Foraging Ecology Predicts Learning Performance in Insectivorous Bats

PubMed Central

Clarin, Theresa M. A.; Ruczyński, Ireneusz; Page, Rachel A.

2013-01-01

Bats are unusual among mammals in showing great ecological diversity even among closely related species and are thus well suited for studies of adaptation to the ecological background. Here we investigate whether behavioral flexibility and simple- and complex-rule learning performance can be predicted by foraging ecology. We predict faster learning and higher flexibility in animals hunting in more complex, variable environments than in animals hunting in more simple, stable environments. To test this hypothesis, we studied three closely related insectivorous European bat species of the genus Myotis that belong to three different functional groups based on foraging habitats: M. capaccinii, an open water forager, M. myotis, a passive listening gleaner, and M. emarginatus, a clutter specialist. We predicted that M. capaccinii would show the least flexibility and slowest learning reflecting its relatively unstructured foraging habitat and the stereotypy of its natural foraging behavior, while the other two species would show greater flexibility and more rapid learning reflecting the complexity of their natural foraging tasks. We used a purposefully unnatural and thus species-fair crawling maze to test simple- and complex-rule learning, flexibility and re-learning performance. We found that M. capaccinii learned a simple rule as fast as the other species, but was slower in complex rule learning and was less flexible in response to changes in reward location. We found no differences in re-learning ability among species. Our results corroborate the hypothesis that animals’ cognitive skills reflect the demands of their ecological niche. PMID:23755146

Characterization and prediction of rate-dependent flexibility in lumbar spine biomechanics at room and body temperature.

PubMed

Stolworthy, Dean K; Zirbel, Shannon A; Howell, Larry L; Samuels, Marina; Bowden, Anton E

2014-05-01

The soft tissues of the spine exhibit sensitivity to strain-rate and temperature, yet current knowledge of spine biomechanics is derived from cadaveric testing conducted at room temperature at very slow, quasi-static rates. The primary objective of this study was to characterize the change in segmental flexibility of cadaveric lumbar spine segments with respect to multiple loading rates within the range of physiologic motion by using specimens at body or room temperature. The secondary objective was to develop a predictive model of spine flexibility across the voluntary range of loading rates. This in vitro study examines rate- and temperature-dependent viscoelasticity of the human lumbar cadaveric spine. Repeated flexibility tests were performed on 21 lumbar function spinal units (FSUs) in flexion-extension with the use of 11 distinct voluntary loading rates at body or room temperature. Furthermore, six lumbar FSUs were loaded in axial rotation, flexion-extension, and lateral bending at both body and room temperature via a stepwise, quasi-static loading protocol. All FSUs were also loaded using a control loading test with a continuous-speed loading-rate of 1-deg/sec. The viscoelastic torque-rotation response for each spinal segment was recorded. A predictive model was developed to accurately estimate spine segment flexibility at any voluntary loading rate based on measured flexibility at a single loading rate. Stepwise loading exhibited the greatest segmental range of motion (ROM) in all loading directions. As loading rate increased, segmental ROM decreased, whereas segmental stiffness and hysteresis both increased; however, the neutral zone remained constant. Continuous-speed tests showed that segmental stiffness and hysteresis are dependent variables to ROM at voluntary loading rates in flexion-extension. To predict the torque-rotation response at different loading rates, the model requires knowledge of the segmental flexibility at a single rate and specified temperature, and a scaling parameter. A Bland-Altman analysis showed high coefficients of determination for the predictive model. The present work demonstrates significant changes in spine segment flexibility as a result of loading rate and testing temperature. Loading rate effects can be accounted for using the predictive model, which accurately estimated ROM, neutral zone, stiffness, and hysteresis within the range of voluntary motion. Copyright © 2014 Elsevier Inc. All rights reserved.

Prediction of Solution Properties of Flexible-Chain Polymers: A Computer Simulation Undergraduate Experiment

ERIC Educational Resources Information Center

de la Torre, Jose Garcia; Cifre, Jose G. Hernandez; Martinez, M. Carmen Lopez

2008-01-01

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer…

Modeling and control of flexible space structures

NASA Technical Reports Server (NTRS)

Wie, B.; Bryson, A. E., Jr.

1981-01-01

The effects of actuator and sensor locations on transfer function zeros are investigated, using uniform bars and beams as generic models of flexible space structures. It is shown how finite element codes may be used directly to calculate transfer function zeros. The impulse response predicted by finite-dimensional models is compared with the exact impulse response predicted by the infinite dimensional models. It is shown that some flexible structures behave as if there were a direct transmission between actuator and sensor (equal numbers of zeros and poles in the transfer function). Finally, natural damping models for a vibrating beam are investigated since natural damping has a strong influence on the appropriate active control logic for a flexible structure.

Dyadic flexibility and positive affect in parent–child coregulation and the development of child behavior problems

PubMed Central

LUNKENHEIMER, ERIKA S.; OLSON, SHERYL L.; HOLLENSTEIN, TOM; SAMEROFF, ARNOLD J.; WINTER, CHARLOTTE

2018-01-01

Parent–child dyadic rigidity and negative affect contribute to children’s higher levels of externalizing problems. The present longitudinal study examined whether the opposite constructs of dyadic flexibility and positive affect predicted lower levels of externalizing behavior problems across the early childhood period. Mother–child (N = 163) and father–child (n = 94) dyads engaged in a challenging block design task at home when children were 3 years old. Dynamic systems methods were used to derive dyadic positive affect and three indicators of dyadic flexibility (range, dispersion, and transitions) from observational coding. We hypothesized that the interaction between dyadic flexibility and positive affect would predict lower levels of externalizing problems at age 5.5 years as rated by mothers and teachers, controlling for stability in externalizing problems, task time, child gender, and the child’s effortful control. The hypothesis was supported in predicting teacher ratings of child externalizing from both mother–child and father–child interactions. There were also differential main effects for mothers and fathers: mother–child flexibility was detrimental and father–child flexibility was beneficial for child outcomes. Results support the inclusion of adaptive and dynamic parent–child coregulation processes in the study of children’s early disruptive behavior. PMID:23786697

The value of radiographs obtained during forced traction under general anaesthesia in predicting flexibility in idiopathic scoliosis with Cobb angles exceeding 60 degree.

PubMed

Ibrahim, T; Gabbar, O A; El-Abed, K; Hutchinson, M J; Nelson, I W

2008-11-01

Our aim in this prospective radiological study was to determine whether the flexibility rate calculated from radiographs obtained during forced traction under general anaesthesia, was better than that of fulcrum-bending radiographs before corrective surgery in predicting the extent of the available correction in patients with idiopathic scoliosis. We evaluated 33 patients with a Cobb angle > 60 degrees on a standing posteroanterior radiograph, who had been treated by posterior correction. Pre-operative standing fulcrum-bending radiographs and those with forced-traction under general anaesthesia were obtained. Post-operative standing radiographs were taken after surgical correction. The mean forced-traction flexibility rate was 55% (SD 11.3) which was significantly higher than the mean fulcrum-bending flexibility rate of 32% (SD 16.1) (p < 0.001). We found no correlation between either the forced-traction or fulcrum-bending flexibility rates and the correction rate post-operatively (p = 0.24 and p = 0.44, respectively). Radiographs obtained during forced traction under general anaesthesia were better at predicting the flexibility of the curve than fulcrum-bending radiographs in curves with a Cobb angle > 60 degrees in the standing position and may identify those patients for whom supplementary anterior surgery can be avoided.

The Ability of Psychological Flexibility and Job Control to Predict Learning, Job Performance, and Mental Health

ERIC Educational Resources Information Center

Bond, Frank W.; Flaxman, Paul E.

2006-01-01

This longitudinal study tested the degree to which an individual characteristic, psychological flexibility, and a work organization variable, job control, predicted ability to learn new skills at work, job performance, and mental health, amongst call center workers in the United Kingdom (N = 448). As hypothesized, results indicated that job…

Turning Potential Flexibility Into Flexible Performance: Moderating Effect of Self-Efficacy and Use of Flexible Cognition

PubMed Central

Liu, Ru-De; Wang, Jia; Star, Jon R.; Zhen, Rui; Jiang, Rong-Huan; Fu, Xin-Chen

2018-01-01

This study examined the relationship between two types of mathematical flexibility – potential flexibility, which indicates individuals’ knowledge of multiple strategies and strategy efficiency, and practical flexibility, which refers to individuals’ flexible performances when solving math problems. Both types of flexibility were assessed in the domain of linear equation solving. Furthermore, two types of beliefs – self-efficacy and use of flexible cognition (UFC) – were investigated as potential moderators between potential and practical flexibility. 121 8th grade students from China took part in this study. Results indicate that potential flexibility positively predicted practical flexibility. Additionally, self-efficacy and UFC might moderate the relationship between these two types of flexibility, suggesting that potential flexibility may lead to different degrees of practical flexibility depending on different levels of beliefs. Implications of these findings for research on mathematical flexibility and for educational practice are discussed. PMID:29780344

Doing the counter-regulation shuffle: The importance of flexibility and hunger for predicting food consumption following a preload.

PubMed

Broadbent, Jaclyn; Fuller-Tyszkiewicz, Matthew; Dennerstein, Michelle; Greenwood, Jesse; Hancock, Naomi; Thavapalan, Nithyyaa; White, Melissa

This study utilised the preload paradigm to evaluate whether trait-like dieting attitudes and behaviours (dietary restraint and flexibility in dieting rules) and context-specific factors (negative mood and hunger) predict food consumption among male and female participants. Following a high calorie preload, 79 participants aged 18-40 completed a deceptive taste test in which they were encouraged to eat as much of the taste test foods as desired, and this ad libitum intake was measured. Although each predictor (except negative mood) predicted consumption when tested individually, regression analyses revealed that dieting flexibility and current hunger were the strongest unique predictors of intake. Mood failed to directly predict food consumption, nor did it moderate the relationship between restraint and food intake. Collectively, findings suggest that emphasis on dietary restraint in preload studies may be misplaced, as other proximal and stable factors may better predict food consumption. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Determination of the criterion-related validity of hip joint angle test for estimating hamstring flexibility using a contemporary statistical approach.

PubMed

Sainz de Baranda, Pilar; Rodríguez-Iniesta, María; Ayala, Francisco; Santonja, Fernando; Cejudo, Antonio

2014-07-01

To examine the criterion-related validity of the horizontal hip joint angle (H-HJA) test and vertical hip joint angle (V-HJA) test for estimating hamstring flexibility measured through the passive straight-leg raise (PSLR) test using contemporary statistical measures. Validity study. Controlled laboratory environment. One hundred thirty-eight professional trampoline gymnasts (61 women and 77 men). Hamstring flexibility. Each participant performed 2 trials of H-HJA, V-HJA, and PSLR tests in a randomized order. The criterion-related validity of H-HJA and V-HJA tests was measured through the estimation equation, typical error of the estimate (TEEST), validity correlation (β), and their respective confidence limits. The findings from this study suggest that although H-HJA and V-HJA tests showed moderate to high validity scores for estimating hamstring flexibility (standardized TEEST = 0.63; β = 0.80), the TEEST statistic reported for both tests was not narrow enough for clinical purposes (H-HJA = 10.3 degrees; V-HJA = 9.5 degrees). Subsequently, the predicted likely thresholds for the true values that were generated were too wide (H-HJA = predicted value ± 13.2 degrees; V-HJA = predicted value ± 12.2 degrees). The results suggest that although the HJA test showed moderate to high validity scores for estimating hamstring flexibility, the prediction intervals between the HJA and PSLR tests are not strong enough to suggest that clinicians and sport medicine practitioners should use the HJA and PSLR tests interchangeably as gold standard measurement tools to evaluate and detect short hamstring muscle flexibility.

The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials

DOE PAGES

Witman, Matthew; Ling, Sanliang; Jawahery, Sudi; ...

2017-03-30

For applications of metal–organic frameworks (MOFs) such as gas storage and separation, flexibility is often seen as a parameter that can tune material performance. In this work we aim to determine the optimal flexibility for the shape selective separation of similarly sized molecules (e.g., Xe/Kr mixtures). To obtain systematic insight into how the flexibility impacts this type of separation, we develop a simple analytical model that predicts a material’s Henry regime adsorption and selectivity as a function of flexibility. We elucidate the complex dependence of selectivity on a framework’s intrinsic flexibility whereby performance is either improved or reduced with increasingmore » flexibility, depending on the material’s pore size characteristics. However, the selectivity of a material with the pore size and chemistry that already maximizes selectivity in the rigid approximation is continuously diminished with increasing flexibility, demonstrating that the globally optimal separation exists within an entirely rigid pore. Molecular simulations show that our simple model predicts performance trends that are observed when screening the adsorption behavior of flexible MOFs. These flexible simulations provide better agreement with experimental adsorption data in a high-performance material that is not captured when modeling this framework as rigid, an approximation typically made in high-throughput screening studies. We conclude that, for shape selective adsorption applications, the globally optimal material will have the optimal pore size/chemistry and minimal intrinsic flexibility even though other nonoptimal materials’ selectivity can actually be improved by flexibility. In conclusion, equally important, we find that flexible simulations can be critical for correctly modeling adsorption in these types of systems.« less

The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials

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

Witman, Matthew; Ling, Sanliang; Jawahery, Sudi

For applications of metal–organic frameworks (MOFs) such as gas storage and separation, flexibility is often seen as a parameter that can tune material performance. In this work we aim to determine the optimal flexibility for the shape selective separation of similarly sized molecules (e.g., Xe/Kr mixtures). To obtain systematic insight into how the flexibility impacts this type of separation, we develop a simple analytical model that predicts a material’s Henry regime adsorption and selectivity as a function of flexibility. We elucidate the complex dependence of selectivity on a framework’s intrinsic flexibility whereby performance is either improved or reduced with increasingmore » flexibility, depending on the material’s pore size characteristics. However, the selectivity of a material with the pore size and chemistry that already maximizes selectivity in the rigid approximation is continuously diminished with increasing flexibility, demonstrating that the globally optimal separation exists within an entirely rigid pore. Molecular simulations show that our simple model predicts performance trends that are observed when screening the adsorption behavior of flexible MOFs. These flexible simulations provide better agreement with experimental adsorption data in a high-performance material that is not captured when modeling this framework as rigid, an approximation typically made in high-throughput screening studies. We conclude that, for shape selective adsorption applications, the globally optimal material will have the optimal pore size/chemistry and minimal intrinsic flexibility even though other nonoptimal materials’ selectivity can actually be improved by flexibility. In conclusion, equally important, we find that flexible simulations can be critical for correctly modeling adsorption in these types of systems.« less

All-phosphorus flexible devices with non-collinear electrodes: a first principles study.

PubMed

Li, Junjun; Ruan, Lufeng; Wu, Zewen; Zhang, Guiling; Wang, Yin

2018-03-07

With the continuous expansion of the family of two-dimensional (2D) materials, flexible electronics based on 2D materials have quickly emerged. Theoretically, predicting the transport properties of the flexible devices made up of 2D materials using first principles is of great importance. Using density functional theory combined with the non-equilibrium Green's function formalism, we calculated the transport properties of all-phosphorus flexible devices with non-collinear electrodes, and the results predicted that the device with compressed metallic phosphorene electrodes sandwiching a P-type semiconducting phosphorene shows a better and robust conducting behavior against the bending of the semiconducting region when the angle between the two electrodes is less than 45°, which indicates that this system is very promising for flexible electronics. The calculation of a quantum transport system with non-collinear electrodes demonstrated in this work will provide more interesting information on mesoscopic material systems and related devices.

An insula-frontostriatal network mediates flexible cognitive control by adaptively predicting changing control demands

PubMed Central

Jiang, Jiefeng; Beck, Jeffrey; Heller, Katherine; Egner, Tobias

2015-01-01

The anterior cingulate and lateral prefrontal cortices have been implicated in implementing context-appropriate attentional control, but the learning mechanisms underlying our ability to flexibly adapt the control settings to changing environments remain poorly understood. Here we show that human adjustments to varying control demands are captured by a reinforcement learner with a flexible, volatility-driven learning rate. Using model-based functional magnetic resonance imaging, we demonstrate that volatility of control demand is estimated by the anterior insula, which in turn optimizes the prediction of forthcoming demand in the caudate nucleus. The caudate's prediction of control demand subsequently guides the implementation of proactive and reactive attentional control in dorsal anterior cingulate and dorsolateral prefrontal cortices. These data enhance our understanding of the neuro-computational mechanisms of adaptive behaviour by connecting the classic cingulate-prefrontal cognitive control network to a subcortical control-learning mechanism that infers future demands by flexibly integrating remote and recent past experiences. PMID:26391305

The interference of flexible working times with the utility of time: a predictor of social impairment?

PubMed

Wirtz, Anna; Giebel, Ole; Schomann, Carsten; Nachreiner, Friedhelm

2008-04-01

Periodic components inherent in actual schedules of flexible working hours and their interference with social rhythms were measured using spectrum analysis. The resulting indicators of periodicity and interference were then related to the reported social impairments of workers. The results show that a suppression of the 24 and the 168 h (seven-day) components (absence of periodicity) in the work schedules predicts reported social impairment. However, even if there are relatively strong 24 and 168 h components left in the work schedules, their interference with the social rhythm (using the phase difference between working hours and the utility of time) further predicts impairment. The results thus indicate that the periodicity of working hours and the amount of (social) desynchronization induced by flexible work schedules can be used both for predicting the impairing effects of the specific work schedules on social well-being as well as for the design of socially acceptable flexible work hours.

Association of grey matter changes with stability and flexibility of prediction in akinetic-rigid Parkinson's disease.

PubMed

Trempler, Ima; Binder, Ellen; El-Sourani, Nadiya; Schiffler, Patrick; Tenberge, Jan-Gerd; Schiffer, Anne-Marike; Fink, Gereon R; Schubotz, Ricarda I

2018-06-01

Parkinson's disease (PD), which is caused by degeneration of dopaminergic neurons in the midbrain, results in a heterogeneous clinical picture including cognitive decline. Since the phasic signal of dopamine neurons is proposed to guide learning by signifying mismatches between subjects' expectations and external events, we here investigated whether akinetic-rigid PD patients without mild cognitive impairment exhibit difficulties in dealing with either relevant (requiring flexibility) or irrelevant (requiring stability) prediction errors. Following our previous study on flexibility and stability in prediction (Trempler et al. J Cogn Neurosci 29(2):298-309, 2017), we then assessed whether deficits would correspond with specific structural alterations in dopaminergic regions as well as in inferior frontal cortex, medial prefrontal cortex, and the hippocampus. Twenty-one healthy controls and twenty-one akinetic-rigid PD patients on and off medication performed a task which required to serially predict upcoming items. Switches between predictable sequences had to be indicated via button press, whereas sequence omissions had to be ignored. Independent of the disease, midbrain volume was related to a general response bias to unexpected events, whereas right putamen volume correlated with the ability to discriminate between relevant and irrelevant prediction errors. However, patients compared with healthy participants showed deficits in stabilisation against irrelevant prediction errors, associated with thickness of right inferior frontal gyrus and left medial prefrontal cortex. Flexible updating due to relevant prediction errors was also affected in patients compared with controls and associated with right hippocampus volume. Dopaminergic medication influenced behavioural performance across, but not within the patients. Our exploratory study warrants further research on deficient prediction error processing and its structural correlates as a core of cognitive symptoms occurring already in early stages of the disease.

Flexibility Considerations on the Hydrodynamic Loading on a Vertical Wedge Drop

NASA Astrophysics Data System (ADS)

Ren, Zhongshu; Wang, Zhaoyuan; Judge, Carolyn; Stern, Fred; Ikeda, Christine

2017-11-01

High-speed craft operating at in waves frequently become airborne and slam into the water surface. This fluid-structure interaction problem is important to understand in order to increase the operating envelope of these craft. The goals of the current work are to investigate both the hydrodynamic loads and the resulting structural response on a planing hull. A V-shaped wedge is dropped vertically into calm water. The hydrodynamic pressure is measured using pressure sensors at discrete points on the hull. Two hulls are studied: one is rigid and one is flexible. Predictions of the hydrodynamic loading are made using Wagner's theory, Vorus's theory, and simulations in CFDShip Iowa. These predictions assume the structure is completely rigid. These predictions of the pressure coefficient match well with the rigid hull, as expected. The spray root is tracked in the rigid experimental set and compared with the theoretical and computational models. The pressure coefficient measured on the flexible hull shows discrepancies with the predictions due to the fluid-structure interaction. These discrepancies are quantified and interpreted in light of the structural flexibility. Funding for this work is from the Office of Naval Research Grant Number N00014-16-1-3188.

Transient dynamics of a flexible rotor with squeeze film dampers

NASA Technical Reports Server (NTRS)

Buono, D. F.; Schlitzer, L. D.; Hall, R. G., III; Hibner, D. H.

1978-01-01

A series of simulated blade loss tests are reported on a test rotor designed to operate above its second bending critical speed. A series of analyses were performed which predicted the transient behavior of the test rig for each of the blade loss tests. The scope of the program included the investigation of transient rotor dynamics of a flexible rotor system, similar to modern flexible jet engine rotors, both with and without squeeze film dampers. The results substantiate the effectiveness of squeeze film dampers and document the ability of available analytical methods to predict their effectiveness and behavior.

Interfacial characterization of flexible hybrid electronics

NASA Astrophysics Data System (ADS)

Najafian, Sara; Amirkhizi, Alireza V.; Stapleton, Scott

2018-03-01

Flexible Hybrid Electronics (FHEs) are the new generation of electronics combining flexible plastic film substrates with electronic devices. Besides the electrical features, design improvements of FHEs depend on the prediction of their mechanical and failure behavior. Debonding of electronic components from the flexible substrate is one of the most common and critical failures of these devices, therefore, the experimental determination of material and interface properties is of great importance in the prediction of failure mechanisms. Traditional interface characterization involves isolated shear and normal mode tests such as the double cantilever beam (DCB) and end notch flexure (ENF) tests. However, due to the thin, flexible nature of the materials and manufacturing restrictions, tests mirroring traditional interface characterization experiments may not always be possible. The ideal goal of this research is to design experiments such that each mode of fracture is isolated. However, due to the complex nonlinear nature of the response and small geometries of FHEs, design of the proper tests to characterize the interface properties can be significantly time and cost consuming. Hence numerical modeling has been implemented to design these novel characterization experiments. This research involves loading case and specimen geometry parametric studies using numerical modeling to design future experiments where either shear or normal fracture modes are dominant. These virtual experiments will provide a foundation for designing similar tests for many different types of flexible electronics and predicting the failure mechanism independent of the specific FHE materials.

Empirical study of the dependence of the results of multivariable flexible survival analyses on model selection strategy.

PubMed

Binquet, C; Abrahamowicz, M; Mahboubi, A; Jooste, V; Faivre, J; Bonithon-Kopp, C; Quantin, C

2008-12-30

Flexible survival models, which avoid assumptions about hazards proportionality (PH) or linearity of continuous covariates effects, bring the issues of model selection to a new level of complexity. Each 'candidate covariate' requires inter-dependent decisions regarding (i) its inclusion in the model, and representation of its effects on the log hazard as (ii) either constant over time or time-dependent (TD) and, for continuous covariates, (iii) either loglinear or non-loglinear (NL). Moreover, 'optimal' decisions for one covariate depend on the decisions regarding others. Thus, some efficient model-building strategy is necessary.We carried out an empirical study of the impact of the model selection strategy on the estimates obtained in flexible multivariable survival analyses of prognostic factors for mortality in 273 gastric cancer patients. We used 10 different strategies to select alternative multivariable parametric as well as spline-based models, allowing flexible modeling of non-parametric (TD and/or NL) effects. We employed 5-fold cross-validation to compare the predictive ability of alternative models.All flexible models indicated significant non-linearity and changes over time in the effect of age at diagnosis. Conventional 'parametric' models suggested the lack of period effect, whereas more flexible strategies indicated a significant NL effect. Cross-validation confirmed that flexible models predicted better mortality. The resulting differences in the 'final model' selected by various strategies had also impact on the risk prediction for individual subjects.Overall, our analyses underline (a) the importance of accounting for significant non-parametric effects of covariates and (b) the need for developing accurate model selection strategies for flexible survival analyses. Copyright 2008 John Wiley & Sons, Ltd.

Neuroendocrine mechanisms underlying behavioral stability: implications for the evolutionary origin of personality.

PubMed

Duckworth, Renée A

2015-12-01

Personality traits are behaviors that show limited flexibility over time and across contexts, and thus understanding their origin requires an understanding of what limits behavioral flexibility. Here, I suggest that insight into the evolutionary origin of personality traits requires determining the relative importance of selection and constraint in producing limits to behavioral flexibility. Natural selection as the primary cause of limits to behavioral flexibility assumes that the default state of behavior is one of high flexibility and predicts that personality variation arises through evolution of buffering mechanisms to stabilize behavioral expression, whereas the constraint hypothesis assumes that the default state is one of limited flexibility and predicts that the neuroendocrine components that underlie personality variation are those most constrained in flexibility. Using recent work on the neurobiology of sensitive periods and maternal programming of offspring behavior, I show that some of the most stable aspects of the neuroendocrine system are structural components and maternally induced epigenetic effects. Evidence of numerous constraints to changes in structural features of the neuroendocrine system and far fewer constraints to flexibility of epigenetic systems suggests that structural constraints play a primary role in the origin of behavioral stability and that epigenetic programming may be more important in generating adaptive variation among individuals. © 2015 New York Academy of Sciences.

Characterization and Predictive Value of Segmental Curve Flexibility in Adolescent Idiopathic Scoliosis Patients.

PubMed

Yao, Guanfeng; Cheung, Jason P Y; Shigematsu, Hideki; Ohrt-Nissen, Søren; Cheung, Kenneth M C; Luk, Keith D K; Samartzis, Dino

2017-11-01

A prospective radiographic analysis of adolescent idiopathic scoliosis (AIS) patients managed with alternate-level pedicle screw fixation was performed. The objective of this study was to characterize segmental curve flexibility and to determine its predictive value in curve correction in AIS patients. Little is known regarding the distinct segmental curve characteristics and their ability to predict curve correction in patients with AIS. The segmental Cobb angle was measured on posteroanterior standing radiographs and on fulcrum bending radiographs. Radiographs were analyzed preoperatively and at 2 years postoperatively and the curve was divided into upper, mid, and lower segments based on predefined criteria. The segmental flexibility and the segmental fulcrum bending correction index (FBCI) were calculated. Eighty patients were included with mean age of 15 years. Preoperative mean segmental Cobb angles were 18, 31, and 17 degrees in the upper, mid, and lower segments, respectively. Segmental bending Cobb angles were 6, 13, and 4 degrees, respectively, corresponding to segmental flexibilities of 50%, 47%, and 83% in the upper, mid, and lower segments, respectively (P < 0.001). At 2-year follow up, the mean segmental FBCI were 155%, 131%, and 100% in the upper, mid, and lower segments, respectively (P < 0.001), which suggested that the lower segment of the curve was more flexible than the other segments and that higher correction was noted in the upper segments. A significant, positive correlation was noted between the segmental bending Cobb angle and the segmental FBCI (P < 0.05), whereby the strength of the correlation varied based on the curve segment. This is the first study to demonstrate the segmental variations in curve flexibility using the fulcrum bending radiograph in AIS patients. Curve flexibility is not uniform throughout the curve and different segments exhibit greater flexibility/correctibility than others. Segmental flexibility should be considered in assessing AIS patients and in the clinical decision-making strategy to optimize curve correction outcomes. 03.

Frontotemporal Functional Connectivity and Executive Functions Contribute to Episodic Memory Performance

PubMed Central

Blankenship, Tashauna L.; O'Neill, Meagan; Deater-Deckard, Kirby; Diana, Rachel A.; Bell, Martha Ann

2016-01-01

The contributions of hemispheric-specific electrophysiology (electroencephalogram or EEG) and independent executive functions (inhibitory control, working memory, cognitive flexibility) to episodic memory performance were examined using abstract paintings. Right hemisphere frontotemporal functional connectivity during encoding and retrieval, measured via EEG alpha coherence, statistically predicted performance on recency but not recognition judgments for the abstract paintings. Theta coherence, however, did not predict performance. Likewise, cognitive flexibility statistically predicted performance on recency judgments, but not recognition. These findings suggest that recognition and recency operate via separate electrophysiological and executive mechanisms. PMID:27388478

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

NASA Astrophysics Data System (ADS)

Bramer, David; Wei, Guo-Wei

2018-02-01

Protein structural fluctuation, measured by Debye-Waller factors or B-factors, is known to correlate to protein flexibility and function. A variety of methods has been developed for protein Debye-Waller factor prediction and related applications to domain separation, docking pose ranking, entropy calculation, hinge detection, stability analysis, etc. Nevertheless, none of the current methodologies are able to deliver an accuracy of 0.7 in terms of the Pearson correlation coefficients averaged over a large set of proteins. In this work, we introduce a paradigm-shifting geometric graph model, multiscale weighted colored graph (MWCG), to provide a new generation of computational algorithms to significantly change the current status of protein structural fluctuation analysis. Our MWCG model divides a protein graph into multiple subgraphs based on interaction types between graph nodes and represents the protein rigidity by generalized centralities of subgraphs. MWCGs not only predict the B-factors of protein residues but also accurately analyze the flexibility of all atoms in a protein. The MWCG model is validated over a number of protein test sets and compared with many standard methods. An extensive numerical study indicates that the proposed MWCG offers an accuracy of over 0.8 and thus provides perhaps the first reliable method for estimating protein flexibility and B-factors. It also simultaneously predicts all-atom flexibility in a molecule.

Age differences in recall and predicting recall of action events and words.

PubMed

McDonald-Miszczak, L; Hubley, A M; Hultsch, D F

1996-03-01

Age differences in recall and prediction of recall were examined with different memory tasks. We asked 36 younger (19-28 yrs) and 36 older (60-81 yrs) women to provide both global and item-by-item predictions of their recall, and then to recall either (a) Subject Performance Tasks (SPTs), (b) verb-noun word-pairs memorized in list-like fashion (Word-Pairs), or (c) nonsense verb-noun word-pairs (Nonsense-Pairs) over three experimental trials. Based on previous research, we hypothesized that these tasks would vary in relative difficulty and flexibility of encoding. The results indicated that (a) age differences in global predictions (task specific self-efficacy) and recall performance across trials were minimized with SPT as compared with verbal materials, (b) global predictions were higher and more accurate for SPT as compared to verbal materials, and (c) item-by-item predictions were most accurate for materials encoded with the most flexibility (Nonsense Pairs). The results suggest that SPTs may provide some level of environmental support to reduce age differences in performance and task-specific self-efficacy, but that memory monitoring may depend on specific characteristics of the stimuli (i.e., flexibility of encoding) rather than their verbal or nonverbal nature.

Language, cognitive flexibility, and explicit false belief understanding: longitudinal analysis in typical development and specific language impairment.

PubMed

Farrant, Brad M; Maybery, Murray T; Fletcher, Janet

2012-01-01

The hypothesis that language plays a role in theory-of-mind (ToM) development is supported by a number of lines of evidence (e.g., H. Lohmann & M. Tomasello, 2003). The current study sought to further investigate the relations between maternal language input, memory for false sentential complements, cognitive flexibility, and the development of explicit false belief understanding in 91 English-speaking typically developing children (M age = 61.3 months) and 30 children with specific language impairment (M age = 63.0 months). Concurrent and longitudinal findings converge in supporting a model in which maternal language input predicts the child's memory for false complements, which predicts cognitive flexibility, which in turn predicts explicit false belief understanding. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc.

Model predictive control of attitude maneuver of a geostationary flexible satellite based on genetic algorithm

NASA Astrophysics Data System (ADS)

TayyebTaher, M.; Esmaeilzadeh, S. Majid

2017-07-01

This article presents an application of Model Predictive Controller (MPC) to the attitude control of a geostationary flexible satellite. SIMO model has been used for the geostationary satellite, using the Lagrange equations. Flexibility is also included in the modelling equations. The state space equations are expressed in order to simplify the controller. Naturally there is no specific tuning rule to find the best parameters of an MPC controller which fits the desired controller. Being an intelligence method for optimizing problem, Genetic Algorithm has been used for optimizing the performance of MPC controller by tuning the controller parameter due to minimum rise time, settling time, overshoot of the target point of the flexible structure and its mode shape amplitudes to make large attitude maneuvers possible. The model included geosynchronous orbit environment and geostationary satellite parameters. The simulation results of the flexible satellite with attitude maneuver shows the efficiency of proposed optimization method in comparison with LQR optimal controller.

Executive function moderates the role of muscular fitness in determining functional mobility in older adults.

PubMed

Forte, Roberta; Pesce, Caterina; Leite, Joao Costa; De Vito, Giuseppe; Gibney, Eileen R; Tomporowski, Phillip D; Boreham, Colin A G

2013-06-01

Both physical and cognitive factors are known to independently predict functional mobility in older people. However, the combined predictive value of both physical fitness and cognitive factors on functional mobility has been less investigated. The aim of the present study was to assess if cognitive executive functions moderate the role of physical fitness in determining functional mobility of older individuals. Fifty-seven 65- to 75-year-old healthy participants performed tests of functional mobility (habitual and maximal walking speed, maximal walking speed while picking up objects/stepping over obstacles), physical fitness (peak power, knee extensors torque, back/lower limb flexibility, aerobic fitness), and executive function (inhibition and cognitive flexibility). Maximal walking speeds were predicted by physical fitness parameters and their interaction with cognitive factors. Knee extensor torque emerged as the main predictor of all tested locomotor performances at maximal speed. The effect of peak power and back/lower limb flexibility was moderated by executive functions. In particular, inhibition and cognitive flexibility differed in the way in which they moderate the role of fitness. High levels of cognitive flexibility seem necessary to take advantage of leg power for walking at maximal speed. In contrast, high levels of inhibitory capacity seem to compensate for low levels of back/lower limb flexibility when picking up movements are added to a locomotor task. These findings may have important practical implications for the design and implementation of multi-component training programs aimed at optimizing functional abilities in older adults.

Cognitive flexibility predicts early reading skills

PubMed Central

Colé, Pascale; Duncan, Lynne G.; Blaye, Agnès

2014-01-01

An important aspect of learning to read is efficiency in accessing different kinds of linguistic information (orthographic, phonological, and semantic) about written words. The present study investigates whether, in addition to the integrity of such linguistic skills, early progress in reading may require a degree of cognitive flexibility in order to manage the coordination of this information effectively. Our study will look for evidence of a link between flexibility and both word reading and passage reading comprehension, and examine whether any such link involves domain-general or reading-specific flexibility. As the only previous support for a predictive relationship between flexibility and early reading comes from studies of reading comprehension in the opaque English orthography, another possibility is that this relationship may be largely orthography-dependent, only coming into play when mappings between representations are complex and polyvalent. To investigate these questions, 60 second-graders learning to read the more transparent French orthography were presented with two multiple classification tasks involving reading-specific cognitive flexibility (based on words) and non-specific flexibility (based on pictures). Reading skills were assessed by word reading, pseudo-word decoding, and passage reading comprehension measures. Flexibility was found to contribute significant unique variance to passage reading comprehension even in the less opaque French orthography. More interestingly, the data also show that flexibility is critical in accounting for one of the core components of reading comprehension, namely, the reading of words in isolation. Finally, the results constrain the debate over whether flexibility has to be reading-specific to be critically involved in reading. PMID:24966842

Effect of flexibility on the growth of concentration fluctuations in a suspension of sedimenting fibers: Particle simulations

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

Manikantan, Harishankar; Saintillan, David

2016-01-15

Three-dimensional numerical simulations are performed to study the stability of a sedimenting suspension of weakly flexible fibers. It is well known that a suspension of rigid rods sedimenting under gravity at low Reynolds number is unstable to concentration fluctuations owing to hydrodynamic interactions. Flexible fibers, however, reorient while settling and even weak flexibility can alter their collective dynamics. In our recent work [Manikantan et al., “The instability of a sedimenting suspension of weakly flexible fibres,” J. Fluid Mech. 756, 935–964 (2014)], we developed a mean-field theory to predict the linear stability of such a system. Here, we verify these predictionsmore » using accurate and efficient particle simulations based on a slender-body model. We also demonstrate the mechanisms by which flexibility-induced reorientation alters suspension microstructure, and through it, its stability. Specifically, we first show that the anisotropy of the base state in the case of a suspension of flexible fibers has a destabilizing effect compared to a suspension of rigid rods. Second, a conflicting effect of flexibility is also shown to suppress particle clustering and slow down the growth of the instability. The relative magnitude of filament flexibility and rotational Brownian motion dictates which effect dominates, and our simulations qualitatively follow theoretically predicted trends. The mechanism for either effects is tied to the flexibility-induced reorientation of particles, which we illustrate using velocity and orientation statistics from our simulations. Finally, we also show that, in the case of an initially homogeneous and isotropic suspension, flexibility always acts to suppress the growth of the instability.« less

How preschool executive functioning predicts several aspects of math achievement in Grades 1 and 3: A longitudinal study.

PubMed

Viterbori, Paola; Usai, M Carmen; Traverso, Laura; De Franchis, Valentina

2015-12-01

This longitudinal study analyzes whether selected components of executive function (EF) measured during the preschool period predict several indices of math achievement in primary school. Six EF measures were assessed in a sample of 5-year-old children (N = 175). The math achievement of the same children was then tested in Grades 1 and 3 using both a composite math score and three single indices of written calculation, arithmetical facts, and problem solving. Using previous results obtained from the same sample of children, a confirmatory factor analysis examining the latent EF structure in kindergarten indicated that a two-factor model provided the best fit for the data. In this model, inhibition and working memory (WM)-flexibility were separate dimensions. A full structural equation model was then used to test the hypothesis that math achievement (the composite math score and single math scores) in Grades 1 and 3 could be explained by the two EF components comprising the kindergarten model. The results indicate that the WM-flexibility component measured during the preschool period substantially predicts mathematical achievement, especially in Grade 3. The math composite scores were predicted by the WM-flexibility factor at both grade levels. In Grade 3, both problem solving and arithmetical facts were predicted by the WM-flexibility component. The results empirically support interventions that target EF as an important component of early childhood mathematics education. Copyright © 2015 Elsevier Inc. All rights reserved.

Aeroelastic Analysis of a Flexible Wing Wind Tunnel Model with Variable Camber Continuous Trailing Edge Flap Design

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Ting, Eric; Lebofsky, Sonia

2015-01-01

This paper presents data analysis of a flexible wing wind tunnel model with a variable camber continuous trailing edge flap (VCCTEF) design for drag minimization tested at the University of Washington Aeronautical Laboratory (UWAL). The wind tunnel test was designed to explore the relative merit of the VCCTEF concept for improved cruise efficiency through the use of low-cost aeroelastic model test techniques. The flexible wing model is a 10%-scale model of a typical transport wing and is constructed of woven fabric composites and foam core. The wing structural stiffness in bending is tailored to be half of the stiffness of a Boeing 757-era transport wing while the torsional stiffness is about the same. This stiffness reduction results in a wing tip deflection of about 10% of the wing semi-span. The VCCTEF is a multi-segment flap design having three chordwise camber segments and five spanwise flap sections for a total of 15 individual flap elements. The three chordwise camber segments can be positioned appropriately to create a desired trailing edge camber. Elastomeric material is used to cover the gaps in between the spanwise flap sections, thereby creating a continuous trailing edge. Wind tunnel data analysis conducted previously shows that the VCCTEF can achieve a drag reduction of up to 6.31% and an improvement in the lift-to-drag ratio (L=D) of up to 4.85%. A method for estimating the bending and torsional stiffnesses of the flexible wingUWAL wind tunnel model from static load test data is presented. The resulting estimation indicates that the stiffness of the flexible wing is significantly stiffer in torsion than in bending by as much as 9 to 1. The lift prediction for the flexible wing is computed by a coupled aerodynamic-structural model. The coupled model is developed by coupling a conceptual aerodynamic tool Vorlax with a finite-element model of the flexible wing via an automated geometry deformation tool. Based on the comparison of the lift curve slope, the lift prediction for the rigid wing is in good agreement with the estimated lift coefficients derived from the wind tunnel test data. Due to the movement of the VCCTEF during the wind tunnel test, uncertainty in the lift prediction due to the indicated variations of the VCCTEF deflection is studied. The results show a significant spread in the lift prediction which contradicts the consistency in the aerodynamic measurements, thus suggesting that the indicated variations as measured by the VICON system may not be reliable. The lift prediction of the flexible wing agrees very well with the measured lift curve for the baseline configuration. The computed bending deflection and wash-out twist of the flexible wing also match reasonably well with the aeroelastic deflection measurements. The results demonstrate the validity of the aerodynamic-structural tool for use to analyze aerodynamic performance of flexible wings.

Wearable, Flexible, and Multifunctional Healthcare Device with an ISFET Chemical Sensor for Simultaneous Sweat pH and Skin Temperature Monitoring.

PubMed

Nakata, Shogo; Arie, Takayuki; Akita, Seiji; Takei, Kuniharu

2017-03-24

Real-time daily healthcare monitoring may increase the chances of predicting and diagnosing diseases in their early stages which, currently, occurs most frequently during medical check-ups. Next-generation noninvasive healthcare devices, such as flexible multifunctional sensor sheets designed to be worn on skin, are considered to be highly suitable candidates for continuous real-time health monitoring. For healthcare applications, acquiring data on the chemical state of the body, alongside physical characteristics such as body temperature and activity, are extremely important for predicting and identifying potential health conditions. To record these data, in this study, we developed a wearable, flexible sweat chemical sensor sheet for pH measurement, consisting of an ion-sensitive field-effect transistor (ISFET) integrated with a flexible temperature sensor: we intend to use this device as the foundation of a fully integrated, wearable healthcare patch in the future. After characterizing the performance, mechanical flexibility, and stability of the sensor, real-time measurements of sweat pH and skin temperature are successfully conducted through skin contact. This flexible integrated device has the potential to be developed into a chemical sensor for sweat for applications in healthcare and sports.

A new approach for evaluating flexible working hours.

PubMed

Giebel, Ole; Janssen, Daniela; Schomann, Carsten; Nachreiner, Friedhelm

2004-01-01

Recent studies on flexible working hours show at least some of these working time arrangements seem to be associated with impairing effects of health and well-being. According to available evidence, variability of working hours seems to play an important role. The question, however, is how this variability can be assessed and used to explain or predict impairments. Based on earlier methods used to assess shift-work effects, a time series analysis approach was applied to the matter of flexible working hours. Data on the working hours of 4 week's length of 137 respondents derived from a survey on flexible work hours involving 15 companies of different production and service sectors in Germany were converted to time series and analyzed by spectral analysis. A cluster analysis of the resulting power spectra yielded 5 clusters of flexible work hours. Analyzing these clusters for differences in reported impairments showed that workers who showed suppression of circadian and weekly rhythms experienced severest impairments, especially in circadian controlled functions like sleep and digestion. The results thus indicate that analyzing the periodicity of flexible working hours seems to be a promising approach for predicting impairments which should be investigated further in the future.

Texas flexible pavements and overlays : year 5 report - complete data documentation.

DOT National Transportation Integrated Search

2017-05-01

Proper calibration and validation of pavement design and performance models to Texas conditions is : essential for cost-effective flexible pavement design, performance predictions, and maintenance/rehab : strategies. The veracity of the calibration o...

Vibrational response analysis of tires using a three-dimensional flexible ring-based model

NASA Astrophysics Data System (ADS)

Matsubara, Masami; Tajiri, Daiki; Ise, Tomohiko; Kawamura, Shozo

2017-11-01

Tire vibration characteristics influence noise, vibration, and harshness. Hence, there have been many investigations of the dynamic responses of tires. In this paper, we present new formulations for the prediction of tire tread vibrations below 150 Hz using a three-dimensional flexible ring-based model. The ring represents the tread including the belt, and the springs represent the tire sidewall stiffness. The equations of motion for lateral, longitudinal, and radial vibration on the tread are derived based on the assumption of inextensional deformation. Many of the associated numerical parameters are identified from experimental tests. Unlike most studies of flexible ring models, which mainly discussed radial and circumferential vibration, this study presents steady response functions concerning not only radial and circumferential but also lateral vibration using the three-dimensional flexible ring-based model. The results of impact tests described confirm the theoretical findings. The results show reasonable agreement with the predictions.

Encompassing receptor flexibility in virtual screening using ensemble docking-based hybrid QSAR: discovery of novel phytochemicals for BACE1 inhibition.

PubMed

Chakraborty, Sandipan; Ramachandran, Balaji; Basu, Soumalee

2014-10-01

Mimicking receptor flexibility during receptor-ligand binding is a challenging task in computational drug design since it is associated with a large increase in the conformational search space. In the present study, we have devised an in silico design strategy incorporating receptor flexibility in virtual screening to identify potential lead compounds as inhibitors for flexible proteins. We have considered BACE1 (β-secretase), a key target protease from a therapeutic perspective for Alzheimer's disease, as the highly flexible receptor. The protein undergoes significant conformational transitions from open to closed form upon ligand binding, which makes it a difficult target for inhibitor design. We have designed a hybrid structure-activity model containing both ligand based descriptors and energetic descriptors obtained from molecular docking based on a dataset of structurally diverse BACE1 inhibitors. An ensemble of receptor conformations have been used in the docking study, further improving the prediction ability of the model. The designed model that shows significant prediction ability judged by several statistical parameters has been used to screen an in house developed 3-D structural library of 731 phytochemicals. 24 highly potent, novel BACE1 inhibitors with predicted activity (Ki) ≤ 50 nM have been identified. Detailed analysis reveals pharmacophoric features of these novel inhibitors required to inhibit BACE1.

Sexual selection and population divergence I: The influence of socially flexible cuticular hydrocarbon expression in male field crickets (Teleogryllus oceanicus).

PubMed

Pascoal, Sonia; Mendrok, Magdalena; Mitchell, Christopher; Wilson, Alastair J; Hunt, John; Bailey, Nathan W

2016-01-01

Debates about how coevolution of sexual traits and preferences might promote evolutionary diversification have permeated speciation research for over a century. Recent work demonstrates that the expression of such traits can be sensitive to variation in the social environment. Here, we examined social flexibility in a sexually selected male trait-cuticular hydrocarbon (CHC) profiles-in the field cricket Teleogryllus oceanicus and tested whether population genetic divergence predicts the extent or direction of social flexibility in allopatric populations. We manipulated male crickets' social environments during rearing and then characterized CHC profiles. CHC signatures varied considerably across populations and also in response to the social environment, but our prediction that increased social flexibility would be selected in more recently founded populations exposed to fluctuating demographic environments was unsupported. Furthermore, models examining the influence of drift and selection failed to support a role of sexual selection in driving population divergence in CHC profiles. Variation in social environments might alter the dynamics of sexual selection, but our results align with theoretical predictions that the role social flexibility plays in modulating evolutionary divergence depends critically on whether responses to variation in the social environment are homogeneous across populations, or whether gene by social environment interactions occur. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

ReactPRED: a tool to predict and analyze biochemical reactions.

PubMed

Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

2016-11-15

Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same. ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application. ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Behavioral flexibility and problem solving in an invasive bird.

PubMed

Logan, Corina J

2016-01-01

Behavioral flexibility is considered an important trait for adapting to environmental change, but it is unclear what it is, how it works, and whether it is a problem solving ability. I investigated behavioral flexibility and problem solving experimentally in great-tailed grackles, an invasive bird species and thus a likely candidate for possessing behavioral flexibility. Grackles demonstrated behavioral flexibility in two contexts, the Aesop's Fable paradigm and a color association test. Contrary to predictions, behavioral flexibility did not correlate across contexts. Four out of 6 grackles exhibited efficient problem solving abilities, but problem solving efficiency did not appear to be directly linked with behavioral flexibility. Problem solving speed also did not significantly correlate with reversal learning scores, indicating that faster learners were not the most flexible. These results reveal how little we know about behavioral flexibility, and provide an immense opportunity for future research to explore how individuals and species can use behavior to react to changing environments.

Performance Prediction Relationships for AM2 Airfield Matting Developed from Full-Scale Accelerated Testing and Laboratory Experimentation

DTIC Science & Technology

2018-01-01

work, the prevailing methods used to predict the performance of AM2 were based on the CBR design procedure for flexible pavements using a small number...suitable for design and evaluation frameworks currently used for airfield pavements and matting systems. DISCLAIMER: The contents of this report...methods used to develop the equivalency curves equated the mat-surfaced area to an equivalent thickness of flexible pavement using the CBR design

Differential Role of CBT Skills, DBT Skills and Psychological Flexibility in Predicting Depressive versus Anxiety Symptom Improvement

PubMed Central

Webb, Christian A.; Beard, Courtney; Kertz, Sarah J.; Hsu, Kean; Björgvinsson, Thröstur

2016-01-01

Objective Studies have reported associations between cognitive behavioral therapy (CBT) skill use and symptom improvement in depressed outpatient samples. However, little is known regarding the temporal relationship between different subsets of therapeutic skills and symptom change among relatively severely depressed patients receiving treatment in psychiatric hospital settings. Method Adult patients with major depression (N=173) receiving combined psychotherapeutic and pharmacological treatment at a psychiatric hospital completed repeated assessments of traditional CBT skills, DBT skills and psychological flexibility, as well as depressive and anxiety symptoms. Results Results indicated that only use of behavioral activation (BA) strategies significantly predicted depressive symptom improvement in this sample; whereas DBT skills and psychological flexibility predicted anxiety symptom change. In addition, a baseline symptom severity X BA strategies interaction emerged indicating that those patients with higher pretreatment depression severity exhibited the strongest association between use of BA strategies and depressive symptom improvement. Conclusions Findings suggest the importance of emphasizing the acquisition and regular use of BA strategies with severely depressed patients in short-term psychiatric settings. In contrast, an emphasis on the development of DBT skills and the cultivation of psychological flexibility may prove beneficial for the amelioration of anxiety symptoms. PMID:27057997

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

PubMed Central

Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

2014-01-01

As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252

Improved prediction of residue flexibility by embedding optimized amino acid grouping into RSA-based linear models.

PubMed

Zhang, Hua; Kurgan, Lukasz

2014-12-01

Knowledge of protein flexibility is vital for deciphering the corresponding functional mechanisms. This knowledge would help, for instance, in improving computational drug design and refinement in homology-based modeling. We propose a new predictor of the residue flexibility, which is expressed by B-factors, from protein chains that use local (in the chain) predicted (or native) relative solvent accessibility (RSA) and custom-derived amino acid (AA) alphabets. Our predictor is implemented as a two-stage linear regression model that uses RSA-based space in a local sequence window in the first stage and a reduced AA pair-based space in the second stage as the inputs. This method is easy to comprehend explicit linear form in both stages. Particle swarm optimization was used to find an optimal reduced AA alphabet to simplify the input space and improve the prediction performance. The average correlation coefficients between the native and predicted B-factors measured on a large benchmark dataset are improved from 0.65 to 0.67 when using the native RSA values and from 0.55 to 0.57 when using the predicted RSA values. Blind tests that were performed on two independent datasets show consistent improvements in the average correlation coefficients by a modest value of 0.02 for both native and predicted RSA-based predictions.

Free Vibration Analysis of a Spinning Flexible DISK-SPINDLE System Supported by Ball Bearing and Flexible Shaft Using the Finite Element Method and Substructure Synthesis

NASA Astrophysics Data System (ADS)

JANG, G. H.; LEE, S. H.; JUNG, M. S.

2002-03-01

Free vibration of a spinning flexible disk-spindle system supported by ball bearing and flexible shaft is analyzed by using Hamilton's principle, FEM and substructure synthesis. The spinning disk is described by using the Kirchhoff plate theory and von Karman non-linear strain. The rotating spindle and stationary shaft are modelled by Rayleigh beam and Euler beam respectively. Using Hamilton's principle and including the rigid body translation and tilting motion, partial differential equations of motion of the spinning flexible disk and spindle are derived consistently to satisfy the geometric compatibility in the internal boundary between substructures. FEM is used to discretize the derived governing equations, and substructure synthesis is introduced to assemble each component of the disk-spindle-bearing-shaft system. The developed method is applied to the spindle system of a computer hard disk drive with three disks, and modal testing is performed to verify the simulation results. The simulation result agrees very well with the experimental one. This research investigates critical design parameters in an HDD spindle system, i.e., the non-linearity of a spinning disk and the flexibility and boundary condition of a stationary shaft, to predict the free vibration characteristics accurately. The proposed method may be effectively applied to predict the vibration characteristics of a spinning flexible disk-spindle system supported by ball bearing and flexible shaft in the various forms of computer storage device, i.e., FDD, CD, HDD and DVD.

Report on the sixth blind test of organic crystal structure prediction methods

PubMed Central

Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.; Bhattacharya, Saswata; Boese, A. Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J.; Bylsma, Rita; Campbell, Josh E.; Car, Roberto; Case, David H.; Chadha, Renu; Cole, Jason C.; Cosburn, Katherine; Cuppen, Herma M.; Curtis, Farren; Day, Graeme M.; DiStasio Jr, Robert A.; Dzyabchenko, Alexander; van Eijck, Bouke P.; Elking, Dennis M.; van den Ende, Joost A.; Facelli, Julio C.; Ferraro, Marta B.; Fusti-Molnar, Laszlo; Gatsiou, Christina-Anna; Gee, Thomas S.; de Gelder, René; Ghiringhelli, Luca M.; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W. M.; Hoja, Johannes; Hylton, Rebecca K.; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T.; Kendrick, John; de Klerk, Niek J. J.; Ko, Hsin-Yu; Kuleshova, Liudmila N.; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J. J.; Lund, Albert M.; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E.; McCabe, Patrick; McMahon, David P.; Meekes, Hugo; Metz, Michael P.; Misquitta, Alston J.; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J.; Neumann, Marcus A.; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R.; Orendt, Anita M.; Pagola, Gabriel I.; Pantelides, Constantinos C.; Pickard, Chris J.; Podeszwa, Rafal; Price, Louise S.; Price, Sarah L.; Pulido, Angeles; Read, Murray G.; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P.; Singh, Pawanpreet; Sugden, Isaac J.; Szalewicz, Krzysztof; Taylor, Christopher R.; Tkatchenko, Alexandre; Tuckerman, Mark E.; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E.; de Wijs, Gilles A.; Yang, Jack; Zhu, Qiang; Groom, Colin R.

2016-01-01

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

Mechanistic-Empirical Pavement Design Guide Flexible Pavement Performance Prediction Models Volume II Reference Manual

DOT National Transportation Integrated Search

2007-08-01

The objective of this research study was to develop performance characteristics or variables (e.g., ride quality, rutting, : fatigue cracking, transverse cracking) of flexible pavements in Montana, and to use these characteristics in the : implementa...

Adaptive Encoding of Outcome Prediction by Prefrontal Cortex Ensembles Supports Behavioral Flexibility.

PubMed

Del Arco, Alberto; Park, Junchol; Wood, Jesse; Kim, Yunbok; Moghaddam, Bita

2017-08-30

The prefrontal cortex (PFC) is thought to play a critical role in behavioral flexibility by monitoring action-outcome contingencies. How PFC ensembles represent shifts in behavior in response to changes in these contingencies remains unclear. We recorded single-unit activity and local field potentials in the dorsomedial PFC (dmPFC) of male rats during a set-shifting task that required them to update their behavior, among competing options, in response to changes in action-outcome contingencies. As behavior was updated, a subset of PFC ensembles encoded the current trial outcome before the outcome was presented. This novel outcome-prediction encoding was absent in a control task, in which actions were rewarded pseudorandomly, indicating that PFC neurons are not merely providing an expectancy signal. In both control and set-shifting tasks, dmPFC neurons displayed postoutcome discrimination activity, indicating that these neurons also monitor whether a behavior is successful in generating rewards. Gamma-power oscillatory activity increased before the outcome in both tasks but did not differentiate between expected outcomes, suggesting that this measure is not related to set-shifting behavior but reflects expectation of an outcome after action execution. These results demonstrate that PFC neurons support flexible rule-based action selection by predicting outcomes that follow a particular action. SIGNIFICANCE STATEMENT Tracking action-outcome contingencies and modifying behavior when those contingencies change is critical to behavioral flexibility. We find that ensembles of dorsomedial prefrontal cortex neurons differentiate between expected outcomes when action-outcome contingencies change. This predictive mode of signaling may be used to promote a new response strategy at the service of behavioral flexibility. Copyright © 2017 the authors 0270-6474/17/378363-11$15.00/0.

Balancing techniques for high-speed flexible rotors

NASA Technical Reports Server (NTRS)

Smalley, A. J.

1978-01-01

Ideal and non-ideal conditions for multiplane balancing are addressed. Methodology and procedures for identifying optimum balancing configurations and for assessing, quantitatively, the penalties associated with non-optimum configurations were developed and demonstrated. The problems introduced when vibration sensors are supported on flexible mounts were assessed experimentally, and the effects of flexural asymmetry in the rotor on balancing were investigated. A general purpose method for predicting the threshold of instability of an asymmetric rotor was developed, and its predictions are compared with measurements under different degrees of asymmetry.

Mechanistic-Empirical Pavement Design Guide Flexible Pavement Performance Prediction Models Volume I Executive Research Summary

DOT National Transportation Integrated Search

2007-08-01

The objective of this research study was to develop performance characteristics or variables (e.g., ride quality, rutting, : fatigue cracking, transverse cracking) of flexible pavements in Montana, and to use these characteristics in the : implementa...

One-dimensional potential of mean force underestimates activation barrier for transport across flexible lipid membranes

NASA Astrophysics Data System (ADS)

Kopelevich, Dmitry I.

2013-10-01

Transport of a fullerene-like nanoparticle across a lipid bilayer is investigated by coarse-grained molecular dynamics (MD) simulations. Potentials of mean force (PMF) acting on the nanoparticle in a flexible bilayer suspended in water and a bilayer restrained to a flat surface are computed by constrained MD simulations. The rate of the nanoparticle transport into the bilayer interior is predicted using one-dimensional Langevin models based on these PMFs. The predictions are compared with the transport rates obtained from a series of direct (unconstrained) MD simulations of the solute transport into the flexible bilayer. It is observed that the PMF acting on the solute in the flexible membrane underestimates the transport rate by more than an order of magnitude while the PMF acting on the solute in the restrained membrane yields an accurate estimate of the activation energy for transport into the flexible membrane. This paradox is explained by a coexistence of metastable membrane configurations for a range of the solute positions inside and near the flexible membrane. This leads to a significant reduction of the contribution of the transition state to the mean force acting on the solute. Restraining the membrane shape ensures that there is only one stable membrane configuration corresponding to each solute position and thus the transition state is adequately represented in the PMF. This mechanism is quite general and thus this phenomenon is expected to occur in a wide range of interfacial systems. A simple model for the free energy landscape of the coupled solute-membrane system is proposed and validated. This model explicitly accounts for effects of the membrane deformations on the solute transport and yields an accurate prediction of the activation energy for the solute transport.

Testing the Link Between Empathy and Lay Theories of Happiness.

