WorldWideScience

Sample records for sequential folding model

  1. Accurately controlled sequential self-folding structures by polystyrene film

    Science.gov (United States)

    Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

    2017-08-01

    Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

  2. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...

  3. Modelling sequentially scored item responses

    NARCIS (Netherlands)

    Akkermans, W.

    2000-01-01

    The sequential model can be used to describe the variable resulting from a sequential scoring process. In this paper two more item response models are investigated with respect to their suitability for sequential scoring: the partial credit model and the graded response model. The investigation is

  4. SDEM modelling of fault-propagation folding

    DEFF Research Database (Denmark)

    Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang

    2009-01-01

    and variations in Mohr-Coulomb parameters including internal friction. Using SDEM modelling, we have mapped the propagation of the tip-line of the fault, as well as the evolution of the fold geometry across sedimentary layers of contrasting rheological parameters, as a function of the increased offset......Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault-propagation...... a precise indication of when faults develop and hence also the sequential evolution of secondary faults. Here we focus on the generation of a fault -propagated fold with a reverse sense of motion at the master fault, and varying only the dip of the master fault and the mechanical behaviour of the deformed...

  5. Domains of Pyrococcus furiosus L-asparaginase fold sequentially and assemble through strong intersubunit associative forces.

    Science.gov (United States)

    Garg, Dushyant K; Tomar, Rachana; Dhoke, Reema R; Srivastava, Ankit; Kundu, Bishwajit

    2015-05-01

    Here, we report the folding and assembly of a Pyrococcus furiosus-derived protein, L-asparaginase (PfA). PfA functions as a homodimer, with each monomer made of distinct N- and C-terminal domains. The purified individual domains as well as single Trp mutant of each domain were subjected to chemical denaturation/renaturation and probed by combination of spectroscopic, chromatographic, quenching and scattering techniques. We found that the N-domain acts like a folding scaffold and assists the folding of remaining polypeptide. The domains displayed sequential folding with the N-domain having higher thermodynamic stability. We report that the extreme thermal stability of PfA is due to the presence of high intersubunit associative forces supported by extensive H-bonding and ionic interactions network. Our results proved that folding cooperativity in a thermophilic, multisubunit protein is dictated by concomitant folding and association of constituent domains directly into a native quaternary structure. This report gives an account of the factors responsible for folding and stability of a therapeutically and industrially important protein.

  6. Simultaneous formation of multiscale hierarchical surface morphologies through sequential wrinkling and folding

    Science.gov (United States)

    Wang, Yu; Sun, Qingyang; Xiao, Jianliang

    2018-02-01

    Highly organized hierarchical surface morphologies possess various intriguing properties that could find important potential applications. In this paper, we demonstrate a facile approach to simultaneously form multiscale hierarchical surface morphologies through sequential wrinkling. This method combines surface wrinkling induced by thermal expansion and mechanical strain on a three-layer structure composed of an aluminum film, a hard Polydimethylsiloxane (PDMS) film, and a soft PDMS substrate. Deposition of the aluminum film on hard PDMS induces biaxial wrinkling due to thermal expansion mismatch, and recovering the prestrain in the soft PDMS substrate leads to wrinkling of the hard PDMS film. In total, three orders of wrinkling patterns form in this process, with wavelength and amplitude spanning 3 orders of magnitude in length scale. By increasing the prestrain in the soft PDMS substrate, a hierarchical wrinkling-folding structure was also obtained. This approach can be easily extended to other thin films for fabrication of multiscale hierarchical surface morphologies with potential applications in different areas.

  7. Sequential and Simultaneous Logit: A Nested Model.

    NARCIS (Netherlands)

    van Ophem, J.C.M.; Schram, A.J.H.C.

    1997-01-01

    A nested model is presented which has both the sequential and the multinomial logit model as special cases. This model provides a simple test to investigate the validity of these specifications. Some theoretical properties of the model are discussed. In the analysis a distribution function is

  8. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  9. Sensitivity Analysis in Sequential Decision Models.

    Science.gov (United States)

    Chen, Qiushi; Ayer, Turgay; Chhatwal, Jagpreet

    2017-02-01

    Sequential decision problems are frequently encountered in medical decision making, which are commonly solved using Markov decision processes (MDPs). Modeling guidelines recommend conducting sensitivity analyses in decision-analytic models to assess the robustness of the model results against the uncertainty in model parameters. However, standard methods of conducting sensitivity analyses cannot be directly applied to sequential decision problems because this would require evaluating all possible decision sequences, typically in the order of trillions, which is not practically feasible. As a result, most MDP-based modeling studies do not examine confidence in their recommended policies. In this study, we provide an approach to estimate uncertainty and confidence in the results of sequential decision models. First, we provide a probabilistic univariate method to identify the most sensitive parameters in MDPs. Second, we present a probabilistic multivariate approach to estimate the overall confidence in the recommended optimal policy considering joint uncertainty in the model parameters. We provide a graphical representation, which we call a policy acceptability curve, to summarize the confidence in the optimal policy by incorporating stakeholders' willingness to accept the base case policy. For a cost-effectiveness analysis, we provide an approach to construct a cost-effectiveness acceptability frontier, which shows the most cost-effective policy as well as the confidence in that for a given willingness to pay threshold. We demonstrate our approach using a simple MDP case study. We developed a method to conduct sensitivity analysis in sequential decision models, which could increase the credibility of these models among stakeholders.

  10. Folding models for elastic and inelastic scattering

    International Nuclear Information System (INIS)

    Satchler, G.R.

    1982-01-01

    The most widely used models are the optical model potential (OMP) for elastic scattering, and its generalization to non-spherical shapes, the deformed optical model potential (DOMP) for inelastic scattering. These models are simple and phenomenological; their parameters are adjusted so as to reproduce empirical data. Nonetheless, there are certain, not always well-defined, constraints to be imposed. The potential shapes and their parameter values must be reasonable and should vary in a smooth and systematic way with the masses of the colliding nuclei and their energy. One way of satisfying these constraints, without going back to a much more fundamental theory, is through the use of folding models. The basic justification for using potentials of the Woods-Saxon shape for nucleon-nucleus scattering, for example, is our knowledge that a nuclear density distribution is more-or-less constant in the nuclear interior with a diffuse surface. When this is folded with a short-range nucleon-nucleon interaction, the result is a similar shape with a more diffuse surface. Folding procedures allow us to incorporate many aspects of nuclear structure (although the nuclear size is one of the most important), as well as theoretical ideas about the effective interaction of two nucleons within nuclear matter. It also provides us with a means of linking information obtained from nuclear (hadronic) interactions with that from other sources, as well as correlating that from the use of different hadronic probes. Folding model potentials, single-folded potentials, and the double-folding model including applications to heavy-ion scattering are discussed

  11. Sequential neural models with stochastic layers

    DEFF Research Database (Denmark)

    Fraccaro, Marco; Sønderby, Søren Kaae; Paquet, Ulrich

    2016-01-01

    How can we efficiently propagate uncertainty in a latent state representation with recurrent neural networks? This paper introduces stochastic recurrent neural networks which glue a deterministic recurrent neural network and a state space model together to form a stochastic and sequential neural...... generative model. The clear separation of deterministic and stochastic layers allows a structured variational inference network to track the factorization of the model's posterior distribution. By retaining both the nonlinear recursive structure of a recurrent neural network and averaging over...

  12. Protein Folding: Search for Basic Physical Models

    Directory of Open Access Journals (Sweden)

    Ivan Y. Torshin

    2003-01-01

    Full Text Available How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context of in vivo protein folding (which has been studied only for a few proteins, the roles of the fundamental physical forces in the in vitro folding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces. Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

  13. Sequential Folding of Transfer RNA. A Nuclear Magnetic Resonance Study of Successively Longer tRNA Fragments with a Common 5’ End

    NARCIS (Netherlands)

    Boyle, John; Robillard, George T.; Kim, Sung-Hou

    1980-01-01

    Most folding studies on proteins and nucleic acids have been addressed to the transition between the folded and unfolded states of an intact molecule, where an entire residue sequence is present during the folding event. However, since these polymers are synthesized sequentially from one terminus to

  14. Folding model analysis of alpha radioactivity

    International Nuclear Information System (INIS)

    Basu, D N

    2003-01-01

    Radioactive decay of nuclei via emission of α-particles has been studied theoretically in the framework of a superasymmetric fission model using the double folding (DF) procedure for obtaining the α-nucleus interaction potential. The DF nuclear potential has been obtained by folding in the density distribution functions of the α nucleus and the daughter nucleus with a realistic effective interaction. The M3Y effective interaction has been used for calculating the nuclear interaction potential which has been supplemented by a zero-range pseudo-potential for exchange along with the density dependence. The nuclear microscopic α-nucleus potential thus obtained has been used along with the Coulomb interaction potential to calculate the action integral within the WKB approximation. This subsequently yields calculations for the half-lives of α decays of nuclei. The density dependence and the exchange effects have not been found to be very significant. These calculations provide reasonable estimates for the lifetimes of α-radioactivity of nuclei

  15. A Rat Excised Larynx Model of Vocal Fold Scar

    Science.gov (United States)

    Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.

    2009-01-01

    Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…

  16. Sequential models for coarsening and missingness

    NARCIS (Netherlands)

    Gill, R.D.; Robins, J.M.

    1997-01-01

    In a companion paper we described what intuitively would seem to be the most general possible way to generate Coarsening at Random mechanisms a sequential procedure called randomized monotone coarsening Counterexamples showed that CAR mechanisms exist which cannot be represented in this way Here we

  17. Sequential and simultaneous choices: testing the diet selection and sequential choice models.

    Science.gov (United States)

    Freidin, Esteban; Aw, Justine; Kacelnik, Alex

    2009-03-01

    We investigate simultaneous and sequential choices in starlings, using Charnov's Diet Choice Model (DCM) and Shapiro, Siller and Kacelnik's Sequential Choice Model (SCM) to integrate function and mechanism. During a training phase, starlings encountered one food-related option per trial (A, B or R) in random sequence and with equal probability. A and B delivered food rewards after programmed delays (shorter for A), while R ('rejection') moved directly to the next trial without reward. In this phase we measured latencies to respond. In a later, choice, phase, birds encountered the pairs A-B, A-R and B-R, the first implementing a simultaneous choice and the second and third sequential choices. The DCM predicts when R should be chosen to maximize intake rate, and SCM uses latencies of the training phase to predict choices between any pair of options in the choice phase. The predictions of both models coincided, and both successfully predicted the birds' preferences. The DCM does not deal with partial preferences, while the SCM does, and experimental results were strongly correlated to this model's predictions. We believe that the SCM may expose a very general mechanism of animal choice, and that its wider domain of success reflects the greater ecological significance of sequential over simultaneous choices.

  18. Approximate self-similarity in models of geological folding

    NARCIS (Netherlands)

    Budd, C.J.; Peletier, M.A.

    2000-01-01

    We propose a model for the folding of rock under the compression of tectonic plates. This models an elastic rock layer imbedded in a viscous foundation by a fourth-order parabolic equation with a nonlinear constraint. The large-time behavior of solutions of this problem is examined and found to be

  19. Visualization of protein folding funnels in lattice models.

    Directory of Open Access Journals (Sweden)

    Antonio B Oliveira

    Full Text Available Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.

  20. Sequential and Parallel Attack Tree Modelling

    NARCIS (Netherlands)

    Arnold, Florian; Guck, Dennis; Kumar, Rajesh; Stoelinga, Mariëlle Ida Antoinette; Koornneef, Floor; van Gulijk, Coen

    The intricacy of socio-technical systems requires a careful planning and utilisation of security resources to ensure uninterrupted, secure and reliable services. Even though many studies have been conducted to understand and model the behaviour of a potential attacker, the detection of crucial

  1. Measurement of flow separation in a human vocal folds model

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Doaré, O.; Cadot, O.; Chaigne, A.

    2011-01-01

    Roč. 51, č. 1 (2011), s. 123-136 ISSN 0723-4864 R&D Projects: GA AV ČR KJB200760801 Institutional research plan: CEZ:AV0Z20760514 Keywords : vocal folds * flow separation * physical model Subject RIV: BI - Acoustics Impact factor: 1.735, year: 2011 http://www.springerlink.com/content/t81114611760jp23/

  2. Mechanical Modeling and Computer Simulation of Protein Folding

    Science.gov (United States)

    Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

    2014-01-01

    In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

  3. Models of sequential decision making in consumer lending

    OpenAIRE

    Kanshukan Rajaratnam; Peter A. Beling; George A. Overstreet

    2016-01-01

    Abstract In this paper, we introduce models of sequential decision making in consumer lending. From the definition of adverse selection in static lending models, we show that homogenous borrowers take-up offers at different instances of time when faced with a sequence of loan offers. We postulate that bounded rationality and diverse decision heuristics used by consumers drive the decisions they make about credit offers. Under that postulate, we show how observation of early decisions in a seq...

  4. Efficient image duplicated region detection model using sequential block clustering

    Czech Academy of Sciences Publication Activity Database

    Sekeh, M. A.; Maarof, M. A.; Rohani, M. F.; Mahdian, Babak

    2013-01-01

    Roč. 10, č. 1 (2013), s. 73-84 ISSN 1742-2876 Institutional support: RVO:67985556 Keywords : Image forensic * Copy–paste forgery * Local block matching Subject RIV: IN - Informatics, Computer Science Impact factor: 0.986, year: 2013 http://library.utia.cas.cz/separaty/2013/ZOI/mahdian-efficient image duplicated region detection model using sequential block clustering.pdf

  5. Glottal aerodynamics in compliant, life-sized vocal fold models

    Science.gov (United States)

    McPhail, Michael; Dowell, Grant; Krane, Michael

    2013-11-01

    This talk presents high-speed PIV measurements in compliant, life-sized models of the vocal folds. A clearer understanding of the fluid-structure interaction of voiced speech, how it produces sound, and how it varies with pathology is required to improve clinical diagnosis and treatment of vocal disorders. Physical models of the vocal folds can answer questions regarding the fundamental physics of speech, as well as the ability of clinical measures to detect the presence and extent of disorder. Flow fields were recorded in the supraglottal region of the models to estimate terms in the equations of fluid motion, and their relative importance. Experiments were conducted over a range of driving pressures with flow rates, given by a ball flowmeter, and subglottal pressures, given by a micro-manometer, reported for each case. Imaging of vocal fold motion, vector fields showing glottal jet behavior, and terms estimated by control volume analysis will be presented. The use of these results for a comparison with clinical measures, and for the estimation of aeroacoustic source strengths will be discussed. Acknowledge support from NIH R01 DC005642.

  6. On the single-mass model of the vocal folds

    International Nuclear Information System (INIS)

    Howe, M S; McGowan, R S

    2010-01-01

    An analysis is made of the fluid-structure interactions necessary to support self-sustained oscillations of a single-mass mechanical model of the vocal folds subject to a nominally steady subglottal overpressure. The single-mass model of Fant and Flanagan is re-examined and an analytical representation of vortex shedding during 'voiced speech' is proposed that promotes cooperative, periodic excitation of the folds by the glottal flow. Positive feedback that sustains glottal oscillations is shown to occur during glottal contraction, when the flow separates from the 'trailing edge' of the glottis producing a low-pressure 'suction' force that tends to pull the folds together. Details are worked out for flow that can be regarded as locally two-dimensional in the glottal region. Predictions of free-streamline theory are used to model the effects of quasi-static variations in the separation point on the glottal wall. Numerical predictions are presented to illustrate the waveform of the sound radiated towards the mouth from the glottis. The theory is easily modified to include feedback on the glottal flow of standing acoustic waves, both in the vocal tract beyond the glottis and in the subglottal region. (invited paper)

  7. Formal modelling and verification of interlocking systems featuring sequential release

    DEFF Research Database (Denmark)

    Vu, Linh Hong; Haxthausen, Anne Elisabeth; Peleska, Jan

    2017-01-01

    In this article, we present a method and an associated toolchain for the formal verification of the new Danish railway interlocking systems that are compatible with the European Train Control System (ETCS) Level 2. We have made a generic and reconfigurable model of the system behaviour and generic...... safety properties. This model accommodates sequential release - a feature in the new Danish interlocking systems. To verify the safety of an interlocking system, first a domain-specific description of interlocking configuration data is constructed and validated. Then the generic model and safety...

  8. Developing guinea pig brain as a model for cortical folding.

    Science.gov (United States)

    Hatakeyama, Jun; Sato, Haruka; Shimamura, Kenji

    2017-05-01

    The cerebral cortex in mammals, the neocortex specifically, is highly diverse among species with respect to its size and morphology, likely reflecting the immense adaptiveness of this lineage. In particular, the pattern and number of convoluted ridges and fissures, called gyri and sulci, respectively, on the surface of the cortex are variable among species and even individuals. However, little is known about the mechanism of cortical folding, although there have been several hypotheses proposed. Recent studies on embryonic neurogenesis revealed the differences in cortical progenitors as a critical factor of the process of gyrification. Here, we investigated the gyrification processes using developing guinea pig brains that form a simple but fundamental pattern of gyri. In addition, we established an electroporation-mediated gene transfer method for guinea pig embryos. We introduce the guinea pig brain as a useful model system to understand the mechanisms and basic principle of cortical folding. © 2017 Japanese Society of Developmental Biologists.

  9. Sequential folding of UmuC by the Hsp70 and Hsp60 chaperone complexes of Escherichia coli.

    Science.gov (United States)

    Petit, M A; Bedale, W; Osipiuk, J; Lu, C; Rajagopalan, M; McInerney, P; Goodman, M F; Echols, H

    1994-09-23

    Replication-blocking lesions generate a signal in Escherichia coli that leads to the induction of the multigene SOS response. Among the SOS-induced genes are umuD and umuC, whose products are necessary for the increased mutation rate in induced bacteria. The mutations are likely to result from replication across the DNA lesion, and such a bypass event has been reconstituted in vitro (Rajagopalan, M., L, C., Woodgate, R., O'Donnel, M., Goodman, M. F., Echols, H. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 10777-10781). In this work, we show that the chaperone proteins promote the proper folding of UmuC protein in vitro. We treated purified and inactive UmuC with Hsp70 and Hsp60. After Hsp70 treatment, the DNA binding activity of UmuC was recovered, but the ability to promote replication across DNA lesions was not. However, lesion bypass activity was recovered upon further treatment with Hsp60. The biological significance of such a folding pathway for UmuC protein is strengthened by in vivo evidence for a role of DnaK in UV-induced mutagenesis.

  10. A continuous-time neural model for sequential action.

    Science.gov (United States)

    Kachergis, George; Wyatte, Dean; O'Reilly, Randall C; de Kleijn, Roy; Hommel, Bernhard

    2014-11-05

    Action selection, planning and execution are continuous processes that evolve over time, responding to perceptual feedback as well as evolving top-down constraints. Existing models of routine sequential action (e.g. coffee- or pancake-making) generally fall into one of two classes: hierarchical models that include hand-built task representations, or heterarchical models that must learn to represent hierarchy via temporal context, but thus far lack goal-orientedness. We present a biologically motivated model of the latter class that, because it is situated in the Leabra neural architecture, affords an opportunity to include both unsupervised and goal-directed learning mechanisms. Moreover, we embed this neurocomputational model in the theoretical framework of the theory of event coding (TEC), which posits that actions and perceptions share a common representation with bidirectional associations between the two. Thus, in this view, not only does perception select actions (along with task context), but actions are also used to generate perceptions (i.e. intended effects). We propose a neural model that implements TEC to carry out sequential action control in hierarchically structured tasks such as coffee-making. Unlike traditional feedforward discrete-time neural network models, which use static percepts to generate static outputs, our biological model accepts continuous-time inputs and likewise generates non-stationary outputs, making short-timescale dynamic predictions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  11. Separable potential approach in the folding model. Pt. 2

    International Nuclear Information System (INIS)

    Lee, C.L.; Robson, D.

    1982-01-01

    A microscopic folding formalism using a separable potential approach is applied to the elastic scattering of the n-α system. Starting with a separable nucleon-nucleon (NN) potential model, a sum of separable nucleon-nucleus potentials is obtained. A simple structure of the α-particle is assumed and the Tabakin, the Doleschall and the Strobel NN potentials are considered. These phenomenological interactions are of Yukawa or gaussian form with variable parameters for each partial wave. Spin-orbit and tensor forces are included. The resulting potentials developed from our folding calculations give approximately the same ssub(1/2) phase shifts for the n-α elastic scattering. However, in the psub(1/2) and psub(3/2) phase-shift analysis, an effective interaction derived from the NN potential is necessary to reproduce the resonances. One free energy independent parameter is introduced in our approximate G-matrix concept to give a good fit for the phase shifts. Single-nucleon knockout exchange (SNKE) is considered throughout. (orig.)

  12. Modeling sequential context effects in diagnostic interpretation of screening mammograms.

    Science.gov (United States)

    Alamudun, Folami; Paulus, Paige; Yoon, Hong-Jun; Tourassi, Georgia

    2018-07-01

    Prior research has shown that physicians' medical decisions can be influenced by sequential context, particularly in cases where successive stimuli exhibit similar characteristics when analyzing medical images. This type of systematic error is known to psychophysicists as sequential context effect as it indicates that judgments are influenced by features of and decisions about the preceding case in the sequence of examined cases, rather than being based solely on the peculiarities unique to the present case. We determine if radiologists experience some form of context bias, using screening mammography as the use case. To this end, we explore correlations between previous perceptual behavior and diagnostic decisions and current decisions. We hypothesize that a radiologist's visual search pattern and diagnostic decisions in previous cases are predictive of the radiologist's current diagnostic decisions. To test our hypothesis, we tasked 10 radiologists of varied experience to conduct blind reviews of 100 four-view screening mammograms. Eye-tracking data and diagnostic decisions were collected from each radiologist under conditions mimicking clinical practice. Perceptual behavior was quantified using the fractal dimension of gaze scanpath, which was computed using the Minkowski-Bouligand box-counting method. To test the effect of previous behavior and decisions, we conducted a multifactor fixed-effects ANOVA. Further, to examine the predictive value of previous perceptual behavior and decisions, we trained and evaluated a predictive model for radiologists' current diagnostic decisions. ANOVA tests showed that previous visual behavior, characterized by fractal analysis, previous diagnostic decisions, and image characteristics of previous cases are significant predictors of current diagnostic decisions. Additionally, predictive modeling of diagnostic decisions showed an overall improvement in prediction error when the model is trained on additional information about

  13. Folded Sheet Versus Transparent Sheet Models for Human Symmetry Judgments

    Directory of Open Access Journals (Sweden)

    Jacques Ninio

    2011-07-01

    Full Text Available As a contribution to the mysteries of human symmetry perception, reaction time data were collected on the detection of symmetry or repetition violations, in the context of short term visual memory studies. The histograms for reaction time distributions are rather narrow in the case of symmetry judgments. Their analysis was performed in terms of a simple kinetic model of a mental process in two steps, a slow one for the construction of the representation of the images to be compared, and a fast one, in the 50 ms range, for the decision. There was no need for an additional ‘mental rotation’ step. Symmetry seems to facilitate the construction step. I also present here original stimuli showing a color equalization effect across a symmetry axis, and its counterpart in periodic patterns. According to a “folded sheet model”, when a shape is perceived, the brain automatically constructs a mirror-image representation of the shape. Based in part on the reaction time analysis, I present here an alternative “transparent sheet” model in which the brain constructs a single representation, which can be accessed from two sides, thus generating simultaneously a pattern and its mirror-symmetric partner. Filtering processes, implied by current models of symmetry perception could intervene at an early stage, by nucleating the propagation of similar perceptual groupings in the two symmetric images.

  14. Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions

    Science.gov (United States)

    Yeo, Zhen Xuan; Wong, Sum Thai; Arjunan, Satya Nanda Vel; Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar; Giuliani, Alessandro; Tsuchiya, Masa

    2007-01-01

    Background Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. Methodology Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM) is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. Principal Findings SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin) during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. Conclusions/Significance The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet providing rich biological

  15. Sequential logic model deciphers dynamic transcriptional control of gene expressions.

    Directory of Open Access Journals (Sweden)

    Zhen Xuan Yeo

    Full Text Available BACKGROUND: Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. METHODOLOGY: Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. PRINCIPAL FINDINGS: SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. CONCLUSIONS/SIGNIFICANCE: The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet

  16. Popularity Modeling for Mobile Apps: A Sequential Approach.

    Science.gov (United States)

    Zhu, Hengshu; Liu, Chuanren; Ge, Yong; Xiong, Hui; Chen, Enhong

    2015-07-01

    The popularity information in App stores, such as chart rankings, user ratings, and user reviews, provides an unprecedented opportunity to understand user experiences with mobile Apps, learn the process of adoption of mobile Apps, and thus enables better mobile App services. While the importance of popularity information is well recognized in the literature, the use of the popularity information for mobile App services is still fragmented and under-explored. To this end, in this paper, we propose a sequential approach based on hidden Markov model (HMM) for modeling the popularity information of mobile Apps toward mobile App services. Specifically, we first propose a popularity based HMM (PHMM) to model the sequences of the heterogeneous popularity observations of mobile Apps. Then, we introduce a bipartite based method to precluster the popularity observations. This can help to learn the parameters and initial values of the PHMM efficiently. Furthermore, we demonstrate that the PHMM is a general model and can be applicable for various mobile App services, such as trend based App recommendation, rating and review spam detection, and ranking fraud detection. Finally, we validate our approach on two real-world data sets collected from the Apple Appstore. Experimental results clearly validate both the effectiveness and efficiency of the proposed popularity modeling approach.

  17. Denatured state is critical in determining the properties of model proteins designed on different folds

    DEFF Research Database (Denmark)

    Amatori, Andrea; Ferkinghoff-Borg, Jesper; Tiana, Guido

    2008-01-01

    The thermodynamics of proteins designed on three common folds (SH3, chymotrypsin inhibitor 2 [CI2], and protein G) is studied with a simplified C alpha, model and compared with the thermodynamics of proteins designed on random-generated folds. The model allows to design sequences to fold within a...

  18. Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

    Science.gov (United States)

    Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

    2017-11-01

    Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

  19. Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

    International Nuclear Information System (INIS)

    Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

    2008-01-01

    Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

  20. Modeling the Biomechanical Influence of Epilaryngeal Stricture on the Vocal Folds: A Low-Dimensional Model of Vocal-Ventricular Fold Coupling

    Science.gov (United States)

    Moisik, Scott R.; Esling, John H.

    2014-01-01

    Purpose: Physiological and phonetic studies suggest that, at moderate levels of epilaryngeal stricture, the ventricular folds impinge upon the vocal folds and influence their dynamical behavior, which is thought to be responsible for constricted laryngeal sounds. In this work, the authors examine this hypothesis through biomechanical modeling.…

  1. Self-organized critical model for protein folding

    Science.gov (United States)

    Moret, M. A.

    2011-09-01

    The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the fractal behavior of 5526 protein structures present in the Brookhaven Protein Data Bank. Power laws of protein mass, volume and solvent-accessible surface area are measured independently. The present findings indicate that self-organized criticality is an alternative explanation for the protein folding. Also we note that the protein packing is an independent and constant value because the self-similar behavior of the volumes and protein masses have the same fractal dimension. This power law guarantees that a protein is a complex system. From the analyzed data, q-Gaussian distributions seem to fit well this class of systems.

  2. Double folding model including the Pauli exclusion principle

    International Nuclear Information System (INIS)

    Gridnev, K.A.; Soubbotin, V.B.; Oertzen, W. von; Bohlen, H.G.; Vinas, X.

    2002-01-01

    A new method to incorporate the Pauli principle into the double folding approach to the heavy ion potential is proposed. It is shown that in order to take into account the Pauli blocking a redefinition of the density matrices of the free isolated nuclei must be one. A solution to the self-consistent incorporation of the Pauli-blocking effects in the mean-field nucleus-nucleus potential is obtained in the Thomas-Fermi approximation [ru

  3. Modeling the Pathophysiology of Phonotraumatic Vocal Hyperfunction with a Triangular Glottal Model of the Vocal Folds

    Science.gov (United States)

    Galindo, Gabriel E.; Peterson, Sean D.; Erath, Byron D.; Castro, Christian; Hillman, Robert E.; Zañartu, Matías

    2017-01-01

    Purpose: Our goal was to test prevailing assumptions about the underlying biomechanical and aeroacoustic mechanisms associated with phonotraumatic lesions of the vocal folds using a numerical lumped-element model of voice production. Method: A numerical model with a triangular glottis, posterior glottal opening, and arytenoid posturing is…

  4. Double-folding model including the Pauli exclusion principle

    International Nuclear Information System (INIS)

    Gridnev, K.A.; Soubbotin, V.B.; Oertzen, W. von; Bohlen, H.G.; Vinas, X.

    2002-01-01

    A new method for incorporating the Pauli exclusion principle into the double-folding approach to the heavy-ion potential is proposed. The description of the exchange terms at the level of the semiclassical one-body density matrix is used. It is shown that, in order to take into account Pauli blocking properly, the density matrices of free isolated nuclei must be redefined. A solution to the self-consistent incorporation of Pauli blocking effects in the mean-field nucleus-nucleus potential is obtained in the Thomas-Fermi approximation

  5. Protein folding simulations: from coarse-grained model to all-atom model.

    Science.gov (United States)

    Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei

    2009-06-01

    Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL

  6. Computational Modeling of Proteins based on Cellular Automata: A Method of HP Folding Approximation.

    Science.gov (United States)

    Madain, Alia; Abu Dalhoum, Abdel Latif; Sleit, Azzam

    2018-06-01

    The design of a protein folding approximation algorithm is not straightforward even when a simplified model is used. The folding problem is a combinatorial problem, where approximation and heuristic algorithms are usually used to find near optimal folds of proteins primary structures. Approximation algorithms provide guarantees on the distance to the optimal solution. The folding approximation approach proposed here depends on two-dimensional cellular automata to fold proteins presented in a well-studied simplified model called the hydrophobic-hydrophilic model. Cellular automata are discrete computational models that rely on local rules to produce some overall global behavior. One-third and one-fourth approximation algorithms choose a subset of the hydrophobic amino acids to form H-H contacts. Those algorithms start with finding a point to fold the protein sequence into two sides where one side ignores H's at even positions and the other side ignores H's at odd positions. In addition, blocks or groups of amino acids fold the same way according to a predefined normal form. We intend to improve approximation algorithms by considering all hydrophobic amino acids and folding based on the local neighborhood instead of using normal forms. The CA does not assume a fixed folding point. The proposed approach guarantees one half approximation minus the H-H endpoints. This lower bound guaranteed applies to short sequences only. This is proved as the core and the folds of the protein will have two identical sides for all short sequences.

  7. Nuclear interaction potential in a folded-Yukawa model with diffuse densities

    International Nuclear Information System (INIS)

    Randrup, J.

    1975-09-01

    The folded-Yukawa model for the nuclear interaction potential is generalized to diffuse density distributions which are generated by folding a Yukawa function into sharp generating distributions. The effect of a finite density diffuseness or of a finite interaction range is studied. The Proximity Formula corresponding to the generalized model is derived and numerical comparison is made with the exact results. (8 figures)

  8. Modeling and imaging of the vocal fold vibration for voice health

    DEFF Research Database (Denmark)

    Granados, Alba

    Identication of abnormalities on the vocal fold by means of dierent diagnostic methods is a key step to determine the cause or causes of a voice disorder, and subsequently give an adequate treatment. To this end, clinical investigations benet from accurate mathematical models for prediction......, analysis and inference. This thesis deals with biomechanical models of the vocal fold, specially of the collision, and laryngeal videoendoscopic analysis procedures suitable for the inference of the underlying vocal fold characteristics. The rst part of this research is devoted to frictionless contact...... modeling during asymmetric vocal fold vibration. The prediction problem is numerically addressed with a self-sustained three-dimensional nite element model of the vocal fold with position-based contact constraints. A novel contact detection mechanism is shown to successfully detect collision in asymmetric...

  9. Sequential Path Model for Grain Yield in Soybean

    Directory of Open Access Journals (Sweden)

    Mohammad SEDGHI

    2010-09-01

    Full Text Available This study was performed to determine some physiological traits that affect soybean,s grain yield via sequential path analysis. In a factorial experiment, two cultivars (Harcor and Williams were sown under four levels of nitrogen and two levels of weed management at the research station of Tabriz University, Iran, during 2004 and 2005. Grain yield, some yield components and physiological traits were measured. Correlation coefficient analysis showed that grain yield had significant positive and negative association with measured traits. A sequential path analysis was done in order to evaluate associations among grain yield and related traits by ordering the various variables in first, second and third order paths on the basis of their maximum direct effects and minimal collinearity. Two first-order variables, namely number of pods per plant and pre-flowering net photosynthesis revealed highest direct effect on total grain yield and explained 49, 44 and 47 % of the variation in grain yield based on 2004, 2005, and combined datasets, respectively. Four traits i.e. post-flowering net photosynthesis, plant height, leaf area index and intercepted radiation at the bottom layer of canopy were found to fit as second-order variables. Pre- and post-flowering chlorophyll content, main root length and intercepted radiation at the middle layer of canopy were placed at the third-order path. From the results concluded that, number of pods per plant and pre-flowering net photosynthesis are the best selection criteria in soybean for grain yield.

  10. 100-fold but not 50-fold dystrophin overexpression aggravates electrocardiographic defects in the mdx model of Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Yongping Yue

    2016-01-01

    Full Text Available Dystrophin gene replacement holds the promise of treating Duchenne muscular dystrophy. Supraphysiological expression is a concern for all gene therapy studies. In the case of Duchenne muscular dystrophy, Chamberlain and colleagues found that 50-fold overexpression did not cause deleterious side effect in skeletal muscle. To determine whether excessive dystrophin expression in the heart is safe, we studied two lines of transgenic mdx mice that selectively expressed a therapeutic minidystrophin gene in the heart at 50-fold and 100-fold of the normal levels. In the line with 50-fold overexpression, minidystrophin showed sarcolemmal localization and electrocardiogram abnormalities were corrected. However, in the line with 100-fold overexpression, we not only detected sarcolemmal minidystrophin expression but also observed accumulation of minidystrophin vesicles in the sarcoplasm. Excessive minidystrophin expression did not correct tachycardia, a characteristic feature of Duchenne muscular dystrophy. Importantly, several electrocardiogram parameters (QT interval, QRS duration and the cardiomyopathy index became worse than that of mdx mice. Our data suggests that the mouse heart can tolerate 50-fold minidystrophin overexpression, but 100-fold overexpression leads to cardiac toxicity.

  11. Scattering of long folded strings and mixed correlators in the two-matrix model

    International Nuclear Information System (INIS)

    Bourgine, J.-E.; Hosomichi, K.; Kostov, I.; Matsuo, Y.

    2008-01-01

    We study the interactions of Maldacena's long folded strings in two-dimensional string theory. We find the amplitude for a state containing two long folded strings to come and go back to infinity. We calculate this amplitude both in the worldsheet theory and in the dual matrix model, the matrix quantum mechanics. The matrix model description allows to evaluate the amplitudes involving any number of long strings, which are given by the mixed trace correlators in an effective two-matrix model

  12. Microwave Ablation: Comparison of Simultaneous and Sequential Activation of Multiple Antennas in Liver Model Systems.

    Science.gov (United States)

    Harari, Colin M; Magagna, Michelle; Bedoya, Mariajose; Lee, Fred T; Lubner, Meghan G; Hinshaw, J Louis; Ziemlewicz, Timothy; Brace, Christopher L

    2016-01-01

    To compare microwave ablation zones created by using sequential or simultaneous power delivery in ex vivo and in vivo liver tissue. All procedures were approved by the institutional animal care and use committee. Microwave ablations were performed in both ex vivo and in vivo liver models with a 2.45-GHz system capable of powering up to three antennas simultaneously. Two- and three-antenna arrays were evaluated in each model. Sequential and simultaneous ablations were created by delivering power (50 W ex vivo, 65 W in vivo) for 5 minutes per antenna (10 and 15 minutes total ablation time for sequential ablations, 5 minutes for simultaneous ablations). Thirty-two ablations were performed in ex vivo bovine livers (eight per group) and 28 in the livers of eight swine in vivo (seven per group). Ablation zone size and circularity metrics were determined from ablations excised postmortem. Mixed effects modeling was used to evaluate the influence of power delivery, number of antennas, and tissue type. On average, ablations created by using the simultaneous power delivery technique were larger than those with the sequential technique (P Simultaneous ablations were also more circular than sequential ablations (P = .0001). Larger and more circular ablations were achieved with three antennas compared with two antennas (P simultaneous power delivery creates larger, more confluent ablations with greater temperatures than those created with sequential power delivery. © RSNA, 2015.

  13. Modeling two-phase ferroelectric composites by sequential laminates

    International Nuclear Information System (INIS)

    Idiart, Martín I

    2014-01-01

    Theoretical estimates are given for the overall dissipative response of two-phase ferroelectric composites with complex particulate microstructures under arbitrary loading histories. The ferroelectric behavior of the constituent phases is described via a stored energy density and a dissipation potential in accordance with the theory of generalized standard materials. An implicit time-discretization scheme is used to generate a variational representation of the overall response in terms of a single incremental potential. Estimates are then generated by constructing sequentially laminated microgeometries of particulate type whose overall incremental potential can be computed exactly. Because they are realizable, by construction, these estimates are guaranteed to conform with any material constraints, to satisfy all pertinent bounds and to exhibit the required convexity properties with no duality gap. Predictions for representative composite and porous systems are reported and discussed in the light of existing experimental data. (paper)

  14. A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision.

    Science.gov (United States)

    Granados, Alba; Misztal, Marek Krzysztof; Brunskog, Jonas; Visseq, Vincent; Erleben, Kenny

    2017-02-01

    Analysis of voice pathologies may require vocal fold models that include relevant features such as vocal fold asymmetric collision. The present study numerically addresses the problem of frictionless asymmetric collision in a self-sustained three-dimensional continuum model of the vocal folds. Theoretical background and numerical analysis of the finite-element position-based contact model are presented, along with validation. A novel contact detection mechanism capable to detect collision in asymmetric oscillations is developed. The effect of inexact contact constraint enforcement on vocal fold dynamics is examined by different variational methods for inequality constrained minimization problems, namely, the Lagrange multiplier method and the penalty method. In contrast to the penalty solution, which is related to classical spring-like contact forces, numerical examples show that the parameter-independent Lagrange multiplier solution is more robust and accurate in the estimation of dynamical and mechanical features at vocal fold contact. Furthermore, special attention is paid to the temporal integration schemes in relation to the contact problem, the results suggesting an advantage of highly diffusive schemes. Finally, vocal fold contact enforcement is shown to affect asymmetric oscillations. The present model may be adapted to existing vocal fold models, which may contribute to a better understanding of the effect of the nonlinear contact phenomenon on phonation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Calculation of real optical model potential for heavy ions in the framework of the folding model

    International Nuclear Information System (INIS)

    Goncharov, S.A.; Timofeyuk, N.K.; Kazacha, G.S.

