds and preexisting particles. Predicted nucleation rates and their dependence on sulfuric acid vapor concentrations are in reasonable agreement with measurements from Mexico City and Atlanta.

Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli.

PubMed Central

Savageau, M A

1998-01-01

Induction of gene expression can be accomplished either by removing a restraining element (negative mode of control) or by providing a stimulatory element (positive mode of control). According to the demand theory of gene regulation, which was first presented in qualitative form in the 1970s, the negative mode will be selected for the control of a gene whose function is in low demand in the organism's natural environment, whereas the positive mode will be selected for the control of a gene whose function is in high demand. This theory has now been further developed in a quantitative form that reveals the importance of two key parameters: cycle time C, which is the average time for a gene to complete an ON/OFF cycle, and demand D, which is the fraction of the cycle time that the gene is ON. Here we estimate nominal values for the relevant mutation rates and growth rates and apply the quantitative demand theory to the lactose and maltose operons of Escherichia coli. The results define regions of the C vs. D plot within which selection for the wild-type regulatory mechanisms is realizable, and these in turn provide the first estimates for the minimum and maximum values of demand that are required for selection of the positive and negative modes of gene control found in these systems. The ratio of mutation rate to selection coefficient is the most relevant determinant of the realizable region for selection, and the most influential parameter is the selection coefficient that reflects the reduction in growth rate when there is superfluous expression of a gene. The quantitative theory predicts the rate and extent of selection for each mode of control. It also predicts three critical values for the cycle time. The predicted maximum value for the cycle time C is consistent with the lifetime of the host. The predicted minimum value for C is consistent with the time for transit through the intestinal tract without colonization. Finally, the theory predicts an optimum value of C that is in agreement with the observed frequency for E. coli colonizing the human intestinal tract. PMID:9691028

Development of an analytical solution for the Budyko watershed parameter in terms of catchment physical features

NASA Astrophysics Data System (ADS)

Reaver, N.; Kaplan, D. A.; Jawitz, J. W.

2017-12-01

The Budyko hypothesis states that a catchment's long-term water and energy balances are dependent on two relatively easy to measure quantities: rainfall depth and potential evaporation. This hypothesis is expressed as a simple function, the Budyko equation, which allows for the prediction of a catchment's actual evapotranspiration and discharge from measured rainfall depth and potential evaporation, data which are widely available. However, the two main analytically derived forms of the Budyko equation contain a single unknown watershed parameter, whose value varies across catchments; variation in this parameter has been used to explain the hydrological behavior of different catchments. The watershed parameter is generally thought of as a lumped quantity that represents the influence of all catchment biophysical features (e.g. soil type and depth, vegetation type, timing of rainfall, etc). Previous work has shown that the parameter is statistically correlated with catchment properties, but an explicit expression has been elusive. While the watershed parameter can be determined empirically by fitting the Budyko equation to measured data in gauged catchments where actual evapotranspiration can be estimated, this limits the utility of the framework for predicting impacts to catchment hydrology due to changing climate and land use. In this study, we developed an analytical solution for the lumped catchment parameter for both forms of the Budyko equation. We combined these solutions with a statistical soil moisture model to obtain analytical solutions for the Budyko equation parameter as a function of measurable catchment physical features, including rooting depth, soil porosity, and soil wilting point. We tested the predictive power of these solutions using the U.S. catchments in the MOPEX database. We also compared the Budyko equation parameter estimates generated from our analytical solutions (i.e. predicted parameters) with those obtained through the calibration of the Budyko equation to discharge data (i.e. empirical parameters), and found good agreement. These results suggest that it is possible to predict the Budyko equation watershed parameter directly from physical features, even for ungauged catchments.

A generic analytical foot rollover model for predicting translational ankle kinematics in gait simulation studies.

PubMed

Ren, Lei; Howard, David; Ren, Luquan; Nester, Chris; Tian, Limei

2010-01-19

The objective of this paper is to develop an analytical framework to representing the ankle-foot kinematics by modelling the foot as a rollover rocker, which cannot only be used as a generic tool for general gait simulation but also allows for case-specific modelling if required. Previously, the rollover models used in gait simulation have often been based on specific functions that have usually been of a simple form. In contrast, the analytical model described here is in a general form that the effective foot rollover shape can be represented by any polar function rho=rho(phi). Furthermore, a normalized generic foot rollover model has been established based on a normative foot rollover shape dataset of 12 normal healthy subjects. To evaluate model accuracy, the predicted ankle motions and the centre of pressure (CoP) were compared with measurement data for both subject-specific and general cases. The results demonstrated that the ankle joint motions in both vertical and horizontal directions (relative RMSE approximately 10%) and CoP (relative RMSE approximately 15% for most of the subjects) are accurately predicted over most of the stance phase (from 10% to 90% of stance). However, we found that the foot cannot be very accurately represented by a rollover model just after heel strike (HS) and just before toe off (TO), probably due to shear deformation of foot plantar tissues (ankle motion can occur without any foot rotation). The proposed foot rollover model can be used in both inverse and forward dynamics gait simulation studies and may also find applications in rehabilitation engineering. Copyright 2009 Elsevier Ltd. All rights reserved.