PubMed

Tullett, Alexa M; Plaks, Jason E

2016-09-20

Happiness is a topic that ignites both considerable interest and considerable disagreement. Thus far, however, there has been little attempt to characterize people's lay theories about happiness or explore their consequences. We examined whether individual differences in lay theories of happiness would predict empathy. In Studies 1a and 1b, we validated the Lay Theories of Happiness Scale (LTHS), which includes three dimensions: flexibility, controllability, and locus. In Study 2, higher dispositional empathy was predicted by the belief that happiness is flexible, controllable, and internal. In Studies 3 and 4, higher empathy toward a specific target was predicted by the belief that happiness is flexible, uncontrollable, and external In conjunction, Studies 2, 3, and 4 provide evidence that trait and state empathy are separable and can have opposing relationships with people's lay theories. Overall, these findings highlight generalized beliefs that may guide empathic reactions to the unhappiness of others. © 2016 by the Society for Personality and Social Psychology, Inc.

Pre-operative prediction of surgical morbidity in children: comparison of five statistical models.

PubMed

Cooper, Jennifer N; Wei, Lai; Fernandez, Soledad A; Minneci, Peter C; Deans, Katherine J

2015-02-01

The accurate prediction of surgical risk is important to patients and physicians. Logistic regression (LR) models are typically used to estimate these risks. However, in the fields of data mining and machine-learning, many alternative classification and prediction algorithms have been developed. This study aimed to compare the performance of LR to several data mining algorithms for predicting 30-day surgical morbidity in children. We used the 2012 National Surgical Quality Improvement Program-Pediatric dataset to compare the performance of (1) a LR model that assumed linearity and additivity (simple LR model) (2) a LR model incorporating restricted cubic splines and interactions (flexible LR model) (3) a support vector machine, (4) a random forest and (5) boosted classification trees for predicting surgical morbidity. The ensemble-based methods showed significantly higher accuracy, sensitivity, specificity, PPV, and NPV than the simple LR model. However, none of the models performed better than the flexible LR model in terms of the aforementioned measures or in model calibration or discrimination. Support vector machines, random forests, and boosted classification trees do not show better performance than LR for predicting pediatric surgical morbidity. After further validation, the flexible LR model derived in this study could be used to assist with clinical decision-making based on patient-specific surgical risks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning

NASA Astrophysics Data System (ADS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-01

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning

PubMed Central

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-01-01

Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate. PMID:28418043

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.

PubMed

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-18

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Behavioral flexibility and problem solving in an invasive bird

PubMed Central

2016-01-01

Behavioral flexibility is considered an important trait for adapting to environmental change, but it is unclear what it is, how it works, and whether it is a problem solving ability. I investigated behavioral flexibility and problem solving experimentally in great-tailed grackles, an invasive bird species and thus a likely candidate for possessing behavioral flexibility. Grackles demonstrated behavioral flexibility in two contexts, the Aesop’s Fable paradigm and a color association test. Contrary to predictions, behavioral flexibility did not correlate across contexts. Four out of 6 grackles exhibited efficient problem solving abilities, but problem solving efficiency did not appear to be directly linked with behavioral flexibility. Problem solving speed also did not significantly correlate with reversal learning scores, indicating that faster learners were not the most flexible. These results reveal how little we know about behavioral flexibility, and provide an immense opportunity for future research to explore how individuals and species can use behavior to react to changing environments. PMID:27168984

The multidirectional bending properties of the human lumbar intervertebral disc.

PubMed

Spenciner, David; Greene, David; Paiva, James; Palumbo, Mark; Crisco, Joseph

2006-01-01

While the biomechanical properties of the isolated intervertebral disc have been well studied in the three principal anatomic directions of flexion/extension, axial rotation, and lateral bending, there is little data on the properties in the more functional directions that are combinations of these principal anatomic directions. To determine the bending flexibility, range of motion (ROM), and neutral zone (NZ) of the human lumbar disc in multiple directions and to determine if the values about the combined moment axes can be predicted from the values about principal moment axes. Three-dimensional biomechanical analysis of the elastic bending properties of human lumbar discs about principal and combined moment axes. Pure, unconstrained moments were applied about multiple axes. The bending properties (flexibility, ROM, and NZ) of isolated lumbar discs (n=4 for L2/L3 and n=3 for L4/L5) were determined in the six principal directions and in 20 combined directions. The experimental values were compared with those predicted from the linear combination of the six principal moment axes. The maximum and minimum values of the biomechanical properties were found at the principal moment axes. Among combined moment axes, ROM and NZ (but not flexibility) values were predicted from the principal moment axis values. The principal moment axes coincide with the primary mechanical axes of the intervertebral disc and demonstrate significant differences in direction for values of flexibility, ROM, and NZ. Not all combined moment axis values can be predicted from principal moment axis values.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

PubMed Central

Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.; Bartashevich, Ekaterina; Boerrigter, Stephan X. M.; Braun, Doris E.; Cruz-Cabeza, Aurora J.; Day, Graeme M.; Della Valle, Raffaele G.; Desiraju, Gautam R.; van Eijck, Bouke P.; Facelli, Julio C.; Ferraro, Marta B.; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W. M.; Hofmann, Fridolin; Jose, K. V. Jovan; Karamertzanis, Panagiotis G.; Kazantsev, Andrei V.; Kendrick, John; Kuleshova, Liudmila N.; Leusen, Frank J. J.; Maleev, Andrey V.; Misquitta, Alston J.; Mohamed, Sharmarke; Needs, Richard J.; Neumann, Marcus A.; Nikylov, Denis; Orendt, Anita M.; Pal, Rumpa; Pantelides, Constantinos C.; Pickard, Chris J.; Price, Louise S.; Price, Sarah L.; Scheraga, Harold A.; van de Streek, Jacco; Thakur, Tejender S.; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K.

2011-01-01

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

PSO-MISMO modeling strategy for multistep-ahead time series prediction.

PubMed

Bao, Yukun; Xiong, Tao; Hu, Zhongyi

2014-05-01

Multistep-ahead time series prediction is one of the most challenging research topics in the field of time series modeling and prediction, and is continually under research. Recently, the multiple-input several multiple-outputs (MISMO) modeling strategy has been proposed as a promising alternative for multistep-ahead time series prediction, exhibiting advantages compared with the two currently dominating strategies, the iterated and the direct strategies. Built on the established MISMO strategy, this paper proposes a particle swarm optimization (PSO)-based MISMO modeling strategy, which is capable of determining the number of sub-models in a self-adaptive mode, with varying prediction horizons. Rather than deriving crisp divides with equal-size s prediction horizons from the established MISMO, the proposed PSO-MISMO strategy, implemented with neural networks, employs a heuristic to create flexible divides with varying sizes of prediction horizons and to generate corresponding sub-models, providing considerable flexibility in model construction, which has been validated with simulated and real datasets.

Differential role of CBT skills, DBT skills and psychological flexibility in predicting depressive versus anxiety symptom improvement.

PubMed

Webb, Christian A; Beard, Courtney; Kertz, Sarah J; Hsu, Kean J; Björgvinsson, Thröstur

2016-06-01

Studies have reported associations between cognitive behavioral therapy (CBT) skill use and symptom improvement in depressed outpatient samples. However, little is known regarding the temporal relationship between different subsets of therapeutic skills and symptom change among relatively severely depressed patients receiving treatment in psychiatric hospital settings. Adult patients with major depression (N = 173) receiving combined psychotherapeutic and pharmacological treatment at a psychiatric hospital completed repeated assessments of traditional CBT skills, DBT skills and psychological flexibility, as well as depressive and anxiety symptoms. Results indicated that only use of behavioral activation (BA) strategies significantly predicted depressive symptom improvement in this sample; whereas DBT skills and psychological flexibility predicted anxiety symptom change. In addition, a baseline symptom severity X BA strategies interaction emerged indicating that those patients with higher pretreatment depression severity exhibited the strongest association between use of BA strategies and depressive symptom improvement. Findings suggest the importance of emphasizing the acquisition and regular use of BA strategies with severely depressed patients in short-term psychiatric settings. In contrast, an emphasis on the development of DBT skills and the cultivation of psychological flexibility may prove beneficial for the amelioration of anxiety symptoms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Increasing work-time influence: consequences for flexibility, variability, regularity and predictability.

PubMed

Nabe-Nielsen, Kirsten; Garde, Anne Helene; Aust, Birgit; Diderichsen, Finn

2012-01-01

This quasi-experimental study investigated how an intervention aiming at increasing eldercare workers' influence on their working hours affected the flexibility, variability, regularity and predictability of the working hours. We used baseline (n = 296) and follow-up (n = 274) questionnaire data and interviews with intervention-group participants (n = 32). The work units in the intervention group designed their own intervention comprising either implementation of computerised self-scheduling (subgroup A), collection of information about the employees' work-time preferences by questionnaires (subgroup B), or discussion of working hours (subgroup C). Only computerised self-scheduling changed the working hours and the way they were planned. These changes implied more flexible but less regular working hours and an experience of less predictability and less continuity in the care of clients and in the co-operation with colleagues. In subgroup B and C, the participants ended up discussing the potential consequences of more work-time influence without actually implementing any changes. Employee work-time influence may buffer the adverse effects of shift work. However, our intervention study suggested that while increasing the individual flexibility, increasing work-time influence may also result in decreased regularity of the working hours and less continuity in the care of clients and co-operation with colleagues.

Individual Differences: Factors Affecting Employee Utilization of Flexible Work Arrangements

ERIC Educational Resources Information Center

Lambert, Alysa D.; Marler, Janet H.; Gueutal, Hal G.

2008-01-01

This study investigated individual and organizational factors that predict an individual's choice to use flexible work arrangements (FWAs). Survey data was collected from 144 employees in two different organizations. The results revealed several significant predictors of FWAs: tenure, hours worked per week, supervisory responsibilities,…

Ventral striatal prediction error signaling is associated with dopamine synthesis capacity and fluid intelligence

PubMed Central

Schlagenhauf, Florian; Rapp, Michael A.; Huys, Quentin J. M.; Beck, Anne; Wüstenberg, Torsten; Deserno, Lorenz; Buchholz, Hans-Georg; Kalbitzer, Jan; Buchert, Ralph; Kienast, Thorsten; Cumming, Paul; Plotkin, Michail; Kumakura, Yoshitaka; Grace, Anthony A.; Dolan, Raymond J.; Heinz, Andreas

2013-01-01

Fluid intelligence represents the capacity for flexible problem solving and rapid behavioral adaptation. Rewards drive flexible behavioral adaptation, in part via a teaching signal expressed as reward prediction errors in the ventral striatum, which has been associated with phasic dopamine release in animal studies. We examined a sample of 28 healthy male adults using multimodal imaging and biological parametric mapping with 1) functional magnetic resonance imaging during a reversal learning task and 2) in a subsample of 17 subjects also with positron emission tomography using 6-[18F]fluoro-L-DOPA to assess dopamine synthesis capacity. Fluid intelligence was measured using a battery of nine standard neuropsychological tests. Ventral striatal BOLD correlates of reward prediction errors were positively correlated with fluid intelligence and, in the right ventral striatum, also inversely correlated with dopamine synthesis capacity (FDOPA Kinapp). When exploring aspects of fluid intelligence, we observed that prediction error signaling correlates with complex attention and reasoning. These findings indicate that individual differences in the capacity for flexible problem solving may be driven by ventral striatal activation during reward-related learning, which in turn proved to be inversely associated with ventral striatal dopamine synthesis capacity. PMID:22344813

The Prediction of Botulinum Toxin Structure Based on in Silico and in Vitro Analysis

NASA Astrophysics Data System (ADS)

Suzuki, Tomonori; Miyazaki, Satoru

2011-01-01

Many of biological system mediated through protein-protein interactions. Knowledge of protein-protein complex structure is required for understanding the function. The determination of huge size and flexible protein-protein complex structure by experimental studies remains difficult, costly and five-consuming, therefore computational prediction of protein structures by homolog modeling and docking studies is valuable method. In addition, MD simulation is also one of the most powerful methods allowing to see the real dynamics of proteins. Here, we predict protein-protein complex structure of botulinum toxin to analyze its property. These bioinformatics methods are useful to report the relation between the flexibility of backbone structure and the activity.

Brain Signal Variability Differentially Affects Cognitive Flexibility and Cognitive Stability.

PubMed

Armbruster-Genç, Diana J N; Ueltzhöffer, Kai; Fiebach, Christian J

2016-04-06

Recent research yielded the intriguing conclusion that, in healthy adults, higher levels of variability in neuronal processes are beneficial for cognitive functioning. Beneficial effects of variability in neuronal processing can also be inferred from neurocomputational theories of working memory, albeit this holds only for tasks requiring cognitive flexibility. However, cognitive stability, i.e., the ability to maintain a task goal in the face of irrelevant distractors, should suffer under high levels of brain signal variability. To directly test this prediction, we studied both behavioral and brain signal variability during cognitive flexibility (i.e., task switching) and cognitive stability (i.e., distractor inhibition) in a sample of healthy human subjects and developed an efficient and easy-to-implement analysis approach to assess BOLD-signal variability in event-related fMRI task paradigms. Results show a general positive effect of neural variability on task performance as assessed by accuracy measures. However, higher levels of BOLD-signal variability in the left inferior frontal junction area result in reduced error rate costs during task switching and thus facilitate cognitive flexibility. In contrast, variability in the same area has a detrimental effect on cognitive stability, as shown in a negative effect of variability on response time costs during distractor inhibition. This pattern was mirrored at the behavioral level, with higher behavioral variability predicting better task switching but worse distractor inhibition performance. Our data extend previous results on brain signal variability by showing a differential effect of brain signal variability that depends on task context, in line with predictions from computational theories. Recent neuroscientific research showed that the human brain signal is intrinsically variable and suggested that this variability improves performance. Computational models of prefrontal neural networks predict differential effects of variability for different behavioral situations requiring either cognitive flexibility or stability. However, this hypothesis has so far not been put to an empirical test. In this study, we assessed cognitive flexibility and cognitive stability, and, besides a generally positive effect of neural variability on accuracy measures, we show that neural variability in a prefrontal brain area at the inferior frontal junction is differentially associated with performance: higher levels of variability are beneficial for the effectiveness of task switching (cognitive flexibility) but detrimental for the efficiency of distractor inhibition (cognitive stability). Copyright © 2016 the authors 0270-6474/16/363978-10$15.00/0.

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.

PubMed

Mottonen, James M; Xu, Minli; Jacobs, Donald J; Livesay, Dennis R

2009-05-15

We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.

Verification of component mode techniques for flexible multibody systems

NASA Technical Reports Server (NTRS)

Wiens, Gloria J.

1990-01-01

Investigations were conducted in the modeling aspects of flexible multibodies undergoing large angular displacements. Models were to be generated and analyzed through application of computer simulation packages employing the 'component mode synthesis' techniques. Multibody Modeling, Verification and Control Laboratory (MMVC) plan was implemented, which includes running experimental tests on flexible multibody test articles. From these tests, data was to be collected for later correlation and verification of the theoretical results predicted by the modeling and simulation process.

Coping with Uncertainty: Woodpecker Finches (Cactospiza pallida) from an Unpredictable Habitat Are More Flexible than Birds from a Stable Habitat

PubMed Central

Tebbich, Sabine; Teschke, Irmgard

2014-01-01

Behavioural flexibility is thought to be a major factor in evolution. It may facilitate the discovery and exploitation of new resources, which in turn may expose populations to novel selective forces and facilitate adaptive radiation. Darwin's finches are a textbook example of adaptive radiation. They are fast learners and show a range of unusual foraging techniques, probably as a result of their flexibility. In this study we aimed to test whether variability of the environment is correlated with flexibility. We compared woodpecker finches from a dry area (hereafter, Arid Zone), where food availability is variable, with individuals from a cloud forest (hereafter, Scalesia zone) where food abundance is stable. As parameters for flexibility, we measured neophilia and neophobia, which are two aspects of reaction to novelty, reversal learning and problem-solving. We found no differences in performance on a problem-solving task but, in line with our prediction, individuals from the Arid Zone were significantly faster reversal learners and more neophilic than their conspecifics from the Scalesia zone. The latter result supports the notion that environmental variability drives flexibility. In contrast to our prediction, Arid Zone birds were even more neophobic than birds from the Scalesia Zone. The latter result could be the consequence of differences in predation pressure between the two vegetation zones. PMID:24638107

Disordered Eating-Related Cognition and Psychological Flexibility as Predictors of Psychological Health among College Students

ERIC Educational Resources Information Center

Masuda, Akihiko; Price, Matthew; Anderson, Page L.; Wendell, Johanna W.

2010-01-01

The present cross-sectional study investigated the relation among disordered eating-related cognition, psychological flexibility, and poor psychological outcomes among a nonclinical college sample. As predicted, conviction of disordered eating-related cognitions was positively associated with general psychological ill-health and emotional distress…

Communication Technology: Pros and Cons of Constant Connection to Work

ERIC Educational Resources Information Center

Diaz, Ismael; Chiaburu, Dan S.; Zimmerman, Ryan D.; Boswell, Wendy R.

2012-01-01

We examined the relationship between employees' attitudes related to communication technology (CT) flexibility, communication technology (CT) use, work-to-life conflict and work satisfaction. Based on data obtained from 193 employees, CT flexibility predicted more CT use. Further, CT use was associated not only with increased work satisfaction,…

Bloc Concentration and Dispute Escalation among the Major Powers, 1830-1965.

ERIC Educational Resources Information Center

Stoll, Richard J.

1984-01-01

In the 1830-1914 era, when the major powers had a high level of political-military interdependence and alliance flexibility, changes in bloc concentration were a good predictor of dispute escalation. But bloc concentration had little predictive ability when this interdependence and alliance flexibility declined (1919-1965). (RM)

Wearable and flexible electronics for continuous molecular monitoring.

PubMed

Yang, Yiran; Gao, Wei

2018-04-03

Wearable biosensors have received tremendous attention over the past decade owing to their great potential in predictive analytics and treatment toward personalized medicine. Flexible electronics could serve as an ideal platform for personalized wearable devices because of their unique properties such as light weight, low cost, high flexibility and great conformability. Unlike most reported flexible sensors that mainly track physical activities and vital signs, the new generation of wearable and flexible chemical sensors enables real-time, continuous and fast detection of accessible biomarkers from the human body, and allows for the collection of large-scale information about the individual's dynamic health status at the molecular level. In this article, we review and highlight recent advances in wearable and flexible sensors toward continuous and non-invasive molecular analysis in sweat, tears, saliva, interstitial fluid, blood, wound exudate as well as exhaled breath. The flexible platforms, sensing mechanisms, and device and system configurations employed for continuous monitoring are summarized. We also discuss the key challenges and opportunities of the wearable and flexible chemical sensors that lie ahead.

Area computer model for transportation noise prediction : phase II--improved noise prediction methods.

DOT National Transportation Integrated Search

1975-01-01

This report recommended that NOISE 3 initially use the same basic logic as the MICNOISE program for highway noise prediction except that additional options be made available, such as flexibility in specifying vehicle noise sources. A choice of six no...

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

Predicting protein concentrations with ELISA microarray assays, monotonic splines and Monte Carlo simulation

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

Daly, Don S.; Anderson, Kevin K.; White, Amanda M.

Background: A microarray of enzyme-linked immunosorbent assays, or ELISA microarray, predicts simultaneously the concentrations of numerous proteins in a small sample. These predictions, however, are uncertain due to processing error and biological variability. Making sound biological inferences as well as improving the ELISA microarray process require require both concentration predictions and creditable estimates of their errors. Methods: We present a statistical method based on monotonic spline statistical models, penalized constrained least squares fitting (PCLS) and Monte Carlo simulation (MC) to predict concentrations and estimate prediction errors in ELISA microarray. PCLS restrains the flexible spline to a fit of assay intensitymore » that is a monotone function of protein concentration. With MC, both modeling and measurement errors are combined to estimate prediction error. The spline/PCLS/MC method is compared to a common method using simulated and real ELISA microarray data sets. Results: In contrast to the rigid logistic model, the flexible spline model gave credible fits in almost all test cases including troublesome cases with left and/or right censoring, or other asymmetries. For the real data sets, 61% of the spline predictions were more accurate than their comparable logistic predictions; especially the spline predictions at the extremes of the prediction curve. The relative errors of 50% of comparable spline and logistic predictions differed by less than 20%. Monte Carlo simulation rendered acceptable asymmetric prediction intervals for both spline and logistic models while propagation of error produced symmetric intervals that diverged unrealistically as the standard curves approached horizontal asymptotes. Conclusions: The spline/PCLS/MC method is a flexible, robust alternative to a logistic/NLS/propagation-of-error method to reliably predict protein concentrations and estimate their errors. The spline method simplifies model selection and fitting, and reliably estimates believable prediction errors. For the 50% of the real data sets fit well by both methods, spline and logistic predictions are practically indistinguishable, varying in accuracy by less than 15%. The spline method may be useful when automated prediction across simultaneous assays of numerous proteins must be applied routinely with minimal user intervention.« less

Testing models of parental investment strategy and offspring size in ants.

PubMed

Gilboa, Smadar; Nonacs, Peter

2006-01-01

Parental investment strategies can be fixed or flexible. A fixed strategy predicts making all offspring a single 'optimal' size. Dynamic models predict flexible strategies with more than one optimal size of offspring. Patterns in the distribution of offspring sizes may thus reveal the investment strategy. Static strategies should produce normal distributions. Dynamic strategies should often result in non-normal distributions. Furthermore, variance in morphological traits should be positively correlated with the length of developmental time the traits are exposed to environmental influences. Finally, the type of deviation from normality (i.e., skewed left or right, or platykurtic) should be correlated with the average offspring size. To test the latter prediction, we used simulations to detect significant departures from normality and categorize distribution types. Data from three species of ants strongly support the predicted patterns for dynamic parental investment. Offspring size distributions are often significantly non-normal. Traits fixed earlier in development, such as head width, are less variable than final body weight. The type of distribution observed correlates with mean female dry weight. The overall support for a dynamic parental investment model has implications for life history theory. Predicted conflicts over parental effort, sex investment ratios, and reproductive skew in cooperative breeders follow from assumptions of static parental investment strategies and omnipresent resource limitations. By contrast, with flexible investment strategies such conflicts can be either absent or maladaptive.

Evidence of common and separate eye and hand accumulators underlying flexible eye-hand coordination

PubMed Central

Jana, Sumitash; Gopal, Atul

2016-01-01

Eye and hand movements are initiated by anatomically separate regions in the brain, and yet these movements can be flexibly coupled and decoupled, depending on the need. The computational architecture that enables this flexible coupling of independent effectors is not understood. Here, we studied the computational architecture that enables flexible eye-hand coordination using a drift diffusion framework, which predicts that the variability of the reaction time (RT) distribution scales with its mean. We show that a common stochastic accumulator to threshold, followed by a noisy effector-dependent delay, explains eye-hand RT distributions and their correlation in a visual search task that required decision-making, while an interactive eye and hand accumulator model did not. In contrast, in an eye-hand dual task, an interactive model better predicted the observed correlations and RT distributions than a common accumulator model. Notably, these two models could only be distinguished on the basis of the variability and not the means of the predicted RT distributions. Additionally, signatures of separate initiation signals were also observed in a small fraction of trials in the visual search task, implying that these distinct computational architectures were not a manifestation of the task design per se. Taken together, our results suggest two unique computational architectures for eye-hand coordination, with task context biasing the brain toward instantiating one of the two architectures. NEW & NOTEWORTHY Previous studies on eye-hand coordination have considered mainly the means of eye and hand reaction time (RT) distributions. Here, we leverage the approximately linear relationship between the mean and standard deviation of RT distributions, as predicted by the drift-diffusion model, to propose the existence of two distinct computational architectures underlying coordinated eye-hand movements. These architectures, for the first time, provide a computational basis for the flexible coupling between eye and hand movements. PMID:27784809

Jumping to Conclusions, a Lack of Belief Flexibility and Delusional Conviction in Psychosis

PubMed Central

So, Suzanne H.; Freeman, Daniel; Dunn, Graham; Kapur, Shitij; Kuipers, Elizabeth; Bebbington, Paul; Fowler, David; Garety, Philippa A.

2012-01-01

Two reasoning biases, jumping to conclusions (JTC) and belief inflexibility, have been found to be associated with delusions. We examined these biases and their relationship with delusional conviction in a longitudinal cohort of people with schizophrenia-spectrum psychosis. We hypothesized that JTC, lack of belief flexibility, and delusional conviction would form distinct factors, and that JTC and lack of belief flexibility would predict less change in delusional conviction over time. Two hundred seventy-three patients with delusions were assessed over twelve months of a treatment trial (Garety et al., 2008). Forty-one percent of the sample had 100% conviction in their delusions, 50% showed a JTC bias, and 50%–75% showed a lack of belief flexibility. Delusional conviction, JTC, and belief flexibility formed distinct factors although conviction was negatively correlated with belief flexibility. Conviction declined slightly over the year in this established psychosis group, whereas the reasoning biases were stable. There was little evidence that reasoning predicted the slight decline in conviction. The degree to which people believe their delusions, their ability to think that they may be mistaken and to consider alternative explanations, and their hastiness in decision making are three distinct processes although belief flexibility and conviction are related. In this established psychosis sample, reasoning biases changed little in response to medication or psychological therapy. Required now is examination of these processes in psychosis groups where there is greater change in delusion conviction, as well as tests of the effects on delusions when these reasoning biases are specifically targeted. PMID:21910515

Touchscreen-paradigm for mice reveals cross-species evidence for an antagonistic relationship of cognitive flexibility and stability

PubMed Central

Richter, S. Helene; Vogel, Anne S.; Ueltzhöffer, Kai; Muzzillo, Chiara; Vogt, Miriam A.; Lankisch, Katja; Armbruster-Genç, Diana J. N.; Riva, Marco A.; Fiebach, Christian J.; Gass, Peter; Vollmayr, Barbara

2014-01-01

The abilities to either flexibly adjust behavior according to changing demands (cognitive flexibility) or to maintain it in the face of potential distractors (cognitive stability) are critical for adaptive behavior in many situations. Recently, a novel human paradigm has found individual differences of cognitive flexibility and stability to be related to common prefrontal networks. The aims of the present study were, first, to translate this paradigm from humans to mice and, second, to test conceptual predictions of a computational model of prefrontal working memory mechanisms, the Dual State Theory, which assumes an antagonistic relation between cognitive flexibility and stability. Mice were trained in a touchscreen-paradigm to discriminate visual cues. The task involved “ongoing” and cued “switch” trials. In addition distractor cues were interspersed to test the ability to resist distraction, and an ambiguous condition assessed the spontaneous switching between two possible responses without explicit cues. While response times did not differ substantially between conditions, error rates (ER) increased from the “ongoing” baseline condition to the most complex condition, where subjects were required to switch between two responses in the presence of a distracting cue. Importantly, subjects switching more often spontaneously were found to be more distractible by task irrelevant cues, but also more flexible in situations, where switching was required. These results support a dichotomy of cognitive flexibility and stability as predicted by the Dual State Theory. Furthermore, they replicate critical aspects of the human paradigm, which indicates the translational potential of the testing procedure and supports the use of touchscreen procedures in preclinical animal research. PMID:24834036

Economic optimization of operations for hybrid energy systems under variable markets

DOE PAGES

Chen, Jen; Garcia, Humberto E.

2016-05-21

We prosed a hybrid energy systems (HES) which is an important element to enable increasing penetration of clean energy. Our paper investigates the operations flexibility of HES, and develops a methodology for operations optimization for maximizing economic value based on predicted renewable generation and market information. A multi-environment computational platform for performing such operations optimization is also developed. In order to compensate for prediction error, a control strategy is accordingly designed to operate a standby energy storage element (ESE) to avoid energy imbalance within HES. The proposed operations optimizer allows systematic control of energy conversion for maximal economic value. Simulationmore » results of two specific HES configurations are included to illustrate the proposed methodology and computational capability. These results demonstrate the economic viability of HES under proposed operations optimizer, suggesting the diversion of energy for alternative energy output while participating in the ancillary service market. Economic advantages of such operations optimizer and associated flexible operations are illustrated by comparing the economic performance of flexible operations against that of constant operations. Sensitivity analysis with respect to market variability and prediction error, are also performed.« less

Economic optimization of operations for hybrid energy systems under variable markets

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

Chen, Jen; Garcia, Humberto E.

We prosed a hybrid energy systems (HES) which is an important element to enable increasing penetration of clean energy. Our paper investigates the operations flexibility of HES, and develops a methodology for operations optimization for maximizing economic value based on predicted renewable generation and market information. A multi-environment computational platform for performing such operations optimization is also developed. In order to compensate for prediction error, a control strategy is accordingly designed to operate a standby energy storage element (ESE) to avoid energy imbalance within HES. The proposed operations optimizer allows systematic control of energy conversion for maximal economic value. Simulationmore » results of two specific HES configurations are included to illustrate the proposed methodology and computational capability. These results demonstrate the economic viability of HES under proposed operations optimizer, suggesting the diversion of energy for alternative energy output while participating in the ancillary service market. Economic advantages of such operations optimizer and associated flexible operations are illustrated by comparing the economic performance of flexible operations against that of constant operations. Sensitivity analysis with respect to market variability and prediction error, are also performed.« less

Walking Flexibility after Hemispherectomy: Split-Belt Treadmill Adaptation and Feedback Control

ERIC Educational Resources Information Center

Choi, Julia T.; Vining, Eileen P. G.; Reisman, Darcy S.; Bastian, Amy J.

2009-01-01

Walking flexibility depends on use of feedback or reactive control to respond to unexpected changes in the environment, and the ability to adapt feedforward or predictive control for sustained alterations. Recent work has demonstrated that cerebellar damage impairs feedforward adaptation, but not feedback control, during human split-belt treadmill…

Mechanistic-Empirical Pavement Design Guide Flexible Pavement Performance Prediction Models Volume III Field Guide - Calibration and User's Guide for the Mechanistic-Empirical Pavement Design Guide

DOT National Transportation Integrated Search

2007-08-01

The objective of this research study was to develop performance characteristics or variables (e.g., ride quality, rutting, : fatigue cracking, transverse cracking) of flexible pavements in Montana, and to use these characteristics in the : implementa...

Impact of a Flexible Evaluation System on Effort and Timing of Study

ERIC Educational Resources Information Center

Pacharn, Parunchana; Bay, Darlene; Felton, Sandra

2012-01-01

This paper examines results of a flexible grading system that allows each student to influence the weight allocated to each performance measure. We construct a stylized model to determine students' optimal responses. Our analytical model predicts different optimal strategies for students with varying academic abilities: a frontloading strategy for…

Theory of energy harvesting from heartbeat including the effects of pleural cavity and respiration.

PubMed

Zhang, Yangyang; Lu, Bingwei; Lü, Chaofeng; Feng, Xue

2017-11-01

Self-powered implantable devices with flexible energy harvesters are of significant interest due to their potential to solve the problem of limited battery life and surgical replacement. The flexible electronic devices made of piezoelectric materials have been employed to harvest energy from the motion of biological organs. Experimental measurements show that the output voltage of the device mounted on porcine left ventricle in chest closed environment decreases significantly compared to the case of chest open. A restricted-space deformation model is proposed to predict the impeding effect of pleural cavity, surrounding tissues, as well as respiration on the efficiency of energy harvesting from heartbeat using flexible piezoelectric devices. The analytical solution is verified by comparing theoretical predictions to experimental measurements. A simple scaling law is established to analyse the intrinsic correlations between the normalized output power and the combined system parameters, i.e. the normalized permitted space and normalized electrical load. The results may provide guidelines for optimization of in vivo energy harvesting from heartbeat or the motions of other biological organs using flexible piezoelectric energy harvesters.

Theory of energy harvesting from heartbeat including the effects of pleural cavity and respiration

NASA Astrophysics Data System (ADS)

Zhang, Yangyang; Lu, Bingwei; Lü, Chaofeng; Feng, Xue

2017-11-01

Self-powered implantable devices with flexible energy harvesters are of significant interest due to their potential to solve the problem of limited battery life and surgical replacement. The flexible electronic devices made of piezoelectric materials have been employed to harvest energy from the motion of biological organs. Experimental measurements show that the output voltage of the device mounted on porcine left ventricle in chest closed environment decreases significantly compared to the case of chest open. A restricted-space deformation model is proposed to predict the impeding effect of pleural cavity, surrounding tissues, as well as respiration on the efficiency of energy harvesting from heartbeat using flexible piezoelectric devices. The analytical solution is verified by comparing theoretical predictions to experimental measurements. A simple scaling law is established to analyse the intrinsic correlations between the normalized output power and the combined system parameters, i.e. the normalized permitted space and normalized electrical load. The results may provide guidelines for optimization of in vivo energy harvesting from heartbeat or the motions of other biological organs using flexible piezoelectric energy harvesters.

Cognitive underpinnings of nationalistic ideology in the context of Brexit.

PubMed

Zmigrod, Leor; Rentfrow, Peter J; Robbins, Trevor W

2018-05-08

Nationalistic identities often play an influential role in citizens' voting behavior and political engagement. Nationalistic ideologies tend to have firm categories and rules for what belongs to and represents the national culture. In a sample of 332 UK citizens, we tested whether strict categorization of stimuli and rules in objective cognitive tasks would be evident in strongly nationalistic individuals. Using voting behavior and attitudes from the United Kingdom's 2016 EU referendum, we found that a flexible representation of national identity and culture was linked to cognitive flexibility in the ideologically neutral Wisconsin Card Sorting Test and Remote Associates Test, and to self-reported flexibility under uncertainty. Path analysis revealed that subjective and objective cognitive inflexibility predicted heightened authoritarianism, nationalism, conservatism, and system justification, and these in turn were predictive of support for Brexit and opposition to immigration, the European Union, and free movement of labor. This model accounted for 47.6% of the variance in support for Brexit. Path analysis models were also predictive of participants' sense of personal attachment to the United Kingdom, signifying that individual differences in cognitive flexibility may contribute toward ideological thinking styles that shape both nationalistic attitudes and personal sense of nationalistic identity. These findings further suggest that emotionally neutral "cold" cognitive information processing-and not just "hot" emotional cognition-may play a key role in ideological behavior and identity.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Caudate Nucleus Volume Mediates the Link between Cardiorespiratory Fitness and Cognitive Flexibility in Older Adults

PubMed Central

Verstynen, Timothy D.; Lynch, Brighid; Miller, Destiny L.; Voss, Michelle W.; Prakash, Ruchika Shaurya; Chaddock, Laura; Basak, Chandramallika; Szabo, Amanda; Olson, Erin A.; Wojcicki, Thomas R.; Fanning, Jason; Gothe, Neha P.; McAuley, Edward; Kramer, Arthur F.; Erickson, Kirk I.

2012-01-01

The basal ganglia play a central role in regulating the response selection abilities that are critical for mental flexibility. In neocortical areas, higher cardiorespiratory fitness levels are associated with increased gray matter volume, and these volumetric differences mediate enhanced cognitive performance in a variety of tasks. Here we examine whether cardiorespiratory fitness correlates with the volume of the subcortical nuclei that make up the basal ganglia and whether this relationship predicts cognitive flexibility in older adults. Structural MRI was used to determine the volume of the basal ganglia nuclei in a group of older, neurologically healthy individuals (mean age 66 years, N = 179). Measures of cardiorespiratory fitness (VO2max), cognitive flexibility (task switching), and attentional control (flanker task) were also collected. Higher fitness levels were correlated with higher accuracy rates in the Task Switching paradigm. In addition, the volume of the caudate nucleus, putamen, and globus pallidus positively correlated with Task Switching accuracy. Nested regression modeling revealed that caudate nucleus volume was a significant mediator of the relationship between cardiorespiratory fitness, and task switching performance. These findings indicate that higher cardiorespiratory fitness predicts better cognitive flexibility in older adults through greater grey matter volume in the dorsal striatum. PMID:22900181

Artificial neural network prediction of ischemic tissue fate in acute stroke imaging

PubMed Central

Huang, Shiliang; Shen, Qiang; Duong, Timothy Q

2010-01-01

Multimodal magnetic resonance imaging of acute stroke provides predictive value that can be used to guide stroke therapy. A flexible artificial neural network (ANN) algorithm was developed and applied to predict ischemic tissue fate on three stroke groups: 30-, 60-minute, and permanent middle cerebral artery occlusion in rats. Cerebral blood flow (CBF), apparent diffusion coefficient (ADC), and spin–spin relaxation time constant (T2) were acquired during the acute phase up to 3 hours and again at 24 hours followed by histology. Infarct was predicted on a pixel-by-pixel basis using only acute (30-minute) stroke data. In addition, neighboring pixel information and infarction incidence were also incorporated into the ANN model to improve prediction accuracy. Receiver-operating characteristic analysis was used to quantify prediction accuracy. The major findings were the following: (1) CBF alone poorly predicted the final infarct across three experimental groups; (2) ADC alone adequately predicted the infarct; (3) CBF+ADC improved the prediction accuracy; (4) inclusion of neighboring pixel information and infarction incidence further improved the prediction accuracy; and (5) prediction was more accurate for permanent occlusion, followed by 60- and 30-minute occlusion. The ANN predictive model could thus provide a flexible and objective framework for clinicians to evaluate stroke treatment options on an individual patient basis. PMID:20424631

Acute stress impairs cognitive flexibility in men, not women.

PubMed

Shields, Grant S; Trainor, Brian C; Lam, Jovian C W; Yonelinas, Andrew P

2016-09-01

Psychosocial stress influences cognitive abilities, such as long-term memory retrieval. However, less is known about the effects of stress on cognitive flexibility, which is mediated by different neurobiological circuits and could thus be regulated by different neuroendocrine pathways. In this study, we randomly assigned healthy adults to an acute stress induction or control condition and subsequently assessed participants' cognitive flexibility using an open-source version of the Wisconsin Card Sort task. Drawing on work in rodents, we hypothesized that stress would have stronger impairing effects on cognitive flexibility in men than women. As predicted, we found that stress impaired cognitive flexibility in men but did not significantly affect women. Our results thus indicate that stress exerts sex-specific effects on cognitive flexibility in humans and add to the growing body of research highlighting the need to consider sex differences in effects of stress.

Functional Specialization and Flexibility in Human Association Cortex

PubMed Central

Yeo, B. T. Thomas; Krienen, Fenna M.; Eickhoff, Simon B.; Yaakub, Siti N.; Fox, Peter T.; Buckner, Randy L.; Asplund, Christopher L.; Chee, Michael W.L.

2015-01-01

The association cortex supports cognitive functions enabling flexible behavior. Here, we explored the organization of human association cortex by mathematically formalizing the notion that a behavioral task engages multiple cognitive components, which are in turn supported by multiple overlapping brain regions. Application of the model to a large data set of neuroimaging experiments (N = 10 449) identified complex zones of frontal and parietal regions that ranged from being highly specialized to highly flexible. The network organization of the specialized and flexible regions was explored with an independent resting-state fMRI data set (N = 1000). Cortical regions specialized for the same components were strongly coupled, suggesting that components function as partially isolated networks. Functionally flexible regions participated in multiple components to different degrees. This heterogeneous selectivity was predicted by the connectivity between flexible and specialized regions. Functionally flexible regions might support binding or integrating specialized brain networks that, in turn, contribute to the ability to execute multiple and varied tasks. PMID:25249407

Limits on efficient human mindreading: convergence across Chinese adults and Semai children.

PubMed

Wang, Bo; Hadi, Nur Shafiqah Abdul; Low, Jason

2015-11-01

We tested Apperly and Butterfill's (2009, Psychological Review, 116, 753) theory that humans have two mindreading systems whereby the efficient-system guiding anticipatory glances displays signature limits that do not apply to the flexible system guiding verbal predictions. Experiments 1 and 2 tested urban Mainland-Chinese adults (n = 64) and Experiment 3 tested Semai children living in the rainforests of Peninsular Malaysia (3- to 4-year-olds, n = 60). Participants - across different ages, groups and methods - anticipated others' false-beliefs about object-location but not object-identity. Convergence in signature limits signalled that the early-developing efficient system involved minimal theory-of-mind. Chinese adults and older Semai children showed flexibility in their direct predictions. The flexible mindreading system in ascribing others' beliefs as such was task-sensitive and implicated maturational and cultural contributions. © 2015 The British Psychological Society.

Universal structural parameter to quantitatively predict metallic glass properties

DOE PAGES

Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; ...

2016-12-12

Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parametermore » correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales.« less

Evaluating scaling models in biology using hierarchical Bayesian approaches

PubMed Central

Price, Charles A; Ogle, Kiona; White, Ethan P; Weitz, Joshua S

2009-01-01

Theoretical models for allometric relationships between organismal form and function are typically tested by comparing a single predicted relationship with empirical data. Several prominent models, however, predict more than one allometric relationship, and comparisons among alternative models have not taken this into account. Here we evaluate several different scaling models of plant morphology within a hierarchical Bayesian framework that simultaneously fits multiple scaling relationships to three large allometric datasets. The scaling models include: inflexible universal models derived from biophysical assumptions (e.g. elastic similarity or fractal networks), a flexible variation of a fractal network model, and a highly flexible model constrained only by basic algebraic relationships. We demonstrate that variation in intraspecific allometric scaling exponents is inconsistent with the universal models, and that more flexible approaches that allow for biological variability at the species level outperform universal models, even when accounting for relative increases in model complexity. PMID:19453621

Buried and accessible surface area control intrinsic protein flexibility.

PubMed

Marsh, Joseph A

2013-09-09

Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the overall flexibility of a protein is demonstrated to be tightly coupled to the total amount of surface area buried within its fold. A simple proxy for this, the relative solvent-accessible surface area (Arel), therefore shows excellent agreement with independent measures of global protein flexibility derived from various experimental and computational methods. Application of Arel on a large scale demonstrates its utility by revealing unique sequence and structural properties associated with intrinsic flexibility. In particular, flexibility as measured by Arel shows little correspondence with intrinsic disorder, but instead tends to be associated with multiple domains and increased α-helical structure. Furthermore, the apparent flexibility of monomeric proteins is found to be useful for identifying quaternary-structure errors in published crystal structures. There is also a strong tendency for the crystal structures of more flexible proteins to be solved to lower resolutions. Finally, local solvent accessibility is shown to be a primary determinant of local residue flexibility. Overall, this work provides both fundamental mechanistic insight into the origin of protein flexibility and a simple, practical method for predicting flexibility from protein structures. © 2013 Elsevier Ltd. All rights reserved.

A study of the limitations of linear theory methods as applied to sonic boom calculations

NASA Technical Reports Server (NTRS)

Darden, Christine M.

1990-01-01

Current sonic boom minimization theories have been reviewed to emphasize the capabilities and flexibilities of the methods. Flexibility is important because it is necessary for the designer to meet optimized area constraints while reducing the impact on vehicle aerodynamic performance. Preliminary comparisons of sonic booms predicted for two Mach 3 concepts illustrate the benefits of shaping. Finally, for very simple bodies of revolution, sonic boom predictions were made using two methods - a modified linear theory method and a nonlinear method - for signature shapes which were both farfield N-waves and midfield waves. Preliminary analysis on these simple bodies verified that current modified linear theory prediction methods become inadequate for predicting midfield signatures for Mach numbers above 3. The importance of impulse is sonic boom disturbance and the importance of three-dimensional effects which could not be simulated with the bodies of revolution will determine the validity of current modified linear theory methods in predicting midfield signatures at lower Mach numbers.

Military Family Coping Project - Phase II

DTIC Science & Technology

2015-05-01

relationship quality, family cohesion, family flexibility, family satisfaction, family communication , social support, will predict Soldier depressed...GF, DAS-14-Marital Adjustment, FACES IV_IF Balanced Cohesion, Balanced Flexibility, and Communication , and FIRA-M Social Support Index) and...depression, the final model retained social support (β = -.221, p = .008); Immediate Family Communication (β = .316, p = .026); Marital Adjustment (β

Contralateral Disconnection of the Rat Prelimbic Cortex and Dorsomedial Striatum Impairs Cue-Guided Behavioral Switching

ERIC Educational Resources Information Center

Baker, Phillip M.; Ragozzino, Michael E.

2014-01-01

Switches in reward outcomes or reward-predictive cues are two fundamental ways in which information is used to flexibly shift response patterns. The rat prelimbic cortex and dorsomedial striatum support behavioral flexibility based on a change in outcomes. The present experiments investigated whether these two brain regions are necessary for…

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Dyadic Affective Flexibility and Emotional Inertia in Relation to Youth Psychopathology: An Integrated Model at Two Timescales.

PubMed

Mancini, Kathryn J; Luebbe, Aaron M

2016-06-01

The current review examines characteristics of temporal affective functioning at both the individual and dyadic level. Specifically, the review examines the following three research questions: (1) How are dyadic affective flexibility and emotional inertia operationalized, and are they related to youth psychopathology? (2) How are dyadic affective flexibility and emotional inertia related, and does this relation occur at micro- and meso-timescales? and (3) How do these constructs combine to predict clinical outcomes? Using the Flex3 model of socioemotional flexibility as a frame, the current study proposes that dyadic affective flexibility and emotional inertia are bidirectionally related at micro- and meso-timescales, which yields psychopathological symptoms for youth. Specific future directions for examining individual, dyadic, and cultural characteristics that may influence relations between these constructs and psychopathology are also discussed.

The effect of loading time on flexible pavement dynamic response: a finite element analysis

NASA Astrophysics Data System (ADS)

Yin, Hao; Solaimanian, Mansour; Kumar, Tanmay; Stoffels, Shelley

2007-12-01

Dynamic response of asphalt concrete (AC) pavements under moving load is a key component for accurate prediction of flexible pavement performance. The time and temperature dependency of AC materials calls for utilizing advanced material characterization and mechanistic theories, such as viscoelasticity and stress/strain analysis. In layered elastic analysis, as implemented in the new Mechanistic-Empirical Pavement Design Guide (MEPDG), the time dependency is accounted for by calculating the loading times at different AC layer depths. In this study, the time effect on pavement response was evaluated by means of the concept of “pseudo temperature.” With the pavement temperature measured from instrumented thermocouples, the time and temperature dependency of AC materials was integrated into one single factor, termed “effective temperature.” Via this effective temperature, pavement responses under a transient load were predicted through finite element analysis. In the finite element model, viscoelastic behavior of AC materials was characterized through relaxation moduli, while the layers with unbound granular material were assumed to be in an elastic mode. The analysis was conducted for two different AC mixtures in a simplified flexible pavement structure at two different seasons. Finite element analysis results reveal that the loading time has a more pronounced impact on pavement response in the summer for both asphalt types. The results indicate that for reasonable prediction of dynamic response in flexible pavements, the effect of the depth-dependent loading time on pavement temperature should be considered.

Tracking changing environments: innovators are fast, but not flexible learners.

PubMed

Griffin, Andrea S; Guez, David; Lermite, Françoise; Patience, Madeleine

2013-01-01

Behavioural innovations are increasingly thought to provide a rich source of phenotypic plasticity and evolutionary change. Innovation propensity shows substantial variation across avian taxa and provides an adaptive mechanism by which behaviour is flexibly adjusted to changing environmental conditions. Here, we tested for the first time the prediction that inter-individual variation in innovation propensity is equally a measure of behavioural flexibility. We used Indian mynas, Sturnus tristis, a highly successful worldwide invader. Results revealed that mynas that solved an extractive foraging task more quickly learnt to discriminate between a cue that predicted food, and one that did not more quickly. However, fast innovators were slower to change their behaviour when the significance of the food cues changed. This unexpected finding appears at odds with the well-established view that avian taxa with larger brains relative to their body size, and therefore greater neural processing power, are both faster, and more flexible learners. We speculate that the existence of this relationship across taxa can be reconciled with its absence within species by assuming that fast, innovative learners and non innovative, slow, flexible learners constitute two separate individual strategies, which are both underpinned by enhanced neural processing power. This idea is consistent with the recent proposal that individuals may differ consistently in 'cognitive style', differentially trading off speed against accuracy in cognitive tasks.

Thrust generation by a heaving flexible foil: Resonance, nonlinearities, and optimality

NASA Astrophysics Data System (ADS)

Paraz, Florine; Schouveiler, Lionel; Eloy, Christophe

2016-01-01

Flexibility of marine animal fins has been thought to enhance swimming performance. However, despite numerous experimental and numerical studies on flapping flexible foils, there is still no clear understanding of the effect of flexibility and flapping amplitude on thrust generation and swimming efficiency. Here, to address this question, we combine experiments on a model system and a weakly nonlinear analysis. Experiments consist in immersing a flexible rectangular plate in a uniform flow and forcing this plate into a heaving motion at its leading edge. A complementary theoretical model is developed assuming a two-dimensional inviscid problem. In this model, nonlinear effects are taken into account by considering a transverse resistive drag. Under these hypotheses, a modal decomposition of the system motion allows us to predict the plate response amplitude and the generated thrust, as a function of the forcing amplitude and frequency. We show that this model can correctly predict the experimental data on plate kinematic response and thrust generation, as well as other data found in the literature. We also discuss the question of efficiency in the context of bio-inspired propulsion. Using the proposed model, we show that the optimal propeller for a given thrust and a given swimming speed is achieved when the actuating frequency is tuned to a resonance of the system, and when the optimal forcing amplitude scales as the square root of the required thrust.

Large-Deformation Displacement Transfer Functions for Shape Predictions of Highly Flexible Slender Aerospace Structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2013-01-01

Large deformation displacement transfer functions were formulated for deformed shape predictions of highly flexible slender structures like aircraft wings. In the formulation, the embedded beam (depth wise cross section of structure along the surface strain sensing line) was first evenly discretized into multiple small domains, with surface strain sensing stations located at the domain junctures. Thus, the surface strain (bending strains) variation within each domain could be expressed with linear of nonlinear function. Such piecewise approach enabled piecewise integrations of the embedded beam curvature equations [classical (Eulerian), physical (Lagrangian), and shifted curvature equations] to yield closed form slope and deflection equations in recursive forms.

Measuring Inhibition and Cognitive Flexibility in Friedreich Ataxia.

PubMed

Corben, Louise A; Klopper, Felicity; Stagnitti, Monique; Georgiou-Karistianis, Nellie; Bradshaw, John L; Rance, Gary; Delatycki, Martin B

2017-08-01

Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder with subtle impact on cognition. Inhibitory processes and cognitive flexibility were examined in FRDA by assessing the ability to suppress a predictable verbal response. We administered the Hayling Sentence Completion Test (HSCT), the Trail Making Test, and the Stroop Test to 43 individuals with FRDA and 42 gender- and age-matched control participants. There were no significant group differences in performance on the Stroop or Trail Making Test whereas significant impairment in cognitive flexibility including the ability to predict and inhibit a pre-potent response as measured in the HSCT was evident in individuals with FRDA. These deficits did not correlate with clinical characteristics of FRDA (age of disease onset, disease duration, number of guanine-adenine-adenine repeats on the shorter or larger FXN allele, or Friedreich Ataxia Rating Scale score), suggesting that such impairment may not be related to the disease process in a straightforward way. The observed specific impairment of inhibition and predictive capacity in individuals with FRDA on the HSCT task, in the absence of impairment in associated executive functions, supports cerebellar dysfunction in conjunction with disturbance to cortico-thalamo-cerebellar connectivity, perhaps via inability to access frontal areas necessary for successful task completion.

Flexible pavement overlay design procedures. Volume 1: Evaluation and modification of the design methods

NASA Astrophysics Data System (ADS)

Majidzadeh, K.; Ilves, G. J.

1981-08-01

A ready reference to design procedures for asphaltic concrete overlay of flexible pavements based on elastic layer theory is provided. The design procedures and the analytical techniques presented were formulated to predict the structural fatigue response of asphaltic concrete overlays for various design conditions, including geometrical and material properties, loading conditions and environmental variables.

Investigation of squeeze-film dampers

NASA Technical Reports Server (NTRS)

Holmes, R.; Dogan, M.

1982-01-01

Squeeze film dampers are a means of curing instabilities in rotating shaft assemblies. Their efficiency depends very much on the condition of the oil, which in turn depends on inlet and outlet arrangements, on damper geometry and on the flexibility of the rotor and surrounding structure. Rig investigations in which structural flexibility is included experimentally are discussed. Comparisons are made between measured and predicted results.

Attitude Control of Flexible Structures.

DTIC Science & Technology

1990-09-01

arm has been determined experimentally and compared with analytical * predictions obtained by using the GIFTS finite element analysis program. The...frequencies of the flexible arm have been determined experimentally and compared with analytical predictiens obtained by using the GIFTS finite element...exception of the first mode. Table V shows the difference between the frequencies obtained from the GIFTS program and the experimental values. TABLE

Specifying Links between Executive Functioning and Theory of Mind during Middle Childhood: Cognitive Flexibility Predicts Social Understanding

ERIC Educational Resources Information Center

Bock, Allison M.; Gallaway, Kristin C.; Hund, Alycia M.

2015-01-01

The purpose of this study was to specify the development of and links between executive functioning and theory of mind during middle childhood. One hundred four 7- to 12-year-old children completed a battery of age-appropriate tasks measuring working memory, inhibition, flexibility, theory of mind, and vocabulary. As expected, spatial working…

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

PubMed

Carstens, Heiko; Renner, Christian; Milbradt, Alexander G; Moroder, Luis; Tavan, Paul

2005-03-29

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

Vibration of rotating-shaft design spindles with flexible bases

NASA Astrophysics Data System (ADS)

Tseng, Chaw-Wu

The purpose of this study is to demonstrate an accurate mathematical model predicting forced vibration of rotating-shaft HDD spindle motors with flexible stationary parts. The mathematical model consists of three parts: a rotating part, a stationary part, and bearings. The rotating part includes a flexible hub, a flexible shaft press-fit into the hub, and N elastic disks mounted on the hub. The stationary part can include motor bracket (stator), base casting, and top cover. The bearings under consideration can be ball bearings or hydrodynamic bearings (HDB). The rotating disks are modelled through the classical plate theory. The rotating part (except the disks) and the stationary part are modelled through finite element analyses (FEA). With mode shapes and natural frequencies obtained from FEA, the kinetic and potential energies of the rotating and stationary parts are formulated and discretized to compensate for the gyroscopic effects from rotation. Finally, use of Lagrange equation results in the equations of motion. To verify the mathematical model, frequency response functions are measured experimentally for an HDB spindle carrying two identical disks at motor and drive levels. Experimental measurements agree very well with theoretical predictions not only in resonance frequency but also in resonance amplitude.

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design.

PubMed

Sinko, William; Lindert, Steffen; McCammon, J Andrew

2013-01-01

Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules. In proteins, these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side-chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient's genetic makeup. © 2012 John Wiley & Sons A/S.

Neurocognitive assessment of emotional context sensitivity.

PubMed

Myruski, Sarah; Bonanno, George A; Gulyayeva, Olga; Egan, Laura J; Dennis-Tiwary, Tracy A

2017-10-01

Sensitivity to emotional context is an emerging construct for characterizing adaptive or maladaptive emotion regulation, but few measurement approaches exist. The current study combined behavioral and neurocognitive measures to assess context sensitivity in relation to self-report measures of adaptive emotional flexibility and well-being. Sixty-six adults completed an emotional go/no-go task using happy, fearful, and neutral faces as go and no-go cues, while EEG was recorded to generate event-related potentials (ERPs) reflecting attentional selection and discrimination (N170) and cognitive control (N2). Context sensitivity was measured as the degree of emotional facilitation or disruption in the go/no-go task and magnitude of ERP response to emotion cues. Participants self-reported on emotional flexibility, anxiety, and depression. Overall participants evidenced emotional context sensitivity, such that when happy faces were go stimuli, accuracy improved (greater behavioral facilitation), whereas when fearful faces were no-go stimuli, errors increased (disrupted behavioral inhibition). These indices predicted emotional flexibility and well-being: Greater behavioral facilitation following happy cues was associated with lower depression and anxiety, whereas greater disruption in behavioral inhibition following fearful cues was associated with lower flexibility. ERP indices of context sensitivity revealed additional associations: Greater N2 to fear go cues was associated with less anxiety and depression, and greater N2 and N170 to happy and fear no-go cues, respectively, were associated with greater emotional flexibility and well-being. Results suggest that pleasant and unpleasant emotions selectively enhance and disrupt components of context sensitivity, and that behavioral and ERP indices of context sensitivity predict flexibility and well-being.

Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.

PubMed

Lee, Hui Sun; Jo, Sunhwan; Lim, Hyun-Suk; Im, Wonpil

2012-07-23

Molecular docking is widely used to obtain binding modes and binding affinities of a molecule to a given target protein. Despite considerable efforts, however, prediction of both properties by docking remains challenging mainly due to protein's structural flexibility and inaccuracy of scoring functions. Here, an integrated approach has been developed to improve the accuracy of binding mode and affinity prediction and tested for small molecule MDM2 and MDMX antagonists. In this approach, initial candidate models selected from docking are subjected to equilibration MD simulations to further filter the models. Free energy perturbation molecular dynamics (FEP/MD) simulations are then applied to the filtered ligand models to enhance the ability in predicting the near-native ligand conformation. The calculated binding free energies for MDM2 complexes are overestimated compared to experimental measurements mainly due to the difficulties in sampling highly flexible apo-MDM2. Nonetheless, the FEP/MD binding free energy calculations are more promising for discriminating binders from nonbinders than docking scores. In particular, the comparison between the MDM2 and MDMX results suggests that apo-MDMX has lower flexibility than apo-MDM2. In addition, the FEP/MD calculations provide detailed information on the different energetic contributions to ligand binding, leading to a better understanding of the sensitivity and specificity of protein-ligand interactions.

Prenatal exposure to testosterone interacts with lifetime physical abuse to predict anger rumination and cognitive flexibility among incarcerated methamphetamine users.

PubMed

Herschl, Laura C; Highland, Krista B; McChargue, Dennis E

2012-01-01

The present pilot study hypothesized that degree of exposure to prenatal testosterone interacts with a history of lifetime physical abuse (LPA) to predict the cognitive (anger rumination) and behavioral (intimate partner and interpersonal violence) components of aggression within incarcerated methamphetamine (MA) users. In addition, we hypothesized that the degree of exposure to prenatal testosterone interacts with LPA to predict cognitive flexibility (Stroop Color-Word performance). Male inmate MA users (N = 60) completed neuropsychological and paper/pencil tests. Hand photocopies were also obtained to index prenatal testosterone exposure. Five covariate-adjusted moderation models were tested using anger rumination, intimate partner violence (IPV) perpetration, interpersonal violence perpetration (before and while incarcerated), and Stroop Color-Word T-score as the criteria, prenatal testosterone exposure as the predictor, and LPA as the moderator. Results indicated that, in individuals with a history of LPA, exposure to higher levels of prenatal testosterone exposure predicted greater anger rumination, lower Stroop Color-Word test T-scores, and lower frequencies of IPV perpetration. Findings were not significant in individuals without a history of LPA. This research suggests that biochemical and psychosocial vulnerabilities influence anger rumination and cognitive flexibility, which may render incarcerated MA users at greater risk to relapse or recidivate upon release from prison. Copyright © American Academy of Addiction Psychiatry.

Urban water supply infrastructure planning under predictive groundwater uncertainty: Bayesian updating and flexible design

NASA Astrophysics Data System (ADS)

Fletcher, S.; Strzepek, K.