    1987-01-01

    The code for calculation of a real optical model potential in the framework of the folding model is realized. The program of numerical Fourier-Bessel transformation based on Filon's integration rule is used. The accuracy of numerical calculations is ∼ 10 -4 for a distance interval up to a bout (2.5-3) times the size of nuclei. The potentials are calculated for interactions of 3,4 He with nuclei from 9 Be to 27 Al with different effective NN-interactions and densities obtained from electron scattering data. Calculated potentials are similar to phenomenological potentials in Woods-Saxon form. With calculated potentials the available elastic scattering data for the considered nuclei in the energy interval 18-56 MeV are analysed. The needed renormalizations for folding potentials are < or approx. 20%

  16. Model-unrestricted scattering potentials for light ions and their interpretation in the folding model

    International Nuclear Information System (INIS)

    Ermer, M.; Clement, H.; Frank, G.; Grabmayr, P.; Heberle, N.; Wagner, G.J.

    1989-01-01

    High-quality data for elastic proton, deuteron and α-particle scattering on 40 Ca and 208 Pb at 26-30 MeV/N have been analyzed in terms of the model-unrestricted Fourier-Bessel concept. While extracted scattering potentials show substantial deviations from Woods-Saxon shapes, their real central parts are well described by folding calculations using a common effective nucleon-nucleon interaction with a weak density dependence. (orig.)

  17. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  18. Fold catastrophe model of dynamic pillar failure in asymmetric mining

    Energy Technology Data Exchange (ETDEWEB)

    Yue Pan; Ai-wu Li; Yun-song Qi [Qingdao Technological University, Qingdao (China). College of Civil Engineering

    2009-01-15

    A rock burst disaster not only destroys the pit facilities and results in economic loss but it also threatens the life of the miners. Pillar rock burst has a higher frequency of occurrence in the pit compared to other kinds of rock burst. Understanding the cause, magnitude and prevention of pillar rock burst is a significant undertaking. Equations describing the bending moment and displacement of the rock beam in asymmetric mining have been deduced for simplified asymmetric beam-pillar systems. Using the symbolic operation software MAPLE 9.5 a catastrophe model of the dynamic failure of an asymmetric rock-beam pillar system has been established. The differential form of the total potential function deduced from the law of conservation of energy was used for this deduction. The critical conditions and the initial and final positions of the pillar during failure have been given in analytical form. The amount of elastic energy released by the rock beam at the instant of failure is determined as well. A diagrammatic form showing the pillar failure was plotted using MATLAB software. This graph contains a wealth of information and is important for understanding the behavior during each deformation phase of the rock-beam pillar system. The graphic also aids in distinguishing the equivalent stiffness of the rock beam in different directions. 11 refs., 8 figs.

  19. Performance of a reduced-order FSI model for flow-induced vocal fold vibration

    Science.gov (United States)

    Luo, Haoxiang; Chang, Siyuan; Chen, Ye; Rousseau, Bernard; PhonoSim Team

    2017-11-01

    Vocal fold vibration during speech production involves a three-dimensional unsteady glottal jet flow and three-dimensional nonlinear tissue mechanics. A full 3D fluid-structure interaction (FSI) model is computationally expensive even though it provides most accurate information about the system. On the other hand, an efficient reduced-order FSI model is useful for fast simulation and analysis of the vocal fold dynamics, which can be applied in procedures such as optimization and parameter estimation. In this work, we study performance of a reduced-order model as compared with the corresponding full 3D model in terms of its accuracy in predicting the vibration frequency and deformation mode. In the reduced-order model, we use a 1D flow model coupled with a 3D tissue model that is the same as in the full 3D model. Two different hyperelastic tissue behaviors are assumed. In addition, the vocal fold thickness and subglottal pressure are varied for systematic comparison. The result shows that the reduced-order model provides consistent predictions as the full 3D model across different tissue material assumptions and subglottal pressures. However, the vocal fold thickness has most effect on the model accuracy, especially when the vocal fold is thin.

  20. FoldEco: A Model for Proteostasis in E. coli

    Directory of Open Access Journals (Sweden)

    Evan T. Powers

    2012-03-01

    Full Text Available To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information—including mechanisms, rate parameters, and equilibrium coefficients—is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at http://foldeco.scripps.edu.

  1. Kinematic evolution of fold and thrust belts. Insights from experimental modeling

    International Nuclear Information System (INIS)

    Ueta, Keiichi

    2011-01-01

    Physical experiments were performed to gain a better understanding on the kinematic evolution of fold and thrust belts. The present study focuses on deformation of sedimentary cover caused by thrust and reverse movements along the basement fault. Our physical models comprise dry quartz sand representing brittle sedimentary rock and viscous silicone polymer representing overpressured mudstone. Computerized X-ray tomography was applied to the experiments to analyze the kinematic evolution of fold and thrust belts. In the sand models, the width of deformation zone above thrust was wider than that above reverse fault, because back thrust developed on the hanging wall of reverse fault. Within the physical models composed of dry sand and silicone polymer, minor folds and thrusts with minor displacement developed on the footwall of the major monoclinal flexure. These results compare well with the geometry and kinematic evolution of the fold and thrust belts in Japan. (author)

  2. Orogen-transverse tectonic window in the Eastern Himalayan fold belt: A superposed buckling model

    Science.gov (United States)

    Bose, Santanu; Mandal, Nibir; Acharyya, S. K.; Ghosh, Subhajit; Saha, Puspendu

    2014-09-01

    The Eastern Lesser Himalayan fold-thrust belt is punctuated by a row of orogen-transverse domal tectonic windows. To evaluate their origin, a variety of thrust-stack models have been proposed, assuming that the crustal shortening occurred dominantly by brittle deformations. However, the Rangit Window (RW) in the Darjeeling-Sikkim Himalaya (DSH) shows unequivocal structural imprints of ductile deformations of multiple episodes. Based on new structural maps, coupled with outcrop-scale field observations, we recognize at least four major episodes of folding in the litho-tectonic units of DSH. The last episode has produced regionally orogen-transverse upright folds (F4), the interference of which with the third-generation (F3) orogen-parallel folds has shaped the large-scale structural patterns in DSH. We propose a new genetic model for the RW, invoking the mechanics of superposed buckling in the mechanically stratified litho-tectonic systems. We substantiate this superposed buckling model with results obtained from analogue experiments. The model explains contrasting F3-F4 interferences in the Lesser Himalayan Sequence (LHS). The lower-order (terrain-scale) folds have undergone superposed buckling in Mode 1, producing large-scale domes and basins, whereas the RW occurs as a relatively higher-order dome nested in the first-order Tista Dome. The Gondwana and the Proterozoic rocks within the RW underwent superposed buckling in Modes 3 and 4, leading to Type 2 fold interferences, as evident from their structural patterns.

  3. An optical flow-based state-space model of the vocal folds

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas

    2017-01-01

    High-speed movies of the vocal fold vibration are valuable data to reveal vocal fold features for voice pathology diagnosis. This work presents a suitable Bayesian model and a purely theoretical discussion for further development of a framework for continuum biomechanical features estimation. A l...... to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters........ A linear and Gaussian nonstationary state-space model is proposed and thoroughly discussed. The evolution model is based on a self-sustained three-dimensional finite element model of the vocal folds, and the observation model involves a dense optical flow algorithm. The results show that the method is able...

  4. An optical flow-based state-space model of the vocal folds.

    Science.gov (United States)

    Granados, Alba; Brunskog, Jonas

    2017-06-01

    High-speed movies of the vocal fold vibration are valuable data to reveal vocal fold features for voice pathology diagnosis. This work presents a suitable Bayesian model and a purely theoretical discussion for further development of a framework for continuum biomechanical features estimation. A linear and Gaussian nonstationary state-space model is proposed and thoroughly discussed. The evolution model is based on a self-sustained three-dimensional finite element model of the vocal folds, and the observation model involves a dense optical flow algorithm. The results show that the method is able to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters.

  5. Prevention of vocal fold scarring by local application of basic fibroblast growth factor in a rat vocal fold injury model.

    Science.gov (United States)

    Suzuki, Ryo; Kawai, Yoshitaka; Tsuji, Takuya; Hiwatashi, Nao; Kishimoto, Yo; Tateya, Ichiro; Nakamura, Tatsuo; Hirano, Shigeru

    2017-02-01

    Vocal fold scarring, which causes severe hoarseness, is intractable. The optimal treatment for vocal fold scarring has not been established; therefore, prevention of scarring is important. The aim of this study was to clarify the effectiveness of basic fibroblast growth factor (bFGF) for prevention of postsurgical vocal fold scarring. Prospective animal experiments with controls. The vocal folds of Sprague-Dawley rats were injured unilaterally or bilaterally after local application of a 10 μL solution of bFGF. Larynges ware harvested for histological and immunohistochemical examination 2 months postoperation and for quantitative real-time polymerase chain reaction (qRT-PCR) analysis 1 week postoperation. Histological examination showed significantly increased hyaluronic acid and decreased deposition of dense collagen in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. Immunohistochemical examination showed significantly decreased collagen type III deposition in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. qRT-PCR revealed that hyaluronan synthase 2 (Has2), Has3, and hepatocyte growth factor were upregulated in bFGF-treated groups compared with sham-treated group. The current results suggest that local application of bFGF at the time of injury has the potential to prevent vocal fold scarring. Preventive injection of bFGF could be applied at the time of phonomicrosurgery to avoid postoperative scar formation. N/A. Laryngoscope, 2016 127:E67-E74, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  6. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

    International Nuclear Information System (INIS)

    Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

    2015-01-01

    The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism

  7. Sequential decoding of intramuscular EMG signals via estimation of a Markov model.

    Science.gov (United States)

    Monsifrot, Jonathan; Le Carpentier, Eric; Aoustin, Yannick; Farina, Dario

    2014-09-01

    This paper addresses the sequential decoding of intramuscular single-channel electromyographic (EMG) signals to extract the activity of individual motor neurons. A hidden Markov model is derived from the physiological generation of the EMG signal. The EMG signal is described as a sum of several action potentials (wavelet) trains, embedded in noise. For each train, the time interval between wavelets is modeled by a process that parameters are linked to the muscular activity. The parameters of this process are estimated sequentially by a Bayes filter, along with the firing instants. The method was tested on some simulated signals and an experimental one, from which the rates of detection and classification of action potentials were above 95% with respect to the reference decomposition. The method works sequentially in time, and is the first to address the problem of intramuscular EMG decomposition online. It has potential applications for man-machine interfacing based on motor neuron activities.

  8. Distinct Element Method modelling of fold-related fractures in a multilayer sequence

    Science.gov (United States)

    Kaserer, Klemens; Schöpfer, Martin P. J.; Grasemann, Bernhard

    2017-04-01

    Natural fractures have a significant impact on the performance of hydrocarbon systems/reservoirs. In a multilayer sequence, both the fracture density within the individual layers and the type of fracture intersection with bedding contacts are key parameters controlling fluid pathways. In the present study the influence of layer stacking and interlayer friction on fracture density and connectivity within a folded sequence is systematically investigated using 2D Distinct Element Method modelling. Our numerical approach permits forward modelling of both fracture nucleation/propagation/arrest and (contemporaneous) frictional slip along bedding planes in a robust and mechanically sound manner. Folding of the multilayer sequence is achieved by enforcing constant curvature folding by means of a velocity boundary condition at the model base, while a constant overburden pressure is maintained at the model top. The modelling reveals that with high bedding plane friction the multilayer stack behaves mechanically as a single layer so that the neutral surface develops in centre of the sequence and fracture spacing is controlled by the total thickness of the folded sequence. In contrast, low bedding plane friction leads to decoupling of the individual layers (flexural slip folding) so that a neutral surface develops in the centre of each layer and fracture spacing is controlled by the thickness of the individual layers. The low interfacial friction models illustrate that stepping of fractures across bedding planes is a common process, which can however have two contrasting origins: The mechanical properties of the interface cause fracture stepping during fracture propagation. Originally through-going fractures are later offset by interfacial slip during folding. A combination of these two different origins may lead to (apparently) inconsistent fracture offsets across bedding planes within a flexural slip fold.

  9. A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

    Science.gov (United States)

    Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

    2017-04-01

    3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

  10. Roles of beta-turns in protein folding: from peptide models to protein engineering.

    Science.gov (United States)

    Marcelino, Anna Marie C; Gierasch, Lila M

    2008-05-01

    Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.

  11. Formal Modeling and Verification of Interlocking Systems Featuring Sequential Release

    DEFF Research Database (Denmark)

    Vu, Linh Hong; Haxthausen, Anne Elisabeth; Peleska, Jan

    2015-01-01

    In this paper, we present a method and an associated tool suite for formal verification of the new ETCS level 2 based Danish railway interlocking systems. We have made a generic and reconfigurable model of the system behavior and generic high-level safety properties. This model accommodates seque...... SMT based bounded model checking (BMC) and inductive reasoning, we are able to verify the properties for model instances corresponding to railway networks of industrial size. Experiments also show that BMC is efficient for finding bugs in the railway interlocking designs....

  12. Formal Modeling and Verification of Interlocking Systems Featuring Sequential Release

    DEFF Research Database (Denmark)

    Vu, Linh Hong; Haxthausen, Anne Elisabeth; Peleska, Jan

    2014-01-01

    In this paper, we present a method and an associated tool suite for formal verification of the new ETCS level 2 based Danish railway interlocking systems. We have made a generic and reconfigurable model of the system behavior and generic high-level safety properties. This model accommodates seque...... SMT based bounded model checking (BMC) and inductive reasoning, we are able to verify the properties for model instances corresponding to railway networks of industrial size. Experiments also show that BMC is efficient for finding bugs in the railway interlocking designs....

  13. A sequential model for the structure of health care utilization.

    NARCIS (Netherlands)

    Herrmann, W.J.; Haarmann, A.; Baerheim, A.

    2017-01-01

    Traditional measurement models of health care utilization are not able to represent the complex structure of health care utilization. In this qualitative study, we, therefore, developed a new model to represent the health care utilization structure. In Norway and Germany, we conducted episodic

  14. Formal modelling and verification of interlocking systems featuring sequential release

    DEFF Research Database (Denmark)

    Vu, Linh Hong; Haxthausen, Anne Elisabeth; Peleska, Jan

    2017-01-01

    checking (BMC) and inductive reasoning, it is verified that the generated model instance satisfies the generated safety properties. Using this method, we are able to verify the safety properties for model instances corresponding to railway networks of industrial size. Experiments show that BMC is also...

  15. Likelihood ratio sequential sampling models of recognition memory.

    Science.gov (United States)

    Osth, Adam F; Dennis, Simon; Heathcote, Andrew

    2017-02-01

    The mirror effect - a phenomenon whereby a manipulation produces opposite effects on hit and false alarm rates - is benchmark regularity of recognition memory. A likelihood ratio decision process, basing recognition on the relative likelihood that a stimulus is a target or a lure, naturally predicts the mirror effect, and so has been widely adopted in quantitative models of recognition memory. Glanzer, Hilford, and Maloney (2009) demonstrated that likelihood ratio models, assuming Gaussian memory strength, are also capable of explaining regularities observed in receiver-operating characteristics (ROCs), such as greater target than lure variance. Despite its central place in theorising about recognition memory, however, this class of models has not been tested using response time (RT) distributions. In this article, we develop a linear approximation to the likelihood ratio transformation, which we show predicts the same regularities as the exact transformation. This development enabled us to develop a tractable model of recognition-memory RT based on the diffusion decision model (DDM), with inputs (drift rates) provided by an approximate likelihood ratio transformation. We compared this "LR-DDM" to a standard DDM where all targets and lures receive their own drift rate parameters. Both were implemented as hierarchical Bayesian models and applied to four datasets. Model selection taking into account parsimony favored the LR-DDM, which requires fewer parameters than the standard DDM but still fits the data well. These results support log-likelihood based models as providing an elegant explanation of the regularities of recognition memory, not only in terms of choices made but also in terms of the times it takes to make them. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Frequency Response of Synthetic Vocal Fold Models with Linear and Nonlinear Material Properties

    Science.gov (United States)

    Shaw, Stephanie M.; Thomson, Scott L.; Dromey, Christopher; Smith, Simeon

    2012-01-01

    Purpose: The purpose of this study was to create synthetic vocal fold models with nonlinear stress-strain properties and to investigate the effect of linear versus nonlinear material properties on fundamental frequency (F[subscript 0]) during anterior-posterior stretching. Method: Three materially linear and 3 materially nonlinear models were…

  17. A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

    A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

  18. Correlation of phonatory behavior with vocal fold structure, observed in a physical model

    Science.gov (United States)

    Krane, Michael; Walters, Gage; McPhail, Michael

    2017-11-01

    The effect of vocal fold shape and internal structure on phonation was studied experimentally using a physical model of the human airway. Model folds used a ``M5'' or a swept ellipse coronal cross-section shape. Models were molded in either 2 or three layers. Two-layer models included a more stiff ``body'' layer and a much softer ``cover'' layer, while the 3-layer models also incorporated an additional, thin, ``ligament/conus'' layer stiffer than the body layer. The elliptical section models were all molded in 3 such layers. Measurements of transglottal pressure, volume flow, mouth sound pressure, and high-speed imaging of vocal fold vibration were performed. These show that models with the ``ligament'' layer experienced much attenuated vertical deformation, that glottal closure was more likely, and that phonation was much easier to initiate. These findings suggest that the combination of the vocal ligament and the conus elasticus stabilize the vocal fold for efficient phonation by limiting vertical deformation, while allowing transverse deformations to occur. Acknowledge support from NIH DC R01005642-11.

  19. Coupled channel folding model description of α scattering from 9Be

    International Nuclear Information System (INIS)

    Roy, S.; Chatterjee, J.M.; Majumdar, H.; Datta, S.K.; Banerjee, S.R.; Chintalapudi, S.N.

    1995-01-01

    Alpha scattering from 9 Be at E α = 65 MeV is described in the coupled channel framework with phenomenological as well as folded potentials. The multipole components of the deformed density of 9 Be are derived from Nilsson model wave functions. Reasonably good agreements are obtained for the angular distributions of 3/2 - (g.s.) and 5/2 - (2.43 MeV) states of the ground state band with folded potentials. The deformation predicted by the model corroborates with that derived from the phenomenological analysis with potentials of different geometries

  20. Coupled channel folding model description of {alpha} scattering from {sup 9}Be

    Energy Technology Data Exchange (ETDEWEB)

    Roy, S.; Chatterjee, J.M.; Majumdar, H. [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Calcutta 700064 (India); Datta, S.K. [Nuclear Science Centre, P.O.10502, New Delhi 110067 (India); Banerjee, S.R. [Variable Energy Cyclotron Centre, 1/AF Bidhannagar, Calcutta 700064 (India); Chintalapudi, S.N. [Inter-University Consortium, Department of Atomic Energy Facilities, Bidhannagar, Calcutta 700064 (India)

    1995-09-01

    Alpha scattering from {sup 9}Be at {ital E}{sub {alpha}}= 65 MeV is described in the coupled channel framework with phenomenological as well as folded potentials. The multipole components of the deformed density of {sup 9}Be are derived from Nilsson model wave functions. Reasonably good agreements are obtained for the angular distributions of 3/2{sup {minus}}(g.s.) and 5/2{sup {minus}}(2.43 MeV) states of the ground state band with folded potentials. The deformation predicted by the model corroborates with that derived from the phenomenological analysis with potentials of different geometries.

  1. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  2. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

    2017-09-01

    We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

  3. Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp

    Science.gov (United States)

    Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.

    2012-11-01

    The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. A recent in-vitro investigation of a model polyp in a driven vocal fold apparatus demonstrated that such a geometric abnormality considerably disrupts the glottal jet behavior and that this flow field adjustment was a likely reason for the severe degradation of the vocal quality in patients. Understanding of the formation and propagation of vortical structures from a geometric protuberance, and their subsequent impact on the aerodynamic loadings that drive vocal fold dynamic, is a critical component in advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp. Unsteady three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  4. Time-resolved transglottal pressure measurements in a scaled up vocal fold model

    Science.gov (United States)

    Ringenberg, Hunter; Krane, Michael; Rogers, Dylan; Misfeldt, Mitchel; Wei, Timothy

    2016-11-01

    Experimental measurements of flow through a scaled up dynamic human vocal fold model are presented. The simplified 10x scale vocal fold model from Krane, et al. (2007) was used to examine fundamental features of vocal fold oscillatory motion. Of particular interest was the temporal variation of transglottal pressure multiplied by the volume flow rate through the glottis throughout an oscillation cycle. Experiments were dynamically scaled to examine a range of frequencies, 100 - 200 Hz, corresponding to the male and female voice. By using water as the working fluid, very high resolution, both spatial and temporal resolution, was achieved. Time resolved movies of flow through symmetrically oscillating vocal folds will be presented. Both individual realizations as well as phase-averaged data will be shown. Key features, such as randomness and development time of the Coanda effect, vortex shedding, and volume flow rate data have been presented in previous APS-DFD meetings. This talk will focus more on the relation between the flow and aeroacoustics associated with vocal fold oscillations. Supported by the NIH.

  5. Heterotic line bundle models on elliptically fibered Calabi-Yau three-folds

    Science.gov (United States)

    Braun, Andreas P.; Brodie, Callum R.; Lukas, Andre

    2018-04-01

    We analyze heterotic line bundle models on elliptically fibered Calabi-Yau three-folds over weak Fano bases. In order to facilitate Wilson line breaking to the standard model group, we focus on elliptically fibered three-folds with a second section and a freely-acting involution. Specifically, we consider toric weak Fano surfaces as base manifolds and identify six such manifolds with the required properties. The requisite mathematical tools for the construction of line bundle models on these spaces, including the calculation of line bundle cohomology, are developed. A computer scan leads to more than 400 line bundle models with the right number of families and an SU(5) GUT group which could descend to standard-like models after taking the ℤ2 quotient. A common and surprising feature of these models is the presence of a large number of vector-like states.

  6. Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference.

    Directory of Open Access Journals (Sweden)

    Dario Cuevas Rivera

    2015-10-01

    Full Text Available The olfactory information that is received by the insect brain is encoded in the form of spatiotemporal patterns in the projection neurons of the antennal lobe. These dense and overlapping patterns are transformed into a sparse code in Kenyon cells in the mushroom body. Although it is clear that this sparse code is the basis for rapid categorization of odors, it is yet unclear how the sparse code in Kenyon cells is computed and what information it represents. Here we show that this computation can be modeled by sequential firing rate patterns using Lotka-Volterra equations and Bayesian online inference. This new model can be understood as an 'intelligent coincidence detector', which robustly and dynamically encodes the presence of specific odor features. We found that the model is able to qualitatively reproduce experimentally observed activity in both the projection neurons and the Kenyon cells. In particular, the model explains mechanistically how sparse activity in the Kenyon cells arises from the dense code in the projection neurons. The odor classification performance of the model proved to be robust against noise and time jitter in the observed input sequences. As in recent experimental results, we found that recognition of an odor happened very early during stimulus presentation in the model. Critically, by using the model, we found surprising but simple computational explanations for several experimental phenomena.

  7. Conditions for Model Matching of Switched Asynchronous Sequential Machines with Output Feedback

    OpenAIRE

    Jung–Min Yang

    2016-01-01

    Solvability of the model matching problem for input/output switched asynchronous sequential machines is discussed in this paper. The control objective is to determine the existence condition and design algorithm for a corrective controller that can match the stable-state behavior of the closed-loop system to that of a reference model. Switching operations and correction procedures are incorporated using output feedback so that the controlled switched machine can show the ...

  8. Finite Element Modelling of Bends and Creases during Folding Ultra Thin Stainless Steel Foils

    NARCIS (Netherlands)

    Datta, K.; Akagi, H.; Geijselaers, Hubertus J.M.; Huetink, Han

    2003-01-01

    Finite Element Modelling of an ultra thin foil of SUS 304 stainless steel is carried out. These foils are 20 mm and below in thickness. The development of stresses and strains during folding of these foils is studied. The objective of this study is to induce qualities of paper in the foils of

  9. A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision

    DEFF Research Database (Denmark)

    Granados, Alba; Misztal, Marek Krzysztof; Brunskog, Jonas

    2016-01-01

    . Theoretical background and numerical analysis of the finite-element position-based contact model are presented, along with validation. A novel contact detection mechanism capable to detect collision in asymmetric oscillations is developed. The effect of inexact contact constraint enforcement on vocal fold...

  10. Cross-tropopause Transport In Tropopause Folds: Mechanisms and Sensitivity To Model Resolution

    Science.gov (United States)

    Gray, S. L.

    The rate and processes of transfer of mass and chemical species between the strato- sphere and troposphere (stratosphere-troposphere exchange) are currently uncertain. In the midlatitudes exchange appears to be dominated by processes associated with tropopause folds and cut-off lows. The development of a tropopause fold is a reversible process and thus irreversible processes must occur for the permanent transfer of ma- terial across the tropopause boundary. Proposed processes include turbulent mixing, quasi-isentropic mixing, convectively breaking gravity waves, deep convection and radiative heating. Numerical models run at typical climate or regional-scale resolutions are unable to re- solve the fine-scale features observed in tropopause folds. It is hypothesised that both the rate of exchange and its partitioning into different processes, as derived from nu- merical model simulations, are sensitive to model resolution. This hypothesis is tested through simulations of a tropopause folding event associated with a vigorous surface cold front which tracked across the British Isles. Climate to high-mesoscale resolution simulations incorporating passive tracers are performed using the mesoscale version of the Met Office Unified Model. The mechanism by which the parametrized convec- tion leads to exchange is the subject of further examination.

  11. Folding model analysis of the nucleus–nucleus scattering based on ...

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Pramana – Journal of Physics; Volume 87; Issue 6. Folding model analysis of the nucleus–nucleus scattering based on Jacobi coordinates. F PAKDEL A A RAJABI L NICKHAH. Regular Volume 87 Issue 6 December 2016 Article ID 90 ...

  12. Sequential Markov chain Monte Carlo filter with simultaneous model selection for electrocardiogram signal modeling.

    Science.gov (United States)

    Edla, Shwetha; Kovvali, Narayan; Papandreou-Suppappola, Antonia

    2012-01-01

    Constructing statistical models of electrocardiogram (ECG) signals, whose parameters can be used for automated disease classification, is of great importance in precluding manual annotation and providing prompt diagnosis of cardiac diseases. ECG signals consist of several segments with different morphologies (namely the P wave, QRS complex and the T wave) in a single heart beat, which can vary across individuals and diseases. Also, existing statistical ECG models exhibit a reliance upon obtaining a priori information from the ECG data by using preprocessing algorithms to initialize the filter parameters, or to define the user-specified model parameters. In this paper, we propose an ECG modeling technique using the sequential Markov chain Monte Carlo (SMCMC) filter that can perform simultaneous model selection, by adaptively choosing from different representations depending upon the nature of the data. Our results demonstrate the ability of the algorithm to track various types of ECG morphologies, including intermittently occurring ECG beats. In addition, we use the estimated model parameters as the feature set to classify between ECG signals with normal sinus rhythm and four different types of arrhythmia.

  13. Characteristics of phonation onset in a two-layer vocal fold model.

    Science.gov (United States)

    Zhang, Zhaoyan

    2009-02-01

    Characteristics of phonation onset were investigated in a two-layer body-cover continuum model of the vocal folds as a function of the biomechanical and geometric properties of the vocal folds. The analysis showed that an increase in either the body or cover stiffness generally increased the phonation threshold pressure and phonation onset frequency, although the effectiveness of varying body or cover stiffness as a pitch control mechanism varied depending on the body-cover stiffness ratio. Increasing body-cover stiffness ratio reduced the vibration amplitude of the body layer, and the vocal fold motion was gradually restricted to the medial surface, resulting in more effective flow modulation and higher sound production efficiency. The fluid-structure interaction induced synchronization of more than one group of eigenmodes so that two or more eigenmodes may be simultaneously destabilized toward phonation onset. At certain conditions, a slight change in vocal fold stiffness or geometry may cause phonation onset to occur as eigenmode synchronization due to a different pair of eigenmodes, leading to sudden changes in phonation onset frequency, vocal fold vibration pattern, and sound production efficiency. Although observed in a linear stability analysis, a similar mechanism may also play a role in register changes at finite-amplitude oscillations.

  14. Modeling programmable deformation of self-folding all-polymer structures with temperature-sensitive hydrogels

    International Nuclear Information System (INIS)

    Guo, Wei; Zhou, Jinxiong; Li, Meie

    2013-01-01

    Combination of soft active hydrogels with hard passive polymers gives rise to all-polymer composites. The hydrogel is sensitive to external stimuli while the passive polymer is inert. Utilizing the different behaviors of two materials subject to environmental variation, for example temperature, results in self-folding soft machines. We report our efforts to model the programmable deformation of self-folding structures with temperature-sensitive hydrogels. The self-folding structures are realized either by constructing a bilayer structure or by incorporating hydrogels as hinges. The methodology and the results may aid the design, control and fabrication of 3D complex structures from 2D simple configurations through self-assembly. (paper)

  15. Modeling eye gaze patterns in clinician-patient interaction with lag sequential analysis.

    Science.gov (United States)

    Montague, Enid; Xu, Jie; Chen, Ping-Yu; Asan, Onur; Barrett, Bruce P; Chewning, Betty

    2011-10-01

    The aim of this study was to examine whether lag sequential analysis could be used to describe eye gaze orientation between clinicians and patients in the medical encounter. This topic is particularly important as new technologies are implemented into multiuser health care settings in which trust is critical and nonverbal cues are integral to achieving trust. This analysis method could lead to design guidelines for technologies and more effective assessments of interventions. Nonverbal communication patterns are important aspects of clinician-patient interactions and may affect patient outcomes. The eye gaze behaviors of clinicians and patients in 110 videotaped medical encounters were analyzed using the lag sequential method to identify significant behavior sequences. Lag sequential analysis included both event-based lag and time-based lag. Results from event-based lag analysis showed that the patient's gaze followed that of the clinician, whereas the clinician's gaze did not follow the patient's. Time-based sequential analysis showed that responses from the patient usually occurred within 2 s after the initial behavior of the clinician. Our data suggest that the clinician's gaze significantly affects the medical encounter but that the converse is not true. Findings from this research have implications for the design of clinical work systems and modeling interactions. Similar research methods could be used to identify different behavior patterns in clinical settings (physical layout, technology, etc.) to facilitate and evaluate clinical work system designs.

  16. A mixed-effects model approach for the statistical analysis of vocal fold viscoelastic shear properties.

    Science.gov (United States)

    Xu, Chet C; Chan, Roger W; Sun, Han; Zhan, Xiaowei

    2017-11-01

    A mixed-effects model approach was introduced in this study for the statistical analysis of rheological data of vocal fold tissues, in order to account for the data correlation caused by multiple measurements of each tissue sample across the test frequency range. Such data correlation had often been overlooked in previous studies in the past decades. The viscoelastic shear properties of the vocal fold lamina propria of two commonly used laryngeal research animal species (i.e. rabbit, porcine) were measured by a linear, controlled-strain simple-shear rheometer. Along with published canine and human rheological data, the vocal fold viscoelastic shear moduli of these animal species were compared to those of human over a frequency range of 1-250Hz using the mixed-effects models. Our results indicated that tissues of the rabbit, canine and porcine vocal fold lamina propria were significantly stiffer and more viscous than those of human. Mixed-effects models were shown to be able to more accurately analyze rheological data generated from repeated measurements. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Generic framework for mining cellular automata models on protein-folding simulations.

    Science.gov (United States)

    Diaz, N; Tischer, I

    2016-05-13

    Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.

  18. Influence of Embedded Fibers and an Epithelium Layer on the Glottal Closure Pattern in a Physical Vocal Fold Model

    Science.gov (United States)

    Xuan, Yue; Zhang, Zhaoyan

    2014-01-01

    Purpose: The purpose of this study was to explore the possible structural and material property features that may facilitate complete glottal closure in an otherwise isotropic physical vocal fold model. Method: Seven vocal fold models with different structural features were used in this study. An isotropic model was used as the baseline model, and…

  19. Mathematical Model for the Sequential Action of Radiation and Heat on Yeast Cells

    International Nuclear Information System (INIS)

    Kim, Jin Kyu; Lee, Yun Jong; Kim, Su Hyoun; Nili, Mohammad; Zhurakovskaya, Galina P.; Petin, Vladislav G.

    2009-01-01

    It is well known that the synergistic interaction of hyperthermia with ionizing radiation and other agents is widely used in hyperthermic oncology. Interaction between two agents may be considered as synergistic or antagonistic when the effect produced is greater or smaller than the sum of the two single responses. It has long be considered that the mechanism of synergistic interaction of hyperthermia and ionizing radiation may be brought about by an inhibition of the repair from sublethal and potentially lethal damage at the cellular level. The inhibition of the recovery process after combined treatments cannot be considered as a reason for the synergy, but rather would be the expected and predicted consequence of the production of irreversible damage. On the basis of it, a simple mathematical model of the synergistic interaction of two agents acting simultaneously has been proposed. However, the model has not been applied to predict the degree of interaction of heat and ionizing radiation after their sequential action. Extension of the model to the sequential treatment of heat and ionizing radiation seems to be of interest for theoretical and practical reasons. Thus, the purposes of the present work is to suggest the simplest mathematical model which would be able to account for the results obtained and currently available experimental information on the sequential action of radiation and heat.

  20. Three-dimensional laryngeal flow fields induced by a model vocal fold polyp

    Energy Technology Data Exchange (ETDEWEB)

    Erath, Byron D., E-mail: erath@gwu.edu [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street NW, 739 Phillips Hall, Washington, DC 20052 (United States); Plesniak, Michael W., E-mail: plesniak@gwu.edu [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street NW, 739 Phillips Hall, Washington, DC 20052 (United States)

    2012-06-15

    Highlights: Black-Right-Pointing-Pointer Pathological speech with a unilateral polyp is modeled in a scaled-up flow facility. Black-Right-Pointing-Pointer Vortex shedding from the polyp disrupts normal flow behavior. Black-Right-Pointing-Pointer Hairpin vortices create spatial velocity asymmetries in the glottal flow. - Abstract: Pathological laryngeal flow fields are investigated in a dynamically-driven, scaled-up model of the vocal folds. Disruption of the flow field due to the presence of a geometric protuberance, representative of a sessile unilateral polyp, is investigated in both the streamwise and transverse flow directions using phase-averaged particle image velocimetry. It is shown that the protuberance disrupts the normal flow behavior of the glottal jet throughout the phonatory cycle. During the divergent portions of the glottal cycle, the flow is characterized by the formation of hairpin vortices downstream of the protuberance. The protuberance also introduces significant velocity gradients in the anterior-posterior direction, which cover {approx}30 - 40% of the vocal fold length. It is proposed that the disruption of the normal velocity behavior owing to the presence of a polyp will adversely impact the aerodynamic loadings that drive vocal fold motion, contributing to the temporal and spatial vocal fold asymmetries that are clinically-observed in patients with unilateral polyps.

  1. Three-dimensional laryngeal flow fields induced by a model vocal fold polyp

    International Nuclear Information System (INIS)

    Erath, Byron D.; Plesniak, Michael W.

    2012-01-01

    Highlights: ► Pathological speech with a unilateral polyp is modeled in a scaled-up flow facility. ► Vortex shedding from the polyp disrupts normal flow behavior. ► Hairpin vortices create spatial velocity asymmetries in the glottal flow. - Abstract: Pathological laryngeal flow fields are investigated in a dynamically-driven, scaled-up model of the vocal folds. Disruption of the flow field due to the presence of a geometric protuberance, representative of a sessile unilateral polyp, is investigated in both the streamwise and transverse flow directions using phase-averaged particle image velocimetry. It is shown that the protuberance disrupts the normal flow behavior of the glottal jet throughout the phonatory cycle. During the divergent portions of the glottal cycle, the flow is characterized by the formation of hairpin vortices downstream of the protuberance. The protuberance also introduces significant velocity gradients in the anterior-posterior direction, which cover ∼30 − 40% of the vocal fold length. It is proposed that the disruption of the normal velocity behavior owing to the presence of a polyp will adversely impact the aerodynamic loadings that drive vocal fold motion, contributing to the temporal and spatial vocal fold asymmetries that are clinically-observed in patients with unilateral polyps.

  2. Development and sensitivity analysis of a fullykinetic model of sequential reductive dechlorination in subsurface

    DEFF Research Database (Denmark)

    Malaguerra, Flavio; Chambon, Julie Claire Claudia; Albrechtsen, Hans-Jørgen

    2010-01-01

    and natural degradation of chlorinated solvents frequently occurs in the subsurface through sequential reductive dechlorination. However, the occurrence and the performance of natural sequential reductive dechlorination strongly depends on environmental factor such as redox conditions, presence of fermenting...... organic matter / electron donors, presence of specific biomass, etc. Here we develop a new fully-kinetic biogeochemical reactive model able to simulate chlorinated solvents degradation as well as production and consumption of molecular hydrogen. The model is validated using batch experiment data......Chlorinated hydrocarbons originating from point sources are amongst the most prevalent contaminants of ground water and often represent a serious threat to groundwater-based drinking water resources. Natural attenuation of contaminant plumes can play a major role in contaminated site management...

  3. A SEQUENTIAL MODEL OF INNOVATION STRATEGY—COMPANY NON-FINANCIAL PERFORMANCE LINKS

    OpenAIRE

    Ciptono, Wakhid Slamet

    2006-01-01

    This study extends the prior research (Zahra and Das 1993) by examining the association between a company’s innovation strategy and its non-financial performance in the upstream and downstream strategic business units (SBUs) of oil and gas companies. The sequential model suggests a causal sequence among six dimensions of innovation strategy (leadership orientation, process innovation, product/service innovation, external innovation source, internal innovation source, and investment) that may ...

  4. [Mathematical modeling of synergistic interaction of sequential thermoradiation action on mammalian cells].

    Science.gov (United States)

    Belkina, S V; Semkina, M A; Kritskiĭ, R O; Petin, V G

    2010-01-01

    Data obtained by other authors for mammalian cells treated by sequential action of ionizing radiation and hyperthermia were used to estimate the dependence of synergistic enhancement ratio on the ratio of damages induced by these agents. Experimental results were described and interpreted by means of the mathematical model of synergism in accordance with which the synergism is expected to result from the additional lethal damage arising from the interaction of sublesions induced by both agents.