Structure-based approach to the prediction of disulfide bonds in proteins.

PubMed

Salam, Noeris K; Adzhigirey, Matvey; Sherman, Woody; Pearlman, David A

2014-10-01

Protein engineering remains an area of growing importance in pharmaceutical and biotechnology research. Stabilization of a folded protein conformation is a frequent goal in projects that deal with affinity optimization, enzyme design, protein construct design, and reducing the size of functional proteins. Indeed, it can be desirable to assess and improve protein stability in order to avoid liabilities such as aggregation, degradation, and immunogenic response that may arise during development. One way to stabilize a protein is through the introduction of disulfide bonds. Here, we describe a method to predict pairs of protein residues that can be mutated to form a disulfide bond. We combine a physics-based approach that incorporates implicit solvent molecular mechanics with a knowledge-based approach. We first assign relative weights to the terms that comprise our scoring function using a genetic algorithm applied to a set of 75 wild-type structures that each contains a disulfide bond. The method is then tested on a separate set of 13 engineered proteins comprising 15 artificial stabilizing disulfides introduced via site-directed mutagenesis. We find that the native disulfide in the wild-type proteins is scored well, on average (within the top 6% of the reasonable pairs of residues that could form a disulfide bond) while 6 out of the 15 artificial stabilizing disulfides scored within the top 13% of ranked predictions. Overall, this suggests that the physics-based approach presented here can be useful for triaging possible pairs of mutations for disulfide bond formation to improve protein stability. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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 ecology and evolution of hominoid molar enamel thickness: Pan troglodytes schweinfurthii and Pongo pygmaeus wurmbii.

PubMed

Vogel, Erin R; van Woerden, Janneke T; Lucas, Peter W; Utami Atmoko, Sri S; van Schaik, Carel P; Dominy, Nathaniel J

2008-07-01

The divergent molar characteristics of Pan troglodytes and Pongo pygmaeus provide an instructive paradigm for examining the adaptive form-function relationship between molar enamel thickness and food hardness. Although both species exhibit a categorical preference for ripe fruit over other food objects, the thick enamel and crenulated occlusal surface of Pongo molar teeth predict a diet that is more resistant to deformation (hard) and fracture (tough) than the diet of Pan. We confirm these predictions with behavioral observations of Pan troglodytes schweinfurthii and Pongo pygmaeus wurmbii in the wild and describe the mechanical properties of foods utilized during periods when preferred foods are scarce. Such fallback foods may have exerted a selective pressure on tooth evolution, particularly molar enamel thinness, which is interpreted as a functional adaptation to seasonal folivory and a derived character trait within the hominoid clade. The thick enamel and crenulated occlusal surface of Pongo molars is interpreted as a functional adaptation to the routine consumption of relatively tough and hard foods. We discuss the implications of these interpretations for inferring the diet of hominin species, which possessed varying degrees of thick molar enamel. These data, which are among the first reported for hominoid primates, fill an important empirical void for evaluating the mechanical plausibility of putative hominin food objects.

Insight in psychotic disorder: relation with psychopathology and frontal lobe function.

PubMed

Kumar, Atmesh; Sharma, Pranjal; Das, Shyamanta; Nath, Kamal; Talukdar, Uddip; Bhagabati, Dipesh

2014-01-01

Through conceptualising poor insight in psychotic disorders as a form of anosognosia, frontal lobe dysfunction is often ascribed a vital role in its pathogenesis. The objective of this study was to compare the relation of insight in patients with psychotic illness to that of psychopathology and frontal lobe function. Forty patients with psychotic disorder were selected from those attending the Department of Psychiatry in a tertiary care teaching hospital. The evaluation of insight was carried out using the Schedule for Assessment of Insight (SAI), that of frontal lobe function by the Frontal Assessment Battery (FAB) and psychopathology by the Brief Psychiatric Rating Scale (BPRS). The correlation coefficients were determined. A negative correlation between SAI and BPRS scores means that the BPRS score is opposite to SAI scores. When the SAI total score was compared with the FAB total score, the correlation coefficient demonstrated a positive correlation. Better insight predicted lesser psychopathology and also that poor insight would exist with greater psychopathology. Better insight predicted a higher functional status of frontal lobes and prefrontal cortex in particular. Insight deficits in schizophrenia and other psychotic illnesses are multidimensional. Integration of different aetiological factors like biological, psychopathological, environmental ones and others are necessary for a better understanding of insight in psychosis. Copyright © 2013 S. Karger AG, Basel.