2017-12-01

Many urban water planners face increased pressure on water supply systems from increasing demands from population and economic growth in combination with uncertain water supply, driven by short-term climate variability and long-term climate change. These uncertainties are often exacerbated in groundwater-dependent water systems due to the extra difficulty in measuring groundwater storage, recharge, and sustainable yield. Groundwater models are typically under-parameterized due to the high data requirements for calibration and limited data availability, leading to uncertainty in the models' predictions. We develop an integrated approach to urban water supply planning that combines predictive groundwater uncertainty analysis with adaptive water supply planning using multi-stage decision analysis. This allows us to compare the value of collecting additional groundwater data and reducing predictive uncertainty with the value of using water infrastructure planning that is flexible, modular, and can react quickly in response to unexpected changes in groundwater availability. We apply this approach to a case from Riyadh, Saudi Arabia. Riyadh relies on fossil groundwater aquifers and desalination for urban use. The main fossil aquifers incur minimal recharge and face depletion as a result of intense withdrawals for urban and agricultural use. As the water table declines and pumping becomes uneconomical, Riyadh will have to build new supply infrastructure, decrease demand, or increase the efficiency of its distribution system. However, poor groundwater characterization has led to severe uncertainty in aquifer parameters such as hydraulic conductivity, and therefore severe uncertainty in how the water table will respond to pumping over time and when these transitions will be necessary: the potential depletion time varies from approximately five years to 100 years. This case is an excellent candidate for flexible planning both because of its severity and the potential for learning: additional information can be collected over time and flexible options exercised in response. Stochastic dynamic programming is used to find optimal policies for using flexibility under different information scenarios. The performance of each strategy is then assessed using a simulation model of Riyadh's water system.

Housing flexibility effects on rotor stability

NASA Technical Reports Server (NTRS)

Davis, L. B.; Wolfe, E. A.; Beatty, R. F.

1985-01-01

Preliminary rotordynamic evaluations are performed with a housing stiffness assumption that is typically determined only after the hardware is built. In addressing rotor stability, a rigid housing assumption was shown to predict an instability at a lower spin speed than a comparable flexible housing analysis. This rigid housing assumption therefore provides a conservative estimate of the stability threshold speed. A flexible housing appears to act as an energy absorber and dissipated some of the destabilizing force. The fact that a flexible housing is usually asymmetric and considerably heavier than the rotor was related to this apparent increase in rotor stability. Rigid housing analysis is proposed as a valuable screening criteria and may save time and money in construction of elaborate housing finite element models for linear stability analyses.

Empathy and nonattachment independently predict peer nominations of prosocial behavior of adolescents

PubMed Central

Sahdra, Baljinder K.; Ciarrochi, Joseph; Parker, Philip D.; Marshall, Sarah; Heaven, Patrick

2015-01-01

There is a plethora of research showing that empathy promotes prosocial behavior among young people. We examined a relatively new construct in the mindfulness literature, nonattachment, defined as a flexible way of relating to one's experiences without clinging to or suppressing them. We tested whether nonattachment could predict prosociality above and beyond empathy. Nonattachment implies high cognitive flexibility and sufficient mental resources to step out of excessive self-cherishing to be there for others in need. Multilevel Poisson models using a sample of 15-year olds (N = 1831) showed that empathy and nonattachment independently predicted prosocial behaviors of helpfulness and kindness, as judged by same-sex and opposite-sex peers, except for when boys nominated girls. The effects of nonattachment remained substantial in more conservative models including self-esteem and peer nominations of liking. PMID:25852590

Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain.

PubMed

Raghav, Pawan Kumar; Verma, Yogesh Kumar; Gangenahalli, Gurudutta U

2012-05-01

B-cell lymphoma (Bcl-2) protein is an anti-apoptotic member of the Bcl-2 family. It is functionally demarcated into four Bcl-2 homology (BH) domains: BH1, BH2, BH3, BH4, one flexible loop domain (FLD), a transmembrane domain (TM), and an X domain. Bcl-2's BH domains have clearly been elucidated from a structural perspective, whereas the conformation of FLD has not yet been predicted, despite its important role in regulating apoptosis through its interactions with JNK-1, PKC, PP2A phosphatase, caspase 3, MAP kinase, ubiquitin, PS1, and FKBP38. Many important residues that regulate Bcl-2 anti-apoptotic activity are present in this domain, for example Asp34, Thr56, Thr69, Ser70, Thr74, and Ser87. The structural elucidation of the FLD would likely help in attempts to accurately predict the effect of mutating these residues on the overall structure of the protein and the interactions of other proteins in this domain. Therefore, we have generated an increased quality model of the Bcl-2 protein including the FLD through modeling. Further, molecular dynamics (MD) simulations were used for FLD optimization, to predict the flexibility, and to determine the stability of the folded FLD. In addition, essential dynamics (ED) was used to predict the collective motions and the essential subspace relevant to Bcl-2 protein function. The predicted average structure and ensemble of MD-simulated structures were submitted to the Protein Model Database (PMDB), and the Bcl-2 structures obtained exhibited enhanced quality. This study should help to elucidate the structural basis for Bcl-2 anti-apoptotic activity regulation through its binding to other proteins via the FLD.

The Association of Dorsiflexion Flexibility on Landing Mechanics during a Drop Vertical Jump

PubMed Central

Malloy, Philip; Meinerz, Carolyn; Geiser, Christopher; Kipp, Kristof

2016-01-01

Purpose While previous studies have examined the association between ankle dorsiflexion flexibility and deleterious landing postures, it is not currently known how landing kinetics are influenced by ankle dorsiflexion flexibility. The purpose of this study was to examine if ankle dorsiflexion flexibility was associated with landing kinematics and kinetics that have been shown to increase the risk of ACL injury in female athletes. Methods Twenty-three female collegiate soccer players participated in a preseason screening that included the assessment of ankle dorsiflexion flexibility and lower-body kinematics and kinetics during a drop vertical jump task. Results The results demonstrated that females with less ankle dorsiflexion flexibility exhibited greater peak knee abduction moments (r = −.442), greater peak knee abduction angles (r = .355), and less peak knee flexion angles (r = −.385) during landing. The range of dorsiflexion flexibility for the current study was between 9°–23° degrees (mean = 15.0°; SD 3.9°). Conclusion Dorsiflexion flexibility may serve as a useful clinical measure to predict poor landing postures and external forces that have been associated with increased knee injury risk. Rehabilitation specialists can provide interventions aimed at improving dorsiflexion flexibility in order to ameliorate the impact of this modifiable factor on deleterious landing kinematics and kinetics in female athletes. PMID:25112598

Sustained selective attention predicts flexible switching in preschoolers

PubMed Central

Benitez, Viridiana L.; Vales, Catarina; Hanania, Rima; Smith, Linda B.

2016-01-01

Stability and flexibility are fundamental to an intelligent cognitive system. Here, we examine the relationship between stability in selective attention and explicit control of flexible attention. Preschoolers were tested on the Dimension-Preference (DP) task, a task that measures the stability of selective attention to an implicitly primed dimension, and the Dimension-Change Card Sort Task (DCCS), a task that measures flexible attention switching between dimensions. Children who successfully switched on the DCCS task were more likely than those who perseverated to sustain attention to the primed dimension on the DP task across trials. We propose that perseverators have less stable attention and distribute their attention between dimensions, while switchers can successfully stabilize attention to individual dimensions and thus show more enduring priming effects. Flexible attention may emerge, in part, from implicit processes that stabilize attention even in tasks not requiring switching. PMID:28024178

Sustained selective attention predicts flexible switching in preschoolers.

PubMed

Benitez, Viridiana L; Vales, Catarina; Hanania, Rima; Smith, Linda B

2017-04-01

Stability and flexibility are fundamental to an intelligent cognitive system. Here, we examined the relationship between stability in selective attention and explicit control of flexible attention. Preschoolers were tested on the Dimension Preference (DP) task, which measures the stability of selective attention to an implicitly primed dimension, and the Dimension Change Card Sort (DCCS) task, which measures flexible attention switching between dimensions. Children who successfully switched on the DCCS task were more likely than those who perseverated to sustain attention to the primed dimension on the DP task across trials. We propose that perseverators have less stable attention and distribute their attention between dimensions, whereas switchers can successfully stabilize attention to individual dimensions and, thus, show more enduring priming effects. Flexible attention may emerge, in part, from implicit processes that stabilize attention even in tasks not requiring switching. Copyright © 2016 Elsevier Inc. All rights reserved.

Addition of flexible body option to the TOLA computer program, part 1

NASA Technical Reports Server (NTRS)

Dick, J. W.; Benda, B. J.

1975-01-01

This report describes a flexible body option that was developed and added to the Takeoff and Landing Analysis (TOLA) computer program. The addition of the flexible body option to TOLA allows it to be used to study essentially any conventional type airplane in the ground operating environment. It provides the capability to predict the total motion of selected points on the analytical methods incorporated in the program and operating instructions for the option are described. A program listing is included along with several example problems to aid in interpretation of the operating instructions and to illustrate program usage.

Simulation of flexible appendage interactions with Mariner Venus/Mercury attitude control and science platform pointing

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1973-01-01

A new computer subroutine, which solves the attitude equations of motion for any vehicle idealized as a topological tree of hinge-connected rigid bodies, is used to simulate and analyze science instrument pointing control interaction with a flexible Mariner Venus/Mercury (MVM) spacecraft. The subroutine's user options include linearized or partially linearized hinge-connected models whose computational advantages are demonstrated for the MVM problem. Results of the pointing control/flexible vehicle interaction simulations, including imaging experiment pointing accuracy predictions and implications for MVM science sequence planning, are described in detail.

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

NASA Astrophysics Data System (ADS)

Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei

2014-06-01

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N^2). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

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

Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei, E-mail: wei@math.msu.edu

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions,more » while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.« less

Investigation of Oil Fluorescence as a Technique for the Remote Sensing of Oil Spills

DOT National Transportation Integrated Search

1971-06-01

The flexibility of remote sensing of oil spills by laser-excited oil fluorescence is investigated. The required parameters are fed into a physical model to predict signal and background levels; and the predictions are verified by field experiments. A...

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.

PubMed

Richardson, Emily J; Escalettes, Franck; Fotheringham, Ian; Wallace, Robert J; Watson, Mick

2013-01-01

Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website, code is available on Github, a cloud image is available, and an example implementation can be seen at.

Classifying short genomic fragments from novel lineages using composition and homology

PubMed Central

2011-01-01

Background The assignment of taxonomic attributions to DNA fragments recovered directly from the environment is a vital step in metagenomic data analysis. Assignments can be made using rank-specific classifiers, which assign reads to taxonomic labels from a predetermined level such as named species or strain, or rank-flexible classifiers, which choose an appropriate taxonomic rank for each sequence in a data set. The choice of rank typically depends on the optimal model for a given sequence and on the breadth of taxonomic groups seen in a set of close-to-optimal models. Homology-based (e.g., LCA) and composition-based (e.g., PhyloPythia, TACOA) rank-flexible classifiers have been proposed, but there is at present no hybrid approach that utilizes both homology and composition. Results We first develop a hybrid, rank-specific classifier based on BLAST and Naïve Bayes (NB) that has comparable accuracy and a faster running time than the current best approach, PhymmBL. By substituting LCA for BLAST or allowing the inclusion of suboptimal NB models, we obtain a rank-flexible classifier. This hybrid classifier outperforms established rank-flexible approaches on simulated metagenomic fragments of length 200 bp to 1000 bp and is able to assign taxonomic attributions to a subset of sequences with few misclassifications. We then demonstrate the performance of different classifiers on an enhanced biological phosphorous removal metagenome, illustrating the advantages of rank-flexible classifiers when representative genomes are absent from the set of reference genomes. Application to a glacier ice metagenome demonstrates that similar taxonomic profiles are obtained across a set of classifiers which are increasingly conservative in their classification. Conclusions Our NB-based classification scheme is faster than the current best composition-based algorithm, Phymm, while providing equally accurate predictions. The rank-flexible variant of NB, which we term ε-NB, is complementary to LCA and can be combined with it to yield conservative prediction sets of very high confidence. The simple parameterization of LCA and ε-NB allows for tuning of the balance between more predictions and increased precision, allowing the user to account for the sensitivity of downstream analyses to misclassified or unclassified sequences. PMID:21827705

Bayesian modeling of flexible cognitive control

PubMed Central

Jiang, Jiefeng; Heller, Katherine; Egner, Tobias

2014-01-01

“Cognitive control” describes endogenous guidance of behavior in situations where routine stimulus-response associations are suboptimal for achieving a desired goal. The computational and neural mechanisms underlying this capacity remain poorly understood. We examine recent advances stemming from the application of a Bayesian learner perspective that provides optimal prediction for control processes. In reviewing the application of Bayesian models to cognitive control, we note that an important limitation in current models is a lack of a plausible mechanism for the flexible adjustment of control over conflict levels changing at varying temporal scales. We then show that flexible cognitive control can be achieved by a Bayesian model with a volatility-driven learning mechanism that modulates dynamically the relative dependence on recent and remote experiences in its prediction of future control demand. We conclude that the emergent Bayesian perspective on computational mechanisms of cognitive control holds considerable promise, especially if future studies can identify neural substrates of the variables encoded by these models, and determine the nature (Bayesian or otherwise) of their neural implementation. PMID:24929218

Dynamic prediction in functional concurrent regression with an application to child growth.

PubMed

Leroux, Andrew; Xiao, Luo; Crainiceanu, Ciprian; Checkley, William

2018-04-15

In many studies, it is of interest to predict the future trajectory of subjects based on their historical data, referred to as dynamic prediction. Mixed effects models have traditionally been used for dynamic prediction. However, the commonly used random intercept and slope model is often not sufficiently flexible for modeling subject-specific trajectories. In addition, there may be useful exposures/predictors of interest that are measured concurrently with the outcome, complicating dynamic prediction. To address these problems, we propose a dynamic functional concurrent regression model to handle the case where both the functional response and the functional predictors are irregularly measured. Currently, such a model cannot be fit by existing software. We apply the model to dynamically predict children's length conditional on prior length, weight, and baseline covariates. Inference on model parameters and subject-specific trajectories is conducted using the mixed effects representation of the proposed model. An extensive simulation study shows that the dynamic functional regression model provides more accurate estimation and inference than existing methods. Methods are supported by fast, flexible, open source software that uses heavily tested smoothing techniques. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

High Speed Civil Transport (HSCT) Isolated Nacelle Transonic Boattail Drag Study and Results Using Computational Fluid Dynamics (CFD)

NASA Technical Reports Server (NTRS)

Midea, Anthony C.; Austin, Thomas; Pao, S. Paul; DeBonis, James R.; Mani, Mori

2005-01-01

Nozzle boattail drag is significant for the High Speed Civil Transport (HSCT) and can be as high as 25 percent of the overall propulsion system thrust at transonic conditions. Thus, nozzle boattail drag has the potential to create a thrust drag pinch and can reduce HSCT aircraft aerodynamic efficiencies at transonic operating conditions. In order to accurately predict HSCT performance, it is imperative that nozzle boattail drag be accurately predicted. Previous methods to predict HSCT nozzle boattail drag were suspect in the transonic regime. In addition, previous prediction methods were unable to account for complex nozzle geometry and were not flexible enough for engine cycle trade studies. A computational fluid dynamics (CFD) effort was conducted by NASA and McDonnell Douglas to evaluate the magnitude and characteristics of HSCT nozzle boattail drag at transonic conditions. A team of engineers used various CFD codes and provided consistent, accurate boattail drag coefficient predictions for a family of HSCT nozzle configurations. The CFD results were incorporated into a nozzle drag database that encompassed the entire HSCT flight regime and provided the basis for an accurate and flexible prediction methodology.

High Speed Civil Transport (HSCT) Isolated Nacelle Transonic Boattail Drag Study and Results Using Computational Fluid Dynamics (CFD)

NASA Technical Reports Server (NTRS)

Midea, Anthony C.; Austin, Thomas; Pao, S. Paul; DeBonis, James R.; Mani, Mori

1999-01-01

Nozzle boattail drag is significant for the High Speed Civil Transport (HSCT) and can be as high as 25% of the overall propulsion system thrust at transonic conditions. Thus, nozzle boattail drag has the potential to create a thrust-drag pinch and can reduce HSCT aircraft aerodynamic efficiencies at transonic operating conditions. In order to accurately predict HSCT performance, it is imperative that nozzle boattail drag be accurately predicted. Previous methods to predict HSCT nozzle boattail drag were suspect in the transonic regime. In addition, previous prediction methods were unable to account for complex nozzle geometry and were not flexible enough for engine cycle trade studies. A computational fluid dynamics (CFD) effort was conducted by NASA and McDonnell Douglas to evaluate the magnitude and characteristics of HSCT nozzle boattail drag at transonic conditions. A team of engineers used various CFD codes and provided consistent, accurate boattail drag coefficient predictions for a family of HSCT nozzle configurations. The CFD results were incorporated into a nozzle drag database that encompassed the entire HSCT flight regime and provided the basis for an accurate and flexible prediction methodology.

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate.

PubMed

Bagno, Alessandro; Rastrelli, Federico; Saielli, Giacomo

2008-06-01

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems. Copyright (c) 2008 John Wiley & Sons, Ltd

Colorectal cancer screening among Mexican Americans at a community clinic.

PubMed

Yepes-Rios, Monica; Reimann, Joachim O F; Talavera, Ana C; Ruiz de Esparza, Antonio; Talavera, Gregory A

2006-03-01

Mexican Americans tend to under-utilize colorectal cancer (CRC) prevention. Yet little is known about sociocultural factors associated with CRC screening. This study assessed predictors of three primary CRC tests among low-income Mexican Americans. From May to December 2003, an availability sample of 287 patients, aged 50 to 89 years, who presented for routine care at a community health center near the U.S.-Mexico border completed surveys on CRC knowledge, awareness, attitudes toward screening, logistic barriers, perceptions of health, locus of control, acculturation, whether their doctor discussed CRC screening, and sociodemographics. Participants also reported whether they had ever had a fecal occult blood test, flexible sigmoidoscopy, or colonoscopy. Logistic regression identified predictors of having had these tests. Overall, 41% reported having ever had any of the three tests; 34.1% had a fecal occult blood test; 6.6%, flexible sigmoidoscopy; and 11.8%, colonoscopy. Few respondents reported any clear knowledge about CRC, and only 41% said their doctor had ever discussed screening with them. Yet "doctor discussed screening" was the only consistent screening predictor across tests. CRC knowledge (p=0.006) and insurance coverage (p=0.009) predicted having had a flexible sigmoidoscopy. Perceptions of general poor health also predicted having had a flexible sigmoidoscopy or a colonoscopy (p=0.04). Being employed marginally predicted whether patient had ever had any of the three tests (p=0.05). Results show that even those in contact with community medical services exhibit low CRC screening rates. They further suggest that interventions focused on clinical settings are an important first step toward CRC prevention in this community.

Improving Separation Assurance Stability Through Trajectory Flexibility Preservation

NASA Technical Reports Server (NTRS)

Idris, Husni; Shen, Ni; Wing, David J.

2010-01-01

New information and automation technologies are enabling the distribution of tasks and decisions from the service providers to the users of the air traffic system, with potential capacity and cost benefits. This distribution of tasks and decisions raises the concern that independent user actions will decrease the predictability and increase the complexity of the traffic system, hence inhibiting and possibly reversing any potential benefits. One such concern is the adverse impact of uncoordinated actions by individual aircraft on the stability of separation assurance. For example, individual aircraft performing self-separation may resolve predicted losses of separation or conflicts with some traffic, only to result in secondary conflicts with other traffic or with the same traffic later in time. In answer to this concern, this paper proposes metrics for preserving user trajectory flexibility to be used in self-separation along with other objectives. The hypothesis is that preserving trajectory flexibility will naturally reduce the creation of secondary conflicts by bringing about implicit coordination between aircraft. The impact of using these metrics on improving self-separation stability is investigated by measuring the impact on secondary conflicts. The scenarios analyzed include aircraft in en route airspace with each aircraft meeting a required time of arrival in a twenty minute time horizon while maintaining separation from the surrounding traffic and using trajectory flexibility metrics to mitigate the risk of secondary conflicts. Preliminary experiments showed promising results in that the trajectory flexibility preservation reduced the potential for secondary conflicts.

Development, calibration, and validation of performance prediction models for the Texas M-E flexible pavement design system.

DOT National Transportation Integrated Search

2010-08-01

This study was intended to recommend future directions for the development of TxDOTs Mechanistic-Empirical : (TexME) design system. For stress predictions, a multi-layer linear elastic system was evaluated and its validity was : verified by compar...

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 1: Analysis methods

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. S.

1985-01-01

As aircraft become larger and lighter due to design requirements for increased payload and improved fuel efficiency, they will also become more flexible. For highly flexible vehicles, the handling qualities may not be accurately predicted by conventional methods. This study applies two analysis methods to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop model analysis technique. This method considers the effects of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Volume 1 consists of the development and application of the two analysis methods described above.

Predictive wall adjustment strategy for two-dimensional flexible walled adaptive wind tunnel: A detailed description of the first one-step method

NASA Technical Reports Server (NTRS)

Wolf, Stephen W. D.; Goodyer, Michael J.

1988-01-01

Following the realization that a simple iterative strategy for bringing the flexible walls of two-dimensional test sections to streamline contours was too slow for practical use, Judd proposed, developed, and placed into service what was the first Predictive Strategy. The Predictive Strategy reduced by 75 percent or more the number of iterations of wall shapes, and therefore the tunnel run-time overhead attributable to the streamlining process, required to reach satisfactory streamlines. The procedures of the Strategy are embodied in the FORTRAN subroutine WAS (standing for Wall Adjustment Strategy) which is written in general form. The essentials of the test section hardware, followed by the underlying aerodynamic theory which forms the basis of the Strategy, are briefly described. The subroutine is then presented as the Appendix, broken down into segments with descriptions of the numerical operations underway in each, with definitions of variables.

Semiparametric Identification of Human Arm Dynamics for Flexible Control of a Functional Electrical Stimulation Neuroprosthesis

PubMed Central

Schearer, Eric M.; Liao, Yu-Wei; Perreault, Eric J.; Tresch, Matthew C.; Memberg, William D.; Kirsch, Robert F.; Lynch, Kevin M.

2016-01-01

We present a method to identify the dynamics of a human arm controlled by an implanted functional electrical stimulation neuroprosthesis. The method uses Gaussian process regression to predict shoulder and elbow torques given the shoulder and elbow joint positions and velocities and the electrical stimulation inputs to muscles. We compare the accuracy of torque predictions of nonparametric, semiparametric, and parametric model types. The most accurate of the three model types is a semiparametric Gaussian process model that combines the flexibility of a black box function approximator with the generalization power of a parameterized model. The semiparametric model predicted torques during stimulation of multiple muscles with errors less than 20% of the total muscle torque and passive torque needed to drive the arm. The identified model allows us to define an arbitrary reaching trajectory and approximately determine the muscle stimulations required to drive the arm along that trajectory. PMID:26955041

Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target.

PubMed

Whalen, Katie L; Chang, Kevin M; Spies, M Ashley

2011-05-16

Existing techniques which attempt to predict the affinity of protein-ligand interactions have demonstrated a direct relationship between computational cost and prediction accuracy. We present here the first application of a hybrid ensemble docking and steered molecular dynamics scheme (with a minimized computational cost), which achieves a binding affinity rank-ordering of ligands with a Spearman correlation coefficient of 0.79 and an RMS error of 0.7 kcal/mol. The scheme, termed Flexible Enzyme Receptor Method by Steered Molecular Dynamics (FERM-SMD), is applied to an in-house collection of 17 validated ligands of glutamate racemase. The resulting improved accuracy in affinity prediction allows elucidation of the key structural components of a heretofore unreported glutamate racemase inhibitor (K(i) = 9 µM), a promising new lead in the development of antibacterial therapeutics.

Approaching Pharmacological Space: Events and Components.

PubMed

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Testa, Bernard

2018-01-01

With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, physicochemical properties and binding spaces, which are seen as the three key elements composing the pharmacological space. While the concept of conformational space is routinely used to encode molecular flexibility, the concepts of property spaces and, particularly, of binding spaces are more innovative. Indeed, their descriptors can find fruitful applications (a) in describing the dynamic adaptability a given ligand experiences when inserted into a specific environment, and (b) in parameterizing the flexibility a ligand retains when bound to a biological target. Overall, these descriptors can conveniently account for the often disregarded entropic factors and as such they prove successful when inserted in ligand- or structure-based predictive models. Notably, and although binding space parameters can clearly be derived from MD simulations, the chapter will illustrate how docking calculations, despite their static nature, are able to evaluate ligand's flexibility by analyzing several poses for each ligand. Such an approach, which represents the founding core of the binding space concept, can find various applications in which the related descriptors show an impressive enhancing effect on the statistical performances of the resulting predictive models.

Biological and cognitive underpinnings of religious fundamentalism.

PubMed

Zhong, Wanting; Cristofori, Irene; Bulbulia, Joseph; Krueger, Frank; Grafman, Jordan

2017-06-01

Beliefs profoundly affect people's lives, but their cognitive and neural pathways are poorly understood. Although previous research has identified the ventromedial prefrontal cortex (vmPFC) as critical to representing religious beliefs, the means by which vmPFC enables religious belief is uncertain. We hypothesized that the vmPFC represents diverse religious beliefs and that a vmPFC lesion would be associated with religious fundamentalism, or the narrowing of religious beliefs. To test this prediction, we assessed religious adherence with a widely-used religious fundamentalism scale in a large sample of 119 patients with penetrating traumatic brain injury (pTBI). If the vmPFC is crucial to modulating diverse personal religious beliefs, we predicted that pTBI patients with lesions to the vmPFC would exhibit greater fundamentalism, and that this would be modulated by cognitive flexibility and trait openness. Instead, we found that participants with dorsolateral prefrontal cortex (dlPFC) lesions have fundamentalist beliefs similar to patients with vmPFC lesions and that the effect of a dlPFC lesion on fundamentalism was significantly mediated by decreased cognitive flexibility and openness. These findings indicate that cognitive flexibility and openness are necessary for flexible and adaptive religious commitment, and that such diversity of religious thought is dependent on dlPFC functionality. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bending induced electrical response variations in ultra-thin flexible chips and device modeling

NASA Astrophysics Data System (ADS)

Heidari, Hadi; Wacker, Nicoleta; Dahiya, Ravinder

2017-09-01

Electronics that conform to 3D surfaces are attracting wider attention from both academia and industry. The research in the field has, thus far, focused primarily on showcasing the efficacy of various materials and fabrication methods for electronic/sensing devices on flexible substrates. As the device response changes are bound to change with stresses induced by bending, the next step will be to develop the capacity to predict the response of flexible systems under various bending conditions. This paper comprehensively reviews the effects of bending on the response of devices on ultra-thin chips in terms of variations in electrical parameters such as mobility, threshold voltage, and device performance (static and dynamic). The discussion also includes variations in the device response due to crystal orientation, applied mechanics, band structure, and fabrication processes. Further, strategies for compensating or minimizing these bending-induced variations have been presented. Following the in-depth analysis, this paper proposes new mathematical relations to simulate and predict the device response under various bending conditions. These mathematical relations have also been used to develop new compact models that have been verified by comparing simulation results with the experimental values reported in the recent literature. These advances will enable next generation computer-aided-design tools to meet the future design needs in flexible electronics.

Biological and cognitive underpinnings of religious fundamentalism

PubMed Central

Zhong, Wanting; Cristofori, Irene; Bulbulia, Joseph; Krueger, Frank; Grafman, Jordan

2017-01-01

Beliefs profoundly affect people's lives, but their cognitive and neural pathways are poorly understood. Although previous research has identified the ventromedial prefrontal cortex (vmPFC) as critical to representing religious beliefs, the means by which vmPFC enables religious belief is uncertain. We hypothesized that the vmPFC represents diverse religious beliefs and that a vmPFC lesion would be associated with religious fundamentalism, or the narrowing ofreligious beliefs. To test this prediction, we assessed religious adherence with a widely-used religious fundamentalism scale in a large sample of 119 patients with penetrating traumatic brain injury (pTBI). If the vmPFC is crucial to modulating diverse personal religious beliefs, we predicted that pTBI patients with lesions to the vmPFC would exhibit greater fundamentalism, and that this would be modulated by cognitive flexibility and trait openness. Instead, we found that participants with dorsolateral prefrontal cortex (dlPFC) lesions have fundamentalist beliefs similar to patients with vmPFC lesions and that the effect of a dlPFC lesion on fundamentalism was significantly mediated by decreased cognitive flexibility and openness. These findings indicate that cognitive flexibility and openness are necessary for flexible and adaptive religious commitment, and that such diversity of religious thought is dependent on dlPFC functionality. PMID:28392301

Simulating Space Capsule Water Landing with Explicit Finite Element Method

NASA Technical Reports Server (NTRS)

Wang, John T.; Lyle, Karen H.

2007-01-01

A study of using an explicit nonlinear dynamic finite element code for simulating the water landing of a space capsule was performed. The finite element model contains Lagrangian shell elements for the space capsule and Eulerian solid elements for the water and air. An Arbitrary Lagrangian Eulerian (ALE) solver and a penalty coupling method were used for predicting the fluid and structure interaction forces. The space capsule was first assumed to be rigid, so the numerical results could be correlated with closed form solutions. The water and air meshes were continuously refined until the solution was converged. The converged maximum deceleration predicted is bounded by the classical von Karman and Wagner solutions and is considered to be an adequate solution. The refined water and air meshes were then used in the models for simulating the water landing of a capsule model that has a flexible bottom. For small pitch angle cases, the maximum deceleration from the flexible capsule model was found to be significantly greater than the maximum deceleration obtained from the corresponding rigid model. For large pitch angle cases, the difference between the maximum deceleration of the flexible model and that of its corresponding rigid model is smaller. Test data of Apollo space capsules with a flexible heat shield qualitatively support the findings presented in this paper.

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

PubMed Central

Kingsley, Laura J.; Lill, Markus A.

2014-01-01

Computational prediction of ligand entry and egress paths in proteins has become an emerging topic in computational biology and has proven useful in fields such as protein engineering and drug design. Geometric tunnel prediction programs, such as Caver3.0 and MolAxis, are computationally efficient methods to identify potential ligand entry and egress routes in proteins. Although many geometric tunnel programs are designed to accommodate a single input structure, the increasingly recognized importance of protein flexibility in tunnel formation and behavior has led to the more widespread use of protein ensembles in tunnel prediction. However, there has not yet been an attempt to directly investigate the influence of ensemble size and composition on geometric tunnel prediction. In this study, we compared tunnels found in a single crystal structure to ensembles of various sizes generated using different methods on both the apo and holo forms of cytochrome P450 enzymes CYP119, CYP2C9, and CYP3A4. Several protein structure clustering methods were tested in an attempt to generate smaller ensembles that were capable of reproducing the data from larger ensembles. Ultimately, we found that by including members from both the apo and holo data sets, we could produce ensembles containing less than 15 members that were comparable to apo or holo ensembles containing over 100 members. Furthermore, we found that, in the absence of either apo or holo crystal structure data, pseudo-apo or –holo ensembles (e.g. adding ligand to apo protein throughout MD simulations) could be used to resemble the structural ensembles of the corresponding apo and holo ensembles, respectively. Our findings not only further highlight the importance of including protein flexibility in geometric tunnel prediction, but also suggest that smaller ensembles can be as capable as larger ensembles at capturing many of the protein motions important for tunnel prediction at a lower computational cost. PMID:24956479

The flexibility and dynamics of protein disulfide isomerase

PubMed Central

Wells, Stephen A.; Emilio Jimenez‐Roldan, J.; Bhattacharyya, Moitrayee; Vishweshwara, Saraswathi; Freedman, Robert B.

2016-01-01

ABSTRACT We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse‐graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures—and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776–1785. © 2016 Wiley Periodicals, Inc. PMID:27616289

Flexible Use of Predictive Cues beyond the Orbitofrontal Cortex: Role of the Submedius Thalamic Nucleus.

PubMed

Alcaraz, Fabien; Marchand, Alain R; Vidal, Elisa; Guillou, Alexandre; Faugère, Angélique; Coutureau, Etienne; Wolff, Mathieu

2015-09-23

The orbitofrontal cortex (OFC) is known to play a crucial role in learning the consequences of specific events. However, the contribution of OFC thalamic inputs to these processes is largely unknown. Using a tract-tracing approach, we first demonstrated that the submedius nucleus (Sub) shares extensive reciprocal connections with the OFC. We then compared the effects of excitotoxic lesions of the Sub or the OFC on the ability of rats to use outcome identity to direct responding. We found that neither OFC nor Sub lesions interfered with the basic differential outcomes effect. However, more specific tests revealed that OFC rats, but not Sub rats, were disproportionally relying on the outcome, rather than on the discriminative stimulus, to guide behavior, which is consistent with the view that the OFC integrates information about predictive cues. In subsequent experiments using a Pavlovian contingency degradation procedure, we found that both OFC and Sub lesions produced a severe deficit in the ability to update Pavlovian associations. Altogether, the submedius therefore appears as a functionally relevant thalamic component in a circuit dedicated to the integration of predictive cues to guide behavior, previously conceived as essentially dependent on orbitofrontal functions. Significance statement: In the present study, we identify a largely unknown thalamic region, the submedius nucleus, as a new functionally relevant component in a circuit supporting the flexible use of predictive cues. Such abilities were previously conceived as largely dependent on the orbitofrontal cortex. Interestingly, this echoes recent findings in the field showing, in research involving an instrumental setup, an additional involvement of another thalamic nuclei, the parafascicular nucleus, when correct responding requires an element of flexibility (Bradfield et al., 2013a). Therefore, the present contribution supports the emerging view that limbic thalamic nuclei may contribute critically to adaptive responding when an element of flexibility is required after the establishment of initial learning. Copyright © 2015 the authors 0270-6474/15/3513183-11$15.00/0.

Handling Qualities of Large Flexible Aircraft. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Poopaka, S.

1980-01-01

The effects on handling qualities of elastic modes interaction with the rigid body dynamics of a large flexible aircraft are studied by a mathematical computer simulation. An analytical method to predict the pilot ratings when there is a severe modes interactions is developed. This is done by extending the optimal control model of the human pilot response to include the mode decomposition mechanism into the model. The handling qualities are determined for a longitudinal tracking task using a large flexible aircraft with parametric variations in the undamped natural frequencies of the two lowest frequency, symmetric elastic modes made to induce varying amounts of mode interaction.

A slewing control experiment for flexible structures

NASA Technical Reports Server (NTRS)

Juang, J.-N.; Horta, L. G.; Robertshaw, H. H.

1985-01-01

A hardware set-up has been developed to study slewing control for flexible structures including a steel beam and a solar panel. The linear optimal terminal control law is used to design active controllers which are implemented in an analog computer. The objective of this experiment is to demonstrate and verify the dynamics and optimal terminal control laws as applied to flexible structures for large angle maneuver. Actuation is provided by an electric motor while sensing is given by strain gages and angle potentiometer. Experimental measurements are compared with analytical predictions in terms of modal parameters of the system stability matrix and sufficient agreement is achieved to validate the theory.

Self-regulation as a moderator of the relation between coping and symptomatology in children of divorce.

PubMed

Lengua, L J; Sandler, I N

1996-12-01

Investigated the effects of self-regulation as a moderator of the relations between coping efforts and psychological symptoms of children of divorce. The interactions of two dimensions of self-regulation (task orientation and approach-flexibility) and two dimensions of coping (active and avoidant) predicting children's postdivorce symptoms were tested using a sample of 199 divorced mothers and their children, ages 8 to 12. The approach-flexibility dimension moderated the relations of both active and avoidant coping with children's self-report of anxiety. At higher levels of approach-flexibility, active coping was negatively related to anxiety, while at lower levels of approach-flexibility, active coping was unrelated to anxiety. Avoidant coping was unrelated to anxiety at higher levels of approach-flexibility, whereas at lower levels of approach-flexibility, avoidant coping was positively related to anxiety. The task orientation dimension did not interact with coping, but had direct, independent effects on children's self-report of conduct problems, depression, and parent-report of internalizing and externalizing behavior problems. The implications for understanding children's coping with divorce and future directions for research are discussed.

Flexibility decline contributes to similarity of past and future thinking in Alzheimer's disease.

PubMed

El Haj, Mohamad; Antoine, Pascal; Kapogiannis, Dimitrios

2015-11-01

A striking similarity has been suggested between past and future thinking in Alzheimer's Disease (AD), a similarity attributable to abnormalities in common modular cognitive functions and neuroanatomical substrates. This study extends this literature by identifying specific executive function deficits underlying past and future thinking in AD. Twenty-four participants with a clinical diagnosis of probable (mild) AD and 26 older controls generated past and future events and underwent tests of binding and the executive functions of flexibility, inhibition, and updating. AD patients showed similar autobiographical performances in past and future event generation, and so did control participants. In each group, the similarity of past and future thinking was predicted by flexibility. Furthermore, AD patients with low flexibility showed higher similarity of past and future thinking than those with high flexibility. These findings are interpreted in terms of involvement of the hippocampus and frontal lobes in future thinking. Deficits in these brain regions in AD are likely to compromise the ability to recombine episodic information into novel and flexible configurations as scenarios for the future. © 2015 Wiley Periodicals, Inc.

Wind-Induced Reconfigurations in Flexible Branched Trees

NASA Astrophysics Data System (ADS)

Ojo, Oluwafemi; Shoele, Kourosh

2017-11-01

Wind induced stresses are the major mechanical cause of failure in trees. We know that the branching mechanism has an important effect on the stress distribution and stability of a tree in the wind. Eloy in PRL 2011, showed that Leonardo da Vinci's original observation which states the total cross section of branches is conserved across branching nodes is the best configuration for resisting wind-induced fracture in rigid trees. However, prediction of the fracture risk and pattern of a tree is also a function of their reconfiguration capabilities and how they mitigate large wind-induced stresses. In this studies through developing an efficient numerical simulation of flexible branched trees, we explore the role of the tree flexibility on the optimal branching. Our results show that the probability of a tree breaking at any point depends on both the cross-section changes in the branching nodes and the level of tree flexibility. It is found that the branching mechanism based on Leonardo da Vinci's original observation leads to a uniform stress distribution over a wide range of flexibilities but the pattern changes for more flexible systems.

Flexibility Decline Contributes to Similarity of Past and Future Thinking in Alzheimer’s Disease

PubMed Central

El Haj, Mohamad; Antoine, Pascal; Kapogiannis, Dimitrios

2017-01-01

A striking similarity has been suggested between past and future thinking in Alzheimer’s Disease (AD), a similarity attributable to abnormalities in common modular cognitive functions and neuroanatomical substrates. This study extends this literature by identifying specific executive function deficits underlying past and future thinking in AD. Twenty-four participants with a clinical diagnosis of probable (mild) AD and 26 older controls generated past and future events and underwent tests of binding and the executive functions of flexibility, inhibition, and updating. AD patients showed similar autobiographical performances in past and future event generation, and so did control participants. In each group, the similarity of past and future thinking was predicted by flexibility. Furthermore, AD patients with low flexibility showed higher similarity of past and future thinking than those with high flexibility. These findings are interpreted in terms of involvement of the hippocampus and frontal lobes in future thinking. Deficits in these brain regions in AD are likely to compromise the ability to recombine episodic information into novel and flexible configurations as scenarios for the future. PMID:25850800

An fMRI investigation of the relationship between future imagination and cognitive flexibility

PubMed Central

Roberts, R.P.; Wiebels, K.; Sumner, R.L.; van Mulukom, V.; Grady, C.L.; Schacter, D.L.; Addis, D.R.

2016-01-01

While future imagination is largely considered to be a cognitive process grounded in default mode network activity, studies have shown that future imagination recruits regions in both default mode and frontoparietal control networks. In addition, it has recently been shown that the ability to imagine the future is associated with cognitive flexibility, and that tasks requiring cognitive flexibility result in increased coupling of the default mode network with frontoparietal control and salience networks. In the current study, we investigated the neural correlates underlying the association between cognitive flexibility and future imagination in two ways. First, we experimentally varied the degree of cognitive flexibility required during future imagination by manipulating the disparateness of episodic details contributing to imagined events. To this end, participants generated episodic details (persons, locations, objects) within three social spheres; during fMRI scanning they were presented with sets of three episodic details all taken from the same social sphere (Congruent condition) or different social spheres (Incongruent condition) and required to imagine a future event involving the three details. We predicted that, relative to the Congruent condition, future simulation in the Incongruent condition would be associated with increased activity in regions of the default mode, frontoparietal and salience networks. Second, we hypothesized that individual differences in cognitive flexibility, as measured by performance on the Alternate Uses Task, would correspond to individual differences in the brain regions recruited during future imagination. A task partial least squares (PLS) analysis showed that the Incongruent condition resulted in an increase in activity in regions in salience networks (e.g. the insula) but, contrary to our prediction, reduced activity in many regions of the default mode network (including the hippocampus). A subsequent functional connectivity (within-subject seed PLS) analysis showed that the insula exhibited increased coupling with default mode regions during the Incongruent condition. Finally, a behavioral PLS analysis showed that individual differences in cognitive flexibility were associated with differences in activity in a number of regions from frontoparietal, salience and default-mode networks during both future imagination conditions, further highlighting that the cognitive flexibility underlying future imagination is grounded in the complex interaction of regions in these networks. PMID:27908591

Piezoresistance of flexible tunneling-percolation networks

NASA Astrophysics Data System (ADS)

Taylor-Harrod, Isaac; Nogaret, Alain

2017-07-01

We model changes in the conductivity of flexible composite films stressed by bending. By treating stress as a perturbation of the effective medium conductivity, we obtain an expression of the piezoresistance as a function of four material parameters. The model correctly predicts resistance spikes and their recovery under the action of viscoelastic forces, in good agreement with experimental observations over stress cycles. The theory may be used to design composite materials for high-sensitivity touch sensors.

Third-order polynomial model for analyzing stickup state laminated structure in flexible electronics

NASA Astrophysics Data System (ADS)

Meng, Xianhong; Wang, Zihao; Liu, Boya; Wang, Shuodao

2018-02-01

Laminated hard-soft integrated structures play a significant role in the fabrication and development of flexible electronics devices. Flexible electronics have advantageous characteristics such as soft and light-weight, can be folded, twisted, flipped inside-out, or be pasted onto other surfaces of arbitrary shapes. In this paper, an analytical model is presented to study the mechanics of laminated hard-soft structures in flexible electronics under a stickup state. Third-order polynomials are used to describe the displacement field, and the principle of virtual work is adopted to derive the governing equations and boundary conditions. The normal strain and the shear stress along the thickness direction in the bi-material region are obtained analytically, which agree well with the results from finite element analysis. The analytical model can be used to analyze stickup state laminated structures, and can serve as a valuable reference for the failure prediction and optimal design of flexible electronics in the future.

Cognitive Flexibility in Juvenile Anorexia Nervosain Relation to Comorbid Symptoms of Depression, Obsessive Compulsive Symptoms and Duration of Illness.

PubMed

Rößner, Anne; Juniak, Izabela; van Noort, Betteke Maria; Pfeiffer, Ernst; Lehmkuhl, Ulrike; Kappel, Viola

2017-09-01

Whereas the evidence in adolescents is inconsistent, anorexia nervosa (AN) in adults is characterized by weak cognitive flexibility. This study investigates cognitive flexibility in adolescents with AN and its potential associations with symptoms of depression, obsessive compulsive disorder (OCD), and duration of illness. 69 patients and 63 age-matched healthy controls (HC) from 9 till 19 years of age were assessed using the Trail-Making Test (TMT) and self-report questionnaires. In hierarchical regression analyses, set-shifting ability did not differ between AN and HC, whereas AN patients reported significantly higher rates of depression symptoms and OCD symptoms. Age significantly predicted set-shifting in the total sample. Only among AN patients aged 14 years and older did set-shifting decline with increasing age. The presence of AN with depression or OCD symptoms or the duration of illness do not influence cognitive flexibility in children and adolescents. Early interventions may be helpful to prevent a decline in cognitive flexibility in adolescent AN with increasing age.

Reciprocal inhibition of inhibition: A circuit motif for flexible categorization in stimulus selection

PubMed Central

Knudsen, Eric I.

2011-01-01

As a precursor to the selection of a stimulus for gaze and attention, a midbrain network categorizes stimuli into “strongest” and “others.” The categorization tracks flexibly, in real-time, the absolute strength of the strongest stimulus. In this study, we take a first principles approach to computations that are essential for such categorization. We demonstrate that classical feedforward lateral inhibition cannot produce flexible categorization. However, circuits in which the strength of lateral inhibition varies with the relative strength of competing stimuli categorize successfully. One particular implementation - reciprocal inhibition of feedforward lateral inhibition – is structurally the simplest, and it outperforms others in flexibly categorizing rapidly and reliably. Strong predictions of this anatomically supported circuit model are validated by neural responses measured in the owl midbrain. The results demonstrate the extraordinary power of a remarkably simple, neurally grounded circuit motif in producing flexible categorization, a computation fundamental to attention, perception, and decision-making. PMID:22243757

Role of Spontaneous Brain Activity in Explicit and Implicit Aspects of Cognitive Flexibility under Socially Conflicting Situations: A Resting-state fMRI Study using Fractional Amplitude of Low-frequency Fluctuations.

PubMed

Fujino, Junya; Tei, Shisei; Jankowski, Kathryn F; Kawada, Ryosaku; Murai, Toshiya; Takahashi, Hidehiko

2017-12-26

We are constantly exposed to socially conflicting situations in everyday life, and cognitive flexibility is essential for adaptively coping with such difficulties. Flexible goal choice and pursuit are not exclusively conscious, and therefore cognitive flexibility involves both explicit and implicit forms of processing. However, it is unclear how individual differences in explicit and implicit aspects of flexibility are associated with neural activity in a resting state. Here, we measured intrinsic fractional amplitude of low-frequency fluctuations (fALFF) by resting-state functional magnetic resonance imaging (RS-fMRI) as an indicator of regional brain spontaneous activity, together with explicit and implicit aspects of cognitive flexibility using the Cognitive Flexibility Scale (CFS) and Implicit Association Test (IAT). Consistent with the dual processing theory, there was a strong association between explicit aspects of flexibility (CFS score) and "rationalism" thinking style and between implicit aspects (IAT effect) and "experientialism." The level of explicit flexibility was also correlated with fALFF values in the left lateral prefrontal cortex, whereas the level of implicit flexibility was correlated with fALFF values in the right cerebellum. Furthermore, the fALFF values in both regions predicted individual preference for flexible decision-making strategy in a vignettes simulation task. These results add to our understanding of the neural mechanisms underlying flexible decision-making for solving social conflicts. More generally, our findings highlight the utility of RS-fMRI combined with both explicit and implicit psychometric measures for better understanding individual differences in social cognition. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Childhood adversity predicts reduced physiological flexibility during the processing of negative affect among adolescents with major depression histories.

PubMed

Daches, Shimrit; Kovacs, Maria; George, Charles J; Yaroslavsky, Ilya; Kiss, Eniko; Vetró, Ágnes; Dochnal, Roberta; Benák, István; Baji, Ildikó; Halas, Kitti; Makai, Attila; Kapornai, Krisztina; Rottenberg, Jonathan

2017-11-01

Adversity during early development has been shown to have enduring negative physiological consequences. In turn, atypical physiological functioning has been associated with maladaptive processing of negative affect, including its regulation. The present study therefore explored whether exposure to adverse life events in childhood predicted maladaptive (less flexible) parasympathetic nervous system functioning during the processing of negative affect among adolescents with depression histories. An initially clinic-referred, pediatric sample (N=189) was assessed at two time points. At Time 1, when subjects were 10.17years old (SD=1.42), on average, and were depressed, parents reported on adverse life events the offspring experienced up to that point. At Time 2, when subjects were 17.18years old (SD=1.28), and were remitted from depression, parents again reported on adverse life events in their offspring's lives for the interim period. At time 2, subjects' parasympathetic nervous system functioning (quantified as respiratory sinus arrhythmia) also was assessed at rest, during sad mood induction, and during instructed mood repair. Extent of adverse life events experienced by T1 (but not events occurring between T1 and T2) predicted less flexible RSA functioning 7years later during the processing of negative affect. Adolescents with more extensive early life adversities exhibited less vagal withdrawal following negative mood induction and tended to show less physiological recovery following mood repair. Early adversities appear to be associated with less flexible physiological regulatory control during negative affect experience, when measured later in development. Stress-related autonomic dysfunction in vulnerable youths may contribute to the unfavorable clinical prognosis associated with juvenile-onset depression. Copyright © 2017 Elsevier B.V. All rights reserved.

Predicting Successful Completion Using Student Delay Indicators in Undergraduate Self-Paced Online Courses

ERIC Educational Resources Information Center

Lim, Janine M.

2016-01-01

Self-paced online courses meet flexibility and learning needs of many students, but skepticism persists regarding the quality and the tendency for students to procrastinate in self-paced courses. Research is needed to understand procrastination and delay patterns of students in online self-paced courses to predict successful completion and…

CABS-flex predictions of protein flexibility compared with NMR ensembles

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-01-01

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. Availability and implementation: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. Contact: sekmi@chem.uw.edu.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24735558

Workplace Policies and Mental Health among Working-Class, New Parents

PubMed Central

Perry-Jenkins, Maureen; Smith, JuliAnna Z.; Wadsworth, Lauren Page; Halpern, Hillary Paul

2017-01-01

Little research has explored linkages between workplace policies and mental health in working-class, employed parents, creating a gap in our knowledge of work-family issues across social class levels. The current U.S. study addresses this gap by employing hierarchical linear modeling techniques to examine how workplace policies and parental leave benefits predicted parents' depressive symptoms and anxiety in a sample of 125, low-income, dual-earner couples interviewed across the transition to parenthood. Descriptive analyses revealed that, on average, parents had few workplace policies, such as schedule flexibility or child care supports, available to them. Results revealed, however, that, when available, schedule flexibility was related to fewer depressive symptoms and less anxiety for new mothers. Greater child care supports predicted fewer depressive symptoms for fathers. In terms of crossover effects, longer maternal leave predicted declines in fathers' anxiety across the first year. Results are discussed with attention to how certain workplace policies may serve to alleviate new parents' lack of time and resources (minimize scarcity of resources) and, in turn, predict better mental health during the sensitive period of new parenthood. PMID:29242705

CABS-flex predictions of protein flexibility compared with NMR ensembles.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-08-01

Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. sekmi@chem.uw.edu.pl Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

The Effect of Executive Function on Science Achievement Among Normally Developing 10-Year Olds

NASA Astrophysics Data System (ADS)

Lederman, Sheri G.

Executive function (EF) is an umbrella term used to identify a set of discrete but interrelated cognitive abilities that enable individuals to engage in goal-directed, future-oriented action in response to a novel context. Developmental studies indicate that EF is predictive of reading and math achievement in middle childhood. The purpose of this study was to identify the association between EF and science achievement among normally developing 10 year olds. A sample of fifth grade students from a Northeastern suburban community participated in tests of EF, science, and intelligence. Consistent with adult models of EF, principal components analysis identified a three-factor model of EF organization in middle childhood, including cognitive flexibility, working memory, and inhibition. Multiple regression analyses revealed that executive function processes of cognitive flexibility, working memory, and inhibition were all predictive of science performance. Post hoc analyses revealed that high-performing science students differed significantly from low-performing students in both cognitive flexibility and working memory. These findings suggest that complex academic demands specific to science achievement rely on the emergence and maturation of EF components.

Self-motivated visual scanning predicts flexible navigation in a virtual environment.

PubMed

Ploran, Elisabeth J; Bevitt, Jacob; Oshiro, Jaris; Parasuraman, Raja; Thompson, James C

2014-01-01

The ability to navigate flexibly (e.g., reorienting oneself based on distal landmarks to reach a learned target from a new position) may rely on visual scanning during both initial experiences with the environment and subsequent test trials. Reliance on visual scanning during navigation harkens back to the concept of vicarious trial and error, a description of the side-to-side head movements made by rats as they explore previously traversed sections of a maze in an attempt to find a reward. In the current study, we examined if visual scanning predicted the extent to which participants would navigate to a learned location in a virtual environment defined by its position relative to distal landmarks. Our results demonstrated a significant positive relationship between the amount of visual scanning and participant accuracy in identifying the trained target location from a new starting position as long as the landmarks within the environment remain consistent with the period of original learning. Our findings indicate that active visual scanning of the environment is a deliberative attentional strategy that supports the formation of spatial representations for flexible navigation.

Metal Building Systems Fit To Be Tried

ERIC Educational Resources Information Center

Nation's Schools, 1974

1974-01-01

Describes the advantages of metal building systems in school construction. These advantages include faster occupancy, lower initial costs, reduced maintenance, flexibility, and predictability of cost. (Author/DN)

Coping with occupational stress: the role of optimism and coping flexibility.

PubMed

Reed, Daniel J

2016-01-01

The current study aimed at measuring whether coping flexibility is a reliable and valid construct in a UK sample and subsequently investigating the association between coping flexibility, optimism, and psychological health - measured by perceived stress and life satisfaction. A UK university undergraduate student sample (N=95) completed an online questionnaire. The study is among the first to examine the validity and reliability of the English version of a scale measuring coping flexibility in a Western population and is also the first to investigate the association between optimism and coping flexibility. The results revealed that the scale had good reliability overall; however, factor analysis revealed no support for the existing two-factor structure of the scale. Coping flexibility and optimism were found to be strongly correlated, and hierarchical regression analyses revealed that the interaction between them predicted a large proportion of the variance in both perceived stress and life satisfaction. In addition, structural equation modeling revealed that optimism completely mediated the relationship between coping flexibility and both perceived stress and life satisfaction. The findings add to the occupational stress literature to further our understanding of how optimism is important in psychological health. Furthermore, given that optimism is a personality trait, and consequently relatively stable, the study also provides preliminary support for the potential of targeting coping flexibility to improve psychological health in Western populations. These findings must be replicated, and further analyses of the English version of the Coping Flexibility Scale are needed.

A Comprehensive Examination of Changes in Psychological Flexibility Following Acceptance and Commitment Therapy for Chronic Pain.

PubMed

Scott, Whitney; Hann, Katie E J; McCracken, Lance M

Acceptance and commitment therapy (ACT) for chronic pain aims to improve patient functioning by fostering greater psychological flexibility. While promising, ACT treatment process research in the context of chronic pain so far has only focused on a few of the processes of psychological flexibility. Therefore, this study aimed to more comprehensively examine changes in processes of psychological flexibility following an ACT-based treatment for chronic pain, and to examine change in these processes in relation to improvements in patient functioning. Individuals with chronic pain attending an interdisciplinary ACT-based rehabilitation program completed measures of pain, functioning, depression, pain acceptance, cognitive fusion, decentering, and committed action at pre- and post-treatment and during a nine-month follow-up. Significant improvements were observed from pre- to post-treatment and pre-treatment to follow-up on each of the treatment outcome and process variables. Regression analyses indicated that change in psychological flexibility processes cumulatively explained 6-27 % of the variance in changes in functioning and depression over both assessment periods, even after controlling for changes in pain intensity. Further research is needed to maximize the effectiveness of ACT for chronic pain, and to determine whether larger improvements in the processes of psychological flexibility under study will produce better patient outcomes, as predicted by the psychological flexibility model.

Side chain flexibility and the pore dimensions in the GABAA receptor

NASA Astrophysics Data System (ADS)

Rossokhin, Alexey V.; Zhorov, Boris S.

2016-07-01

Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α1β2γ2 GABAA receptor (GABAAR). The models are based, respectively, on the X-ray structure of α3 glycine receptor (α3 GlyR), cryo-EM structure of α1 GlyR and X-ray structure of β3 GABAAR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of -2', 9' and 20' residues. Residues around the -2' and 9' rings are known to form the desensitization and activation gates of GABAAR. Our computations predict that the 20' ring may also serve as GABAAR gate whose physiological role is unclear. The side chain flexibility of residues -2', 9' and 20' and hence the dimensions of the constrictions depend on the GABAAR functional state.

Identifying and describing feelings and psychological flexibility predict mental health in men with HIV.

PubMed

Landstra, Jodie M B; Ciarrochi, Joseph; Deane, Frank P; Hillman, Richard J

2013-11-01

Difficulty identifying and describing feelings (DIDF) and psychological flexibility (PF) predict poor emotional adjustment. To examine the relationship between DIDF and PF and whether DIDF and low PF would put men undergoing cancer screening at risk for poor adjustment. Longitudinal self-report survey. Two hundred and one HIV-infected men who have sex with men participated in anal cancer screening at two time points over 14 weeks. Psychological flexibility was assessed by the Acceptance and Action Questionnaire II and DIDF by the Toronto Alexithymia Scale-20. We also measured depression, anxiety, stress (DASS) and health-related quality of life (QOL; SF-12). Both DIDF and PF were reliable predictors of mental health. When levels of baseline mental health were controlled, greater DIDF predicted increases in Time 2 depression, anxiety and stress and decreases in mental and physical QOL. The link between PF and mental health was entirely mediated by DIDF. Being chronically low in PF could lead to greater DIDF and thereby worse mental health. Having more PF promotes the ability to identify and differentiate the nuances of pleasant and unpleasant emotions, which enhances an individual's mental health. Intentionally enhancing men's ability to identify and describe feelings or PF may assist them to better manage a range of difficult life experiences such as health screenings and other potentially threatening information. © 2013 The British Psychological Society.

HCP: A Flexible CNN Framework for Multi-label Image Classification.

PubMed

Wei, Yunchao; Xia, Wei; Lin, Min; Huang, Junshi; Ni, Bingbing; Dong, Jian; Zhao, Yao; Yan, Shuicheng

2015-10-26

Convolutional Neural Network (CNN) has demonstrated promising performance in single-label image classification tasks. However, how CNN best copes with multi-label images still remains an open problem, mainly due to the complex underlying object layouts and insufficient multi-label training images. In this work, we propose a flexible deep CNN infrastructure, called Hypotheses-CNN-Pooling (HCP), where an arbitrary number of object segment hypotheses are taken as the inputs, then a shared CNN is connected with each hypothesis, and finally the CNN output results from different hypotheses are aggregated with max pooling to produce the ultimate multi-label predictions. Some unique characteristics of this flexible deep CNN infrastructure include: 1) no ground-truth bounding box information is required for training; 2) the whole HCP infrastructure is robust to possibly noisy and/or redundant hypotheses; 3) the shared CNN is flexible and can be well pre-trained with a large-scale single-label image dataset, e.g., ImageNet; and 4) it may naturally output multi-label prediction results. Experimental results on Pascal VOC 2007 and VOC 2012 multi-label image datasets well demonstrate the superiority of the proposed HCP infrastructure over other state-of-the-arts. In particular, the mAP reaches 90.5% by HCP only and 93.2% after the fusion with our complementary result in [44] based on hand-crafted features on the VOC 2012 dataset.