  5. The importance of examining movements within the US health care system: sequential logit modeling

    Directory of Open Access Journals (Sweden)

    Lee Chioun

    2010-09-01

    Full Text Available Abstract Background Utilization of specialty care may not be a discrete, isolated behavior but rather, a behavior of sequential movements within the health care system. Although patients may often visit their primary care physician and receive a referral before utilizing specialty care, prior studies have underestimated the importance of accounting for these sequential movements. Methods The sample included 6,772 adults aged 18 years and older who participated in the 2001 Survey on Disparities in Quality of Care, sponsored by the Commonwealth Fund. A sequential logit model was used to account for movement in all stages of utilization: use of any health services (i.e., first stage, having a perceived need for specialty care (i.e., second stage, and utilization of specialty care (i.e., third stage. In the sequential logit model, all stages are nested within the previous stage. Results Gender, race/ethnicity, education and poor health had significant explanatory effects with regard to use of any health services and having a perceived need for specialty care, however racial/ethnic, gender, and educational disparities were not present in utilization of specialty care. After controlling for use of any health services and having a perceived need for specialty care, inability to pay for specialty care via income (AOR = 1.334, CI = 1.10 to 1.62 or health insurance (unstable insurance: AOR = 0.26, CI = 0.14 to 0.48; no insurance: AOR = 0.12, CI = 0.07 to 0.20 were significant barriers to utilization of specialty care. Conclusions Use of a sequential logit model to examine utilization of specialty care resulted in a detailed representation of utilization behaviors and patient characteristics that impact these behaviors at all stages within the health care system. After controlling for sequential movements within the health care system, the biggest barrier to utilizing specialty care is the inability to pay, while racial, gender, and educational disparities

  6. Employees’ Perceptions of Corporate Social Responsibility and Job Performance: A Sequential Mediation Model

    Directory of Open Access Journals (Sweden)

    Inyong Shin

    2016-05-01

    Full Text Available In spite of the increasing importance of corporate social responsibility (CSR and employee job performance, little is still known about the links between the socially responsible actions of organizations and the job performance of their members. In order to explain how employees’ perceptions of CSR influence their job performance, this study first examines the relationships between perceived CSR, organizational identification, job satisfaction, and job performance, and then develops a sequential mediation model by fully integrating these links. The results of structural equation modeling analyses conducted for 250 employees at hotels in South Korea offered strong support for the proposed model. We found that perceived CSR was indirectly and positively associated with job performance sequentially mediated first through organizational identification and then job satisfaction. This study theoretically contributes to the CSR literature by revealing the sequential mechanism through which employees’ perceptions of CSR affect their job performance, and offers practical implications by stressing the importance of employees’ perceptions of CSR. Limitations of this study and future research directions are discussed.

  7. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Fabrizio Marinelli

    2009-08-01

    Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

  8. Multimodal imaging of vocal fold scarring in a rabbit model by multiphoton microscopy

    Science.gov (United States)

    Kazarine, Alexei; Bouhabel, Sarah; Douillette, Annie H.; Kost, Karen; Li-Jessen, Nicole Y. K.; Mongeau, Luc; Wiseman, Paul W.

    2017-02-01

    Vocal fold scarring as a result of injury or disease can lead to voice disorders which can significantly affect the quality of life. During the scarring process, the normally elastic tissue of the vocal fold lamina propria is replaced by a much stiffer collagen-based fibrotic tissue, which impacts the fold's ability to vibrate. Surgical removal of this tissue is often ineffective and can result in further scarring. Injectable biomaterials, a form of tissue engineering, have been proposed as a potential solution to reduce existing scars or prevent scarring altogether. In order to properly evaluate the effectiveness of these new materials, multiphoton microscopy emerges as an effective tool due to its intrinsic multiple label free contrast mechanisms that highlight extracellular matrix elements. In this study, we evaluate the spatial distribution of collagen and elastin fibers in a rabbit model using second harmonic generation (SHG), third harmonic generation (THG) and two photon autofluorescence (TPAF) applied to unlabeled tissue sections. In comparison to traditional methods that rely on histological staining or immunohistochemistry, SHG, THG and TPAF provide a more reliable detection of these native proteins. The evaluation of collagen levels allows us to follow the extent of scarring, while the presence of elastin fibers is thought to be indicative of the level of healing of the injured fold. Using these imaging modalities, we characterize the outcome of injectable biomaterial treatments in order to direct future treatments for tissue engineering.

  9. The parametrization of Coulomb barrier heights and positions using the double folding model

    International Nuclear Information System (INIS)

    Qu, W.W.; Zhang, G.L.; Le, X.Y.

    2011-01-01

    The Coulomb barrier heights and positions are systematically shown with mass numbers and charge radii of the interacting nuclei. The nuclear potential is calculated by using the double folding model with the density-dependence nucleon-nucleon interaction (CDM3Y6). The pocket formulas are obtained for the Coulomb barrier heights and positions by analyzing several hundreds of heavy-ion systems with mass numbers from light nuclei to heavy nuclei. The parameterized formulas can reproduce the calculated barrier heights and positions by using the double folding model within the accuracy of ±1%. Moreover, the results are agreeable with the experimental data. The relation between the barrier height and the barrier position is also studied.

  10. Encoding Sequential Information in Semantic Space Models: Comparing Holographic Reduced Representation and Random Permutation

    Directory of Open Access Journals (Sweden)

    Gabriel Recchia

    2015-01-01

    Full Text Available Circular convolution and random permutation have each been proposed as neurally plausible binding operators capable of encoding sequential information in semantic memory. We perform several controlled comparisons of circular convolution and random permutation as means of encoding paired associates as well as encoding sequential information. Random permutations outperformed convolution with respect to the number of paired associates that can be reliably stored in a single memory trace. Performance was equal on semantic tasks when using a small corpus, but random permutations were ultimately capable of achieving superior performance due to their higher scalability to large corpora. Finally, “noisy” permutations in which units are mapped to other units arbitrarily (no one-to-one mapping perform nearly as well as true permutations. These findings increase the neurological plausibility of random permutations and highlight their utility in vector space models of semantics.

  11. Cluster folding-model for quasi-elastic scattering of 23Na from 208Pb

    International Nuclear Information System (INIS)

    Kabir, A.; Johnson, R.C.; Tostevin, M.H.

    1991-01-01

    A cluster model of 23 Na is used to calculate the 23 Na-target interaction potentials by folding the cluster wavefunction with the cluster-target interaction potentials. Coupled channels calculations are carried out for the quasi-elastic scattering of polarized 23 Na from 208 Pb at 170 MeV and compared with recent experiments. Qualitative agreement with experiment is obtained when the interaction is adjusted by a single overall normalization constant. (author)

  12. A Self-Folding Hydrogel In Vitro Model for Ductal Carcinoma.

    Science.gov (United States)

    Kwag, Hye Rin; Serbo, Janna V; Korangath, Preethi; Sukumar, Saraswati; Romer, Lewis H; Gracias, David H

    2016-04-01

    A significant challenge in oncology is the need to develop in vitro models that accurately mimic the complex microenvironment within and around normal and diseased tissues. Here, we describe a self-folding approach to create curved hydrogel microstructures that more accurately mimic the geometry of ducts and acini within the mammary glands, as compared to existing three-dimensional block-like models or flat dishes. The microstructures are composed of photopatterned bilayers of poly (ethylene glycol) diacrylate (PEGDA), a hydrogel widely used in tissue engineering. The PEGDA bilayers of dissimilar molecular weights spontaneously curve when released from the underlying substrate due to differential swelling ratios. The photopatterns can be altered via AutoCAD-designed photomasks so that a variety of ductal and acinar mimetic structures can be mass-produced. In addition, by co-polymerizing methacrylated gelatin (methagel) with PEGDA, microstructures with increased cell adherence are synthesized. Biocompatibility and versatility of our approach is highlighted by culturing either SUM159 cells, which were seeded postfabrication, or MDA-MB-231 cells, which were encapsulated in hydrogels; cell viability is verified over 9 and 15 days, respectively. We believe that self-folding processes and associated tubular, curved, and folded constructs like the ones demonstrated here can facilitate the design of more accurate in vitro models for investigating ductal carcinoma.

  13. Folding-type coupling potentials in the context of the generalized rotation-vibration model

    Science.gov (United States)

    Chamon, L. C.; Morales Botero, D. F.

    2018-03-01

    The generalized rotation-vibration model was proposed in previous works to describe the structure of heavy nuclei. The model was successfully tested in the description of experimental results related to the electron-nucleus elastic and inelastic scattering. In the present work, we consider heavy-ion collisions and assume this model to calculate folding-type coupling potentials for inelastic states, through the corresponding transition densities. As an example, the method is applied to coupled-channel data analyses for the α + 70,72,74,76Ge systems.

  14. How to fold a spin chain: Integrable boundaries of the Heisenberg XXX and Inozemtsev hyperbolic models

    Science.gov (United States)

    De La Rosa Gomez, Alejandro; MacKay, Niall; Regelskis, Vidas

    2017-04-01

    We present a general method of folding an integrable spin chain, defined on a line, to obtain an integrable open spin chain, defined on a half-line. We illustrate our method through two fundamental models with sl2 Lie algebra symmetry: the Heisenberg XXX and the Inozemtsev hyperbolic spin chains. We obtain new long-range boundary Hamiltonians and demonstrate that they exhibit Yangian symmetries, thus ensuring integrability of the models we obtain. The method presented provides a ;bottom-up; approach for constructing integrable boundaries and can be applied to any spin chain model.

  15. The ModFOLD4 server for the quality assessment of 3D protein models

    OpenAIRE

    McGuffin, Liam J.; Buenavista, Maria T.; Roche, Daniel B.

    2013-01-01

    Once you have generated a 3D model of a protein,\\ud how do you know whether it bears any resemblance\\ud to the actual structure? To determine the usefulness\\ud of 3D models of proteins, they must be assessed in\\ud terms of their quality by methods that predict their\\ud similarity to the native structure. The ModFOLD4\\ud server is the latest version of our leading independent\\ud server for the estimation of both the global and\\ud local (per-residue) quality of 3D protein models. The\\ud server ...

  16. Sequential updating of a new dynamic pharmacokinetic model for caffeine in premature neonates.

    Science.gov (United States)

    Micallef, Sandrine; Amzal, Billy; Bach, Véronique; Chardon, Karen; Tourneux, Pierre; Bois, Frédéric Y

    2007-01-01

    Caffeine treatment is widely used in nursing care to reduce the risk of apnoea in premature neonates. To check the therapeutic efficacy of the treatment against apnoea, caffeine concentration in blood is an important indicator. The present study was aimed at building a pharmacokinetic model as a basis for a medical decision support tool. In the proposed model, time dependence of physiological parameters is introduced to describe rapid growth of neonates. To take into account the large variability in the population, the pharmacokinetic model is embedded in a population structure. The whole model is inferred within a Bayesian framework. To update caffeine concentration predictions as data of an incoming patient are collected, we propose a fast method that can be used in a medical context. This involves the sequential updating of model parameters (at individual and population levels) via a stochastic particle algorithm. Our model provides better predictions than the ones obtained with models previously published. We show, through an example, that sequential updating improves predictions of caffeine concentration in blood (reduce bias and length of credibility intervals). The update of the pharmacokinetic model using body mass and caffeine concentration data is studied. It shows how informative caffeine concentration data are in contrast to body mass data. This study provides the methodological basis to predict caffeine concentration in blood, after a given treatment if data are collected on the treated neonate.

  17. Study of elastic scattering of polarized proton with 6He by folding model

    International Nuclear Information System (INIS)

    Iseri, Y.; Tanifuji, M.; Ishikawa, S.; Hiyama, E.; Yamamoto, Y.

    2005-01-01

    Experimental data of the elastic scattering of 6 He with polarized proton target has been analyzed using a simple folding model. As we regard 6 He as three bodies consisting of 4 He+n+n, the potential between the proton and 6 He is obtained by folding the two potentials, one between a proton and 4 He and another between a proton and a neutron, with the density distribution of 6 He. Calculated results of both the differential cross section and the vector analyzing power reproduce the experimental data satisfactorily. It is shown that the vector analyzing power of the p- 6 He scattering is mainly due to the spin orbit interaction between the proton and 4 He. (S. Funahashi)

  18. Folding paper swans, modeling lives: the ritual of Filipina eldercare in Israel.

    Science.gov (United States)

    Mazuz, Keren

    2013-06-01

    This article examines the practices of folding paper swans by Filipina migrants employed as live-in caregivers for elderly, dying patients in Israel. These practices create a microsystem model of adjustment through precise, small-scale, and repetitive movements. This microsystem synchronizes a tripartite process: the swan's process of construction, the patient's process of decay, and the caregiver's process of self-creation. In the short term, the microsystem is sustained, but in the long term, the microsystem contains within it the seeds of its own self-destruction, as the patient eventually dies, the caregiver is reassigned to another patient or deported, and the swans are gifted. Therefore, the swan folding expands both medical anthropology understanding of caregiving as a ritual and the phenomenology of global caregivers who use immediately accessible materials-paper and glue-as an imaginative tool for ordering their daily experiences as dislocated and marginalized workers. © 2013 by the American Anthropological Association.

  19. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

    Science.gov (United States)

    Maghrabi, Ali H A; McGuffin, Liam J

    2017-07-03

    Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

    Science.gov (United States)

    Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin

    2005-01-01

    In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.

  1. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    Science.gov (United States)

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  2. A new moving strategy for the sequential Monte Carlo approach in optimizing the hydrological model parameters

    Science.gov (United States)

    Zhu, Gaofeng; Li, Xin; Ma, Jinzhu; Wang, Yunquan; Liu, Shaomin; Huang, Chunlin; Zhang, Kun; Hu, Xiaoli

    2018-04-01

    Sequential Monte Carlo (SMC) samplers have become increasing popular for estimating the posterior parameter distribution with the non-linear dependency structures and multiple modes often present in hydrological models. However, the explorative capabilities and efficiency of the sampler depends strongly on the efficiency in the move step of SMC sampler. In this paper we presented a new SMC sampler entitled the Particle Evolution Metropolis Sequential Monte Carlo (PEM-SMC) algorithm, which is well suited to handle unknown static parameters of hydrologic model. The PEM-SMC sampler is inspired by the works of Liang and Wong (2001) and operates by incorporating the strengths of the genetic algorithm, differential evolution algorithm and Metropolis-Hasting algorithm into the framework of SMC. We also prove that the sampler admits the target distribution to be a stationary distribution. Two case studies including a multi-dimensional bimodal normal distribution and a conceptual rainfall-runoff hydrologic model by only considering parameter uncertainty and simultaneously considering parameter and input uncertainty show that PEM-SMC sampler is generally superior to other popular SMC algorithms in handling the high dimensional problems. The study also indicated that it may be important to account for model structural uncertainty by using multiplier different hydrological models in the SMC framework in future study.

  3. Modeling and experimental verification of a fan-folded vibration energy harvester for leadless pacemakers

    Science.gov (United States)

    Ansari, M. H.; Karami, M. Amin

    2016-03-01

    This paper studies energy harvesting from heartbeat vibrations for powering leadless pacemakers. Unlike traditional pacemakers, leadless pacemakers are implanted inside the heart and the pacemaker is in direct contact with the myocardium. A leadless pacemaker is in the shape of a cylinder. Thus, in order to utilize the available 3-dimensional space for the energy harvester, we choose a fan-folded 3D energy harvester. The proposed device consists of several piezoelectric beams stacked on top of each other. The volume of the energy harvester is 1 cm3 and its dimensions are 2 cm × 0.5 cm × 1 cm. Although high natural frequency is generally a major concern with micro-scale energy harvesters, by utilizing the fan-folded geometry and adding tip mass and link mass to the configuration, we reduced the natural frequency to the desired range. This fan-folded design makes it possible to generate more than 10 μ W of power per cubic centimeter. The proposed device is compatible with Magnetic Resonance Imaging. Although the proposed device is a linear energy harvester, it is relatively insensitive to the heart rate. The natural frequencies and the mode shapes of the device are calculated analytically. The accuracy of the analytical model is verified by experimental investigations. We use a closed loop shaker system to precisely replicate heartbeat vibrations in vitro.

  4. A sequential threshold cure model for genetic analysis of time-to-event data

    DEFF Research Database (Denmark)

    Ødegård, J; Madsen, Per; Labouriau, Rodrigo S.

    2011-01-01

    In analysis of time-to-event data, classical survival models ignore the presence of potential nonsusceptible (cured) individuals, which, if present, will invalidate the inference procedures. Existence of nonsusceptible individuals is particularly relevant under challenge testing with specific...... pathogens, which is a common procedure in aquaculture breeding schemes. A cure model is a survival model accounting for a fraction of nonsusceptible individuals in the population. This study proposes a mixed cure model for time-to-event data, measured as sequential binary records. In a simulation study...... survival data were generated through 2 underlying traits: susceptibility and endurance (risk of dying per time-unit), associated with 2 sets of underlying liabilities. Despite considerable phenotypic confounding, the proposed model was largely able to distinguish the 2 traits. Furthermore, if selection...

  5. DUAL STATE-PARAMETER UPDATING SCHEME ON A CONCEPTUAL HYDROLOGIC MODEL USING SEQUENTIAL MONTE CARLO FILTERS

    Science.gov (United States)

    Noh, Seong Jin; Tachikawa, Yasuto; Shiiba, Michiharu; Kim, Sunmin

    Applications of data assimilation techniques have been widely used to improve upon the predictability of hydrologic modeling. Among various data assimilation techniques, sequential Monte Carlo (SMC) filters, known as "particle filters" provide the capability to handle non-linear and non-Gaussian state-space models. This paper proposes a dual state-parameter updating scheme (DUS) based on SMC methods to estimate both state and parameter variables of a hydrologic model. We introduce a kernel smoothing method for the robust estimation of uncertain model parameters in the DUS. The applicability of the dual updating scheme is illustrated using the implementation of the storage function model on a middle-sized Japanese catchment. We also compare performance results of DUS combined with various SMC methods, such as SIR, ASIR and RPF.

  6. Communication: Role of explicit water models in the helix folding/unfolding processes

    Science.gov (United States)

    Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

    2016-09-01

    In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

  7. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    Science.gov (United States)

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. A SEQUENTIAL MODEL OF INNOVATION STRATEGY—COMPANY NON-FINANCIAL PERFORMANCE LINKS

    Directory of Open Access Journals (Sweden)

    Wakhid Slamet Ciptono

    2006-05-01

    Full Text Available This study extends the prior research (Zahra and Das 1993 by examining the association between a company’s innovation strategy and its non-financial performance in the upstream and downstream strategic business units (SBUs of oil and gas companies. The sequential model suggests a causal sequence among six dimensions of innovation strategy (leadership orientation, process innovation, product/service innovation, external innovation source, internal innovation source, and investment that may lead to higher company non-financial performance (productivity and operational reliability. The study distributed a questionnaire (by mail, e-mailed web system, and focus group discussion to three levels of managers (top, middle, and first-line of 49 oil and gas companies with 140 SBUs in Indonesia. These qualified samples fell into 47 upstream (supply-chain companies with 132 SBUs, and 2 downstream (demand-chain companies with 8 SBUs. A total of 1,332 individual usable questionnaires were returned thus qualified for analysis, representing an effective response rate of 50.19 percent. The researcher conducts structural equation modeling (SEM and hierarchical multiple regression analysis to assess the goodness-of-fit between the research models and the sample data and to test whether innovation strategy mediates the impact of leadership orientation on company non-financial performance. SEM reveals that the models have met goodness-of-fit criteria, thus the interpretation of the sequential models fits with the data. The results of SEM and hierarchical multiple regression: (1 support the importance of innovation strategy as a determinant of company non-financial performance, (2 suggest that the sequential model is appropriate for examining the relationships between six dimensions of innovation strategy and company non-financial performance, and (3 show that the sequential model provides additional insights into the indirect contribution of the individual

  9. Folding model analysis of Λ binding energies and three-body ΛNN force

    International Nuclear Information System (INIS)

    Mian, M.; Rahman Khan, M.Z.

    1988-02-01

    Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ 5 He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs

  10. Learning of state-space models with highly informative observations: A tempered sequential Monte Carlo solution

    Science.gov (United States)

    Svensson, Andreas; Schön, Thomas B.; Lindsten, Fredrik

    2018-05-01

    Probabilistic (or Bayesian) modeling and learning offers interesting possibilities for systematic representation of uncertainty using probability theory. However, probabilistic learning often leads to computationally challenging problems. Some problems of this type that were previously intractable can now be solved on standard personal computers thanks to recent advances in Monte Carlo methods. In particular, for learning of unknown parameters in nonlinear state-space models, methods based on the particle filter (a Monte Carlo method) have proven very useful. A notoriously challenging problem, however, still occurs when the observations in the state-space model are highly informative, i.e. when there is very little or no measurement noise present, relative to the amount of process noise. The particle filter will then struggle in estimating one of the basic components for probabilistic learning, namely the likelihood p (data | parameters). To this end we suggest an algorithm which initially assumes that there is substantial amount of artificial measurement noise present. The variance of this noise is sequentially decreased in an adaptive fashion such that we, in the end, recover the original problem or possibly a very close approximation of it. The main component in our algorithm is a sequential Monte Carlo (SMC) sampler, which gives our proposed method a clear resemblance to the SMC2 method. Another natural link is also made to the ideas underlying the approximate Bayesian computation (ABC). We illustrate it with numerical examples, and in particular show promising results for a challenging Wiener-Hammerstein benchmark problem.

  11. Behavioral Modeling of WSN MAC Layer Security Attacks: A Sequential UML Approach

    DEFF Research Database (Denmark)

    Pawar, Pranav M.; Nielsen, Rasmus Hjorth; Prasad, Neeli R.

    2012-01-01

    is the vulnerability to security attacks/threats. The performance and behavior of a WSN are vastly affected by such attacks. In order to be able to better address the vulnerabilities of WSNs in terms of security, it is important to understand the behavior of the attacks. This paper addresses the behavioral modeling...... of medium access control (MAC) security attacks in WSNs. The MAC layer is responsible for energy consumption, delay and channel utilization of the network and attacks on this layer can introduce significant degradation of the individual sensor nodes due to energy drain and in performance due to delays....... The behavioral modeling of attacks will be beneficial for designing efficient and secure MAC layer protocols. The security attacks are modeled using a sequential diagram approach of Unified Modeling Language (UML). Further, a new attack definition, specific to hybrid MAC mechanisms, is proposed....

  12. Macroscopic Dynamic Modeling of Sequential Batch Cultures of Hybridoma Cells: An Experimental Validation

    Directory of Open Access Journals (Sweden)

    Laurent Dewasme

    2017-02-01

    Full Text Available Hybridoma cells are commonly grown for the production of monoclonal antibodies (MAb. For monitoring and control purposes of the bioreactors, dynamic models of the cultures are required. However these models are difficult to infer from the usually limited amount of available experimental data and do not focus on target protein production optimization. This paper explores an experimental case study where hybridoma cells are grown in a sequential batch reactor. The simplest macroscopic reaction scheme translating the data is first derived using a maximum likelihood principal component analysis. Subsequently, nonlinear least-squares estimation is used to determine the kinetic laws. The resulting dynamic model reproduces quite satisfactorily the experimental data, as evidenced in direct and cross-validation tests. Furthermore, model predictions can also be used to predict optimal medium renewal time and composition.

  13. Corpus Callosum Analysis using MDL-based Sequential Models of Shape and Appearance

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille; Davies, Rhodri H.; Ryberg, Charlotte

    2004-01-01

    are proposed, but all remain applicable to other domain problems. The well-known multi-resolution AAM optimisation is extended to include sequential relaxations on texture resolution, model coverage and model parameter constraints. Fully unsupervised analysis is obtained by exploiting model parameter...... that show that the method produces accurate, robust and rapid segmentations in a cross sectional study of 17 subjects, establishing its feasibility as a fully automated clinical tool for analysis and segmentation.......This paper describes a method for automatically analysing and segmenting the corpus callosum from magnetic resonance images of the brain based on the widely used Active Appearance Models (AAMs) by Cootes et al. Extensions of the original method, which are designed to improve this specific case...

  14. A model in which heat shock protein 90 targets protein-folding clefts: rationale for a new approach to neuroprotective treatment of protein folding diseases.

    Science.gov (United States)

    Pratt, William B; Morishima, Yoshihiro; Gestwicki, Jason E; Lieberman, Andrew P; Osawa, Yoichi

    2014-11-01

    In an EBM Minireview published in 2010, we proposed that the heat shock protein (Hsp)90/Hsp70-based chaperone machinery played a major role in determining the selection of proteins that have undergone oxidative or other toxic damage for ubiquitination and proteasomal degradation. The proposal was based on a model in which the Hsp90 chaperone machinery regulates signaling by modulating ligand-binding clefts. The model provides a framework for thinking about the development of neuroprotective therapies for protein-folding diseases like Alzheimer's disease (AD), Parkinson's disease (PD), and the polyglutamine expansion disorders, such as Huntington's disease (HD) and spinal and bulbar muscular atrophy (SBMA). Major aberrant proteins that misfold and accumulate in these diseases are "client" proteins of the abundant and ubiquitous stress chaperone Hsp90. These Hsp90 client proteins include tau (AD), α-synuclein (PD), huntingtin (HD), and the expanded glutamine androgen receptor (polyQ AR) (SBMA). In this Minireview, we update our model in which Hsp90 acts on protein-folding clefts and show how it forms a rational basis for developing drugs that promote the targeted elimination of these aberrant proteins. © 2014 by the Society for Experimental Biology and Medicine.

  15. Use of the peritracheal fold in the dog tracheal transplantation model.

    Science.gov (United States)

    Gannon, P J; Costantino, P D; Lueg, E A; Chaplin, J M; Brandwein, M S; Passalaqua, P J; Fliegelman, L J; Laitman, J T; Marquez, S; Urken, M L

    1999-09-01

    To investigate the technical aspects of the canine model of human tracheal transplantation for potential application to reconstruction of extremely long tracheal defects (> 10 cm). In phase 1, long tracheal segments were skeletonized and pedicled with the thyroid glands, cranial thyroid arteries and veins, and internal jugular vein branches. The segments were elevated completely, attached to the vascular pedicle only, and replaced with primary tracheal anastomoses. In phase 2, long segments were elevated along with a diffuse soft tissue "blanket" that envelops the trachea and thyroid glands. Because this study was designed to primarily address, in situ, tracheal perfusion territories of a cranially located vascular pedicle, microvascular anastomoses were not conducted. Two small-bodied beagles (10-15 kg) and 5 large-bodied mixed-breed dogs (20-30 kg) were humanely killed 2 to 41 days after surgery, and anatomic and histological analyses were conducted. Unlike that of humans, the thyroid gland complex of dogs is not intimately associated with the trachea but is conjoined with a peritracheal soft tissue "fold." Within this fold, blood is transmitted to the trachea via a diffuse, segmental vascular plexus. In phase 1, pronounced tracheal necrosis occurred within 2 to 5 days. In phase 2, extremely long tracheal segments (10-12 cm), based only on a cranially located pedicle, were still viable at 2 to 6 weeks. Preservation of the "peritracheal fold" in the dog model of tracheal transplantation is critical to the onset and maintenance of vascular perfusion in a long tracheal segment. Furthermore, the use of large-bodied dogs is necessary to provide for a usable venous efflux component.

  16. Spherical aberration correction with an in-lens N-fold symmetric line currents model.

    Science.gov (United States)

    Hoque, Shahedul; Ito, Hiroyuki; Nishi, Ryuji

    2018-04-01

    In our previous works, we have proposed N-SYLC (N-fold symmetric line currents) models for aberration correction. In this paper, we propose "in-lens N-SYLC" model, where N-SYLC overlaps rotationally symmetric lens. Such overlap is possible because N-SYLC is free of magnetic materials. We analytically prove that, if certain parameters of the model are optimized, an in-lens 3-SYLC (N = 3) doublet can correct 3rd order spherical aberration. By computer simulation, we show that the required excitation current for correction is less than 0.25 AT for beam energy 5 keV, and the beam size after correction is smaller than 1 nm at the corrector image plane for initial slope less than 4 mrad. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. A replica exchange Monte Carlo algorithm for protein folding in the HP model

    Directory of Open Access Journals (Sweden)

    Shmygelska Alena

    2007-09-01

    Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

  18. Exposure assessment of mobile phone base station radiation in an outdoor environment using sequential surrogate modeling.

    Science.gov (United States)

    Aerts, Sam; Deschrijver, Dirk; Joseph, Wout; Verloock, Leen; Goeminne, Francis; Martens, Luc; Dhaene, Tom

    2013-05-01

    Human exposure to background radiofrequency electromagnetic fields (RF-EMF) has been increasing with the introduction of new technologies. There is a definite need for the quantification of RF-EMF exposure but a robust exposure assessment is not yet possible, mainly due to the lack of a fast and efficient measurement procedure. In this article, a new procedure is proposed for accurately mapping the exposure to base station radiation in an outdoor environment based on surrogate modeling and sequential design, an entirely new approach in the domain of dosimetry for human RF exposure. We tested our procedure in an urban area of about 0.04 km(2) for Global System for Mobile Communications (GSM) technology at 900 MHz (GSM900) using a personal exposimeter. Fifty measurement locations were sufficient to obtain a coarse street exposure map, locating regions of high and low exposure; 70 measurement locations were sufficient to characterize the electric field distribution in the area and build an accurate predictive interpolation model. Hence, accurate GSM900 downlink outdoor exposure maps (for use in, e.g., governmental risk communication and epidemiological studies) are developed by combining the proven efficiency of sequential design with the speed of exposimeter measurements and their ease of handling. Copyright © 2013 Wiley Periodicals, Inc.

  19. Modeling and Predicting AD Progression by Regression Analysis of Sequential Clinical Data

    KAUST Repository

    Xie, Qing

    2016-02-23

    Alzheimer\\'s Disease (AD) is currently attracting much attention in elders\\' care. As the increasing availability of massive clinical diagnosis data, especially the medical images of brain scan, it is highly significant to precisely identify and predict the potential AD\\'s progression based on the knowledge in the diagnosis data. In this paper, we follow a novel sequential learning framework to model the disease progression for AD patients\\' care. Different from the conventional approaches using only initial or static diagnosis data to model the disease progression for different durations, we design a score-involved approach and make use of the sequential diagnosis information in different disease stages to jointly simulate the disease progression. The actual clinical scores are utilized in progress to make the prediction more pertinent and reliable. We examined our approach by extensive experiments on the clinical data provided by the Alzheimer\\'s Disease Neuroimaging Initiative (ADNI). The results indicate that the proposed approach is more effective to simulate and predict the disease progression compared with the existing methods.

  20. Modeling and Predicting AD Progression by Regression Analysis of Sequential Clinical Data

    KAUST Repository

    Xie, Qing; Wang, Su; Zhu, Jia; Zhang, Xiangliang

    2016-01-01

    Alzheimer's Disease (AD) is currently attracting much attention in elders' care. As the increasing availability of massive clinical diagnosis data, especially the medical images of brain scan, it is highly significant to precisely identify and predict the potential AD's progression based on the knowledge in the diagnosis data. In this paper, we follow a novel sequential learning framework to model the disease progression for AD patients' care. Different from the conventional approaches using only initial or static diagnosis data to model the disease progression for different durations, we design a score-involved approach and make use of the sequential diagnosis information in different disease stages to jointly simulate the disease progression. The actual clinical scores are utilized in progress to make the prediction more pertinent and reliable. We examined our approach by extensive experiments on the clinical data provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI). The results indicate that the proposed approach is more effective to simulate and predict the disease progression compared with the existing methods.

  1. Assessing groundwater availability in a folded carbonate aquifer through the development of a numerical model

    Science.gov (United States)

    Di Salvo, Cristina; Romano, Emanuele; Guyennon, Nicolas; Bruna Petrangeli, Anna; Preziosi, Elisabetta

    2015-04-01

    The study of aquifer systems from a quantitative point of view is fundamental for adopting water management plans aiming at preserving water resources and reducing environmental risks related to groundwater level and discharge changes. This is also what the European Union Water Framework Directive (WFD, 2000/60/EC) states, holding the development of numerical models as a key aspect for groundwater management. The objective of this research is to i) define a methodology for modeling a complex hydrogeological structure in a structurally folded carbonate area and ii) estimate the concurrent effects of exploitation and climate changes on groundwater availability through the implementation of a 3D groundwater flow model. This study concerns the Monte Coscerno karst aquifer located in the Apennine chain in Central Italy in the Nera River Valley.This aquifer, is planned to be exploited in the near future for water supply. Negative trends of precipitation in Central Italy have been reported in relation to global climate changes, which are expected to affect the availability of recharge to carbonate aquifers throughout the region . A great concern is the combined impact of climate change and groundwater exploitation, hence scenarios are needed taking into account the effect of possible temperature and precipitation trends on recharge rates. Following a previous experience with model conceptualization and long-term simulation of groundwater flow, an integrated three-dimensional groundwater model has been developed for the Monte Coscerno aquifer. In a previous paper (Preziosi et al 2014) the spatial distribution of recharge to this aquifer was estimated through the Thornthwaite Mather model at a daily time step using as inputs past precipitation and temperature values (1951-2013) as well as soil and landscape properties. In this paper the numerical model development is described. On the basis of well logs from private consulting companies and literature cross sections the

  2. Factors controlling the evolution of the Perdido Fold Belt, northwestern Gulf of Mexico, determined from numerical models

    Science.gov (United States)

    Gradmann, Sofie; Beaumont, Christopher; Albertz, Markus

    2009-04-01

    The Perdido Fold Belt (PFB) is a prominent salt-cored deep water structure in the northwestern Gulf of Mexico. It is characterized by symmetric, kink-banded folds of a ˜4.5 km thick prekinematic layer and its vicinity to the extensive Sigsbee Salt Canopy. We use 2-D finite element numerical models to study the evolution of the PFB as a gravity-driven fold belt both in a local context and in the context of the larger-scale passive margin, influenced by adjacent allochthonous salt structures. We show that parameters such as overburden strength, salt geometry, or salt viscosity determine timing, extent, and location of the modeled fold belt. Simplified models of the Gulf of Mexico show that toe-of-slope folding is a viable mechanism to develop diapirs in the deep salt basin and to delay folding of the distal overburden. In this scenario, the PFB likely represents the terminal folding of a much larger, diachronously formed fold belt system.

  3. The Efficacy of Fibroblast Growth Factor for the Treatment of Chronic Vocal Fold Scarring: From Animal Model to Clinical Application.

    Science.gov (United States)

    Ban, Myung Jin; Park, Jae Hong; Kim, Jae Wook; Park, Ki Nam; Lee, Jae Yong; Kim, Hee Kyung; Lee, Seung Won

    2017-12-01

    This study assessed the regenerative efficacy of basic fibroblast growth factor (FGF) in a rabbit model of chronic vocal fold scarring and then confirmed its utility and safety in a prospective trial of patients with this condition. FGF was injected three times, at 1-week intervals, into a chronic vocal fold scar created in a rabbit model. After 1 month, mRNA level of procollagen I, hyaluronic acid synthetase 2 (HAS 2), and matrix metalloproteinase 2 (MMP 2) were analyzed by real-time polymerase chain reaction. The relative densities of hyaluronic acid (HA) and collagen were examined 3 months post-injection. From April 2012 to September 2014, a prospective clinical trial was conducted at a tertiary hospital in Korea. FGF was injected into the mild vocal fold scar of 17 consecutive patients with a small glottic gap. The patients underwent perceptual, stroboscopic, acoustic aerodynamic test, and Voice Handicap Index (VHI) survey prior to and 3, 6, and 12 months after FGF injection. FGF injection of the vocal fold scar decreased the density of collagen and increased mRNA level of HAS 2 and MMP 2 expression significantly compared to the control group injected with phosphate buffered solution in a rabbit model (Pvocal fold injections of FGF in patients with mild chronic vocal fold scarring can significantly improve voice quality for as long as 1 year and without side effects. Our results recommend the use of FGF vocal fold injection as an alternative treatment modality for mild chronic vocal fold scarring.

  4. Multiple sequential failure model: A probabilistic approach to quantifying human error dependency

    International Nuclear Information System (INIS)

    Samanta

    1985-01-01

    This paper rpesents a probabilistic approach to quantifying human error dependency when multiple tasks are performed. Dependent human failures are dominant contributors to risks from nuclear power plants. An overview of the Multiple Sequential Failure (MSF) model developed and its use in probabilistic risk assessments (PRAs) depending on the available data are discussed. A small-scale psychological experiment was conducted on the nature of human dependency and the interpretation of the experimental data by the MSF model show remarkable accommodation of the dependent failure data. The model, which provides an unique method for quantification of dependent failures in human reliability analysis, can be used in conjunction with any of the general methods currently used for performing the human reliability aspect in PRAs

  5. Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

    Science.gov (United States)

    Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

    2012-09-01

    Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

  6. Three-dimensional biomechanical properties of human vocal folds: Parameter optimization of a numerical model to match in vitro dynamics

    Science.gov (United States)

    Yang, Anxiong; Berry, David A.; Kaltenbacher, Manfred; Döllinger, Michael

    2012-01-01

    The human voice signal originates from the vibrations of the two vocal folds within the larynx. The interactions of several intrinsic laryngeal muscles adduct and shape the vocal folds to facilitate vibration in response to airflow. Three-dimensional vocal fold dynamics are extracted from in vitro hemilarynx experiments and fitted by a numerical three-dimensional-multi-mass-model (3DM) using an optimization procedure. In this work, the 3DM dynamics are optimized over 24 experimental data sets to estimate biomechanical vocal fold properties during phonation. Accuracy of the optimization is verified by low normalized error (0.13 ± 0.02), high correlation (83% ± 2%), and reproducible subglottal pressure values. The optimized, 3DM parameters yielded biomechanical variations in tissue properties along the vocal fold surface, including variations in both the local mass and stiffness of vocal folds. That is, both mass and stiffness increased along the superior-to-inferior direction. These variations were statistically analyzed under different experimental conditions (e.g., an increase in tension as a function of vocal fold elongation and an increase in stiffness and a decrease in mass as a function of glottal airflow). The study showed that physiologically relevant vocal fold tissue properties, which cannot be directly measured during in vivo human phonation, can be captured using this 3D-modeling technique. PMID:22352511

  7. Validation studies on indexed sequential modeling for the Colorado River Basin

    International Nuclear Information System (INIS)

    Labadie, J.W.; Fontane, D.G.; Salas, J.D.; Ouarda, T.

    1991-01-01

    This paper reports on a method called indexed sequential modeling (ISM) that has been developed by the Western Area Power Administration to estimate reliable levels of project dependable power capacity (PDC) and applied to several federal hydro systems in the Western U.S. The validity of ISM in relation to more commonly accepted stochastic modeling approaches is analyzed by applying it to the Colorado River Basin using the Colorado River Simulation System (CRSS) developed by the U.S. Bureau of Reclamation. Performance of ISM is compared with results from input of stochastically generated data using the LAST Applied Stochastic Techniques Package. Results indicate that output generated from ISM synthetically generated sequences display an acceptable correspondence with results obtained from final convergent stochastically generated hydrology for the Colorado River Basin

  8. Modeling Search Behaviors during the Acquisition of Expertise in a Sequential Decision-Making Task

    Directory of Open Access Journals (Sweden)

    Cristóbal Moënne-Loccoz

    2017-09-01

    Full Text Available Our daily interaction with the world is plagued of situations in which we develop expertise through self-motivated repetition of the same task. In many of these interactions, and especially when dealing with computer and machine interfaces, we must deal with sequences of decisions and actions. For instance, when drawing cash from an ATM machine, choices are presented in a step-by-step fashion and a specific sequence of choices must be performed in order to produce the expected outcome. But, as we become experts in the use of such interfaces, is it possible to identify specific search and learning strategies? And if so, can we use this information to predict future actions? In addition to better understanding the cognitive processes underlying sequential decision making, this could allow building adaptive interfaces that can facilitate interaction at different moments of the learning curve. Here we tackle the question of modeling sequential decision-making behavior in a simple human-computer interface that instantiates a 4-level binary decision tree (BDT task. We record behavioral data from voluntary participants while they attempt to solve the task. Using a Hidden Markov Model-based approach that capitalizes on the hierarchical structure of behavior, we then model their performance during the interaction. Our results show that partitioning the problem space into a small set of hierarchically related stereotyped strategies can potentially capture a host of individual decision making policies. This allows us to follow how participants learn and develop expertise in the use of the interface. Moreover, using a Mixture of Experts based on these stereotyped strategies, the model is able to predict the behavior of participants that master the task.