Knowledge-based prediction of protein backbone conformation using a structural alphabet.

PubMed

Vetrivel, Iyanar; Mahajan, Swapnil; Tyagi, Manoj; Hoffmann, Lionel; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; de Brevern, Alexandre G; Cadet, Frédéric; Offmann, Bernard

2017-01-01

Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. Predicting the local structure of a protein in terms of protein blocks is the general objective of this work. A new approach, PB-kPRED is proposed towards this aim. It involves (i) organizing the structural knowledge in the form of a database of pentapeptide fragments extracted from all protein structures in the PDB and (ii) applying a knowledge-based algorithm that does not rely on any secondary structure predictions and/or sequence alignment profiles, to scan this database and predict most probable backbone conformations for the protein local structures. Though PB-kPRED uses the structural information from homologues in preference, if available. The predictions were evaluated rigorously on 15,544 query proteins representing a non-redundant subset of the PDB filtered at 30% sequence identity cut-off. We have shown that the kPRED method was able to achieve mean accuracies ranging from 40.8% to 66.3% depending on the availability of homologues. The impact of the different strategies for scanning the database on the prediction was evaluated and is discussed. Our results highlight the usefulness of the method in the context of proteins without any known structural homologues. A scoring function that gives a good estimate of the accuracy of prediction was further developed. This score estimates very well the accuracy of the algorithm (R2 of 0.82). An online version of the tool is provided freely for non-commercial usage at http://www.bo-protscience.fr/kpred/.

MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

PubMed

Yu, Haoyu S; He, Xiao; Truhlar, Donald G

2016-03-08

Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology.

Prediction of dissolved oxygen in the Mediterranean Sea along Gaza, Palestine - an artificial neural network approach.

PubMed

Zaqoot, Hossam Adel; Ansari, Abdul Khalique; Unar, Mukhtiar Ali; Khan, Shaukat Hyat

2009-01-01

Artificial Neural Networks (ANNs) are flexible tools which are being used increasingly to predict and forecast water resources variables. The human activities in areas surrounding enclosed and semi-enclosed seas such as the Mediterranean Sea always produce in the long term a strong environmental impact in the form of coastal and marine degradation. The presence of dissolved oxygen is essential for the survival of most organisms in the water bodies. This paper is concerned with the use of ANNs - Multilayer Perceptron (MLP) and Radial Basis Function neural networks for predicting the next fortnight's dissolved oxygen concentrations in the Mediterranean Sea water along Gaza. MLP and Radial Basis Function (RBF) neural networks are trained and developed with reference to five important oceanographic variables including water temperature, wind velocity, turbidity, pH and conductivity. These variables are considered as inputs of the network. The data sets used in this study consist of four years and collected from nine locations along Gaza coast. The network performance has been tested with different data sets and the results show satisfactory performance. Prediction results prove that neural network approach has good adaptability and extensive applicability for modelling the dissolved oxygen in the Mediterranean Sea along Gaza. We hope that the established model will help in assisting the local authorities in developing plans and policies to reduce the pollution along Gaza coastal waters to acceptable levels.

Investigating the impact of pain, age, Gross Motor Function Classification System, and sex on health-related quality of life in children with cerebral palsy.

PubMed

Findlay, Briar; Switzer, Lauren; Narayanan, Unni; Chen, Shiyi; Fehlings, Darcy

2016-03-01

To explore whether health-related quality of life (HRQOL) can be predicted by pain, age, Gross Motor Function Classification System (GMFCS) level, and sex in children with cerebral palsy (CP) and whether different pain etiologies have varying effects on HRQOL. Children with CP aged 3 to 19 years and their caregivers were consecutively recruited. Caregivers reported their child's pain (Health Utilities Index 3 [HUI3] pain subset) and HRQOL (DISABKIDS questionnaires). Physicians identified pain etiologies. A multiple linear regression model determined whether pain, GMFCS level, sex, and age predicted HRQOL. An ANOVA evaluated the effects of pain etiologies on HRQOL. Three hundred and forty-four participants were approached and 87% (n=300) participated. Sufficient data were available on 248 (72% of total sample). Sixty-six participants (27%) formed the pain group with HUI3 pain scores of at least 3. The presence of pain and increasing age significantly negatively predicted HRQOL (p<0.001, R(2) =0.141), while GMFCS and sex did not. Musculoskeletal deformity (24%) and hypertonia (18%) were the most frequent pain causes. HRQOL statistically differed depending on the pain etiology (p=0.028) with musculoskeletal deformity showing the lowest mean HRQOL. The presence of pain and increasing age negatively predict HRQOL in CP. musculoskeletal deformity has the greatest negative impact on HRQOL. © 2015 Mac Keith Press.