A system identification approach for developing model predictive controllers of antibody quality attributes in cell culture processes

PubMed Central

Schmitt, John; Beller, Justin; Russell, Brian; Quach, Anthony; Hermann, Elizabeth; Lyon, David; Breit, Jeffrey

2017-01-01

As the biopharmaceutical industry evolves to include more diverse protein formats and processes, more robust control of Critical Quality Attributes (CQAs) is needed to maintain processing flexibility without compromising quality. Active control of CQAs has been demonstrated using model predictive control techniques, which allow development of processes which are robust against disturbances associated with raw material variability and other potentially flexible operating conditions. Wide adoption of model predictive control in biopharmaceutical cell culture processes has been hampered, however, in part due to the large amount of data and expertise required to make a predictive model of controlled CQAs, a requirement for model predictive control. Here we developed a highly automated, perfusion apparatus to systematically and efficiently generate predictive models using application of system identification approaches. We successfully created a predictive model of %galactosylation using data obtained by manipulating galactose concentration in the perfusion apparatus in serialized step change experiments. We then demonstrated the use of the model in a model predictive controller in a simulated control scenario to successfully achieve a %galactosylation set point in a simulated fed‐batch culture. The automated model identification approach demonstrated here can potentially be generalized to many CQAs, and could be a more efficient, faster, and highly automated alternative to batch experiments for developing predictive models in cell culture processes, and allow the wider adoption of model predictive control in biopharmaceutical processes. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 33:1647–1661, 2017 PMID:28786215

Analytical and numerical modeling for flexible pipes

NASA Astrophysics Data System (ADS)

Wang, Wei; Chen, Geng

2011-12-01

The unbonded flexible pipe of eight layers, in which all the layers except the carcass layer are assumed to have isotropic properties, has been analyzed. Specifically, the carcass layer shows the orthotropic characteristics. The effective elastic moduli of the carcass layer have been developed in terms of the influence of deformation to stiffness. With consideration of the effective elastic moduli, the structure can be properly analyzed. Also the relative movements of tendons and relative displacements of wires in helical armour layer have been investigated. A three-dimensional nonlinear finite element model has been presented to predict the response of flexible pipes under axial force and torque. Further, the friction and contact of interlayer have been considered. Comparison between the finite element model and experimental results obtained in literature has been given and discussed, which might provide practical and technical support for the application of unbonded flexible pipes.

Children’s Beliefs in Reciprocation of Biases and Flexibility

PubMed Central

Rennels, Jennifer L.

2015-01-01

Children display positive and negative biases based on peers’ attractiveness, gender, and race, but it is unclear whether children who associate positive attributes with certain peers also believe those peers think positively of them. In each domain (attractiveness, gender, race), we measured 3- to 11-year-olds’ (N=102) biases and flexibility and their beliefs in reciprocity of bias and flexibility by asking who would think positively of them. Children could choose one of two unfamiliar peers (forced choice assessment) or had the additional options of choosing both or neither peer (non-forced choice assessment). We found children often displayed beliefs in reciprocation, with beliefs in positive bias reciprocation from attractive girls showing the largest effect sizes. These beliefs significantly correlated with and were predictive of children’s positive and negative biases and flexibility. The duality of children’s beliefs may contribute to strengthening their biases and segregating social groups. PMID:25918015

Inflexible daily behaviour is associated with the ability to control an automatic reaction in autism spectrum disorder.

PubMed

Tei, Shisei; Fujino, Junya; Hashimoto, Ryu-Ichiro; Itahashi, Takashi; Ohta, Haruhisa; Kanai, Chieko; Kubota, Manabu; Nakamura, Motoaki; Kato, Nobumasa; Takahashi, Hidehiko

2018-05-24

Inflexible behaviours in people with autism spectrum disorder (ASD) broadly obstruct social communication. Meanwhile, flexibility implicates cognitive control to resolve socially conflicting situations; however, it remains unclear how people with ASD behave in the face of these conflicts in this respect. We used the ultimatum game (UG) and the implicit-association test (IAT) to examine goal-directed/economic flexibility, both of which involve conflict and cognitive control. In addition, we used the Detail and Flexibility Questionnaire (DFlex) to measure inflexible everyday behaviour with diminished cognitive control and attention shifting. We observed the decreased flexibility in participants with ASD (DFlex and IAT); further, their IAT scores positively correlated with DFlex. However, in the UG, contrary to our prediction, participants with ASD accepted unfair offers more frequently than TD. These results suggest that assessing the automatic/attention processing level with the IAT could be a useful approach to study behavioural flexibility among ASD compared with the UG, which might comprise multiple response strategies besides economic rationality. Overall, the severity of inflexible daily behaviours in people with ASD may be associated with a reduced flexible attitude at an automatic level, altered attention processing and decreased cognitive control.

Fluid and flexible minds: Intelligence reflects synchrony in the brain’s intrinsic network architecture

PubMed Central

Ferguson, Michael A.; Anderson, Jeffrey S.; Spreng, R. Nathan

2017-01-01

Human intelligence has been conceptualized as a complex system of dissociable cognitive processes, yet studies investigating the neural basis of intelligence have typically emphasized the contributions of discrete brain regions or, more recently, of specific networks of functionally connected regions. Here we take a broader, systems perspective in order to investigate whether intelligence is an emergent property of synchrony within the brain’s intrinsic network architecture. Using a large sample of resting-state fMRI and cognitive data (n = 830), we report that the synchrony of functional interactions within and across distributed brain networks reliably predicts fluid and flexible intellectual functioning. By adopting a whole-brain, systems-level approach, we were able to reliably predict individual differences in human intelligence by characterizing features of the brain’s intrinsic network architecture. These findings hold promise for the eventual development of neural markers to predict changes in intellectual function that are associated with neurodevelopment, normal aging, and brain disease.

Choose and choose again: appearance-reality errors, pragmatics and logical ability.

PubMed

Deák, Gedeon O; Enright, Brian

2006-05-01

In the Appearance/Reality (AR) task some 3- and 4-year-old children make perseverative errors: they choose the same word for the appearance and the function of a deceptive object. Are these errors specific to the AR task, or signs of a general question-answering problem? Preschoolers completed five tasks: AR; simple successive forced-choice question pairs (QP); flexible naming of objects (FN); working memory (WM) span; and indeterminacy detection (ID). AR errors correlated with QP errors. Insensitivity to indeterminacy predicted perseveration in both tasks. Neither WM span nor flexible naming predicted other measures. Age predicted sensitivity to indeterminacy. These findings suggest that AR tests measure a pragmatic understanding; specifically, different questions about a topic usually call for different answers. This understanding is related to the ability to detect indeterminacy of each question in a series. AR errors are unrelated to the ability to represent an object as belonging to multiple categories, to working memory span, or to inhibiting previously activated words.

Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.

PubMed

Peterson, Lenna; Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2017-01-01

The conventional view of a protein structure as static provides only a limited picture. There is increasing evidence that protein dynamics are often vital to protein function including interaction with partners such as other proteins, nucleic acids, and small molecules. Considering flexibility is also important in applications such as computational protein docking and protein design. While residue flexibility is partially indicated by experimental measures such as the B-factor from X-ray crystallography and ensemble fluctuation from nuclear magnetic resonance (NMR) spectroscopy as well as computational molecular dynamics (MD) simulation, these techniques are resource-intensive. In this chapter, we describe the web server and stand-alone version of FlexPred, which rapidly predicts absolute per-residue fluctuation from a three-dimensional protein structure. On a set of 592 nonredundant structures, comparing the fluctuations predicted by FlexPred to the observed fluctuations in MD simulations showed an average correlation coefficient of 0.669 and an average root mean square error of 1.07 Å. FlexPred is available at http://kiharalab.org/flexPred/ .

Thermal math model analysis of FRSI test article subjected to cold soak and entry environments. [Flexible Reuseable Surface Insulation in Space Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Gallegos, J. J.

1978-01-01

A multi-objective test program was conducted at the NASA/JSC Radiant Heat Test Facility in which an aluminum skin/stringer test panel insulated with FRSI (Flexible Reusable Surface Insulation) was subjected to 24 simulated Space Shuttle Orbiter ascent/entry heating cycles with a cold soak in between in the 10th and 20th cycles. A two-dimensional thermal math model was developed and utilized to predict the thermal performance of the FRSI. Results are presented which indicate that the modeling techniques and property values have been proven adequate in predicting peak structure temperatures and entry thermal responses from both an ambient and cold soak condition of an FRSI covered aluminum structure.

Molecular dynamics, flexible docking, virtual screening, ADMET predictions, and molecular interaction field studies to design novel potential MAO-B inhibitors.

PubMed

Braun, Glaucia H; Jorge, Daniel M M; Ramos, Henrique P; Alves, Raquel M; da Silva, Vinicius B; Giuliatti, Silvana; Sampaio, Suley Vilela; Taft, Carlton A; Silva, Carlos H T P

2008-02-01

Monoamine oxidase is a flavoenzyme bound to the mitochondrial outer membranes of the cells, which is responsible for the oxidative deamination of neurotransmitter and dietary amines. It has two distinct isozymic forms, designated MAO-A and MAO-B, each displaying different substrate and inhibitor specificities. They are the well-known targets for antidepressant, Parkinson's disease, and neuroprotective drugs. Elucidation of the x-ray crystallographic structure of MAO-B has opened the way for the molecular modeling studies. In this work we have used molecular modeling, density functional theory with correlation, virtual screening, flexible docking, molecular dynamics, ADMET predictions, and molecular interaction field studies in order to design new molecules with potential higher selectivity and enzymatic inhibitory activity over MAO-B.

Experimental and Predicted Longitudinal and Lateral-Directional Response Characteristics of a Large Flexible 35 Degree Swept-Wing Airplane at an Altitude of 35,000 Feet

NASA Technical Reports Server (NTRS)

Cole, Henry A , Jr; Brown, Stuart C; Holleman, Euclid C

1957-01-01

Measured and predicted dynamic response characteristics of a large flexible swept-wing airplane to control surface inputs are presented for flight conditions of 0.6 to 0.85 Mach number at an altitude of 35,000 feet. The report is divided into two parts. The first part deals with the response of the airplane to elevator control inputs with principal responses contained in a band of frequencies including the longitudinal short-period mode and several symmetrical structural modes. The second part deals with the response of the airplane to aileron and rudder control inputs with principal responses contained in a band of frequencies including the dutch roll mode, the rolling mode, and three antisymmetrical structural modes.

Gender Attitudes in Early Childhood: Behavioral Consequences and Cognitive Antecedents

PubMed Central

Halim, May Ling D.; Ruble, Diane N.; Tamis-LeMonda, Catherine S.; Shrout, Patrick E.; Amodio, David M.

2016-01-01

This study examined factors that predicted children’s gender intergroup attitudes at age 5 and the implications of these attitudes for intergroup behavior. Ethnically-diverse children from low-income backgrounds (N=246, Mexican-, Chinese-, Dominican-, and African-American) were assessed at ages 4 and 5. On average, children reported positive same-gender and negative other-gender attitudes. Positive same-gender attitudes were associated with knowledge of gender stereotypes. In contrast, positive other-gender attitudes were associated with flexibility in gender cognitions (stereotype flexibility, gender consistency). Other-gender attitudes predicted gender-biased behavior. These patterns were observed in all ethnic groups. These findings suggest that early learning about gender categories shape young children’s gender attitudes, and that these gender attitudes already have consequences for children’s intergroup behavior at age 5. PMID:27759886

Multi-scale Modeling of the Evolution of a Large-Scale Nourishment

NASA Astrophysics Data System (ADS)

Luijendijk, A.; Hoonhout, B.

2016-12-01

Morphological predictions are often computed using a single morphological model commonly forced with schematized boundary conditions representing the time scale of the prediction. Recent model developments are now allowing us to think and act differently. This study presents some recent developments in coastal morphological modeling focusing on flexible meshes, flexible coupling between models operating at different time scales, and a recently developed morphodynamic model for the intertidal and dry beach. This integrated modeling approach is applied to the Sand Engine mega nourishment in The Netherlands to illustrate the added-values of this integrated approach both in accuracy and computational efficiency. The state-of-the-art Delft3D Flexible Mesh (FM) model is applied at the study site under moderate wave conditions. One of the advantages is that the flexibility of the mesh structure allows a better representation of the water exchange with the lagoon and corresponding morphological behavior than with the curvilinear grid used in the previous version of Delft3D. The XBeach model is applied to compute the morphodynamic response to storm events in detail incorporating the long wave effects on bed level changes. The recently developed aeolian transport and bed change model AeoLiS is used to compute the bed changes in the intertidal and dry beach area. In order to enable flexible couplings between the three abovementioned models, a component-based environment has been developed using the BMI method. This allows a serial coupling of Delft3D FM and XBeach steered by a control module that uses a hydrodynamic time series as input (see figure). In addition, a parallel online coupling, with information exchange in each timestep will be made with the AeoLiS model that predicts the bed level changes at the intertidal and dry beach area. This study presents the first years of evolution of the Sand Engine computed with the integrated modelling approach. Detailed comparisons are made between the observed and computed morphological behaviour for the Sand Engine on an aggregated as well as sub-system level.

Nuclear quantum effects in water clusters: the role of the molecular flexibility.

PubMed

González, Briesta S; Noya, Eva G; Vega, Carlos; Sesé, Luis M

2010-02-25

With the objective of establishing the importance of water flexibility in empirical models which explicitly include nuclear quantum effects, we have carried out path integral Monte Carlo simulations in water clusters with up to seven molecules. Two recently developed models have been used for comparison: the rigid TIP4PQ/2005 and the flexible q-TIP4P/F models, both inspired by the rigid TIP4P/2005 model. To obtain a starting configuration for our simulations, we have located the global minima for the rigid TIP4P/2005 and TIP4PQ/2005 models and for the flexible q-TIP4P/F model. All the structures are similar to those predicted by the rigid TIP4P potential showing that the charge distribution mainly determines the global minimum structure. For the flexible q-TIP4P/F model, we have studied the geometrical distortion upon isotopic substitution by studying tritiated water clusters. Our results show that tritiated water clusters exhibit an r(OT) distance shorter than the r(OH) distance in water clusters, not significant changes in the Phi(HOH) angle, and a lower average dipole moment than water clusters. We have also carried out classical simulations with the rigid TIP4PQ/2005 model showing that the rotational kinetic energy is greatly affected by quantum effects, but the translational kinetic energy is only slightly modified. The potential energy is also noticeably higher than in classical simulations. Finally, as a concluding remark, we have calculated the formation energies of water clusters using both models, finding that the formation energies predicted by the rigid TIP4PQ/2005 model are lower by roughly 0.6 kcal/mol than those of the flexible q-TIP4P/F model for clusters of moderate size, the origin of this difference coming mainly from the geometrical distortion of the water molecule in the clusters that causes an increase in the intramolecular potential energy.

Profiling Coping Strategies in Male and Female Rats: Potential neurobehavioral markers of increased resilience to depressive symptoms

PubMed Central

Kent, Molly; Bardi, Massimo; Hazelgrove, Ashley; Sewell, Kaitlyn; Kirk, Emily; Thompson, Brooke; Trexler, Kristen; Terhune-Cotter, Brennan; Lambert, Kelly

2018-01-01

Coping strategies have been associated with differential stress responsivity, perhaps providing a valuable neurobiological marker for susceptibility to the emergence of depressogenic symptoms or vulnerability to other anxiety-related disorders. Rats profiled with a flexible coping phenotype, for example, exhibit increased neurobiological markers of emotional regulation compared to active and passive copers (Bardi et al., 2012; Lambert et al., 2014). In the current study, responses of male and female rats to prediction errors in a spatial foraging task (dry land maze; DLM) were examined after animals were exposed to chronic unpredictable stress (CUS). Brains were processed following the DLM training/assessment for fos-activation patterns and several measures of neuroplasticity in relevant areas. Behavioral responses observed during both the CUS and DLM phases of testing suggested that males and females employ different means of gathering information such as increased ambulatory exploration in males and rear responses in females. Fecal samples collected during baseline and following CUS swim exposure revealed higher corticosterone (CORT) in active copers, whereas flexible copers had higher dehydroepiandrosterone (DHEA) and DHEA/CORT ratios, both indications of enhanced emotional regulation. Focusing on the neural analysis, flexible copers exhibited fewer fos-immunoreactive cells in the basolateral amygdala and a trend toward lower activation in the insula while encountering the prediction error associated with the DLM probe trial. Coping profiles also differentially influenced markers of neuroplasticity; specifically, flexible copers exhibited higher levels nestin-immunoreactivity (ir). Further, less hippocampal glucocorticoid receptor-ir was observed in the flexible copers than the active and passive copers. In sum, flexible coping rats exhibited evidence of emotional resilience as indicated by several neurobiological measures; however, despite increased rates of depression and related symptoms reported in human females, sex effects weren’t as pervasive as coping strategy profiles in the analysis of neurobiological markers employed in the current study. PMID:28755980

Model predictive control of a wind turbine modelled in Simpack

NASA Astrophysics Data System (ADS)

Jassmann, U.; Berroth, J.; Matzke, D.; Schelenz, R.; Reiter, M.; Jacobs, G.; Abel, D.

2014-06-01

Wind turbines (WT) are steadily growing in size to increase their power production, which also causes increasing loads acting on the turbine's components. At the same time large structures, such as the blades and the tower get more flexible. To minimize this impact, the classical control loops for keeping the power production in an optimum state are more and more extended by load alleviation strategies. These additional control loops can be unified by a multiple-input multiple-output (MIMO) controller to achieve better balancing of tuning parameters. An example for MIMO control, which has been paid more attention to recently by wind industry, is Model Predictive Control (MPC). In a MPC framework a simplified model of the WT is used to predict its controlled outputs. Based on a user-defined cost function an online optimization calculates the optimal control sequence. Thereby MPC can intrinsically incorporate constraints e.g. of actuators. Turbine models used for calculation within the MPC are typically simplified. For testing and verification usually multi body simulations, such as FAST, BLADED or FLEX5 are used to model system dynamics, but they are still limited in the number of degrees of freedom (DOF). Detailed information about load distribution (e.g. inside the gearbox) cannot be provided by such models. In this paper a Model Predictive Controller is presented and tested in a co-simulation with SlMPACK, a multi body system (MBS) simulation framework used for detailed load analysis. The analysis are performed on the basis of the IME6.0 MBS WT model, described in this paper. It is based on the rotor of the NREL 5MW WT and consists of a detailed representation of the drive train. This takes into account a flexible main shaft and its main bearings with a planetary gearbox, where all components are modelled flexible, as well as a supporting flexible main frame. The wind loads are simulated using the NREL AERODYN v13 code which has been implemented as a routine to SlMPACK. This modeling approach allows to investigate the nonlinear behavior of wind loads and nonlinear drive train dynamics. Thereby the MPC's impact on specific loads and effects not covered by standard simulation tools can be assessed and investigated. Keywords. wind turbine simulation, model predictive control, multi body simulation, MIMO, load alleviation

A flexible Bayesian assessment for the expected impact of data on prediction confidence for optimal sampling designs

NASA Astrophysics Data System (ADS)

Leube, Philipp; Geiges, Andreas; Nowak, Wolfgang

2010-05-01

Incorporating hydrogeological data, such as head and tracer data, into stochastic models of subsurface flow and transport helps to reduce prediction uncertainty. Considering limited financial resources available for the data acquisition campaign, information needs towards the prediction goal should be satisfied in a efficient and task-specific manner. For finding the best one among a set of design candidates, an objective function is commonly evaluated, which measures the expected impact of data on prediction confidence, prior to their collection. An appropriate approach to this task should be stochastically rigorous, master non-linear dependencies between data, parameters and model predictions, and allow for a wide variety of different data types. Existing methods fail to fulfill all these requirements simultaneously. For this reason, we introduce a new method, denoted as CLUE (Cross-bred Likelihood Uncertainty Estimator), that derives the essential distributions and measures of data utility within a generalized, flexible and accurate framework. The method makes use of Bayesian GLUE (Generalized Likelihood Uncertainty Estimator) and extends it to an optimal design method by marginalizing over the yet unknown data values. Operating in a purely Bayesian Monte-Carlo framework, CLUE is a strictly formal information processing scheme free of linearizations. It provides full flexibility associated with the type of measurements (linear, non-linear, direct, indirect) and accounts for almost arbitrary sources of uncertainty (e.g. heterogeneity, geostatistical assumptions, boundary conditions, model concepts) via stochastic simulation and Bayesian model averaging. This helps to minimize the strength and impact of possible subjective prior assumptions, that would be hard to defend prior to data collection. Our study focuses on evaluating two different uncertainty measures: (i) expected conditional variance and (ii) expected relative entropy of a given prediction goal. The applicability and advantages are shown in a synthetic example. Therefor, we consider a contaminant source, posing a threat on a drinking water well in an aquifer. Furthermore, we assume uncertainty in geostatistical parameters, boundary conditions and hydraulic gradient. The two mentioned measures evaluate the sensitivity of (1) general prediction confidence and (2) exceedance probability of a legal regulatory threshold value on sampling locations.

Interaction Dynamics Between a Flexible Rotor and an Auxiliary Clearance Bearing

NASA Technical Reports Server (NTRS)

Lawen, James L., Jr.; Flowers, George T.

1996-01-01

This study investigates the application of synchronous interaction dynamics methodology to the design of auxiliary bearing systems. The technique is applied to a flexible rotor system and comparisons are made between the behavior predicted by this analysis method and the observed simulation response characteristics. Of particular interest is the influence of coupled shaft/bearing vibration modes on rotordynamical behavior. Experimental studies are also perFormed to validate the simulation results and provide insight into the expected behavior of such a system.

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

PubMed Central

Trellet, Mikael; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.

2013-01-01

Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II), flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking. PMID:23516555

A unified conformational selection and induced fit approach to protein-peptide docking.

PubMed

Trellet, Mikael; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2013-01-01

Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II), flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking.

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

PubMed

Jacobs, Donald J; Livesay, Dennis R; Hules, Jeremy; Tasayco, Maria Luisa

2006-05-05

Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability, and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data.

Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.

PubMed

Vorobjev, Yury N; Scheraga, Harold A; Vila, Jorge A

2018-02-01

A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins. The pKa-prediction test shows that, on average, 57, 86, and 95% of all predictions have an error lower than 0.5, 1.0, and 1.5 pKa units, respectively. This work contributes to our general understanding of the importance of protein flexibility for an accurate computation of pKa, providing critical insight about the significance of the multiple neutral states of acid and histidine residues for pKa-prediction, and may spur significant progress in our effort to develop a fast and accurate electrostatic-based method for pKa-predictions of proteins as a function of pH.

How does symmetry impact the flexibility of proteins?

PubMed

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-02-13

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures-and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body-bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body-bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains.

How does symmetry impact the flexibility of proteins?

PubMed Central

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-01-01

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures—and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body–bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body–bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains. PMID:24379431

The social transmission of metacontrol policies: Mechanisms underlying the interpersonal transfer of persistence and flexibility.

PubMed

Hommel, Bernhard; Colzato, Lorenza S

2017-10-01

Humans often face binary cognitive-control dilemmas, with the choice between persistence and flexibility being a crucial one. Tackling these dilemmas requires metacontrol, i.e., the control of the current cognitive-control policy. As predicted from functional, psychometric, neuroscientific, and modeling approaches, interindividual variability in metacontrol biases towards persistence or flexibility could be demonstrated in metacontrol-sensitive tasks. These biases covary systematically with genetic predispositions regarding mesofrontal and nigrostriatal dopaminergic functioning and the individualistic or collectivistic nature of the cultural background. However, there is also evidence for mood- and meditation-induced intraindividual variability (with negative mood and focused-attention meditation being associated with a bias towards persistence, and positive mood and open-monitoring meditation being associated with a bias towards flexibility), suggesting that genetic and cultural factors do not determine metacontrol settings entirely. We suggest a theoretical framework that explains how genetic predisposition and cultural learning can lead to the implementation of metacontrol defaults, which however can be shifted towards persistence or flexibility by situational factors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Manipulating flexible parts using a teleoperated system with time delay: An experiment

NASA Technical Reports Server (NTRS)

Kotoku, T.; Takamune, K.; Tanie, K.; Komoriya, K.; Matsuhira, N.; Asakura, M.; Bamba, H.

1994-01-01

This paper reports experiments involving the handling of flexible parts (e.g. wires) when using a teleoperated system with time delay. The task is principally a peg-in-hole task involving the wrapping of a wire around two posts on the task-board. It is difficult to estimate the effects of the flexible parts; therefore, on-line teleoperation is indispensable for this class of unpredictable task. We first propose a teleoperation system based on the predictive image display, then describe an experimental teleoperation testbed with a four second transmission time delay. Finally, we report on wire handling operations that were performed to evaluate the performance of this system. Those experiments will contribute to future advanced experiments for the MITI ETS-7 mission.

Obesity and unhealthy lifestyle associated with poor executive function among Malaysian adolescents.

PubMed

Tee, Joyce Ying Hui; Gan, Wan Ying; Tan, Kit-Aun; Chin, Yit Siew

2018-01-01

The understanding on the roles of obesity and lifestyle behaviors in predicting executive function of adolescents has been limited. Low executive function proficiency may have adverse effects on adolescents' school academic performance. This cross-sectional study aimed to examine the relationship between BMI-for-age and multiple lifestyle behaviors (operationalized as meal consumption, physical activity, and sleep quality) with executive function (operationalized as inhibition, working memory, and cognitive flexibility) on a sample of Malaysian adolescents aged between 12 and 16 years (N = 513). Participants were recruited from two randomly selected schools in the state of Selangor in Malaysia. Using a self-administered questionnaire, parent participants provided information concerning their sociodemographic data, whereas adolescent participants provided information regarding their meal consumptions, physical activity, and sleep quality. The modified Harvard step test was used to assess adolescents' aerobic fitness, while Stroop color-word, digit span, and trail-making tests were used to assess adolescents' inhibition, working memory, and cognitive flexibility, respectively. Three separate hierarchical regression analyses were conducted for each outcome namely, inhibition, working memory, and cognitive flexibility. After adjusted for sociodemographic factors and BMI-for-age, differential predictors of inhibition and working memory were found. Habitual sleep efficiency significantly and positively predicted inhibition. Regular dinner intakes, physical activity levels, and sleep quality significantly and positively predicted working memory. Household income emerged as a consistent predictor for all executive function domains. In conclusion, an increased trend of obesity and unhealthy lifestyles among adolescents were found to be associated with poorer executive function. Regular dinner intakes, higher physical activity levels and better sleep quality predicted better executive function despite the inverse relationship between obesity and executive function. Future studies may explore how lifestyle modifications can optimize the development of executive function in adolescents as well as relieve the burden of obesity.

Passive cyclic pitch control for horizontal axis wind turbines

NASA Technical Reports Server (NTRS)

Bottrell, G. W.

1981-01-01

A flexible rotor concept, called the balanced pitch rotor, is described. The system provides passive adjustment of cyclic pitch in response to unbalanced pitching moments across the rotor disk. Various applications are described and performance predictions are made for wind shear and cross wind operating conditions. Comparisons with the teetered hub are made and significant cost savings are predicted.

The Predictive Validity of the Torrance Figural Test (Form B) of Creative Thinking in the College of Fine and Applied Arts.

ERIC Educational Resources Information Center

Stallings, William M.

In an effort to improve the predictability of course grades in the College of Fine and Applied Arts the Torrance Figural Test (Form B) of Creative Thinking was administered to entering 1968 freshmen. Four figural creativity variables (Fluency, Flexibility, Originality, and Elaboration) were correlated with course grades, American College Testing…

WEPPCAT: An Online tool for assessing and managing the potential impacts of climate change on sediment loading to streams using the Water Erosion Prediction Project (WEPP) Model

EPA Science Inventory

WEPPCAT is an on-line tool that provides a flexible capability for creating user-determined climate change scenarios for assessing the potential impacts of climate change on sediment loading to streams using the USDA’s Water Erosion Prediction Project (WEPP) Model. In combination...

Adjustments of individual-tree survival and diameter-growth equations to match whole-stand attributes

Treesearch

Quang V. Cao

2010-01-01

Individual-tree models are flexible and can perform well in predicting tree survival and diameter growth for a certain growing period. However, the resulting stand-level outputs often suffer from accumulation of errors and subsequently cannot compete with predictions from whole-stand models, especially when the projection period lengthens. Evaluated in this study were...

Negative impacts of climate change on cereal yields: statistical evidence from France

NASA Astrophysics Data System (ADS)

Gammans, Matthew; Mérel, Pierre; Ortiz-Bobea, Ariel

2017-05-01

In several world regions, climate change is predicted to negatively affect crop productivity. The recent statistical yield literature emphasizes the importance of flexibly accounting for the distribution of growing-season temperature to better represent the effects of warming on crop yields. We estimate a flexible statistical yield model using a long panel from France to investigate the impacts of temperature and precipitation changes on wheat and barley yields. Winter varieties appear sensitive to extreme cold after planting. All yields respond negatively to an increase in spring-summer temperatures and are a decreasing function of precipitation about historical precipitation levels. Crop yields are predicted to be negatively affected by climate change under a wide range of climate models and emissions scenarios. Under warming scenario RCP8.5 and holding growing areas and technology constant, our model ensemble predicts a 21.0% decline in winter wheat yield, a 17.3% decline in winter barley yield, and a 33.6% decline in spring barley yield by the end of the century. Uncertainty from climate projections dominates uncertainty from the statistical model. Finally, our model predicts that continuing technology trends would counterbalance most of the effects of climate change.

Developmental Steps in Metaphorical Language Abilities: The Influence of Age, Gender, Cognitive Flexibility, Information Processing Speed, and Analogical Reasoning.

PubMed

Willinger, Ulrike; Deckert, Matthias; Schmöger, Michaela; Schaunig-Busch, Ines; Formann, Anton K; Auff, Eduard

2017-12-01

Metaphor is a specific type of figurative language that is used in various important fields such as in the work with children in clinical or teaching contexts. The aim of the study was to investigate the developmental course, developmental steps, and possible cognitive predictors regarding metaphor processing in childhood and early adolescence. One hundred sixty-four typically developing children (7-year-olds, 9-year-olds) and early adolescents (11-year-olds) were tested for metaphor identification, comprehension, comprehension quality, and preference by the Metaphoric Triads Task as well as for analogical reasoning, information processing speed, cognitive flexibility under time pressure, and cognitive flexibility without time pressure. Metaphor identification and comprehension consecutively increased with age. Eleven-year-olds showed significantly higher metaphor comprehension quality and preference scores than seven- and nine-year-olds, whilst these younger age groups did not differ. Age, cognitive flexibility under time pressure, information processing speed, analogical reasoning, and cognitive flexibility without time pressure significantly predicted metaphor comprehension. Metaphorical language ability shows an ongoing development and seemingly changes qualitatively at the beginning of early adolescence. These results can possibly be explained by a greater synaptic reorganization in early adolescents. Furthermore, cognitive flexibility under time pressure and information processing speed possibly facilitate the ability to adapt metaphor processing strategies in a flexible, quick, and appropriate way.

Near-Ideal Xylene Selectivity in Adaptive Molecular Pillar[ n]arene Crystals.

PubMed

Jie, Kecheng; Liu, Ming; Zhou, Yujuan; Little, Marc A; Pulido, Angeles; Chong, Samantha Y; Stephenson, Andrew; Hughes, Ashlea R; Sakakibara, Fumiyasu; Ogoshi, Tomoki; Blanc, Frédéric; Day, Graeme M; Huang, Feihe; Cooper, Andrew I

2018-06-06

The energy-efficient separation of alkylaromatic compounds is a major industrial sustainability challenge. The use of selectively porous extended frameworks, such as zeolites or metal-organic frameworks, is one solution to this problem. Here, we studied a flexible molecular material, perethylated pillar[ n]arene crystals ( n = 5, 6), which can be used to separate C8 alkylaromatic compounds. Pillar[6]arene is shown to separate para-xylene from its structural isomers, meta-xylene and ortho-xylene, with 90% specificity in the solid state. Selectivity is an intrinsic property of the pillar[6]arene host, with the flexible pillar[6]arene cavities adapting during adsorption thus enabling preferential adsorption of para-xylene in the solid state. The flexibility of pillar[6]arene as a solid sorbent is rationalized using molecular conformer searches and crystal structure prediction (CSP) combined with comprehensive characterization by X-ray diffraction and 13 C solid-state NMR spectroscopy. The CSP study, which takes into account the structural variability of pillar[6]arene, breaks new ground in its own right and showcases the feasibility of applying CSP methods to understand and ultimately to predict the behavior of soft, adaptive molecular crystals.

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

PubMed

Gainza, Pablo; Roberts, Kyle E; Georgiev, Ivelin; Lilien, Ryan H; Keedy, Daniel A; Chen, Cheng-Yu; Reza, Faisal; Anderson, Amy C; Richardson, David C; Richardson, Jane S; Donald, Bruce R

2013-01-01

We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling of proteins and ligands as ensembles of low-energy structures to better approximate binding affinity; and (3) a globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect to the input model. Here, we illustrate the importance of these three characteristics. We then describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been used prospectively, with experimental validation, in several biomedically relevant settings. We show in detail how OSPREY has been used to predict resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application. OSPREY is free and open source under a Lesser GPL license. The latest version is OSPREY 2.0. The program, user manual, and source code are available at www.cs.duke.edu/donaldlab/software.php. osprey@cs.duke.edu. Copyright © 2013 Elsevier Inc. All rights reserved.

Testing the predictions of coping styles theory in threespined sticklebacks

PubMed Central

Bensky, Miles K.; Paitz, Ryan; Pereira, Laura; Bell, Alison M.

2017-01-01

Coping styles theory provides a framework for understanding individual variation in how animals respond to environmental change, and predicts how individual differences in stress responsiveness and behavior might relate to cognitive differences. According to coping styles theory, proactive individuals are bolder, less reactive to stressors, and more routinized than their reactive counterparts. A key tenet of coping styles theory is that variation in coping styles is maintained by tradeoffs with behavioral flexibility: proactive individuals excel in stable environments while more flexible, reactive individuals perform better in variable environments. Here, we assess evidence for coping styles within a natural population of threespined sticklebacks (Gasterosteus aculeatus). We developed a criterion-based learning paradigm to evaluate individual variation in initial and reversal learning. We observed strong individual differences in boldness, cortisol production, and learning performance. Consistent with coping styles, fish that released more cortisol were more timid in response to a predator attack and slower to learn a color discrimination task. However, there was no evidence that reactive individuals performed better when the environment changed (when the rewarded color was reversed). The failure to detect trade-offs between behavioral routinization and flexibility prompts other explanations for the maintenance of differing coping styles. PMID:28017848

Maternal play behaviors, child negativity, and preterm or low birthweight toddlers' visual-spatial outcomes: testing a differential susceptibility hypothesis.

PubMed

Dilworth-Bart, Janean E; Miller, Kyle E; Hane, Amanda

2012-04-01

We examined the joint roles of child negative emotionality and parenting in the visual-spatial development of toddlers born preterm or with low birthweights (PTLBW). Neonatal risk data were collected at hospital discharge, observer- and parent-rated child negative emotionality was assessed at 9-months postterm, and mother-initiated task changes and flexibility during play were observed during a dyadic play interaction at 16-months postterm. Abbreviated IQ scores, and verbal/nonverbal and visual-spatial processing data were collected at 24-months postterm. Hierarchical regression analyses did not support our hypothesis that the visual-spatial processing of PTLBW toddlers with higher negative emotionality would be differentially susceptible to parenting behaviors during play. Instead, observer-rated distress and a negativity composite score were associated with less optimal visual-spatial processing when mothers were more flexible during the 16-month play interaction. Mother-initiated task changes did not interact with any of the negative emotionality variables to predict any of the 24-month neurocognitive outcomes, nor did maternal flexibility interact with mother-rated difficult temperament to predict the visual-spatial processing outcomes. Copyright © 2011 Elsevier Inc. All rights reserved.

Contralateral disconnection of the rat prelimbic cortex and dorsomedial striatum impairs cue-guided behavioral switching

PubMed Central

Baker, Phillip M.

2014-01-01

Switches in reward outcomes or reward-predictive cues are two fundamental ways in which information is used to flexibly shift response patterns. The rat prelimbic cortex and dorsomedial striatum support behavioral flexibility based on a change in outcomes. The present experiments investigated whether these two brain regions are necessary for conditional discrimination performance in which a switch in reward-predictive cues occurs every three to six trials. The GABA agonists baclofen and muscimol infused into the prelimbic cortex significantly impaired performance leading rats to adopt an inappropriate turn strategy. The NMDA receptor antagonist D-AP5 infused into the dorsomedial striatum or prelimbic cortex and dorsomedial striatum contralateral disconnection impaired performance due to a rat failing to switch a response choice for an entire trial block in about two out of 13 test blocks. In an additional study, contralateral disconnection did not affect nonswitch discrimination performance. The results suggest that the prelimbic cortex and dorsomedial striatum are necessary to support cue-guided behavioral switching. The prelimbic cortex may be critical for generating alternative response patterns while the dorsomedial striatum supports the selection of an appropriate response when cue information must be used to flexibly switch response patterns. PMID:25028395

Correlation of Lateral Cephalogram and Flexible Laryngoscopy with Sleep Study in Obstructive Sleep Apnea

PubMed Central

Narayanan, Anila; Faizal, Bini

2015-01-01

Objective. To study the correlation between lateral cephalogram, flexible laryngoscopy, and sleep study in patients diagnosed with obstructive sleep apnea (OSA). Background. Screening tools should be devised for predicting OSA which could be performed on an outpatient basis. With this aim we studied the skeletal and soft tissue characteristics of proven OSA patients. Methods. A prospective study was performed in patients diagnosed with obstructive sleep apnea by sleep study. They were evaluated clinically and subjected to lateral cephalometry and nasopharyngolaryngoscopy. The findings were matched to see if they corresponded to AHI of sleep study in severity. An attempt was made to see whether the data predicted the patients who would benefit from oral appliance or surgery as the definitive treatment in indicated cases. Results. A retropalatal collapse seen on endoscopy could be equated to the distance from mandibular plane to hyoid (MP-H) of lateral cephalometry and both corresponded to severity of AHI. At the retroglossal region, there was a significant correlation with MP-H, length of the soft palate, and AHI. Conclusion. There is significant correlation of lateral cephalogram and awake flexible nasopharyngolaryngoscopy with AHI in OSA. In unison they form an excellent screening tool for snorers. PMID:26689652

Correlation of Lateral Cephalogram and Flexible Laryngoscopy with Sleep Study in Obstructive Sleep Apnea.

PubMed

Narayanan, Anila; Faizal, Bini

2015-01-01

Objective. To study the correlation between lateral cephalogram, flexible laryngoscopy, and sleep study in patients diagnosed with obstructive sleep apnea (OSA). Background. Screening tools should be devised for predicting OSA which could be performed on an outpatient basis. With this aim we studied the skeletal and soft tissue characteristics of proven OSA patients. Methods. A prospective study was performed in patients diagnosed with obstructive sleep apnea by sleep study. They were evaluated clinically and subjected to lateral cephalometry and nasopharyngolaryngoscopy. The findings were matched to see if they corresponded to AHI of sleep study in severity. An attempt was made to see whether the data predicted the patients who would benefit from oral appliance or surgery as the definitive treatment in indicated cases. Results. A retropalatal collapse seen on endoscopy could be equated to the distance from mandibular plane to hyoid (MP-H) of lateral cephalometry and both corresponded to severity of AHI. At the retroglossal region, there was a significant correlation with MP-H, length of the soft palate, and AHI. Conclusion. There is significant correlation of lateral cephalogram and awake flexible nasopharyngolaryngoscopy with AHI in OSA. In unison they form an excellent screening tool for snorers.

Attentional fluctuations in preschoolers: Direct and indirect relations with task accuracy, academic readiness, and school performance.

PubMed

Isbell, Elif; Calkins, Susan D; Swingler, Margaret M; Leerkes, Esther M

2018-03-01

Attentional control fluctuates in the presence of internal and external distractors, wandering on and off a given task. The current study investigated individual differences in attentional fluctuations in 250 preschoolers. Attentional fluctuations were assessed via intra-individual variability in response time in a Go/No-Go task. Greater fluctuations in attentional control were linked to lower task accuracy. In addition, greater attentional fluctuations predicted lower performance in a task of cognitive flexibility, the Dimensional Change Card Sort task. Attentional fluctuations were also associated with laboratory measures of academic readiness in preschool, as assessed by the Applied Problems and Letter-Word Identification subscales of the Woodcock-Johnson III Tests of Achievement, which in turn predicted teacher reports of academic performance in first grade. Attentional fluctuations also had indirect associations with emergent math skills in preschool, via cognitive flexibility, as well as indirect associations with first-grade teacher reports of academic performance, via the relations between cognitive flexibility and emergent math skills in preschool. These results suggest that consistency is an important aspect of attentional control during early childhood. Copyright © 2017 Elsevier Inc. All rights reserved.

A system identification approach for developing model predictive controllers of antibody quality attributes in cell culture processes.

PubMed

Downey, Brandon; Schmitt, John; Beller, Justin; Russell, Brian; Quach, Anthony; Hermann, Elizabeth; Lyon, David; Breit, Jeffrey

2017-11-01

As the biopharmaceutical industry evolves to include more diverse protein formats and processes, more robust control of Critical Quality Attributes (CQAs) is needed to maintain processing flexibility without compromising quality. Active control of CQAs has been demonstrated using model predictive control techniques, which allow development of processes which are robust against disturbances associated with raw material variability and other potentially flexible operating conditions. Wide adoption of model predictive control in biopharmaceutical cell culture processes has been hampered, however, in part due to the large amount of data and expertise required to make a predictive model of controlled CQAs, a requirement for model predictive control. Here we developed a highly automated, perfusion apparatus to systematically and efficiently generate predictive models using application of system identification approaches. We successfully created a predictive model of %galactosylation using data obtained by manipulating galactose concentration in the perfusion apparatus in serialized step change experiments. We then demonstrated the use of the model in a model predictive controller in a simulated control scenario to successfully achieve a %galactosylation set point in a simulated fed-batch culture. The automated model identification approach demonstrated here can potentially be generalized to many CQAs, and could be a more efficient, faster, and highly automated alternative to batch experiments for developing predictive models in cell culture processes, and allow the wider adoption of model predictive control in biopharmaceutical processes. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 33:1647-1661, 2017. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers.

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.

PubMed

Pallara, Chiara; Rueda, Manuel; Abagyan, Ruben; Fernández-Recio, Juan

2016-07-12

To understand cellular processes at the molecular level we need to improve our knowledge of protein-protein interactions, from a structural, mechanistic, and energetic point of view. Current theoretical studies and computational docking simulations show that protein dynamics plays a key role in protein association and support the need for including protein flexibility in modeling protein interactions. Assuming the conformational selection binding mechanism, in which the unbound state can sample bound conformers, one possible strategy to include flexibility in docking predictions would be the use of conformational ensembles originated from unbound protein structures. Here we present an exhaustive computational study about the use of precomputed unbound ensembles in the context of protein docking, performed on a set of 124 cases of the Protein-Protein Docking Benchmark 3.0. Conformational ensembles were generated by conformational optimization and refinement with MODELLER and by short molecular dynamics trajectories with AMBER. We identified those conformers providing optimal binding and investigated the role of protein conformational heterogeneity in protein-protein recognition. Our results show that a restricted conformational refinement can generate conformers with better binding properties and improve docking encounters in medium-flexible cases. For more flexible cases, a more extended conformational sampling based on Normal Mode Analysis was proven helpful. We found that successful conformers provide better energetic complementarity to the docking partners, which is compatible with recent views of binding association. In addition to the mechanistic considerations, these findings could be exploited for practical docking predictions of improved efficiency.

Measuring ability to enhance and suppress emotional expression: The Flexible Regulation of Emotional Expression (FREE) Scale.

PubMed

Burton, Charles L; Bonanno, George A

2016-08-01

Flexibility in self-regulatory behaviors has proved to be an important quality for adjusting to stressful life events and requires individuals to have a diverse repertoire of emotion regulation abilities. However, the most commonly used emotion regulation questionnaires assess frequency of behavior rather than ability, with little evidence linking these measures to observable capacity to enact a behavior. The aim of the current investigation was to develop and validate a Flexible Regulation of Emotional Expression (FREE) Scale that measures a person's ability to enhance and suppress displayed emotion across an array of hypothetical contexts. In Studies 1 and 2, a series of confirmatory factor analyses revealed that the FREE Scale consists of 4 first-order factors divided by regulation and emotional valence type that can contribute to 2 higher order factors: expressive enhancement ability and suppression ability. In Study 1, we also compared the FREE Scale to other commonly used emotion regulation measures, which revealed that suppression ability is conceptually distinct from suppression frequency. In Study 3, we compared the FREE Scale with a composite of traditional frequency-based indices of expressive regulation to predict performance in a previously validated emotional modulation paradigm. Participants' enhancement and suppression ability scores on the FREE Scale predicted their corresponding performance on the laboratory task, even when controlling for baseline expressiveness. These studies suggest that the FREE Scale is a valid and flexible measure of expressive regulation ability. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Random walk on a leash: a simple single-molecule diffusion model for surface-tethered redox molecules with flexible linkers.

PubMed

Huang, Kuan-Chun; White, Ryan J

2013-08-28

We develop a random walk model to simulate the Brownian motion and the electrochemical response of a single molecule confined to an electrode surface via a flexible molecular tether. We use our simple model, which requires no prior knowledge of the physics of the molecular tether, to predict and better understand the voltammetric response of surface-confined redox molecules when motion of the redox molecule becomes important. The single molecule is confined to a hemispherical volume with a maximum radius determined by the flexible molecular tether (5-20 nm) and is allowed to undergo true three-dimensional diffusion. Distance- and potential-dependent electron transfer probabilities are evaluated throughout the simulations to generate cyclic voltammograms of the model system. We find that at sufficiently slow cyclic voltammetric scan rates the electrochemical reaction behaves like an adsorbed redox molecule with no mass transfer limitation; thus, the peak current is proportional to the scan rate. Conversely, at faster scan rates the diffusional motion of the molecule limits the simulated peak current, which exhibits a linear dependence on the square root of the scan rate. The switch between these two limiting regimes occurs when the diffusion layer thickness, (2Dt)(1/2), is ~10 times the tether length. Finally, we find that our model predicts the voltammetric behavior of a redox-active methylene blue tethered to an electrode surface via short flexible single-stranded, polythymine DNAs, allowing the estimation of diffusion coefficients for the end-tethered molecule.

Rigid dietary control, flexible dietary control, and intuitive eating: Evidence for their differential relationship to disordered eating and body image concerns.

PubMed

Linardon, Jake; Mitchell, Sarah

2017-08-01

This study aimed to replicate and extend from Tylka, Calogero, and Daníelsdóttir (2015) findings by examining the relationship between rigid control, flexible control, and intuitive eating on various indices of disordered eating (i.e., binge eating, disinhibition) and body image concerns (i.e., shape and weight over-evaluation, body checking, and weight-related exercise motivations). This study also examined whether the relationship between intuitive eating and outcomes was mediated by dichotomous thinking and body appreciation. Analysing data from a sample of 372 men and women recruited through the community, this study found that, in contrast to rigid dietary control, intuitive eating uniquely and consistently predicted lower levels of disordered eating and body image concerns. This intuitive eating-disordered eating relationship was mediated by low levels of dichotomous thinking and the intuitive eating-body image relationship was mediated by high levels of body appreciation. Flexible control predicted higher levels of body image concerns and lower levels of disordered eating only when rigid control was accounted for. Findings suggest that until the adaptive properties of flexible control are further elucidated, it may be beneficial to promote intuitive eating within public health approaches to eating disorder prevention. In addition to this, particular emphasis should also be made toward promoting body acceptance and eradicating a dichotomous thinking style around food and eating. Copyright © 2017 Elsevier Ltd. All rights reserved.

Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans

PubMed Central

Keramati, Mehdi

2017-01-01

Decision-making in the real world presents the challenge of requiring flexible yet prompt behavior, a balance that has been characterized in terms of a trade-off between a slower, prospective goal-directed model-based (MB) strategy and a fast, retrospective habitual model-free (MF) strategy. Theory predicts that flexibility to changes in both reward values and transition contingencies can determine the relative influence of the two systems in reinforcement learning, but few studies have manipulated the latter. Therefore, we developed a novel two-level contingency change task in which transition contingencies between states change every few trials; MB and MF control predict different responses following these contingency changes, allowing their relative influence to be inferred. Additionally, we manipulated the rate of contingency changes in order to determine whether contingency change volatility would play a role in shifting subjects between a MB and MF strategy. We found that human subjects employed a hybrid MB/MF strategy on the task, corroborating the parallel contribution of MB and MF systems in reinforcement learning. Further, subjects did not remain at one level of MB/MF behaviour but rather displayed a shift towards more MB behavior over the first two blocks that was not attributable to the rate of contingency changes but rather to the extent of training. We demonstrate that flexibility to contingency changes can distinguish MB and MF strategies, with human subjects utilizing a hybrid strategy that shifts towards more MB behavior over blocks, consequently corresponding to a higher payoff. PMID:28957319

Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans.

PubMed

Lee, Julie J; Keramati, Mehdi

2017-09-01

Decision-making in the real world presents the challenge of requiring flexible yet prompt behavior, a balance that has been characterized in terms of a trade-off between a slower, prospective goal-directed model-based (MB) strategy and a fast, retrospective habitual model-free (MF) strategy. Theory predicts that flexibility to changes in both reward values and transition contingencies can determine the relative influence of the two systems in reinforcement learning, but few studies have manipulated the latter. Therefore, we developed a novel two-level contingency change task in which transition contingencies between states change every few trials; MB and MF control predict different responses following these contingency changes, allowing their relative influence to be inferred. Additionally, we manipulated the rate of contingency changes in order to determine whether contingency change volatility would play a role in shifting subjects between a MB and MF strategy. We found that human subjects employed a hybrid MB/MF strategy on the task, corroborating the parallel contribution of MB and MF systems in reinforcement learning. Further, subjects did not remain at one level of MB/MF behaviour but rather displayed a shift towards more MB behavior over the first two blocks that was not attributable to the rate of contingency changes but rather to the extent of training. We demonstrate that flexibility to contingency changes can distinguish MB and MF strategies, with human subjects utilizing a hybrid strategy that shifts towards more MB behavior over blocks, consequently corresponding to a higher payoff.

Prediction of flow-induced failures of braided flexible hoses and bellows

NASA Technical Reports Server (NTRS)

Sack, L. E.; Nelson, R. L.; Mason, D. R.; Cooper, R. A.

1972-01-01

Analytical techniques were developed to evaluate braided hoses and bellows for possibility of flow induced resonance. These techniques determine likelihood of high cycle fatigue failure when such resonance exists.

Using transonic small disturbance theory for predicting the aeroelastic stability of a flexible wind-tunnel model

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Bennett, Robert M.

1990-01-01

The CAP-TSD (Computational Aeroelasticity Program - Transonic Small Disturbance) code, developed at the NASA - Langley Research Center, is applied to the Active Flexible Wing (AFW) wind tunnel model for prediction of the model's transonic aeroelastic behavior. Static aeroelastic solutions using CAP-TSD are computed. Dynamic (flutter) analyses are then performed as perturbations about the static aeroelastic deformations of the AFW. The accuracy of the static aeroelastic procedure is investigated by comparing analytical results to those from previous AFW wind tunnel experiments. Dynamic results are presented in the form of root loci at different Mach numbers for a heavy gas and air. The resultant flutter boundaries for both gases are also presented. The effects of viscous damping and angle-of-attack, on the flutter boundary in air, are presented as well.

ARPA-E: Advancing the Electric Grid

ScienceCinema

Lemmon, John; Ruiz, Pablo; Sommerer, Tim; Aziz, Michael

2018-06-07

The electric grid was designed with the assumption that all energy generation sources would be relatively controllable, and grid operators would always be able to predict when and where those sources would be located. With the addition of renewable energy sources like wind and solar, which can be installed faster than traditional generation technologies, this is no longer the case. Furthermore, the fact that renewable energy sources are imperfectly predictable means that the grid has to adapt in real-time to changing patterns of power flow. We need a dynamic grid that is far more flexible. This video highlights three ARPA-E-funded approaches to improving the grid's flexibility: topology control software from Boston University that optimizes power flow, gas tube switches from General Electric that provide efficient power conversion, and flow batteries from Harvard University that offer grid-scale energy storage.

DAT/SERT Selectivity of Flexible GBR 12909 Analogs Modeled Using 3D-QSAR Methods

PubMed Central

Gilbert, Kathleen M.; Boos, Terrence L.; Dersch, Christina M.; Greiner, Elisabeth; Jacobson, Arthur E.; Lewis, David; Matecka, Dorota; Prisinzano, Thomas E.; Zhang, Ying; Rothman, Richard B.; Rice, Kenner C.; Venanzi, Carol A.

2007-01-01

The dopamine reuptake inhibitor GBR 12909 (1-{2-[bis(4-fluorophenyl)methoxy]ethyl}-4-(3-phenylpropyl)piperazine, 1) and its analogs have been developed as tools to test the hypothesis that selective dopamine transporter (DAT) inhibitors will be useful therapeutics for cocaine addiction. This 3D-QSAR study focuses on the effect of substitutions in the phenylpropyl region of 1. CoMFA and CoMSIA techniques were used to determine a predictive and stable model for the DAT/serotonin transporter (SERT) selectivity (represented by pKi (DAT/SERT)) of a set of flexible analogs of 1, most of which have eight rotatable bonds. In the absence of a rigid analog to use as a 3D-QSAR template, six conformational families of analogs were constructed from six pairs of piperazine and piperidine template conformers identified by hierarchical clustering as representative molecular conformations. Three models stable to y-value scrambling were identified after a comprehensive CoMFA and CoMSIA survey with Region Focusing. Test set correlation validation led to an acceptable model, with q2 = 0.508, standard error of prediction = 0.601, two components, r2 = 0.685, standard error of estimate = 0.481, F value = 39, percent steric contribution = 65, and percent electrostatic contribution = 35. A CoMFA contour map identified areas of the molecule that affect pKi (DAT/SERT). This work outlines a protocol for deriving a stable and predictive model of the biological activity of a set of very flexible molecules. PMID:17127069

BMI predicts emotion-driven impulsivity and cognitive inflexibility in adolescents with excess weight.

PubMed

Delgado-Rico, Elena; Río-Valle, Jacqueline S; González-Jiménez, Emilio; Campoy, Cristina; Verdejo-García, Antonio

2012-08-01

Adolescent obesity is increasingly viewed as a brain-related dysfunction, whereby reward-driven urges for pleasurable foods "hijack" response selection systems, such that behavioral control progressively shifts from impulsivity to compulsivity. In this study, we aimed to examine the link between personality factors (sensitivity to reward (SR) and punishment (SP), BMI, and outcome measures of impulsivity vs. flexibility in--otherwise healthy--excessive weight adolescents. Sixty-three adolescents (aged 12-17) classified as obese (n = 26), overweight (n = 16), or normal weight (n = 21) participated in the study. We used psychometric assessments of the SR and SP motivational systems, impulsivity (using the UPPS-P scale), and neurocognitive measures with discriminant validity to dissociate inhibition vs. flexibility deficits (using the process-approach version of the Stroop test). We tested the relative contribution of age, SR/SP, and BMI on estimates of impulsivity and inhibition vs. switching performance using multistep hierarchical regression models. BMI significantly predicted elevations in emotion-driven impulsivity (positive and negative urgency) and inferior flexibility performance in adolescents with excess weight--exceeding the predictive capacity of SR and SP. SR was the main predictor of elevations in sensation seeking and lack of premeditation. These findings demonstrate that increases in BMI are specifically associated with elevations in emotion-driven impulsivity and cognitive inflexibility, supporting a dimensional path in which adolescents with excess weight increase their proneness to overindulge when under strong affective states, and their difficulties to switch or reverse habitual behavioral patterns.

Do Flexible Goal Adjustment and Acceptance Help Preserve Quality of Life in Patients with Multiple Sclerosis?

PubMed

Van Damme, Stefaan; De Waegeneer, Annelies; Debruyne, Jan

2016-06-01

Goal regulation strategies such as flexible goal adjustment and acceptance are believed to be protective factors in persons with chronic illness, but research on their relative contributions to quality of life in multiple sclerosis (MS) is lacking. We aimed to test the idea that acceptance and flexible goal adjustment (in contrast to tenacious goal pursuit) may help preserve the quality of life in persons with MS. A sample of 117 patients with MS was recruited. They completed questionnaires measuring quality of life (physical functioning, psychological distress), acceptance, flexible goal adjustment, and tenacious goal pursuit. Acceptance significantly accounted for variance in all three indexes of quality of life, beyond the effects of demographic and illness characteristics. The role of goal regulation style was less clear. Flexible goal adjustment significantly accounted for psychological well-being only. Surprisingly, tenacious goal pursuit predicted better psychological functioning and less psychological distress. No support was found for the hypothesis that acceptance and flexible goal adjustment would moderate the relation between illness severity and quality of life. The findings suggest the potential importance of acceptance in understanding MS patients' quality of life, although its hypothesized protective function could not be confirmed. Further conceptual work on acceptance and goal regulation style is needed, as well as prospective work investigating their causal status.

Flutter Phenomenon in Flow Driven Energy Harvester-A Unified Theoretical Model for "Stiff" and "Flexible" Materials.

PubMed

Chen, Yu; Mu, Xiaojing; Wang, Tao; Ren, Weiwei; Yang, Ya; Wang, Zhong Lin; Sun, Chengliang; Gu, Alex Yuandong

2016-10-14

Here, we report a stable and predictable aero-elastic motion in the flow-driven energy harvester, which is different from flapping and vortex-induced-vibration (VIV). A unified theoretical frame work that describes the flutter phenomenon observed in both "stiff" and "flexible" materials for flow driven energy harvester was presented in this work. We prove flutter in both types of materials is the results of the coupled effects of torsional and bending modes. Compared to "stiff" materials, which has a flow velocity-independent flutter frequency, flexible material presents a flutter frequency that almost linearly scales with the flow velocity. Specific to "flexible" materials, pre-stress modulates the frequency range in which flutter occurs. It is experimentally observed that a double-clamped "flexible" piezoelectric P(VDF-TrFE) thin belt, when driven into the flutter state, yields a 1,000 times increase in the output voltage compared to that of the non-fluttered state. At a fixed flow velocity, increase in pre-stress level of the P(VDF-TrFE) thin belt up-shifts the flutter frequency. In addition, this work allows the rational design of flexible piezoelectric devices, including flow-driven energy harvester, triboelectric energy harvester, and self-powered wireless flow speed sensor.

Prediction of pavement remaining service life based on repetition of load and permanent deformation

NASA Astrophysics Data System (ADS)

Usman, R. S.; Setyawan, A.; Suprapto, M.