  9. Improving multiple-point-based a priori models for inverse problems by combining Sequential Simulation with the Frequency Matching Method

    DEFF Research Database (Denmark)

    Cordua, Knud Skou; Hansen, Thomas Mejer; Lange, Katrine

    In order to move beyond simplified covariance based a priori models, which are typically used for inverse problems, more complex multiple-point-based a priori models have to be considered. By means of marginal probability distributions ‘learned’ from a training image, sequential simulation has...... proven to be an efficient way of obtaining multiple realizations that honor the same multiple-point statistics as the training image. The frequency matching method provides an alternative way of formulating multiple-point-based a priori models. In this strategy the pattern frequency distributions (i.......e. marginals) of the training image and a subsurface model are matched in order to obtain a solution with the same multiple-point statistics as the training image. Sequential Gibbs sampling is a simulation strategy that provides an efficient way of applying sequential simulation based algorithms as a priori...

  10. Theoretical models for designing a 220-GHz folded waveguide backward wave oscillator

    International Nuclear Information System (INIS)

    Cai Jin-Chi; Chen Huai-Bi; Hu Lin-Lin; Ma Guo-Wu; Chen Hong-Bin; Jin Xiao

    2015-01-01

    In this paper, the basic equations of beam-wave interaction for designing the 220 GHz folded waveguide (FW) backward wave oscillator (BWO) are described. On the whole, these equations are mainly classified into small signal model (SSM), large signal model (LSM), and simplified small signal model (SSSM). Using these linear and nonlinear one-dimensional (1D) models, the oscillation characteristics of the FW BWO of a given configuration of slow wave structure (SWS) can be calculated by numerical iteration algorithm, which is more time efficient than three-dimensional (3D) particle-in-cell (PIC) simulation. The SSSM expressed by analytical formulas is innovatively derived for determining the initial values of the FW SWS conveniently. The dispersion characteristics of the FW are obtained by equivalent circuit analysis. The space charge effect, the end reflection effect, the lossy wall effect, and the relativistic effect are all considered in our models to offer more accurate results. The design process of the FW BWO tube with output power of watt scale in a frequency range between 215 GHz and 225 GHz based on these 1D models is demonstrated. The 3D PIC method is adopted to verify the theoretical design results, which shows that they are in good agreement with each other. (paper)

  11. Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Fábio L. Custódio

    2004-01-01

    Full Text Available An approach to the hydrophobic-polar (HP protein folding model was developed using a genetic algorithm (GA to find the optimal structures on a 3D cubic lattice. A modification was introduced to the scoring system of the original model to improve the model's capacity to generate more natural-like structures. The modification was based on the assumption that it may be preferable for a hydrophobic monomer to have a polar neighbor than to be in direct contact with the polar solvent. The compactness and the segregation criteria were used to compare structures created by the original HP model and by the modified one. An islands' algorithm, a new selection scheme and multiple-points crossover were used to improve the performance of the algorithm. Ten sequences, seven with length 27 and three with length 64 were analyzed. Our results suggest that the modified model has a greater tendency to form globular structures. This might be preferable, since the original HP model does not take into account the positioning of long polar segments. The algorithm was implemented in the form of a program with a graphical user interface that might have a didactical potential in the study of GA and on the understanding of hydrophobic core formation.

  12. Rf modeling and design of a folded waveguide launcher for the Alcator C-Mod tokamak

    International Nuclear Information System (INIS)

    Bigelow, T.S.; Fogelman, C.F.; Baity, F.W.; Carter, M.D.; Hoffman, D.J.; Ryan, P.M.; Yugo, J.J.; Golovato, S.N.; Bonoli, P.

    1993-01-01

    The folded waveguide (FWG) launcher is being investigated as an improved antenna configuration for plasma heating in the ion cyclotron range of frequencies (ICRF). A development FWG launcher was successfully tested at Oak Ridge National Laboratory (ORNL) with a low-density plasma load and found to have significantly greater power density capability than current strap-type antennas operating in similar plasmas. To further test the concept on a high density tokamak plasma, a collaboration has been set up between ORNL and Massachusetts Institute of Technology (MIT) to develop and test an 80-MHz, 2-MW FWG on the Alcator C-Mod tokamak at MIT. The radio frequency (rf) electromagnetic modeling techniques and laboratory measurements used in the design of this antenna are described in this paper. A companion paper describes the mechanical design of the FWG

  13. Mind-to-mind heteroclinic coordination: Model of sequential episodic memory initiation

    Science.gov (United States)

    Afraimovich, V. S.; Zaks, M. A.; Rabinovich, M. I.

    2018-05-01

    Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated with specific events directly experienced by single members, are encoded, recalled, and shared by all participants. Here, we construct and study the dynamical model for the formation and maintaining of episodic memory in small ensembles of interacting minds. We prove that the unconventional dynamical attractor of this process—the nonsmooth heteroclinic torus—is structurally stable within the Lotka-Volterra-like sets of equations. Dynamics on this torus combines the absence of chaos with asymptotic instability of every separate trajectory; its adequate quantitative characteristics are length-related Lyapunov exponents. Variation of the coupling strength between the participants results in different types of sequential switching between metastable states; we interpret them as stages in formation and modification of the episodic memory.

  14. Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment

    DEFF Research Database (Denmark)

    Ahmad, Amais; Zachariasen, Camilla; Christiansen, Lasse Engbo

    2016-01-01

    generated by a mathematical model of the competitive growth of multiple strains of Escherichia coli.Results: Simulation studies showed that sequential use of tetracycline and ampicillin reduced the level of double resistance, when compared to the combination treatment. The effect of the cycling frequency...... frequency did not play a role in suppressing the growth of resistant strains, but the specific order of the two antimicrobials did. Predictions made from the study could be used to redesign multidrug treatment strategies not only for intramuscular treatment in pigs, but also for other dosing routes.......Background: Combination treatment is increasingly used to fight infections caused by bacteria resistant to two or more antimicrobials. While multiple studies have evaluated treatment strategies to minimize the emergence of resistant strains for single antimicrobial treatment, fewer studies have...

  15. Modelling sequential Biosphere systems under Climate change for radioactive waste disposal. Project BIOCLIM

    International Nuclear Information System (INIS)

    Texier, D.; Degnan, P.; Loutre, M.F.; Lemaitre, G.; Paillard, D.; Thorne, M.

    2000-01-01

    The BIOCLIM project (Modelling Sequential Biosphere systems under Climate change for Radioactive Waste Disposal) is part of the EURATOM fifth European framework programme. The project was launched in October 2000 for a three-year period. It is coordinated by ANDRA, the French national radioactive waste management agency. The project brings together a number of European radioactive waste management organisations that have national responsibilities for the safe disposal of radioactive wastes, and several highly experienced climate research teams. Waste management organisations involved are: NIREX (UK), GRS (Germany), ENRESA (Spain), NRI (Czech Republic) and ANDRA (France). Climate research teams involved are: LSCE (CEA/CNRS, France), CIEMAT (Spain), UPMETSIMM (Spain), UCL/ASTR (Belgium) and CRU (UEA, UK). The Environmental Agency for England and Wales provides a regulatory perspective. The consulting company Enviros Consulting (UK) assists ANDRA by contributing to both the administrative and scientific aspects of the project. This paper describes the project and progress to date. (authors)

  16. On Modeling Large-Scale Multi-Agent Systems with Parallel, Sequential and Genuinely Asynchronous Cellular Automata

    International Nuclear Information System (INIS)

    Tosic, P.T.

    2011-01-01

    We study certain types of Cellular Automata (CA) viewed as an abstraction of large-scale Multi-Agent Systems (MAS). We argue that the classical CA model needs to be modified in several important respects, in order to become a relevant and sufficiently general model for the large-scale MAS, and so that thus generalized model can capture many important MAS properties at the level of agent ensembles and their long-term collective behavior patterns. We specifically focus on the issue of inter-agent communication in CA, and propose sequential cellular automata (SCA) as the first step, and genuinely Asynchronous Cellular Automata (ACA) as the ultimate deterministic CA-based abstract models for large-scale MAS made of simple reactive agents. We first formulate deterministic and nondeterministic versions of sequential CA, and then summarize some interesting configuration space properties (i.e., possible behaviors) of a restricted class of sequential CA. In particular, we compare and contrast those properties of sequential CA with the corresponding properties of the classical (that is, parallel and perfectly synchronous) CA with the same restricted class of update rules. We analytically demonstrate failure of the studied sequential CA models to simulate all possible behaviors of perfectly synchronous parallel CA, even for a very restricted class of non-linear totalistic node update rules. The lesson learned is that the interleaving semantics of concurrency, when applied to sequential CA, is not refined enough to adequately capture the perfect synchrony of parallel CA updates. Last but not least, we outline what would be an appropriate CA-like abstraction for large-scale distributed computing insofar as the inter-agent communication model is concerned, and in that context we propose genuinely asynchronous CA. (author)

  17. Methamphetamine-alcohol interactions in murine models of sequential and simultaneous oral drug-taking.

    Science.gov (United States)

    Fultz, Elissa K; Martin, Douglas L; Hudson, Courtney N; Kippin, Tod E; Szumlinski, Karen K

    2017-08-01

    A high degree of co-morbidity exists between methamphetamine (MA) addiction and alcohol use disorders and both sequential and simultaneous MA-alcohol mixing increases risk for co-abuse. As little preclinical work has focused on the biobehavioral interactions between MA and alcohol within the context of drug-taking behavior, we employed simple murine models of voluntary oral drug consumption to examine how prior histories of either MA- or alcohol-taking influence the intake of the other drug. In one study, mice with a 10-day history of binge alcohol-drinking [5,10, 20 and 40% (v/v); 2h/day] were trained to self-administer oral MA in an operant-conditioning paradigm (10-40mg/L). In a second study, mice with a 10-day history of limited-access oral MA-drinking (5, 10, 20 and 40mg/L; 2h/day) were presented with alcohol (5-40% v/v; 2h/day) and then a choice between solutions of 20% alcohol, 10mg/L MA or their mix. Under operant-conditioning procedures, alcohol-drinking mice exhibited less MA reinforcement overall, than water controls. However, when drug availability was not behaviorally-contingent, alcohol-drinking mice consumed more MA and exhibited greater preference for the 10mg/L MA solution than drug-naïve and combination drug-experienced mice. Conversely, prior MA-drinking history increased alcohol intake across a range of alcohol concentrations. These exploratory studies indicate the feasibility of employing procedurally simple murine models of sequential and simultaneous oral MA-alcohol mixing of relevance to advancing our biobehavioral understanding of MA-alcohol co-abuse. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. A discrete event modelling framework for simulation of long-term outcomes of sequential treatment strategies for ankylosing spondylitis

    NARCIS (Netherlands)

    A. Tran-Duy (An); A. Boonen (Annelies); M.A.F.J. van de Laar (Mart); A. Franke (Andre); J.L. Severens (Hans)

    2011-01-01

    textabstractObjective: To develop a modelling framework which can simulate long-term quality of life, societal costs and cost-effectiveness as affected by sequential drug treatment strategies for ankylosing spondylitis (AS). Methods: Discrete event simulation paradigm was selected for model

  19. A discrete event modelling framework for simulation of long-term outcomes of sequential treatment strategies for ankylosing spondylitis

    NARCIS (Netherlands)

    Tran-Duy, A.; Boonen, A.; Laar, M.A.F.J.; Franke, A.C.; Severens, J.L.

    2011-01-01

    Objective To develop a modelling framework which can simulate long-term quality of life, societal costs and cost-effectiveness as affected by sequential drug treatment strategies for ankylosing spondylitis (AS). Methods Discrete event simulation paradigm was selected for model development. Drug

  20. Histological Effect of Basic Fibroblast Growth Factor on Chronic Vocal Fold Scarring in a Rat Model.

    Science.gov (United States)

    Tateya, Ichiro; Tateya, Tomoko; Sohn, Jin-Ho; Bless, Diane M

    2016-03-01

    Vocal fold scarring is one of the most challenging laryngeal disorders to treat and there are currently no consistently effective treatments available. Our previous studies have shown the therapeutic potential of basic fibroblast growth factor (bFGF) for vocal fold scarring. However, the histological effects of bFGF on scarred vocal fold have not been elucidated. The aim of this study was to examine the histological effects of bFGF on chronic vocal fold scarring. Sprague-Dawley rats were divided into phosphate buffered saline (sham) and bFGF groups. Unilateral vocal fold stripping was performed and the drug was injected into the scarred vocal fold for each group 2 months postoperatively. Injections were performed weekly for 4 weeks. Two months after the last injection, larynges were harvested and histologically analyzed. A significant increase of hyaluronic acid was observed in the vocal fold of the bFGF group compared with that of the sham group. However, there was no remarkable change in collagen expression nor in vocal fold contraction. Significant increase of hyaluronic acid by local bFGF injection was thought to contribute to the therapeutic effects on chronic vocal fold scarring.

  1. New insights into chromatin folding and dynamics from multi-scale modeling

    Science.gov (United States)

    Olson, Wilma

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

  2. The influence of material anisotropy on vibration at onset in a three-dimensional vocal fold model

    Science.gov (United States)

    Zhang, Zhaoyan

    2014-01-01

    Although vocal folds are known to be anisotropic, the influence of material anisotropy on vocal fold vibration remains largely unknown. Using a linear stability analysis, phonation onset characteristics were investigated in a three-dimensional anisotropic vocal fold model. The results showed that isotropic models had a tendency to vibrate in a swing-like motion, with vibration primarily along the superior-inferior direction. Anterior-posterior (AP) out-of-phase motion was also observed and large vocal fold vibration was confined to the middle third region along the AP length. In contrast, increasing anisotropy or increasing AP-transverse stiffness ratio suppressed this swing-like motion and allowed the vocal fold to vibrate in a more wave-like motion with strong medial-lateral motion over the entire medial surface. Increasing anisotropy also suppressed the AP out-of-phase motion, allowing the vocal fold to vibrate in phase along the entire AP length. Results also showed that such improvement in vibration pattern was the most effective with large anisotropy in the cover layer alone. These numerical predictions were consistent with previous experimental observations using self-oscillating physical models. It was further hypothesized that these differences may facilitate complete glottal closure in finite-amplitude vibration of anisotropic models as observed in recent experiments. PMID:24606284

  3. AUTOMATIC 3D BUILDING MODEL GENERATION FROM LIDAR AND IMAGE DATA USING SEQUENTIAL MINIMUM BOUNDING RECTANGLE

    Directory of Open Access Journals (Sweden)

    E. Kwak

    2012-07-01

    Full Text Available Digital Building Model is an important component in many applications such as city modelling, natural disaster planning, and aftermath evaluation. The importance of accurate and up-to-date building models has been discussed by many researchers, and many different approaches for efficient building model generation have been proposed. They can be categorised according to the data source used, the data processing strategy, and the amount of human interaction. In terms of data source, due to the limitations of using single source data, integration of multi-senor data is desired since it preserves the advantages of the involved datasets. Aerial imagery and LiDAR data are among the commonly combined sources to obtain 3D building models with good vertical accuracy from laser scanning and good planimetric accuracy from aerial images. The most used data processing strategies are data-driven and model-driven ones. Theoretically one can model any shape of buildings using data-driven approaches but practically it leaves the question of how to impose constraints and set the rules during the generation process. Due to the complexity of the implementation of the data-driven approaches, model-based approaches draw the attention of the researchers. However, the major drawback of model-based approaches is that the establishment of representative models involves a manual process that requires human intervention. Therefore, the objective of this research work is to automatically generate building models using the Minimum Bounding Rectangle algorithm and sequentially adjusting them to combine the advantages of image and LiDAR datasets.

  4. Analysis of membrane fusion as a two-state sequential process: evaluation of the stalk model.

    Science.gov (United States)

    Weinreb, Gabriel; Lentz, Barry R

    2007-06-01

    We propose a model that accounts for the time courses of PEG-induced fusion of membrane vesicles of varying lipid compositions and sizes. The model assumes that fusion proceeds from an initial, aggregated vesicle state ((A) membrane contact) through two sequential intermediate states (I(1) and I(2)) and then on to a fusion pore state (FP). Using this model, we interpreted data on the fusion of seven different vesicle systems. We found that the initial aggregated state involved no lipid or content mixing but did produce leakage. The final state (FP) was not leaky. Lipid mixing normally dominated the first intermediate state (I(1)), but content mixing signal was also observed in this state for most systems. The second intermediate state (I(2)) exhibited both lipid and content mixing signals and leakage, and was sometimes the only leaky state. In some systems, the first and second intermediates were indistinguishable and converted directly to the FP state. Having also tested a parallel, two-intermediate model subject to different assumptions about the nature of the intermediates, we conclude that a sequential, two-intermediate model is the simplest model sufficient to describe PEG-mediated fusion in all vesicle systems studied. We conclude as well that a fusion intermediate "state" should not be thought of as a fixed structure (e.g., "stalk" or "transmembrane contact") of uniform properties. Rather, a fusion "state" describes an ensemble of similar structures that can have different mechanical properties. Thus, a "state" can have varying probabilities of having a given functional property such as content mixing, lipid mixing, or leakage. Our data show that the content mixing signal may occur through two processes, one correlated and one not correlated with leakage. Finally, we consider the implications of our results in terms of the "modified stalk" hypothesis for the mechanism of lipid pore formation. We conclude that our results not only support this hypothesis but

  5. Distributed data access in the sequential access model at the D0 experiment at Fermilab

    International Nuclear Information System (INIS)

    Terekhov, Igor; White, Victoria

    2000-01-01

    The authors present the Sequential Access Model (SAM), which is the data handling system for D0, one of two primary High Energy Experiments at Fermilab. During the next several years, the D0 experiment will store a total of about 1 PByte of data, including raw detector data and data processed at various levels. The design of SAM is not specific to the D0 experiment and carries few assumptions about the underlying mass storage level; its ideas are applicable to any sequential data access. By definition, in the sequential access mode a user application needs to process a stream of data, by accessing each data unit exactly once, the order of data units in the stream being irrelevant. The units of data are laid out sequentially in files. The adopted model allows for significant optimizations of system performance, decrease of user file latency and increase of overall throughput. In particular, caching is done with the knowledge of all the files needed in the near future, defined as all the files of the already running or submitted jobs. The bulk of the data is stored in files on tape in the mass storage system (MSS) called Enstore[2] and also developed at Fermilab. (The tape drives are served by an ADIC AML/2 Automated Tape Library). At any given time, SAM has a small fraction of the data cached on disk for processing. In the present paper, the authors discuss how data is delivered onto disk and how it is accessed by user applications. They will concentrate on data retrieval (consumption) from the MSS; when SAM is used for storing of data, the mechanisms are rather symmetrical. All of the data managed by SAM is cataloged in great detail in a relational database (ORACLE). The database also serves as the persistency mechanism for the SAM servers described in this paper. Any client or server in the SAM system which needs to store or retrieve information from the database does so through the interfaces of a CORBA-based database server. The users (physicists) use the

  6. Expression of tenascin-C in a rat vocal fold injury model and its regulation of fibroblasts.

    Science.gov (United States)

    Li, Juan; Liu, Yiqiong; Wang, Yiming; Xu, Wen

    2018-03-23

    Tenascin-C (Tnc) is an extracellular matrix (ECM) glycoprotein that plays a vital role in wound healing and fibrotic disease. Tnc is highly upregulated soon after vocal fold injury, but its function in the vocal fold has not yet been defined. In this study, we investigated Tnc expression in a rat vocal fold injury model in vivo and its roles in fibroblasts in vitro. In vivo and in vitro. Tnc mRNA and protein expression levels were quantified on days 3, 7, 14, 28, and 56 after vocal fold injury in Sprague-Dawley rats. In vitro, immunocytochemistry, Western blot, and quantitative real-time polymerase chain reaction (qRT-PCR) analyses were performed in primary rat vocal fold fibroblasts following Tnc or transforming growth factor (TGF)-β1 stimulation to investigate the phenotypic effects. Tnc mRNA and protein expression was upregulated dramatically on days 3 and 7 after injury, and significant differences were observed by qRT-PCR (P vocal fold fibroblasts. Following incubation with Tnc for 72 hours, α-smooth muscle actin, collagen I, and fibronectin expression was significantly upregulated (P vocal fold fibroblast migration, transdifferentiation, and ECM protein synthesis in vitro. Tnc was induced by TGF-β1 in a SMAD3-dependent manner. Transient expression of Tnc is likely to promote regeneration, but its potential role in fibrosis requires further study. NA Laryngoscope, 2018. © 2018 The American Laryngological, Rhinological and Otological Society, Inc.

  7. SPRINT: A Tool to Generate Concurrent Transaction-Level Models from Sequential Code

    Directory of Open Access Journals (Sweden)

    Richard Stahl

    2007-01-01

    Full Text Available A high-level concurrent model such as a SystemC transaction-level model can provide early feedback during the exploration of implementation alternatives for state-of-the-art signal processing applications like video codecs on a multiprocessor platform. However, the creation of such a model starting from sequential code is a time-consuming and error-prone task. It is typically done only once, if at all, for a given design. This lack of exploration of the design space often leads to a suboptimal implementation. To support our systematic C-based design flow, we have developed a tool to generate a concurrent SystemC transaction-level model for user-selected task boundaries. Using this tool, different parallelization alternatives have been evaluated during the design of an MPEG-4 simple profile encoder and an embedded zero-tree coder. Generation plus evaluation of an alternative was possible in less than six minutes. This is fast enough to allow extensive exploration of the design space.

  8. Patient specific dynamic geometric models from sequential volumetric time series image data.

    Science.gov (United States)

    Cameron, B M; Robb, R A

    2004-01-01

    Generating patient specific dynamic models is complicated by the complexity of the motion intrinsic and extrinsic to the anatomic structures being modeled. Using a physics-based sequentially deforming algorithm, an anatomically accurate dynamic four-dimensional model can be created from a sequence of 3-D volumetric time series data sets. While such algorithms may accurately track the cyclic non-linear motion of the heart, they generally fail to accurately track extrinsic structural and non-cyclic motion. To accurately model these motions, we have modified a physics-based deformation algorithm to use a meta-surface defining the temporal and spatial maxima of the anatomic structure as the base reference surface. A mass-spring physics-based deformable model, which can expand or shrink with the local intrinsic motion, is applied to the metasurface, deforming this base reference surface to the volumetric data at each time point. As the meta-surface encompasses the temporal maxima of the structure, any extrinsic motion is inherently encoded into the base reference surface and allows the computation of the time point surfaces to be performed in parallel. The resultant 4-D model can be interactively transformed and viewed from different angles, showing the spatial and temporal motion of the anatomic structure. Using texture maps and per-vertex coloring, additional data such as physiological and/or biomechanical variables (e.g., mapping electrical activation sequences onto contracting myocardial surfaces) can be associated with the dynamic model, producing a 5-D model. For acquisition systems that may capture only limited time series data (e.g., only images at end-diastole/end-systole or inhalation/exhalation), this algorithm can provide useful interpolated surfaces between the time points. Such models help minimize the number of time points required to usefully depict the motion of anatomic structures for quantitative assessment of regional dynamics.

  9. Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Balaji Petety V

    2006-04-01

    Full Text Available Abstract Background The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Results Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. Conclusion The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate

  10. Assessing sequential data assimilation techniques for integrating GRACE data into a hydrological model

    KAUST Repository

    Khaki, M.

    2017-07-06

    The time-variable terrestrial water storage (TWS) products from the Gravity Recovery And Climate Experiment (GRACE) have been increasingly used in recent years to improve the simulation of hydrological models by applying data assimilation techniques. In this study, for the first time, we assess the performance of the most popular data assimilation sequential techniques for integrating GRACE TWS into the World-Wide Water Resources Assessment (W3RA) model. We implement and test stochastic and deterministic ensemble-based Kalman filters (EnKF), as well as Particle filters (PF) using two different resampling approaches of Multinomial Resampling and Systematic Resampling. These choices provide various opportunities for weighting observations and model simulations during the assimilation and also accounting for error distributions. Particularly, the deterministic EnKF is tested to avoid perturbing observations before assimilation (that is the case in an ordinary EnKF). Gaussian-based random updates in the EnKF approaches likely do not fully represent the statistical properties of the model simulations and TWS observations. Therefore, the fully non-Gaussian PF is also applied to estimate more realistic updates. Monthly GRACE TWS are assimilated into W3RA covering the entire Australia. To evaluate the filters performances and analyze their impact on model simulations, their estimates are validated by independent in-situ measurements. Our results indicate that all implemented filters improve the estimation of water storage simulations of W3RA. The best results are obtained using two versions of deterministic EnKF, i.e. the Square Root Analysis (SQRA) scheme and the Ensemble Square Root Filter (EnSRF), respectively improving the model groundwater estimations errors by 34% and 31% compared to a model run without assimilation. Applying the PF along with Systematic Resampling successfully decreases the model estimation error by 23%.

  11. Particle rejuvenation of Rao-Blackwellized sequential Monte Carlo smoothers for conditionally linear and Gaussian models

    Science.gov (United States)

    Nguyen, Ngoc Minh; Corff, Sylvain Le; Moulines, Éric

    2017-12-01

    This paper focuses on sequential Monte Carlo approximations of smoothing distributions in conditionally linear and Gaussian state spaces. To reduce Monte Carlo variance of smoothers, it is typical in these models to use Rao-Blackwellization: particle approximation is used to sample sequences of hidden regimes while the Gaussian states are explicitly integrated conditional on the sequence of regimes and observations, using variants of the Kalman filter/smoother. The first successful attempt to use Rao-Blackwellization for smoothing extends the Bryson-Frazier smoother for Gaussian linear state space models using the generalized two-filter formula together with Kalman filters/smoothers. More recently, a forward-backward decomposition of smoothing distributions mimicking the Rauch-Tung-Striebel smoother for the regimes combined with backward Kalman updates has been introduced. This paper investigates the benefit of introducing additional rejuvenation steps in all these algorithms to sample at each time instant new regimes conditional on the forward and backward particles. This defines particle-based approximations of the smoothing distributions whose support is not restricted to the set of particles sampled in the forward or backward filter. These procedures are applied to commodity markets which are described using a two-factor model based on the spot price and a convenience yield for crude oil data.

  12. Sequential assimilation of multi-mission dynamical topography into a global finite-element ocean model

    Directory of Open Access Journals (Sweden)

    S. Skachko

    2008-12-01

    Full Text Available This study focuses on an accurate estimation of ocean circulation via assimilation of satellite measurements of ocean dynamical topography into the global finite-element ocean model (FEOM. The dynamical topography data are derived from a complex analysis of multi-mission altimetry data combined with a referenced earth geoid. The assimilation is split into two parts. First, the mean dynamic topography is adjusted. To this end an adiabatic pressure correction method is used which reduces model divergence from the real evolution. Second, a sequential assimilation technique is applied to improve the representation of thermodynamical processes by assimilating the time varying dynamic topography. A method is used according to which the temperature and salinity are updated following the vertical structure of the first baroclinic mode. It is shown that the method leads to a partially successful assimilation approach reducing the rms difference between the model and data from 16 cm to 2 cm. This improvement of the mean state is accompanied by significant improvement of temporal variability in our analysis. However, it remains suboptimal, showing a tendency in the forecast phase of returning toward a free run without data assimilation. Both the mean difference and standard deviation of the difference between the forecast and observation data are reduced as the result of assimilation.

  13. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

    Science.gov (United States)

    Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

    2015-10-01

    Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

  14. A cervid vocal fold model suggests greater glottal efficiency in calling at high frequencies.

    Directory of Open Access Journals (Sweden)

    Ingo R Titze

    2010-08-01

    Full Text Available Male Rocky Mountain elk (Cervus elaphus nelsoni produce loud and high fundamental frequency bugles during the mating season, in contrast to the male European Red Deer (Cervus elaphus scoticus who produces loud and low fundamental frequency roaring calls. A critical step in understanding vocal communication is to relate sound complexity to anatomy and physiology in a causal manner. Experimentation at the sound source, often difficult in vivo in mammals, is simulated here by a finite element model of the larynx and a wave propagation model of the vocal tract, both based on the morphology and biomechanics of the elk. The model can produce a wide range of fundamental frequencies. Low fundamental frequencies require low vocal fold strain, but large lung pressure and large glottal flow if sound intensity level is to exceed 70 dB at 10 m distance. A high-frequency bugle requires both large muscular effort (to strain the vocal ligament and high lung pressure (to overcome phonation threshold pressure, but at least 10 dB more intensity level can be achieved. Glottal efficiency, the ration of radiated sound power to aerodynamic power at the glottis, is higher in elk, suggesting an advantage of high-pitched signaling. This advantage is based on two aspects; first, the lower airflow required for aerodynamic power and, second, an acoustic radiation advantage at higher frequencies. Both signal types are used by the respective males during the mating season and probably serve as honest signals. The two signal types relate differently to physical qualities of the sender. The low-frequency sound (Red Deer call relates to overall body size via a strong relationship between acoustic parameters and the size of vocal organs and body size. The high-frequency bugle may signal muscular strength and endurance, via a 'vocalizing at the edge' mechanism, for which efficiency is critical.

  15. Multimodality pH imaging in a mouse dorsal skin fold window chamber model

    Science.gov (United States)

    Leung, Hui Min; Schafer, Rachel; Pagel, Mark M.; Robey, Ian F.; Gmitro, Arthur F.

    2013-03-01

    Upregulate levels of expression and activity of membrane H+ ion pumps in cancer cells drives the extracellular pH (pHe,) to values lower than normal. Furthermore, disregulated pH is indicative of the changes in glycolytic metabolism in tumor cells and has been shown to facilitate extracellular tissue remodeling during metastasis Therefore, measurement of pHe could be a useful cancer biomarker for diagnostic and therapy monitoring evaluation. Multimodality in-vivo imaging of pHe in tumorous tissue in a mouse dorsal skin fold window chamber (DSFWC) model is described. A custom-made plastic window chamber structure was developed that is compatible with both imaging optical and MR imaging modalities and provides a model system for continuous study of the same tissue microenvironment on multiple imaging platforms over a 3-week period. For optical imaging of pHe, SNARF-1 carboxylic acid is injected intravenously into a SCID mouse with an implanted tumor. A ratiometric measurement of the fluorescence signal captured on a confocal microscope reveals the pHe of the tissue visible within the window chamber. This imaging method was used in a preliminary study to evaluate sodium bicarbonate as a potential drug treatment to reverse tissue acidosis. For MR imaging of pHe the chemical exchange saturation transfer (CEST) was used as an alternative way of measuring pHe in a DSFWC model. ULTRAVIST®, a FDA approved x-ray/CT contrast agent has been shown to have a CEST effect that is pH dependent. A ratiometric analysis of water saturation at 5.6 and 4.2 ppm chemical shift provides a means to estimate the local pHe.

  16. Airflow visualization in a model of human glottis near the self-oscillating vocal folds model

    Czech Academy of Sciences Publication Activity Database

    Horáček, Jaromír; Uruba, Václav; Radolf, Vojtěch; Veselý, Jan; Bula, Vítězslav

    2011-01-01

    Roč. 5, č. 1 (2011), s. 21-28 ISSN 1802-680X R&D Projects: GA ČR GA101/08/1155 Institutional research plan: CEZ:AV0Z20760514 Keywords : biomechanics of human voice * voice production modelling * PIV measurement of streamline patterns Subject RIV: BI - Acoustics

  17. Limit Theory for Panel Data Models with Cross Sectional Dependence and Sequential Exogeneity.

    Science.gov (United States)

    Kuersteiner, Guido M; Prucha, Ingmar R

    2013-06-01

    The paper derives a general Central Limit Theorem (CLT) and asymptotic distributions for sample moments related to panel data models with large n . The results allow for the data to be cross sectionally dependent, while at the same time allowing the regressors to be only sequentially rather than strictly exogenous. The setup is sufficiently general to accommodate situations where cross sectional dependence stems from spatial interactions and/or from the presence of common factors. The latter leads to the need for random norming. The limit theorem for sample moments is derived by showing that the moment conditions can be recast such that a martingale difference array central limit theorem can be applied. We prove such a central limit theorem by first extending results for stable convergence in Hall and Hedye (1980) to non-nested martingale arrays relevant for our applications. We illustrate our result by establishing a generalized estimation theory for GMM estimators of a fixed effect panel model without imposing i.i.d. or strict exogeneity conditions. We also discuss a class of Maximum Likelihood (ML) estimators that can be analyzed using our CLT.

  18. Prospectivity Modeling of Karstic Groundwater Using a Sequential Exploration Approach in Tepal Area, Iran

    Science.gov (United States)

    Sharifi, Fereydoun; Arab-Amiri, Ali Reza; Kamkar-Rouhani, Abolghasem; Yousefi, Mahyar; Davoodabadi-Farahani, Meysam

    2017-09-01

    The purpose of this study is water prospectivity modeling (WPM) for recognizing karstic water-bearing zones by using analyses of geo-exploration data in Kal-Qorno valley, located in Tepal area, north of Iran. For this, a sequential exploration method applied on geo-evidential data to delineate target areas for further exploration. In this regard, two major exploration phases including regional and local scales were performed. In the first phase, indicator geological features, structures and lithological units, were used to model groundwater prospectivity as a regional scale. In this phase, for karstic WPM, fuzzy lithological and structural evidence layers were generated and combined using fuzzy operators. After generating target areas using WPM, in the second phase geophysical surveys including gravimetry and geoelectrical resistivity were carried out on the recognized high potential zones as a local scale exploration. Finally the results of geophysical analyses in the second phase were used to select suitable drilling locations to access and extract karstic groundwater in the study area.

  19. Double folding model of nucleus-nucleus potential: formulae, iteration method and computer code

    International Nuclear Information System (INIS)

    Luk'yanov, K.V.

    2008-01-01

    Method of construction of the nucleus-nucleus double folding potential is described. Iteration procedure for the corresponding integral equation is presented. Computer code and numerical results are presented

  20. Work–Family Conflict and Mental Health Among Female Employees: A Sequential Mediation Model via Negative Affect and Perceived Stress

    Science.gov (United States)

    Zhou, Shiyi; Da, Shu; Guo, Heng; Zhang, Xichao

    2018-01-01

    After the implementation of the universal two-child policy in 2016, more and more working women have found themselves caught in the dilemma of whether to raise a baby or be promoted, which exacerbates work–family conflicts among Chinese women. Few studies have examined the mediating effect of negative affect. The present study combined the conservation of resources model and affective events theory to examine the sequential mediating effect of negative affect and perceived stress in the relationship between work–family conflict and mental health. A valid sample of 351 full-time Chinese female employees was recruited in this study, and participants voluntarily answered online questionnaires. Pearson correlation analysis, structural equation modeling, and multiple mediation analysis were used to examine the relationships between work–family conflict, negative affect, perceived stress, and mental health in full-time female employees. We found that women’s perceptions of both work-to-family conflict and family-to-work conflict were significant negatively related to mental health. Additionally, the results showed that negative affect and perceived stress were negatively correlated with mental health. The 95% confidence intervals indicated the sequential mediating effect of negative affect and stress in the relationship between work–family conflict and mental health was significant, which supported the hypothesized sequential mediation model. The findings suggest that work–family conflicts affected the level of self-reported mental health, and this relationship functioned through the two sequential mediators of negative affect and perceived stress. PMID:29719522

  1. Work-Family Conflict and Mental Health Among Female Employees: A Sequential Mediation Model via Negative Affect and Perceived Stress.

    Science.gov (United States)

    Zhou, Shiyi; Da, Shu; Guo, Heng; Zhang, Xichao

    2018-01-01

    After the implementation of the universal two-child policy in 2016, more and more working women have found themselves caught in the dilemma of whether to raise a baby or be promoted, which exacerbates work-family conflicts among Chinese women. Few studies have examined the mediating effect of negative affect. The present study combined the conservation of resources model and affective events theory to examine the sequential mediating effect of negative affect and perceived stress in the relationship between work-family conflict and mental health. A valid sample of 351 full-time Chinese female employees was recruited in this study, and participants voluntarily answered online questionnaires. Pearson correlation analysis, structural equation modeling, and multiple mediation analysis were used to examine the relationships between work-family conflict, negative affect, perceived stress, and mental health in full-time female employees. We found that women's perceptions of both work-to-family conflict and family-to-work conflict were significant negatively related to mental health. Additionally, the results showed that negative affect and perceived stress were negatively correlated with mental health. The 95% confidence intervals indicated the sequential mediating effect of negative affect and stress in the relationship between work-family conflict and mental health was significant, which supported the hypothesized sequential mediation model. The findings suggest that work-family conflicts affected the level of self-reported mental health, and this relationship functioned through the two sequential mediators of negative affect and perceived stress.

  2. Work–Family Conflict and Mental Health Among Female Employees: A Sequential Mediation Model via Negative Affect and Perceived Stress

    Directory of Open Access Journals (Sweden)

    Shiyi Zhou

    2018-04-01

    Full Text Available After the implementation of the universal two-child policy in 2016, more and more working women have found themselves caught in the dilemma of whether to raise a baby or be promoted, which exacerbates work–family conflicts among Chinese women. Few studies have examined the mediating effect of negative affect. The present study combined the conservation of resources model and affective events theory to examine the sequential mediating effect of negative affect and perceived stress in the relationship between work–family conflict and mental health. A valid sample of 351 full-time Chinese female employees was recruited in this study, and participants voluntarily answered online questionnaires. Pearson correlation analysis, structural equation modeling, and multiple mediation analysis were used to examine the relationships between work–family conflict, negative affect, perceived stress, and mental health in full-time female employees. We found that women’s perceptions of both work-to-family conflict and family-to-work conflict were significant negatively related to mental health. Additionally, the results showed that negative affect and perceived stress were negatively correlated with mental health. The 95% confidence intervals indicated the sequential mediating effect of negative affect and stress in the relationship between work–family conflict and mental health was significant, which supported the hypothesized sequential mediation model. The findings suggest that work–family conflicts affected the level of self-reported mental health, and this relationship functioned through the two sequential mediators of negative affect and perceived stress.