MnNiO3 revisited with modern theoretical and experimental methods

NASA Astrophysics Data System (ADS)

Dzubak, Allison L.; Mitra, Chandrima; Chance, Michael; Kuhn, Stephen; Jellison, Gerald E.; Sefat, Athena S.; Krogel, Jaron T.; Reboredo, Fernando A.

2017-11-01

MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.

Mapping the core mass function to the initial mass function

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Hopkins, Philip F.

2015-07-01

It has been shown that fragmentation within self-gravitating, turbulent molecular clouds (`turbulent fragmentation') can naturally explain the observed properties of protostellar cores, including the core mass function (CMF). Here, we extend recently developed analytic models for turbulent fragmentation to follow the time-dependent hierarchical fragmentation of self-gravitating cores, until they reach effectively infinite density (and form stars). We show that turbulent fragmentation robustly predicts two key features of the initial mass function (IMF). First, a high-mass power-law scaling very close to the Salpeter slope, which is a generic consequence of the scale-free nature of turbulence and self-gravity. We predict the IMF slope (-2.3) is slightly steeper than the CMF slope (-2.1), owing to the slower collapse and easier fragmentation of large cores. Secondly, a turnover mass, which is set by a combination of the CMF turnover mass (a couple solar masses, determined by the `sonic scale' of galactic turbulence, and so weakly dependent on galaxy properties), and the equation of state (EOS). A `soft' EOS with polytropic index γ < 1.0 predicts that the IMF slope becomes `shallow' below the sonic scale, but fails to produce the full turnover observed. An EOS, which becomes `stiff' at sufficiently low surface densities Σgas ˜ 5000 M⊙ pc-2, and/or models, where each collapsing core is able to heat and effectively stiffen the EOS of a modest mass (˜0.02 M⊙) of surrounding gas, are able to reproduce the observed turnover. Such features are likely a consequence of more detailed chemistry and radiative feedback.

Age-related decline in the matrix contents and functional properties of human periodontal ligament stem cell sheets.

PubMed

Wu, Rui-Xin; Bi, Chun-Sheng; Yu, Yang; Zhang, Lin-Lin; Chen, Fa-Ming

2015-08-01

In this study, periodontal ligament (PDL) stem cells (PDLSCs) derived from different-aged donors were used to evaluate the effect of aging on cell sheet formation. The activity of PDLSCs was first determined based on their colony-forming ability, surface markers, proliferative/differentiative potentials, senescence-associated β-galactosidase (SA-βG) staining, and expression of pluripotency-associated transcription factors. The ability of these cells to form sheets, based on their extracellular matrix (ECM) contents and their functional properties necessary for osteogenic differentiation, was evaluated to predict the age-related changes in the regenerative capacity of the cell sheets in their further application. It was found that human PDLSCs could be isolated from the PDL tissue of different-aged subjects. However, the ability of the PDLSCs to proliferate and to undergo osteogenic differentiation and their expression of pluripotency-associated transcription factors displayed age-related decreases. In addition, these cells exhibited an age-related increase in SA-βG expression. Aged cells showed an impaired ability to form functional cell sheets, as determined by morphological observations and Ki-67 immunohistochemistry staining. Based on the production of ECM proteins, such as fibronectin, integrin β1, and collagen type I; alkaline phosphatase (ALP) activity; and the expression of osteogenic genes, such as ALP, Runt-related transcription factor 2, and osteocalcin, cell sheets formed by PDLSCs derived from older donors demonstrated a less potent osteogenic capacity compared to those formed by PDLSCs from younger donors. Our data suggest that the age-associated decline in the matrix contents and osteogenic properties of PDLSC sheets should be taken into account in cell sheet engineering research and clinical periodontal regenerative therapy. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Physical Intrepretation of Mathematically Invariant K(r,P) Type Equations of State for Hydrodynamically Driven Flow

NASA Astrophysics Data System (ADS)