2018-03-01

One of the methods which was applied in the assessment of flexible pavement performance was mechanistic method assuming structures of road pavement to become multi-layer structure for flexible pavement, that the vehicle load working on the pavement layer under repetition with power failure worth 1 (one) unit which was assumed as evenly distributed static load, and therefore the pavement material would provide response in the form of stress, strain, and deflection. This is closely related in order to assess the structure of flexible pavement and to predict the remaining service life on the roads of Pulau Indah sta 0 + 000 to sta. 0 + 845 in Kota Kupang, Nusa Tenggara Timur. The performance appraisal indicator which was used was fatigue cracking happening bottom of the asphalt layer and permanent deformation (rutting) on the surface of subgrade. The strain estimate on the flexible pavement layer structure needs carefulness and high accuracy and therefore a software like KENPAVE which produces horizontal tensile strain of 8,802E-05 and vertical compressive strain of 2,642E-04 was used. By applying equation of The Asphalt Instituteit was obtained repetition of permit load when reaching fatigue cracking (Nf) was 16.071.516 ESAL and permanent deformation (rutting) was 14.703.867 ESAL and also it was predicted the remaining service life of pavement applied the equation of AASTHO 1993 by considering Traffic Multiplier factor (TM 1.8, TM 1.9 and TM 2.0) obtained the remaining life service due to fatigue of 5.51% in the year of 13th (TM 1.8), 7.95% in the year of12th (TM 1.9) and 3.11% (TM 2.0) in the year of 12th, also the remaining service life due to rutting of 4.69% in the year of 12th(TM 1.8), 7.79% in the year of 11th (TM 1.9), and 2.94 in the year of 11th (TM 2.0).

Children's beliefs in reciprocation of biases and flexibility.

PubMed

Rennels, Jennifer L; Langlois, Judith H

2015-09-01

Children display positive and negative biases based on peers' attractiveness, gender, and race, but it is unclear whether children who associate positive attributes with certain peers also believe those peers think positively of them. In each domain (attractiveness, gender, and race), we measured 3- to 11-year-olds' (N = 102) biases and flexibility and their beliefs in reciprocity of bias and flexibility by asking who would think positively of them. Children could choose one of two unfamiliar peers (forced choice assessment) or had the additional options of choosing both peers or neither peer (non-forced choice assessment). We found that children often displayed beliefs in reciprocation, with beliefs in positive bias reciprocation from attractive girls showing the largest effect sizes. These beliefs were significantly correlated with and were predictive of children's positive and negative biases and flexibility. The duality of children's beliefs may contribute to strengthening their biases and segregating social groups. Copyright © 2015 Elsevier Inc. All rights reserved.

Children's classification and lexicalization of attractiveness, gender, and race: differential displays of these concepts and relatedness to bias and flexibility.

PubMed

Rennels, Jennifer L; Langlois, Judith H

2014-10-01

Minimal research has examined children's functional use of attractiveness to classify and label others, an important step in the development of children's biases. This study compared 3- to 11-year-olds' classification, sorting, and labeling of others and themselves based on attractiveness, gender, and race and also investigated whether these abilities and other characteristics predicted children's bias and flexibility. Relative to gender and race, children rarely used attractiveness to spontaneously classify people and were less accurate at sorting and labeling others and themselves by attractiveness, suggesting that they have a less explicit concept of attractiveness. Predictors of bias differed depending on domain and assessment method (forced choice or non-forced choice), showing that children's bias is affected by both individual differences and task characteristics. Predictors of flexibility differed based on whether children were assigning positive or negative traits to target children, demonstrating that the valence of attributes is an important consideration when conceptualizing children's flexibility. Copyright © 2014 Elsevier Inc. All rights reserved.

Children’s Classification and Lexicalization of Attractiveness, Gender, and Race: Differential Displays of These Concepts and Relatedness to Bias and Flexibility

PubMed Central

Rennels, Jennifer L.; Langlois, Judith H.

2014-01-01

Minimal research has examined children’s functional use of attractiveness to classify and label others, an important step in the development of children’s biases. This study compared 3-to 11-year-olds’ classification, sorting, and labeling of others and themselves based on attractiveness, gender, and race, and investigated whether these abilities and other characteristics predicted children’s bias and flexibility. Relative to gender and race, children rarely used attractiveness to spontaneously classify people and were less accurate at sorting and labeling others and themselves by attractiveness, suggesting they have a less explicit concept of attractiveness. Predictors of bias differed depending upon domain and assessment method (forced choice or non-forced choice), showing that children’s bias is affected by both individual differences and task characteristics. Predictors of flexibility differed based on whether children were assigning positive or negative traits to target children, demonstrating that the valence of attributes is an important consideration when conceptualizing children’s flexibility. PMID:24842583

CFD Analysis of Flexible Thermal Protection System Shear Configuration Testing in the LCAT Facility

NASA Technical Reports Server (NTRS)

Ferlemann, Paul G.

2014-01-01

This paper documents results of computational analysis performed after flexible thermal protection system shear configuration testing in the LCAT facility. The primary objectives were to predict the shear force on the sample and the sensitivity of all surface properties to the shape of the sample. Bumps of 0.05, 0.10,and 0.15 inches were created to approximate the shape of some fabric samples during testing. A large amount of information was extracted from the CFD solutions for comparison between runs and also current or future flight simulations.

Comments on ;An improved Cauchy number approach for predicting the drag and reconfiguration of flexible vegetation; by Peter Whittaker, Catherine A.M.E. Wilson, and Jochen Aberle

NASA Astrophysics Data System (ADS)

Chen, Li; Chen, Xiaobing

2017-07-01

Whittaker et al. (2015) presented a modified Cauchy number approach for the estimate of flow resistance induced by flexible vegetation. The approach represents a noteworthy effort in quantifying vegetation resistance to streamflow. Here we briefly discuss some theoretical and practical issues of this approach, and show how it is related to the approach developed by Kouwen and others (Kouwen et al., 1969; Kouwen and Unny, 1973) and recently revised by Chen et al. (2014).

A new bead-spring model for simulation of semi-flexible macromolecules

NASA Astrophysics Data System (ADS)

Saadat, Amir; Khomami, Bamin

2016-11-01

A bead-spring model for semi-flexible macromolecules is developed to overcome the deficiencies of the current coarse-grained bead-spring models. Specifically, model improvements are achieved through incorporation of a bending potential. The new model is designed to accurately describe the correlation along the backbone of the chain, segmental length, and force-extension behavior of the macromolecule even at the limit of 1 Kuhn step per spring. The relaxation time of different Rouse modes is used to demonstrate the capabilities of the new model in predicting chain dynamics.

A study of the dynamics of rotating space stations with elastically connected counterweight and attached flexible appendages. Volume 1: Theory

NASA Technical Reports Server (NTRS)

Austin, F.; Markowitz, J.; Goldenberg, S.; Zetkov, G. A.

1973-01-01

The formulation of a mathematical model for predicting the dynamic behavior of rotating flexible space station configurations was conducted. The overall objectives of the study were: (1) to develop the theoretical techniques for determining the behavior of a realistically modeled rotating space station, (2) to provide a versatile computer program for the numerical analysis, and (3) to present practical concepts for experimental verification of the analytical results. The mathematical model and its associated computer program are described.

Dynamic analysis of space structures including elastic, multibody, and control behavior

NASA Technical Reports Server (NTRS)

Pinson, Larry; Soosaar, Keto

1989-01-01

The problem is to develop analysis methods, modeling stategies, and simulation tools to predict with assurance the on-orbit performance and integrity of large complex space structures that cannot be verified on the ground. The problem must incorporate large reliable structural models, multi-body flexible dynamics, multi-tier controller interaction, environmental models including 1g and atmosphere, various on-board disturbances, and linkage to mission-level performance codes. All areas are in serious need of work, but the weakest link is multi-body flexible dynamics.

The role of material flexibility on the drying transition of water between hydrophobic objects: A thermodynamic analysis

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

Altabet, Y. Elia; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

2014-11-14

Liquid water confined between hydrophobic objects of sufficient size becomes metastable with respect to its vapor at separations smaller than a critical drying distance. Macroscopic thermodynamic arguments predicting this distance have been restricted to the limit of perfectly rigid confining materials. However, no material is perfectly rigid and it is of interest to account for this fact in the thermodynamic analysis. We present a theory that combines the current macroscopic theory with the thermodynamics of elasticity to derive an expression for the critical drying distance for liquids confined between flexible materials. The resulting expression is the sum of the well-knownmore » drying distance for perfectly rigid confining materials and a new term that accounts for flexibility. Thermodynamic arguments show that this new term is necessarily positive, meaning that flexibility increases the critical drying distance. To study the expected magnitude and scaling behavior of the flexible term, we consider the specific case of water and present an example of drying between thin square elastic plates that are simply supported along two opposite edges and free at the remaining two. We find that the flexible term can be the same order of magnitude or greater than the rigid solution for materials of biological interest at ambient conditions. In addition, we find that when the rigid solution scales with the characteristic size of the immersed objects, the flexible term is independent of size and vice versa. Thus, the scaling behavior of the overall drying distance will depend on the relative weights of the rigid and flexible contributions.« less

Automated Docking with Protein Flexibility in the Design of Femtomolar “Click Chemistry” Inhibitors of Acetylcholinesterase

PubMed Central

Morris, Garrett M.; Green, Luke G.; Radić, Zoran; Taylor, Palmer; Sharpless, K. Barry; Olson, Arthur J.; Grynszpan, Flavio

2013-01-01

The use of computer-aided structure-based drug design prior to synthesis has proven to be generally valuable in suggesting improved binding analogues of existing ligands.1 Here we describe the application of the program AutoDock2 to the design of a focused library that was used in the “click chemistry in-situ” generation of the most potent non-covalent inhibitor of the enzyme acetylcholinesterase (AChE) yet developed (Kd = ~100 fM).3 AutoDock version 3.0.5 has been widely distributed and successfully used to predict bound conformations of flexible ligands. Here, we also used a version of AutoDock which permits additional conformational flexibility in selected amino acid sidechains of the target protein. PMID:23451944

Meteorological Measurements from Satellite Platforms. [stability and control of flexible stochastic satellites

NASA Technical Reports Server (NTRS)

Suomi, V. E.

1975-01-01

The stability of stochastic satellites and the stability and control of flexible satellites were investigated. The effects of random environmental torques and noises in the moments of inertia of spinning and three-axes stabilized satellites were first compared analytically by four methods and by analog simulations. Among the analytical methods, it was shown that the Fokker-Planck formulation yields predictions which most coincide with the simulation results. It was then shown that the required stability criterion of a satellite is quite different from that obtained by a deterministic approach, under the assumption that the environmental and control torques experienced by the satellite are random. Finally, it was demonstrated that, by monitoring the deformations of the flexible elements of a satellite, the effectiveness of the satellite control system can be increased considerably.

Examining the mediational role of psychological flexibility, pain catastrophizing, and visceral sensitivity in the relationship between psychological distress, irritable bowel symptom frequency, and quality of life.

PubMed

Cassar, G E; Knowles, S; Youssef, G J; Moulding, R; Uiterwijk, D; Waters, L; Austin, D W

2018-06-08

The aim of the current study was to use Structural Equation Modelling (SEM) to examine whether psychological flexibility (i.e. mindfulness, acceptance, valued-living) mediates the relationship between distress, irritable bowel syndrome (IBS) symptom frequency, and quality of life (QoL). Ninety-two individuals participated in the study (12 male, 80 female, M age  = 36.24) by completing an online survey including measures of visceral sensitivity, distress, IBS-related QoL, mindfulness, bowel symptoms, pain catastrophizing, acceptance, and valued-living. A final model with excellent fit was identified. Psychological distress significantly and directly predicted pain catastrophizing, valued-living, and IBS symptom frequency. Pain catastrophizing directly predicted visceral sensitivity and acceptance, while visceral sensitivity significantly and directly predicted IBS symptom frequency and QoL. Symptom frequency also had a direct and significant relationship with QoL. The current findings suggest that interventions designed to address unhelpful cognitive processes related to visceral sensitivity, pain catastrophizing, and psychological distress may be of most benefit to IBS-related QoL.

Homeostatic Regulation of Memory Systems and Adaptive Decisions

PubMed Central

Mizumori, Sheri JY; Jo, Yong Sang

2013-01-01

While it is clear that many brain areas process mnemonic information, understanding how their interactions result in continuously adaptive behaviors has been a challenge. A homeostatic-regulated prediction model of memory is presented that considers the existence of a single memory system that is based on a multilevel coordinated and integrated network (from cells to neural systems) that determines the extent to which events and outcomes occur as predicted. The “multiple memory systems of the brain” have in common output that signals errors in the prediction of events and/or their outcomes, although these signals differ in terms of what the error signal represents (e.g., hippocampus: context prediction errors vs. midbrain/striatum: reward prediction errors). The prefrontal cortex likely plays a pivotal role in the coordination of prediction analysis within and across prediction brain areas. By virtue of its widespread control and influence, and intrinsic working memory mechanisms. Thus, the prefrontal cortex supports the flexible processing needed to generate adaptive behaviors and predict future outcomes. It is proposed that prefrontal cortex continually and automatically produces adaptive responses according to homeostatic regulatory principles: prefrontal cortex may serve as a controller that is intrinsically driven to maintain in prediction areas an experience-dependent firing rate set point that ensures adaptive temporally and spatially resolved neural responses to future prediction errors. This same drive by prefrontal cortex may also restore set point firing rates after deviations (i.e. prediction errors) are detected. In this way, prefrontal cortex contributes to reducing uncertainty in prediction systems. An emergent outcome of this homeostatic view may be the flexible and adaptive control that prefrontal cortex is known to implement (i.e. working memory) in the most challenging of situations. Compromise to any of the prediction circuits should result in rigid and suboptimal decision making and memory as seen in addiction and neurological disease. © 2013 The Authors. Hippocampus Published by Wiley Periodicals, Inc. PMID:23929788

Homeostatic regulation of memory systems and adaptive decisions.

PubMed

Mizumori, Sheri J Y; Jo, Yong Sang

2013-11-01

While it is clear that many brain areas process mnemonic information, understanding how their interactions result in continuously adaptive behaviors has been a challenge. A homeostatic-regulated prediction model of memory is presented that considers the existence of a single memory system that is based on a multilevel coordinated and integrated network (from cells to neural systems) that determines the extent to which events and outcomes occur as predicted. The "multiple memory systems of the brain" have in common output that signals errors in the prediction of events and/or their outcomes, although these signals differ in terms of what the error signal represents (e.g., hippocampus: context prediction errors vs. midbrain/striatum: reward prediction errors). The prefrontal cortex likely plays a pivotal role in the coordination of prediction analysis within and across prediction brain areas. By virtue of its widespread control and influence, and intrinsic working memory mechanisms. Thus, the prefrontal cortex supports the flexible processing needed to generate adaptive behaviors and predict future outcomes. It is proposed that prefrontal cortex continually and automatically produces adaptive responses according to homeostatic regulatory principles: prefrontal cortex may serve as a controller that is intrinsically driven to maintain in prediction areas an experience-dependent firing rate set point that ensures adaptive temporally and spatially resolved neural responses to future prediction errors. This same drive by prefrontal cortex may also restore set point firing rates after deviations (i.e. prediction errors) are detected. In this way, prefrontal cortex contributes to reducing uncertainty in prediction systems. An emergent outcome of this homeostatic view may be the flexible and adaptive control that prefrontal cortex is known to implement (i.e. working memory) in the most challenging of situations. Compromise to any of the prediction circuits should result in rigid and suboptimal decision making and memory as seen in addiction and neurological disease. Copyright © 2013 Wiley Periodicals, Inc.

Predicting bioactive conformations and binding modes of macrocycles

NASA Astrophysics Data System (ADS)

Anighoro, Andrew; de la Vega de León, Antonio; Bajorath, Jürgen

2016-10-01

Macrocyclic compounds experience increasing interest in drug discovery. It is often thought that these large and chemically complex molecules provide promising candidates to address difficult targets and interfere with protein-protein interactions. From a computational viewpoint, these molecules are difficult to treat. For example, flexible docking of macrocyclic compounds is hindered by the limited ability of current docking approaches to optimize conformations of extended ring systems for pose prediction. Herein, we report predictions of bioactive conformations of macrocycles using conformational search and binding modes using docking. Conformational ensembles generated using specialized search technique of about 70 % of the tested macrocycles contained accurate bioactive conformations. However, these conformations were difficult to identify on the basis of conformational energies. Moreover, docking calculations with limited ligand flexibility starting from individual low energy conformations rarely yielded highly accurate binding modes. In about 40 % of the test cases, binding modes were approximated with reasonable accuracy. However, when conformational ensembles were subjected to rigid body docking, an increase in meaningful binding mode predictions to more than 50 % of the test cases was observed. Electrostatic effects did not contribute to these predictions in a positive or negative manner. Rather, achieving shape complementarity at macrocycle-target interfaces was a decisive factor. In summary, a combined computational protocol using pre-computed conformational ensembles of macrocycles as a starting point for docking shows promise in modeling binding modes of macrocyclic compounds.

Validation of TxDOT flexible pavement skid prediction model : workshop : student guide.

DOT National Transportation Integrated Search

2017-05-01

Course Materials: : Background summary of Research Project 0-5627. : Short presentation of research tasks and findings from Research Project 0-6746. : Aggregate characterization with Aggregate Imaging Measurement System (AIMS) and Micro-D...

An improved Cauchy number approach for predicting the drag and reconfiguration of flexible vegetation

NASA Astrophysics Data System (ADS)

Whittaker, Peter; Wilson, Catherine A. M. E.; Aberle, Jochen

2015-09-01

An improved model to describe the drag and reconfiguration of flexible riparian vegetation is proposed. The key improvement over previous models is the use of a refined 'vegetative' Cauchy number to explicitly determine the magnitude and rate of the vegetation's reconfiguration. After being derived from dimensional consideration, the model is applied to two experimental data sets. The first contains high-resolution drag force and physical property measurements for twenty-one foliated and defoliated full-scale trees, including specimens of Alnus glutinosa, Populus nigra and Salix alba. The second data set is independent and of a different scale, consisting of drag force and physical property measurements for natural and artificial branches of willow and poplar, under partially and fully submerged flow conditions. Good agreement between the measured and predicted drag forces is observed for both data sets, especially when compared to a more typical 'rigid' approximation, where the effects of reconfiguration are neglected.

The potential effects of climate-change-associated temperature increases on the metabolic rate of a small Afrotropical bird.

PubMed

Thompson, Lindy J; Brown, Mark; Downs, Colleen T

2015-05-15

Studies have only recently begun to underline the importance of including data on the physiological flexibility of a species when modelling its vulnerability to extinction from climate change. We investigated the effects of a 4°C increase in ambient temperature (Ta), similar to that predicted for southern Africa by the year 2080, on certain physiological variables of a 10-12 g passerine bird endemic to southern Africa, the Cape white-eye Zosterops virens. There was no significant difference in resting metabolism, body mass and intraperitoneal body temperature between birds housed indoors at 4°C above outside ambient temperature and those housed indoors at outside ambient temperature. We conclude that the physiological flexibility of Cape white-eyes will aid them in coping with the 4°C increase predicted for their range by 2080. © 2015. Published by The Company of Biologists Ltd.

Young's Modulus of Wurtzite and Zinc Blende InP Nanowires.

PubMed

Dunaevskiy, Mikhail; Geydt, Pavel; Lähderanta, Erkki; Alekseev, Prokhor; Haggrén, Tuomas; Kakko, Joona-Pekko; Jiang, Hua; Lipsanen, Harri

2017-06-14

The Young's modulus of thin conical InP nanowires with either wurtzite or mixed "zinc blende/wurtzite" structures was measured. It has been shown that the value of Young's modulus obtained for wurtzite InP nanowires (E [0001] = 130 ± 30 GPa) was similar to the theoretically predicted value for the wurtzite InP material (E [0001] = 120 ± 10 GPa). The Young's modulus of mixed "zinc blende/wurtzite" InP nanowires (E [111] = 65 ± 10 GPa) appeared to be 40% less than the theoretically predicted value for the zinc blende InP material (E [111] = 110 GPa). An advanced method for measuring the Young's modulus of thin and flexible nanostructures is proposed. It consists of measuring the flexibility (the inverse of stiffness) profiles 1/k(x) by the scanning probe microscopy with precise control of loading force in nanonewton range followed by simulations.

Gender Attitudes in Early Childhood: Behavioral Consequences and Cognitive Antecedents.

PubMed

Halim, May Ling D; Ruble, Diane N; Tamis-LeMonda, Catherine S; Shrout, Patrick E; Amodio, David M

2017-05-01

This study examined factors that predicted children's gender intergroup attitudes at age 5 and the implications of these attitudes for intergroup behavior. Ethnically diverse children from low-income backgrounds (N = 246; Mexican-, Chinese-, Dominican-, and African American) were assessed at ages 4 and 5. On average, children reported positive same-gender and negative other-gender attitudes. Positive same-gender attitudes were associated with knowledge of gender stereotypes. In contrast, positive other-gender attitudes were associated with flexibility in gender cognitions (stereotype flexibility, gender consistency). Other-gender attitudes predicted gender-biased behavior. These patterns were observed in all ethnic groups. These findings suggest that early learning about gender categories shape young children's gender attitudes and that these gender attitudes already have consequences for children's intergroup behavior at age 5. © 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.

PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes.

PubMed

Li, Ginny X H; Vogel, Christine; Choi, Hyungwon

2018-06-07

While tandem mass spectrometry can detect post-translational modifications (PTM) at the proteome scale, reported PTM sites are often incomplete and include false positives. Computational approaches can complement these datasets by additional predictions, but most available tools use prediction models pre-trained for single PTM type by the developers and it remains a difficult task to perform large-scale batch prediction for multiple PTMs with flexible user control, including the choice of training data. We developed an R package called PTMscape which predicts PTM sites across the proteome based on a unified and comprehensive set of descriptors of the physico-chemical microenvironment of modified sites, with additional downstream analysis modules to test enrichment of individual or pairs of PTMs in protein domains. PTMscape is flexible in the ability to process any major modifications, such as phosphorylation and ubiquitination, while achieving the sensitivity and specificity comparable to single-PTM methods and outperforming other multi-PTM tools. Applying this framework, we expanded proteome-wide coverage of five major PTMs affecting different residues by prediction, especially for lysine and arginine modifications. Using a combination of experimentally acquired sites (PSP) and newly predicted sites, we discovered that the crosstalk among multiple PTMs occur more frequently than by random chance in key protein domains such as histone, protein kinase, and RNA recognition motifs, spanning various biological processes such as RNA processing, DNA damage response, signal transduction, and regulation of cell cycle. These results provide a proteome-scale analysis of crosstalk among major PTMs and can be easily extended to other types of PTM.

Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions

NASA Astrophysics Data System (ADS)

Crivelli, Joseph J.; Lemmon, Gordon; Kaufmann, Kristian W.; Meiler, Jens

2013-12-01

Interactions between protein domains and linear peptides underlie many biological processes. Among these interactions, the recognition of C-terminal peptides by PDZ domains is one of the most ubiquitous. In this work, we present a mathematical model for PDZ domain-peptide interactions capable of predicting both affinity and specificity of binding based on X-ray crystal structures and comparative modeling with R osetta. We developed our mathematical model using a large phage display dataset describing binding specificity for a wild type PDZ domain and 91 single mutants, as well as binding affinity data for a wild type PDZ domain binding to 28 different peptides. Structural refinement was carried out through several R osetta protocols, the most accurate of which included flexible peptide docking and several iterations of side chain repacking and backbone minimization. Our findings emphasize the importance of backbone flexibility and the energetic contributions of side chain-side chain hydrogen bonds in accurately predicting interactions. We also determined that predicting PDZ domain-peptide interactions became increasingly challenging as the length of the peptide increased in the N-terminal direction. In the training dataset, predicted binding energies correlated with those derived through calorimetry and specificity switches introduced through single mutations at interface positions were recapitulated. In independent tests, our best performing protocol was capable of predicting dissociation constants well within one order of magnitude of the experimental values and specificity profiles at the level of accuracy of previous studies. To our knowledge, this approach represents the first integrated protocol for predicting both affinity and specificity for PDZ domain-peptide interactions.

Exploiting protein flexibility to predict the location of allosteric sites

PubMed Central

2012-01-01

Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity), by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing that this simple coarse-grained methodology is able to capture the effects triggered by allosteric ligands already described in the literature. Conclusions We introduce a simple computational approach to predict the presence and position of allosteric sites in a protein based on the analysis of changes in protein normal modes upon the binding of a coarse-grained ligand at predicted cavities. Its performance has been demonstrated using a newly curated non-redundant set of 91 proteins with reported allosteric properties. The software developed in this work is available upon request from the authors. PMID:23095452

Exploiting protein flexibility to predict the location of allosteric sites.

PubMed

Panjkovich, Alejandro; Daura, Xavier

2012-10-25

Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity), by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing that this simple coarse-grained methodology is able to capture the effects triggered by allosteric ligands already described in the literature. We introduce a simple computational approach to predict the presence and position of allosteric sites in a protein based on the analysis of changes in protein normal modes upon the binding of a coarse-grained ligand at predicted cavities. Its performance has been demonstrated using a newly curated non-redundant set of 91 proteins with reported allosteric properties. The software developed in this work is available upon request from the authors.

Variable selection for confounder control, flexible modeling and Collaborative Targeted Minimum Loss-based Estimation in causal inference

PubMed Central

Schnitzer, Mireille E.; Lok, Judith J.; Gruber, Susan

2015-01-01

This paper investigates the appropriateness of the integration of flexible propensity score modeling (nonparametric or machine learning approaches) in semiparametric models for the estimation of a causal quantity, such as the mean outcome under treatment. We begin with an overview of some of the issues involved in knowledge-based and statistical variable selection in causal inference and the potential pitfalls of automated selection based on the fit of the propensity score. Using a simple example, we directly show the consequences of adjusting for pure causes of the exposure when using inverse probability of treatment weighting (IPTW). Such variables are likely to be selected when using a naive approach to model selection for the propensity score. We describe how the method of Collaborative Targeted minimum loss-based estimation (C-TMLE; van der Laan and Gruber, 2010) capitalizes on the collaborative double robustness property of semiparametric efficient estimators to select covariates for the propensity score based on the error in the conditional outcome model. Finally, we compare several approaches to automated variable selection in low-and high-dimensional settings through a simulation study. From this simulation study, we conclude that using IPTW with flexible prediction for the propensity score can result in inferior estimation, while Targeted minimum loss-based estimation and C-TMLE may benefit from flexible prediction and remain robust to the presence of variables that are highly correlated with treatment. However, in our study, standard influence function-based methods for the variance underestimated the standard errors, resulting in poor coverage under certain data-generating scenarios. PMID:26226129

Variable Selection for Confounder Control, Flexible Modeling and Collaborative Targeted Minimum Loss-Based Estimation in Causal Inference.

PubMed

Schnitzer, Mireille E; Lok, Judith J; Gruber, Susan

2016-05-01

This paper investigates the appropriateness of the integration of flexible propensity score modeling (nonparametric or machine learning approaches) in semiparametric models for the estimation of a causal quantity, such as the mean outcome under treatment. We begin with an overview of some of the issues involved in knowledge-based and statistical variable selection in causal inference and the potential pitfalls of automated selection based on the fit of the propensity score. Using a simple example, we directly show the consequences of adjusting for pure causes of the exposure when using inverse probability of treatment weighting (IPTW). Such variables are likely to be selected when using a naive approach to model selection for the propensity score. We describe how the method of Collaborative Targeted minimum loss-based estimation (C-TMLE; van der Laan and Gruber, 2010 [27]) capitalizes on the collaborative double robustness property of semiparametric efficient estimators to select covariates for the propensity score based on the error in the conditional outcome model. Finally, we compare several approaches to automated variable selection in low- and high-dimensional settings through a simulation study. From this simulation study, we conclude that using IPTW with flexible prediction for the propensity score can result in inferior estimation, while Targeted minimum loss-based estimation and C-TMLE may benefit from flexible prediction and remain robust to the presence of variables that are highly correlated with treatment. However, in our study, standard influence function-based methods for the variance underestimated the standard errors, resulting in poor coverage under certain data-generating scenarios.

Analysis and experiments for delay compensation in attitude control of flexible spacecraft

NASA Astrophysics Data System (ADS)

Sabatini, Marco; Palmerini, Giovanni B.; Leonangeli, Nazareno; Gasbarri, Paolo

2014-11-01

Space vehicles are often characterized by highly flexible appendages, with low natural frequencies which can generate coupling phenomena during orbital maneuvering. The stability and delay margins of the controlled system are deeply affected by the presence of bodies with different elastic properties, assembled to form a complex multibody system. As a consequence, unstable behavior can arise. In this paper the problem is first faced from a numerical point of view, developing accurate multibody mathematical models, as well as relevant navigation and control algorithms. One of the main causes of instability is identified with the unavoidable presence of time delays in the GNC loop. A strategy to compensate for these delays is elaborated and tested using the simulation tool, and finally validated by means of a free floating platform, replicating the flexible spacecraft attitude dynamics (single axis rotation). The platform is equipped with thrusters commanded according to the on-off modulation of the Linear Quadratic Regulator (LQR) control law. The LQR is based on the estimate of the full state vector, i.e. including both rigid - attitude - and elastic variables, that is possible thanks to the on line measurement of the flexible displacements, realized by processing the images acquired by a dedicated camera. The accurate mathematical model of the system and the rigid and elastic measurements enable a prediction of the state, so that the control is evaluated taking the predicted state relevant to a delayed time into account. Both the simulations and the experimental campaign demonstrate that by compensating in this way the time delay, the instability is eliminated, and the maneuver is performed accurately.

Stress attenuates the flexible updating of aversive value

PubMed Central

Raio, Candace M.; Hartley, Catherine A.; Orederu, Temidayo A.; Li, Jian; Phelps, Elizabeth A.

2017-01-01

In a dynamic environment, sources of threat or safety can unexpectedly change, requiring the flexible updating of stimulus−outcome associations that promote adaptive behavior. However, aversive contexts in which we are required to update predictions of threat are often marked by stress. Acute stress is thought to reduce behavioral flexibility, yet its influence on the modulation of aversive value has not been well characterized. Given that stress exposure is a prominent risk factor for anxiety and trauma-related disorders marked by persistent, inflexible responses to threat, here we examined how acute stress affects the flexible updating of threat responses. Participants completed an aversive learning task, in which one stimulus was probabilistically associated with an electric shock, while the other stimulus signaled safety. A day later, participants underwent an acute stress or control manipulation before completing a reversal learning task during which the original stimulus−outcome contingencies switched. Skin conductance and neuroendocrine responses provided indices of sympathetic arousal and stress responses, respectively. Despite equivalent initial learning, stressed participants showed marked impairments in reversal learning relative to controls. Additionally, reversal learning deficits across participants were related to heightened levels of alpha-amylase, a marker of noradrenergic activity. Finally, fitting arousal data to a computational reinforcement learning model revealed that stress-induced reversal learning deficits emerged from stress-specific changes in the weight assigned to prediction error signals, disrupting the adaptive adjustment of learning rates. Our findings provide insight into how stress renders individuals less sensitive to changes in aversive reinforcement and have implications for understanding clinical conditions marked by stress-related psychopathology. PMID:28973957

Revolutionize Situational Awareness in Emergencies

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

Hehlen, Markus Peter

This report describes an integrated system that provides real-time actionable information to first responders. LANL will integrate three technologies to form an advanced predictive real-time sensor network including compact chemical and wind sensor sin low cost rugged package for outdoor installation; flexible robust communication architecture linking sensors in near-real time to globally accessible servers; and the QUIC code which predicts contamination transport and dispersal in urban environments in near real time.

Progress in Finite Element Modeling of the Lower Extremities

DTIC Science & Technology

2015-06-01

bending and subsequent injury , e.g., the distal tibia motion results in bending of the tibia rather than the tibia rotating about the knee joint...layers, rich anisotropy, and wide variability. Developing a model for predictive injury capability, therefore, needs to be versatile and flexible to... injury capability presents many challenges, the first of which is identifying the types of conditions where injury prediction is needed. Our focus

Repeatability and degree of territorial aggression differs among urban and rural great tits (Parus major).

PubMed

Hardman, Samuel I; Dalesman, Sarah

2018-03-22

Animals in urban habitats face many novel selection pressures such as increased human population densities and human disturbance. This is predicted to favour bolder and more aggressive individuals together with greater flexibility in behaviour. Previous work has focussed primarily on studying these traits in captive birds and has shown increased aggression and reduced consistency between traits (behavioural syndromes) in birds from urban populations. However, personality (consistency within a behavioural trait) has not been well studied in the wild. Here we tested whether urban free-living male great tits show greater territorial aggression than rural counterparts. We also tested predictions that both behavioural syndromes and personality would show lower consistency in urban populations. We found that urban populations were more aggressive than rural populations and urban birds appeared to show lower levels of individual behavioural repeatability (personality) as predicted. However, we found no effect of urbanisation on behavioural syndromes (correlations between multiple behavioural traits). Our results indicate that urban environments may favour individuals which exhibit increased territorial aggression and greater within-trait flexibility which may be essential to success in holding urban territories. Determining how urban environments impact key fitness traits will be important in predicting how animals cope with ongoing urbanisation.

Validation of Models Used to Inform Colorectal Cancer Screening Guidelines: Accuracy and Implications.

PubMed

Rutter, Carolyn M; Knudsen, Amy B; Marsh, Tracey L; Doria-Rose, V Paul; Johnson, Eric; Pabiniak, Chester; Kuntz, Karen M; van Ballegooijen, Marjolein; Zauber, Ann G; Lansdorp-Vogelaar, Iris

2016-07-01

Microsimulation models synthesize evidence about disease processes and interventions, providing a method for predicting long-term benefits and harms of prevention, screening, and treatment strategies. Because models often require assumptions about unobservable processes, assessing a model's predictive accuracy is important. We validated 3 colorectal cancer (CRC) microsimulation models against outcomes from the United Kingdom Flexible Sigmoidoscopy Screening (UKFSS) Trial, a randomized controlled trial that examined the effectiveness of one-time flexible sigmoidoscopy screening to reduce CRC mortality. The models incorporate different assumptions about the time from adenoma initiation to development of preclinical and symptomatic CRC. Analyses compare model predictions to study estimates across a range of outcomes to provide insight into the accuracy of model assumptions. All 3 models accurately predicted the relative reduction in CRC mortality 10 years after screening (predicted hazard ratios, with 95% percentile intervals: 0.56 [0.44, 0.71], 0.63 [0.51, 0.75], 0.68 [0.53, 0.83]; estimated with 95% confidence interval: 0.56 [0.45, 0.69]). Two models with longer average preclinical duration accurately predicted the relative reduction in 10-year CRC incidence. Two models with longer mean sojourn time accurately predicted the number of screen-detected cancers. All 3 models predicted too many proximal adenomas among patients referred to colonoscopy. Model accuracy can only be established through external validation. Analyses such as these are therefore essential for any decision model. Results supported the assumptions that the average time from adenoma initiation to development of preclinical cancer is long (up to 25 years), and mean sojourn time is close to 4 years, suggesting the window for early detection and intervention by screening is relatively long. Variation in dwell time remains uncertain and could have important clinical and policy implications. © The Author(s) 2016.

Single drug biomarker prediction for ER- breast cancer outcome from chemotherapy.

PubMed

Chen, Yong-Zi; Kim, Youngchul; Soliman, Hatem H; Ying, GuoGuang; Lee, Jae K

2018-06-01

ER-negative breast cancer includes most aggressive subtypes of breast cancer such as triple negative (TN) breast cancer. Excluded from hormonal and targeted therapies effectively used for other subtypes of breast cancer, standard chemotherapy is one of the primary treatment options for these patients. However, as ER- patients have shown highly heterogeneous responses to different chemotherapies, it has been difficult to select most beneficial chemotherapy treatments for them. In this study, we have simultaneously developed single drug biomarker models for four standard chemotherapy agents: paclitaxel (T), 5-fluorouracil (F), doxorubicin (A) and cyclophosphamide (C) to predict responses and survival of ER- breast cancer patients treated with combination chemotherapies. We then flexibly combined these individual drug biomarkers for predicting patient outcomes of two independent cohorts of ER- breast cancer patients who were treated with different drug combinations of neoadjuvant chemotherapy. These individual and combined drug biomarker models significantly predicted chemotherapy response for 197 ER- patients in the Hatzis cohort (AUC = 0.637, P  = 0.002) and 69 ER- patients in the Hess cohort (AUC = 0.635, P  = 0.056). The prediction was also significant for the TN subgroup of both cohorts (AUC = 0.60, 0.72, P  = 0.043, 0.009). In survival analysis, our predicted responder patients showed significantly improved survival with a >17 months longer median PFS than the predicted non-responder patients for both ER- and TN subgroups (log-rank test P -value = 0.018 and 0.044). This flexible prediction capability based on single drug biomarkers may allow us to even select new drug combinations most beneficial to individual patients with ER- breast cancer. © 2018 The authors.

A flexible docking scheme to explore the binding selectivity of PDZ domains.

PubMed

Gerek, Z Nevin; Ozkan, S Banu

2010-05-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 A. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

A flexible docking scheme to explore the binding selectivity of PDZ domains

PubMed Central

Gerek, Z Nevin; Ozkan, S Banu

2010-01-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using RosettaLigand, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately. PMID:20196074

First order coupled dynamic model of flexible space structures with time-varying configurations

NASA Astrophysics Data System (ADS)

Wang, Jie; Li, Dongxu; Jiang, Jianping

2017-03-01

This paper proposes a first order coupled dynamic modeling method for flexible space structures with time-varying configurations for the purpose of deriving the characteristics of the system. The model considers the first time derivative of the coordinate transformation matrix between the platform's body frame and the appendage's floating frame. As a result it can accurately predict characteristics of the system even if flexible appendages rotate with complex trajectory relative to the rigid part. In general, flexible appendages are fixed on the rigid platform or forced to rotate with a slow angular velocity. So only the zero order of the transformation matrix is considered in conventional models. However, due to neglecting of time-varying terms of the transformation matrix, these models introduce severe error when appendages, like antennas, for example, rotate with a fast speed relative to the platform. The first order coupled dynamic model for flexible space structures proposed in this paper resolve this problem by introducing the first time derivative of the transformation matrix. As a numerical example, a central core with a rotating solar panel is considered and the results are compared with those given by the conventional model. It has been shown that the first order terms are of great importance on the attitude of the rigid body and dynamic response of the flexible appendage.

A Contextual Behavior Science Framework for Understanding How Behavioral Flexibility Relates to Anxiety.

PubMed

Palm Reed, Kathleen M; Cameron, Amy Y; Ameral, Victoria E

2017-09-01

There is a growing literature focusing on the emerging idea that behavioral flexibility, rather than particular emotion regulation strategies per se, provides greater promise in predicting and influencing anxiety-related psychopathology. Yet this line of research and theoretical analysis appear to be plagued by its own challenges. For example, middle-level constructs, such as behavioral flexibility, are difficult to define, difficult to measure, and difficult to interpret in relation to clinical interventions. A key point that some researchers have made is that previous studies examining flexible use of emotion regulation strategies (or, more broadly, coping) have failed due to a lack of focus on context. That is, examining strategies in isolation of the context in which they are used provides limited information on the suitability, rigid adherence, or effectiveness of a given strategy in that situation. Several of these researchers have proposed the development of new models to define and measure various types of behavioral flexibility. We would like to suggest that an explanation of the phenomenon already exists and that we can go back to our behavioral roots to understand this phenomenon rather than focusing on defining and capturing a new process. Indeed, thorough contextual behavioral analyses already yield a useful account of what has been observed. We will articulate a model explaining behavioral flexibility using a functional, contextual framework, with anxiety-related disorders as an example.

Modulation of HIV Protease Flexibility by the T80N Mutation

PubMed Central

Zhou, Hao; Li, Shangyang; Badger, John; Nalivaika, Ellen; Cai, Yufeng; Foulkes-Murzycki, Jennifer; Schiffer, Celia; Makowski, Lee

2015-01-01

The flexibility of HIV protease plays a critical role in enabling enzymatic activity and is required for substrate access to the active site. While the importance of flexibility in the flaps that cover the active site is well known, flexibility in other parts of the enzyme is also critical for function. One key region is a loop containing Thr 80 which forms the walls of the active site. Although not situated within the active site, amino acid Thr80 is absolutely conserved. The mutation T80N preserves the structure of the enzyme but catalytic activity is completely lost. To investigate the potential influence of the T80N mutation on HIVp flexibility, wide-angle scattering (WAXS) data was measured for a series of HIV protease variants. Starting with a calculated WAXS pattern from a rigid atomic model, the modulations in the intensity distribution caused by structural fluctuations in the protein were predicted by simple analytic methods and compared to the experimental data. An analysis of T80N WAXS data shows that this variant is significantly more rigid than the WT across all length scales. The effects of this single point mutation extend throughout the protein, so as to alter the mobility of amino acids in the enzymatic core. These results support the contentions that significant protein flexibility extends throughout HIV protease and is critical to catalytic function. PMID:25488402

Preliminary analysis of the PreFlexMS molten salt once-through steam generator dynamics and control strategy

NASA Astrophysics Data System (ADS)

Trabucchi, Stefano; Casella, Francesco; Maioli, Tommaso; Elsido, Cristina; Franzini, Davide; Ramond, Mathieu

2017-06-01

Concentrated Solar Power plants (CSP) coupled with thermal storage have the potential to guarantee both flexible and continuous energy production, thus being competitive with conventional fossil fuel and hydro power plants, in terms of dispatchability and provision of ancillary services. Hence, the plant equipment and control design have to be focused on flexible operation on one hand, and on plant safety concerning the molten salt freezing on the other hand. The PreFlexMS European project aims to introduce a molten salt Once-Through Steam Generator (OTSG) within a Rankine cycle based power unit, a technology that has greater flexibility potential if compared to steam drum boilers, currently used in CSP plants. The dynamic modelling and simulation from the early design stages is, thus, of paramount importance, to assess the plant dynamic behavior and controllability, and to predict the achievable closed-loop dynamic performance, potentially saving money and time during the detailed design, construction and commissioning phases. The present paper reports the main results of the analysis carried out during the first part of the project, regarding the system analysis and control design. In particular, two different control systems have been studied and tested with the plant dynamic model: a decentralized control strategy based on PI controllers and a Linear Model Predictive Control (LMPC).

Behavioral and Neural Markers of Flexible Attention over Working Memory in Aging.

PubMed

Mok, Robert M; Myers, Nicholas E; Wallis, George; Nobre, Anna Christina

2016-04-01

Working memory (WM) declines as we age and, because of its fundamental role in higher order cognition, this can have highly deleterious effects in daily life. We investigated whether older individuals benefit from flexible orienting of attention within WM to mitigate cognitive decline. We measured magnetoencephalography (MEG) in older adults performing a WM precision task with cues during the maintenance period that retroactively predicted the location of the relevant items for performance (retro-cues). WM performance of older adults significantly benefitted from retro-cues. Whereas WM maintenance declined with age, retro-cues conferred strong attentional benefits. A model-based analysis revealed an increase in the probability of recalling the target, a lowered probability of retrieving incorrect items or guessing, and an improvement in memory precision. MEG recordings showed that retro-cues induced a transient lateralization of alpha (8-14 Hz) and beta (15-30 Hz) oscillatory power. Interestingly, shorter durations of alpha/beta lateralization following retro-cues predicted larger cueing benefits, reinforcing recent ideas about the dynamic nature of access to WM representations. Our results suggest that older adults retain flexible control over WM, but individual differences in control correspond to differences in neural dynamics, possibly reflecting the degree of preservation of control in healthy aging. © The Author 2016. Published by Oxford University Press.

Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

PubMed

Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

2013-01-01

The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

Behavioral and Neural Markers of Flexible Attention over Working Memory in Aging

PubMed Central

Mok, Robert M.; Myers, Nicholas E.; Wallis, George; Nobre, Anna Christina

2016-01-01

Working memory (WM) declines as we age and, because of its fundamental role in higher order cognition, this can have highly deleterious effects in daily life. We investigated whether older individuals benefit from flexible orienting of attention within WM to mitigate cognitive decline. We measured magnetoencephalography (MEG) in older adults performing a WM precision task with cues during the maintenance period that retroactively predicted the location of the relevant items for performance (retro-cues). WM performance of older adults significantly benefitted from retro-cues. Whereas WM maintenance declined with age, retro-cues conferred strong attentional benefits. A model-based analysis revealed an increase in the probability of recalling the target, a lowered probability of retrieving incorrect items or guessing, and an improvement in memory precision. MEG recordings showed that retro-cues induced a transient lateralization of alpha (8–14 Hz) and beta (15–30 Hz) oscillatory power. Interestingly, shorter durations of alpha/beta lateralization following retro-cues predicted larger cueing benefits, reinforcing recent ideas about the dynamic nature of access to WM representations. Our results suggest that older adults retain flexible control over WM, but individual differences in control correspond to differences in neural dynamics, possibly reflecting the degree of preservation of control in healthy aging. PMID:26865653

Adjustment latitude and attendance requirements as determinants of sickness absence or attendance. Empirical tests of the illness flexibility model.

PubMed

Johansson, Gun; Lundberg, Ingvar

2004-05-01

This study investigates whether the two dimensions of illness flexibility at work, adjustment latitude and attendance requirements are associated to sickness absence and sickness attendance. Adjustment latitude describes the opportunities people have to reduce or in other ways change their work-effort when ill. Such opportunities can be to choose among work tasks or work at a slower pace. Attendance requirements describe negative consequences of being away from work that can affect either the subject, work mates or a third party. In a cross-sectional design data based on self-reports from a questionnaire from 4924 inhabitants in the county of Stockholm were analysed. The results showed that low adjustment latitude, as predicted, increased women's sickness absence. However, it did not show any relation to men's sickness absence and men's and women's sickness attendance. Attendance requirements were strongly associated to both men's and women's sickness absence and sickness attendance in the predicted way. Those more often required to attend were less likely to be absent and more likely to attend work at illness. As this is the first study of how illness flexibility at work affects behaviour at illness, it was concluded that more studies are needed.

Cofilin-Linked Changes in Actin Filament Flexibility Promote Severing

PubMed Central

McCullough, Brannon R.; Grintsevich, Elena E.; Chen, Christine K.; Kang, Hyeran; Hutchison, Alan L.; Henn, Arnon; Cao, Wenxiang; Suarez, Cristian; Martiel, Jean-Louis; Blanchoin, Laurent; Reisler, Emil; De La Cruz, Enrique M.

2011-01-01

The actin regulatory protein, cofilin, increases the bending and twisting elasticity of actin filaments and severs them. It has been proposed that filaments partially decorated with cofilin accumulate stress from thermally driven shape fluctuations at bare (stiff) and decorated (compliant) boundaries, thereby promoting severing. This mechanics-based severing model predicts that changes in actin filament compliance due to cofilin binding affect severing activity. Here, we test this prediction by evaluating how the severing activities of vertebrate and yeast cofilactin scale with the flexural rigidities determined from analysis of shape fluctuations. Yeast actin filaments are more compliant in bending than vertebrate actin filaments. Severing activities of cofilactin isoforms correlate with changes in filament flexibility. Vertebrate cofilin binds but does not increase the yeast actin filament flexibility, and does not sever them. Imaging of filament thermal fluctuations reveals that severing events are associated with local bending and fragmentation when deformations attain a critical angle. The critical severing angle at boundaries between bare and cofilin-decorated segments is smaller than in bare or fully decorated filaments. These measurements support a cofilin-severing mechanism in which mechanical asymmetry promotes local stress accumulation and fragmentation at boundaries of bare and cofilin-decorated segments, analogous to failure of some nonprotein materials. PMID:21723825

The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains

PubMed Central

Münz, Márton; Hein, Jotun; Biggin, Philip C.

2012-01-01

In molecular recognition, it is often the case that ligand binding is coupled to conformational change in one or both of the binding partners. Two hypotheses describe the limiting cases involved; the first is the induced fit and the second is the conformational selection model. The conformational selection model requires that the protein adopts conformations that are similar to the ligand-bound conformation in the absence of ligand, whilst the induced-fit model predicts that the ligand-bound conformation of the protein is only accessible when the ligand is actually bound. The flexibility of the apo protein clearly plays a major role in these interpretations. For many proteins involved in signaling pathways there is the added complication that they are often promiscuous in that they are capable of binding to different ligand partners. The relationship between protein flexibility and promiscuity is an area of active research and is perhaps best exemplified by the PDZ domain family of proteins. In this study we use molecular dynamics simulations to examine the relationship between flexibility and promiscuity in five PDZ domains: the human Dvl2 (Dishevelled-2) PDZ domain, the human Erbin PDZ domain, the PDZ1 domain of InaD (inactivation no after-potential D protein) from fruit fly, the PDZ7 domain of GRIP1 (glutamate receptor interacting protein 1) from rat and the PDZ2 domain of PTP-BL (protein tyrosine phosphatase) from mouse. We show that despite their high structural similarity, the PDZ binding sites have significantly different dynamics. Importantly, the degree of binding pocket flexibility was found to be closely related to the various characteristics of peptide binding specificity and promiscuity of the five PDZ domains. Our findings suggest that the intrinsic motions of the apo structures play a key role in distinguishing functional properties of different PDZ domains and allow us to make predictions that can be experimentally tested. PMID:23133356

Building flexible real-time systems using the Flex language

NASA Technical Reports Server (NTRS)

Kenny, Kevin B.; Lin, Kwei-Jay

1991-01-01

The design and implementation of a real-time programming language called Flex, which is a derivative of C++, are presented. It is shown how different types of timing requirements might be expressed and enforced in Flex, how they might be fulfilled in a flexible way using different program models, and how the programming environment can help in making binding and scheduling decisions. The timing constraint primitives in Flex are easy to use yet powerful enough to define both independent and relative timing constraints. Program models like imprecise computation and performance polymorphism can carry out flexible real-time programs. In addition, programmers can use a performance measurement tool that produces statistically correct timing models to predict the expected execution time of a program and to help make binding decisions. A real-time programming environment is also presented.

Dense granular flow around a rigid or flexible intruder

NASA Astrophysics Data System (ADS)

Kolb, Evelyne; Adda-Bedia, Mokhtar

2012-02-01

We experimentally studied the flow of a dense granular material around an obstacle (rigid cylinder or flexible plate) placed in a 2 dimensional confined cell at a packing fraction near the 2D jamming threshold. In the case of the rigid obstacle, the displacement field of grains as well as the drag force experienced by the obstacle were simultaneously recorded and a parametric study was done by changing the cell size, the intruder diameter or the packing fraction. The drag force experienced by the intruder and the formation of a wake behind the obstacle were very sensitive to the approach to jamming. The same experimental set-up was adapted to a flexible intruder and coupling between the granular flow and fibre deflexion were imaged. The deformation of the fibre could be compared with theoretical predictions from elastica.

Information Technology.

ERIC Educational Resources Information Center

Reynolds, Roger

1983-01-01

Describes important information-handling products, predicting future devices in light of convergence and greater flexibility offered through use of microchip technology. Contends that information technology and its impact of privacy depends on how information systems are used, arguing that the privacy issue deals more with moral/physiological…

Incorporating operational flexibility into electric generation planning Impacts and methods for system design and policy analysis

NASA Astrophysics Data System (ADS)

Palmintier, Bryan S.

This dissertation demonstrates how flexibility in hourly electricity operations can impact long-term planning and analysis for future power systems, particularly those with substantial variable renewables (e.g., wind) or strict carbon policies. Operational flexibility describes a power system's ability to respond to predictable and unexpected changes in generation or demand. Planning and policy models have traditionally not directly captured the technical operating constraints that determine operational flexibility. However, as demonstrated in this dissertation, this capability becomes increasingly important with the greater flexibility required by significant renewables (>= 20%) and the decreased flexibility inherent in some low-carbon generation technologies. Incorporating flexibility can significantly change optimal generation and energy mixes, lower system costs, improve policy impact estimates, and enable system designs capable of meeting strict regulatory targets. Methodologically, this work presents a new clustered formulation that tractably combines a range of normally distinct power system models, from hourly unit-commitment operations to long-term generation planning. This formulation groups similar generators into clusters to reduce problem size, while still retaining the individual unit constraints required to accurately capture operating reserves and other flexibility drivers. In comparisons against traditional unit commitment formulations, errors were generally less than 1% while run times decreased by several orders of magnitude (e.g., 5000x). Extensive numerical simulations, using a realistic Texas-based power system show that ignoring flexibility can underestimate carbon emissions by 50% or result in significant load and wind shedding to meet environmental regulations. Contributions of this dissertation include: 1. Demonstrating that operational flexibility can have an important impact on power system planning, and describing when and how these impacts occur; 2. Demonstrating that a failure to account for operational flexibility can result in undesirable outcomes for both utility planners and policy analysts; and 3. Extending the state of the art for electric power system models by introducing a tractable method for incorporating unit commitment based operational flexibility at full 876o hourly resolution directly into planning optimization. Together these results encourage and offer a new flexibility-aware approach for capacity planning and accompanying policy design that can enable cleaner, less expensive electric power systems for the future. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

Architecture of cognitive flexibility revealed by lesion mapping

PubMed Central

Barbey, Aron K.; Colom, Roberto; Grafman, Jordan

2013-01-01

Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism–Extraversion–Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R2 = 0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

Immortality of cancers

PubMed Central

Duesberg, Peter; McCormack, Amanda

2013-01-01

Immortality is a common characteristic of cancers, but its origin and purpose are still unclear. Here we advance a karyotypic theory of immortality based on the theory that carcinogenesis is a form of speciation. Accordingly, cancers are generated from normal cells by random karyotypic rearrangements and selection for cancer-specific reproductive autonomy. Since such rearrangements unbalance long-established mitosis genes, cancer karyotypes vary spontaneously but are stabilized perpetually by clonal selections for autonomy. To test this theory we have analyzed neoplastic clones, presumably immortalized by transfection with overexpressed telomerase or with SV40 tumor virus, for the predicted clonal yet flexible karyotypes. The following results were obtained: (1) All immortal tumorigenic lines from cells transfected with overexpressed telomerase had clonal and flexible karyotypes; (2) Searching for the origin of such karyotypes, we found spontaneously increasing, random aneuploidy in human fibroblasts early after transfection with overexpressed telomerase; (3) Late after transfection, new immortal tumorigenic clones with new clonal and flexible karyotypes were found; (4) Testing immortality of one clone during 848 unselected generations showed the chromosome number was stable, but the copy numbers of 36% of chromosomes drifted ± 1; (5) Independent immortal tumorigenic clones with individual, flexible karyotypes arose after individual latencies; (6) Immortal tumorigenic clones with new flexible karyotypes also arose late from cells of a telomerase-deficient mouse rendered aneuploid by SV40 virus. Because immortality and tumorigenicity: (1) correlated exactly with individual clonal but flexible karyotypes; (2) originated simultaneously with such karyotypes; and (3) arose in the absence of telomerase, we conclude that clonal and flexible karyotypes generate the immortality of cancers. PMID:23388461

The stability of a flexible cantilever in viscous channel flow

NASA Astrophysics Data System (ADS)

Cisonni, Julien; Lucey, Anthony D.; Elliott, Novak S. J.; Heil, Matthias

2017-05-01

Most studies of the flow-induced flutter instability of a flexible cantilever have assumed inviscid flow because of the high flow speeds and the large scale of the structures encountered in the wide range of applications of this fluid-structure interaction (FSI) system. However, for instance, in the fields of energy harvesting and biomechanics, low flow speeds and small- and micro-scale systems can give relatively low Reynolds numbers so that fluid viscosity needs to be explicitly accounted for to provide reliable predictions of channel-immersed-cantilever stability. In this study, we employ a numerical model coupling the Navier-Stokes equations and a one-dimensional elastic beam model. We conduct a parametric investigation to determine the conditions leading to flutter instability of a slender flexible cantilever immersed in two-dimensional viscous channel flow for Reynolds numbers lower than 1000. The large set of numerical simulations carried out allows predictions of the influence of decreasing Reynolds numbers and of the cantilever confinement on the single-mode neutral stability of the FSI system and on the pre- and post-critical cantilever motion. This model's predictions are also compared to those of a FSI model containing a two-dimensional solid model in order to assess, primarily, the effect of the cantilever slenderness in the simulations. Results show that an increasing contribution of viscosity to the hydrodynamic forces significantly alters the instability boundaries. In general, a decrease in Reynolds number is predicted to produce a stabilisation of the FSI system, which is more pronounced for high fluid-to-solid mass ratios. For particular fluid-to-solid mass ratios, viscous effects can lower the critical velocity and lead to a change in the first unstable structural mode. However, at constant Reynolds number, the effects of viscosity on the system stability are diminished by the confinement of the cantilever, which strengthens the importance of flow inertia.

A new flexible plug and play scheme for modeling, simulating, and predicting gastric emptying

PubMed Central

2014-01-01

Background In-silico models that attempt to capture and describe the physiological behavior of biological organisms, including humans, are intrinsically complex and time consuming to build and simulate in a computing environment. The level of detail of description incorporated in the model depends on the knowledge of the system’s behavior at that level. This knowledge is gathered from the literature and/or improved by knowledge obtained from new experiments. Thus model development is an iterative developmental procedure. The objective of this paper is to describe a new plug and play scheme that offers increased flexibility and ease-of-use for modeling and simulating physiological behavior of biological organisms. Methods This scheme requires the modeler (user) first to supply the structure of the interacting components and experimental data in a tabular format. The behavior of the components described in a mathematical form, also provided by the modeler, is externally linked during simulation. The advantage of the plug and play scheme for modeling is that it requires less programming effort and can be quickly adapted to newer modeling requirements while also paving the way for dynamic model building. Results As an illustration, the paper models the dynamics of gastric emptying behavior experienced by humans. The flexibility to adapt the model to predict the gastric emptying behavior under varying types of nutrient infusion in the intestine (ileum) is demonstrated. The predictions were verified with a human intervention study. The error in predicting the half emptying time was found to be less than 6%. Conclusions A new plug-and-play scheme for biological systems modeling was developed that allows changes to the modeled structure and behavior with reduced programming effort, by abstracting the biological system into a network of smaller sub-systems with independent behavior. In the new scheme, the modeling and simulation becomes an automatic machine readable and executable task. PMID:24917054

Flexible parametric survival models built on age-specific antimüllerian hormone percentiles are better predictors of menopause.

PubMed

Ramezani Tehrani, Fahimeh; Mansournia, Mohammad Ali; Solaymani-Dodaran, Masoud; Steyerberg, Ewout; Azizi, Fereidoun

2016-06-01

This study aimed to improve existing prediction models for age at menopause. We identified all reproductive aged women with regular menstrual cycles who met our eligibility criteria (n = 1,015) in the Tehran Lipid and Glucose Study-an ongoing population-based cohort study initiated in 1998. Participants were examined every 3 years and their reproductive histories were recorded. Blood levels of antimüllerian hormone (AMH) were measured at the time of recruitment. Age at menopause was estimated based on serum concentrations of AMH using flexible parametric survival models. The optimum model was selected according to Akaike Information Criteria and the realness of the range of predicted median menopause age. We followed study participants for a median of 9.8 years during which 277 women reached menopause and found that a spline-based proportional odds model including age-specific AMH percentiles as the covariate performed well in terms of statistical criteria and provided the most clinically relevant and realistic predictions. The range of predicted median age at menopause for this model was 47.1 to 55.9 years. For those who reached menopause, the median of the absolute mean difference between actual and predicted age at menopause was 1.9 years (interquartile range 2.9). The model including the age-specific AMH percentiles as the covariate and using proportional odds as its covariate metrics meets all the statistical criteria for the best model and provides the most clinically relevant and realistic predictions for age at menopause for reproductive-aged women.