  3. A sequential Monte Carlo model of the combined GB gas and electricity network

    International Nuclear Information System (INIS)

    Chaudry, Modassar; Wu, Jianzhong; Jenkins, Nick

    2013-01-01

    A Monte Carlo model of the combined GB gas and electricity network was developed to determine the reliability of the energy infrastructure. The model integrates the gas and electricity network into a single sequential Monte Carlo simulation. The model minimises the combined costs of the gas and electricity network, these include gas supplies, gas storage operation and electricity generation. The Monte Carlo model calculates reliability indices such as loss of load probability and expected energy unserved for the combined gas and electricity network. The intention of this tool is to facilitate reliability analysis of integrated energy systems. Applications of this tool are demonstrated through a case study that quantifies the impact on the reliability of the GB gas and electricity network given uncertainties such as wind variability, gas supply availability and outages to energy infrastructure assets. Analysis is performed over a typical midwinter week on a hypothesised GB gas and electricity network in 2020 that meets European renewable energy targets. The efficacy of doubling GB gas storage capacity on the reliability of the energy system is assessed. The results highlight the value of greater gas storage facilities in enhancing the reliability of the GB energy system given various energy uncertainties. -- Highlights: •A Monte Carlo model of the combined GB gas and electricity network was developed. •Reliability indices are calculated for the combined GB gas and electricity system. •The efficacy of doubling GB gas storage capacity on reliability of the energy system is assessed. •Integrated reliability indices could be used to assess the impact of investment in energy assets

  4. Implementation of a 3d numerical model of a folded multilayer carbonate aquifer

    Science.gov (United States)

    Di Salvo, Cristina; Guyennon, Nicolas; Romano, Emanuele; Bruna Petrangeli, Anna; Preziosi, Elisabetta

    2016-04-01

    The main objective of this research is to present a case study of the numerical model implementation of a complex carbonate, structurally folded aquifer, with a finite difference, porous equivalent model. The case study aquifer (which extends over 235 km2 in the Apennine chain, Central Italy) provides a long term average of 3.5 m3/s of good quality groundwater to the surface river network, sustaining the minimum vital flow, and it is planned to be exploited in the next years for public water supply. In the downstream part of the river in the study area, a "Site of Community Importance" include the Nera River for its valuable aquatic fauna. However, the possible negative effects of the foreseen exploitation on groundwater dependent ecosystems are a great concern and model grounded scenarios are needed. This multilayer aquifer was conceptualized as five hydrostratigraphic units: three main aquifers (the uppermost unconfined, the central and the deepest partly confined), are separated by two locally discontinuous aquitards. The Nera river cuts through the two upper aquifers and acts as the main natural sink for groundwater. An equivalent porous medium approach was chosen. The complex tectonic structure of the aquifer requires several steps in defining the conceptual model; the presence of strongly dipping layers with very heterogeneous hydraulic conductivity, results in different thicknesses of saturated portions. Aquifers can have both unconfined or confined zones; drying and rewetting must be allowed when considering recharge/discharge cycles. All these characteristics can be included in the conceptual and numerical model; however, being the number of flow and head target scarce, the over-parametrization of the model must be avoided. Following the principle of parsimony, three steady state numerical models were developed, starting from a simple model, and then adding complexity: 2D (single layer), QUASI -3D (with leackage term simulating flow through aquitards) and

  5. Space-time evolution of a growth fold (Betic Cordillera, Spain). Evidences from 3D geometrical modelling

    Science.gov (United States)

    Martin-Rojas, Ivan; Alfaro, Pedro; Estévez, Antonio

    2014-05-01

    We present a study that encompasses several software tools (iGIS©, ArcGIS©, Autocad©, etc.) and data (geological mapping, high resolution digital topographic data, high resolution aerial photographs, etc.) to create a detailed 3D geometric model of an active fault propagation growth fold. This 3D model clearly shows structural features of the analysed fold, as well as growth relationships and sedimentary patterns. The results obtained permit us to discuss the kinematics and structural evolution of the fold and the fault in time and space. The study fault propagation fold is the Crevillente syncline. This fold represents the northern limit of the Bajo Segura Basin, an intermontane basin in the Eastern Betic Cordillera (SE Spain) developed from upper Miocene on. 3D features of the Crevillente syncline, including growth pattern, indicate that limb rotation and, consequently, fault activity was higher during Messinian than during Tortonian; consequently, fault activity was also higher. From Pliocene on our data point that limb rotation and fault activity steadies or probably decreases. This in time evolution of the Crevillente syncline is not the same all along the structure; actually the 3D geometric model indicates that observed lateral heterogeneity is related to along strike variation of fault displacement.

  6. 3D Reservoir Modeling of Semutang Gas Field: A lonely Gas field in Chittagong-Tripura Fold Belt, with Integrated Well Log, 2D Seismic Reflectivity and Attributes.

    Science.gov (United States)

    Salehin, Z.; Woobaidullah, A. S. M.; Snigdha, S. S.

    2015-12-01

    Bengal Basin with its prolific gas rich province provides needed energy to Bangladesh. Present energy situation demands more Hydrocarbon explorations. Only 'Semutang' is discovered in the high amplitude structures, where rest of are in the gentle to moderate structures of western part of Chittagong-Tripura Fold Belt. But it has some major thrust faults which have strongly breached the reservoir zone. The major objectives of this research are interpretation of gas horizons and faults, then to perform velocity model, structural and property modeling to obtain reservoir properties. It is needed to properly identify the faults and reservoir heterogeneities. 3D modeling is widely used to reveal the subsurface structure in faulted zone where planning and development drilling is major challenge. Thirteen 2D seismic and six well logs have been used to identify six gas bearing horizons and a network of faults and to map the structure at reservoir level. Variance attributes were used to identify faults. Velocity model is performed for domain conversion. Synthetics were prepared from two wells where sonic and density logs are available. Well to seismic tie at reservoir zone shows good match with Direct Hydrocarbon Indicator on seismic section. Vsh, porosity, water saturation and permeability have been calculated and various cross plots among porosity logs have been shown. Structural modeling is used to make zone and layering accordance with minimum sand thickness. Fault model shows the possible fault network, those liable for several dry wells. Facies model have been constrained with Sequential Indicator Simulation method to show the facies distribution along the depth surfaces. Petrophysical models have been prepared with Sequential Gaussian Simulation to estimate petrophysical parameters away from the existing wells to other parts of the field and to observe heterogeneities in reservoir. Average porosity map for each gas zone were constructed. The outcomes of the research

  7. In vivo comparison of simultaneous versus sequential injection technique for thermochemical ablation in a porcine model.

    Science.gov (United States)

    Cressman, Erik N K; Shenoi, Mithun M; Edelman, Theresa L; Geeslin, Matthew G; Hennings, Leah J; Zhang, Yan; Iaizzo, Paul A; Bischof, John C

    2012-01-01

    To investigate simultaneous and sequential injection thermochemical ablation in a porcine model, and compare them to sham and acid-only ablation. This IACUC-approved study involved 11 pigs in an acute setting. Ultrasound was used to guide placement of a thermocouple probe and coaxial device designed for thermochemical ablation. Solutions of 10 M acetic acid and NaOH were used in the study. Four injections per pig were performed in identical order at a total rate of 4 mL/min: saline sham, simultaneous, sequential, and acid only. Volume and sphericity of zones of coagulation were measured. Fixed specimens were examined by H&E stain. Average coagulation volumes were 11.2 mL (simultaneous), 19.0 mL (sequential) and 4.4 mL (acid). The highest temperature, 81.3°C, was obtained with simultaneous injection. Average temperatures were 61.1°C (simultaneous), 47.7°C (sequential) and 39.5°C (acid only). Sphericity coefficients (0.83-0.89) had no statistically significant difference among conditions. Thermochemical ablation produced substantial volumes of coagulated tissues relative to the amounts of reagents injected, considerably greater than acid alone in either technique employed. The largest volumes were obtained with sequential injection, yet this came at a price in one case of cardiac arrest. Simultaneous injection yielded the highest recorded temperatures and may be tolerated as well as or better than acid injection alone. Although this pilot study did not show a clear advantage for either sequential or simultaneous methods, the results indicate that thermochemical ablation is attractive for further investigation with regard to both safety and efficacy.

  8. Simultaneous temporally resolved DPIV and pressure measurements of symmetric oscillations in a scaled-up vocal fold model

    Science.gov (United States)

    Ringenberg, Hunter; Rogers, Dylan; Wei, Nathaniel; Krane, Michael; Wei, Timothy

    2017-11-01

    The objective of this study is to apply experimental data to theoretical framework of Krane (2013) in which the principal aeroacoustic source is expressed in terms of vocal fold drag, glottal jet dynamic head, and glottal exit volume flow, reconciling formal theoretical aeroacoustic descriptions of phonation with more traditional lumped-element descriptions. These quantities appear in the integral equations of motion for phonatory flow. In this way time resolved velocity field measurements can be used to compute time-resolved estimates of the relevant terms in the integral equations of motion, including phonation aeroacoustic source strength. A simplified 10x scale vocal fold model from Krane, et al. (2007) was used to examine symmetric, i.e. `healthy', oscillatory motion of the vocal folds. By using water as the working fluid, very high spatial and temporal resolution was achieved. Temporal variation of transglottal pressure was simultaneously measured with flow on the vocal fold model mid-height. Experiments were dynamically scaled to examine a range of frequencies corresponding to male and female voice. The simultaneity of the pressure and flow provides new insights into the aeroacoustics associated with vocal fold oscillations. Supported by NIH Grant No. 2R01 DC005642-11.

  9. Sequential and joint hydrogeophysical inversion using a field-scale groundwater model with ERT and TDEM data

    DEFF Research Database (Denmark)

    Herckenrath, Daan; Fiandaca, G.; Auken, Esben

    2013-01-01

    hydrogeophysical inversion approaches to inform a field-scale groundwater model with time domain electromagnetic (TDEM) and electrical resistivity tomography (ERT) data. In a sequential hydrogeophysical inversion (SHI) a groundwater model is calibrated with geophysical data by coupling groundwater model parameters...... with the inverted geophysical models. We subsequently compare the SHI with a joint hydrogeophysical inversion (JHI). In the JHI, a geophysical model is simultaneously inverted with a groundwater model by coupling the groundwater and geophysical parameters to explicitly account for an established petrophysical...

  10. Sequential and joint hydrogeophysical inversion using a field-scale groundwater model with ERT and TDEM data

    DEFF Research Database (Denmark)

    Herckenrath, Daan; Fiandaca, G.; Auken, Esben

    2013-01-01

    with the inverted geophysical models. We subsequently compare the SHI with a joint hydrogeophysical inversion (JHI). In the JHI, a geophysical model is simultaneously inverted with a groundwater model by coupling the groundwater and geophysical parameters to explicitly account for an established petrophysical...... hydrogeophysical inversion approaches to inform a field-scale groundwater model with time domain electromagnetic (TDEM) and electrical resistivity tomography (ERT) data. In a sequential hydrogeophysical inversion (SHI) a groundwater model is calibrated with geophysical data by coupling groundwater model parameters...

  11. Use of integrated analogue and numerical modelling to predict tridimensional fracture intensity in fault-related-folds.

    Science.gov (United States)

    Pizzati, Mattia; Cavozzi, Cristian; Magistroni, Corrado; Storti, Fabrizio

    2016-04-01

    Fracture density pattern predictions with low uncertainty is a fundamental issue for constraining fluid flow pathways in thrust-related anticlines in the frontal parts of thrust-and-fold belts and accretionary prisms, which can also provide plays for hydrocarbon exploration and development. Among the drivers that concur to determine the distribution of fractures in fold-and-thrust-belts, the complex kinematic pathways of folded structures play a key role. In areas with scarce and not reliable underground information, analogue modelling can provide effective support for developing and validating reliable hypotheses on structural architectures and their evolution. In this contribution, we propose a working method that combines analogue and numerical modelling. We deformed a sand-silicone multilayer to eventually produce a non-cylindrical thrust-related anticline at the wedge toe, which was our test geological structure at the reservoir scale. We cut 60 serial cross-sections through the central part of the deformed model to analyze faults and folds geometry using dedicated software (3D Move). The cross-sections were also used to reconstruct the 3D geometry of reference surfaces that compose the mechanical stratigraphy thanks to the use of the software GoCad. From the 3D model of the experimental anticline, by using 3D Move it was possible to calculate the cumulative stress and strain underwent by the deformed reference layers at the end of the deformation and also in incremental steps of fold growth. Based on these model outputs it was also possible to predict the orientation of three main fractures sets (joints and conjugate shear fractures) and their occurrence and density on model surfaces. The next step was the upscaling of the fracture network to the entire digital model volume, to create DFNs.

  12. Finite element modeling of the vocal folds with deformable interface tracking

    DEFF Research Database (Denmark)

    Granados Corsellas, Alba; Brunskog, Jonas; Misztal, Marek Krzysztof

    2014-01-01

    Continuous and prolonged use of the sp eaking voice may lead to functional sp eech disorders that are not apparent for voice clinicians from high-sp eed imaging of the vo cal folds' vibration. However, it is hyp othesized that time dep endent tissue prop erties provide some insight into the injury...... pro cess. To infer material parameters via an inverse optimization problem from recorded deformation, a self sustained theoretical mo del of the vo cal folds is needed. With this purp ose, a transversely isotropic three-dimensional nite element mo del is prop osed and investigated. Sp ecial attention...

  13. Normative personality trait development in adulthood: A 6-year cohort-sequential growth model.

    Science.gov (United States)

    Milojev, Petar; Sibley, Chris G

    2017-03-01

    The present study investigated patterns of normative change in personality traits across the adult life span (19 through 74 years of age). We examined change in extraversion, agreeableness, conscientiousness, neuroticism, openness to experience and honesty-humility using data from the first 6 annual waves of the New Zealand Attitudes and Values Study (N = 10,416; 61.1% female, average age = 49.46). We present a cohort-sequential latent growth model assessing patterns of mean-level change due to both aging and cohort effects. Extraversion decreased as people aged, with the most pronounced declines occurring in young adulthood, and then again in old age. Agreeableness, indexed with a measure focusing on empathy, decreased in young adulthood and remained relatively unchanged thereafter. Conscientiousness increased among young adults then leveled off and remained fairly consistent for the rest of the adult life span. Neuroticism and openness to experience decreased as people aged. However, the models suggest that these latter effects may also be partially due to cohort differences, as older people showed lower levels of neuroticism and openness to experience more generally. Honesty-humility showed a pronounced and consistent increase across the adult life span. These analyses of large-scale longitudinal national probability panel data indicate that different dimensions of personality follow distinct developmental processes throughout adulthood. Our findings also highlight the importance of young adulthood (up to about the age of 30) in personality trait development, as well as continuing change throughout the adult life span. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  14. Relation of Structural and Vibratory Kinematics of the Vocal Folds to Two Acoustic Measures of Breathy Voice Based on Computational Modeling

    Science.gov (United States)

    Samlan, Robin A.; Story, Brad H.

    2011-01-01

    Purpose: To relate vocal fold structure and kinematics to 2 acoustic measures: cepstral peak prominence (CPP) and the amplitude of the first harmonic relative to the second (H1-H2). Method: The authors used a computational, kinematic model of the medial surfaces of the vocal folds to specify features of vocal fold structure and vibration in a…

  15. Examining diseased states in a scaled-up vocal fold model using simultaneous temporally resolved DPIV and pressure measurements

    Science.gov (United States)

    Rogers, Dylan; Wei, Nathaniel; Ringenber, Hunter; Krane, Michael; Wei, Timothy

    2017-11-01

    This study builds on the parallel presentation of Ringenberg, et al. (APS-DFD 2017) involving simultaneous, temporally and spatially resolved flow and pressure measurements in a scaled-up vocal fold model. In this talk, data from experiments replicating characteristics of diseased vocal folds are presented. This begins with vocal folds that do not fully close and continues with asymmetric oscillations. Data are compared to symmetric, i.e. `healthy', oscillatory motions presented in the companion talk. Having pressure and flow data for individual as well as phase averaged oscillations for these diseased cases highlights the potential for aeroacoustic analysis in this complex system. Supported by NIH Grant No. 2R01 DC005642-11.

  16. Geometry of human vocal folds and glottal channel for mathematical and biomechanical modeling of voice production

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Švec, J. G.; Horáček, Jaromír; Veselý, Jan; Klepáček, I.; Havlík, R.

    2008-01-01

    Roč. 41, - (2008), s. 985-995 ISSN 0021-9290 R&D Projects: GA AV ČR IAA2076401 Institutional research plan: CEZ:AV0Z20760514 Keywords : vocal fold geometry * glottal channel shape * quantitative description Subject RIV: BI - Acoustics Impact factor: 2.784, year: 2008

  17. Self-similar voiding solutions for a single layered model of folding rocks

    NARCIS (Netherlands)

    Dodwell, T.J.; Peletier, M.A.; Budd, C.J.; Hunt, G.W.

    2011-01-01

    In this paper we derive an obstacle problem with a free boundary to describe the formation of voids at areas of intense geological folding. An elastic layer is forced by overburden pressure against a V-shaped rigid obstacle. Energy minimization leads to representation as a non-linear fourth-order

  18. Numerical Simulation of Interaction of Fluid Flow and Elastic Structure Modelling Vocal Fold

    Czech Academy of Sciences Publication Activity Database

    Valášek, J.; Sváček, P.; Horáček, Jaromír

    2016-01-01

    Roč. 821, č. 2016 (2016), s. 693-700 ISSN 1660-9336 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional support: RVO:61388998 Keywords : finite element method * 2D Navier-Stokes equations * vocal folds * aeroelasticity Subject RIV: BI - Acoustics

  19. The human vocal fold layers. Their delineation inside vocal fold as a background to create 3D digital and synthetic glottal model

    Czech Academy of Sciences Publication Activity Database

    Klepáček, I.; Jirák, D.; Dušková-Smrčková, Miroslava; Janoušková, Olga; Vampola, T.

    2016-01-01

    Roč. 30, č. 5 (2016), s. 529-537 ISSN 0892-1997 R&D Projects: GA ČR(CZ) GAP101/12/1306 Institutional support: RVO:61389013 Keywords : human vocal fold * vocal ligamentous complex * lamina propria Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.381, year: 2016

  20. Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

    Science.gov (United States)

    Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

    2011-06-09

    Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

  1. Bootstrap Sequential Determination of the Co-integration Rank in VAR Models

    DEFF Research Database (Denmark)

    Guiseppe, Cavaliere; Rahbæk, Anders; Taylor, A.M. Robert

    with empirical rejection frequencies often very much in excess of the nominal level. As a consequence, bootstrap versions of these tests have been developed. To be useful, however, sequential procedures for determining the co-integrating rank based on these bootstrap tests need to be consistent, in the sense...... in the literature by proposing a bootstrap sequential algorithm which we demonstrate delivers consistent cointegration rank estimation for general I(1) processes. Finite sample Monte Carlo simulations show the proposed procedure performs well in practice....

  2. Work–Family Conflict and Mental Health Among Female Employees: A Sequential Mediation Model via Negative Affect and Perceived Stress

    OpenAIRE

    Shiyi Zhou; Shu Da; Heng Guo; Xichao Zhang

    2018-01-01

    After the implementation of the universal two-child policy in 2016, more and more working women have found themselves caught in the dilemma of whether to raise a baby or be promoted, which exacerbates work–family conflicts among Chinese women. Few studies have examined the mediating effect of negative affect. The present study combined the conservation of resources model and affective events theory to examine the sequential mediating effect of negative affect and perceived stress in the relat...

  3. Structurally and functionally characterized in vitro model of rabbit vocal fold epithelium.

    Science.gov (United States)

    Mizuta, Masanobu; Kurita, Takashi; Kimball, Emily E; Rousseau, Bernard

    2017-06-01

    In this paper, we describe a method for primary culture of a well differentiated electrically tight rabbit vocal fold epithelial cell multilayer and the measurement of transepithelial electrical resistance (TEER) for the evaluation of epithelial barrier function in vitro. Rabbit larynges were harvested and enzymatically treated to isolate vocal fold epithelial cells and to establish primary culture. Vocal fold epithelial cells were co-cultured with mitomycin C-treated feeder cells on collagen-coated plates. After 10-14 days in primary culture, cells were passaged and cultured until they achieved 70-90% confluence on collagen-coated plates. Epithelial cells were then passaged onto collagen-coated cell culture inserts using 4.5cm 2 membrane filters (1.0μm pore size) with 10% fetal bovine serum or 30μg/mL bovine pituitary extract to investigate the effects of growth-promoting additives on TEER. Additional experiments were performed to investigate optimal seeding density (1.1, 2.2, 4.4, or 8.9×10 5 cells/cm 2 ), the effect of co-culture with feeder cells, and the effect of passage number on epithelial barrier function. Characterization of in vitro cultures was performed using hematoxylin and eosin staining and immunostaining for vocal fold epithelial cell markers and tight junctions. Results revealed higher TEER in cells supplemented with fetal bovine serum compared to bovine pituitary extract. TEER was highest in cells passaged at a seeding density of 2.2×10 4 cells/cm 2 , and TEER was higher in cells at passage two than passage three. Ultrastructural experiments revealed a well-differentiated epithelial cell multilayer, expressing the epithelial cell markers CK13, CK14 and the tight junction proteins occludin and ZO-1. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment

    DEFF Research Database (Denmark)

    Ahmad, Amais; Zachariasen, Camilla; Christiansen, Lasse Engbo

    2016-01-01

    Background: Combination treatment is increasingly used to fight infections caused by bacteria resistant to two or more antimicrobials. While multiple studies have evaluated treatment strategies to minimize the emergence of resistant strains for single antimicrobial treatment, fewer studies have...... the sensitive fraction of the commensal flora.Growth parameters for competing bacterial strains were estimated from the combined in vitro pharmacodynamic effect of two antimicrobials using the relationship between concentration and net bacterial growth rate. Predictions of in vivo bacterial growth were...... (how frequently antibiotics are alternated in a sequential treatment) of the two drugs was dependent upon the order in which the two drugs were used.Conclusion: Sequential treatment was more effective in preventing the growth of resistant strains when compared to the combination treatment. The cycling...

  5. A meta-analysis of response-time tests of the sequential two-systems model of moral judgment.

    Science.gov (United States)

    Baron, Jonathan; Gürçay, Burcu

    2017-05-01

    The (generalized) sequential two-system ("default interventionist") model of utilitarian moral judgment predicts that utilitarian responses often arise from a system-two correction of system-one deontological intuitions. Response-time (RT) results that seem to support this model are usually explained by the fact that low-probability responses have longer RTs. Following earlier results, we predicted response probability from each subject's tendency to make utilitarian responses (A, "Ability") and each dilemma's tendency to elicit deontological responses (D, "Difficulty"), estimated from a Rasch model. At the point where A = D, the two responses are equally likely, so probability effects cannot account for any RT differences between them. The sequential two-system model still predicts that many of the utilitarian responses made at this point will result from system-two corrections of system-one intuitions, hence should take longer. However, when A = D, RT for the two responses was the same, contradicting the sequential model. Here we report a meta-analysis of 26 data sets, which replicated the earlier results of no RT difference overall at the point where A = D. The data sets used three different kinds of moral judgment items, and the RT equality at the point where A = D held for all three. In addition, we found that RT increased with A-D. This result holds for subjects (characterized by Ability) but not for items (characterized by Difficulty). We explain the main features of this unanticipated effect, and of the main results, with a drift-diffusion model.

  6. A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

    Directory of Open Access Journals (Sweden)

    Konstantin B Zeldovich

    2007-07-01

    Full Text Available In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species--subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

  7. Parallel CFD simulation of flow in a 3D model of vibrating human vocal folds

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Horáček, Jaromír; Řidký, V.

    2013-01-01

    Roč. 80, č. 1 (2013), s. 290-300 ISSN 0045-7930 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional research plan: CEZ:AV0Z20760514 Keywords : numerical simulation * vocal folds * glottal airflow * inite volume method * parallel CFD Subject RIV: BI - Acoustics Impact factor: 1.532, year: 2013 http://www.sciencedirect.com/science?_ob=ArticleListURL&_method=list&_ArticleListID=-268060849&_sort=r&_st=13&view=c&_acct=C000034318&_version=1&_urlVersion=0&_userid=640952&md5=7c5b5539857ee9a02af5e690585b3126&searchtype=a

  8. Sequential Banking.

    OpenAIRE

    Bizer, David S; DeMarzo, Peter M

    1992-01-01

    The authors study environments in which agents may borrow sequentially from more than one leader. Although debt is prioritized, additional lending imposes an externality on prior debt because, with moral hazard, the probability of repayment of prior loans decreases. Equilibrium interest rates are higher than they would be if borrowers could commit to borrow from at most one bank. Even though the loan terms are less favorable than they would be under commitment, the indebtedness of borrowers i...

  9. Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

    Science.gov (United States)

    Kapoor, Abhijeet; Travesset, Alex

    2014-03-01

    We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

  10. Group theoretical classification of broken symmetry states of the two-fold degenerate Hubbard model on a triangular lattice

    International Nuclear Information System (INIS)

    Masago, Akira; Suzuki, Naoshi

    2001-01-01

    By a group theoretical procedure we derive the possible spontaneously broken-symmetry states for the two-fold degenerate Hubbard model on a two-dimensional triangular lattice. For ordering wave vectors corresponding to the points Γ and K in the first BZ we find 22 states which include 16 collinear and six non-collinear states. The collinear states include the usual SDW and CDW states which appear also in the single-band Hubbard model. The non-collinear states include exotic ordering states of orbitals and spins as well as the triangular arrangement of spins

  11. Systems-level modeling the effects of arsenic exposure with sequential pulsed and fluctuating patterns for tilapia and freshwater clam

    International Nuclear Information System (INIS)

    Chen, W.-Y.; Tsai, J.-W.; Ju, Y.-R.; Liao, C.-M.

    2010-01-01

    The purpose of this paper was to use quantitative systems-level approach employing biotic ligand model based threshold damage model to examine physiological responses of tilapia and freshwater clam to sequential pulsed and fluctuating arsenic concentrations. We tested present model and triggering mechanisms by carrying out a series of modeling experiments where we used periodic pulses and sine-wave as featured exposures. Our results indicate that changes in the dominant frequencies and pulse timing can shift the safe rate distributions for tilapia, but not for that of freshwater clam. We found that tilapia increase bioenergetic costs to maintain the acclimation during pulsed and sine-wave exposures. Our ability to predict the consequences of physiological variation under time-varying exposure patterns has also implications for optimizing species growing, cultivation strategies, and risk assessment in realistic situations. - Systems-level modeling the pulsed and fluctuating arsenic exposures.

  12. Systems-level modeling the effects of arsenic exposure with sequential pulsed and fluctuating patterns for tilapia and freshwater clam

    Energy Technology Data Exchange (ETDEWEB)

    Chen, W.-Y. [Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan (China); Tsai, J.-W. [Institute of Ecology and Evolutionary Ecology, China Medical University, Taichung 40402, Taiwan (China); Ju, Y.-R. [Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan (China); Liao, C.-M., E-mail: cmliao@ntu.edu.t [Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan (China)

    2010-05-15

    The purpose of this paper was to use quantitative systems-level approach employing biotic ligand model based threshold damage model to examine physiological responses of tilapia and freshwater clam to sequential pulsed and fluctuating arsenic concentrations. We tested present model and triggering mechanisms by carrying out a series of modeling experiments where we used periodic pulses and sine-wave as featured exposures. Our results indicate that changes in the dominant frequencies and pulse timing can shift the safe rate distributions for tilapia, but not for that of freshwater clam. We found that tilapia increase bioenergetic costs to maintain the acclimation during pulsed and sine-wave exposures. Our ability to predict the consequences of physiological variation under time-varying exposure patterns has also implications for optimizing species growing, cultivation strategies, and risk assessment in realistic situations. - Systems-level modeling the pulsed and fluctuating arsenic exposures.

  13. Polyphase tertiary fold-and-thrust tectonics in the Belluno Dolomites: new mapping, kinematic analysis, and 3D modelling

    Science.gov (United States)

    Chistolini, Filippo; Bistacchi, Andrea; Massironi, Matteo; Consonni, Davide; Cortinovis, Silvia

    2014-05-01

    performed a dip-domain analysis that allowed to categorize the different fold limbs and reduce the uncertainty in the reconstruction of the fault network topology in map view. This enabled us to reconstruct a high-quality, low-uncertainty 3D structural and geological model, which unambiguously proves that deformations with a top-to-WSW Dinaric transport direction propagate farther to the west than previously supposed in this part of the Southern Alps. Our new structural reconstruction of the Vajont valley have also clarified the structural control on the 1963 catastrophic landslide (which caused over 2000 losses). Besides being a challenging natural laboratory for testing analysis and modelling methodologies to be used when reconstructing in 3D this kind of complex interference structures, the Vajont area also provides useful clues on the still-enigmatic structures in the frontal part of the Friuli-Venetian Southern Alps, buried in the Venetian Plain foredeep. These include active seismogenic thrust-faults and, at the same time, represent a growing interest for the oil industry.

  14. AdOn HDP-HMM: An Adaptive Online Model for Segmentation and Classification of Sequential Data.

    Science.gov (United States)

    Bargi, Ava; Xu, Richard Yi Da; Piccardi, Massimo

    2017-09-21

    Recent years have witnessed an increasing need for the automated classification of sequential data, such as activities of daily living, social media interactions, financial series, and others. With the continuous flow of new data, it is critical to classify the observations on-the-fly and without being limited by a predetermined number of classes. In addition, a model should be able to update its parameters in response to a possible evolution in the distributions of the classes. This compelling problem, however, does not seem to have been adequately addressed in the literature, since most studies focus on offline classification over predefined class sets. In this paper, we present a principled solution for this problem based on an adaptive online system leveraging Markov switching models and hierarchical Dirichlet process priors. This adaptive online approach is capable of classifying the sequential data over an unlimited number of classes while meeting the memory and delay constraints typical of streaming contexts. In this paper, we introduce an adaptive ''learning rate'' that is responsible for balancing the extent to which the model retains its previous parameters or adapts to new observations. Experimental results on stationary and evolving synthetic data and two video data sets, TUM Assistive Kitchen and collated Weizmann, show a remarkable performance in terms of segmentation and classification, particularly for sequences from evolutionary distributions and/or those containing previously unseen classes.

  15. Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

    Science.gov (United States)

    de Oliveira, Saulo H P; Law, Eleanor C; Shi, Jiye; Deane, Charlotte M

    2018-04-01

    Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2. saulo.deoliveira@dtc.ox.ac.uk. Supplementary data are available at Bioinformatics online.

  16. Tibetan Microblog Emotional Analysis Based on Sequential Model in Online Social Platforms

    Directory of Open Access Journals (Sweden)

    Lirong Qiu

    2017-01-01

    Full Text Available With the development of microblogs, selling and buying appear in online social platforms such as Sina Weibo and Wechat. Besides Mandarin, Tibetan language is also used to describe products and customers’ opinions. In this paper, we are interested in analyzing the emotions of Tibetan microblogs, which are helpful to understand opinions and product reviews for Tibetan customers. It is challenging since existing studies paid little attention to Tibetan language. Our key idea is to express Tibetan microblogs as vectors and then classify them. To express microblogs more fully, we select two kinds of features, which are sequential features and semantic features. In addition, our experimental results on the Sina Weibo dataset clearly demonstrate the effectiveness of feature selection and the efficiency of our classification method.

  17. An extended Kalman filter approach to non-stationary Bayesian estimation of reduced-order vocal fold model parameters.

    Science.gov (United States)

    Hadwin, Paul J; Peterson, Sean D

    2017-04-01

    The Bayesian framework for parameter inference provides a basis from which subject-specific reduced-order vocal fold models can be generated. Previously, it has been shown that a particle filter technique is capable of producing estimates and associated credibility intervals of time-varying reduced-order vocal fold model parameters. However, the particle filter approach is difficult to implement and has a high computational cost, which can be barriers to clinical adoption. This work presents an alternative estimation strategy based upon Kalman filtering aimed at reducing the computational cost of subject-specific model development. The robustness of this approach to Gaussian and non-Gaussian noise is discussed. The extended Kalman filter (EKF) approach is found to perform very well in comparison with the particle filter technique at dramatically lower computational cost. Based upon the test cases explored, the EKF is comparable in terms of accuracy to the particle filter technique when greater than 6000 particles are employed; if less particles are employed, the EKF actually performs better. For comparable levels of accuracy, the solution time is reduced by 2 orders of magnitude when employing the EKF. By virtue of the approximations used in the EKF, however, the credibility intervals tend to be slightly underpredicted.

  18. Joint Data Assimilation and Parameter Calibration in on-line groundwater modelling using Sequential Monte Carlo techniques

    Science.gov (United States)

    Ramgraber, M.; Schirmer, M.

    2017-12-01

    As computational power grows and wireless sensor networks find their way into common practice, it becomes increasingly feasible to pursue on-line numerical groundwater modelling. The reconciliation of model predictions with sensor measurements often necessitates the application of Sequential Monte Carlo (SMC) techniques, most prominently represented by the Ensemble Kalman Filter. In the pursuit of on-line predictions it seems advantageous to transcend the scope of pure data assimilation and incorporate on-line parameter calibration as well. Unfortunately, the interplay between shifting model parameters and transient states is non-trivial. Several recent publications (e.g. Chopin et al., 2013, Kantas et al., 2015) in the field of statistics discuss potential algorithms addressing this issue. However, most of these are computationally intractable for on-line application. In this study, we investigate to what extent compromises between mathematical rigour and computational restrictions can be made within the framework of on-line numerical modelling of groundwater. Preliminary studies are conducted in a synthetic setting, with the goal of transferring the conclusions drawn into application in a real-world setting. To this end, a wireless sensor network has been established in the valley aquifer around Fehraltorf, characterized by a highly dynamic groundwater system and located about 20 km to the East of Zürich, Switzerland. By providing continuous probabilistic estimates of the state and parameter distribution, a steady base for branched-off predictive scenario modelling could be established, providing water authorities with advanced tools for assessing the impact of groundwater management practices. Chopin, N., Jacob, P.E. and Papaspiliopoulos, O. (2013): SMC2: an efficient algorithm for sequential analysis of state space models. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 75 (3), p. 397-426. Kantas, N., Doucet, A., Singh, S

  19. Modelling the sequential geographical exploitation and potential collapse of marine fisheries through economic globalization, climate change and management alternatives

    Directory of Open Access Journals (Sweden)

    Gorka Merino

    2011-07-01

    Full Text Available Global marine fisheries production has reached a maximum and may even be declining. Underlying this trend is a well-understood sequence of development, overexploitation, depletion and in some instances collapse of individual fish stocks, a pattern that can sequentially link geographically distant populations. Ineffective governance, economic considerations and climate impacts are often responsible for this sequence, although the relative contribution of each factor is contentious. In this paper we use a global bioeconomic model to explore the synergistic effects of climate variability, economic pressures and management measures in causing or avoiding this sequence. The model shows how a combination of climate-induced variability in the underlying fish population production, particular patterns of demand for fish products and inadequate management is capable of driving the world’s fisheries into development, overexploitation, collapse and recovery phases consistent with observations. Furthermore, it demonstrates how a sequential pattern of overexploitation can emerge as an endogenous property of the interaction between regional environmental fluctuations and a globalized trade system. This situation is avoidable through adaptive management measures that ensure the sustainability of regional production systems in the face of increasing global environmental change and markets. It is concluded that global management measures are needed to ensure that global food supply from marine products is optimized while protecting long-term ecosystem services across the world’s oceans.

  20. Sequential fragmentation of Pleistocene forests in an East Africa biodiversity hotspot: chameleons as a model to track forest history.

    Directory of Open Access Journals (Sweden)

    G John Measey

    Full Text Available The Eastern Arc Mountains (EAM is an example of naturally fragmented tropical forests, which contain one of the highest known concentrations of endemic plants and vertebrates. Numerous paleo-climatic studies have not provided direct evidence for ancient presence of Pleistocene forests, particularly in the regions in which savannah presently occurs. Knowledge of the last period when forests connected EAM would provide a sound basis for hypothesis testing of vicariance and dispersal models of speciation. Dated phylogenies have revealed complex patterns throughout EAM, so we investigated divergence times of forest fauna on four montane isolates in close proximity to determine whether forest break-up was most likely to have been simultaneous or sequential, using population genetics of a forest restricted arboreal chameleon, Kinyongia boehmei.We used mitochondrial and nuclear genetic sequence data and mutation rates from a fossil-calibrated phylogeny to estimate divergence times between montane isolates using a coalescent approach. We found that chameleons on all mountains are most likely to have diverged sequentially within the Pleistocene from 0.93-0.59 Ma (95% HPD 0.22-1.84 Ma. In addition, post-hoc tests on chameleons on the largest montane isolate suggest a population expansion ∼182 Ka.Sequential divergence is most likely to have occurred after the last of three wet periods within the arid Plio-Pleistocene era, but was not correlated with inter-montane distance. We speculate that forest connection persisted due to riparian corridors regardless of proximity, highlighting their importance in the region's historic dispersal events. The population expansion coincides with nearby volcanic activity, which may also explain the relative paucity of the Taita's endemic fauna. Our study shows that forest chameleons are an apposite group to track forest fragmentation, with the inference that forest extended between some EAM during the Pleistocene 1

  1. Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

    Science.gov (United States)

    Paul, Fabian; Noé, Frank; Weikl, Thomas R

    2018-03-27

    Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

  2. A Three Dimension Model to Demonstrate Head and Tail Fold Formation in Mammalian Embryos

    Science.gov (United States)

    Bressler, Robert S.

    1977-01-01

    Many students have difficulty visualizing the delineation of the embryonic body from the flat germ disc. An easily-constructed model is described that has been used successfully to convey the dynamics of embryological events at Mount Sinai School of Medicine. (LBH)

  3. Sequential super-stereotypy of an instinctive fixed action pattern in hyper-dopaminergic mutant mice: a model of obsessive compulsive disorder and Tourette's

    Directory of Open Access Journals (Sweden)

    Houchard Kimberly R

    2005-02-01

    Full Text Available Abstract Background Excessive sequential stereotypy of behavioral patterns (sequential super-stereotypy in Tourette's syndrome and obsessive compulsive disorder (OCD is thought to involve dysfunction in nigrostriatal dopamine systems. In sequential super-stereotypy, patients become trapped in overly rigid sequential patterns of action, language, or thought. Some instinctive behavioral patterns of animals, such as the syntactic grooming chain pattern of rodents, have sufficiently complex and stereotyped serial structure to detect potential production of overly-rigid sequential patterns. A syntactic grooming chain is a fixed action pattern that serially links up to 25 grooming movements into 4 predictable phases that follow 1 syntactic rule. New mutant mouse models allow gene-based manipulation of brain function relevant to sequential patterns, but no current animal model of spontaneous OCD-like behaviors has so far been reported to exhibit sequential super-stereotypy in the sense of a whole complex serial pattern that becomes stronger and excessively rigid. Here we used a hyper-dopaminergic mutant mouse to examine whether an OCD-like behavioral sequence in animals shows sequential super-stereotypy. Knockdown mutation of the dopamine transporter gene (DAT causes extracellular dopamine levels in the neostriatum of these adult mutant mice to rise to 170% of wild-type control levels. Results We found that the serial pattern of this instinctive behavioral sequence becomes strengthened as an entire entity in hyper-dopaminergic mutants, and more resistant to interruption. Hyper-dopaminergic mutant mice have stronger and more rigid syntactic grooming chain patterns than wild-type control mice. Mutants showed sequential super-stereotypy in the sense of having more stereotyped and predictable syntactic grooming sequences, and were also more likely to resist disruption of the pattern en route, by returning after a disruption to complete the pattern from the

  4. Impact stress in a self-oscillating model of human vocal folds

    Czech Academy of Sciences Publication Activity Database

    Horáček, Jaromír; Bula, Vítězslav; Radolf, Vojtěch; Šidlof, Petr

    2016-01-01

    Roč. 4, č. 3 (2016), s. 183-190 ISSN 2321-3558 R&D Projects: GA ČR(CZ) GAP101/12/1306 Institutional support: RVO:61388998 Keywords : fluid-structure interaction * flutter * biomechanics of voice modeling * phonation * aeroelasticity Subject RIV: BI - Acoustics Impact factor: 0.259, year: 2016 http://www.tvi-in.com/Journals/journaldetail.aspx?Id=2016062811045074383592dcc719793

  5. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    International Nuclear Information System (INIS)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-01-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space

  6. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    Energy Technology Data Exchange (ETDEWEB)

    Nedialkova, Lilia V.; Amat, Miguel A. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States); Hummer, Gerhard, E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main (Germany)

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  7. Numerical seismic modelling of fault-fold structures in a mountainous setting

    Energy Technology Data Exchange (ETDEWEB)

    Kirtland Grech, M.G.; Lawton, D.C.; Spratt, D.A. (Calgary Univ., AB (Canada))

    1999-01-01

    Experiments were conducted to determine the performance of different prestack migration algorithms in complex structural areas, particularly in the presence of rugged topography and thrust faults that result in severe lateral and vertical velocity changes, using a series of numerical seismic models. The numerical model used was based on a cross section through the Rocky Mountains Front Ranges of Western Canada and is 33 km wide and 11 km deep. The best migrated section was obtained with FD shot migration in depth and from topography, using the known velocity model. This result was superior to Kirchhoff depth migration from topography and from a flat datum. As the velocities departed from their true value, the deeper events were most affected, because of the accumulation of velocity errors with depth. The small-scale features of Target A, in the shallower part of the section, could still be interpreted even when the velocities were inaccurate. In the presence of velocity errors, the different structures could still be interpreted, but were at the wrong depth and had the wrong structural shape and size. Layers that were of the order of 1 km in width and 500 km in thickness, such as Layer 4, were the most poorly imaged and focussed, both with time migration and with depth migration. Fault planes were not imaged in the absence of a velocity contrast across them, making some FW cutoffs difficult to interpret. 2 refs.