Hrbek, George

2001-06-01

At SCCM Shock 99, Lie Group Theory was applied to the problem of temperature independent, hydrodynamic shock in a Birch-Murnaghan continuum. (1) Ratios of the group parameters were shown to be linked to the physical parameters specified in the second, third, and fourth order BM-EOS approximations. This effort has subsequently been extended to provide a general formalism for a wide class of mathematical forms (i.e., K(r,P)) of the equation of state. Variations in material expansion and resistance (i.e., counter pressure) are shown to be functions of compression and material variation ahead of the expanding front. Specific examples included the Birch-Murnaghan, Vinet, Brennan-Stacey, Shanker, Tait, Poirier, and Jones-Wilkins-Lee (JWL) forms. (2) With these ratios defined, the next step is to predict the behavior of these K(r,P) type solids. To do this, one must introduce the group ratios into a numerical simulation for the flow and generate the density, pressure, and particle velocity profiles as the shock moves through the material. This will allow the various equations of state, and their respective fitting coefficients, to be compared with experiments, and additionally, allow the empirical coefficients for these EOS forms to be adjusted accordingly. (1) Hrbek, G. M., Invariant Functional Forms For The Second, Third, And Fourth Order Birch-Murnaghan Equation of State For Materials Subject to Hydrodynamic Shock, Proceedings of the 11th American Physical Society Topical Group Meeting on Shock Compression of Condensed Matter (SCCM Shock 99), Snowbird, Utah (2) Hrbek, G. M., Invariant Functional Forms For K(r,P) Type Equations Of State For Hydrodynamically Driven Flows, Submitted to the 12th American Physical Society Topical Group Meeting on Shock Compression of Condensed Matter (SCCM Shock 01), Atlanta, Georgia

Characterization and dynamic charge dependent modeling of conducting polymer trilayer bending

NASA Astrophysics Data System (ADS)

Farajollahi, Meisam; Sassani, Farrokh; Naserifar, Naser; Fannir, Adelyne; Plesse, Cédric; Nguyen, Giao T. M.; Vidal, Frédéric; Madden, John D. W.

2016-11-01

Trilayer bending actuators are charge driven devices that have the ability to function in air and provide large mechanical amplification. The electronic and mechanical properties of these actuators are known to be functions of their charge state making prediction of their responses more difficult when they operate over their full range of deformation. In this work, a combination of state space representation and a two-dimensional RC transmission line model are used to implement a nonlinear time variant model for conducting polymer-based trilayer actuators. Electrical conductivity and Young’s modulus of electromechanically active PEDOT conducting polymer containing films as a function of applied voltage were measured and incorporated into the model. A 16% drop in Young’s modulus and 24 times increase in conductivity are observed by oxidizing the PEDOT. A closed form formulation for radius of curvature of trilayer actuators considering asymmetric and location dependent Young’s modulus and conductivity in the conducting polymer layers is derived and implemented in the model. The nonlinear model shows the capability to predict the radius of curvature as a function of time and position with reasonable consistency (within 4%). The formulation is useful for general trilayer configurations to calculate the radius of curvature as a function of time. The proposed electrochemical modeling approach may also be useful for modeling energy storage devices.

Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.

PubMed

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De; Qin, Cheng-Feng

2013-06-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

PubMed Central

Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Zhao, Hui; Wang, Hong-Jiang; Ye, Qing; Zhu, Shun-Ya; Qiu, Yang; Zhou, Xi; Qin, E-De

2013-01-01

cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5′ cyclization sequence (5′CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5′CS, and the presence of DCS-PK facilitates the formation of 5′-3′ RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution. PMID:23576500

Risk Assessment and Prediction of Heavy Metal Pollution in Groundwater and River Sediment: A Case Study of a Typical Agricultural Irrigation Area in Northeast China

PubMed Central

Zhong, Shuang; Geng, Hui; Zhang, Fengjun; Liu, Zhaoying; Wang, Tianye; Song, Boyu

2015-01-01

The areas with typical municipal sewage discharge river and irrigation water function were selected as study sites in northeast China. The samples from groundwater and river sediment in this area were collected for the concentrations and forms of heavy metals (Cr(VI), Cd, As, and Pb) analysis. The risk assessment of heavy metal pollution was conducted based on single-factor pollution index (I) and Nemerow pollution index (NI). The results showed that only one groundwater sampling site reached a polluted level of heavy metals. There was a high potential ecological risk of Cd on the N21-2 sampling site in river sediment. The morphological analysis results of heavy metals in sediment showed that the release of heavy metals can be inferred as one of the main pollution sources of groundwater. In addition, the changes in the concentration and migration scope of As were predicted by using the Groundwater Modeling System (GMS). The predicted results showed that As will migrate downstream in the next decade, and the changing trend of As polluted areas was changed with As content districts because of some pump wells downstream to form groundwater depression cone, which made the solute transfer upstream. PMID:26366176