Relations among conceptual knowledge, procedural knowledge, and procedural flexibility in two samples differing in prior knowledge.

PubMed

Schneider, Michael; Rittle-Johnson, Bethany; Star, Jon R

2011-11-01

Competence in many domains rests on children developing conceptual and procedural knowledge, as well as procedural flexibility. However, research on the developmental relations between these different types of knowledge has yielded unclear results, in part because little attention has been paid to the validity of the measures or to the effects of prior knowledge on the relations. To overcome these problems, we modeled the three constructs in the domain of equation solving as latent factors and tested (a) whether the predictive relations between conceptual and procedural knowledge were bidirectional, (b) whether these interrelations were moderated by prior knowledge, and (c) how both constructs contributed to procedural flexibility. We analyzed data from 2 measurement points each from two samples (Ns = 228 and 304) of middle school students who differed in prior knowledge. Conceptual and procedural knowledge had stable bidirectional relations that were not moderated by prior knowledge. Both kinds of knowledge contributed independently to procedural flexibility. The results demonstrate how changes in complex knowledge structures contribute to competence development.

Aspects of workplace flexibility and mothers' satisfaction with their husbands' contributions to household labor.

PubMed

Alger, Vanessa M; Crowley, Jocelyn Elise

2012-01-01

This article explores whether mothers’ perceived control over their own workplace flexibility options has any relationship to their satisfaction with their husbands’ contributions to household labor in the United States. We hypothesize that flexibility enhances their ability to more adeptly engage in role management in multiple life areas, thus enabling them to be more satisfied with their partners’ domestic input as well. We use a unique data set of 1,078 randomly sampled women involved in mothers’ organizations that generally attract members based on their current level of participation in the paid labor market. We then link nine distinct workplace flexibility policies with mothers’ satisfaction related to their husbands’ participation in all household tasks, as well as a subset of female-typed tasks. We find that across both arrays of tasks, mothers with more perceived control over work-related schedule predictability and those that had the ability to secure employment again after an extended break had higher levels of satisfaction with their husbands’ participation in household labor. In addition, short-term time off to address unexpected needs was important for all tasks considered together only.

Dynamic analysis of horizontal axis wind turbine by thin-walled beam theory

NASA Astrophysics Data System (ADS)

Wang, Jianhong; Qin, Datong; Lim, Teik C.

2010-08-01

A mixed flexible-rigid multi-body mathematical model is applied to predict the dynamic performance of a wind turbine system. Since the tower and rotor are both flexible thin-walled structures, a consistent expression for their deformations is applied, which employs a successive series of transformations to locate any point on the blade and tower relative to an inertial coordinate system. The kinetic and potential energy terms of each flexible body and rigid body are derived for use in the Lagrange approach to formulate the wind turbine system's governing equation. The mode shapes are then obtained from the free vibration solution, while the distributions of dynamic stress and displacement of the tower and rotor are computed from the forced vibration response analysis. Using this dynamic model, the influence of the tower's stiffness on the blade tip deformation is studied. From the analysis, it is evident that the proposed model not only inherits the simplicity of the traditional 1-D beam element, but also able to provide detailed information about the tower and rotor response due to the incorporation of the flexible thin-walled beam theory.

Prediction of relative and absolute permeabilities for gas and water from soil water retention curves using a pore-scale network model

NASA Astrophysics Data System (ADS)

Fischer, Ulrich; Celia, Michael A.

1999-04-01

Functional relationships for unsaturated flow in soils, including those between capillary pressure, saturation, and relative permeabilities, are often described using analytical models based on the bundle-of-tubes concept. These models are often limited by, for example, inherent difficulties in prediction of absolute permeabilities, and in incorporation of a discontinuous nonwetting phase. To overcome these difficulties, an alternative approach may be formulated using pore-scale network models. In this approach, the pore space of the network model is adjusted to match retention data, and absolute and relative permeabilities are then calculated. A new approach that allows more general assignments of pore sizes within the network model provides for greater flexibility to match measured data. This additional flexibility is especially important for simultaneous modeling of main imbibition and drainage branches. Through comparisons between the network model results, analytical model results, and measured data for a variety of both undisturbed and repacked soils, the network model is seen to match capillary pressure-saturation data nearly as well as the analytical model, to predict water phase relative permeabilities equally well, and to predict gas phase relative permeabilities significantly better than the analytical model. The network model also provides very good estimates for intrinsic permeability and thus for absolute permeabilities. Both the network model and the analytical model lost accuracy in predicting relative water permeabilities for soils characterized by a van Genuchten exponent n≲3. Overall, the computational results indicate that reliable predictions of both relative and absolute permeabilities are obtained with the network model when the model matches the capillary pressure-saturation data well. The results also indicate that measured imbibition data are crucial to good predictions of the complete hysteresis loop.

Interindividual differences in cognitive flexibility: influence of gray matter volume, functional connectivity and trait impulsivity

PubMed Central

Langner, Robert; Cieslik, Edna C.; Rottschy, Claudia; Eickhoff, Simon B.

2016-01-01

Cognitive flexibility, a core aspect of executive functioning, is required for the speeded shifting between different tasks and sets. Using an interindividual differences approach, we examined whether cognitive flexibility, as assessed by the Delis–Kaplan card-sorting test, is associated with gray matter volume (GMV) and functional connectivity (FC) of regions of a core network of multiple cognitive demands as well as with different facets of trait impulsivity. The core multiple-demand network was derived from three large-scale neuroimaging meta-analyses and only included regions that showed consistent associations with sustained attention, working memory as well as inhibitory control. We tested to what extent self-reported impulsivity as well as GMV and resting-state FC in this core network predicted cognitive flexibility independently and incrementally. Our analyses revealed that card-sorting performance correlated positively with GMV of the right anterior insula, FC between bilateral anterior insula and midcingulate cortex/supplementary motor area as well as the impulsivity dimension “Premeditation.” Importantly, GMV, FC and impulsivity together accounted for more variance of card-sorting performance than every parameter alone. Our results therefore indicate that various factors contribute individually to cognitive flexibility, underlining the need to search across multiple modalities when aiming to unveil the mechanisms behind executive functioning. PMID:24878823

Study of Flexible Load Dispatch to Improve the Capacity of Wind Power Absorption

NASA Astrophysics Data System (ADS)

Yunlei, Yang; Shifeng, Zhang; Xiao, Chang; Da, Lei; Min, Zhang; Jinhao, Wang; Shengwen, Li; Huipeng, Li

2017-05-01

The dispatch method which track the trend of load demand by arranging the generation scheme of controllable hydro or thermal units faces great difficulties and challenges. With the increase of renewable energy sources such as wind power and photovoltaic power introduced to grid, system has to arrange much more spinning reserve units to compensate the unbalanced power. How to exploit the peak-shaving potential of flexible load which can be shifted with time or storage energy has become many scholars’ research direction. However, the modelling of different kinds of load and control strategy is considerably difficult, this paper choose the Air Conditioner with compressor which can storage energy in fact to study. The equivalent thermal parameters of Air Conditioner has been established. And with the use of “loop control” strategies, we can predict the regulated power of Air Conditioner. Then we established the Gen-Load optimal scheduling model including flexible load based on traditional optimal scheduling model. At last, an improved IEEE-30 case is used to verify. The result of simulation shows that flexible load can fast-track renewable power changes. More than that, with flexible load and reasonable incentive method to consumers, the operating cost of the system can be greatly cut down.

Protein flexibility in the light of structural alphabets

PubMed Central

Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

2015-01-01

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy.

PubMed

Therrien, Eric; Weill, Nathanael; Tomberg, Anna; Corbeil, Christopher R; Lee, Devin; Moitessier, Nicolas

2014-11-24

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.

Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin.

PubMed

Tripathi, Swarnendu; Portman, John J

2009-02-17

We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals "cracking" or local partial unfolding during the open/closed transition. This result is in harmony with the picture that cracking relieves local stresses caused by conformational deformations of a sufficiently rigid protein. We also compare the conformational transition in a recently studied even-odd paired fragment of CaM. Our results rationalize the different relative binding affinities of the EF-hands in the engineered fragment compared with the intact odd-even paired EF-hands (nCaM and cCaM) in terms of changes in flexibility along the transition route. Aside from elucidating general theoretical ideas about the cracking mechanism, these studies also emphasize how the remarkable intrinsic plasticity of CaM underlies conformational dynamics essential for its diverse functions.

Disaggregating census data for population mapping using random forests with remotely-sensed and ancillary data.

PubMed

Stevens, Forrest R; Gaughan, Andrea E; Linard, Catherine; Tatem, Andrew J

2015-01-01

High resolution, contemporary data on human population distributions are vital for measuring impacts of population growth, monitoring human-environment interactions and for planning and policy development. Many methods are used to disaggregate census data and predict population densities for finer scale, gridded population data sets. We present a new semi-automated dasymetric modeling approach that incorporates detailed census and ancillary data in a flexible, "Random Forest" estimation technique. We outline the combination of widely available, remotely-sensed and geospatial data that contribute to the modeled dasymetric weights and then use the Random Forest model to generate a gridded prediction of population density at ~100 m spatial resolution. This prediction layer is then used as the weighting surface to perform dasymetric redistribution of the census counts at a country level. As a case study we compare the new algorithm and its products for three countries (Vietnam, Cambodia, and Kenya) with other common gridded population data production methodologies. We discuss the advantages of the new method and increases over the accuracy and flexibility of those previous approaches. Finally, we outline how this algorithm will be extended to provide freely-available gridded population data sets for Africa, Asia and Latin America.

PREDICTING ER BINDING AFFINITY FOR EDC RANKING AND PRIORITIZATION: MODEL I

EPA Science Inventory

A Common Reactivity Pattern (COREPA) model, based on consideration of multiple energetically reasonable conformations of flexible chemicals was developed using a training set of 232 rat estrogen receptor (rER) relative binding affinity (RBA) measurements. The training set include...

Validation of TxDOT flexible pavement skid prediction model : project summary.

DOT National Transportation Integrated Search

2017-01-01

This study had two main objectives: : Investigate and examine surface and friction characteristics of 35 test sections of asphalt mixtures and 35 test sections of surface-treated roads in Texas. The test sections covered a wide range of mixtures ...

The novel appearance of low rectal anastomosis on contrast enema following laparoscopic anterior resection: discriminating anastomotic leaks from "dog-ears" on water-soluble contrast enema and flexible sigmoidoscopy.

PubMed

Katory, Mark; McLean, Ross; Osman, Khalid; Ahmad, Mukhtar; Hughes, Tracey; Newby, Mike; Dennison, Christopher; O'Loughlin, Paul

2017-02-01

Interpretation of water-soluble contrast enema following laparoscopic low anterior resection can be very challenging for both radiologists and colorectal surgeons. Discriminating the radiological appearances secondary to anastomotic configuration from those caused by actual anastomotic dehiscence is a common problem and may be made worse with the advent of laparoscopic surgery. The aim of this study is to identify potential novel appearances of the water-soluble contrast enema (WSCE) images of rectal anastomosis following laparoscopic low anterior resection to radiologists and surgeons. We enrolled 45 patients who underwent laparoscopic low anterior resection with proximal de-functioning loop ileostomy within a specialized colorectal unit. The water-soluble contrast enema reports were reviewed. Two blinded colorectal radiologists independently reviewed the images of patients suspected of anastomotic leak. All of these patients also underwent a flexible sigmoidoscopy to confirm or exclude anastomotic leak before reversal of loop ileostomy. Inter-observer concordance was calculated. Seven out of eighteen patients (38.9%) were found to have true anastomotic leaks on flexible sigmoidoscopy (15% overall leak rate). In the remaining eleven patients the image appearances were attributed to the appearance of the anastomotic 'dog-ear effect', created by the anastomotic configuration due to multiple firing of the intra-corporeal laparoscopic stapling device. Radiologist inter-observer concordance was 83%. Sensitivity was 100%, specificity 71%, positive-predictive value (38.9%) and negative-predictive value (100%). The novel appearances of laparoscopic-stapled rectal anastomoses in WSCE can be mistaken for anastomotic leak. To avoid delay in reversal of ileostomy, a flexible sigmoidoscopy can be used to confirm or exclude a leak.

Flexible Meta-Regression to Assess the Shape of the Benzene–Leukemia Exposure–Response Curve

PubMed Central

Vlaanderen, Jelle; Portengen, Lützen; Rothman, Nathaniel; Lan, Qing; Kromhout, Hans; Vermeulen, Roel

2010-01-01

Background Previous evaluations of the shape of the benzene–leukemia exposure–response curve (ERC) were based on a single set or on small sets of human occupational studies. Integrating evidence from all available studies that are of sufficient quality combined with flexible meta-regression models is likely to provide better insight into the functional relation between benzene exposure and risk of leukemia. Objectives We used natural splines in a flexible meta-regression method to assess the shape of the benzene–leukemia ERC. Methods We fitted meta-regression models to 30 aggregated risk estimates extracted from nine human observational studies and performed sensitivity analyses to assess the impact of a priori assessed study characteristics on the predicted ERC. Results The natural spline showed a supralinear shape at cumulative exposures less than 100 ppm-years, although this model fitted the data only marginally better than a linear model (p = 0.06). Stratification based on study design and jackknifing indicated that the cohort studies had a considerable impact on the shape of the ERC at high exposure levels (> 100 ppm-years) but that predicted risks for the low exposure range (< 50 ppm-years) were robust. Conclusions Although limited by the small number of studies and the large heterogeneity between studies, the inclusion of all studies of sufficient quality combined with a flexible meta-regression method provides the most comprehensive evaluation of the benzene–leukemia ERC to date. The natural spline based on all data indicates a significantly increased risk of leukemia [relative risk (RR) = 1.14; 95% confidence interval (CI), 1.04–1.26] at an exposure level as low as 10 ppm-years. PMID:20064779

Transport properties of carbon dioxide and methane from molecular dynamics simulations.

PubMed

Aimoli, C G; Maginn, E J; Abreu, C R A

2014-10-07

Transport properties of carbon dioxide and methane are predicted for temperatures between (273.15 and 573.15) K and pressures up to 800 MPa by molecular dynamics simulations. Viscosities and thermal conductivities were obtained through the Green-Kubo formalism, whereas the Einstein relation was used to provide self-diffusion coefficient estimates. The differences in property predictions due to the force field nature and parametrization were investigated by the comparison of seven different CO2 models (two single-site models, three rigid three-site models, and two fully flexible three-site models) and three different CH4 models (two single-site models and one fully flexible five-site model). The simulation results show good agreement with experimental data, except for thermal conductivities at low densities. The molecular structure and force field parameters play an important role in the accuracy of the simulations, which is within the experimental deviations reported for viscosities and self-diffusion coefficients considering the most accurate CO2 and CH4 models studied. On the other hand, the molecular flexibility does not seem to improve accuracy, since the explicit account of vibrational and bending degrees of freedom in the CO2 flexible models leads to slightly less accurate results. Nonetheless, the use of a correctional term to account for vibrational modes in rigid models generally improves estimations of thermal conductivity values. At extreme densities, the caging effect observed with single-site representations of the molecules restrains mobility and leads to an unphysical overestimation of viscosities and, conversely, to the underestimation of self-diffusion coefficients. This result may help to better understand the limits of applicability of such force fields concerning structural and transport properties of dense systems.

The effects of a flexible visual acuity-driven ranibizumab treatment regimen in age-related macular degeneration: outcomes of a drug and disease model.

PubMed

Holz, Frank G; Korobelnik, Jean-François; Lanzetta, Paolo; Mitchell, Paul; Schmidt-Erfurth, Ursula; Wolf, Sebastian; Markabi, Sabri; Schmidli, Heinz; Weichselberger, Andreas

2010-01-01

Differences in treatment responses to ranibizumab injections observed within trials involving monthly (MARINA and ANCHOR studies) and quarterly (PIER study) treatment suggest that an individualized treatment regimen may be effective in neovascular age-related macular degeneration. In the present study, a drug and disease model was used to evaluate the impact of an individualized, flexible treatment regimen on disease progression. For visual acuity (VA), a model was developed on the 12-month data from ANCHOR, MARINA, and PIER. Data from untreated patients were used to model patient-specific disease progression in terms of VA loss. Data from treated patients from the period after the three initial injections were used to model the effect of predicted ranibizumab vitreous concentration on VA loss. The model was checked by comparing simulations of VA outcomes after monthly and quarterly injections during this period with trial data. A flexible VA-guided regimen (after the three initial injections) in which treatment is initiated by loss of >5 letters from best previously observed VA scores was simulated. Simulated monthly and quarterly VA-guided regimens showed good agreement with trial data. Simulation of VA-driven individualized treatment suggests that this regimen, on average, sustains the initial gains in VA seen in clinical trials at month 3. The model predicted that, on average, to maintain initial VA gains, an estimated 5.1 ranibizumab injections are needed during the 9 months after the three initial monthly injections, which amounts to a total of 8.1 injections during the first year. A flexible, individualized VA-guided regimen after the three initial injections may sustain vision improvement with ranibizumab and could improve cost-effectiveness and convenience and reduce drug administration-associated risks.

Contingency-based emotional resilience: effort-based reward training and flexible coping lead to adaptive responses to uncertainty in male rats

PubMed Central

Lambert, Kelly G.; Hyer, Molly M.; Rzucidlo, Amanda A.; Bergeron, Timothy; Landis, Timothy; Bardi, Massimo

2014-01-01

Emotional resilience enhances an animal's ability to maintain physiological allostasis and adaptive responses in the midst of challenges ranging from cognitive uncertainty to chronic stress. In the current study, neurobiological factors related to strategic responses to uncertainty produced by prediction errors were investigated by initially profiling male rats as passive, active or flexible copers (n = 12 each group) and assigning to either a contingency-trained or non-contingency trained group. Animals were subsequently trained in a spatial learning task so that problem solving strategies in the final probe task, as well-various biomarkers of brain activation and plasticity in brain areas associated with cognition and emotional regulation, could be assessed. Additionally, fecal samples were collected to further determine markers of stress responsivity and emotional resilience. Results indicated that contingency-trained rats exhibited more adaptive responses in the probe trial (e.g., fewer interrupted grooming sequences and more targeted search strategies) than the noncontingent-trained rats; additionally, increased DHEA/CORT ratios were observed in the contingent-trained animals. Diminished activation of the habenula (i.e., fos-immunoreactivity) was correlated with resilience factors such as increased levels of DHEA metabolites during cognitive training. Of the three coping profiles, flexible copers exhibited enhanced neuroplasticity (i.e., increased dentate gyrus doublecortin-immunoreactivity) compared to the more consistently responding active and passive copers. Thus, in the current study, contingency training via effort-based reward (EBR) training, enhanced by a flexible coping style, provided neurobiological resilience and adaptive responses to prediction errors in the final probe trial. These findings have implications for psychiatric illnesses that are influenced by altered stress responses and decision-making abilities (e.g., depression). PMID:24808837

Contingency-based emotional resilience: effort-based reward training and flexible coping lead to adaptive responses to uncertainty in male rats.

PubMed

Lambert, Kelly G; Hyer, Molly M; Rzucidlo, Amanda A; Bergeron, Timothy; Landis, Timothy; Bardi, Massimo

2014-01-01

Emotional resilience enhances an animal's ability to maintain physiological allostasis and adaptive responses in the midst of challenges ranging from cognitive uncertainty to chronic stress. In the current study, neurobiological factors related to strategic responses to uncertainty produced by prediction errors were investigated by initially profiling male rats as passive, active or flexible copers (n = 12 each group) and assigning to either a contingency-trained or non-contingency trained group. Animals were subsequently trained in a spatial learning task so that problem solving strategies in the final probe task, as well-various biomarkers of brain activation and plasticity in brain areas associated with cognition and emotional regulation, could be assessed. Additionally, fecal samples were collected to further determine markers of stress responsivity and emotional resilience. Results indicated that contingency-trained rats exhibited more adaptive responses in the probe trial (e.g., fewer interrupted grooming sequences and more targeted search strategies) than the noncontingent-trained rats; additionally, increased DHEA/CORT ratios were observed in the contingent-trained animals. Diminished activation of the habenula (i.e., fos-immunoreactivity) was correlated with resilience factors such as increased levels of DHEA metabolites during cognitive training. Of the three coping profiles, flexible copers exhibited enhanced neuroplasticity (i.e., increased dentate gyrus doublecortin-immunoreactivity) compared to the more consistently responding active and passive copers. Thus, in the current study, contingency training via effort-based reward (EBR) training, enhanced by a flexible coping style, provided neurobiological resilience and adaptive responses to prediction errors in the final probe trial. These findings have implications for psychiatric illnesses that are influenced by altered stress responses and decision-making abilities (e.g., depression).

Individual differences in children's innovative problem-solving are not predicted by divergent thinking or executive functions

PubMed Central

2016-01-01

Recent studies of children's tool innovation have revealed that there is variation in children's success in middle-childhood. In two individual differences studies, we sought to identify personal characteristics that might predict success on an innovation task. In Study 1, we found that although measures of divergent thinking were related to each other they did not predict innovation success. In Study 2, we measured executive functioning including: inhibition, working memory, attentional flexibility and ill-structured problem-solving. None of these measures predicted innovation, but, innovation was predicted by children's performance on a receptive vocabulary scale that may function as a proxy for general intelligence. We did not find evidence that children's innovation was predicted by specific personal characteristics. PMID:26926280

Measurement of Residual Flexibility for Substructures Having Prominent Flexible Interfaces

NASA Technical Reports Server (NTRS)

Tinker, Michael L.; Bookout, Paul S.

1994-01-01

Verification of a dynamic model of a constrained structure requires a modal survey test of the physical structure and subsequent modification of the model to obtain the best agreement possible with test data. Constrained-boundary or fixed-base testing has historically been the most common approach for verifying constrained mathematical models, since the boundary conditions of the test article are designed to match the actual constraints in service. However, there are difficulties involved with fixed-base testing, in some cases making the approach impractical. It is not possible to conduct a truly fixed-base test due to coupling between the test article and the fixture. In addition, it is often difficult to accurately simulate the actual boundary constraints, and the cost of designing and constructing the fixture may be prohibitive. For use when fixed-base testing proves impractical or undesirable, alternate free-boundary test methods have been investigated, including the residual flexibility technique. The residual flexibility approach has been treated analytically in considerable detail and has had limited frequency response measurements for the method. This concern is well-justified for a number of reasons. First, residual flexibilities are very small numbers, typically on the order of 1.0E-6 in/lb for translational diagonal terms, and orders of magnitude smaller for off-diagonal values. This poses difficulty in obtaining accurate and noise-free measurements, especially for points removed from the excitation source. A second difficulty encountered in residual measurements lies in obtaining a clean residual function in the process of subtracting synthesized modal data from a measured response function. Inaccuracies occur since modes are not subtracted exactly, but only to the accuracy of the curve fits for each mode; these errors are compounded with increasing distance from the excitation point. In this paper, the residual flexibility method is applied to a simple structure in both test and analysis. Measured and predicted residual functions are compared, and regions of poor data in the measured curves are described. It is found that for accurate residual measurements, frequency response functions having prominent stiffness lines in the acceleration/force format are needed. The lack of such stiffness lines increases measurement errors. Interface drive point frequency respose functions for shuttle orbiter payloads exhibit dominant stiffness lines, making the residual test approach a good candidate for payload modal tests when constrained tests are inappropriate. Difficulties in extracting a residual flexibility value from noisy test data are discussed. It is shown that use of a weighted second order least-squares curve fit of the measured residual function allows identification of residual flexibility that compares very well with predictions for the simple structure. This approach also provides an estimate of second order residual mass effects.

How wing compliance drives the efficiency of self-propelled flapping flyers.

PubMed

Thiria, Benjamin; Godoy-Diana, Ramiro

2010-07-01

Wing flexibility governs the flying performance of flapping-wing flyers. Here, we use a self-propelled flapping-wing model mounted on a "merry go round" to investigate the effect of wing compliance on the propulsive efficiency of the system. Our measurements show that the elastic nature of the wings can lead not only to a substantial reduction in the consumed power, but also to an increment of the propulsive force. A scaling analysis using a flexible plate model for the wings points out that, for flapping flyers in air, the time-dependent shape of the elastic bending wing is governed by the wing inertia. Based on this prediction, we define the ratio of the inertial forces deforming the wing to the elastic restoring force that limits the deformation as the elastoinertial number N(ei). Our measurements with the self-propelled model confirm that it is the appropriate structural parameter to describe flapping flyers with flexible wings.

Persistent neuronal activity in human prefrontal cortex links perception and action

PubMed Central

Haller, Matar; Case, John; Crone, Nathan E.; Chang, Edward F.; King-Stephens, David; Laxer, Kenneth D.; Weber, Peter B.; Parvizi, Josef; Knight, Robert T.; Shestyuk, Avgusta Y.

2017-01-01

How do humans flexibly respond to changing environmental demands on a sub-second temporal scale? Extensive research has highlighted the key role of the prefrontal cortex in flexible decision-making and adaptive behavior, yet the core mechanisms that translate sensory information into behavior remain undefined. Utilizing direct human cortical recordings, we investigated the temporal and spatial evolution of neuronal activity, indexed by the broadband gamma signal, while sixteen participants performed a broad range of self-paced cognitive tasks. Here we describe a robust domain- and modality-independent pattern of persistent stimulus-to-response neural activation that encodes stimulus features and predicts motor output on a trial-by-trial basis with near-perfect accuracy. Observed across a distributed network of brain areas, this persistent neural activation is centered in the prefrontal cortex and is required for successful response implementation, providing a functional substrate for domain-general transformation of perception into action, critical for flexible behavior.

Expected Utility Distributions for Flexible, Contingent Execution

NASA Technical Reports Server (NTRS)

Bresina, John L.; Washington, Richard

2000-01-01

This paper presents a method for using expected utility distributions in the execution of flexible, contingent plans. A utility distribution maps the possible start times of an action to the expected utility of the plan suffix starting with that action. The contingent plan encodes a tree of possible courses of action and includes flexible temporal constraints and resource constraints. When execution reaches a branch point, the eligible option with the highest expected utility at that point in time is selected. The utility distributions make this selection sensitive to the runtime context, yet still efficient. Our approach uses predictions of action duration uncertainty as well as expectations of resource usage and availability to determine when an action can execute and with what probability. Execution windows and probabilities inevitably change as execution proceeds, but such changes do not invalidate the cached utility distributions, thus, dynamic updating of utility information is minimized.

Control of a flexible planar truss using proof mass actuators

NASA Technical Reports Server (NTRS)

Minas, Constantinos; Garcia, Ephrahim; Inman, Daniel J.

1989-01-01

A flexible structure was modeled and actively controlled by using a single space realizable linear proof mass actuator. The NASA/UVA/UB actuator was attached to a flexible planar truss structure at an optimal location and it was considered as both passive and active device. The placement of the actuator was specified by examining the eigenvalues of the modified model that included the actuator dynamics, and the frequency response functions of the modified system. The electronic stiffness of the actuator was specified, such that the proof mass actuator system was tuned to the fourth structural mode of the truss by using traditional vibration absorber design. The active control law was limited to velocity feedback by integrating of the signals of two accelerometers attached to the structure. The two lower modes of the closed-loop structure were placed further in the LHS of the complex plane. The theoretically predicted passive and active control law was experimentally verified.

Influence of charge and flexibility on smectic phase formation in filamentous virus suspensions

NASA Astrophysics Data System (ADS)

Purdy, Kirstin R.; Fraden, Seth

2007-07-01

We present experimental measurements of the cholesteric-smectic phase transition of suspensions of charged semiflexible rods as a function of rod flexibility and surface charge. The rod particles consist of the bacteriophage M13 and closely related mutants, which are structurally identical to M13, but vary either in contour length and therefore ratio of persistence length to contour length, or surface charge. Surface charge is altered in two ways; by changing solution pH and by comparing M13 with fd virus, a virus which differs from M13 only by the substitution of a single charged amino acid for a neutral one per viral coat protein. Phase diagrams are measured as a function of particle length, particle charge, and ionic strength. The experimental results are compared with existing theoretical predictions for the phase behavior of flexible rods and charged rods.

Spatially confined polymer chains: implications of chromatin fibre flexibility and peripheral anchoring on telomere telomere interaction

NASA Astrophysics Data System (ADS)

Gehlen, L. R.; Rosa, A.; Klenin, K.; Langowski, J.; Gasser, S. M.; Bystricky, K.

2006-04-01

We simulate the extension of spatially confined chromatin fibres modelled as polymer chains and examine the effect of the flexibility of the fibre and its degree of freedom. The developed formalism was used to analyse experimental data of telomere-telomere distances in living yeast cells in the absence of confining factors as identified by the proteins Sir4 and yKu70. Our analysis indicates that intrinsic properties of the chromatin fibre, in particular its elastic properties and flexibility, can influence the juxtaposition of the telomeric ends of chromosomes. However, measurements in intact yeast cells showed that the telomeres of chromosomes 3 and 6 come even closer together than the parameters of constraint imposed on the simulations would predict. This juxtaposition was specific to telomeres on one contiguous chromosome and overrode a tendency for separation that is imposed by anchoring.

Control of Flexible Structures (COFS) Flight Experiment Background and Description

NASA Technical Reports Server (NTRS)

Hanks, B. R.

1985-01-01

A fundamental problem in designing and delivering large space structures to orbit is to provide sufficient structural stiffness and static configuration precision to meet performance requirements. These requirements are directly related to control requirements and the degree of control system sophistication available to supplement the as-built structure. Background and rationale are presented for a research study in structures, structural dynamics, and controls using a relatively large, flexible beam as a focus. This experiment would address fundamental problems applicable to large, flexible space structures in general and would involve a combination of ground tests, flight behavior prediction, and instrumented orbital tests. Intended to be multidisciplinary but basic within each discipline, the experiment should provide improved understanding and confidence in making design trades between structural conservatism and control system sophistication for meeting static shape and dynamic response/stability requirements. Quantitative results should be obtained for use in improving the validity of ground tests for verifying flight performance analyses.

The role of anxiety and depression on acceptance and action, considering emotional schemas in diabetics of Birjand (Iran)

PubMed Central

Imani, Elham; Shahabizadeh, Fatemeh; Mahmoodirad, Alireza

2017-01-01

Background Diabetes is one of the most common noncommunicable diseases around the world that accompanies assorted psychiatric disorders including anxiety and depression due to being chronic. Objective The aim of this study was to evaluate the effect of anxiety and depression on acceptance and action, considering emotional schemas of diabetics referring to diabetes clinics of health centers in Birjand, Iran. Methods This study was conducted in 2016 and was a correlational study with a structural equation modeling approach. The statistical population of this study were all men and women with type 2 diabetes in Birjand, with an active health record in health centers of this county. To collect data, Depression, Anxiety, and Stress Scale (DASS-21), Acceptance and Action Questionnaire-II (AAQ-II) and Leahy Emotional Schema Scale (LESS) were employed. Using SPSS19 and LISREL, data were analyzed via multiple regression and modeling at p≤0.05. Results In general, 350 subjects entered the study, most of whom were between 50 and 60 years of age and of whom, (47.7%) were women. Results show that depression has had a negative contribution in predicting quality of life (p=0.0001). In addition, results demonstrated the negative relation of anxiety and depression in predicting no emotional avoidance (flexibility) (p=0.0001). Anxiety and rumination had a positive effect and emotional unawareness had a negative effect on predicting no emotional avoidance (p=0.0001). Conclusion Results of this study showed that by reducing adaptive emotional schemas, emotions reduce psychological flexibility and increase emotional avoidance. In addition, by increasing non-adaptive emotional schemas, it increases no flexibility and emotional avoidance that finally reduces quality of life as well as acceptance and action. PMID:29238497

Modeling Individual Patient Preferences for Colorectal Cancer Screening Based on Their Tolerance for Complications Risk.

PubMed

Taksler, Glen B; Perzynski, Adam T; Kattan, Michael W

2017-04-01

Recommendations for colorectal cancer screening encourage patients to choose among various screening methods based on individual preferences for benefits, risks, screening frequency, and discomfort. We devised a model to illustrate how individuals with varying tolerance for screening complications risk might decide on their preferred screening strategy. We developed a discrete-time Markov mathematical model that allowed hypothetical individuals to maximize expected lifetime utility by selecting screening method, start age, stop age, and frequency. Individuals could choose from stool-based testing every 1 to 3 years, flexible sigmoidoscopy every 1 to 20 years with annual stool-based testing, colonoscopy every 1 to 20 years, or no screening. We compared the life expectancy gained from the chosen strategy with the life expectancy available from a benchmark strategy of decennial colonoscopy. For an individual at average risk of colorectal cancer who was risk neutral with respect to screening complications (and therefore was willing to undergo screening if it would actuarially increase life expectancy), the model predicted that he or she would choose colonoscopy every 10 years, from age 53 to 73 years, consistent with national guidelines. For a similar individual who was moderately averse to screening complications risk (and therefore required a greater increase in life expectancy to accept potential risks of colonoscopy), the model predicted that he or she would prefer flexible sigmoidoscopy every 12 years with annual stool-based testing, with 93% of the life expectancy benefit of decennial colonoscopy. For an individual with higher risk aversion, the model predicted that he or she would prefer 2 lifetime flexible sigmoidoscopies, 20 years apart, with 70% of the life expectancy benefit of decennial colonoscopy. Mathematical models may formalize how individuals with different risk attitudes choose between various guideline-recommended colorectal cancer screening strategies.

Aerodynamics of a bio-inspired flexible flapping-wing micro air vehicle.

PubMed

Nakata, T; Liu, H; Tanaka, Y; Nishihashi, N; Wang, X; Sato, A

2011-12-01

MAVs (micro air vehicles) with a maximal dimension of 15 cm and nominal flight speeds of around 10 m s⁻¹, operate in a Reynolds number regime of 10⁵ or lower, in which most natural flyers including insects, bats and birds fly. Furthermore, due to their light weight and low flight speed, the MAVs' flight characteristics are substantially affected by environmental factors such as wind gust. Like natural flyers, the wing structures of MAVs are often flexible and tend to deform during flight. Consequently, the aero/fluid and structural dynamics of these flyers are closely linked to each other, making the entire flight vehicle difficult to analyze. We have recently developed a hummingbird-inspired, flapping flexible wing MAV with a weight of 2.4-3.0 g and a wingspan of 10-12 cm. In this study, we carry out an integrated study of the flexible wing aerodynamics of this flapping MAV by combining an in-house computational fluid dynamic (CFD) method and wind tunnel experiments. A CFD model that has a realistic wing planform and can mimic realistic flexible wing kinematics is established, which provides a quantitative prediction of unsteady aerodynamics of the four-winged MAV in terms of vortex and wake structures and their relationship with aerodynamic force generation. Wind tunnel experiments further confirm the effectiveness of the clap and fling mechanism employed in this bio-inspired MAV as well as the importance of the wing flexibility in designing small flapping-wing MAVs.

Experimentally determined stiffness and damping of an inherently compensated air squeeze-film damper

NASA Technical Reports Server (NTRS)

Cunningham, R. E.

1975-01-01

Values of damping and stiffness were determined experimentally for an externally pressurized, inherently compensated, compressible squeeze-film damper up to excitation frequencies of 36,000 cycles per minute. Experimental damping values were higher than theory predicted at low squeeze numbers and less than predicted at high squeeze numbers. Experimental values of air film stiffness were less than theory predicted at low squeeze numbers and much greater at higher squeeze numbers. Results also indicate sufficient damping to attenuate amplitudes and forces at the critical speed when using three dampers in the flexible support system of a small, lightweight turborotor.

Data governance in predictive toxicology: A review.

PubMed

Fu, Xin; Wojak, Anna; Neagu, Daniel; Ridley, Mick; Travis, Kim

2011-07-13

Due to recent advances in data storage and sharing for further data processing in predictive toxicology, there is an increasing need for flexible data representations, secure and consistent data curation and automated data quality checking. Toxicity prediction involves multidisciplinary data. There are hundreds of collections of chemical, biological and toxicological data that are widely dispersed, mostly in the open literature, professional research bodies and commercial companies. In order to better manage and make full use of such large amount of toxicity data, there is a trend to develop functionalities aiming towards data governance in predictive toxicology to formalise a set of processes to guarantee high data quality and better data management. In this paper, data quality mainly refers in a data storage sense (e.g. accuracy, completeness and integrity) and not in a toxicological sense (e.g. the quality of experimental results). This paper reviews seven widely used predictive toxicology data sources and applications, with a particular focus on their data governance aspects, including: data accuracy, data completeness, data integrity, metadata and its management, data availability and data authorisation. This review reveals the current problems (e.g. lack of systematic and standard measures of data quality) and desirable needs (e.g. better management and further use of captured metadata and the development of flexible multi-level user access authorisation schemas) of predictive toxicology data sources development. The analytical results will help to address a significant gap in toxicology data quality assessment and lead to the development of novel frameworks for predictive toxicology data and model governance. While the discussed public data sources are well developed, there nevertheless remain some gaps in the development of a data governance framework to support predictive toxicology. In this paper, data governance is identified as the new challenge in predictive toxicology, and a good use of it may provide a promising framework for developing high quality and easy accessible toxicity data repositories. This paper also identifies important research directions that require further investigation in this area.

Data governance in predictive toxicology: A review

PubMed Central

2011-01-01

Background Due to recent advances in data storage and sharing for further data processing in predictive toxicology, there is an increasing need for flexible data representations, secure and consistent data curation and automated data quality checking. Toxicity prediction involves multidisciplinary data. There are hundreds of collections of chemical, biological and toxicological data that are widely dispersed, mostly in the open literature, professional research bodies and commercial companies. In order to better manage and make full use of such large amount of toxicity data, there is a trend to develop functionalities aiming towards data governance in predictive toxicology to formalise a set of processes to guarantee high data quality and better data management. In this paper, data quality mainly refers in a data storage sense (e.g. accuracy, completeness and integrity) and not in a toxicological sense (e.g. the quality of experimental results). Results This paper reviews seven widely used predictive toxicology data sources and applications, with a particular focus on their data governance aspects, including: data accuracy, data completeness, data integrity, metadata and its management, data availability and data authorisation. This review reveals the current problems (e.g. lack of systematic and standard measures of data quality) and desirable needs (e.g. better management and further use of captured metadata and the development of flexible multi-level user access authorisation schemas) of predictive toxicology data sources development. The analytical results will help to address a significant gap in toxicology data quality assessment and lead to the development of novel frameworks for predictive toxicology data and model governance. Conclusions While the discussed public data sources are well developed, there nevertheless remain some gaps in the development of a data governance framework to support predictive toxicology. In this paper, data governance is identified as the new challenge in predictive toxicology, and a good use of it may provide a promising framework for developing high quality and easy accessible toxicity data repositories. This paper also identifies important research directions that require further investigation in this area. PMID:21752279

Molecular determinants of the interactions between proteins and ssDNA.

PubMed

Mishra, Garima; Levy, Yaakov

2015-04-21

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.

Static and free-vibrational response of semi-circular graphite-epoxy frames with thin-walled open sections

NASA Technical Reports Server (NTRS)

Collins, J. Scott; Johnson, Eric R.

1989-01-01

Experiments were conducted to measure the three-dimensional static and free vibrational response of two graphite-epoxy, thin-walled, open section frames. The frames are semi-circular with a radius of three feet, and one specimen has an I cross section and the other has a channel cross section. The flexibility influence coefficients were measured in static tests for loads applied at midspan with the ends of the specimens clamped. Natural frequencies and modes were determined from vibrational tests for free and clamped end conditions. The experimental data is used to evaluate a new finite element which was developed specifically for the analysis of curved, thin-walled structures. The formulation of the element is based on a Vlasov-type, thin-walled, curved beam theory. The predictions from the finite element program generally correlated well with the experimental data for the symmetric I-specimen. Discrepancies in some of the data were found to be due to flexibility in the clamped end conditions. With respect to the data for the channel specimen, the correlation was less satisfactory. The finite element analysis predicted the out-of-plane response of the channel specimen reasonably well, but large discrepancies occurred between the predicted in-plane response and the experimental data. The analysis predicted a much more compliant in-plane response than was observed in the experiments.

Target specific proteochemometric model development for BACE1 - protein flexibility and structural water are critical in virtual screening.

PubMed

Manoharan, Prabu; Chennoju, Kiranmai; Ghoshal, Nanda

2015-07-01

BACE1 is an attractive target in Alzheimer's disease (AD) treatment. A rational drug design effort for the inhibition of BACE1 is actively pursued by researchers in both academic and pharmaceutical industries. This continued effort led to the steady accumulation of BACE1 crystal structures, co-complexed with different classes of inhibitors. This wealth of information is used in this study to develop target specific proteochemometric models and these models are exploited for predicting the prospective BACE1 inhibitors. The models developed in this study have performed excellently in predicting the computationally generated poses, separately obtained from single and ensemble docking approaches. The simple protein-ligand contact (SPLC) model outperforms other sophisticated high end models, in virtual screening performance, developed during this study. In an attempt to account for BACE1 protein active site flexibility information in predictive models, we included the change in the area of solvent accessible surface and the change in the volume of solvent accessible surface in our models. The ensemble and single receptor docking results obtained from this study indicate that the structural water mediated interactions improve the virtual screening results. Also, these waters are essential for recapitulating bioactive conformation during docking study. The proteochemometric models developed in this study can be used for the prediction of BACE1 inhibitors, during the early stage of AD drug discovery.

FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

PubMed

Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

2003-07-01

We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.

Design of overlays for flexible pavements based on AASHTO road test data.

DOT National Transportation Integrated Search

1978-01-01

The need for a suitable method of designing the thickness of overlays and predicting the performance of the overlaid pavement has recently been recognized. The AASHTO Road Tests included studies on 99 overlays, but they failed to produce conclusive r...

Impressions about Communication Styles and Competence in Nursing Relationships.

ERIC Educational Resources Information Center

Honeycutt, James M.; Worobey, Jacqueline Lowe

1987-01-01

Indicates that viewing oneself as a friendly and flexible communicator predicts an effective communicator across nursing relationships. Provides evidence for ascribing importance of communication skills depending on work relationship. Concludes that listening is the most important skill in relationships while managing conflict with hospital…

Community Colleges Put Their Best Faces Forward for Students of Tomorrow.

ERIC Educational Resources Information Center

Aslanian, Carol B.

1998-01-01

Suggests a positive future for community colleges as the educational needs of high school students, business organizations, graduate students, and diverse others stimulate enrollment. Predicts high demand for community colleges for reasons including convenience, quality of instruction, and flexibility in scheduling. (VWC)

Structure and Sequence Search on Aptamer-Protein Docking

NASA Astrophysics Data System (ADS)

Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

2015-03-01

Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

Criterion and incremental validity of the emotion regulation questionnaire

PubMed Central

Ioannidis, Christos A.; Siegling, A. B.

2015-01-01

Although research on emotion regulation (ER) is developing, little attention has been paid to the predictive power of ER strategies beyond established constructs. The present study examined the incremental validity of the Emotion Regulation Questionnaire (ERQ; Gross and John, 2003), which measures cognitive reappraisal and expressive suppression, over and above the Big Five personality factors. It also extended the evidence for the measure's criterion validity to yet unexamined criteria. A university student sample (N = 203) completed the ERQ, a measure of the Big Five, and relevant cognitive and emotion-laden criteria. Cognitive reappraisal predicted positive affect beyond personality, as well as experiential flexibility and constructive self-assertion beyond personality and affect. Expressive suppression explained incremental variance in negative affect beyond personality and in experiential flexibility beyond personality and general affect. No incremental effects were found for worry, social anxiety, rumination, reflection, and preventing negative emotions. Implications for the construct validity and utility of the ERQ are discussed. PMID:25814967

Structural Dynamics of Electronic Systems

NASA Astrophysics Data System (ADS)

Suhir, E.

2013-03-01

The published work on analytical ("mathematical") and computer-aided, primarily finite-element-analysis (FEA) based, predictive modeling of the dynamic response of electronic systems to shocks and vibrations is reviewed. While understanding the physics of and the ability to predict the response of an electronic structure to dynamic loading has been always of significant importance in military, avionic, aeronautic, automotive and maritime electronics, during the last decade this problem has become especially important also in commercial, and, particularly, in portable electronics in connection with accelerated testing of various surface mount technology (SMT) systems on the board level. The emphasis of the review is on the nonlinear shock-excited vibrations of flexible printed circuit boards (PCBs) experiencing shock loading applied to their support contours during drop tests. At the end of the review we provide, as a suitable and useful illustration, the exact solution to a highly nonlinear problem of the dynamic response of a "flexible-and-heavy" PCB to an impact load applied to its support contour during drop testing.

Development of hypersonic engine seals: Flow effects of preload and engine pressures

NASA Technical Reports Server (NTRS)

Cai, Zhong; Mutharasan, Rajakkannu; Ko, Frank K.; Steinetz, Bruce M.

1993-01-01

A new type of engine seal is being developed to meet the needs of advanced hypersonic engines. A seal braided of emerging high temperature ceramic fibers comprised of a sheath-core construction was selected for study based on its low leakage rates. Flexible, low-leakage, high temperature seals are required to seal the movable engine panels of advanced ramjet-scramjet engines either preventing potentially dangerous leakage into backside engine cavities or limiting the purge coolant flow rates through the seals. To predict the leakage through these flexible, porous seal structures as a function of preload and engine pressures, new analytical flow models are required. An empirical leakage resistance/preload model is proposed to characterize the observed decrease in leakage with increasing preload. Empirically determined compression modulus and preload factor are used to correlate experimental leakage data for a wide range of seal architectures. Good agreement between measured and predicted values are observed over a range of engine pressures and seal preloads.

Bayesian Approach for Flexible Modeling of Semicompeting Risks Data

PubMed Central

Han, Baoguang; Yu, Menggang; Dignam, James J.; Rathouz, Paul J.

2016-01-01

Summary Semicompeting risks data arise when two types of events, non-terminal and terminal, are observed. When the terminal event occurs first, it censors the non-terminal event, but not vice versa. To account for possible dependent censoring of the non-terminal event by the terminal event and to improve prediction of the terminal event using the non-terminal event information, it is crucial to model their association properly. Motivated by a breast cancer clinical trial data analysis, we extend the well-known illness-death models to allow flexible random effects to capture heterogeneous association structures in the data. Our extension also represents a generalization of the popular shared frailty models that usually assume that the non-terminal event does not affect the hazards of the terminal event beyond a frailty term. We propose a unified Bayesian modeling approach that can utilize existing software packages for both model fitting and individual specific event prediction. The approach is demonstrated via both simulation studies and a breast cancer data set analysis. PMID:25274445

More Than the Sum of Its Parts: A Role for the Hippocampus in Configural Reinforcement Learning.

PubMed

Duncan, Katherine; Doll, Bradley B; Daw, Nathaniel D; Shohamy, Daphna

2018-05-02

People often perceive configurations rather than the elements they comprise, a bias that may emerge because configurations often predict outcomes. But how does the brain learn to associate configurations with outcomes and how does this learning differ from learning about individual elements? We combined behavior, reinforcement learning models, and functional imaging to understand how people learn to associate configurations of cues with outcomes. We found that configural learning depended on the relative predictive strength of elements versus configurations and was related to both the strength of BOLD activity and patterns of BOLD activity in the hippocampus. Configural learning was further related to functional connectivity between the hippocampus and nucleus accumbens. Moreover, configural learning was associated with flexible knowledge about associations and differential eye movements during choice. Together, this suggests that configural learning is associated with a distinct computational, cognitive, and neural profile that is well suited to support flexible and adaptive behavior. Copyright © 2018 Elsevier Inc. All rights reserved.

Acquiring and Producing Sentences: Whether Learners Use Verb-Specific or Verb-General Information Depends on Cue Validity

PubMed Central

Thothathiri, Malathi; Rattinger, Michelle G.

2016-01-01

Learning to produce sentences involves learning patterns that enable the generation of new utterances. Language contains both verb-specific and verb-general regularities that are relevant to this capacity. Previous research has focused on whether one source is more important than the other. We tested whether the production system can flexibly learn to use either source, depending on the predictive validity of different cues in the input. Participants learned new sentence structures in a miniature language paradigm. In three experiments, we manipulated whether individual verbs or verb-general mappings better predicted the structures heard during learning. Evaluation of participants’ subsequent production revealed that they could use either the structural preferences of individual verbs or abstract meaning-to-form mappings to construct new sentences. Further, this choice varied according to cue validity. These results demonstrate flexibility within the production architecture and the importance of considering how language was learned when discussing how language is used. PMID:27047428

Docking and scoring with ICM: the benchmarking results and strategies for improvement

PubMed Central

Neves, Marco A. C.; Totrov, Maxim; Abagyan, Ruben

2012-01-01

Flexible docking and scoring using the Internal Coordinate Mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91% and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC= 82.2 and ROC(2%)= 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target. PMID:22569591

Invigoration of reward-seeking by cue and proximity encoding in the nucleus accumbens

PubMed Central

McGinty, Vincent B.; Lardeux, Sylvie; Taha, Sharif A.; Kim, James J.; Nicola, Saleem M.

2014-01-01

Summary A key function of the nucleus accumbens is to promote vigorous reward-seeking, but the corresponding neural mechanism has not been identified despite many years of research. Here we study cued flexible approach behavior, a form of reward-seeking that strongly depends on the accumbens, and we describe a robust, single-cell neural correlate of behavioral vigor in the excitatory response of accumbens neurons to reward-predictive cues. Well before locomotion begins, this cue-evoked excitation predicts both the movement initiation latency and speed of subsequent flexible approach responses, but not of stereotyped, inflexible responses. Moreover, the excitation simultaneously signals the subject’s proximity to the approach target, a signal that appears to mediate greater response vigor on trials that begin with the subject closer to the target. These results demonstrate a neural mechanism for response invigoration whereby accumbens neuronal encoding of reward availability and target proximity together drive the onset and speed of reward-seeking locomotion. PMID:23764290

Structural response of a rotating bladed disk to rotor whirl

NASA Technical Reports Server (NTRS)

Crawley, E. F.

1985-01-01

A set of high speed rotating whirl experiments were performed in the vacuum of the MIT Blowdown Compressor Facility on the MIT Aeroelastic Rotor, which is structurally typical of a modern high bypass ratio turbofan stage. These tests identified the natural frequencies of whirl of the rotor system by forcing its response using an electromagnetic shaker whirl excitation system. The excitation was slowly swept in frequency at constant amplitude for several constant rotor speeds in both a forward and backward whirl direction. The natural frequencies of whirl determined by these experiments were compared to those predicted by an analytical 6 DOF model of a flexible blade-rigid disk-flexible shaft rotor. The model is also presented in terms of nondimensional parameters in order to assess the importance of the interation between the bladed disk dynamics and the shaft-disk dynamics. The correlation between the experimental and predicted natural frequencies is reasonable, given the uncertainty involved in determining the stiffness parameters of the system.

Metal oxide semiconductor thin-film transistors for flexible electronics

NASA Astrophysics Data System (ADS)

Petti, Luisa; Münzenrieder, Niko; Vogt, Christian; Faber, Hendrik; Büthe, Lars; Cantarella, Giuseppe; Bottacchi, Francesca; Anthopoulos, Thomas D.; Tröster, Gerhard

2016-06-01

The field of flexible electronics has rapidly expanded over the last decades, pioneering novel applications, such as wearable and textile integrated devices, seamless and embedded patch-like systems, soft electronic skins, as well as imperceptible and transient implants. The possibility to revolutionize our daily life with such disruptive appliances has fueled the quest for electronic devices which yield good electrical and mechanical performance and are at the same time light-weight, transparent, conformable, stretchable, and even biodegradable. Flexible metal oxide semiconductor thin-film transistors (TFTs) can fulfill all these requirements and are therefore considered the most promising technology for tomorrow's electronics. This review reflects the establishment of flexible metal oxide semiconductor TFTs, from the development of single devices, large-area circuits, up to entirely integrated systems. First, an introduction on metal oxide semiconductor TFTs is given, where the history of the field is revisited, the TFT configurations and operating principles are presented, and the main issues and technological challenges faced in the area are analyzed. Then, the recent advances achieved for flexible n-type metal oxide semiconductor TFTs manufactured by physical vapor deposition methods and solution-processing techniques are summarized. In particular, the ability of flexible metal oxide semiconductor TFTs to combine low temperature fabrication, high carrier mobility, large frequency operation, extreme mechanical bendability, together with transparency, conformability, stretchability, and water dissolubility is shown. Afterward, a detailed analysis of the most promising metal oxide semiconducting materials developed to realize the state-of-the-art flexible p-type TFTs is given. Next, the recent progresses obtained for flexible metal oxide semiconductor-based electronic circuits, realized with both unipolar and complementary technology, are reported. In particular, the realization of large-area digital circuitry like flexible near field communication tags and analog integrated circuits such as bendable operational amplifiers is presented. The last topic of this review is devoted for emerging flexible electronic systems, from foldable displays, power transmission elements to integrated systems for large-area sensing and data storage and transmission. Finally, the conclusions are drawn and an outlook over the field with a prediction for the future is provided.

Metal oxide semiconductor thin-film transistors for flexible electronics

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

Petti, Luisa; Vogt, Christian; Büthe, Lars

The field of flexible electronics has rapidly expanded over the last decades, pioneering novel applications, such as wearable and textile integrated devices, seamless and embedded patch-like systems, soft electronic skins, as well as imperceptible and transient implants. The possibility to revolutionize our daily life with such disruptive appliances has fueled the quest for electronic devices which yield good electrical and mechanical performance and are at the same time light-weight, transparent, conformable, stretchable, and even biodegradable. Flexible metal oxide semiconductor thin-film transistors (TFTs) can fulfill all these requirements and are therefore considered the most promising technology for tomorrow's electronics. This reviewmore » reflects the establishment of flexible metal oxide semiconductor TFTs, from the development of single devices, large-area circuits, up to entirely integrated systems. First, an introduction on metal oxide semiconductor TFTs is given, where the history of the field is revisited, the TFT configurations and operating principles are presented, and the main issues and technological challenges faced in the area are analyzed. Then, the recent advances achieved for flexible n-type metal oxide semiconductor TFTs manufactured by physical vapor deposition methods and solution-processing techniques are summarized. In particular, the ability of flexible metal oxide semiconductor TFTs to combine low temperature fabrication, high carrier mobility, large frequency operation, extreme mechanical bendability, together with transparency, conformability, stretchability, and water dissolubility is shown. Afterward, a detailed analysis of the most promising metal oxide semiconducting materials developed to realize the state-of-the-art flexible p-type TFTs is given. Next, the recent progresses obtained for flexible metal oxide semiconductor-based electronic circuits, realized with both unipolar and complementary technology, are reported. In particular, the realization of large-area digital circuitry like flexible near field communication tags and analog integrated circuits such as bendable operational amplifiers is presented. The last topic of this review is devoted for emerging flexible electronic systems, from foldable displays, power transmission elements to integrated systems for large-area sensing and data storage and transmission. Finally, the conclusions are drawn and an outlook over the field with a prediction for the future is provided.« less

Visual arts training is linked to flexible attention to local and global levels of visual stimuli.

PubMed

Chamberlain, Rebecca; Wagemans, Johan

2015-10-01

Observational drawing skill has been shown to be associated with the ability to focus on local visual details. It is unclear whether superior performance in local processing is indicative of the ability to attend to, and flexibly switch between, local and global levels of visual stimuli. It is also unknown whether these attentional enhancements remain specific to observational drawing skill or are a product of a wide range of artistic activities. The current study aimed to address these questions by testing if flexible visual processing predicts artistic group membership and observational drawing skill in a sample of first-year bachelor's degree art students (n=23) and non-art students (n=23). A pattern of local and global visual processing enhancements was found in relation to artistic group membership and drawing skill, with local processing ability found to be specifically related to individual differences in drawing skill. Enhanced global processing and more fluent switching between local and global levels of hierarchical stimuli predicted both drawing skill and artistic group membership, suggesting that these are beneficial attentional mechanisms for art-making in a range of domains. These findings support a top-down attentional model of artistic expertise and shed light on the domain specific and domain-general attentional enhancements induced by proficiency in the visual arts. Copyright © 2015 Elsevier B.V. All rights reserved.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.

PubMed

Schreck, John S; Romano, Flavio; Zimmer, Matthew H; Louis, Ard A; Doye, Jonathan P K

2016-04-26

We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.

An openstack-based flexible video transcoding framework in live

NASA Astrophysics Data System (ADS)

Shi, Qisen; Song, Jianxin

2017-08-01

With the rapid development of mobile live business, transcoding HD video is often a challenge for mobile devices due to their limited processing capability and bandwidth-constrained network connection. For live service providers, it's wasteful for resources to delay lots of transcoding server because some of them are free to work sometimes. To deal with this issue, this paper proposed an Openstack-based flexible transcoding framework to achieve real-time video adaption for mobile device and make computing resources used efficiently. To this end, we introduced a special method of video stream splitting and VMs resource scheduling based on access pressure prediction,which is forecasted by an AR model.

Dynamics of Rotating Multi-component Turbomachinery Systems

NASA Technical Reports Server (NTRS)

Lawrence, Charles

1993-01-01

The ultimate objective of turbomachinery vibration analysis is to predict both the overall, as well as component dynamic response. To accomplish this objective requires complete engine structural models, including multistages of bladed disk assemblies, flexible rotor shafts and bearings, and engine support structures and casings. In the present approach each component is analyzed as a separate structure and boundary information is exchanged at the inter-component connections. The advantage of this tactic is that even though readily available detailed component models are utilized, accurate and comprehensive system response information may be obtained. Sample problems, which include a fixed base rotating blade and a blade on a flexible rotor, are presented.

Contrived Role Playing and Attitude Change.

ERIC Educational Resources Information Center

Schwartz, Henrietta S.

This study asked whether structured role playing and attendant experiences in extracurricular play productions were predictably associated with attitude changes in high school students. The major hypothesis was that students who participated in plays would become more open-minded and flexible and would show greater change toward more positive…

School Administration.

ERIC Educational Resources Information Center

Bete, Tim, Ed.

1998-01-01

Presents predictions from four administration experts on what the future holds for U.S. schools. Questions addressed concern the following: will schools ever include pre-K programs; will standardized testing disappear; will high schools adopt the flexible, independent study model; will K-12 education ever be run by big business, and will…

Hybrid and Electric Advanced Vehicle Systems Simulation

NASA Technical Reports Server (NTRS)

Beach, R. F.; Hammond, R. A.; Mcgehee, R. K.

1985-01-01

Predefined components connected to represent wide variety of propulsion systems. Hybrid and Electric Advanced Vehicle System (HEAVY) computer program is flexible tool for evaluating performance and cost of electric and hybrid vehicle propulsion systems. Allows designer to quickly, conveniently, and economically predict performance of proposed drive train.

Emotion Regulation in Children with Down Syndrome.

ERIC Educational Resources Information Center

Smith, Maureen C.; Walden, Tedra A.

This study presents a preliminary exploration of emotion regulation in a sample of 20 children (ages 3-18 years) with Down Syndrome. Three aspects of emotion regulation (modulation, organization, flexibility) were predicted from emotion variables (affect intensity, affective expression, and autonomy-curiosity and motivation) in backward regression…

Predicting readmission risk with institution-specific prediction models.