  8. Numerical seismic modelling of fault-fold structures in a mountainous setting

    Energy Technology Data Exchange (ETDEWEB)

    Kirtland Grech, M.G.; Lawton, D.C.; Spratt, D.A. [Calgary Univ., AB (Canada)

    1999-11-01

    Experiments were conducted to determine the performance of different prestack migration algorithms in complex structural areas, particularly in the presence of rugged topography and thrust faults that result in severe lateral and vertical velocity changes, using a series of numerical seismic models. The numerical model used was based on a cross section through the Rocky Mountains Front Ranges of Western Canada and is 33 km wide and 11 km deep. The best migrated section was obtained with FD shot migration in depth and from topography, using the known velocity model. This result was superior to Kirchhoff depth migration from topography and from a flat datum. As the velocities departed from their true value, the deeper events were most affected, because of the accumulation of velocity errors with depth. The small-scale features of Target A, in the shallower part of the section, could still be interpreted even when the velocities were inaccurate. In the presence of velocity errors, the different structures could still be interpreted, but were at the wrong depth and had the wrong structural shape and size. Layers that were of the order of 1 km in width and 500 km in thickness, such as Layer 4, were the most poorly imaged and focussed, both with time migration and with depth migration. Fault planes were not imaged in the absence of a velocity contrast across them, making some FW cutoffs difficult to interpret. 2 refs.

  9. Three-dimensional classical-ensemble modeling of non-sequential double ionization

    International Nuclear Information System (INIS)

    Haan, S.L.; Breen, L.; Tannor, D.; Panfili, R.; Ho, Phay J.; Eberly, J.H.

    2005-01-01

    Full text: We have been using 1d ensembles of classical two-electron atoms to simulate helium atoms that are exposed to pulses of intense laser radiation. In this talk we discuss the challenges in setting up a 3d classical ensemble that can mimic the quantum ground state of helium. We then report studies in which each one of 500,000 two-electron trajectories is followed in 3d through a ten-cycle (25 fs) 780 nm laser pulse. We examine double-ionization yield for various intensities, finding the familiar knee structure. We consider the momentum spread of outcoming electrons in directions both parallel and perpendicular to the direction of laser polarization, and find results that are consistent with experiment. We examine individual trajectories and recollision processes that lead to double ionization, considering the best phases of the laser cycle for recollision events and looking at the possible time delay between recollision and emergence. We consider also the number of recollision events, and find that multiple recollisions are common in the classical ensemble. We investigate which collisional processes lead to various final electron momenta. We conclude with comments regarding the ability of classical mechanics to describe non-sequential double ionization, and a quick summary of similarities and differences between 1d and 3d classical double ionization using energy-trajectory comparisons. Refs. 3 (author)

  10. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  11. Kinetic Modeling of Synthetic Wastewater Treatment by the Moving-bed Sequential Continuous-inflow Reactor (MSCR

    Directory of Open Access Journals (Sweden)

    Mohammadreza Khani

    2016-11-01

    Full Text Available It was the objective of the present study to conduct a kinetic modeling of a Moving-bed Sequential Continuous-inflow Reactor (MSCR and to develop its best prediction model. For this purpose, a MSCR consisting of an aerobic-anoxic pilot 50 l in volume and an anaerobic pilot of 20 l were prepared. The MSCR was fed a variety of organic loads and operated at different hydraulic retention times (HRT using synthetic wastewater at input COD concentrations of 300 to 1000 mg/L with HRTs of 2 to 5 h. Based on the results and the best system operation conditions, the highest COD removal (98.6% was obtained at COD=500 mg/L. The three well-known first order, second order, and Stover-Kincannon models were utilized for the kinetic modeling of the reactor. Based on the kinetic analysis of organic removal, the Stover-Kincannon model was chosen for the kinetic modeling of the moving bed biofilm. Given its advantageous properties in the statisfactory prediction of organic removal at different organic loads, this model is recommended for the design and operation of MSCR systems.

  12. The Complexity of Folding Self-Folding Origami

    Directory of Open Access Journals (Sweden)

    Menachem Stern

    2017-12-01

    Full Text Available Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of “distractor” folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal’s paradox and other NP-hard satisfiability (SAT problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out (“folding islands”. Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  13. The Complexity of Folding Self-Folding Origami

    Science.gov (United States)

    Stern, Menachem; Pinson, Matthew B.; Murugan, Arvind

    2017-10-01

    Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of "distractor" folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out ("folding islands"). Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  14. Reflex vocal fold adduction in the porcine model: the effects of stimuli delivered to various sensory nerves.

    Science.gov (United States)

    Woo, Jeong-Soo; Hundal, Jagdeep S; Sasaki, Clarence T; Abdelmessih, Mikhail W; Kelleher, Stephen P

    2008-10-01

    The aim of this study was to identify a panel of sensory nerves capable of eliciting an evoked glottic closure reflex (GCR) and to quantify the glottic closing force (GCF) of these responses in a porcine model. In 5 pigs, the internal branch of the superior laryngeal nerve (iSLN) and the trigeminal, pharyngeal plexus, glossopharyngeal, radial, and intercostal nerves were surgically isolated and electrically stimulated. During stimulation of each nerve, the GCR was detected by laryngeal electromyography and the GCF was measured with a pressure transducer. The only nerve that elicited the GCR in the 5 pigs was the iSLN. The average GCF was 288.9 mm Hg. This study demonstrates that the only afferent nerve that elicits the GCR in pigs is the iSLN, and that it should remain the focus of research for the rehabilitation of patients with absent or defective reflex vocal fold adduction.

  15. Adaptive decision making in a dynamic environment: a test of a sequential sampling model of relative judgment.

    Science.gov (United States)

    Vuckovic, Anita; Kwantes, Peter J; Neal, Andrew

    2013-09-01

    Research has identified a wide range of factors that influence performance in relative judgment tasks. However, the findings from this research have been inconsistent. Studies have varied with respect to the identification of causal variables and the perceptual and decision-making mechanisms underlying performance. Drawing on the ecological rationality approach, we present a theory of the judgment and decision-making processes involved in a relative judgment task that explains how people judge a stimulus and adapt their decision process to accommodate their own uncertainty associated with those judgments. Undergraduate participants performed a simulated air traffic control conflict detection task. Across two experiments, we systematically manipulated variables known to affect performance. In the first experiment, we manipulated the relative distances of aircraft to a common destination while holding aircraft speeds constant. In a follow-up experiment, we introduced a direct manipulation of relative speed. We then fit a sequential sampling model to the data, and used the best fitting parameters to infer the decision-making processes responsible for performance. Findings were consistent with the theory that people adapt to their own uncertainty by adjusting their criterion and the amount of time they take to collect evidence in order to make a more accurate decision. From a practical perspective, the paper demonstrates that one can use a sequential sampling model to understand performance in a dynamic environment, allowing one to make sense of and interpret complex patterns of empirical findings that would otherwise be difficult to interpret using standard statistical analyses. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  16. Sequential and joint hydrogeophysical inversion using a field-scale groundwater model with ERT and TDEM data

    Directory of Open Access Journals (Sweden)

    D. Herckenrath

    2013-10-01

    Full Text Available Increasingly, ground-based and airborne geophysical data sets are used to inform groundwater models. Recent research focuses on establishing coupling relationships between geophysical and groundwater parameters. To fully exploit such information, this paper presents and compares different hydrogeophysical inversion approaches to inform a field-scale groundwater model with time domain electromagnetic (TDEM and electrical resistivity tomography (ERT data. In a sequential hydrogeophysical inversion (SHI a groundwater model is calibrated with geophysical data by coupling groundwater model parameters with the inverted geophysical models. We subsequently compare the SHI with a joint hydrogeophysical inversion (JHI. In the JHI, a geophysical model is simultaneously inverted with a groundwater model by coupling the groundwater and geophysical parameters to explicitly account for an established petrophysical relationship and its accuracy. Simulations for a synthetic groundwater model and TDEM data showed improved estimates for groundwater model parameters that were coupled to relatively well-resolved geophysical parameters when employing a high-quality petrophysical relationship. Compared to a SHI these improvements were insignificant and geophysical parameter estimates became slightly worse. When employing a low-quality petrophysical relationship, groundwater model parameters improved less for both the SHI and JHI, where the SHI performed relatively better. When comparing a SHI and JHI for a real-world groundwater model and ERT data, differences in parameter estimates were small. For both cases investigated in this paper, the SHI seems favorable, taking into account parameter error, data fit and the complexity of implementing a JHI in combination with its larger computational burden.

  17. A Summary of Coupled, Uncoupled, and Hybrid Tectonic Models for the Yakima Fold Belt--Topical Report

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Michele A.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize the range of opinions and supporting information expressed by the expert community regarding whether a coupled or uncoupled model, or a combination of both, best represents structures in the Yakima Fold Belt. This issue was assessed to have a high level of contention with up to moderate potential for impact on the hazard estimate. This report defines the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some possible approaches for reducing uncertainties regarding this issue.

  18. Modelling "reality" in tectonics: Simulation of the mechanical evolution of the Jura Mountains-Molasse Basin system, and routes to forward-inverse modelling of fold thrust belts.

    Science.gov (United States)

    Hindle, David; Kley, Jonas

    2016-04-01

    The ultimate validation of any numerical model of any geological process comes when it can accurately forward model a case study from the geological record. However, as the example of the Jura-Molasse fold thrust belt demonstrates, geological information on even the most basic aspects of the present day state of such systems is highly incomplete and usually known only with large uncertainties. Fold thrust-belts are studied and understood by geologists in an iterative process of constructing their subsurface geometries and structures (folds, faults, bedding etc) based on limited subsurface information from boreholes, tunnels or seismic data where available, and surface information on outcrops of different layers and their dips. This data is usually processed through geometric models which involve conservation of line length of different beds over the length of an entire cross section. Constructing such sections is the art of cross section balancing. A balanced cross section can be easily restored to its pre-deformation state, assuming (usually) originally horizontal bedding to remove the effects of folding and faulting. Such a pre-deformation state can then form an initial condition for a forward mechanical model of the section. A mechanical model introduces new parameters into the system such as rock elasticity, cohesion, and frictional properties. However, a forward mechanical model can also potentially show the continuous evolution of a fold thrust belt, including dynamic quantities like stress. Moreover, a forward mechanical model, if correct in most aspects, should match in its final state, the present day geological cross section it is simulating. However, when attempting to achieve a match between geometric and mechanical models, it becomes clear that many more aspects of the geodynamic history of a fold thrust belt have to be taken into account. Erosion of the uppermost layers of an evolving thrust belt is the most obvious one of these. This can potentially

  19. Sequential change in T2* values of cartilage, meniscus, and subchondral bone marrow in a rat model of knee osteoarthritis.

    Directory of Open Access Journals (Sweden)

    Ping-Huei Tsai

    Full Text Available BACKGROUND: There is an emerging interest in using magnetic resonance imaging (MRI T2* measurement for the evaluation of degenerative cartilage in osteoarthritis (OA. However, relatively few studies have addressed OA-related changes in adjacent knee structures. This study used MRI T2* measurement to investigate sequential changes in knee cartilage, meniscus, and subchondral bone marrow in a rat OA model induced by anterior cruciate ligament transection (ACLX. MATERIALS AND METHODS: Eighteen male Sprague Dawley rats were randomly separated into three groups (n = 6 each group. Group 1 was the normal control group. Groups 2 and 3 received ACLX and sham-ACLX, respectively, of the right knee. T2* values were measured in the knee cartilage, the meniscus, and femoral subchondral bone marrow of all rats at 0, 4, 13, and 18 weeks after surgery. RESULTS: Cartilage T2* values were significantly higher at 4, 13, and 18 weeks postoperatively in rats of the ACLX group than in rats of the control and sham groups (p<0.001. In the ACLX group (compared to the sham and control groups, T2* values increased significantly first in the posterior horn of the medial meniscus at 4 weeks (p = 0.001, then in the anterior horn of the medial meniscus at 13 weeks (p<0.001, and began to increase significantly in the femoral subchondral bone marrow at 13 weeks (p = 0.043. CONCLUSION: Quantitative MR T2* measurements of OA-related tissues are feasible. Sequential change in T2* over time in cartilage, meniscus, and subchondral bone marrow were documented. This information could be potentially useful for in vivo monitoring of disease progression.

  20. Effects of model complexity and priors on estimation using sequential importance sampling/resampling for species conservation

    Science.gov (United States)

    Dunham, Kylee; Grand, James B.

    2016-01-01

    We examined the effects of complexity and priors on the accuracy of models used to estimate ecological and observational processes, and to make predictions regarding population size and structure. State-space models are useful for estimating complex, unobservable population processes and making predictions about future populations based on limited data. To better understand the utility of state space models in evaluating population dynamics, we used them in a Bayesian framework and compared the accuracy of models with differing complexity, with and without informative priors using sequential importance sampling/resampling (SISR). Count data were simulated for 25 years using known parameters and observation process for each model. We used kernel smoothing to reduce the effect of particle depletion, which is common when estimating both states and parameters with SISR. Models using informative priors estimated parameter values and population size with greater accuracy than their non-informative counterparts. While the estimates of population size and trend did not suffer greatly in models using non-informative priors, the algorithm was unable to accurately estimate demographic parameters. This model framework provides reasonable estimates of population size when little to no information is available; however, when information on some vital rates is available, SISR can be used to obtain more precise estimates of population size and process. Incorporating model complexity such as that required by structured populations with stage-specific vital rates affects precision and accuracy when estimating latent population variables and predicting population dynamics. These results are important to consider when designing monitoring programs and conservation efforts requiring management of specific population segments.

  1. Sequential optimization of a terrestrial biosphere model constrained by multiple satellite based products

    Science.gov (United States)

    Ichii, K.; Kondo, M.; Wang, W.; Hashimoto, H.; Nemani, R. R.

    2012-12-01

    Various satellite-based spatial products such as evapotranspiration (ET) and gross primary productivity (GPP) are now produced by integration of ground and satellite observations. Effective use of these multiple satellite-based products in terrestrial biosphere models is an important step toward better understanding of terrestrial carbon and water cycles. However, due to the complexity of terrestrial biosphere models with large number of model parameters, the application of these spatial data sets in terrestrial biosphere models is difficult. In this study, we established an effective but simple framework to refine a terrestrial biosphere model, Biome-BGC, using multiple satellite-based products as constraints. We tested the framework in the monsoon Asia region covered by AsiaFlux observations. The framework is based on the hierarchical analysis (Wang et al. 2009) with model parameter optimization constrained by satellite-based spatial data. The Biome-BGC model is separated into several tiers to minimize the freedom of model parameter selections and maximize the independency from the whole model. For example, the snow sub-model is first optimized using MODIS snow cover product, followed by soil water sub-model optimized by satellite-based ET (estimated by an empirical upscaling method; Support Vector Regression (SVR) method; Yang et al. 2007), photosynthesis model optimized by satellite-based GPP (based on SVR method), and respiration and residual carbon cycle models optimized by biomass data. As a result of initial assessment, we found that most of default sub-models (e.g. snow, water cycle and carbon cycle) showed large deviations from remote sensing observations. However, these biases were removed by applying the proposed framework. For example, gross primary productivities were initially underestimated in boreal and temperate forest and overestimated in tropical forests. However, the parameter optimization scheme successfully reduced these biases. Our analysis

  2. Modeling of Activated Sludge Process Using Sequential Adaptive Neuro-fuzzy Inference System

    Directory of Open Access Journals (Sweden)

    Mahsa Vajedi

    2014-10-01

    Full Text Available In this study, an adaptive neuro-fuzzy inference system (ANFIS has been applied to model activated sludge wastewater treatment process of Mobin petrochemical company. The correlation coefficients between the input variables and the output variable were calculated to determine the input with the highest influence on the output (the quality of the outlet flow in order to compare three neuro-fuzzy structures with different number of parameters. The predictions of the neuro-fuzzy models were compared with those of multilayer artificial neural network models with similar structure. The comparison indicated that both methods resulted in flexible, robust and effective models for the activated sludge system. Moreover, the root mean square of the error for neuro-fuzzy and neural network models were 5.14 and 6.59, respectively, which means the former is the superior method.

  3. Topology optimization of induction heating model using sequential linear programming based on move limit with adaptive relaxation

    Science.gov (United States)

    Masuda, Hiroshi; Kanda, Yutaro; Okamoto, Yoshifumi; Hirono, Kazuki; Hoshino, Reona; Wakao, Shinji; Tsuburaya, Tomonori

    2017-12-01

    It is very important to design electrical machineries with high efficiency from the point of view of saving energy. Therefore, topology optimization (TO) is occasionally used as a design method for improving the performance of electrical machinery under the reasonable constraints. Because TO can achieve a design with much higher degree of freedom in terms of structure, there is a possibility for deriving the novel structure which would be quite different from the conventional structure. In this paper, topology optimization using sequential linear programming using move limit based on adaptive relaxation is applied to two models. The magnetic shielding, in which there are many local minima, is firstly employed as firstly benchmarking for the performance evaluation among several mathematical programming methods. Secondly, induction heating model is defined in 2-D axisymmetric field. In this model, the magnetic energy stored in the magnetic body is maximized under the constraint on the volume of magnetic body. Furthermore, the influence of the location of the design domain on the solutions is investigated.

  4. The economic, environmental and public health impacts of new power plants: a sequential inter industry model integrated with GIS data

    Energy Technology Data Exchange (ETDEWEB)

    Avelino, Andre F.T.; Hewings, Geoffrey J.D.; Guilhoto, Joaquim J.M. [Universidade de Sao Paulo (FEA/USP), SE (Brazil). Fac. de Administracao e Contabilidade

    2010-07-01

    The electrical sector is responsible for a considerable amount of greenhouse gases emissions worldwide, but also the one in which modern society depends the most for maintenance of quality of life as well as the functioning of economic and social activities. Invariably, even CO2 emission-free power plants have some indirect environmental impacts due to the economic effects they produce during their life cycle (construction, O and M and decommissioning). Thus, sustainability issues should be always considered in energy planning, by evaluating the balance of positive/negative externalities on different areas of the country. This study aims to introduce a social-environmental economic model, based on a Regional Sequential Inter industry Model (SIM) integrated with geoprocessing data, in order to identify economic, pollution and public health impacts in state level for energy planning analysis. The model is based on the Impact Pathway Approach Methodology, using geoprocessing to locate social-environmental variables for dispersion and health evaluations. The final goal is to provide an auxiliary tool for policy makers to assess energy planning scenarios in Brazil. (author)

  5. Model Predictive Engine Air-Ratio Control Using Online Sequential Relevance Vector Machine

    Directory of Open Access Journals (Sweden)

    Hang-cheong Wong

    2012-01-01

    Full Text Available Engine power, brake-specific fuel consumption, and emissions relate closely to air ratio (i.e., lambda among all the engine variables. An accurate and adaptive model for lambda prediction is essential to effective lambda control for long term. This paper utilizes an emerging technique, relevance vector machine (RVM, to build a reliable time-dependent lambda model which can be continually updated whenever a sample is added to, or removed from, the estimated lambda model. The paper also presents a new model predictive control (MPC algorithm for air-ratio regulation based on RVM. This study shows that the accuracy, training, and updating time of the RVM model are superior to the latest modelling methods, such as diagonal recurrent neural network (DRNN and decremental least-squares support vector machine (DLSSVM. Moreover, the control algorithm has been implemented on a real car to test. Experimental results reveal that the control performance of the proposed relevance vector machine model predictive controller (RVMMPC is also superior to DRNNMPC, support vector machine-based MPC, and conventional proportional-integral (PI controller in production cars. Therefore, the proposed RVMMPC is a promising scheme to replace conventional PI controller for engine air-ratio control.

  6. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  7. An Efficient Constraint Boundary Sampling Method for Sequential RBDO Using Kriging Surrogate Model

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jihoon; Jang, Junyong; Kim, Shinyu; Lee, Tae Hee [Hanyang Univ., Seoul (Korea, Republic of); Cho, Sugil; Kim, Hyung Woo; Hong, Sup [Korea Research Institute of Ships and Ocean Engineering, Busan (Korea, Republic of)

    2016-06-15

    Reliability-based design optimization (RBDO) requires a high computational cost owing to its reliability analysis. A surrogate model is introduced to reduce the computational cost in RBDO. The accuracy of the reliability depends on the accuracy of the surrogate model of constraint boundaries in the surrogated-model-based RBDO. In earlier researches, constraint boundary sampling (CBS) was proposed to approximate accurately the boundaries of constraints by locating sample points on the boundaries of constraints. However, because CBS uses sample points on all constraint boundaries, it creates superfluous sample points. In this paper, efficient constraint boundary sampling (ECBS) is proposed to enhance the efficiency of CBS. ECBS uses the statistical information of a kriging surrogate model to locate sample points on or near the RBDO solution. The efficiency of ECBS is verified by mathematical examples.

  8. Assessing sequential data assimilation techniques for integrating GRACE data into a hydrological model

    KAUST Repository

    Khaki, M.; Hoteit, Ibrahim; Kuhn, M.; Awange, J.; Forootan, E.; van Dijk, A.; Schumacher, M.; Pattiaratchi, C.

    2017-01-01

    The time-variable terrestrial water storage (TWS) products from the Gravity Recovery And Climate Experiment (GRACE) have been increasingly used in recent years to improve the simulation of hydrological models by applying data assimilation techniques

  9. A discrete event modelling framework for simulation of long-term outcomes of sequential treatment strategies for ankylosing spondylitis.

    Science.gov (United States)

    Tran-Duy, An; Boonen, Annelies; van de Laar, Mart A F J; Franke, Angelinus C; Severens, Johan L

    2011-12-01

    To develop a modelling framework which can simulate long-term quality of life, societal costs and cost-effectiveness as affected by sequential drug treatment strategies for ankylosing spondylitis (AS). Discrete event simulation paradigm was selected for model development. Drug efficacy was modelled as changes in disease activity (Bath Ankylosing Spondylitis Disease Activity Index (BASDAI)) and functional status (Bath Ankylosing Spondylitis Functional Index (BASFI)), which were linked to costs and health utility using statistical models fitted based on an observational AS cohort. Published clinical data were used to estimate drug efficacy and time to events. Two strategies were compared: (1) five available non-steroidal anti-inflammatory drugs (strategy 1) and (2) same as strategy 1 plus two tumour necrosis factor α inhibitors (strategy 2). 13,000 patients were followed up individually until death. For probability sensitivity analysis, Monte Carlo simulations were performed with 1000 sets of parameters sampled from the appropriate probability distributions. The models successfully generated valid data on treatments, BASDAI, BASFI, utility, quality-adjusted life years (QALYs) and costs at time points with intervals of 1-3 months during the simulation length of 70 years. Incremental cost per QALY gained in strategy 2 compared with strategy 1 was €35,186. At a willingness-to-pay threshold of €80,000, it was 99.9% certain that strategy 2 was cost-effective. The modelling framework provides great flexibility to implement complex algorithms representing treatment selection, disease progression and changes in costs and utilities over time of patients with AS. Results obtained from the simulation are plausible.

  10. Effectiveness of maritime safety control in different navigation zones using a spatial sequential DEA model: Yangtze River case.

    Science.gov (United States)

    Wu, Bing; Wang, Yang; Zhang, Jinfen; Savan, Emanuel Emil; Yan, Xinping

    2015-08-01

    This paper aims to analyze the effectiveness of maritime safety control from the perspective of safety level along the Yangtze River with special considerations for navigational environments. The influencing variables of maritime safety are reviewed, including ship condition, maritime regulatory system, human reliability and navigational environment. Because the former three variables are generally assumed to be of the same level of safety, this paper focuses on studying the impact of navigational environments on the level of safety in different waterways. An improved data envelopment analysis (DEA) model is proposed by treating the navigational environment factors as inputs and ship accident data as outputs. Moreover, because the traditional DEA model cannot provide an overall ranking of different decision making units (DMUs), the spatial sequential frontiers and grey relational analysis are incorporated into the DEA model to facilitate a refined assessment. Based on the empirical study results, the proposed model is able to solve the problem of information missing in the prior models and evaluate the level of safety with a better accuracy. The results of the proposed DEA model are further compared with an evidential reasoning (ER) method, which has been widely used for level of safety evaluations. A sensitivity analysis is also conducted to better understand the relationship between the variation of navigational environments and level of safety. The sensitivity analysis shows that the level of safety varies in terms of traffic flow. It indicates that appropriate traffic control measures should be adopted for different waterways to improve their safety. This paper presents a practical method of conducting maritime level of safety assessments under dynamic navigational environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. A dynamic general disequilibrium model of a sequential monetary production economy

    International Nuclear Information System (INIS)

    Raberto, Marco; Teglio, Andrea; Cincotti, Silvano

    2006-01-01

    A discrete, deterministic, economic model, based on the framework of non-Walrasian or disequilibrium economics, is presented. The main feature of this approach is the presence of non-clearing markets, where not all demands and supplies are satisfied and some agents may be rationed. The model is characterized by three agents (i.e., a representative firm, a representative consumer, and a central bank), three commodities (i.e., goods, labour and money, each homogeneous) and three markets for their exchange. The imbalance between demand and supply in each market determines the dynamics of price, nominal wage and nominal interest rate. The central bank provides the money supply according to an operating target interest rate that is fixed accordingly to Taylor's rule. The model has been studied by means of computer simulations. Results pointed out the presence of business cycles that can be controlled by proper policies of the central bank

  12. Sequential Monte Carlo filter for state estimation of LiFePO4 batteries based on an online updated model

    Science.gov (United States)

    Li, Jiahao; Klee Barillas, Joaquin; Guenther, Clemens; Danzer, Michael A.

    2014-02-01

    Battery state monitoring is one of the key techniques in battery management systems e.g. in electric vehicles. An accurate estimation can help to improve the system performance and to prolong the battery remaining useful life. Main challenges for the state estimation for LiFePO4 batteries are the flat characteristic of open-circuit-voltage over battery state of charge (SOC) and the existence of hysteresis phenomena. Classical estimation approaches like Kalman filtering show limitations to handle nonlinear and non-Gaussian error distribution problems. In addition, uncertainties in the battery model parameters must be taken into account to describe the battery degradation. In this paper, a novel model-based method combining a Sequential Monte Carlo filter with adaptive control to determine the cell SOC and its electric impedance is presented. The applicability of this dual estimator is verified using measurement data acquired from a commercial LiFePO4 cell. Due to a better handling of the hysteresis problem, results show the benefits of the proposed method against the estimation with an Extended Kalman filter.

  13. Effect of anaerobic digestion on sequential pyrolysis kinetics of organic solid wastes using thermogravimetric analysis and distributed activation energy model.

    Science.gov (United States)

    Li, Xiaowei; Mei, Qingqing; Dai, Xiaohu; Ding, Guoji

    2017-03-01

    Thermogravimetric analysis, Gaussian-fit-peak model (GFPM), and distributed activation energy model (DAEM) were firstly used to explore the effect of anaerobic digestion on sequential pyrolysis kinetic of four organic solid wastes (OSW). Results showed that the OSW weight loss mainly occurred in the second pyrolysis stage relating to organic matter decomposition. Compared with raw substrate, the weight loss of corresponding digestate was lower in the range of 180-550°C, but was higher in 550-900°C. GFPM analysis revealed that organic components volatized at peak temperatures of 188-263, 373-401 and 420-462°C had a faster degradation rate than those at 274-327°C during anaerobic digestion. DAEM analysis showed that anaerobic digestion had discrepant effects on activation energy for four OSW pyrolysis, possibly because of their different organic composition. It requires further investigation for the special organic matter, i.e., protein-like and carbohydrate-like groups, to confirm the assumption. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Development and Sensitivity Analysis of a Fully Kinetic Model of Sequential Reductive Dechlorination in Groundwater

    DEFF Research Database (Denmark)

    Malaguerra, Flavio; Chambon, Julie Claire Claudia; Bjerg, Poul Løgstrup

    2011-01-01

    experiments of complete trichloroethene (TCE) degradation in natural sediments. Global sensitivity analysis was performed using the Morris method and Sobol sensitivity indices to identify the most influential model parameters. Results show that the sulfate concentration and fermentation kinetics are the most...

  15. A model of type 2 diabetes in the guinea pig using sequential diet-induced glucose intolerance and streptozotocin treatment

    Science.gov (United States)

    Ackart, David F.; Richardson, Michael A.; DiLisio, James E.; Pulford, Bruce; Basaraba, Randall J.

    2017-01-01

    ABSTRACT Type 2 diabetes is a leading cause of morbidity and mortality among noncommunicable diseases, and additional animal models that more closely replicate the pathogenesis of human type 2 diabetes are needed. The goal of this study was to develop a model of type 2 diabetes in guinea pigs, in which diet-induced glucose intolerance precedes β-cell cytotoxicity, two processes that are crucial to the development of human type 2 diabetes. Guinea pigs developed impaired glucose tolerance after 8 weeks of feeding on a high-fat, high-carbohydrate diet, as determined by oral glucose challenge. Diet-induced glucose intolerance was accompanied by β-cell hyperplasia, compensatory hyperinsulinemia, and dyslipidemia with hepatocellular steatosis. Streptozotocin (STZ) treatment alone was ineffective at inducing diabetic hyperglycemia in guinea pigs, which failed to develop sustained glucose intolerance or fasting hyperglycemia and returned to euglycemia within 21 days after treatment. However, when high-fat, high-carbohydrate diet-fed guinea pigs were treated with STZ, glucose intolerance and fasting hyperglycemia persisted beyond 21 days post-STZ treatment. Guinea pigs with diet-induced glucose intolerance subsequently treated with STZ demonstrated an insulin-secretory capacity consistent with insulin-independent diabetes. This insulin-independent state was confirmed by response to oral antihyperglycemic drugs, metformin and glipizide, which resolved glucose intolerance and extended survival compared with guinea pigs with uncontrolled diabetes. In this study, we have developed a model of sequential glucose intolerance and β-cell loss, through high-fat, high-carbohydrate diet and extensive optimization of STZ treatment in the guinea pig, which closely resembles human type 2 diabetes. This model will prove useful in the study of insulin-independent diabetes pathogenesis with or without comorbidities, where the guinea pig serves as a relevant model species. PMID:28093504

  16. A model of type 2 diabetes in the guinea pig using sequential diet-induced glucose intolerance and streptozotocin treatment.

    Science.gov (United States)

    Podell, Brendan K; Ackart, David F; Richardson, Michael A; DiLisio, James E; Pulford, Bruce; Basaraba, Randall J

    2017-02-01

    Type 2 diabetes is a leading cause of morbidity and mortality among noncommunicable diseases, and additional animal models that more closely replicate the pathogenesis of human type 2 diabetes are needed. The goal of this study was to develop a model of type 2 diabetes in guinea pigs, in which diet-induced glucose intolerance precedes β-cell cytotoxicity, two processes that are crucial to the development of human type 2 diabetes. Guinea pigs developed impaired glucose tolerance after 8 weeks of feeding on a high-fat, high-carbohydrate diet, as determined by oral glucose challenge. Diet-induced glucose intolerance was accompanied by β-cell hyperplasia, compensatory hyperinsulinemia, and dyslipidemia with hepatocellular steatosis. Streptozotocin (STZ) treatment alone was ineffective at inducing diabetic hyperglycemia in guinea pigs, which failed to develop sustained glucose intolerance or fasting hyperglycemia and returned to euglycemia within 21 days after treatment. However, when high-fat, high-carbohydrate diet-fed guinea pigs were treated with STZ, glucose intolerance and fasting hyperglycemia persisted beyond 21 days post-STZ treatment. Guinea pigs with diet-induced glucose intolerance subsequently treated with STZ demonstrated an insulin-secretory capacity consistent with insulin-independent diabetes. This insulin-independent state was confirmed by response to oral antihyperglycemic drugs, metformin and glipizide, which resolved glucose intolerance and extended survival compared with guinea pigs with uncontrolled diabetes. In this study, we have developed a model of sequential glucose intolerance and β-cell loss, through high-fat, high-carbohydrate diet and extensive optimization of STZ treatment in the guinea pig, which closely resembles human type 2 diabetes. This model will prove useful in the study of insulin-independent diabetes pathogenesis with or without comorbidities, where the guinea pig serves as a relevant model species. © 2017. Published by

  17. Parameter optimisation for a better representation of drought by LSMs: inverse modelling vs. sequential data assimilation

    Science.gov (United States)

    Dewaele, Hélène; Munier, Simon; Albergel, Clément; Planque, Carole; Laanaia, Nabil; Carrer, Dominique; Calvet, Jean-Christophe

    2017-09-01

    Soil maximum available water content (MaxAWC) is a key parameter in land surface models (LSMs). However, being difficult to measure, this parameter is usually uncertain. This study assesses the feasibility of using a 15-year (1999-2013) time series of satellite-derived low-resolution observations of leaf area index (LAI) to estimate MaxAWC for rainfed croplands over France. LAI interannual variability is simulated using the CO2-responsive version of the Interactions between Soil, Biosphere and Atmosphere (ISBA) LSM for various values of MaxAWC. Optimal value is then selected by using (1) a simple inverse modelling technique, comparing simulated and observed LAI and (2) a more complex method consisting in integrating observed LAI in ISBA through a land data assimilation system (LDAS) and minimising LAI analysis increments. The evaluation of the MaxAWC estimates from both methods is done using simulated annual maximum above-ground biomass (Bag) and straw cereal grain yield (GY) values from the Agreste French agricultural statistics portal, for 45 administrative units presenting a high proportion of straw cereals. Significant correlations (p value Bag and GY are found for up to 36 and 53 % of the administrative units for the inverse modelling and LDAS tuning methods, respectively. It is found that the LDAS tuning experiment gives more realistic values of MaxAWC and maximum Bag than the inverse modelling experiment. Using undisaggregated LAI observations leads to an underestimation of MaxAWC and maximum Bag in both experiments. Median annual maximum values of disaggregated LAI observations are found to correlate very well with MaxAWC.

  18. Vocal Fold Paralysis

    Science.gov (United States)

    ... here Home » Health Info » Voice, Speech, and Language Vocal Fold Paralysis On this page: What is vocal fold ... Where can I get additional information? What is vocal fold paralysis? Structures involved in speech and voice production ...

  19. Discrete gauge groups in F-theory models on genus-one fibered Calabi-Yau 4-folds without section

    International Nuclear Information System (INIS)

    Kimura, Yusuke

    2017-01-01

    We determine the discrete gauge symmetries that arise in F-theory compactifications on examples of genus-one fibered Calabi-Yau 4-folds without a section. We construct genus-one fibered Calabi-Yau 4-folds using Fano manifolds, cyclic 3-fold covers of Fano 4-folds, and Segre embeddings of products of projective spaces. Discrete ℤ 5 , ℤ 4 , ℤ 3 and ℤ 2 symmetries arise in these constructions. We introduce a general method to obtain multisections for several constructions of genus-one fibered Calabi-Yau manifolds. The pullbacks of hyperplane classes under certain projections represent multisections to these genus-one fibrations. We determine the degrees of these multisections by computing the intersection numbers with fiber classes. As a result, we deduce the discrete gauge symmetries that arise in F-theory compactifications. This method applies to various Calabi-Yau genus-one fibrations.

  20. A Data-Driven Method for Selecting Optimal Models Based on Graphical Visualisation of Differences in Sequentially Fitted ROC Model Parameters

    Directory of Open Access Journals (Sweden)

    K S Mwitondi

    2013-05-01

    Full Text Available Differences in modelling techniques and model performance assessments typically impinge on the quality of knowledge extraction from data. We propose an algorithm for determining optimal patterns in data by separately training and testing three decision tree models in the Pima Indians Diabetes and the Bupa Liver Disorders datasets. Model performance is assessed using ROC curves and the Youden Index. Moving differences between sequential fitted parameters are then extracted, and their respective probability density estimations are used to track their variability using an iterative graphical data visualisation technique developed for this purpose. Our results show that the proposed strategy separates the groups more robustly than the plain ROC/Youden approach, eliminates obscurity, and minimizes over-fitting. Further, the algorithm can easily be understood by non-specialists and demonstrates multi-disciplinary compliance.

  1. Sequential modelling of the effects of mass drug treatments on anopheline-mediated lymphatic filariasis infection in Papua New Guinea.

    Directory of Open Access Journals (Sweden)

    Brajendra K Singh

    Full Text Available Lymphatic filariasis (LF has been targeted by the WHO for global eradication leading to the implementation of large scale intervention programs based on annual mass drug administrations (MDA worldwide. Recent work has indicated that locality-specific bio-ecological complexities affecting parasite transmission may complicate the prediction of LF extinction endpoints, casting uncertainty on the achievement of this initiative. One source of difficulty is the limited quantity and quality of data used to parameterize models of parasite transmission, implying the important need to update initially-derived parameter values. Sequential analysis of longitudinal data following annual MDAs will also be important to gaining new understanding of the persistence dynamics of LF. Here, we apply a Bayesian statistical-dynamical modelling framework that enables assimilation of information in human infection data recorded from communities in Papua New Guinea that underwent annual MDAs, into our previously developed model of parasite transmission, in order to examine these questions in LF ecology and control.Biological parameters underlying transmission obtained by fitting the model to longitudinal data remained stable throughout the study period. This enabled us to reliably reconstruct the observed baseline data in each community. Endpoint estimates also showed little variation. However, the updating procedure showed a shift towards higher and less variable values for worm kill but not for any other drug-related parameters. An intriguing finding is that the stability in key biological parameters could be disrupted by a significant reduction in the vector biting rate prevailing in a locality.Temporal invariance of biological parameters in the face of intervention perturbations indicates a robust adaptation of LF transmission to local ecological conditions. The results imply that understanding the mechanisms that underlie locally adapted transmission dynamics will

  2. Predictive modelling of survival and length of stay in critically ill patients using sequential organ failure scores.

    Science.gov (United States)

    Houthooft, Rein; Ruyssinck, Joeri; van der Herten, Joachim; Stijven, Sean; Couckuyt, Ivo; Gadeyne, Bram; Ongenae, Femke; Colpaert, Kirsten; Decruyenaere, Johan; Dhaene, Tom; De Turck, Filip

    2015-03-01

    The length of stay of critically ill patients in the intensive care unit (ICU) is an indication of patient ICU resource usage and varies considerably. Planning of postoperative ICU admissions is important as ICUs often have no nonoccupied beds available. Estimation of the ICU bed availability for the next coming days is entirely based on clinical judgement by intensivists and therefore too inaccurate. For this reason, predictive models have much potential for improving planning for ICU patient admission. Our goal is to develop and optimize models for patient survival and ICU length of stay (LOS) based on monitored ICU patient data. Furthermore, these models are compared on their use of sequential organ failure (SOFA) scores as well as underlying raw data as input features. Different machine learning techniques are trained, using a 14,480 patient dataset, both on SOFA scores as well as their underlying raw data values from the first five days after admission, in order to predict (i) the patient LOS, and (ii) the patient mortality. Furthermore, to help physicians in assessing the prediction credibility, a probabilistic model is tailored to the output of our best-performing model, assigning a belief to each patient status prediction. A two-by-two grid is built, using the classification outputs of the mortality and prolonged stay predictors to improve the patient LOS regression models. For predicting patient mortality and a prolonged stay, the best performing model is a support vector machine (SVM) with GA,D=65.9% (area under the curve (AUC) of 0.77) and GS,L=73.2% (AUC of 0.82). In terms of LOS regression, the best performing model is support vector regression, achieving a mean absolute error of 1.79 days and a median absolute error of 1.22 days for those patients surviving a nonprolonged stay. Using a classification grid based on the predicted patient mortality and prolonged stay, allows more accurate modeling of the patient LOS. The detailed models allow to support

  3. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Osmark, Peter; Neergaard, Thomas B.

    1999-01-01

    The acyl-coenzyme A-binding proteins (ACBPs) contain 26 highly conserved sequence positions. The majority of these have been mutated in the bovine protein, and their influence on the rate of two-state folding and unfolding has been measured. The results identify eight sequence positions, out of 24...... probed, that are critical for fast productive folding. The residues are all hydrophobic and located in the interface between the N- and C-terminal helices. The results suggest that one specific site dominated by conserved hydrophobic residues forms the structure of the productive rate-determining folding...... step and that a sequential framework model can describe the protein folding reaction....

  4. Effects of Combined Simultaneous and Sequential Endostar and Cisplatin Treatment in a Mice Model of Gastric Cancer Peritoneal Metastases

    Directory of Open Access Journals (Sweden)

    Lin Jia

    2017-01-01

    Full Text Available Objective. Aimed to study the effects of endostar and cisplatin using an in vivo imaging system (IVIS in a model of peritoneal metastasis of gastric cancer. Methods. NUGC-4 gastric cancer cells transfected with luciferase gene (NUGC-4-Luc were injected i.p. into nude mice. One week later, mice were randomly injected i.p.: group 1, cisplatin (d1–3 + endostar (d4–7; group 2, endostar (d1–4 + cisplatin (d5–7; group 3, endostar + cisplatin d1, 4, and 7; group 4, saline for two weeks. One week after the final administration, mice were sacrificed. Bioluminescent data, microvessel density (MVD, and lymphatic vessel density (LVD were analyzed. Results. Among the four groups, there were no significant differences in the weights and in the number of cancer cell photons on days 1 and 8 (P>0.05. On day 15, the numbers in groups 3 and 1 were less than that in group 2 (P0.05 or in LVD number among the four groups (P>0.05. Conclusions. IVIS® was more useful than weight, volume of ascites, and number of peritoneal nodules. The simultaneous group was superior to sequential groups in killing cancer cells and inhibiting vascular endothelium. Cisplatin-endostar was superior to endostar-cisplatin in killing cancer cells, while the latter in inhibiting peritoneal vascular endothelium.

  5. Effects of Combined Simultaneous and Sequential Endostar and Cisplatin Treatment in a Mice Model of Gastric Cancer Peritoneal Metastases.

    Science.gov (United States)

    Jia, Lin; Ren, Shuguang; Li, Tao; Wu, Jianing; Zhou, Xinliang; Zhang, Yan; Wu, Jianhua; Liu, Wei

    2017-01-01

    Objective . Aimed to study the effects of endostar and cisplatin using an in vivo imaging system (IVIS) in a model of peritoneal metastasis of gastric cancer. Methods . NUGC-4 gastric cancer cells transfected with luciferase gene (NUGC-4-Luc) were injected i.p. into nude mice. One week later, mice were randomly injected i.p.: group 1, cisplatin (d1-3) + endostar (d4-7); group 2, endostar (d1-4) + cisplatin (d5-7); group 3, endostar + cisplatin d1, 4, and 7; group 4, saline for two weeks. One week after the final administration, mice were sacrificed. Bioluminescent data, microvessel density (MVD), and lymphatic vessel density (LVD) were analyzed. Results . Among the four groups, there were no significant differences in the weights and in the number of cancer cell photons on days 1 and 8 ( P > 0.05). On day 15, the numbers in groups 3 and 1 were less than that in group 2 ( P 0.05) or in LVD number among the four groups ( P > 0.05). Conclusions . IVIS® was more useful than weight, volume of ascites, and number of peritoneal nodules. The simultaneous group was superior to sequential groups in killing cancer cells and inhibiting vascular endothelium. Cisplatin-endostar was superior to endostar-cisplatin in killing cancer cells, while the latter in inhibiting peritoneal vascular endothelium.

  6. Flips for 3-folds and 4-folds

    CERN Document Server

    Corti, Alessio

    2007-01-01

    This edited collection of chapters, authored by leading experts, provides a complete and essentially self-contained construction of 3-fold and 4-fold klt flips. A large part of the text is a digest of Shokurov's work in the field and a concise, complete and pedagogical proof of the existence of 3-fold flips is presented. The text includes a ten page glossary and is accessible to students and researchers in algebraic geometry.

  7. Dual Binding Site and Selective Acetylcholinesterase Inhibitors Derived from Integrated Pharmacophore Models and Sequential Virtual Screening

    Directory of Open Access Journals (Sweden)

    Shikhar Gupta

    2014-01-01

    Full Text Available In this study, we have employed in silico methodology combining double pharmacophore based screening, molecular docking, and ADME/T filtering to identify dual binding site acetylcholinesterase inhibitors that can preferentially inhibit acetylcholinesterase and simultaneously inhibit the butyrylcholinesterase also but in the lesser extent than acetylcholinesterase. 3D-pharmacophore models of AChE and BuChE enzyme inhibitors have been developed from xanthostigmine derivatives through HypoGen and validated using test set, Fischer’s randomization technique. The best acetylcholinesterase and butyrylcholinesterase inhibitors pharmacophore hypotheses Hypo1_A and Hypo1_B, with high correlation coefficient of 0.96 and 0.94, respectively, were used as 3D query for screening the Zinc database. The screened hits were then subjected to the ADME/T and molecular docking study to prioritise the compounds. Finally, 18 compounds were identified as potential leads against AChE enzyme, showing good predicted activities and promising ADME/T properties.

  8. CHIRP-Like Signals: Estimation, Detection and Processing A Sequential Model-Based Approach

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J. V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-08-04

    Chirp signals have evolved primarily from radar/sonar signal processing applications specifically attempting to estimate the location of a target in surveillance/tracking volume. The chirp, which is essentially a sinusoidal signal whose phase changes instantaneously at each time sample, has an interesting property in that its correlation approximates an impulse function. It is well-known that a matched-filter detector in radar/sonar estimates the target range by cross-correlating a replicant of the transmitted chirp with the measurement data reflected from the target back to the radar/sonar receiver yielding a maximum peak corresponding to the echo time and therefore enabling the desired range estimate. In this application, we perform the same operation as a radar or sonar system, that is, we transmit a “chirp-like pulse” into the target medium and attempt to first detect its presence and second estimate its location or range. Our problem is complicated by the presence of disturbance signals from surrounding broadcast stations as well as extraneous sources of interference in our frequency bands and of course the ever present random noise from instrumentation. First, we discuss the chirp signal itself and illustrate its inherent properties and then develop a model-based processing scheme enabling both the detection and estimation of the signal from noisy measurement data.

  9. Vehicle speed detection based on gaussian mixture model using sequential of images

    Science.gov (United States)

    Setiyono, Budi; Ratna Sulistyaningrum, Dwi; Soetrisno; Fajriyah, Farah; Wahyu Wicaksono, Danang

    2017-09-01

    Intelligent Transportation System is one of the important components in the development of smart cities. Detection of vehicle speed on the highway is supporting the management of traffic engineering. The purpose of this study is to detect the speed of the moving vehicles using digital image processing. Our approach is as follows: The inputs are a sequence of frames, frame rate (fps) and ROI. The steps are following: First we separate foreground and background using Gaussian Mixture Model (GMM) in each frames. Then in each frame, we calculate the location of object and its centroid. Next we determine the speed by computing the movement of centroid in sequence of frames. In the calculation of speed, we only consider frames when the centroid is inside the predefined region of interest (ROI). Finally we transform the pixel displacement into a time unit of km/hour. Validation of the system is done by comparing the speed calculated manually and obtained by the system. The results of software testing can detect the speed of vehicles with the highest accuracy is 97.52% and the lowest accuracy is 77.41%. And the detection results of testing by using real video footage on the road is included with real speed of the vehicle.

  10. Seasonal climate variation and caribou availability: Modeling sequential movement using satellite-relocation data

    Science.gov (United States)

    Nicolson, Craig; Berman, Matthew; West, Colin Thor; Kofinas, Gary P.; Griffith, Brad; Russell, Don; Dugan, Darcy

    2013-01-01

    Livelihood systems that depend on mobile resources must constantly adapt to change. For people living in permanent settlements, environmental changes that affect the distribution of a migratory species may reduce the availability of a primary food source, with the potential to destabilize the regional social-ecological system. Food security for Arctic indigenous peoples harvesting barren ground caribou (Rangifer tarandus granti) depends on movement patterns of migratory herds. Quantitative assessments of physical, ecological, and social effects on caribou distribution have proven difficult because of the significant interannual variability in seasonal caribou movement patterns. We developed and evaluated a modeling approach for simulating the distribution of a migratory herd throughout its annual cycle over a multiyear period. Beginning with spatial and temporal scales developed in previous studies of the Porcupine Caribou Herd of Canada and Alaska, we used satellite collar locations to compute and analyze season-by-season probabilities of movement of animals between habitat zones under two alternative weather conditions for each season. We then built a set of transition matrices from these movement probabilities, and simulated the sequence of movements across the landscape as a Markov process driven by externally imposed seasonal weather states. Statistical tests showed that the predicted distributions of caribou were consistent with observed distributions, and significantly correlated with subsistence harvest levels for three user communities. Our approach could be applied to other caribou herds and could be adapted for simulating the distribution of other ungulates and species with similarly large interannual variability in the use of their range.

  11. Seasonal Climate Variation and Caribou Availability: Modeling Sequential Movement Using Satellite-Relocation Data

    Directory of Open Access Journals (Sweden)

    Craig Nicolson

    2013-06-01

    Full Text Available Livelihood systems that depend on mobile resources must constantly adapt to change. For people living in permanent settlements, environmental changes that affect the distribution of a migratory species may reduce the availability of a primary food source, with the potential to destabilize the regional social-ecological system. Food security for Arctic indigenous peoples harvesting barren ground caribou (Rangifer tarandus granti depends on movement patterns of migratory herds. Quantitative assessments of physical, ecological, and social effects on caribou distribution have proven difficult because of the significant interannual variability in seasonal caribou movement patterns. We developed and evaluated a modeling approach for simulating the distribution of a migratory herd throughout its annual cycle over a multiyear period. Beginning with spatial and temporal scales developed in previous studies of the Porcupine Caribou Herd of Canada and Alaska, we used satellite collar locations to compute and analyze season-by-season probabilities of movement of animals between habitat zones under two alternative weather conditions for each season. We then built a set of transition matrices from these movement probabilities, and simulated the sequence of movements across the landscape as a Markov process driven by externally imposed seasonal weather states. Statistical tests showed that the predicted distributions of caribou were consistent with observed distributions, and significantly correlated with subsistence harvest levels for three user communities. Our approach could be applied to other caribou herds and could be adapted for simulating the distribution of other ungulates and species with similarly large interannual variability in the use of their range.

  12. Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism.

    Directory of Open Access Journals (Sweden)

    Matteo Pappalardo

    Full Text Available The human histamine H4 receptor (hH4R, a member of the G-protein coupled receptors (GPCR family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH4R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH4R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE and Iterative Stochastic Elimination (ISE approach, were used to index chemicals for their hH4R bioactivity. An application of the prediction model on external test set composed of more than 160 hH4R antagonists picked from the chEMBL database gave enrichment factor of 16.4. A virtual high throughput screening on ZINC database was carried out, picking ∼ 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH4R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH4R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and

  13. Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism.

    Science.gov (United States)

    Pappalardo, Matteo; Shachaf, Nir; Basile, Livia; Milardi, Danilo; Zeidan, Mouhammed; Raiyn, Jamal; Guccione, Salvatore; Rayan, Anwar

    2014-01-01

    The human histamine H4 receptor (hH4R), a member of the G-protein coupled receptors (GPCR) family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH4R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH4R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE) and Iterative Stochastic Elimination (ISE) approach, were used to index chemicals for their hH4R bioactivity. An application of the prediction model on external test set composed of more than 160 hH4R antagonists picked from the chEMBL database gave enrichment factor of 16.4. A virtual high throughput screening on ZINC database was carried out, picking ∼ 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH4R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH4R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and increase the

  14. A sequential vesicle pool model with a single release sensor and a ca(2+)-dependent priming catalyst effectively explains ca(2+)-dependent properties of neurosecretion

    DEFF Research Database (Denmark)

    Walter, Alexander M; da Silva Pinheiro, Paulo César; Verhage, Matthijs

    2013-01-01

    identified. We here propose a Sequential Pool Model (SPM), assuming a novel Ca(2+)-dependent action: a Ca(2+)-dependent catalyst that accelerates both forward and reverse priming reactions. While both models account for fast fusion from the Readily-Releasable Pool (RRP) under control of synaptotagmin-1...... the simultaneous changes in release rate and amplitude seen when mutating the SNARE-complex. Finally, it can account for the loss of fast- and the persistence of slow release in the synaptotagmin-1 knockout by assuming that the RRP is depleted, leading to slow and Ca(2+)-dependent fusion from the NRP. We conclude...... that the elusive 'alternative Ca(2+) sensor' for slow release might be the upstream priming catalyst, and that a sequential model effectively explains Ca(2+)-dependent properties of secretion without assuming parallel pools or sensors....

  15. Physics of protein folding

    Science.gov (United States)

    Finkelstein, A. V.; Galzitskaya, O. V.

    2004-04-01

    Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

  16. Observation of a tropopause fold by MARA VHF wind-profiler radar and ozonesonde at Wasa, Antarctica: comparison with ECMWF analysis and a WRF model simulation

    Directory of Open Access Journals (Sweden)

    M. Mihalikova

    2012-09-01

    Full Text Available Tropopause folds are one of the mechanisms of stratosphere–troposphere exchange, which can bring ozone rich stratospheric air to low altitudes in the extra-tropical regions. They have been widely studied at northern mid- or high latitudes, but so far almost no studies have been made at mid- or high southern latitudes. The Moveable Atmospheric Radar for Antarctica (MARA, a 54.5 MHz wind-profiler radar, has operated at the Swedish summer station Wasa, Antarctica (73° S, 13.5° W during austral summer seasons from 2007 to 2011 and has observed on several occasions signatures similar to those caused by tropopause folds at comparable Arctic latitudes. Here a case study is presented of one of these events when an ozonesonde successfully sampled the fold. Analysis from European Center for Medium Range Weather Forecasting (ECMWF is used to study the circumstances surrounding the event, and as boundary conditions for a mesoscale simulation using the Weather Research and Forecasting (WRF model. The fold is well resolved by the WRF simulation, and occurs on the poleward side of the polar jet stream. However, MARA resolves fine-scale layering associated with the fold better than the WRF simulation.

  17. Sequential Management of Commercial Rosewood (Aniba rosaeodora Ducke Plantations in Central Amazonia: Seeking Sustainable Models for Essential Oil Production

    Directory of Open Access Journals (Sweden)

    Pedro Medrado Krainovic

    2017-11-01

    Full Text Available Rosewood (Aniba rosaeodora Ducke is an endangered tree that produces essential oil of high commercial value. However, technical-scientific knowledge about cultivation is scarce and studies are needed to examine the management viability. The current study evaluated rosewood aboveground biomass management, measuring the export of nutrients resulting from harvesting and testing sustainable management models. The crown of 36 rosewood trees were pruned and 108 trees cut at 50 cm above the soil in two regions in Central Amazonia. Post-harvest performance of sprouting shoots was evaluated and after, sprouting shoots were pruned so that the development of two, three and all shoots was permitted. Nutrient stock estimation was calculated as the product of mass and nutrient concentration, which allowed nutritional replacement to be estimated. The pruning facilitates regrowth by 40.11% of the initial mass while by cut regrow 1.45%. Chemical attributes of regrowth biomass differed significantly prior to management and regrowth had a significant correlation with the reserves in root tissues and with the pre -management status of the individual tree. Driving sprouts resulted in significantly larger growth increments and may provide a form of management that can viably be adopted. Biomass sequential management resulted in high nutrient exports and the amount of fertilizer needed for replenishment depended on the intensity and frequency of cropping. Compared with the cut of the tree, pruning the canopy reduces fertilizers that are required to replenish amount by 44%, decreasing to 26.37% in the second rotation. The generated knowledge contributes to this silvicultural practice as it becomes ecologically and economically viable.

  18. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling

    NARCIS (Netherlands)

    Tark-Dame, M.; Jerabek, H.; Manders, E.M.M.; Heermann, D.W.; van Driel, R.

    2014-01-01

    Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control

  19. Influence of pre-existing basement faults on the structural evolution of the Zagros Simply Folded belt: 3D numerical modelling

    Science.gov (United States)

    Ruh, Jonas B.; Gerya, Taras

    2015-04-01

    The Simply Folded Belt of the Zagros orogen is characterized by elongated fold trains symptomatically defining the geomorphology along this mountain range. The Zagros orogen results from the collision of the Arabian and the Eurasian plates. The Simply Folded Belt is located southwest of the Zagros suture zone. An up to 2 km thick salt horizon below the sedimentary sequence enables mechanical and structural detachment from the underlying Arabian basement. Nevertheless, deformation within the basement influences the structural evolution of the Simply Folded Belt. It has been shown that thrusts in form of reactivated normal faults can trigger out-of-sequence deformation within the sedimentary stratigraphy. Furthermore, deeply rooted strike-slip faults, such as the Kazerun faults between the Fars zone in the southeast and the Dezful embayment and the Izeh zone, are largely dispersing into the overlying stratigraphy, strongly influencing the tectonic evolution and mechanical behaviour. The aim of this study is to reveal the influence of basement thrusts and strike-slip faults on the structural evolution of the Simply Folded Belt depending on the occurrence of intercrustal weak horizons (Hormuz salt) and the rheology and thermal structure of the basement. Therefore, we present high-resolution 3D thermo-mechnical models with pre-existing, inversively reactivated normal faults or strike-slip faults within the basement. Numerical models are based on finite difference, marker-in-cell technique with (power-law) visco-plastic rheology accounting for brittle deformation. Preliminary results show that deep tectonic structures present in the basement may have crucial effects on the morphology and evolution of a fold-and-thrust belt above a major detachment horizon.

  20. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  1. Using a Simple Binomial Model to Assess Improvement in Predictive Capability: Sequential Bayesian Inference, Hypothesis Testing, and Power Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sigeti, David E. [Los Alamos National Laboratory; Pelak, Robert A. [Los Alamos National Laboratory

    2012-09-11

    We present a Bayesian statistical methodology for identifying improvement in predictive simulations, including an analysis of the number of (presumably expensive) simulations that will need to be made in order to establish with a given level of confidence that an improvement has been observed. Our analysis assumes the ability to predict (or postdict) the same experiments with legacy and new simulation codes and uses a simple binomial model for the probability, {theta}, that, in an experiment chosen at random, the new code will provide a better prediction than the old. This model makes it possible to do statistical analysis with an absolute minimum of assumptions about the statistics of the quantities involved, at the price of discarding some potentially important information in the data. In particular, the analysis depends only on whether or not the new code predicts better than the old in any given experiment, and not on the magnitude of the improvement. We show how the posterior distribution for {theta} may be used, in a kind of Bayesian hypothesis testing, both to decide if an improvement has been observed and to quantify our confidence in that decision. We quantify the predictive probability that should be assigned, prior to taking any data, to the possibility of achieving a given level of confidence, as a function of sample size. We show how this predictive probability depends on the true value of {theta} and, in particular, how there will always be a region around {theta} = 1/2 where it is highly improbable that we will be able to identify an improvement in predictive capability, although the width of this region will shrink to zero as the sample size goes to infinity. We show how the posterior standard deviation may be used, as a kind of 'plan B metric' in the case that the analysis shows that {theta} is close to 1/2 and argue that such a plan B should generally be part of hypothesis testing. All the analysis presented in the paper is done with a

  2. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    Science.gov (United States)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  3. Fault-related-folding structure and reflection seismic sections. Construction of earth model using balanced cross section; Danso ga kaizaisuru shukyoku kozo no keitai to jishin tansa danmen. 1. Balanced cross section wo mochiita chika model no kochiku

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, T; Tamagawa, T [Japan Petroleum Exploration Corp., Tokyo (Japan); Tsukui, R [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

    1997-05-27

    Pre-stacking depth migration treatment is studied for the estimation of the fold configuration from seismic survey cross sections. The estimation of a velocity structure is necessary for the execution of such treatment, and the utilization of structural-geological knowledge is required for its interpretation. The concept of balanced cross section in relation to the fault-bend fold constructs a stratum structure model under conditions that the deformation during fold and fault formation is a planar strain, that there is no change in volume due to deformation, and that a fold is a parallel fold. In addition to the above geometric and kinetic approach, there is another fold formation process simulation model using a Newtonian fluid for study from the viewpoint of dynamics. This simulation stands on the presumption that the boundary contains a ramp that had been in presence before fold formation and that an incompressible viscous matter is mounted on the top surface. The viscous matter flows and deforms for the formation of an anticline on the ramp. Such enables the reproduction of a fault-bend fold formation process, and helpful discussion may be furthered on the dynamic aspect of this simulation. 5 refs., 4 figs.

  4. Exploring the sequential lineup advantage using WITNESS.

    Science.gov (United States)

    Goodsell, Charles A; Gronlund, Scott D; Carlson, Curt A

    2010-12-01

    Advocates claim that the sequential lineup is an improvement over simultaneous lineup procedures, but no formal (quantitatively specified) explanation exists for why it is better. The computational model WITNESS (Clark, Appl Cogn Psychol 17:629-654, 2003) was used to develop theoretical explanations for the sequential lineup advantage. In its current form, WITNESS produced a sequential advantage only by pairing conservative sequential choosing with liberal simultaneous choosing. However, this combination failed to approximate four extant experiments that exhibited large sequential advantages. Two of these experiments became the focus of our efforts because the data were uncontaminated by likely suspect position effects. Decision-based and memory-based modifications to WITNESS approximated the data and produced a sequential advantage. The next step is to evaluate the proposed explanations and modify public policy recommendations accordingly.

  5. Simulation modeling analysis of sequential relations among therapeutic alliance, symptoms, and adherence to child-centered play therapy between a child with autism spectrum disorder and two therapists.

    Science.gov (United States)

    Goodman, Geoff; Chung, Hyewon; Fischel, Leah; Athey-Lloyd, Laura

    2017-07-01

    This study examined the sequential relations among three pertinent variables in child psychotherapy: therapeutic alliance (TA) (including ruptures and repairs), autism symptoms, and adherence to child-centered play therapy (CCPT) process. A 2-year CCPT of a 6-year-old Caucasian boy diagnosed with autism spectrum disorder was conducted weekly with two doctoral-student therapists, working consecutively for 1 year each, in a university-based community mental-health clinic. Sessions were video-recorded and coded using the Child Psychotherapy Process Q-Set (CPQ), a measure of the TA, and an autism symptom measure. Sequential relations among these variables were examined using simulation modeling analysis (SMA). In Therapist 1's treatment, unexpectedly, autism symptoms decreased three sessions after a rupture occurred in the therapeutic dyad. In Therapist 2's treatment, adherence to CCPT process increased 2 weeks after a repair occurred in the therapeutic dyad. The TA decreased 1 week after autism symptoms increased. Finally, adherence to CCPT process decreased 1 week after autism symptoms increased. The authors concluded that (1) sequential relations differ by therapist even though the child remains constant, (2) therapeutic ruptures can have an unexpected effect on autism symptoms, and (3) changes in autism symptoms can precede as well as follow changes in process variables.

  6. Attack Trees with Sequential Conjunction

    NARCIS (Netherlands)

    Jhawar, Ravi; Kordy, Barbara; Mauw, Sjouke; Radomirović, Sasa; Trujillo-Rasua, Rolando

    2015-01-01

    We provide the first formal foundation of SAND attack trees which are a popular extension of the well-known attack trees. The SAND at- tack tree formalism increases the expressivity of attack trees by intro- ducing the sequential conjunctive operator SAND. This operator enables the modeling of

  7. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chunhua [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States); Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Su, Jiguo, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [College of Science, Yanshan University, Qinhuangdao 066004 (China); Zhang, Yang, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States)

    2016-07-07

    Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

  8. Folding model analysis of 58Ni + 64Ni elastic and inelastic scattering at Elab=203.8 and 219.2 MeV

    International Nuclear Information System (INIS)

    Ruiz, J.A.; Ferrero, J.L.; Bilwes, B.; Bilwes, R.

    1992-01-01

    Angular distributions of elastic scattering of 58 Ni by 64 Ni and inelastic scattering leading to the first 2 + state in 58 Ni or in 64 Ni were measured at E lab =203.8 and 219.2 MeV. The data were analyzed in the frame of the folding model. A renormalization N of the folding potential consistently lower than unity (N∼0.65) is needed to reproduce the elastic scattering data. Coupled-channel calculations including the main inelastic channels explain partly this discrepancy. They reproduce the elastic and inelastic scattering data with a renormalization of N∼0.8 at both energies. Interference between Coulomb and nuclear excitation is shown to play an important role in the repulsive character of the polarization potential. (author) 38 refs.; 6 figs.; 1 tab

  9. A comparison of sequential and information-based methods for determining the co-integration rank in heteroskedastic VAR MODELS

    DEFF Research Database (Denmark)

    Cavaliere, Giuseppe; Angelis, Luca De; Rahbek, Anders

    2015-01-01

    In this article, we investigate the behaviour of a number of methods for estimating the co-integration rank in VAR systems characterized by heteroskedastic innovation processes. In particular, we compare the efficacy of the most widely used information criteria, such as Akaike Information Criterion....... The relative finite-sample properties of the different methods are investigated by means of a Monte Carlo simulation study. For the simulation DGPs considered in the analysis, we find that the BIC-based procedure and the bootstrap sequential test procedure deliver the best overall performance in terms......-based method to over-estimate the co-integration rank in relatively small sample sizes....

  10. The structure and evolution of galacto-detonation waves - Some analytic results in sequential star formation models of spiral galaxies

    Science.gov (United States)

    Cowie, L. L.; Rybicki, G. B.

    1982-01-01

    Waves of star formation in a uniform, differentially rotating disk galaxy are treated analytically as a propagating detonation wave front. It is shown, that if single solitary waves could be excited, they would evolve asymptotically to one of two stable spiral forms, each of which rotates with a fixed pattern speed. Simple numerical solutions confirm these results. However, the pattern of waves that develop naturally from an initially localized disturbance is more complex and dies out within a few rotation periods. These results suggest a conclusive observational test for deciding whether sequential star formation is an important determinant of spiral structure in some class of galaxies.

  11. The four-fold way

    International Nuclear Information System (INIS)

    Terazawa, H.

    1986-01-01

    The four-fold way is proposed in a minimal composite model of quarks and leptons. Various new pictures and consequences are presented and discussed. They include 1) generation, 2) quark-lepton mass spectrum, 3) quark mixing, 4) supersymmetry, 5) effective gauge theory. (author)

  12. Effects of a combined parent-student alcohol prevention program on intermediate factors and adolescents' drinking behavior: A sequential mediation model.

    Science.gov (United States)

    Koning, Ina M; Maric, Marija; MacKinnon, David; Vollebergh, Wilma A M

    2015-08-01

    Previous work revealed that the combined parent-student alcohol prevention program (PAS) effectively postponed alcohol initiation through its hypothesized intermediate factors: increase in strict parental rule setting and adolescents' self-control (Koning, van den Eijnden, Verdurmen, Engels, & Vollebergh, 2011). This study examines whether the parental strictness precedes an increase in adolescents' self-control by testing a sequential mediation model. A cluster randomized trial including 3,245 Dutch early adolescents (M age = 12.68, SD = 0.50) and their parents randomized over 4 conditions: (1) parent intervention, (2) student intervention, (3) combined intervention, and (4) control group. Outcome measure was amount of weekly drinking measured at age 12 to 15; baseline assessment (T0) and 3 follow-up assessments (T1-T3). Main effects of the combined and parent intervention on weekly drinking at T3 were found. The effect of the combined intervention on weekly drinking (T3) was mediated via an increase in strict rule setting (T1) and adolescents' subsequent self-control (T2). In addition, the indirect effect of the combined intervention via rule setting (T1) was significant. No reciprocal sequential mediation (self-control at T1 prior to rules at T2) was found. The current study is 1 of the few studies reporting sequential mediation effects of youth intervention outcomes. It underscores the need of involving parents in youth alcohol prevention programs, and the need to target both parents and adolescents, so that change in parents' behavior enables change in their offspring. (c) 2015 APA, all rights reserved).

  13. Optimal Sequential Rules for Computer-Based Instruction.

    Science.gov (United States)

    Vos, Hans J.

    1998-01-01

    Formulates sequential rules for adapting the appropriate amount of instruction to learning needs in the context of computer-based instruction. Topics include Bayesian decision theory, threshold and linear-utility structure, psychometric model, optimal sequential number of test questions, and an empirical example of sequential instructional…

  14. RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup

    DEFF Research Database (Denmark)

    Jin, Emma Yu; Nebel, M. E.

    2016-01-01

    that the corresponding conditional probabilities behave according to a polymer-zeta probability model. We show that even if some of the structural parameters exhibit an almost realistic behavior on average, the expected shape of a folding in that model must be assumed to highly differ from those observed in nature. More...... sparsification) may reduce the runtime to n2 on average, assuming that nucleotides of distance d form a hydrogen bond (i.e. are paired) with probability (Formula Presented.) for some constants b > 0, c > 1. The latter is called the polymer-zeta model and plays a crucial role in speeding up the above mentioned...... algorithm. In this paper we discuss the application of the polymer-zeta property for the analysis of sparsification, showing that it must be applied conditionally on first and last positions to pair. Afterwards, we will investigate the combinatorics of RNA secondary structures assuming...

  15. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed

    2017-09-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order, and folding angles for each part of the model, enabling it to transform into a spatially efficient configuration while keeping its original functionality as intact as possible. That is, if a model is supposed to withstand several forces in its initial state to serve its functionality, our framework places the joints between the parts of the model such that the model can withstand forces with magnitudes that are comparable to the magnitudes applied on the unedited model. Furthermore, if the folded shape is not compact, our framework proposes further segmentation of the model to improve its compactness in its folded state.

  16. Sequential charged particle reaction

    International Nuclear Information System (INIS)

    Hori, Jun-ichi; Ochiai, Kentaro; Sato, Satoshi; Yamauchi, Michinori; Nishitani, Takeo

    2004-01-01

    The effective cross sections for producing the sequential reaction products in F82H, pure vanadium and LiF with respect to the 14.9-MeV neutron were obtained and compared with the estimation ones. Since the sequential reactions depend on the secondary charged particles behavior, the effective cross sections are corresponding to the target nuclei and the material composition. The effective cross sections were also estimated by using the EAF-libraries and compared with the experimental ones. There were large discrepancies between estimated and experimental values. Additionally, we showed the contribution of the sequential reaction on the induced activity and dose rate in the boundary region with water. From the present study, it has been clarified that the sequential reactions are of great importance to evaluate the dose rates around the surface of cooling pipe and the activated corrosion products. (author)

  17. Application of sequential fragmentation/transport theory to deposits of 1723 and 1963-65 eruptions of Volcan Irazu, Costa Rica: positive dispersion case and fractal model

    International Nuclear Information System (INIS)

    Brenes, Jose; Alvarado, Guillermo E.

    2013-01-01

    The theory of Fragmentation and Sequential Transport (FST) was applied to the granulometric analyzes of the deposits from the eruptions of 1723 and 1963-65 of the Volcan Irazu. An appreciable number of cases of positive dispersion was showed, associated in the literature with aggregation processes. A new fractal dimension defined in research has shown to be the product of secondary fragmentation. The application of the new dimension is used in the analyses of the eruptions of 1723 and 1963-65. A fractal model of a volcanic activity is formulated for the first time. The Hurst coefficient and the exponent of the law of powers are incorporated. The existence of values of dissidence near zero have been indicators of an effusive process, as would be the lava pools. The results derived from the model were agreed with field observations. (author) [es

  18. Random sequential adsorption of cubes

    Science.gov (United States)

    Cieśla, Michał; Kubala, Piotr

    2018-01-01

    Random packings built of cubes are studied numerically using a random sequential adsorption algorithm. To compare the obtained results with previous reports, three different models of cube orientation sampling were used. Also, three different cube-cube intersection algorithms were tested to find the most efficient one. The study focuses on the mean saturated packing fraction as well as kinetics of packing growth. Microstructural properties of packings were analyzed using density autocorrelation function.

  19. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  20. Swelling pressure induced phase-volume transition in hybrid biopolymer gels caused by unfolding of folded crosslinks: A model

    Czech Academy of Sciences Publication Activity Database

    Dušek, Karel; Dušková, Miroslava; Ilavský, Michal; Steward, R.; Kopeček, J.

    2003-01-01

    Roč. 4, č. 6 (2003), s. 1818-1826 ISSN 1525-7797 R&D Projects: GA AV ČR KSK4050111 Keywords : thermodynamic model * swelling transitions * hybrid gels Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.824, year: 2003

  1. Coherent structures in the flow inside a model of the human vocal tract with self-oscillating vocal folds

    Czech Academy of Sciences Publication Activity Database

    Horáček, Jaromír; Šidlof, Petr; Uruba, Václav; Veselý, Jan; Radolf, Vojtěch; Bula, Vítězslav

    2010-01-01

    Roč. 55, č. 4 (2010), s. 327-343 ISSN 0001-7043 R&D Projects: GA ČR GA101/08/1155 Institutional research plan: CEZ:AV0Z20760514 Keywords : biomechanics of voice * voice production modeling * PIV method * coherent structures Subject RIV: BI - Acoustics

  2. Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation.

    Directory of Open Access Journals (Sweden)

    Niklas Berliner

    Full Text Available Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases.

  3. From Holonomy of the Ising Model Form Factors to n-Fold Integrals and the Theory of Elliptic Curves

    Directory of Open Access Journals (Sweden)

    Salah Boukraa

    2007-10-01

    Full Text Available We recall the form factors $f^(j_{N,N}$ corresponding to the $lambda$-extension $C(N,N; lambda$ of the two-point diagonal correlation function of the Ising model on the square lattice and their associated linear differential equations which exhibit both a "Russian-doll" nesting, and a decomposition of the linear differential operators as a direct sum of operators (equivalent to symmetric powers of the differential operator of the complete elliptic integral $E$. The scaling limit of these differential operators breaks the direct sum structure but not the "Russian doll" structure, the "scaled" linear differential operators being no longer Fuchsian. We then introduce some multiple integrals of the Ising class expected to have the same singularities as the singularities of the $n$-particle contributions $chi^{(n}$ to the susceptibility of the square lattice Ising model. We find the Fuchsian linear differential equations satisfied by these multiple integrals for $n = 1, 2, 3, 4$ and, only modulo a prime, for $n = 5$ and 6, thus providing a large set of (possible new singularities of the $chi^{(n}$. We get the location of these singularities by solving the Landau conditions. We discuss the mathematical, as well as physical, interpretation of these new singularities. Among the singularities found, we underline the fact that the quadratic polynomial condition $1 + 3w + 4w^2 = 0$, that occurs in the linear differential equation of $chi^{(3}$, actually corresponds to the occurrence of complex multiplication for elliptic curves. The interpretation of complex multiplication for elliptic curves as complex fixed points of generators of the exact renormalization group is sketched. The other singularities occurring in our multiple integrals are not related to complex multiplication situations, suggesting a geometric interpretation in terms of more general (motivic mathematical structures beyond the theory of elliptic curves. The scaling limit of the (lattice

  4. Quantification of Porcine Vocal Fold Geometry.

    Science.gov (United States)

    Stevens, Kimberly A; Thomson, Scott L; Jetté, Marie E; Thibeault, Susan L

    2016-07-01

    The aim of this study was to quantify porcine vocal fold medial surface geometry and three-dimensional geometric distortion induced by freezing the larynx, especially in the region of the vocal folds. The medial surface geometries of five excised porcine larynges were quantified and reported. Five porcine larynges were imaged in a micro-CT scanner, frozen, and rescanned. Segmentations and three-dimensional reconstructions were used to quantify and characterize geometric features. Comparisons were made with geometry data previously obtained using canine and human vocal folds as well as geometries of selected synthetic vocal fold models. Freezing induced an overall expansion of approximately 5% in the transverse plane and comparable levels of nonuniform distortion in sagittal and coronal planes. The medial surface of the porcine vocal folds was found to compare reasonably well with other geometries, although the compared geometries exhibited a notable discrepancy with one set of published human female vocal fold geometry. Porcine vocal folds are qualitatively geometrically similar to data available for canine and human vocal folds, as well as commonly used models. Freezing of tissue in the larynx causes distortion of around 5%. The data can provide direction in estimating uncertainty due to bulk distortion of tissue caused by freezing, as well as quantitative geometric data that can be directly used in developing vocal fold models. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  5. Evaluating realized seed dispersal across fragmented tropical landscapes: a two-fold approach using parentage analysis and the neighbourhood model.