PubMed

Yu, Shipeng; Farooq, Faisal; van Esbroeck, Alexander; Fung, Glenn; Anand, Vikram; Krishnapuram, Balaji

2015-10-01

The ability to predict patient readmission risk is extremely valuable for hospitals, especially under the Hospital Readmission Reduction Program of the Center for Medicare and Medicaid Services which went into effect starting October 1, 2012. There is a plethora of work in the literature that deals with developing readmission risk prediction models, but most of them do not have sufficient prediction accuracy to be deployed in a clinical setting, partly because different hospitals may have different characteristics in their patient populations. We propose a generic framework for institution-specific readmission risk prediction, which takes patient data from a single institution and produces a statistical risk prediction model optimized for that particular institution and, optionally, for a specific condition. This provides great flexibility in model building, and is also able to provide institution-specific insights in its readmitted patient population. We have experimented with classification methods such as support vector machines, and prognosis methods such as the Cox regression. We compared our methods with industry-standard methods such as the LACE model, and showed the proposed framework is not only more flexible but also more effective. We applied our framework to patient data from three hospitals, and obtained some initial results for heart failure (HF), acute myocardial infarction (AMI), pneumonia (PN) patients as well as patients with all conditions. On Hospital 2, the LACE model yielded AUC 0.57, 0.56, 0.53 and 0.55 for AMI, HF, PN and All Cause readmission prediction, respectively, while the proposed model yielded 0.66, 0.65, 0.63, 0.74 for the corresponding conditions, all significantly better than the LACE counterpart. The proposed models that leverage all features at discharge time is more accurate than the models that only leverage features at admission time (0.66 vs. 0.61 for AMI, 0.65 vs. 0.61 for HF, 0.63 vs. 0.56 for PN, 0.74 vs. 0.60 for All Cause). Furthermore, the proposed admission-time models already outperform the performance of LACE, which is a discharge-time model (0.61 vs. 0.57 for AMI, 0.61 vs. 0.56 for HF, 0.56 vs. 0.53 for PN, 0.60 vs. 0.55 for All Cause). Similar conclusions can be drawn from other hospitals as well. The same performance comparison also holds for precision and recall at top-decile predictions. Most of the performance improvements are statistically significant. The institution-specific readmission risk prediction framework is more flexible and more effective than the one-size-fit-all models like the LACE, sometimes twice and three-time more effective. The admission-time models are able to give early warning signs compared to the discharge-time models, and may be able to help hospital staff intervene early while the patient is still in the hospital. Copyright © 2015 Elsevier B.V. All rights reserved.

Prediction of conformationally dependent atomic multipole moments in carbohydrates

PubMed Central

Cardamone, Salvatore

2015-01-01

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an “atom in a molecule,” thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol−1 for open chains and just over 90% an error of maximum 4 kJ mol−1 for rings. © 2015 Wiley Periodicals, Inc. PMID:26547500

Prediction of conformationally dependent atomic multipole moments in carbohydrates.

PubMed

Cardamone, Salvatore; Popelier, Paul L A

2015-12-15

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.

Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2

NASA Astrophysics Data System (ADS)

Baumgartner, Matthew P.; Evans, David A.

2018-01-01

Two of the major ongoing challenges in computational drug discovery are predicting the binding pose and affinity of a compound to a protein. The Drug Design Data Resource Grand Challenge 2 was developed to address these problems and to drive development of new methods. The challenge provided the 2D structures of compounds for which the organizers help blinded data in the form of 35 X-ray crystal structures and 102 binding affinity measurements and challenged participants to predict the binding pose and affinity of the compounds. We tested a number of pose prediction methods as part of the challenge; we found that docking methods that incorporate protein flexibility (Induced Fit Docking) outperformed methods that treated the protein as rigid. We also found that using binding pose metadynamics, a molecular dynamics based method, to score docked poses provided the best predictions of our methods with an average RMSD of 2.01 Å. We tested both structure-based (e.g. docking) and ligand-based methods (e.g. QSAR) in the affinity prediction portion of the competition. We found that our structure-based methods based on docking with Smina (Spearman ρ = 0.614), performed slightly better than our ligand-based methods (ρ = 0.543), and had equivalent performance with the other top methods in the competition. Despite the overall good performance of our methods in comparison to other participants in the challenge, there exists significant room for improvement especially in cases such as these where protein flexibility plays such a large role.

Androgen responses to reproductive competition of males pursuing either fixed or plastic alternative reproductive tactics.

PubMed

von Kuerthy, Corinna; Ros, Albert F H; Taborsky, Michael

2016-11-15

Alternative reproductive tactics (ARTs), which can be plastic or fixed for life, may be characterized by distinct hormonal profiles. The relative plasticity hypothesis predicts flexible androgen regulation for adult males pursuing plastic tactics, but a less flexible regulation for males using a fixed tactic throughout life. Furthermore, androgen profiles may respond to changes in the social environment, as predicted by the social reciprocity models of hormone/behaviour interactions. The cichlid fish Lamprologus callipterus provides a rare opportunity to study the roles of androgens for male ARTs within a single species, because fixed and plastic ARTs coexist. We experimentally exposed males to competitors pursuing either the same or different tactics to test predictions of the relative plasticity and the social reciprocity models. Androgen profiles of different male types partly comply with predictions derived from the relative plasticity hypothesis: males of the plastic bourgeois/sneaker male trajectory showed different 11-ketotestosterone (11-KT) levels when pursuing either bourgeois or parasitic sneaker male behaviours. Surprisingly, males pursuing the fixed dwarf male tactic showed the highest free and conjugated 11-KT and testosterone (T) levels. Our experimental social challenges significantly affected the free 11-KT levels of bourgeois males, but the androgen responses did not differ between challenges involving different types of competitors. Furthermore, the free T-responses of the bourgeois males correlated with their aggressive behaviour exhibited against competitors. Our results provide new insights into the endocrine responsiveness of fixed and plastic ARTs, confirming and refuting some predictions of both the relative plasticity and the social reciprocity models. © 2016. Published by The Company of Biologists Ltd.

Artificial neural network prediction of aircraft aeroelastic behavior

NASA Astrophysics Data System (ADS)

Pesonen, Urpo Juhani

An Artificial Neural Network that predicts aeroelastic behavior of aircraft is presented. The neural net was designed to predict the shape of a flexible wing in static flight conditions using results from a structural analysis and an aerodynamic analysis performed with traditional computational tools. To generate reliable training and testing data for the network, an aeroelastic analysis code using these tools as components was designed and validated. To demonstrate the advantages and reliability of Artificial Neural Networks, a network was also designed and trained to predict airfoil maximum lift at low Reynolds numbers where wind tunnel data was used for the training. Finally, a neural net was designed and trained to predict the static aeroelastic behavior of a wing without the need to iterate between the structural and aerodynamic solvers.

Analysis of Trajectory Flexibility Preservation Impact on Traffic Complexity

NASA Technical Reports Server (NTRS)

Idris, Husni; El-Wakil, Tarek; Wing, David J.

2009-01-01

The growing demand for air travel is increasing the need for mitigation of air traffic congestion and complexity problems, which are already at high levels. At the same time new information and automation technologies are enabling the distribution of tasks and decisions from the service providers to the users of the air traffic system, with potential capacity and cost benefits. This distribution of tasks and decisions raises the concern that independent user actions will decrease the predictability and increase the complexity of the traffic system, hence inhibiting and possibly reversing any potential benefits. In answer to this concern, the authors proposed the introduction of decision-making metrics for preserving user trajectory flexibility. The hypothesis is that such metrics will make user actions naturally mitigate traffic complexity. In this paper, the impact of using these metrics on traffic complexity is investigated. The scenarios analyzed include aircraft in en route airspace with each aircraft meeting a required time of arrival in a one-hour time horizon while mitigating the risk of loss of separation with the other aircraft, thus preserving its trajectory flexibility. The experiments showed promising results in that the individual trajectory flexibility preservation induced self-separation and self-organization effects in the overall traffic situation. The effects were quantified using traffic complexity metrics, namely dynamic density indicators, which indicated that using the flexibility metrics reduced aircraft density and the potential of loss of separation.

Two strategies to engineer flexible loops for improved enzyme thermostability

PubMed Central

Yu, Haoran; Yan, Yihan; Zhang, Cheng; Dalby, Paul A.

2017-01-01

Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a “back to consensus mutations” approach, and the second was computational design based on ΔΔG calculations in Rosetta. Forty-nine single variants were generated and characterised experimentally. From these, three single-variants I189H, A282P, D143K were found to be more thermostable than wild-type TK. The combination of A282P with H192P, a variant constructed previously, resulted in the best all-round variant with a 3-fold improved half-life at 60 °C, 5-fold increased specific activity at 65 °C, 1.3-fold improved kcat and a Tm increased by 5 °C above that of wild type. Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%. Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes. PMID:28145457

An analytical model and scaling of chordwise flexible flapping wings in forward flight.

PubMed

Kodali, Deepa; Kang, Chang-Kwon

2016-12-13

Aerodynamic performance of biological flight characterized by the fluid structure interaction of a flapping wing and the surrounding fluid is affected by the wing flexibility. One of the main challenges to predict aerodynamic forces is that the wing shape and motion are a priori unknown. In this study, we derive an analytical fluid-structure interaction model for a chordwise flexible flapping two-dimensional airfoil in forward flight. A plunge motion is imposed on the rigid leading-edge (LE) of teardrop shape and the flexible tail dynamically deforms. The resulting unsteady aeroelasticity is modeled with the Euler-Bernoulli-Theodorsen equation under a small deformation assumption. The two-way coupling is realized by considering the trailing-edge deformation relative to the LE as passive pitch, affecting the unsteady aerodynamics. The resulting wing deformation and the aerodynamic performance including lift and thrust agree well with high-fidelity numerical results. Under the dynamic balance, the aeroelastic stiffness decreases, whereas the aeroelastic stiffness increases with the reduced frequency. A novel aeroelastic frequency ratio is derived, which scales with the wing deformation, lift, and thrust. Finally, the dynamic similarity between flapping in water and air is established.

Exploring the Role of Receptor Flexibility in Structure-Based Drug Discovery

PubMed Central

Feixas, Ferran; Lindert, Steffen; Sinko, William; McCammon, J. Andrew

2015-01-01

The proper understanding of biomolecular recognition mechanisms that take place in a drug target is of paramount importance to improve the efficiency of drug discovery and development. The intrinsic dynamic character of proteins has a strong influence on biomolecular recognition mechanisms and models such as conformational selection have been widely used to account for this dynamic association process. However, conformational changes occurring in the receptor prior and upon association with other molecules are diverse and not obvious to predict when only a few structures of the receptor are available. In view of the prominent role of protein flexibility in ligand binding and its implications for drug discovery, it is of great interest to identify receptor conformations that play a major role in biomolecular recognition before starting rational drug design efforts. In this review, we discuss a number of recent advances in computer-aided drug discovery techniques that have been proposed to incorporate receptor flexibility into structure-based drug design. The allowance for receptor flexibility provided by computational techniques such as molecular dynamics simulations or enhanced sampling techniques helps to improve the accuracy of methods used to estimate binding affinities and, thus, such methods can contribute to the discovery of novel drug leads. PMID:24332165

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Polymer flexibility and turbulent drag reduction.

PubMed

Gillissen, J J J

2008-10-01

Polymer-induced drag reduction is the phenomenon by which the friction factor of a turbulent flow is reduced by the addition of small amounts of high-molecular-weight linear polymers, which conformation in solution at rest can vary between randomly coiled and rodlike. It is well known that drag reduction is positively correlated to viscous stresses, which are generated by extended polymers. Rodlike polymers always assume this favorable conformation, while randomly coiling chains need to be unraveled by fluid strain rate in order to become effective. The coiling and stretching of flexible polymers in turbulent flow produce an additional elastic component in the polymer stress. The effect of the elastic stresses on drag reduction is unclear. To study this issue, we compare direct numerical simulations of turbulent drag reduction in channel flow using constitutive equations describing solutions of rigid and flexible polymers. When compared at constant phi r2, both simulations predict the same amount of drag reduction. Here phi is the polymer volume fraction and r is the polymer aspect ratio, which for flexible polymers is based on average polymer extension at the channel wall. This demonstrates that polymer elasticity plays a marginal role in the mechanism for drag reduction.

A combinatorial approach to protein docking with flexible side chains.

PubMed

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans-Peter; Müller, Peter

2002-01-01

Rigid-body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side chains while keeping the protein backbone rigid. Starting from candidates created by a rigid-docking algorithm, we demangle the side chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side chain demangling. Both approaches are based on a discrete representation of the side chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem, we propose a fast heuristic approach and an exact, albeit slower, method that uses branch-and-cut techniques. As a test set, we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples, the highest-ranking conformation produced was a good approximation of the true complex structure.

Efficient Skin Temperature Sensor and Stable Gel-Less Sticky ECG Sensor for a Wearable Flexible Healthcare Patch.

PubMed

Yamamoto, Yuki; Yamamoto, Daisuke; Takada, Makoto; Naito, Hiroyoshi; Arie, Takayuki; Akita, Seiji; Takei, Kuniharu

2017-09-01

Wearable, flexible healthcare devices, which can monitor health data to predict and diagnose disease in advance, benefit society. Toward this future, various flexible and stretchable sensors as well as other components are demonstrated by arranging materials, structures, and processes. Although there are many sensor demonstrations, the fundamental characteristics such as the dependence of a temperature sensor on film thickness and the impact of adhesive for an electrocardiogram (ECG) sensor are yet to be explored in detail. In this study, the effect of film thickness for skin temperature measurements, adhesive force, and reliability of gel-less ECG sensors as well as an integrated real-time demonstration is reported. Depending on the ambient conditions, film thickness strongly affects the precision of skin temperature measurements, resulting in a thin flexible film suitable for a temperature sensor in wearable device applications. Furthermore, by arranging the material composition, stable gel-less sticky ECG electrodes are realized. Finally, real-time simultaneous skin temperature and ECG signal recordings are demonstrated by attaching an optimized device onto a volunteer's chest. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nonlinear vibration absorption for a flexible arm via a virtual vibration absorber

NASA Astrophysics Data System (ADS)

Bian, Yushu; Gao, Zhihui

2017-07-01

A semi-active vibration absorption method is put forward to attenuate nonlinear vibration of a flexible arm based on the internal resonance. To maintain the 2:1 internal resonance condition and the desirable damping characteristic, a virtual vibration absorber is suggested. It is mathematically equivalent to a vibration absorber but its frequency and damping coefficients can be readily adjusted by simple control algorithms, thereby replacing those hard-to-implement mechanical designs. Through theoretical analyses and numerical simulations, it is proven that the internal resonance can be successfully established for the flexible arm, and the vibrational energy of flexible arm can be transferred to and dissipated by the virtual vibration absorber. Finally, experimental results are presented to validate the theoretical predictions. Since the proposed method absorbs rather than suppresses vibrational energy of the primary system, it is more convenient to reduce strong vibration than conventional active vibration suppression methods based on smart material actuators with limited energy output. Furthermore, since it aims to establish an internal vibrational energy transfer channel from the primary system to the vibration absorber rather than directly respond to external excitations, it is especially applicable for attenuating nonlinear vibration excited by unpredictable excitations.

Learning outdoors: male lizards show flexible spatial learning under semi-natural conditions

PubMed Central

Noble, Daniel W. A.; Carazo, Pau; Whiting, Martin J.

2012-01-01

Spatial cognition is predicted to be a fundamental component of fitness in many lizard species, and yet some studies suggest that it is relatively slow and inflexible. However, such claims are based on work conducted using experimental designs or in artificial contexts that may underestimate their cognitive abilities. We used a biologically realistic experimental procedure (using simulated predatory attacks) to study spatial learning and its flexibility in the lizard Eulamprus quoyii in semi-natural outdoor enclosures under similar conditions to those experienced by lizards in the wild. To evaluate the flexibility of spatial learning, we conducted a reversal spatial-learning task in which positive and negative reinforcements of learnt spatial stimuli were switched. Nineteen (32%) male lizards learnt both tasks within 10 days (spatial task mean: 8.16 ± 0.69 (s.e.) and reversal spatial task mean: 10.74 ± 0.98 (s.e.) trials). We demonstrate that E. quoyii are capable of flexible spatial learning and suggest that future studies focus on a range of lizard species which differ in phylogeny and/or ecology, using biologically relevant cognitive tasks, in an effort to bridge the cognitive divide between ecto- and endotherms. PMID:23075525

Experimental validation of damping properties and solar pressure effects on flexible, high area-to-mass ratio debris model

NASA Astrophysics Data System (ADS)

Channumsin, Sittiporn; Ceriotti, Matteo; Radice, Gianmarco; Watson, Ian

2017-09-01

Multilayer insulation (MLI) is a recently-discovered type of debris originating from delamination of aging spacecraft; it is mostly detected near the geosynchronous orbit (GEO). Observation data indicates that these objects are characterised by high reflectivity, high area-to-mass ratio (HAMR), fast rotation, high sensitivity to perturbations (especially solar radiation pressure) and change of area-to-mass ratio (AMR) over time. As a result, traditional models (e.g. cannonball) are unsuitable to represent and predict this debris' orbital evolution. Previous work by the authors effectively modelled the flexible debris by means of multibody dynamics to improve the prediction accuracy. The orbit evolution with the flexible model resulted significantly different from using the rigid model. This paper aims to present a methodology to determine the dynamic properties of thin membranes with the purpose to validate the deformation characteristics of the flexible model. A high-vacuum chamber (10-4 mbar) to significantly decrease air friction, inside which a thin membrane is hinged at one end but free at the other provides the experimental setup. A free motion test is used to determine the damping characteristics and natural frequency of the thin membrane via logarithmic decrement and frequency response. The membrane can swing freely in the chamber and the motion is tracked by a static, optical camera, and a Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. Then, the effect of solar radiation pressure on the thin membrane is investigated: a high power spotlight (500-2000 W) is used to illuminate the sample and any displacement of the membrane is measured by means of a high-resolution laser sensor. Analytic methods from the natural frequency response and Finite Element Analysis (FEA) including multibody simulations of both experimental setups are used for the validation of the flexible model by comparing the experimental results of amplitude decay, natural frequencies and deformation. The experimental results show good agreement with both analytical results and finite element methods.

When repetitive mental sets increase cognitive flexibility in adolescent obsessive-compulsive disorder.

PubMed

Wolff, Nicole; Giller, Franziska; Buse, Judith; Roessner, Veit; Beste, Christian

2018-03-30

A major facet of obsessive-compulsive disorder (OCD) is cognitive inflexibility. However, sometimes, cognitive flexibility can be needed to reuse recently abandoned mental sets. Therefore, cognitive flexibility can in certain cases be useful to reinstate some form of rigid, repetitive behavior characterizing OCD. We test the counterintuitive hypothesis that under such circumstances, cognitive flexibility is better in OCD patients than controls. We examined N = 20 adolescent OCD patients and N = 22 controls in a backward inhibition (BI) paradigm. This was combined with event-related potential (ERP) recordings and source localization. The BI effect describes the cost of overcoming the inhibition of a recently abandoned mental set that is relevant again. Therefore, a strong BI effect is disadvantageous for cognitive flexibility. Compared to controls, OCD patients revealed a smaller backward inhibition effect. The EEG data revealed larger P1 amplitudes in backward inhibition trials in the OCD group, which was due to activation differences in the inferior frontal gyrus (BA47). The severity of clinical symptoms predicted these neurophysiological modulations. The power of the observed effects was about 95%. The study shows that cognitive flexibility can be better in OCD than controls. This may be the case in situations where superior abilities in the reactivation of repeating mental sets and difficulties to process new ones coincide. This may be accomplished by intensified inhibitory control mechanisms. The results challenge the view on OCD, since OCD is not generally associated with cognitive inflexibility. © 2018 Association for Child and Adolescent Mental Health.

Arctic Engineering--Through Human Eyes.

ERIC Educational Resources Information Center

Simmonds, W. H. C.

Adopting technology to people and examining projects through the eyes of those concerned are two ways new technology and engineering can be installed and successfully operated under the adverse conditions of northern Canada and in the face of predicted labor shortages in the 1980's. Adopting a more flexible technology provides the opportunity for…

A Two-Process Model of Paragraph Development.

ERIC Educational Resources Information Center

Woodson, Linda

Paragraph writing mediated by imagery is richer, more flexible, and more creative than that produced by the somewhat impoverished, predictable, one-process model usually taught in composition classes. Since the writing advice given students differs considerably from the practice of professional writers, students should be given exercises that not…

A review of performance models and test procedures with recommendations for use in the Texas m-e design program.

DOT National Transportation Integrated Search

2008-09-01

In the first year of this project, a comprehensive review was made of the available models for : predicting the major distresses in flexible pavements, including cracking of asphalt layers and chemically : bound layers, permanent deformation of aspha...

Field verification of KDOT's Superpave mixture properties to be used as inputs in the NCHRP mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2009-01-01

In the MechanisticEmpirical Pavement Design Guide (M-EPDG), prediction of flexible pavement response and performance needs an input of dynamic modulus of hot-mix asphalt (HMA) at all three levels of hierarchical inputs. This study was intended to ...

Linguo-Intercultural Sensitivity and Its Predictors in EFL in a Bosnian Sample

ERIC Educational Resources Information Center

Aydogan, Hakan; Akbarov, Azamat

2015-01-01

In this article, the predictive power of five variables relevant for Linguo-intercultural sensitivity (flexibility) is examined. Communication aspect of intercultural interactions, specifically, the role of English as an international language are emphasized. Attitudes Towards English and Its Usage Scale (ATEUS) was applied to 194 students who…

Representing, Running, and Revising Mental Models: A Computational Model

ERIC Educational Resources Information Center

Friedman, Scott; Forbus, Kenneth; Sherin, Bruce

2018-01-01

People use commonsense science knowledge to flexibly explain, predict, and manipulate the world around them, yet we lack computational models of how this commonsense science knowledge is represented, acquired, utilized, and revised. This is an important challenge for cognitive science: Building higher order computational models in this area will…

Thump, Ring: The Sound of a Bouncing Ball

ERIC Educational Resources Information Center

Katz, J. I.

2010-01-01

A basketball bounced on a stiff surface produces a characteristic loud thump, followed by a high-pitched ringing. Describing the ball as an inextensible but flexible membrane containing compressed air, I formulate an approximate theory of the generation of these sounds and predict their amplitudes and waveforms. (Contains 3 figures.)

Flexible stocking as a strategy for enhancing ranch profitability in the face of a changing and variable climate

USDA-ARS?s Scientific Manuscript database

Predicted climate change impacts include increased weather variability and increased occurrences of extreme events such as drought. Such climate changes potentially affect cattle performance as well as pasture and range productivity. These climate induced risks are often coupled with variable market...

Changing Role of the Personnel Manager

ERIC Educational Resources Information Center

Schein, Edgar H.

1975-01-01

Arguing that the personnel manager will increasingly have to become a change agent and process consultant, the author discusses tasks involved and skills required for the new role. A shift in focus toward top management as the primary client and utilization of more flexible intervention into organizational processes are predicted. (JT)

Superpave in-situ stress/strain investigation--phase II implementing (SISSI II) : draft report, evaluating the sensitivity of MEPDG to SISSI data.

DOT National Transportation Integrated Search

2009-01-01

The objective of the sensitivity study was to evaluate the input parameters related to AC material properties, traffic, and climate that significantly or insignificantly influence the predicted performance for two specific SISSI flexible pavements: W...

Competitive actions of small firms in a declining market

Treesearch

Matthew Bumgardner; Urs Buehlmann; Albert Schuler; Jeff Crissey

2011-01-01

Small firms, through their flexibility advantages and closeness to customers, potentially can increase their sales volume in economic downturns. The decline in U.S. housing construction (beginning in 2006) provided an opportunity to develop and test four hypotheses predicting the attributes and marketing actions associated with successful companies supplying housing...

Adaptive vehicle motion estimation and prediction

NASA Astrophysics Data System (ADS)

Zhao, Liang; Thorpe, Chuck E.

1999-01-01

Accurate motion estimation and reliable maneuver prediction enable an automated car to react quickly and correctly to the rapid maneuvers of the other vehicles, and so allow safe and efficient navigation. In this paper, we present a car tracking system which provides motion estimation, maneuver prediction and detection of the tracked car. The three strategies employed - adaptive motion modeling, adaptive data sampling, and adaptive model switching probabilities - result in an adaptive interacting multiple model algorithm (AIMM). The experimental results on simulated and real data demonstrate that our tracking system is reliable, flexible, and robust. The adaptive tracking makes the system intelligent and useful in various autonomous driving tasks.

Rapid recipe formulation for plasma etching of new materials

NASA Astrophysics Data System (ADS)

Chopra, Meghali; Zhang, Zizhuo; Ekerdt, John; Bonnecaze, Roger T.

2016-03-01

A fast and inexpensive scheme for etch rate prediction using flexible continuum models and Bayesian statistics is demonstrated. Bulk etch rates of MgO are predicted using a steady-state model with volume-averaged plasma parameters and classical Langmuir surface kinetics. Plasma particle and surface kinetics are modeled within a global plasma framework using single component Metropolis Hastings methods and limited data. The accuracy of these predictions is evaluated with synthetic and experimental etch rate data for magnesium oxide in an ICP-RIE system. This approach is compared and superior to factorial models generated from JMP, a software package frequently employed for recipe creation and optimization.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

PubMed Central

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

2016-01-01

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

Mechanical Model of Dexterous Continuum Manipulators with Compliant Joints and Tendon/External Force Interactions

PubMed Central

Murphy, Ryan J.; Liu, Hao; Iordachita, Iulian I.; Armand, Mehran

2017-01-01

Dexterous continuum manipulators (DCMs) have been widely adopted for minimally- and less-invasive surgery. During the operation, these DCMs interact with surrounding anatomy actively or passively. The interaction force will inevitably affect the tip position and shape of DCMs, leading to potentially inaccurate control near critical anatomy. In this paper, we demonstrated a 2D mechanical model for a tendon actuated, notched DCM with compliant joints. The model predicted deformation of the DCM accurately in the presence of tendon force, friction force, and external force. A partition approach was proposed to describe the DCM as a series of interconnected rigid and flexible links. Beam mechanics, taking into consideration tendon interaction and external force on the tip and the body, was applied to obtain the deformation of each flexible link of the DCM. The model results were compared with experiments for free bending as well as bending in the presence of external forces acting at either the tip or body of the DCM. The overall mean error of tip position between model predictions and all of the experimental results was 0.62±0.41mm. The results suggest that the proposed model can effectively predict the shape of the DCM. PMID:28989273

Accelerated probabilistic inference of RNA structure evolution

PubMed Central

Holmes, Ian

2005-01-01

Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387

Analytical design model for a piezo-composite unimorph actuator and its verification using lightweight piezo-composite curved actuators

NASA Astrophysics Data System (ADS)

Yoon, K. J.; Park, K. H.; Lee, S. K.; Goo, N. S.; Park, H. C.

2004-06-01

This paper describes an analytical design model for a layered piezo-composite unimorph actuator and its numerical and experimental verification using a LIPCA (lightweight piezo-composite curved actuator) that is lighter than other conventional piezo-composite type actuators. The LIPCA is composed of top fiber composite layers with high modulus and low CTE (coefficient of thermal expansion), a middle PZT ceramic wafer, and base layers with low modulus and high CTE. The advantages of the LIPCA design are to replace the heavy metal layer of THUNDER by lightweight fiber-reinforced plastic layers without compromising the generation of high force and large displacement and to have design flexibility by selecting the fiber direction and the number of prepreg layers. In addition to the lightweight advantage and design flexibility, the proposed device can be manufactured without adhesive layers when we use a resin prepreg system. A piezo-actuation model for a laminate with piezo-electric material layers and fiber composite layers is proposed to predict the curvature and residual stress of the LIPCA. To predict the actuation displacement of the LIPCA with curvature, a finite element analysis method using the proposed piezo-actuation model is introduced. The predicted deformations are in good agreement with the experimental ones.

Disaggregating Census Data for Population Mapping Using Random Forests with Remotely-Sensed and Ancillary Data

PubMed Central

Stevens, Forrest R.; Gaughan, Andrea E.; Linard, Catherine; Tatem, Andrew J.

2015-01-01

High resolution, contemporary data on human population distributions are vital for measuring impacts of population growth, monitoring human-environment interactions and for planning and policy development. Many methods are used to disaggregate census data and predict population densities for finer scale, gridded population data sets. We present a new semi-automated dasymetric modeling approach that incorporates detailed census and ancillary data in a flexible, “Random Forest” estimation technique. We outline the combination of widely available, remotely-sensed and geospatial data that contribute to the modeled dasymetric weights and then use the Random Forest model to generate a gridded prediction of population density at ~100 m spatial resolution. This prediction layer is then used as the weighting surface to perform dasymetric redistribution of the census counts at a country level. As a case study we compare the new algorithm and its products for three countries (Vietnam, Cambodia, and Kenya) with other common gridded population data production methodologies. We discuss the advantages of the new method and increases over the accuracy and flexibility of those previous approaches. Finally, we outline how this algorithm will be extended to provide freely-available gridded population data sets for Africa, Asia and Latin America. PMID:25689585

node2vec: Scalable Feature Learning for Networks

PubMed Central

Grover, Aditya; Leskovec, Jure

2016-01-01

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node’s network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks. PMID:27853626

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

PubMed Central

2014-01-01

Background Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site’s Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site’s LPD with its rate of evolution. Results We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein’s potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant’s active conformation. We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. Conclusions We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship between LPD and evolutionary rate. Moreover, the model also accounts for the nonlinear dependence between evolutionary rate and dynamical flexibility. PMID:24716445

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

PubMed

Curtis, Darren S; Phillips, Aaron R; Callister, Stephen J; Conlan, Sean; McCue, Lee Ann

2013-10-15

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

Predicting Flory-Huggins χ from Simulations

NASA Astrophysics Data System (ADS)

Zhang, Wenlin; Gomez, Enrique D.; Milner, Scott T.

2017-07-01

We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10-3k T for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends. Our SCFT results agree with MD simulations, validating both the predicted χ values and our thermodynamic integration method. Combined with atomistic simulations, our method can be applied to predict χ for new polymers from their chemical structures.

Development of braided rope seals for hypersonic engine applications: Flow modeling

NASA Technical Reports Server (NTRS)

Mutharasan, Rajakkannu; Steinetz, Bruce M.; Tao, Xiaoming; Du, Guang-Wu; Ko, Frank

1992-01-01

A new type of engine seal is being developed to meet the needs of advanced hypersonic engines. A seal braided of emerging high temperature ceramic fibers comprised of a sheath-core construction was selected for study based on its low leakage rates. Flexible, low-leakage, high temperature seals are required to seal the movable engine panels of advanced ramjet-scramjet engines either preventing potentially dangerous leakage into backside engine cavities or limiting the purge coolant flow rates through the seals. To predict the leakage through these flexible, porous seal structures new analytical flow models are required. Two such models based on the Kozeny-Carman equations are developed herein and are compared to experimental leakage measurements for simulated pressure and seal gap conditions. The models developed allow prediction of the gas leakage rate as a function of fiber diameter, fiber packing density, gas properties, and pressure drop across the seal. The first model treats the seal as a homogeneous fiber bed. The second model divides the seal into two homogeneous fiber beds identified as the core and the sheath of the seal. Flow resistances of each of the main seal elements are combined to determine the total flow resistance. Comparisons between measured leakage rates and model predictions for seal structures covering a wide range of braid architectures show good agreement. Within the experimental range, the second model provides a prediction within 6 to 13 percent of the flow for many of the cases examined. Areas where future model refinements are required are identified.

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

Hao, He; Sun, Yannan; Carroll, Thomas E.

We propose a coordination algorithm for cooperative power allocation among a collection of commercial buildings within a campus. We introduced thermal and power models of a typical commercial building Heating, Ventilation, and Air Conditioning (HVAC) system, and utilize model predictive control to characterize their power flexibility. The power allocation problem is formulated as a cooperative game using the Nash Bargaining Solution (NBS) concept, in which buildings collectively maximize the product of their utilities subject to their local flexibility constraints and a total power limit set by the campus coordinator. To solve the optimal allocation problem, a distributed protocol is designedmore » using dual decomposition of the Nash bargaining problem. Numerical simulations are performed to demonstrate the efficacy of our proposed allocation method« less

Experimental and theoretical study of fluid-structure interactions in plunging hydrofoils and gravity-driven falling plates

NASA Astrophysics Data System (ADS)

Tian, Ruijun

Two typical unsteady fluid-structure interaction problems have been investigated in the present study. One of them was about actively plunged flexible hydrofoil; the other was about gravity-driven falling plates in water. Real-time velocity field and dynamic response on the moving objects were measured to study these unsteady and highly nonlinear problems. For a long time, scientists have believed that bird and insect flight benefits greatly from the flexibility and morphing facility of their wings via flapping motion. A significant advantage flexible wing models have over quasi-steady rigid wing models is a much higher lift generation capability. Both experimental and computational studies have shown that the leading and trailing edge vortexes (LEV and TEV) play a major role in the efficient generation of such unconventionally high lift force. In this study, two NACA0012 miniature hydrofoils, one flexible and the other rigid, were actively plunged at various frequencies in a viscous glycerol-water solution to study the influence of flexibility. Two-dimensional, phase-locked particle image velocimetry (PIV) measurements were conducted to investigate the temporal and spacial development of LEVs and TEVs. Simultaneous measurements of lift and thrust forces were recorded to reveal the relationship between hydrodynamic force and the evolution of the surrounding flow field. Results from the flexible hydrofoil were compared to those from the rigid one in order to quantitatively analyze the effects of flexibility. The second problem focused on fluid-structure interaction of gravity driven falling plates. Falling leaves and paper cards in air has drawn plenty of research interest in the past decades to investigate the interaction between the fluid flow and the falling object. In this research, time-resolved PIV were employed to experimentally visualize the flow field evolution around the gravity-driven falling plates. The plates were made of different materials with various geometric dimensions, in order to investigate the effects of non-dimensional parameters such as Reynolds number (Re) and dimensionless moment of inertia (I*). Within the range of relative high Reynolds numbers (Re > 500), three types of falling modes were observed: i.e., periodic fluttering, periodic tumbling and marginal chaotic motion. It was found that the nondimensional moment of inertia controlled the falling mode. The flow features through the falling path of the plate were characterized and compared with their corresponding kinematics. Based on theoretical analysis and experimental results, a semi-analytic model was developed to calculate the real-time hydrodynamic force and moment applied on falling plates. With this model, the falling trajectory of 2D plates with arbitrary material/dimension combinations can be predicted. The model yielded a good match for both the dynamic force simulation and trajectory prediction.

Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders

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

Bao, Y., E-mail: ybao@sjtu.edu.cn; Department of Aeronautics, Imperial College London, South Kensington Campus, London; Palacios, R., E-mail: r.palacios@imperial.ac.uk

2016-09-15

We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural modelmore » of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.« less

The emergent executive: a dynamic field theory of the development of executive function.

PubMed

Buss, Aaron T; Spencer, John P

2014-06-01

Executive function (EF) is a central aspect of cognition that undergoes significant changes in early childhood. Changes in EF in early childhood are robustly predictive of academic achievement and general quality of life measures later in adulthood. We present a dynamic neural field (DNF) model that provides a process-based account of behavior and developmental change in a key task used to probe the early development of executive function—the Dimensional Change Card Sort (DCCS) task. In the DCCS, children must flexibly switch from sorting cards either by shape or color to sorting by the other dimension. Typically, 3-year-olds, but not 5-year-olds, lack the flexibility to do so and perseverate on the first set of rules when instructed to switch. Using the DNF model, we demonstrate how rule-use and behavioral flexibility come about through a form of dimensional attention. Further, developmental change is captured by increasing the robustness and precision of dimensional attention. Note that although this enables the model to effectively switch tasks, the dimensional attention system does not “know” the details of task-specific performance. Rather, correct performance emerges as a property of system–wide interactions. We show how this captures children’s behavior in quantitative detail across 14 versions of the DCCS task. Moreover, we successfully test a set of novel predictions with 3-year-old children from a version of the task not explained by other theories.

A Neural Circuit Model of Flexible Sensori-motor Mapping: Learning and Forgetting on Multiple Timescales

PubMed Central

Fusi, Stefano; Asaad, Wael F.; Miller, Earl K.; Wang, Xiao-Jing

2007-01-01

Summary Volitional behavior relies on the brain’s ability to remap sensory flow to motor programs whenever demanded by a changed behavioral context. To investigate the circuit basis of such flexible behavior, we have developed a biophysically-based decision-making network model of spiking neurons for arbitrary sensorimotor mapping. The model quantitatively reproduces behavioral and prefrontal single-cell data from an experiment in which monkeys learn visuo-motor associations that are reversed unpredictably from time to time. We show that when synaptic modifications occur on multiple timescales, the model behavior becomes flexible only when needed: slow components of learning usually dominate the decision process. However, if behavioral contexts change frequently enough, fast components of plasticity take over, and the behavior exhibits a quick forget-and-learn pattern. This model prediction is confirmed by monkey data. Therefore, our work reveals a scenario for conditional associative learning that is distinct from instant switching between sets of well established sensorimotor associations. PMID:17442251

Activity patterns of serotonin neurons underlying cognitive flexibility

PubMed Central

Matias, Sara; Lottem, Eran; Dugué, Guillaume P; Mainen, Zachary F

2017-01-01

Serotonin is implicated in mood and affective disorders. However, growing evidence suggests that a core endogenous role is to promote flexible adaptation to changes in the causal structure of the environment, through behavioral inhibition and enhanced plasticity. We used long-term photometric recordings in mice to study a population of dorsal raphe serotonin neurons, whose activity we could link to normal reversal learning using pharmacogenetics. We found that these neurons are activated by both positive and negative prediction errors, and thus report signals similar to those proposed to promote learning in conditions of uncertainty. Furthermore, by comparing the cue responses of serotonin and dopamine neurons, we found differences in learning rates that could explain the importance of serotonin in inhibiting perseverative responding. Our findings show how the activity patterns of serotonin neurons support a role in cognitive flexibility, and suggest a revised model of dopamine–serotonin opponency with potential clinical implications. DOI: http://dx.doi.org/10.7554/eLife.20552.001 PMID:28322190

Modeling and controller design of a 6-DOF precision positioning system

NASA Astrophysics Data System (ADS)

Cai, Kunhai; Tian, Yanling; Liu, Xianping; Fatikow, Sergej; Wang, Fujun; Cui, Liangyu; Zhang, Dawei; Shirinzadeh, Bijan

2018-05-01

A key hurdle to meet the needs of micro/nano manipulation in some complex cases is the inadequate workspace and flexibility of the operation ends. This paper presents a 6-degree of freedom (DOF) serial-parallel precision positioning system, which consists of two compact type 3-DOF parallel mechanisms. Each parallel mechanism is driven by three piezoelectric actuators (PEAs), guided by three symmetric T-shape hinges and three elliptical flexible hinges, respectively. It can extend workspace and improve flexibility of the operation ends. The proposed system can be assembled easily, which will greatly reduce the assembly errors and improve the positioning accuracy. In addition, the kinematic and dynamic model of the 6-DOF system are established, respectively. Furthermore, in order to reduce the tracking error and improve the positioning accuracy, the Discrete-time Model Predictive Controller (DMPC) is applied as an effective control method. Meanwhile, the effectiveness of the DMCP control method is verified. Finally, the tracking experiment is performed to verify the tracking performances of the 6-DOF stage.

Roll Damping Derivatives from Generalized Lifting-Surface Theory and Wind Tunnel Forced-Oscillation Tests

NASA Technical Reports Server (NTRS)

Pototzky, Anthony S; Murphy, Patrick C.

2014-01-01

Improving aerodynamic models for adverse loss-of-control conditions in flight is an area being researched under the NASA Aviation Safety Program. Aerodynamic models appropriate for loss of control conditions require a more general mathematical representation to predict nonlinear unsteady behaviors. As more general aerodynamic models are studied that include nonlinear higher order effects, the possibility of measurements that confound aerodynamic and structural responses are probable. In this study an initial step is taken to look at including structural flexibility in analysis of rigid-body forced-oscillation testing that accounts for dynamic rig, sting and balance flexibility. Because of the significant testing required and associated costs in a general study, it makes sense to capitalize on low cost analytical methods where possible, especially where structural flexibility can be accounted for by a low cost method. This paper provides an initial look at using linear lifting surface theory applied to rigid-body aircraft roll forced-oscillation tests.

Modeling and control for vibration suppression of a flexible smart structure

NASA Technical Reports Server (NTRS)

Dosch, J.; Leo, D.; Inman, D.

1993-01-01

Theoretical and experimental results of the modeling and control of a flexible ribbed antenna are presented. The antenna consists of eight flexible ribs which constitutes a smart antenna in the sense that the actuator and sensors are an integral part of the structure. The antenna exhibits closely space and repeated modes, thus multi-input multi-output (MIMO) control is necessary for controllability and observability of the structure. The structure also exhibits mode localization phenomenon and contains post buckled members making an accurate finite element model of the structure difficult to obtain. An identified MIMO minimum order model of the antenna is synthesized from identified single-input single-output (SISO) transfer functions curve fit in the frequency domain. The identified model is used to design a positive position feedback (PPF) controller that increases damping in all of the modes in the targeted frequency range. Due to the accuracy of the open loop model of the antenna, the closed loop response predicted by the identified model correlates well wtih experimental results.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

PubMed

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Solder creep-fatigue interactions with flexible leaded parts

NASA Technical Reports Server (NTRS)

Ross, R. G., Jr.; Wen, L. C.; Mon, G. R.; Jetter, E.

1992-01-01

With flexible leaded parts, the solder-joint failure process involves a complex interplay of creep and fatigue mechanisms. To better understand the role of creep in typical multi-hour cyclic loading conditions, a specialized non-linear finite-element creep simulation computer program has been formulated. The numerical algorithm includes the complete part-lead-solder-PWB system, accounting for strain-rate dependence of creep on applied stress and temperature, and the role of the part-lead dimensions and flexibility that determine the total creep deflection (solder strain range) during stress relaxation. The computer program has been used to explore the effects of various solder creep-fatigue parameters such as lead height and stiffness, thermal-cycle test profile, and part/board differential thermal expansion properties. One of the most interesting findings is the strong presence of unidirectional creep-ratcheting that occurs during thermal cycling due to temperature dominated strain-rate effects. To corroborate the solder fatigue model predictions, a number of carefully controlled thermal-cycle tests have been conducted using special bimetallic test boards.

Residual stress analysis for oxide thin film deposition on flexible substrate using finite element method

NASA Astrophysics Data System (ADS)

Chen, Hsi-Chao; Huang, Chen-Yu; Lin, Ssu-Fan; Chen, Sheng-Hui

2011-09-01

Residual or internal stresses directly affect a variety of phenomena including adhesion, generation of crystalline defects, perfection of epitaxial layers and formation of film surface growths such as hillocks and whiskers. Sputtering oxide films with high density promote high compressive stress, and it offers researchers a reference if the value of residual stress could be analyzed directly. Since, the study of residual stress of SiO2 and Nb2O5 thin film deposited by DC magnetron sputtered on hard substrate (BK7) and flexible substrate (PET and PC). A finite element method (FEM) with an equivalent-reference-temperature (ERT) technique had been proposed and used to model and evaluate the intrinsic strains of layered structures. The research has improved the equivalent reference temperature (ERT) technique of the simulation of intrinsic strain for oxygen film. The results have also generalized two models connecting to the lattice volume to predict the residual stress of hard substrate and flexible substrate with error of 3% and 6%, respectively.

A neural circuit model of flexible sensorimotor mapping: learning and forgetting on multiple timescales.

PubMed

Fusi, Stefano; Asaad, Wael F; Miller, Earl K; Wang, Xiao-Jing

2007-04-19

Volitional behavior relies on the brain's ability to remap sensory flow to motor programs whenever demanded by a changed behavioral context. To investigate the circuit basis of such flexible behavior, we have developed a biophysically based decision-making network model of spiking neurons for arbitrary sensorimotor mapping. The model quantitatively reproduces behavioral and prefrontal single-cell data from an experiment in which monkeys learn visuomotor associations that are reversed unpredictably from time to time. We show that when synaptic modifications occur on multiple timescales, the model behavior becomes flexible only when needed: slow components of learning usually dominate the decision process. However, if behavioral contexts change frequently enough, fast components of plasticity take over, and the behavior exhibits a quick forget-and-learn pattern. This model prediction is confirmed by monkey data. Therefore, our work reveals a scenario for conditional associative learning that is distinct from instant switching between sets of well-established sensorimotor associations.

Pesticide Environmental Fate Research for the 21st Century: Building Bridges Between Laboratory and Field Studies at Varying Scales

USDA-ARS?s Scientific Manuscript database

Accurate determination of predicted environmental concentrations (PECs) is a continuing and often elusive goal of pesticide risk assessment. PECs are typically derived using simulation models that depend on laboratory generated data for key input parameters (t1/2, Koc, etc.). Model flexibility in ...

Pesticide Environmental Fate Research for the 21st Century: Building Bridges Between Laboratory and Field Studies at Varying Scales

USDA-ARS?s Scientific Manuscript database

Accurate determination of predicted environmental concentrations (PECs) is a continuing and often elusive goal of pesticide risk assessment. PECs are typically derived using simulation models that depend on laboratory generated data for key input parameters (t1/2, Koc, etc.). Model flexibility in ev...

Willingness to Seek Help as a Function of Self-Disclosure and Problem Severity.

ERIC Educational Resources Information Center

Hinson, Janise A.; Swanson, Jane L.

1993-01-01

Examined effects of problem severity, amount of self-disclosure, and self-disclosure flexibility on willingness to seek help for problem. Findings from 101 college students indicated that factors that predicted greatest amount of variance in willingness to seek help were interaction of problem severity with willingness to self-disclose to…

Does Preschool Education Exposure Predict Children's Academic and Behavioural Outcomes in China?

ERIC Educational Resources Information Center

Li, Yanfang; Lv, Ying; Huntsinger, Carol S.

2015-01-01

Relationships between exposure to preschool education and children's academic and social outcomes have been documented in Western countries. There is a lack of comparable research in China, where preschool education is relatively formal, but rather flexible in arrangement. We conducted research at six public kindergartens in a large Chinese city…

Ground-penetrating radar calibration at the Virginia Smart Road and signal analysis to improve prediction of flexible pavement layer thicknesses.

DOT National Transportation Integrated Search

2005-01-01

A ground-penetrating radar (GPR) system was used to collect data over the different pavement sections of the Virginia Smart Road from June 1999 until December 2002. Three antennae at different frequencies were used for this research. The collected da...

Lignin and Fiber digestibility in Caffeic Acid 3-O-Methyltransferase and Caffeoyl CoA 3-O-Methyltransferase Downregulated Alfalfa

USDA-ARS?s Scientific Manuscript database

Alfalfa (Medicago sativa L.) is one of the most important forages in the United States. Increasing alfalfa fiber digestibility would improve forage management and ration formulation flexibility. Currently, growers and breeders rely on near infrared spectroscopy (NIRS) to predict forage quality tra...

Feed-in Tariffs: Good Practices and Design Considerations

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

Cox, Sadie; Esterly, Sean

2016-01-02

In recent years, feed-in tariff (FIT) activity has focused primarily on revisions to current policies, underscoring the need for stable and predictable, yet flexible, policy environments. This policy brief provides a primer on key FIT design elements, lessons from country experience, and support resources to enable more detailed and country-specific FIT policy design.

Predicting Performance on a Firefighter's Ability Test from Fitness Parameters

ERIC Educational Resources Information Center

Michaelides, Marcos A.; Parpa, Koulla M.; Thompson, Jerald; Brown, Barry

2008-01-01

The purpose of this project was to identify the relationships between various fitness parameters such as upper body muscular endurance, upper and lower body strength, flexibility, body composition and performance on an ability test (AT) that included simulated firefighting tasks. A second intent was to create a regression model that would predict…

Social Support and Gender Role Attitude among Teenage Mothers.

ERIC Educational Resources Information Center

Kissman, Kris

1990-01-01

Identified some factors accounting for relatively flexible gender role orientation among adolescent mothers (n=118). Education and support from family, peers, and the father of the child(ren) were predictive of positive attitude toward combining career and child-care roles and competing in labor market on equal basis with males. (Author/NB)

Using thermography to detect misalignment in coupled equipment

NASA Astrophysics Data System (ADS)

Kelch, Craig K.; Grover, Paul E.

1996-03-01

This paper describes and reports the findings of a study performed by the Miller Brewing Company. The researchers assembled a test bed consisting of a motor and generator linked by seven different interchangeable flexible couplings. They then misaligned the motor and generator and used different predictive technologies to monitor any coupling changes.

When Simple Things Are Meaningful: Working Memory Strength Predicts Children's Cognitive Flexibility

ERIC Educational Resources Information Center

Blackwell, Katharine A.; Cepeda, Nicholas J.; Munakata, Yuko

2009-01-01

People often perseverate, repeating outdated behaviors despite correctly answering questions about rules they should be following. Children who perseverate are slower to respond to such questions than children who successfully switch to new rules, even after controlling for age and processing speed. Thus, switchers may have stronger working memory…

Strategy Generalization across Orientation Tasks: Testing a Computational Cognitive Model

ERIC Educational Resources Information Center

Gunzelmann, Glenn

2008-01-01

Humans use their spatial information processing abilities flexibly to facilitate problem solving and decision making in a variety of tasks. This article explores the question of whether a general strategy can be adapted for performing two different spatial orientation tasks by testing the predictions of a computational cognitive model. Human…

Development and validation of a habitat suitability model for the non-indigenous seagrass Zostera japonica in North America

EPA Science Inventory

We developed a spatially-explicit, flexible 3-parameter habitat suitability model that can be used to identify and predict areas at higher risk for non-native dwarf eelgrass (Zostera japonica) invasion. The model uses simple environmental parameters (depth, nearshore slope, and s...

Benchmarking performance measurement and lean manufacturing in the rough mill

Treesearch

Dan Cumbo; D. Earl Kline; Matthew S. Bumgardner

2006-01-01

Lean manufacturing represents a set of tools and a stepwise strategy for achieving smooth, predictable product flow, maximum product flexibility, and minimum system waste. While lean manufacturing principles have been successfully applied to some components of the secondary wood products value stream (e.g., moulding, turning, assembly, and finishing), the rough mill is...

The Costs of Supervised Classification: The Effect of Learning Task on Conceptual Flexibility

ERIC Educational Resources Information Center

Hoffman, Aaron B.; Rehder, Bob

2010-01-01

Research has shown that learning a concept via standard supervised classification leads to a focus on diagnostic features, whereas learning by inferring missing features promotes the acquisition of within-category information. Accordingly, we predicted that classification learning would produce a deficit in people's ability to draw "novel…

Controlling the stream of thought: working memory capacity predicts adjustment of mind-wandering to situational demands.

PubMed

Rummel, Jan; Boywitt, C Dennis

2014-10-01

Although engaging in task-unrelated thoughts can be enjoyable and functional under certain circumstances, allowing one's mind to wander off-task will come at a cost to performance in many situations. Given that task-unrelated thoughts need to be blocked out when the current task requires full attention, it has been argued that cognitive control is necessary to prevent mind-wandering from becoming maladaptive. Extending this idea, we exposed participants to tasks of different demands and assessed mind-wandering via thought probes. Employing a latent-change model, we found mind-wandering to be adjusted to current task demands. As hypothesized, the degree of adjustment was predicted by working memory capacity, indicating that participants with higher working memory capacity were more flexible in their coordination of on- and off-task thoughts. Notably, the better the adjustment, the smaller performance decrements due to increased task demands were. On the basis of these findings, we argue that cognitive control does not simply allow blocking out task-unrelated thoughts but, rather, allows one to flexibly adjust mind-wandering to situational demands.

Higgs mass prediction in the MSSM at three-loop level in a pure \\overline{{ {DR}}} context

NASA Astrophysics Data System (ADS)

Harlander, Robert V.; Klappert, Jonas; Voigt, Alexander

2017-12-01

The impact of the three-loop effects of order α _tα _s^2 on the mass of the light CP-even Higgs boson in the { {MSSM}} is studied in a pure \\overline{{ {DR}}} context. For this purpose, we implement the results of Kant et al. (JHEP 08:104, 2010) into the C++ module Himalaya and link it to FlexibleSUSY, a Mathematica and C++ package to create spectrum generators for BSM models. The three-loop result is compared to the fixed-order two-loop calculations of the original FlexibleSUSY and of FeynHiggs, as well as to the result based on an EFT approach. Aside from the expected reduction of the renormalization scale dependence with respect to the lower-order results, we find that the three-loop contributions significantly reduce the difference from the EFT prediction in the TeV-region of the { {SUSY}} scale {M_S}. Himalaya can be linked also to other two-loop \\overline{{ {DR}}} codes, thus allowing for the elevation of these codes to the three-loop level.

An Ensemble-Based Forecasting Framework to Optimize Reservoir Releases

NASA Astrophysics Data System (ADS)

Ramaswamy, V.; Saleh, F.

2017-12-01

Increasing frequency of extreme precipitation events are stressing the need to manage water resources on shorter timescales. Short-term management of water resources becomes proactive when inflow forecasts are available and this information can be effectively used in the control strategy. This work investigates the utility of short term hydrological ensemble forecasts for operational decision making during extreme weather events. An advanced automated hydrologic prediction framework integrating a regional scale hydrologic model, GIS datasets and the meteorological ensemble predictions from the European Center for Medium Range Weather Forecasting (ECMWF) was coupled to an implicit multi-objective dynamic programming model to optimize releases from a water supply reservoir. The proposed methodology was evaluated by retrospectively forecasting the inflows to the Oradell reservoir in the Hackensack River basin in New Jersey during the extreme hydrologic event, Hurricane Irene. Additionally, the flexibility of the forecasting framework was investigated by forecasting the inflows from a moderate rainfall event to provide important perspectives on using the framework to assist reservoir operations during moderate events. The proposed forecasting framework seeks to provide a flexible, assistive tool to alleviate the complexity of operational decision-making.

Aeroservoelastic Stability Analysis of the X-43A Stack

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2008-01-01

The first air launch attempt of an X-43A stack, consisting of the booster, adapter and Hyper-X research vehicle, ended in failure shortly after the successful drop from the National Aeronautics and Space Administration Dryden Flight Research Center (Edwards, California) B-52B airplane and ignition of the booster. The stack was observed to begin rolling and yawing violently upon reaching transonic speeds, and the grossly oscillating fins of the booster separated shortly thereafter. The flight then had to be terminated with the stack out of control. Very careful linear flutter and aeroservoelastic analyses were subsequently performed as reported herein to numerically duplicate the observed instability. These analyses properly identified the instability mechanism and demonstrated the importance of including the flight control laws, rigid-body modes, structural flexible modes and control surface flexible modes. In spite of these efforts, however, the predicted instability speed remained more than 25 percent higher than that observed in flight. It is concluded that transonic shock phenomena, which linear analyses cannot take into account, are also important for accurate prediction of this mishap instability.

Clinical validation of three short forms of the Dutch Wechsler Memory Scale-Fourth Edition (WMS-IV-NL) in a mixed clinical sample.

PubMed

Bouman, Zita; Hendriks, Marc P H; Van Der Veld, William M; Aldenkamp, Albert P; Kessels, Roy P C

2016-06-01

The reliability and validity of three short forms of the Dutch version of the Wechsler Memory Scale-Fourth Edition (WMS-IV-NL) were evaluated in a mixed clinical sample of 235 patients. The short forms were based on the WMS-IV Flexible Approach, that is, a 3-subtest combination (Older Adult Battery for Adults) and two 2-subtest combinations (Logical Memory and Visual Reproduction and Logical Memory and Designs), which can be used to estimate the Immediate, Delayed, Auditory and Visual Memory Indices. All short forms showed good reliability coefficients. As expected, for adults (16-69 years old) the 3-subtest short form was consistently more accurate (predictive accuracy ranged from 73% to 100%) than both 2-subtest short forms (range = 61%-80%). Furthermore, for older adults (65-90 years old), the predictive accuracy of the 2-subtest short form ranged from 75% to 100%. These results suggest that caution is warranted when using the WMS-IV-NL Flexible Approach short forms to estimate all four indices. © The Author(s) 2015.

Establishing the relationship between manufacturing and component performance in stretch formed thermoplastic composites

NASA Technical Reports Server (NTRS)

Santare, Michael H.; Pipes, R. Byron; Beaussart, A. J.; Coffin, D. W.; Otoole, B. J.; Shuler, S. F.

1993-01-01

Flexible manufacturing methods are needed to reduce the cost of using advanced composites in structural applications. One method that allows for this is the stretch forming of long discontinuous fiber materials with thermoplastic matrices. In order to exploit this flexibility in an economical way, a thorough understanding of the relationship between manufacturing and component performance must be developed. This paper reviews some of the recent work geared toward establishing this understanding. Micromechanics models have been developed to predict the formability of the material during processing. The latest improvement of these models includes the viscoelastic nature of the matrix and comparison with experimental data. A finite element scheme is described which can be used to model the forming process. This model uses equivalent anisotropic viscosities from the micromechanics models and predicts the microstructure in the formed part. In addition, structural models have been built to account for the material property gradients that can result from the manufacturing procedures. Recent developments in this area include the analysis of stress concentrations and a failure model each accounting for the heterogeneous material fields.

Zooming into creativity: individual differences in attentional global-local biases are linked to creative thinking.

PubMed

Zmigrod, Sharon; Zmigrod, Leor; Hommel, Bernhard

2015-01-01

While recent studies have investigated how processes underlying human creativity are affected by particular visual-attentional states, we tested the impact of more stable attention-related preferences. These were assessed by means of Navon's global-local task, in which participants respond to the global or local features of large letters constructed from smaller letters. Three standard measures were derived from this task: the sizes of the global precedence effect, the global interference effect (i.e., the impact of incongruent letters at the global level on local processing), and the local interference effect (i.e., the impact of incongruent letters at the local level on global processing). These measures were correlated with performance in a convergent-thinking creativity task (the Remote Associates Task), a divergent-thinking creativity task (the Alternate Uses Task), and a measure of fluid intelligence (Raven's matrices). Flexibility in divergent thinking was predicted by the local interference effect while convergent thinking was predicted by intelligence only. We conclude that a stronger attentional bias to visual information about the "bigger picture" promotes cognitive flexibility in searching for multiple solutions.

Does the ability to express different emotions predict different indices of physical health? A skill-based study of physical symptoms and heart rate variability.

PubMed

Tuck, Natalie L; Adams, Kathryn S; Consedine, Nathan S

2017-09-01

The outward expression of emotion has been frequently associated with better health outcomes, whereas suppressing emotion is thought to contribute to worse physical health. However, work has typically focused on trait expressive tendencies and the possibility that individual differences in the ability to express specific emotions may also be associated with health has not been widely tested. A cross-sectional study of community dwelling adults. One hundred and twenty-eight participants aged 18-88 years completed questionnaires assessing demographics and health status, before attending a testing session in which resting heart rate variability (HRV) was assessed. Participants then completed a performance-based test of expressive regulatory skill in which they were instructed to enhance and suppress their emotional expressions while they watched film clips validated to elicit amusement, sadness, and anger. Participants rated subjective emotional experience before and after each clip, and their degree of expressivity was scored using FACS-based Noldus FaceReader. Missing data resulted in a final sample size of 117. Linear regressions controlling for age, sex, diagnoses, and trait emotion revealed that greater ability to enhance sad expressions was associated with higher HRV while the ability to enhance expressions of joy was associated with lower symptom interference. In parallel models, the ability to flexibly regulate (both enhance and suppress) expressions of joy and sadness was also associated with lower symptom interference. Findings suggest that the ability to regulate expressions of both sadness and joy is associated with health indices even when controlling for trait affect and potential confounds. The present findings offer early evidence that individual differences in the ability to regulate the outward expression of emotion may be relevant to health and suggest that expressive regulatory skills offer a novel avenue for research and intervention. Statement of contribution What is already known on this subject The tendency to outwardly express felt emotion generally predicts better health, whereas expressive suppression typically predicts worse health outcomes. Most work has been based on trait assessments; however, the ability to regulate the expression of felt emotion can be objectively assessed using performance-based tests. Prior work in mental health suggests that the ability to flexibly up- and downregulate the expression of emotion predicts better outcomes. What does this study add The first evidence that the ability to flexibly regulate expressions predicts indices of health. Skill in both expressing and suppressing facial expressions predicts better reported health. Skills with different emotions differentially predict symptom interference and cardiac vagal tone. © 2017 The British Psychological Society.

Over-imitation is not automatic: context sensitivity in children's overimitation and action interpretation of causally irrelevant actions.

PubMed

Keupp, Stefanie; Behne, Tanya; Zachow, Joanna; Kasbohm, Alina; Rakoczy, Hannes

2015-02-01

Recent research has documented the robust tendency of children to "over-imitate," that is, to copy causally irrelevant action elements in goal-directed action sequences. Different explanations for over-imitation have been proposed. Causal accounts claim that children mistakenly perceive such action elements as causally relevant and, therefore, imitate them. Affiliation accounts claim that children over-imitate to affiliate with the model. Normative accounts claim that children conceive of causally irrelevant actions as essential parts of an overarching conventional activity. These different accounts generally hold the same predictions regarding children's imitative response. However, it is possible to distinguish between them when one considers additional parameters. The normative account predicts wide-ranging flexibility with regard to action interpretation and the occurrence of over-imitation. First, it predicts spontaneous protest against norm violators who omit the causally irrelevant actions. Second, children should perform the causally irrelevant actions less frequently, and criticize others less frequently for omitting them, when the actions take place in a different context from the one of the initial demonstration. Such flexibility is not predicted by causal accounts and is predicted for only a limited range of contexts by affiliation accounts. Study 1 investigated children's own imitative response and found less over-imitation when children acted in a different context from when they acted in the same context as the initial demonstration. In Study 2, children criticized a puppet less frequently for omitting irrelevant actions when the puppet acted in a different context. The results support the notion that over-imitation is not an automatic and inflexible phenomenon. Copyright © 2014 Elsevier Inc. All rights reserved.

Research on Novel High-Power Microwave/Millimeter Wave Sources and Applications

DTIC Science & Technology

2010-08-28

density with acceptable operating temperature and lifetime. The MIG is optimized with the EGUN code for a cath- ode voltage Vb of 100 kV and a beam...emission suppression. Figure 2 is an EGUN drawing of the MIG configuration/ dimensions and electron trajectories. The design is flexible TABLE I. Predicted...and measured MIG parameters. EGUN prediction smooth cathode Measurement Voltage kV 100.0 100.0 Current A 8.0 8.0 0 1.40 1.40 vz /vz0 3.5% 4.6

Robust functional regression model for marginal mean and subject-specific inferences.

PubMed

Cao, Chunzheng; Shi, Jian Qing; Lee, Youngjo

2017-01-01

We introduce flexible robust functional regression models, using various heavy-tailed processes, including a Student t-process. We propose efficient algorithms in estimating parameters for the marginal mean inferences and in predicting conditional means as well as interpolation and extrapolation for the subject-specific inferences. We develop bootstrap prediction intervals (PIs) for conditional mean curves. Numerical studies show that the proposed model provides a robust approach against data contamination or distribution misspecification, and the proposed PIs maintain the nominal confidence levels. A real data application is presented as an illustrative example.

Loads and aeroelasticity division research and technology accomplishments for FY 1983 and plans for FY 1984

NASA Technical Reports Server (NTRS)

Gardner, J. E.; Dixon, S. C.

1984-01-01

Research was done in the following areas: development and validation of solution algorithms, modeling techniques, integrated finite elements for flow-thermal-structural analysis and design, optimization of aircraft and spacecraft for the best performance, reduction of loads and increase in the dynamic structural stability of flexible airframes by the use of active control, methods for predicting steady and unsteady aerodynamic loads and aeroelastic characteristics of flight vehicles with emphasis on the transonic range, and methods for predicting and reducing helicoper vibrations.

Flexibility of orthographic and graphomotor coordination during a handwritten copy task: effect of time pressure

PubMed Central

Sausset, Solen; Lambert, Eric; Olive, Thierry

2013-01-01

The coordination of the various processes involved in language production is a subject of keen debate in writing research. Some authors hold that writing processes can be flexibly coordinated according to task demands, whereas others claim that process coordination is entirely inflexible. For instance, orthographic planning has been shown to be resource-dependent during handwriting, but inflexible in typing, even under time pressure. The present study therefore went one step further in studying flexibility in the coordination of orthographic processing and graphomotor execution, by measuring the impact of time pressure during a handwritten copy task. Orthographic and graphomotor processes were observed via syllable processing. Writers copied out two- and three-syllable words three times in a row, with and without time pressure. Latencies and letter measures at syllable boundaries were analyzed. We hypothesized that if coordination is flexible and varies according to task demands, it should be modified by time pressure, affecting both latency before execution and duration of execution. We therefore predicted that the extent of syllable processing before execution would be reduced under time pressure and, as a consequence, syllable effects during execution would be more salient. Results showed, however, that time pressure interacted neither with syllable number nor with syllable structure. Accordingly, syllable processing appears to remain the same regardless of time pressure. The flexibility of process coordination during handwriting is discussed, as is the operationalization of time pressure constraints. PMID:24319435

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes.

PubMed

Brown, Jenna R; Livesay, Dennis R

2015-01-01

β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme.

Mediated moderation in combined cognitive behavioral therapy versus component treatments for generalized anxiety disorder.

PubMed

Newman, Michelle G; Fisher, Aaron J

2013-06-01

This study examined (a) duration of generalized anxiety disorder (GAD) as a moderator of cognitive behavioral therapy (CBT) versus its components (cognitive therapy and self-control desensitization) and (b) increases in dynamic flexibility of anxious symptoms during the course of psychotherapy as a mediator of this moderation. Degree of dynamic flexibility in daily symptoms was quantified as the inverse of spectral power due to daily to intradaily oscillations in four-times-daily diary data (Fisher, Newman, & Molenaar, 2011). This was a secondary analysis of the data of Borkovec, Newman, Pincus, and Lytle (2002). Seventy-six participants with a principle diagnosis of GAD were assigned randomly to combined CBT (n = 24), cognitive therapy (n = 25), or self-control desensitization (n = 27). Duration of GAD moderated outcome such that those with longer duration showed greater reliable change from component treatments than they showed from CBT, whereas those with shorter duration fared better in response to CBT. Decreasing predictability in daily and intradaily oscillations of anxiety symptoms during therapy reflected less rigidity and more flexible responding. Increases in flexibility over the course of therapy fully mediated the moderating effect of GAD duration on condition, indicating a mediated moderation process. Individuals with longer duration of GAD may respond better to more focused treatments, whereas those with shorter duration of GAD may respond better to a treatment that offers more coping strategies. Importantly, the mechanism by which this moderation occurs appears to be the establishment of flexible responding during treatment.

Flexibility of resource allocation in a hermaphroditic-gynomonoecious herb through deployment of female and male resources in perfect flowers.

PubMed

Mamut, Jannathan; Xiong, Ying-Ze; Tan, Dun-Yan; Huang, Shuang-Quan

2017-03-01

It has been hypothesized that two flower types permit flexible allocation of resources to female and male functions, yet empirical evidence for the sex-allocation hypothesis remains scarce in gynomonoecious species. To characterize resource allocation to pistillate and perfect flowers and allocation of perfect flowers between gynomonoecious and hermaphroditic individuals, we examined the flexibility and whether female-biased allocation increases with plant size in the hermaphroditic-gynomonoecious herb Eremurus anisopterus . Frequency of gynomonoecious individuals, flower production, and plant size were investigated in different populations. Floral allocation was compared among the three flower types of E. anisopterus . Frequency of gynomonoecious plants varied from 2-17% in nine populations. Only larger plants produced female flowers at the bottom of racemes. Both female and perfect flower production tended to increase proportionately with plant size in gynomonoecious individuals. Female flowers did not produce less biomass than perfect flowers from hermaphroditic or gynomonoecious plants. However, both female and perfect flowers from gynomonoecious individuals had lighter stamen mass, but larger pistil mass, than perfect flowers from hermaphrodites. Although the prediction of an increase in female flower number with plant size was not observed in E. anisopterus , the flexibility of sex allocation in gynomonoecious species was confirmed in that gynomonoecious individuals had a female-biased floral allocation compared to hermaphroditic individuals. Such comparisons of gynomonoecious to hermaphroditic individuals permit us to unveil a sexual adjustment strategy: flexibility of sexual investments within plants. © 2017 Botanical Society of America.

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

PubMed Central

Brown, Jenna R.; Livesay, Dennis R.

2015-01-01

β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme. PMID:26018804

A cost analysis of reusable and disposable flexible optical scopes for intubation.

PubMed

Tvede, M F; Kristensen, M S; Nyhus-Andreasen, M

2012-05-01

Intubation using a flexible optical scope (FOS) is a cornerstone technique for managing the predicted and unpredicted difficult airway. The term FOS covers both fibre-optic scopes and videoscopes. The total costs of using flexible scopes for intubation are unknown. The recent introduction of a disposable flexible scope for intubation merits closer scrutiny of the total costs associated with both modalities. The costs incurred during intubations using FOSs at a large anaesthesia department were identified, and a series of intubations using a disposable scope were analyzed for comparison. Recognized health-economic methodology was applied. During a 1-year period, 360 FOS intubations were performed. In this clinical setting, the average cost of an intubation using a reusable FOS was €177.7. When using the disposable Ambu(®) aScope (Ambu A/S, Ballerup, Denmark), the cost was €204.4. The break-even point, i.e. the number of intubations per month where the cost of using disposable and non-disposable equipment is identical, was 22.5/month. A subgroup analysis looking solely at intubations performed with flexible videoscopes revealed that the cost per intubation was equal for disposable and reusable videoscopes. At our institution, the total cost of an intubation is greater when using disposable compared with reusable equipment (€204.4 vs. €177.7). If video equipment with an external monitor is considered mandatory, the expenses are of equal magnitude. The cost analysis is particularly sensitive to the actual number of flexible optic intubations performed; with fewer intubations, the total cost will begin to favour disposable equipment. © 2012 The Authors. Acta Anaesthesiologica Scandinavica © 2012 The Acta Anaesthesiologica Scandinavica Foundation.

Medium-scale carbon nanotube thin-film integrated circuits on flexible plastic substrates.

PubMed

Cao, Qing; Kim, Hoon-sik; Pimparkar, Ninad; Kulkarni, Jaydeep P; Wang, Congjun; Shim, Moonsub; Roy, Kaushik; Alam, Muhammad A; Rogers, John A

2008-07-24

The ability to form integrated circuits on flexible sheets of plastic enables attributes (for example conformal and flexible formats and lightweight and shock resistant construction) in electronic devices that are difficult or impossible to achieve with technologies that use semiconductor wafers or glass plates as substrates. Organic small-molecule and polymer-based materials represent the most widely explored types of semiconductors for such flexible circuitry. Although these materials and those that use films or nanostructures of inorganics have promise for certain applications, existing demonstrations of them in circuits on plastic indicate modest performance characteristics that might restrict the application possibilities. Here we report implementations of a comparatively high-performance carbon-based semiconductor consisting of sub-monolayer, random networks of single-walled carbon nanotubes to yield small- to medium-scale integrated digital circuits, composed of up to nearly 100 transistors on plastic substrates. Transistors in these integrated circuits have excellent properties: mobilities as high as 80 cm(2) V(-1) s(-1), subthreshold slopes as low as 140 m V dec(-1), operating voltages less than 5 V together with deterministic control over the threshold voltages, on/off ratios as high as 10(5), switching speeds in the kilohertz range even for coarse (approximately 100-microm) device geometries, and good mechanical flexibility-all with levels of uniformity and reproducibility that enable high-yield fabrication of integrated circuits. Theoretical calculations, in contexts ranging from heterogeneous percolative transport through the networks to compact models for the transistors to circuit level simulations, provide quantitative and predictive understanding of these systems. Taken together, these results suggest that sub-monolayer films of single-walled carbon nanotubes are attractive materials for flexible integrated circuits, with many potential areas of application in consumer and other areas of electronics.

A deformation model of flexible, HAMR objects for accurate propagation under perturbations and the self-shadowing effects

NASA Astrophysics Data System (ADS)

Channumsin, Sittiporn; Ceriotti, Matteo; Radice, Gianmarco

2018-02-01

A new type of space debris in near geosynchronous orbit (GEO) was recently discovered and later identified as exhibiting unique characteristics associated with high area-to-mass ratio (HAMR) objects, such as high rotation rates and high reflection properties. Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that its motion depends on the actual effective area, orientation of that effective area, reflection properties and the area-to-mass ratio of the object is not stable over time. Previous investigations have modelled this type of debris as rigid bodies (constant area-to-mass ratios) or discrete deformed body; however, these simplifications will lead to inaccurate long term orbital predictions. This paper proposes a simple yet reliable model of a thin, deformable membrane based on multibody dynamics. The membrane is modelled as a series of flat plates, connected through joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account through lump masses at the joints. The attitude and orbital motion of this flexible membrane model is then propagated near GEO to predict its orbital evolution under the perturbations of solar radiation pressure, Earth's gravity field (J2), third body gravitational fields (the Sun and Moon) and self-shadowing. These results are then compared to those obtained for two rigid body models (cannonball and flat rigid plate). In addition, Monte Carlo simulations of the flexible model by varying initial attitude and deformation angle (different shape) are investigated and compared with the two rigid models (cannonball and flat rigid plate) over a period of 100 days. The numerical results demonstrate that cannonball and rigid flat plate are not appropriate to capture the true dynamical evolution of these objects, at the cost of increased computational time.

Prey density and the behavioral flexibility of a marine predator: The common murre (Uria aalge)

USGS Publications Warehouse

Harding, A.M.A.; Piatt, John F.; Schmutz, J.A.; Shultz, M.T.; van Pelt, Thomas I.; Kettle, Arthur B.; Speckman, Suzann G.

2007-01-01

Flexible time budgets allow individual animals to buffer the effects of variable food availability by allocating more time to foraging when food density decreases. This trait should be especially important for marine predators that forage on patchy and ephemeral food resources. We examined flexible time allocation by a long-lived marine predator, the Common Murre (Uria aalge), using data collected in a five-year study at three colonies in Alaska (USA) with contrasting environmental conditions. Annual hydroacoustic surveys revealed an order-of-magnitude variation in food density among the 15 colony-years of study. We used data on parental time budgets and local prey density to test predictions from two hypotheses: Hypothesis A, the colony attendance of seabirds varies nonlinearly with food density; and Hypothesis B, flexible time allocation of parent murres buffers chicks against variable food availability. Hypothesis A was supported; colony attendance by murres was positively correlated with food over a limited range of poor-to-moderate food densities, but independent of food over a broader range of higher densities. This is the first empirical evidence for a nonlinear response of a marine predator's time budget to changes in prey density. Predictions from Hypothesis B were largely supported: (1) chick-feeding rates were fairly constant over a wide range of densities and only dropped below 3.5 meals per day at the low end of prey density, and (2) there was a nonlinear relationship between chick-feeding rates and time spent at the colony, with chick-feeding rates only declining after time at the colony by the nonbrooding parent was reduced to a minimum. The ability of parents to adjust their foraging time by more than 2 h/d explains why they were able to maintain chick-feeding rates of more than 3.5 meals/d across a 10-fold range in local food density. ?? 2007 by the Ecological Society of America.

Stochastic Dynamics Underlying Cognitive Stability and Flexibility

PubMed Central

Ueltzhöffer, Kai; Armbruster-Genç, Diana J. N.; Fiebach, Christian J.

2015-01-01

Cognitive stability and flexibility are core functions in the successful pursuit of behavioral goals. While there is evidence for a common frontoparietal network underlying both functions and for a key role of dopamine in the modulation of flexible versus stable behavior, the exact neurocomputational mechanisms underlying those executive functions and their adaptation to environmental demands are still unclear. In this work we study the neurocomputational mechanisms underlying cue based task switching (flexibility) and distractor inhibition (stability) in a paradigm specifically designed to probe both functions. We develop a physiologically plausible, explicit model of neural networks that maintain the currently active task rule in working memory and implement the decision process. We simplify the four-choice decision network to a nonlinear drift-diffusion process that we canonically derive from a generic winner-take-all network model. By fitting our model to the behavioral data of individual subjects, we can reproduce their full behavior in terms of decisions and reaction time distributions in baseline as well as distractor inhibition and switch conditions. Furthermore, we predict the individual hemodynamic response timecourse of the rule-representing network and localize it to a frontoparietal network including the inferior frontal junction area and the intraparietal sulcus, using functional magnetic resonance imaging. This refines the understanding of task-switch-related frontoparietal brain activity as reflecting attractor-like working memory representations of task rules. Finally, we estimate the subject-specific stability of the rule-representing attractor states in terms of the minimal action associated with a transition between different rule states in the phase-space of the fitted models. This stability measure correlates with switching-specific thalamocorticostriatal activation, i.e., with a system associated with flexible working memory updating and dopaminergic modulation of cognitive flexibility. These results show that stochastic dynamical systems can implement the basic computations underlying cognitive stability and flexibility and explain neurobiological bases of individual differences. PMID:26068119

Coupled Fluid-Structure Interaction Analysis of Solid Rocket Motor with Flexible Inhibitors

NASA Technical Reports Server (NTRS)

Yang, H. Q.; West, Jeff; Harris, Robert E.

2014-01-01

Flexible inhibitors are generally used in solid rocket motors (SRMs) as a means to control the burning of propellant. Vortices generated by the flow of propellant around the flexible inhibitors have been identified as a driving source of instabilities that can lead to thrust oscillations in launch vehicles. Potential coupling between the SRM thrust oscillations and structural vibration modes is an important risk factor in launch vehicle design. As a means to predict and better understand these phenomena, a multidisciplinary simulation capability that couples the NASA production CFD code, Loci/CHEM, with CFDRC's structural finite element code, CoBi, has been developed. This capability is crucial to the development of NASA's new space launch system (SLS). This paper summarizes the efforts in applying the coupled software to demonstrate and investigate fluid-structure interaction (FSI) phenomena between pressure waves and flexible inhibitors inside reusable solid rocket motors (RSRMs). The features of the fluid and structural solvers are described in detail, and the coupling methodology and interfacial continuity requirements are then presented in a general Eulerian-Lagrangian framework. The simulations presented herein utilize production level CFD with hybrid RANS/LES turbulence modeling and grid resolution in excess of 80 million cells. The fluid domain in the SRM is discretized using a general mixed polyhedral unstructured mesh, while full 3D shell elements are utilized in the structural domain for the flexible inhibitors. Verifications against analytical solutions for a structural model under a steady uniform pressure condition and under dynamic modal analysis show excellent agreement in terms of displacement distribution and eigenmode frequencies. The preliminary coupled results indicate that due to acoustic coupling, the dynamics of one of the more flexible inhibitors shift from its first modal frequency to the first acoustic frequency of the solid rocket motor. This insight could have profound implications for SRM and flexible inhibitor designs for current and future launch vehicles including SLS.

Individual differences in choice (in)flexibility but not impulsivity in the common marmoset: an automated, operant-behavior choice task.

PubMed

Adriani, Walter; Romani, Chiara; Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni

2013-11-01

Individual differences in behavioural flexibility are a significant issue in human psychopathology as well as in its animal models. We aimed to investigate individual variations of operant-choice behaviour in the common marmoset (Callithrix jacchus), a small New World primate, using a new operant panel with two hand-poking holes. Experimental subjects (N=16) were presented with a choice between a Small & Soon (SS) vs a Large & Late (LL) food reward. After extensive training (31 daily sessions with no delay, during which a basal, large-reward preference developed), the delay before release of LL was progressively increased (from 0 to 60 s, during 16 daily sessions; indifferent point at delay=9 s). Subjects were classified as either "flexible" or "non-flexible", respectively, based on a decrease (or not) in the preference for LL with increasing delays. Each subject was also classified as "maximizer" (or "non-maximizer") based on capacity (or not) to maximize the food payoff as delay increased. Upon delays shorter than the indifferent point (<9s), none of the subjects showed a shift from LL to SS, denoting a lack of delay-induced, cognitive impulsivity. Individual differences only emerged upon delays longer than the indifferent point (>9 s), when a preference shift could be interpreted as economically-driven. In general, a profile of few unrewarded hand-pokes in reaction to initial delays (i.e., a low motor impulsivity) and of clear-cut basal LL preference seemed to predict elevated flexibility of choices and better food payoff, which was typical of subjects classified as both "flexible & maximizer". These results provide normative data on the marmosets, which can be used as a model for the investigation of 1) individual differences in behavioural flexibility, as well as 2) biological mechanisms rooted in our evolutionary history. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity.

PubMed

Qin, Lingyun; Liu, Huili; Chen, Rong; Zhou, Jingjing; Cheng, Xiyao; Chen, Yao; Huang, Yongqi; Su, Zhengding

2017-11-07

The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays pivotal roles in determining and predicting the binding properties and the design of inhibitors. Although the molecular dynamics simulation approach enables us to understand protein-ligand interactions, the mechanism underlying how a flexible binding pocket adapts an inhibitor has been less explored experimentally. In this work, we have investigated how the intrinsic flexible regions of the N-terminal domain of MdmX (N-MdmX) affect the affinity of the Mdm2 inhibitor nutlin-3a using protein engineering. Guided by heteronuclear nuclear Overhauser effect measurements, we identified the flexible regions that affect inhibitor binding affinity around the ligand-binding pocket on N-MdmX. A disulfide engineering mutant, N-MdmX C25-C110/C76-C88 , which incorporated two staples to rigidify the ligand-binding pocket, allowed an affinity for nutlin-3a higher than that of wild-type N-MdmX (K d ∼ 0.48 vs K d ∼ 20.3 μM). Therefore, this mutant provides not only an effective protein model for screening and designing of MdmX inhibitors but also a valuable clue for enhancing the intermolecular interactions of the pharmacophores of a ligand with pronounced flexible regions. In addition, our results revealed an allosteric ligand-binding mechanism of N-MdmX in which the ligand initially interacts with a compact core, followed by augmenting intermolecular interactions with intrinsic flexible regions. This strategy should also be applicable to many other protein targets to accelerate drug discovery.

The predictive protective control of the heat exchanger

NASA Astrophysics Data System (ADS)

Nevriva, Pavel; Filipova, Blanka; Vilimec, Ladislav

2016-06-01

The paper deals with the predictive control applied to flexible cogeneration energy system FES. FES was designed and developed by the VITKOVICE POWER ENGINEERING joint-stock company and represents a new solution of decentralized cogeneration energy sources. In FES, the heating medium is flue gas generated by combustion of a solid fuel. The heated medium is power gas, which is a gas mixture of air and water steam. Power gas is superheated in the main heat exchanger and led to gas turbines. To protect the main heat exchanger against damage by overheating, the novel predictive protective control based on the mathematical model of exchanger was developed. The paper describes the principle, the design and the simulation of the predictive protective method applied to main heat exchanger of FES.

Update of the ATTRACT force field for the prediction of protein-protein binding affinity.

PubMed

Chéron, Jean-Baptiste; Zacharias, Martin; Antonczak, Serge; Fiorucci, Sébastien

2017-06-05

Determining the protein-protein interactions is still a major challenge for molecular biology. Docking protocols has come of age in predicting the structure of macromolecular complexes. However, they still lack accuracy to estimate the binding affinities, the thermodynamic quantity that drives the formation of a complex. Here, an updated version of the protein-protein ATTRACT force field aiming at predicting experimental binding affinities is reported. It has been designed on a dataset of 218 protein-protein complexes. The correlation between the experimental and predicted affinities reaches 0.6, outperforming most of the available protocols. Focusing on a subset of rigid and flexible complexes, the performance raises to 0.76 and 0.69, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

PubMed

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A; Ryu, Seong Eon; Kim, Deok-Soo

2016-07-08

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Model Update of a Micro Air Vehicle (MAV) Flexible Wing Frame with Uncertainty Quantification

NASA Technical Reports Server (NTRS)

Reaves, Mercedes C.; Horta, Lucas G.; Waszak, Martin R.; Morgan, Benjamin G.

2004-01-01

This paper describes a procedure to update parameters in the finite element model of a Micro Air Vehicle (MAV) to improve displacement predictions under aerodynamics loads. Because of fabrication, materials, and geometric uncertainties, a statistical approach combined with Multidisciplinary Design Optimization (MDO) is used to modify key model parameters. Static test data collected using photogrammetry are used to correlate with model predictions. Results show significant improvements in model predictions after parameters are updated; however, computed probabilities values indicate low confidence in updated values and/or model structure errors. Lessons learned in the areas of wing design, test procedures, modeling approaches with geometric nonlinearities, and uncertainties quantification are all documented.

Physical signals for protein-DNA recognition

NASA Astrophysics Data System (ADS)

Cao, Xiao-Qin; Zeng, Jia; Yan, Hong

2009-09-01

This paper discovers consensus physical signals around eukaryotic splice sites, transcription start sites, and replication origin start and end sites on a genome-wide scale based on their DNA flexibility profiles calculated by three different flexibility models. These salient physical signals are localized highly rigid and flexible DNAs, which may play important roles in protein-DNA recognition by the sliding search mechanism. The found physical signals lead us to a detailed hypothetical view of the search process in which a DNA-binding protein first finds a genomic region close to the target site from an arbitrary starting location by three-dimensional (3D) hopping and intersegment transfer mechanisms for long distances, and subsequently uses the one-dimensional (1D) sliding mechanism facilitated by the localized highly rigid DNAs to accurately locate the target flexible binding site within 30 bp (base pair) short distances. Guided by these physical signals, DNA-binding proteins rapidly search the entire genome to recognize a specific target site from the 3D to 1D pathway. Our findings also show that current promoter prediction programs (PPPs) based on DNA physical properties may suffer from lots of false positives because other functional sites such as splice sites and replication origins have similar physical signals as promoters do.

Competing while cooperating with the same others: The consequences of conflicting demands in co-opetition.

PubMed

Landkammer, Florian; Sassenberg, Kai

2016-12-01

Numerous studies comparing the effects of competition and cooperation demonstrated that competition is detrimental on the social level. However, instead of purely competing, many social contexts require competing while cooperating with the same social target. The current work examined the consequences of such "co-opetition" situations between individuals. Because having to compete and to cooperate with the same social target constitutes conflicting demands, co-opetition should lead to more flexibility, such as (a) less rigid transfer effects of competitive behavior and (b) less rigidity/more flexibility in general. Supporting these predictions, Studies 1a and 1b demonstrated that co-opetition did not elicit competitive behavior in a subsequent task (here: enhanced deceiving of uninvolved others). Study 2 showed that adding conflicting demands (independent of social interdependence) to competition likewise elicits less competitive transfer than competition without such conflicting demands. Beyond that, co-opetition reduced rigid response tendencies during a classification task in Studies 3a and 3b and enhanced flexibility during brainstorming in Study 4, compared with other forms of interdependence. Together, these results suggest that co-opetition leads to more flexible behavior when individuals have to reconcile conflicting demands. Implications for research on social priming, interdependence and competition in everyday life are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

High-Frequency Binaural Beats Increase Cognitive Flexibility: Evidence from Dual-Task Crosstalk.

PubMed

Hommel, Bernhard; Sellaro, Roberta; Fischer, Rico; Borg, Saskia; Colzato, Lorenza S

2016-01-01

Increasing evidence suggests that cognitive-control processes can be configured to optimize either persistence of information processing (by amplifying competition between decision-making alternatives and top-down biasing of this competition) or flexibility (by dampening competition and biasing). We investigated whether high-frequency binaural beats, an auditory illusion suspected to act as a cognitive enhancer, have an impact on cognitive-control configuration. We hypothesized that binaural beats in the gamma range bias the cognitive-control style toward flexibility, which in turn should increase the crosstalk between tasks in a dual-task paradigm. We replicated earlier findings that the reaction time in the first-performed task is sensitive to the compatibility between the responses in the first and the second task-an indication of crosstalk. As predicted, exposing participants to binaural beats in the gamma range increased this effect as compared to a control condition in which participants were exposed to a continuous tone of 340 Hz. These findings provide converging evidence that the cognitive-control style can be systematically biased by inducing particular internal states; that high-frequency binaural beats bias the control style toward more flexibility; and that different styles are implemented by changing the strength of local competition and top-down bias.

High-Frequency Binaural Beats Increase Cognitive Flexibility: Evidence from Dual-Task Crosstalk

PubMed Central

Hommel, Bernhard; Sellaro, Roberta; Fischer, Rico; Borg, Saskia; Colzato, Lorenza S.

2016-01-01

Increasing evidence suggests that cognitive-control processes can be configured to optimize either persistence of information processing (by amplifying competition between decision-making alternatives and top-down biasing of this competition) or flexibility (by dampening competition and biasing). We investigated whether high-frequency binaural beats, an auditory illusion suspected to act as a cognitive enhancer, have an impact on cognitive-control configuration. We hypothesized that binaural beats in the gamma range bias the cognitive-control style toward flexibility, which in turn should increase the crosstalk between tasks in a dual-task paradigm. We replicated earlier findings that the reaction time in the first-performed task is sensitive to the compatibility between the responses in the first and the second task—an indication of crosstalk. As predicted, exposing participants to binaural beats in the gamma range increased this effect as compared to a control condition in which participants were exposed to a continuous tone of 340 Hz. These findings provide converging evidence that the cognitive-control style can be systematically biased by inducing particular internal states; that high-frequency binaural beats bias the control style toward more flexibility; and that different styles are implemented by changing the strength of local competition and top-down bias. PMID:27605922

The effects of organizational flexibility on nurse utilization and vacancy statistics in Ontario hospitals.

PubMed

Fisher, Anita; Baumann, Andrea; Blythe, Jennifer

2007-01-01

Social and economic changes in industrial societies during the past quarter-century encouraged organizations to develop greater flexibility in their employment systems in order to adapt to organizational restructuring and labour market shifts (Kallenberg 2003). During the 1990s this trend became evident in healthcare organizations. Before healthcare restructuring, employment in the acute hospital sector was more stable, with higher levels of full-time staff. However, in the downsizing era, employers favoured more flexible, contingent workforces (Zeytinoglu 1999). As healthcare systems evolved, staffing patterns became more chaotic and predicting staffing requirements more complex. Increased use of casual and part-time staff, overtime and agency nurses, as well as alterations in skills mix, masked vacancy counts and thus rendered this measurement of nursing demand increasingly difficult. This study explores flexible nurse staffing practices and demonstrates how data such as nurse vacancy statistics, considered in isolation from nurse utilization information, are inaccurate indicators of nursing demand and nurse shortage. It develops an algorithm that provides a standard methodology for improved monitoring and management of nurse utilization data and better quantification of vacancy statistics. Use of standard methodology promotes more accurate measurement of nurse utilization and shortage. Furthermore, it provides a solid base for improved nursing workforce planning, production and management.

Distributed Trajectory Flexibility Preservation for Traffic Complexity Mitigation

NASA Technical Reports Server (NTRS)

Idris, Husni; Wing, David; Delahaye, Daniel

2009-01-01

The growing demand for air travel is increasing the need for mitigation of air traffic congestion and complexity problems, which are already at high levels. At the same time new information and automation technologies are enabling the distribution of tasks and decisions from the service providers to the users of the air traffic system, with potential capacity and cost benefits. This distribution of tasks and decisions raises the concern that independent user actions will decrease the predictability and increase the complexity of the traffic system, hence inhibiting and possibly reversing any potential benefits. In answer to this concern, the authors propose the introduction of decision-making metrics for preserving user trajectory flexibility. The hypothesis is that such metrics will make user actions naturally mitigate traffic complexity. In this paper, the impact of using these metrics on traffic complexity is investigated. The scenarios analyzed include aircraft in en route airspace with each aircraft meeting a required time of arrival in a one-hour time horizon while mitigating the risk of loss of separation with the other aircraft, thus preserving its trajectory flexibility. The experiments showed promising results in that the individual trajectory flexibility preservation induced self-separation and self-organization effects in the overall traffic situation. The effects were quantified using traffic complexity metrics based on Lyapunov exponents and traffic proximity.

PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.

PubMed

Li, Haiou; Lu, Liyao; Chen, Rong; Quan, Lijun; Xia, Xiaoyan; Lü, Qiang

2014-01-01

Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

PubMed Central

Tu, Chao; Tan, Yu-Hong; Shaw, Gary; Zhou, Zheng; Bai, Yawen; Luo, Ray; Ji, Xinhua

2008-01-01

Tumor suppressor p53 is a sequence-specific DNA-binding protein and its central DNA-binding domain (DBD) harbors six hotspots (Arg175, Gly245, Arg248, Arg249, Arg273 and Arg282) for human cancers. Here, the crystal structure of a low-frequency hotspot mutant, p53DBD(R282Q), is reported at 1.54 Å resolution together with the results of molecular-dynamics simulations on the basis of the structure. In addition to eliminating a salt bridge, the R282Q mutation has a significant impact on the properties of two DNA-binding loops (L1 and L3). The L1 loop is flexible in the wild type, but it is not flexible in the mutant. The L3 loop of the wild type is not flexible, whereas it assumes two conformations in the mutant. Molecular-dynamics simulations indicated that both conformations of the L3 loop are accessible under biological conditions. It is predicted that the elimination of the salt bridge and the inversion of the flexibility of L1 and L3 are directly or indirectly responsible for deactivating the tumor suppressor p53. PMID:18453682

Intra-Seasonal Flexibility in Avian Metabolic Performance Highlights the Uncoupling of Basal Metabolic Rate and Thermogenic Capacity

PubMed Central

Petit, Magali; Lewden, Agnès; Vézina, François

2013-01-01

Stochastic winter weather events are predicted to increase in occurrence and amplitude at northern latitudes and organisms are expected to cope through phenotypic flexibility. Small avian species wintering in these environments show acclimatization where basal metabolic rate (BMR) and maximal thermogenic capacity (MSUM) are typically elevated. However, little is known on intra-seasonal variation in metabolic performance and on how population trends truly reflect individual flexibility. Here we report intra-seasonal variation in metabolic parameters measured at the population and individual levels in black-capped chickadees ( Poecile atricapillus ). Results confirmed that population patterns indeed reflect flexibility at the individual level. They showed the expected increase in BMR (6%) and MSUM (34%) in winter relative to summer but also, and most importantly, that these parameters changed differently through time. BMR began its seasonal increase in November, while MSUM had already achieved more than 20% of its inter-seasonal increase by October, and declined to its starting level by March, while MSUM remained high. Although both parameters co-vary on a yearly scale, this mismatch in the timing of variation in winter BMR and MSUM likely reflects different constraints acting on different physiological components and therefore suggests a lack of functional link between these parameters. PMID:23840843

Body image flexibility: A predictor and moderator of outcome in transdiagnostic outpatient eating disorder treatment.

PubMed

Pellizzer, Mia L; Waller, Glenn; Wade, Tracey D

2018-04-01

Predictors of attrition and predictors and moderators of outcome were explored in a transdiagnostic sample of patients who received ten-session cognitive behavioral therapy (CBT-T) for nonunderweight eating disorders. Body image flexibility, a protective positive body image construct, was hypothesized to be a significant moderator. Data from two case series were combined to form a sample of 78 participants who received CBT-T. Baseline measures of body image, negative affect, personality, and motivation (readiness to change and self-efficacy) were included as potential predictors. Global eating disorder psychopathology at each assessment point (baseline, mid- and post-treatment, 1- and 3-month follow-up) was the outcome variable. Predictors of attrition were assessed using logistic regression, and multilevel modeling was applied for predictors and moderators of outcome. Body image flexibility emerged as the strongest predictor and moderator of global eating disorder psychopathology, followed by body image avoidance. Body checking, negative affect, personality beliefs, and self-efficacy were significant predictors of global eating disorder psychopathology. Higher body image flexibility predicted lower global eating disorder psychopathology at every assessment point. Further research is required to replicate findings and explore the benefit of focusing on positive body image in treatment. © 2018 Wiley Periodicals, Inc.

A flexible framework for process-based hydraulic and water ...

EPA Pesticide Factsheets

Background Models that allow for design considerations of green infrastructure (GI) practices to control stormwater runoff and associated contaminants have received considerable attention in recent years. While popular, generally, the GI models are relatively simplistic. However, GI model predictions are being relied upon by many municipalities and State/Local agencies to make decisions about grey vs. green infrastructure improvement planning. Adding complexity to GI modeling frameworks may preclude their use in simpler urban planning situations. Therefore, the goal here was to develop a sophisticated, yet flexible tool that could be used by design engineers and researchers to capture and explore the effect of design factors and properties of the media used in the performance of GI systems at a relatively small scale. We deemed it essential to have a flexible GI modeling tool that is capable of simulating GI system components and specific biophysical processes affecting contaminants such as reactions, and particle-associated transport accurately while maintaining a high degree of flexibly to account for the myriad of GI alternatives. The mathematical framework for a stand-alone GI performance assessment tool has been developed and will be demonstrated.Framework Features The process-based model framework developed here can be used to model a diverse range of GI practices such as green roof, retention pond, bioretention, infiltration trench, permeable pavement and

The utility of Bayesian predictive probabilities for interim monitoring of clinical trials

PubMed Central

Connor, Jason T.; Ayers, Gregory D; Alvarez, JoAnn

2014-01-01

Background Bayesian predictive probabilities can be used for interim monitoring of clinical trials to estimate the probability of observing a statistically significant treatment effect if the trial were to continue to its predefined maximum sample size. Purpose We explore settings in which Bayesian predictive probabilities are advantageous for interim monitoring compared to Bayesian posterior probabilities, p-values, conditional power, or group sequential methods. Results For interim analyses that address prediction hypotheses, such as futility monitoring and efficacy monitoring with lagged outcomes, only predictive probabilities properly account for the amount of data remaining to be observed in a clinical trial and have the flexibility to incorporate additional information via auxiliary variables. Limitations Computational burdens limit the feasibility of predictive probabilities in many clinical trial settings. The specification of prior distributions brings additional challenges for regulatory approval. Conclusions The use of Bayesian predictive probabilities enables the choice of logical interim stopping rules that closely align with the clinical decision making process. PMID:24872363

Memory Flexibility training (MemFlex) to reduce depressive symptomatology in individuals with major depressive disorder: study protocol for a randomised controlled trial.

PubMed

Hitchcock, Caitlin; Hammond, Emily; Rees, Catrin; Panesar, Inderpal; Watson, Peter; Werner-Seidler, Aliza; Dalgleish, Tim

2015-11-03

Major depressive disorder (MDD) is associated with chronic biases in the allocation of attention and recollection of personal memories. Impaired flexibility in attention and autobiographical memory retrieval is seen to both maintain current symptoms and predict future depression. Development of innovative interventions to reduce maladaptive cognitive patterns and improve cognitive flexibility in the domain of memory may therefore advance current treatment approaches for depression. Memory specificity training and cognitive bias modification techniques have both shown some promise in improving cognitive flexibility. Here we outline plans for a trial of an innovative memory flexibility training programme, MemFlex, which advances current training techniques with the aim of improving flexibility of autobiographical memory retrieval. This trial seeks to estimate the efficacy of MemFlex, provide data on feasibility, and begin to explore mechanisms of change. We plan a single-blind, randomised, controlled, patient-level trial in which 50 individuals with MDD will complete either psychoeducation (n = 25) or MemFlex (n = 25). After completing pre-treatment measures and an orientation session, participants complete eight workbook-based sessions at home. Participants will then be assessed at post-treatment and at 3 month follow-up. The co-primary outcomes are depressive symptoms and diagnostic status at 3 month follow-up. The secondary outcomes are memory flexibility at post-treatment and number of depression free days at 3 month follow-up. Other process outcomes and mediators of any treatment effects will also be explored. This trial will establish the efficacy of MemFlex in improving memory flexibility, and reducing depressive symptoms. Any effects on process measures related to relapse may also indicate whether MemFlex may be helpful in reducing vulnerability to future depressive episodes. The low-intensity and workbook-based format of the programme may improve access to psychological therapies, and, if encouraging, the results of this study will provide a platform for later-phase trials. NCT02371291 (ClinicalTrials.gov), registered 9 February 2015.

Bladed disk assemblies; Proceedings of the Eleventh Biennial Conference on Mechanical Vibration and Noise, Boston, MA, Sept. 27-30, 1987

NASA Technical Reports Server (NTRS)

Kielb, R. (Editor); Crawley, E. (Editor); Simonis, J. C. (Editor)

1987-01-01

The present conference on bladed disk assemblies discusses aerodynamic indicial reponse and stability derivatives for a rotor annulus, an analysis of aerodynamically forced turbomachine vibration, the effect of downwash on the nonsteady forces in a turbomachine stage, the vibration of turbomachine blades with root flexibility effects, mistuned bladed disk assembly vibrations, and the model-generation and modal analysis of flexible bladed disk assemblies. Also discussed are the vibration characteristics of a mistuned bladed disk, free and forced vibrations associated with localization phenomena in mistuned assemblies with cyclic symmetry, steam turbine cyclic symmetry through constraint equations, and the interpretation of experimental and theoretical results predicting vibrating turbocharger blade mode shapes.

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

Design and experimental validation of a flutter suppression controller for the active flexible wing

NASA Technical Reports Server (NTRS)

Waszak, Martin R.; Srinathkumar, S.

1992-01-01

The synthesis and experimental validation of an active flutter suppression controller for the Active Flexible Wing wind tunnel model is presented. The design is accomplished with traditional root locus and Nyquist methods using interactive computer graphics tools and extensive simulation based analysis. The design approach uses a fundamental understanding of the flutter mechanism to formulate a simple controller structure to meet stringent design specifications. Experimentally, the flutter suppression controller succeeded in simultaneous suppression of two flutter modes, significantly increasing the flutter dynamic pressure despite modeling errors in predicted flutter dynamic pressure and flutter frequency. The flutter suppression controller was also successfully operated in combination with another controller to perform flutter suppression during rapid rolling maneuvers.

Surrogate endpoints for cancer screening trials: general principles and an illustration using the UK Flexible Sigmoidoscopy Screening Trial.

PubMed

Cuzick, Jack; Cafferty, Fay H; Edwards, Robert; Møller, Henrik; Duffy, Stephen W

2007-01-01

Cancer screening is aimed primarily at reducing deaths. Thus, site-specific cancer mortality is the appropriate endpoint for evaluating screening interventions. However, it is also the most demanding endpoint, requiring follow-up and a large numbers of patients order to have adequate power. Therefore, it is highly desirable to have surrogate endpoints that can reliably predict mortality reductions many years earlier. We here review a range of surrogate markers in terms of their potential advantages and pitfalls, and argue that a measure which weights incident cancers according to their predicted mortality has many advantages over other measures and should be used more routinely. Application to the UK Flexible Sigmoidoscopy Screening Trial data suggests that predicted colorectal cancer mortality, based on stage-specific incidence, is a more powerful endpoint than actual mortality and could advance the analysis time by about three years. Total colorectal cancer incidence as a surrogate endpoint provides little advance in the analysis time over actual mortality. The approach requires reliable prognostic data, (e.g. stage), for both the study cohort and a representative sample of the whole population. The routine collection of such data should be a priority for cancer registries. Surrogate endpoints should not replace a long-term analysis based directly on mortality, but can provide reliable early indicators which can be useful both for monitoring ongoing screening programmes and for making policy decisions.

Enroute NASA/FAA low-frequency propfan test in Alabama (October 1987): A versatile atmospheric aircraft long-range noise prediction system

NASA Astrophysics Data System (ADS)

Tsouka, Despina G.

In order to obtain a flight-to-static noise prediction of an advanced Turboprop (propfan) Aircraft, FAA went on an elaboration of the data that were measured during a full scale measuring program that was conducted by NASA and FAA/DOT/TSC on October 1987 in Alabama. The elaboration process was based on aircraft simulation to a point source, on an atmospheric two dimensional noise model, on the American National Standard algorithm for the calculation of atmospheric absortion, and on the DOT/TSC convention for ground reflection effects. Using the data of the Alabama measurements, the present paper examines the development of a generalized, flexible and more accurate process for the evaluation of the static and flight low-frequency long-range noise data. This paper also examines the applicability of the assumptions made by the Integrated Noise Model about linear propagation, of the three dimensional Hamiltonian Rays Tracing model and of the Weyl-Van der Pol model. The model proposes some assumptions in order to increase the calculations flexibility without significant loss of accuracy. In addition, it proposes the usage of the three dimensional Hamiltonian Rays Tracing model and the Weyl-Van der Pol model in order to increase the accuracy and to ensure the generalization of noise propagation prediction over grounds with variable impedance.

Measuring Complexity and Predictability of Time Series with Flexible Multiscale Entropy for Sensor Networks

PubMed Central

Zhou, Renjie; Yang, Chen; Wan, Jian; Zhang, Wei; Guan, Bo; Xiong, Naixue

2017-01-01

Measurement of time series complexity and predictability is sometimes the cornerstone for proposing solutions to topology and congestion control problems in sensor networks. As a method of measuring time series complexity and predictability, multiscale entropy (MSE) has been widely applied in many fields. However, sample entropy, which is the fundamental component of MSE, measures the similarity of two subsequences of a time series with either zero or one, but without in-between values, which causes sudden changes of entropy values even if the time series embraces small changes. This problem becomes especially severe when the length of time series is getting short. For solving such the problem, we propose flexible multiscale entropy (FMSE), which introduces a novel similarity function measuring the similarity of two subsequences with full-range values from zero to one, and thus increases the reliability and stability of measuring time series complexity. The proposed method is evaluated on both synthetic and real time series, including white noise, 1/f noise and real vibration signals. The evaluation results demonstrate that FMSE has a significant improvement in reliability and stability of measuring complexity of time series, especially when the length of time series is short, compared to MSE and composite multiscale entropy (CMSE). The proposed method FMSE is capable of improving the performance of time series analysis based topology and traffic congestion control techniques. PMID:28383496

Measuring Complexity and Predictability of Time Series with Flexible Multiscale Entropy for Sensor Networks.

PubMed

Zhou, Renjie; Yang, Chen; Wan, Jian; Zhang, Wei; Guan, Bo; Xiong, Naixue

2017-04-06

Measurement of time series complexity and predictability is sometimes the cornerstone for proposing solutions to topology and congestion control problems in sensor networks. As a method of measuring time series complexity and predictability, multiscale entropy (MSE) has been widely applied in many fields. However, sample entropy, which is the fundamental component of MSE, measures the similarity of two subsequences of a time series with either zero or one, but without in-between values, which causes sudden changes of entropy values even if the time series embraces small changes. This problem becomes especially severe when the length of time series is getting short. For solving such the problem, we propose flexible multiscale entropy (FMSE), which introduces a novel similarity function measuring the similarity of two subsequences with full-range values from zero to one, and thus increases the reliability and stability of measuring time series complexity. The proposed method is evaluated on both synthetic and real time series, including white noise, 1/f noise and real vibration signals. The evaluation results demonstrate that FMSE has a significant improvement in reliability and stability of measuring complexity of time series, especially when the length of time series is short, compared to MSE and composite multiscale entropy (CMSE). The proposed method FMSE is capable of improving the performance of time series analysis based topology and traffic congestion control techniques.

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.

PubMed

Zhang, Dong; Xue, Xingran; Malmberg, Russell L; Cai, Liming

2012-10-15

TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species. The web server TRFolder-W is available at http://rna-informatics.uga.edu/?f=software&p=TRFolder-w.

Modelling proteins' hidden conformations to predict antibiotic resistance

NASA Astrophysics Data System (ADS)

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-10-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.

COSIM: A Finite-Difference Computer Model to Predict Ternary Concentration Profiles Associated With Oxidation and Interdiffusion of Overlay-Coated Substrates

NASA Technical Reports Server (NTRS)

Nesbitt, James A.

2001-01-01

A finite-difference computer program (COSIM) has been written which models the one-dimensional, diffusional transport associated with high-temperature oxidation and interdiffusion of overlay-coated substrates. The program predicts concentration profiles for up to three elements in the coating and substrate after various oxidation exposures. Surface recession due to solute loss is also predicted. Ternary cross terms and concentration-dependent diffusion coefficients are taken into account. The program also incorporates a previously-developed oxide growth and spalling model to simulate either isothermal or cyclic oxidation exposures. In addition to predicting concentration profiles after various oxidation exposures, the program can also be used to predict coating life based on a concentration dependent failure criterion (e.g., surface solute content drops to 2%). The computer code is written in FORTRAN and employs numerous subroutines to make the program flexible and easily modifiable to other coating oxidation problems.

When is an error not a prediction error? An electrophysiological investigation.

PubMed

Holroyd, Clay B; Krigolson, Olave E; Baker, Robert; Lee, Seung; Gibson, Jessica

2009-03-01

A recent theory holds that the anterior cingulate cortex (ACC) uses reinforcement learning signals conveyed by the midbrain dopamine system to facilitate flexible action selection. According to this position, the impact of reward prediction error signals on ACC modulates the amplitude of a component of the event-related brain potential called the error-related negativity (ERN). The theory predicts that ERN amplitude is monotonically related to the expectedness of the event: It is larger for unexpected outcomes than for expected outcomes. However, a recent failure to confirm this prediction has called the theory into question. In the present article, we investigated this discrepancy in three trial-and-error learning experiments. All three experiments provided support for the theory, but the effect sizes were largest when an optimal response strategy could actually be learned. This observation suggests that ACC utilizes dopamine reward prediction error signals for adaptive decision making when the optimal behavior is, in fact, learnable.

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

RBind: computational network method to predict RNA binding sites.

PubMed

Wang, Kaili; Jian, Yiren; Wang, Huiwen; Zeng, Chen; Zhao, Yunjie

2018-04-26

Non-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA-ligand and RNA-protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions. Current RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites. Here, we present a network approach, RBind, to predict the RNA binding sites. We benchmarked RBind in RNA-ligand and RNA-protein datasets. The average accuracy of 0.82 in RNA-ligand and 0.63 in RNA-protein testing showed that this network strategy has a reliable accuracy for binding sites prediction. The codes and datasets are available at https://zhaolab.com.cn/RBind. yjzhaowh@mail.ccnu.edu.cn. Supplementary data are available at Bioinformatics online.

Modelling proteins’ hidden conformations to predict antibiotic resistance

PubMed Central

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-01-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM’s specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models’ prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design. PMID:27708258

Impulsiveness, postprandial blood glucose, and glucoregulation affect measures of behavioral flexibility.

PubMed

Riby, Leigh M; Lai Teik Ong, Derek; Azmie, Nurulnadia Binti Mohamad; Ooi, Ee Lyn; Regina, Caroline; Yeo, Eugene Ki Wai; Massa, Jacqueline; Aquili, Luca

2017-12-01

Behavioral flexibility (BF) performance is influenced by both psychological and physiological factors. Recent evidence suggests that impulsivity and blood glucose can affect executive function, of which BF is a subdomain. Here, we hypothesized that impulsivity, fasting blood glucose (FBG), glucose changes (ie, glucoregulation) from postprandial blood glucose (PBG) following the intake of a 15-g glucose beverage could account for variability in BF performance. The Stroop Color-Word Test and the Wisconsin Card Sorting Test (WCST) were used as measures of BF, and the Barratt Impulsiveness Scale (BIS-11) to quantify participants' impulsivity. In Study 1, neither impulsivity nor FBG could predict performance on the Stroop or the WCST. In Study 2, we tested whether blood glucose levels following the intake of a sugary drink, and absolute changes in glucose levels following the intake of the glucose beverage could better predict BF. Results showed that impulsivity and the difference in blood glucose between time 1 (postprandial) and time 2, but not blood glucose levels at time 2 per se could account for variation in performance on the WCST but not on the Stroop task. More specifically, lower impulsivity scores on the BIS-11, and smaller differences in blood glucose levels from time 1 to time 2 predicted a decrease in the number of total and perseverative errors on the WCST. Our results show that measures of impulsivity and glucoregulation can be used to predict BF. Importantly our data extend the work on glucose and cognition to a clinically relevant domain of cognition. Copyright © 2017 Elsevier Inc. All rights reserved.

Task Effects Reveal Cognitive Flexibility Responding to Frequency and Predictability: Evidence from Eye Movements in Reading and Proofreading

PubMed Central

Schotter, Elizabeth R.; Bicknell, Klinton; Howard, Ian; Levy, Roger; Rayner, Keith

2014-01-01

It is well-known that word frequency and predictability affect processing time. These effects change magnitude across tasks, but studies testing this use tasks with different response types (e.g., lexical decision, naming, and fixation time during reading; Schilling, Rayner & Chumbley, 1998), preventing direct comparison. Recently, Kaakinen and Hyönä (2010) overcame this problem, comparing fixation times in reading for comprehension and proofreading, showing that the frequency effect was larger in proofreading than in reading. This result could be explained by readers exhibiting substantial cognitive flexibility, and qualitatively changing how they process words in the proofreading task in a way that magnifies effects of word frequency. Alternatively, readers may not change word processing so dramatically, and instead may perform more careful identification generally, increasing the magnitude of many word processing effects (e.g., both frequency and predictability). We tested these possibilities with two experiments: subjects read for comprehension and then proofread for spelling errors (letter transpositions) that produce nonwords (e.g., trcak for track as in Kaakinen & Hyönä) or that produce real but unintended words (e.g., trial for trail) to compare how the task changes these effects. Replicating Kaakinen and Hyönä, frequency effects increased during proofreading. However, predictability effects only increased when integration with the sentence context was necessary to detect errors (i.e., when spelling errors produced words that were inappropriate in the sentence; trial for trail). The results suggest that readers adopt sophisticated word processing strategies to accommodate task demands. PMID:24434024

Parsing trait and state effects of depression severity on neurocognition: Evidence from a 26-year longitudinal study.

PubMed

Sarapas, Casey; Shankman, Stewart A; Harrow, Martin; Goldberg, Joseph F

2012-11-01

Cognitive dysfunction in mood disorders falls along a continuum, such that more severe current depression is associated with greater cognitive impairment. It is not clear whether this association reflects transient state effects of current symptoms on cognitive performance, or persistent, trait-like differences in cognition that are related to overall disorder severity. We addressed this question in 42 unipolar and 47 bipolar participants drawn from a 26-year longitudinal study of psychopathology, using measures of attention/psychomotor processing speed, cognitive flexibility, verbal fluency, and verbal memory. We assessed (a) the extent to which current symptom severity and past average disorder severity predicted unique variance in cognitive performance; (b) whether cognitive performance covaried with within-individual changes in symptom severity; and (c) the stability of neurocognitive measures over six years. We also tested for differences among unipolar and bipolar groups and published norms. Past average depression severity predicted performance on attention/psychomotor processing speed in both groups, and in cognitive flexibility among unipolar participants, even after controlling for current symptom severity, which did not independently predict cognition. Within-participant state changes in depressive symptoms did not predict change in any cognitive domain. All domains were stable over the course of six years. Both groups showed generalized impairment relative to published norms, and bipolar participants performed more poorly than unipolar participants on attention/psychomotor processing speed. The results suggest a stable relationship between mood disorder severity and cognitive deficits. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

Intraoperative laryngeal electromyography in children with vocal fold immobility: results of a multicenter longitudinal study.

PubMed

Maturo, Stephen C; Braun, Nicole; Brown, David J; Chong, Peter Siao Tick; Kerschner, Joseph E; Hartnick, Christopher J

2011-12-01

To determine whether laryngeal electromyography (LEMG) can predict recurrent laryngeal nerve function return in children and whether LEMG can aid in the management of vocal fold immobility (VFI). Prospective case series. Tertiary pediatric aerodigestive centers. Twenty-five children aged 14 days to 7 years at the time of first LEMG (mean age, 21.4 months) with VFI who underwent flexible fiberoptic laryngeal examination, intraoperative LEMG of the thyroarytenoid muscles, and 12-month follow-up. To compare results of LEMG with flexible fiberoptic laryngeal examination in children with vocal fold paresis and to determine if LEMG can predict vocal fold return. In children who had a patent ductus arteriosus ligation, the LEMG data suggest that if there is no activity 6 months after injury, then the nerve is unlikely to regain function. In 3 of 3 children with central causes of VFI, normal LEMG findings predicted return of nerve function 2 to 7 months before vocal fold movement on fiberoptic examination. Finally, in 3 of 3 children with idiopathic VFI, LEMG predicted return within 2 to 14 months of vocal folds with normal findings. Intraoperative LEMG is a safe, easy-to-use method for determining the likelihood of recurrent laryngeal nerve function return in children who have undergone patent ductus arteriosus ligation, in children with centrally correctable lesions, and in children with idiopathic VFI. More work is needed in the area of pediatric LEMG, but it is possible that LEMG data can be used to aid in management strategies and provide families with more information to make better informed decisions regarding their child's care.

Predicting and Priming Thematic Roles: Flexible Use of Verbal and Nonverbal Cues during Relative Clause Comprehension

ERIC Educational Resources Information Center

Kowalski, Alix; Huang, Yi Ting

2017-01-01

Relative-clause sentences (RCs) have been a key test case for psycholinguistic models of comprehension. While object-relative clauses (e.g., ORCs: "The bear that 'the horse' . . .") are distinguished from subject-relative clauses (SRCs) after the second noun phrase (NP2; e.g., SRCs: "The bear that 'pushed' . . ."), role…

Learning to Manage Change in the Third Age

ERIC Educational Resources Information Center

Innocent, Natasha

2010-01-01

Everyone is living through a period of considerable demographic change, which is predicted to continue and escalate. People are living longer and, generally, healthier lives, and the lifelong learning system in the UK needs to catch-up with this new reality. There is a need for a much more flexible approach that offers choice and opportunities to…

Evaluating Teleworkers' Acceptance of Mobile Technology: A Study Based on the Utaut Model

ERIC Educational Resources Information Center

Mills, Jamia Sharie

2016-01-01

Mobile technology has provided flexible methods for employees to complete work-related tasks without being tied to an office. Research has predicted the level of training on mobile technology may impact a user's ability to complete work responsibilities accurately. This study intended to examine what behavior factors from the unified theory of…