    Science.gov (United States)

    Ismail, Sascha A; Ghazoul, Jaboury; Ravikanth, Gudasalamani; Kushalappa, Cheppudira G; Uma Shaanker, Ramanan; Kettle, Chris J

    2017-05-01

    Despite the importance of seed dispersal for survival of plant species in fragmented landscapes, data on seed dispersal at landscape scales remain sparse. Effective seed dispersal among fragments determines recolonization and plant species persistence in such landscapes. We present the first large-scale (216-km 2 ) direct estimates of realized seed dispersal of a high-value timber tree (Dysoxylum malabaricum) across an agro-forest landscape in the Western Ghats, India. Based upon an exhaustive inventory of adult trees and a sample of 488 seedlings all genotyped at 10 microsatellite loci, we estimated realized seed dispersal using parentage analysis and the neighbourhood model. Our estimates found that most realized seed dispersal was within 200 m, which is insufficient to effectively bridge the distances between forest patches. We conclude that using mobility of putative animal dispersers can be misleading when estimating tropical tree species vulnerability to habitat fragmentation. This raises serious concerns about the potential of many tropical trees to recolonize isolated forest patches where high-value tree species have already been removed. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  6. Folding worlds between pages

    CERN Multimedia

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  7. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  8. Modelling and sequential simulation of multi-tubular metallic membrane and techno-economics of a hydrogen production process employing thin-layer membrane reactor

    KAUST Repository

    Shafiee, Alireza

    2016-09-24

    A theoretical model for multi-tubular palladium-based membrane is proposed in this paper and validated against experimental data for two different sized membrane modules that operate at high temperatures. The model is used in a sequential simulation format to describe and analyse pure hydrogen and hydrogen binary mixture separations, and then extended to simulate an industrial scale membrane unit. This model is used as a sub-routine within an ASPEN Plus model to simulate a membrane reactor in a steam reforming hydrogen production plant. A techno-economic analysis is then conducted using the validated model for a plant producing 300 TPD of hydrogen. The plant utilises a thin (2.5 μm) defect-free and selective layer (Pd75Ag25 alloy) membrane reactor. The economic sensitivity analysis results show usefulness in finding the optimum operating condition that achieves minimum hydrogen production cost at break-even point. A hydrogen production cost of 1.98 $/kg is estimated while the cost of the thin-layer selective membrane is found to constitute 29% of total process capital cost. These results indicate the competiveness of this thin-layer membrane process against conventional methods of hydrogen production. © 2016 Hydrogen Energy Publications LLC

  9. Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

    International Nuclear Information System (INIS)

    Khoa, Dao T.; Thang, Dang Ngoc; Loc, Bui Minh

    2014-01-01

    The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ( 3 He, t) reaction, can be considered as ''elastic'' scattering of proton or 3 He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ( 3 He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or 3 He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or 3 He optical potential to the cross section of the charge-exchange (p, n) or ( 3 He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ( 3 He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

  10. Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

    Energy Technology Data Exchange (ETDEWEB)

    Khoa, Dao T.; Thang, Dang Ngoc [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); Loc, Bui Minh [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); University of Pedagogy, Ho Chi Minh City (Viet Nam)

    2014-02-15

    The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ({sup 3}He, t) reaction, can be considered as ''elastic'' scattering of proton or {sup 3}He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ({sup 3}He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or {sup 3}He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or {sup 3}He optical potential to the cross section of the charge-exchange (p, n) or ({sup 3}He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ({sup 3}He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

  11. Approaching climate-adaptive facades with foldings

    DEFF Research Database (Denmark)

    Sack-Nielsen, Torsten

    2014-01-01

    envelopes based on folding principles such as origami. Three major aspects cover the project’s interest in this topic: Shape, kinetics and the application of new multi-functional materials form the interdisciplinary framework of this research. Shape// Initially small paper sketch models demonstrate folding...

  12. Sequential stochastic optimization

    CERN Document Server

    Cairoli, Renzo

    1996-01-01

    Sequential Stochastic Optimization provides mathematicians and applied researchers with a well-developed framework in which stochastic optimization problems can be formulated and solved. Offering much material that is either new or has never before appeared in book form, it lucidly presents a unified theory of optimal stopping and optimal sequential control of stochastic processes. This book has been carefully organized so that little prior knowledge of the subject is assumed; its only prerequisites are a standard graduate course in probability theory and some familiarity with discrete-paramet

  13. Kinematics of large scale asymmetric folds and associated smaller ...

    Indian Academy of Sciences (India)

    The present work reiterates the importance of analysis of ... these models is the assumption that the folds are passive folds ... applicability of these models is thus limited in the case of ...... with contrasted rheological properties, a theory for the.

  14. Sequential Dependencies in Driving

    Science.gov (United States)

    Doshi, Anup; Tran, Cuong; Wilder, Matthew H.; Mozer, Michael C.; Trivedi, Mohan M.

    2012-01-01

    The effect of recent experience on current behavior has been studied extensively in simple laboratory tasks. We explore the nature of sequential effects in the more naturalistic setting of automobile driving. Driving is a safety-critical task in which delayed response times may have severe consequences. Using a realistic driving simulator, we find…

  15. Mining compressing sequential problems

    NARCIS (Netherlands)

    Hoang, T.L.; Mörchen, F.; Fradkin, D.; Calders, T.G.K.

    2012-01-01

    Compression based pattern mining has been successfully applied to many data mining tasks. We propose an approach based on the minimum description length principle to extract sequential patterns that compress a database of sequences well. We show that mining compressing patterns is NP-Hard and

  16. Image Quality of 3rd Generation Spiral Cranial Dual-Source CT in Combination with an Advanced Model Iterative Reconstruction Technique: A Prospective Intra-Individual Comparison Study to Standard Sequential Cranial CT Using Identical Radiation Dose.

    Science.gov (United States)

    Wenz, Holger; Maros, Máté E; Meyer, Mathias; Förster, Alex; Haubenreisser, Holger; Kurth, Stefan; Schoenberg, Stefan O; Flohr, Thomas; Leidecker, Christianne; Groden, Christoph; Scharf, Johann; Henzler, Thomas

    2015-01-01

    To prospectively intra-individually compare image quality of a 3rd generation Dual-Source-CT (DSCT) spiral cranial CT (cCT) to a sequential 4-slice Multi-Slice-CT (MSCT) while maintaining identical intra-individual radiation dose levels. 35 patients, who had a non-contrast enhanced sequential cCT examination on a 4-slice MDCT within the past 12 months, underwent a spiral cCT scan on a 3rd generation DSCT. CTDIvol identical to initial 4-slice MDCT was applied. Data was reconstructed using filtered backward projection (FBP) and 3rd-generation iterative reconstruction (IR) algorithm at 5 different IR strength levels. Two neuroradiologists independently evaluated subjective image quality using a 4-point Likert-scale and objective image quality was assessed in white matter and nucleus caudatus with signal-to-noise ratios (SNR) being subsequently calculated. Subjective image quality of all spiral cCT datasets was rated significantly higher compared to the 4-slice MDCT sequential acquisitions (pspiral compared to sequential cCT datasets with mean SNR improvement of 61.65% (p*Bonferroni0.05spiral cCT with an advanced model IR technique significantly improves subjective and objective image quality compared to a standard sequential cCT acquisition acquired at identical dose levels.

  17. Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing.

    Science.gov (United States)

    Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

    2016-05-01

    We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.

  18. Evidence for the statistical and sequential nature of 16O breakup into four alphas

    International Nuclear Information System (INIS)

    Pouliot, J.; Beaulieu, L.; Djerroud, B.; Dore, D.; Laforest, R.; Roy, R.; St-Pierre, C.; Lopez, J.A.

    1993-01-01

    The relation between the folding angle distributions observed in the decay of 16 O into four alphas and the final alpha-alpha interactions is discussed and inferred from model calculations. Likewise, the excitation energy dependence of the four-alpha decay channel probability is studied. A lack of alpha-alpha interactions is deduced from the analysis and the observed energy dependence is found to be characteristic of a statistical decay. This reveals the statistical nature of the disassembly and suggests a sequential breakup as the decay method

  19. Charge and angular distributions as well as sequential decay and γ-ray emission in heavy ion collisions viewed in the light of the diffusion model

    International Nuclear Information System (INIS)

    Moretto, L.G.

    1977-08-01

    The hierarchy of the collective relaxation times in heavy ion reactions is briefly reviewed. An improved diffusion model is introduced and applied to interpret the fragment Z and angular distributions for some typical reactions. The equilibrium in the neutron-to-proton ratio as well as the sharing of the excitation energy between fragments is studied by a coincidence method which leads to the measurement of the charge, mass and mean number of nucleons emitted by each fragment. The final destiny of the dissipative energy is determined by measuring the atomic number of two coincident fragments, thus obtaining the missing charge as a function of bombarding energy and the Q of the reaction. The sequential fission probability of the heavy recoil is established as a function of the Z and kinetic energy of the light partner. The out-of-plane angular distribution of the fission fragments is correlated with the fissionability and interpreted in terms of various sources of angular momentum misalignment. The γ-ray multiplicities and the γ-ray angular distributions associated with deep inelastic event are discussed in terms of the angular momentum transfer and in terms of the diffusion model

  20. Quantum Chemical Examination of the Sequential Halogen Incorporation Scheme for the Modeling of Speciation of I/Br/Cl-Containing Trihalomethanes.

    Science.gov (United States)

    Zhang, Chenyang; Li, Maodong; Han, Xuze; Yan, Mingquan

    2018-02-20

    The recently developed three-step ternary halogenation model interprets the incorporation of chlorine, bromine, and iodine ions into natural organic matter (NOM) and formation of iodine-, bromine-, and chlorine-containing trihalomethanes (THMs) based on the competition of iodine, bromine, and chlorine species at each node of the halogenation sequence. This competition is accounted for using the dimensionless ratios (denoted as γ) of kinetic rates of reactions of the initial attack sites or halogenated intermediates with chlorine, bromine, and iodine ions. However, correlations between the model predictions made and mechanistic aspects of the incorporation of halogen species need to be ascertained in more detail. In this study, quantum chemistry calculations were first used to probe the formation mechanism of 10 species of Cl-/Br-/I- THMs. The HOMO energy (E HOMO ) of each mono-, bi-, or trihalomethanes were calculated by B3LYP method in Gaussian 09 software. Linear correlations were found to exist between the logarithms of experimentally determined kinetic preference coefficients γ reported in prior research and, on the other hand, differences of E HOMO values between brominated/iodinated and chlorinated halomethanes. One notable exception from this trend was that observed for the incorporation of iodine into mono- and di-iodinated intermediates. These observations confirm the three-step halogen incorporation sequence and the factor γ in the statistical model. The combined use of quantum chemistry calculations and the ternary sequential halogenation model provides a new insight into the microscopic nature of NOM-halogen interactions and the trends seen in the behavior of γ factors incorporated in the THM speciation models.

  1. High resolution 2D numerical models from rift to break-up: Crustal hyper-extension, Margin asymmetry, Sequential faulting

    Science.gov (United States)

    Brune, Sascha; Heine, Christian; Pérez-Gussinyé, Marta; Sobolev, Stephan

    2013-04-01

    Numerical modelling is a powerful tool to integrate a multitude of geological and geophysical data while addressing fundamental questions of passive margin formation such as the occurrence of crustal hyper-extension, (a-)symmetries between conjugate margin pairs, and the sometimes significant structural differences between adjacent margin segments. This study utilises knowledge gathered from two key examples of non-magmatic, asymmetric, conjugate margin pairs, i.e. Iberia-New Foundland and Southern Africa-Brazil, where many published seismic lines provide solid knowledge on individual margin geometry. While both margins involve crustal hyper-extension, it is much more pronounced in the South Atlantic. We investigate the evolution of these two margin pairs by carefully constraining our models with detailed plate kinematic history, laboratory-based rheology, and melt fraction evaluation of mantle upwelling. Our experiments are consistent with observed fault patterns, crustal thickness, and basin stratigraphy. We conduct 2D thermomechanical rift models using the finite element code SLIM3D that operates with nonlinear stress- and temperature-dependent elasto-visco-plastic rheology, with parameters provided by laboratory experiments on major crustal and upper mantle rocks. In our models we also calculate the melt fraction within the upwelling asthenosphere, which allows us to control whether the model indeed corresponds to the non-magmatic margin type or not. Our modelling highlights two processes as fundamental for the formation of hyper-extension and margin asymmetry at non-magmatic margins: (1) Strain hardening in the rift center due to cooling of upwelling mantle material (2) The formation of a weak crustal domain adjacent to the rift center caused by localized viscous strain softening and heat transfer from the mantle. Simultaneous activity of both processes promotes lateral rift migration in a continuous way that generates a wide layer of hyper-extended crust on

  2. The folding mechanism and key metastable state identification of the PrP127-147 monomer studied by molecular dynamics simulations and Markov state model analysis.

    Science.gov (United States)

    Zhou, Shuangyan; Wang, Qianqian; Wang, Yuwei; Yao, Xiaojun; Han, Wei; Liu, Huanxiang

    2017-05-10

    The structural transition of prion proteins from a native α-helix (PrP C ) to a misfolded β-sheet-rich conformation (PrP Sc ) is believed to be the main cause of a number of prion diseases in humans and animals. Understanding the molecular basis of misfolding and aggregation of prion proteins will be valuable for unveiling the etiology of prion diseases. However, due to the limitation of conventional experimental techniques and the heterogeneous property of oligomers, little is known about the molecular architecture of misfolded PrP Sc and the mechanism of structural transition from PrP C to PrP Sc . The prion fragment 127-147 (PrP127-147) has been reported to be a critical region for PrP Sc formation in Gerstmann-Straussler-Scheinker (GSS) syndrome and thus has been used as a model for the study of prion aggregation. In the present study, we employ molecular dynamics (MD) simulation techniques to study the conformational change of this fragment that could be relevant to the PrP C -PrP Sc transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127-147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136-His140 and Pro137-His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond

  3. Random and cooperative sequential adsorption

    Science.gov (United States)

    Evans, J. W.

    1993-10-01

    Irreversible random sequential adsorption (RSA) on lattices, and continuum "car parking" analogues, have long received attention as models for reactions on polymer chains, chemisorption on single-crystal surfaces, adsorption in colloidal systems, and solid state transformations. Cooperative generalizations of these models (CSA) are sometimes more appropriate, and can exhibit richer kinetics and spatial structure, e.g., autocatalysis and clustering. The distribution of filled or transformed sites in RSA and CSA is not described by an equilibrium Gibbs measure. This is the case even for the saturation "jammed" state of models where the lattice or space cannot fill completely. However exact analysis is often possible in one dimension, and a variety of powerful analytic methods have been developed for higher dimensional models. Here we review the detailed understanding of asymptotic kinetics, spatial correlations, percolative structure, etc., which is emerging for these far-from-equilibrium processes.

  4. Geometric U-folds in four dimensions

    Science.gov (United States)

    Lazaroiu, C. I.; Shahbazi, C. S.

    2018-01-01

    We describe a general construction of geometric U-folds compatible with a non-trivial extension of the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain flat fiber bundles which encode how supergravity fields are globally glued together. We show that smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the scalar map of the solution is homotopically non-trivial. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of \

  5. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis

    In this thesis we describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon codes with non-uniform profile. With this scheme decoding with good performance...... is possible as low as Eb/No=0.6 dB, which is about 1.7 dB below the signal-to-noise ratio that marks the cut-off rate for the convolutional code. This is possible since the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability...... of computational overflow. Analytical results for the probability that the first Reed-Solomon word is decoded after C computations are presented. This is supported by simulation results that are also extended to other parameters....

  6. Sequential Power-Dependence Theory

    NARCIS (Netherlands)

    Buskens, Vincent; Rijt, Arnout van de

    2008-01-01

    Existing methods for predicting resource divisions in laboratory exchange networks do not take into account the sequential nature of the experimental setting. We extend network exchange theory by considering sequential exchange. We prove that Sequential Power-Dependence Theory—unlike

  7. Muscular anatomy of the human ventricular folds.

    Science.gov (United States)

    Moon, Jerald; Alipour, Fariborz

    2013-09-01

    Our purpose in this study was to better understand the muscular anatomy of the ventricular folds in order to help improve biomechanical modeling of phonation and to better understand the role of these muscles during phonatory and nonphonatory tasks. Four human larynges were decalcified, sectioned coronally from posterior to anterior by a CryoJane tape transfer system, and stained with Masson's trichrome. The total and relative areas of muscles observed in each section were calculated and used for characterizing the muscle distribution within the ventricular folds. The ventricular folds contained anteriorly coursing thyroarytenoid and ventricularis muscle fibers that were in the lower half of the ventricular fold posteriorly, and some ventricularis muscle was evident in the upper and lateral portions of the fold more anteriorly. Very little muscle tissue was observed in the medial half of the fold, and the anterior half of the ventricular fold was largely devoid of any muscle tissue. All 4 larynges contained muscle bundles that coursed superiorly and medially through the upper half of the fold, toward the lateral margin of the epiglottis. Although variability of expression was evident, a well-defined thyroarytenoid muscle was readily apparent lateral to the arytenoid cartilage in all specimens.

  8. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis; Paaske, Erik

    1998-01-01

    We describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon (RS) codes with nonuniform profile. With this scheme decoding with good performance is possible as low...... as Eb/N0=0.6 dB, which is about 1.25 dB below the signal-to-noise ratio (SNR) that marks the cutoff rate for the full system. Accounting for about 0.45 dB due to the outer codes, sequential decoding takes place at about 1.7 dB below the SNR cutoff rate for the convolutional code. This is possible since...... the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability of computational overflow. Analytical results for the probability that the first RS word is decoded after C computations are presented. These results are supported...

  9. Frustration in Condensed Matter and Protein Folding

    Science.gov (United States)

    Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.

    2014-03-01

    By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.

  10. Folding model analyses of 12C-12C and 16O-16O elastic scattering using the density-dependent LOCV-averaged effective interaction

    Science.gov (United States)

    Rahmat, M.; Modarres, M.

    2018-03-01

    The averaged effective two-body interaction (AEI), which can be generated through the lowest order constrained variational (LOCV) method for symmetric nuclear matter (SNM) with the input [Reid68, Ann. Phys. 50, 411 (1968), 10.1016/0003-4916(68)90126-7] nucleon-nucleon potential, is used as the effective nucleon-nucleon potential in the folding model to describe the heavy-ion (HI) elastic scattering cross sections. The elastic scattering cross sections of 12C-12C and 16O-16O systems are calculated in the above framework. The results are compared with the corresponding calculations coming from the fitting procedures with the input finite range D D M 3 Y 1 -Reid potential and the available experimental data at different incident energies. It is shown that a reasonable description of the elastic 12C-12C and 16O-16O scattering data at the low and medium energies can be obtained by using the above LOCV AEI, without any need to define a parametrized density-dependent function in the effective nucleon-nucleon potential, which is formally considered in the typical D D M 3 Y 1 -Reid interactions.

  11. Simulation Modeling Method and Experimental Investigation on the Uniflow Scavenging System of an Opposed-Piston Folded-Cranktrain Diesel Engine

    Directory of Open Access Journals (Sweden)

    Fukang Ma

    2017-05-01

    Full Text Available The scavenging process for opposed-piston folded-cranktrain (OPFC diesel engines can be described by the time evolution of the in-cylinder and exhaust chamber residual gas rates. The relation curve of in-cylinder and exhaust chamber residual gas rate is called scavenging profile, which is calculated through the changes of in-cylinder and exhaust chamber gas compositions determined by computational fluid dynamics (CFD simulation. The scavenging profile is used to calculate the scavenging process by mono-dimensional (1D simulation. The tracer gas method (TGM is employed to validate the accuracy of the scavenging profile. At the same time, the gas exchange performance under different intake and exhaust state parameters was examined based on the TGM. The results show that the scavenging process from 1D simulation and experiment match well, which means the scavenging model obtained by CFD simulation performs well and validation of its effectiveness by TGM is possible. The difference between intake and exhaust pressure has a significant positive effect on the gas exchange performance and trapped gas mass, but the pressure difference has little effect on the scavenging efficiency and the trapped air mass if the delivery ratio exceeds 1.4.

  12. Sequential modelling of ICRF wave near RF fields and asymptotic RF sheaths description for AUG ICRF antennas

    Directory of Open Access Journals (Sweden)

    Jacquot Jonathan

    2017-01-01

    Full Text Available A sequence of simulations is performed with RAPLICASOL and SSWICH to compare two AUG ICRF antennas. RAPLICASOL outputs have been used as input to SSWICH-SW for the AUG ICRF antennas. Using parallel electric field maps and the scattering matrix produced by RAPLICASOL, SSWICH-SW, reduced to its asymptotic part, is able to produce a 2D radial/poloidal map of the DC plasma potential accounting for the antenna input settings (total power, power balance, phasing. Two models of antennas are compared: 2-strap antenna vs 3-strap antenna. The 2D DC potential structures are correlated to structures of the parallel electric field map for different phasing and power balance. The overall DC plasma potential on the 3-strap antenna is lower due to better global RF currents compensation. Spatial proximity between regions of high RF electric field and regions where high DC plasma potentials are observed is an important factor for sheath rectification.

  13. Kinematics of tectonic fracture development during regional folding in sandstones of the Kamlial Formation, Khushalgarh, northern Pakistan

    International Nuclear Information System (INIS)

    Sayab, M.

    2005-01-01

    Systematic relationships between the fracture orientation and fold geometry in sedimentary rocks have been used to explain the development of synfolding fractures. Based on field observations at the Khushalgarh syncline, located east of the Kohat Plateau, we proposed that the orientation of fractures was influenced dominantly by two tectonic fracture sets, that is, the NE-SW and NW-SE. The NE-SW fracture set dominantly formed as mode 1 (tensile), where as, the NW-SE fracture set developed as mode 11 (shear) conjugate fractures. The NE-SW trending fractures follow the axis of the syncline, whereas, the NW-SE fracture about crosscuts the fold axis. Most of the NE-SW fractures abut against the NW-SW fracture set. Based on the orientation and crosscutting relationship, their modes in response to stress, we conclude that the NE-SW trending fractures formed early than those of NW-SE fracture set. Though, both the fracture sets are formed during the folding, we suggest that they were not formed at the same time. Their crosscutting relationship suggests that they developed sequentially rather than synchronously. Our interpretations support the laboratory-based models where only one fracture orientation (or set of fractures with one orientation) form in response to single stress. However, as the stress distribution in folded strata changes over time new fractures of distinct orientations can form during or late in the folding history. We conclude that the sandstone units underwent bedding-parallel extension during folding, where bedding is stretched to accommodate extension. Parallel to the fold axis orientation. Bending of the limbs is a likely mechanism for the development of observed NE-SW trending fractures during folding, whereas the NW-SE fractures developed late in the folded history. (author)

  14. Distinct effects of perceptual quality on auditory word recognition, memory formation and recall in a neural model of sequential memory

    Directory of Open Access Journals (Sweden)

    Paul Miller

    2010-06-01

    Full Text Available Adults with sensory impairment, such as reduced hearing acuity, have impaired ability to recall identifiable words, even when their memory is otherwise normal. We hypothesize that poorer stimulus quality causes weaker activity in neurons responsive to the stimulus and more time to elapse between stimulus onset and identification. The weaker activity and increased delay to stimulus identification reduce the necessary strengthening of connections between neurons active before stimulus presentation and neurons active at the time of stimulus identification. We test our hypothesis through a biologically motivated computational model, which performs item recognition, memory formation and memory retrieval. In our simulations, spiking neurons are distributed into pools representing either items or context, in two separate, but connected winner-takes-all (WTA networks. We include associative, Hebbian learning, by comparing multiple forms of spike-timing dependent plasticity (STDP, which strengthen synapses between coactive neurons during stimulus identification. Synaptic strengthening by STDP can be sufficient to reactivate neurons during recall if their activity during a prior stimulus rose strongly and rapidly. We find that a single poor quality stimulus impairs recall of neighboring stimuli as well as the weak stimulus itself. We demonstrate that within the WTA paradigm of word recognition, reactivation of separate, connected sets of non-word, context cells permits reverse recall. Also, only with such coactive context cells, does slowing the rate of stimulus presentation increase recall probability. We conclude that significant temporal overlap of neural activity patterns, absent from individual WTA networks, is necessary to match behavioral data for word recall.

  15. The Bacterial Sequential Markov Coalescent.

    Science.gov (United States)

    De Maio, Nicola; Wilson, Daniel J

    2017-05-01

    Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e. , using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)-an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is

  16. Sequential decay of Reggeons

    International Nuclear Information System (INIS)

    Yoshida, Toshihiro

    1981-01-01

    Probabilities of meson production in the sequential decay of Reggeons, which are formed from the projectile and the target in the hadron-hadron to Reggeon-Reggeon processes, are investigated. It is assumed that pair creation of heavy quarks and simultaneous creation of two antiquark-quark pairs are negligible. The leading-order terms with respect to ratio of creation probabilities of anti s s to anti u u (anti d d) are calculated. The production cross sections in the target fragmentation region are given in terms of probabilities in the initial decay of the Reggeons and an effect of manyparticle production. (author)

  17. Fault-related-folding structures and reflection seismic sections. Study by seismic modeling and balanced cross section; Danso ga kaizaisuru shukyoku kozo no keitai to jishin tansa danmen. 2. Seismic modeling oyobi balanced cross section ni yoru study

    Energy Technology Data Exchange (ETDEWEB)

    Tamagawa, T; Matsuoka, T [Japan Petroleum Exploration Corp., Tokyo (Japan); Tsukui, R [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

    1997-05-27

    It occasionally happens that there exists a part where reflection near the thrust is not clearly observed in a thrust zone seismic survey cross section. For the effective interpretation of such an occurrence, the use of geological structures as well as the reflected pattern is effective. When the velocity structures for a fold structure having a listric fault caused anticline (unidirectionally inclined with a backlimb, without a forelimb) and for a fault propagation fold are involved, a wrong interpretation may be made since they look alike in reflection wave pattern despite their difference in geological structure. In the concept of balanced cross section, a check is performed, when the stratum after deformation is recovered to the time of deposition, as to whether the geologic stratum area is conserved without excess or shortage. An excess or shortage occurs if there is an error in the model, and this shows that the fault surface or fold structure is not correctly reflected. Positive application of geological knowledge is required in the processing and interpreting of data from a seismic survey. 6 refs., 6 figs.

  18. Asynchronous Operators of Sequential Logic Venjunction & Sequention

    CERN Document Server

    Vasyukevich, Vadim

    2011-01-01

    This book is dedicated to new mathematical instruments assigned for logical modeling of the memory of digital devices. The case in point is logic-dynamical operation named venjunction and venjunctive function as well as sequention and sequentional function. Venjunction and sequention operate within the framework of sequential logic. In a form of the corresponding equations, they organically fit analytical expressions of Boolean algebra. Thus, a sort of symbiosis is formed using elements of asynchronous sequential logic on the one hand and combinational logic on the other hand. So, asynchronous

  19. Synthetic Aperture Sequential Beamforming

    DEFF Research Database (Denmark)

    Kortbek, Jacob; Jensen, Jørgen Arendt; Gammelmark, Kim Løkke

    2008-01-01

    A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective is to im......A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective...... is to improve and obtain a more range independent lateral resolution compared to conventional dynamic receive focusing (DRF) without compromising frame rate. SASB is a two-stage procedure using two separate beamformers. First a set of Bmode image lines using a single focal point in both transmit and receive...... is stored. The second stage applies the focused image lines from the first stage as input data. The SASB method has been investigated using simulations in Field II and by off-line processing of data acquired with a commercial scanner. The performance of SASB with a static image object is compared with DRF...

  20. Effects of gravity in folding

    Science.gov (United States)

    Minkel, Donald Howe

    Effects of gravity on buckle folding are studied using a Newtonian fluid finite element model of a single layer embedded between two thicker less viscous layers. The methods allow arbitrary density jumps, surface tension coefficients, resistance to slip at the interfaces, and tracking of fold growth to a large amplitudes. When density increases downward in two equal jumps, a layer buckles less and thickens more than with uniform density. When density increases upward in two equal jumps, it buckles more and thickens less. A low density layer with periodic thickness variations buckles more, sometimes explosively. Thickness variations form, even if not present initially. These effects are greater with; smaller viscosities, larger density jump, larger length scale, and slower shortening rate. They also depend on wavelength and amplitude, and these dependencies are described in detail. The model is applied to the explosive growth of the salt anticlines of the Paradox Basin, Colorado and Utah. There, shale (higher density) overlies salt (lower density). Methods for simulating realistic earth surface erosion and deposition conditions are introduced. Growth rates increase both with ease of slip at the salt-shale interface, and when earth surface relief stays low due to erosion and deposition. Model anticlines grow explosively, attaining growth rates and amplitudes close to those of the field examples. Fastest growing wavelengths are the same as seen in the field. It is concluded that a combination of partial-slip at the salt-shale interface, with reasonable earth surface conditions, promotes sufficiently fast buckling of the salt-shale interface due to density inversion alone. Neither basement faulting, nor tectonic shortening is required to account for the observed structures. Of fundamental importance is the strong tendency of gravity to promote buckling in low density layers with thickness variations. These develop, even if not present initially. folds

  1. Campbell and moment measures for finite sequential spatial processes

    NARCIS (Netherlands)

    M.N.M. van Lieshout (Marie-Colette)

    2006-01-01

    textabstractWe define moment and Campbell measures for sequential spatial processes, prove a Campbell-Mecke theorem, and relate the results to their counterparts in the theory of point processes. In particular, we show that any finite sequential spatial process model can be derived as the vector

  2. Dynamics-based sequential memory: Winnerless competition of patterns

    International Nuclear Information System (INIS)

    Seliger, Philip; Tsimring, Lev S.; Rabinovich, Mikhail I.

    2003-01-01

    We introduce a biologically motivated dynamical principle of sequential memory which is based on winnerless competition (WLC) of event images. This mechanism is implemented in a two-layer neural model of sequential spatial memory. We present the learning dynamics which leads to the formation of a WLC network. After learning, the system is capable of associative retrieval of prerecorded sequences of patterns

  3. Accounting for Heterogeneous Returns in Sequential Schooling Decisions

    NARCIS (Netherlands)

    Zamarro, G.

    2006-01-01

    This paper presents a method for estimating returns to schooling that takes into account that returns may be heterogeneous among agents and that educational decisions are made sequentially.A sequential decision model is interesting because it explicitly considers that the level of education of each

  4. Geostatistical modeling of the gas emission zone and its in-place gas content for Pittsburgh-seam mines using sequential Gaussian simulation

    Science.gov (United States)

    Karacan, C.O.; Olea, R.A.; Goodman, G.

    2012-01-01

    Determination of the size of the gas emission zone, the locations of gas sources within, and especially the amount of gas retained in those zones is one of the most important steps for designing a successful methane control strategy and an efficient ventilation system in longwall coal mining. The formation of the gas emission zone and the potential amount of gas-in-place (GIP) that might be available for migration into a mine are factors of local geology and rock properties that usually show spatial variability in continuity and may also show geometric anisotropy. Geostatistical methods are used here for modeling and prediction of gas amounts and for assessing their associated uncertainty in gas emission zones of longwall mines for methane control.This study used core data obtained from 276 vertical exploration boreholes drilled from the surface to the bottom of the Pittsburgh coal seam in a mining district in the Northern Appalachian basin. After identifying important coal and non-coal layers for the gas emission zone, univariate statistical and semivariogram analyses were conducted for data from different formations to define the distribution and continuity of various attributes. Sequential simulations performed stochastic assessment of these attributes, such as gas content, strata thickness, and strata displacement. These analyses were followed by calculations of gas-in-place and their uncertainties in the Pittsburgh seam caved zone and fractured zone of longwall mines in this mining district. Grid blanking was used to isolate the volume over the actual panels from the entire modeled district and to calculate gas amounts that were directly related to the emissions in longwall mines.Results indicated that gas-in-place in the Pittsburgh seam, in the caved zone and in the fractured zone, as well as displacements in major rock units, showed spatial correlations that could be modeled and estimated using geostatistical methods. This study showed that GIP volumes may

  5. Portal vein ligation is as effective as sequential portal vein and hepatic artery ligation in inducing contralateral liver hypertrophy in a rat model

    NARCIS (Netherlands)

    Veteläinen, Reeta; Dinant, Sander; van Vliet, Arlène; van Gulik, Thomas M.

    2006-01-01

    PURPOSE: Dual embolization of the hepatic artery and portal vein (PV) has been proposed to enhance contralateral liver regeneration before resection. The aim of this study was to evaluate the effect of PV ligation compared with simultaneous or sequential dual ligation on regeneration,

  6. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  7. Vocal fold injection medialization laryngoplasty.

    Science.gov (United States)

    Modi, Vikash K

    2012-01-01

    Unilateral vocal fold paralysis (UVFP) can cause glottic insufficiency that can result in hoarseness, chronic cough, dysphagia, and/or aspiration. In rare circumstances, UVFP can cause airway obstruction necessitating a tracheostomy. The treatment options for UVFP include observation, speech therapy, vocal fold injection medialization laryngoplasty, thyroplasty, and laryngeal reinnervation. In this chapter, the author will discuss the technique of vocal fold injection for medialization of a UVFP. Copyright © 2012 S. Karger AG, Basel.

  8. The review on tessellation origami inspired folded structure

    Science.gov (United States)

    Chu, Chai Chen; Keong, Choong Kok

    2017-10-01

    Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

  9. Sequential radioimmunotherapy with 177Lu- and 211At-labeled monoclonal antibody BR96 in a syngeneic rat colon carcinoma model

    DEFF Research Database (Denmark)

    Eriksson, Sophie E; Elgström, Erika; Bäck, Tom

    2014-01-01

    for small, established tumors. A combination of such radionuclides may be successful in regimens of radioimmunotherapy. In this study, rats were treated by sequential administration of first a 177Lu-labeled antibody, followed by a 211At-labeled antibody 25 days later. METHODS: Rats bearing solid colon...... carcinoma tumors were treated with 400 MBq/kg body weight 177Lu-BR96. After 25 days, three groups of animals were given either 5 or 10 MBq/kg body weight of 211At-BR96 simultaneously with or without a blocking agent reducing halogen uptake in normal tissues. Control animals were not given any 211At-BR96....... The rats suffered from reversible myelotoxicity after treatment. CONCLUSIONS: Sequential administration of 177Lu-BR96 and 211At-BR96 resulted in tolerable toxicity providing halogen blocking but did not enhance the therapeutic effect....

  10. Solvent Effects on Protein Folding/Unfolding

    Science.gov (United States)

    García, A. E.; Hillson, N.; Onuchic, J. N.

    Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.

  11. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  12. How old is your fold?

    NARCIS (Netherlands)

    Winstanley, Henry F.; Abeln, Sanne; Deane, Charlotte M.

    Motivation: At present there exists no age estimate for the different protein structures found in nature. It has become clear from occurrence studies that different folds arose at different points in evolutionary time. An estimation of the age of different folds would be a starting point for many

  13. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  14. Adaptive sequential controller

    Energy Technology Data Exchange (ETDEWEB)

    El-Sharkawi, Mohamed A. (Renton, WA); Xing, Jian (Seattle, WA); Butler, Nicholas G. (Newberg, OR); Rodriguez, Alonso (Pasadena, CA)

    1994-01-01

    An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

  15. Adaptive sequential controller

    Science.gov (United States)

    El-Sharkawi, Mohamed A.; Xing, Jian; Butler, Nicholas G.; Rodriguez, Alonso

    1994-01-01

    An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

  16. Periodic folding of viscous sheets

    Science.gov (United States)

    Ribe, Neil M.

    2003-09-01

    The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

  17. Factors that affect coseismic folds in an overburden layer

    Science.gov (United States)

    Zeng, Shaogang; Cai, Yongen

    2018-03-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.

  18. Quantum Inequalities and Sequential Measurements

    International Nuclear Information System (INIS)

    Candelpergher, B.; Grandouz, T.; Rubinx, J.L.

    2011-01-01

    In this article, the peculiar context of sequential measurements is chosen in order to analyze the quantum specificity in the two most famous examples of Heisenberg and Bell inequalities: Results are found at some interesting variance with customary textbook materials, where the context of initial state re-initialization is described. A key-point of the analysis is the possibility of defining Joint Probability Distributions for sequential random variables associated to quantum operators. Within the sequential context, it is shown that Joint Probability Distributions can be defined in situations where not all of the quantum operators (corresponding to random variables) do commute two by two. (authors)

  19. Sequential Foreign Investments, Regional Technology Platforms and the Evolution of Japanese Multinationals in East Asia

    OpenAIRE

    Song, Jaeyong

    2001-01-01

    IVABSTRACTIn this paper, we investigate the firm-level mechanisms that underlie the sequential foreign direct investment (FDI) decisions of multinational corporations (MNCs). To understand inter-firm heterogeneity in the sequential FDI behaviors of MNCs, we develop a firm capability-based model of sequential FDI decisions. In the setting of Japanese electronics MNCs in East Asia, we empirically examine how prior investments in firm capabilities affect sequential investments into existingprodu...

  20. Framework for sequential approximate optimization

    NARCIS (Netherlands)

    Jacobs, J.H.; Etman, L.F.P.; Keulen, van F.; Rooda, J.E.

    2004-01-01

    An object-oriented framework for Sequential Approximate Optimization (SAO) isproposed. The framework aims to provide an open environment for thespecification and implementation of SAO strategies. The framework is based onthe Python programming language and contains a toolbox of Python

  1. Sequential Monte Carlo with Highly Informative Observations

    OpenAIRE

    Del Moral, Pierre; Murray, Lawrence M.

    2014-01-01

    We propose sequential Monte Carlo (SMC) methods for sampling the posterior distribution of state-space models under highly informative observation regimes, a situation in which standard SMC methods can perform poorly. A special case is simulating bridges between given initial and final values. The basic idea is to introduce a schedule of intermediate weighting and resampling times between observation times, which guide particles towards the final state. This can always be done for continuous-...

  2. A new class of compact high sensitive tiltmeter based on the UNISA folded pendulum mechanical architecture

    Science.gov (United States)

    Barone, Fabrizio; Giordano, Gerardo

    2018-02-01

    We present the Extended Folded Pendulum Model (EFPM), a model developed for a quantitative description of the dynamical behavior of a folded pendulum generically oriented in space. This model, based on the Tait-Bryan angular reference system, highlights the relationship between the folded pendulum orientation in the gravitational field and its natural resonance frequency. Tis model validated by tests performed with a monolithic UNISA Folded Pendulum, highlights a new technique of implementation of folded pendulum based tiltmeters.

  3. Sequentially pulsed traveling wave accelerator

    Science.gov (United States)

    Caporaso, George J [Livermore, CA; Nelson, Scott D [Patterson, CA; Poole, Brian R [Tracy, CA

    2009-08-18

    A sequentially pulsed traveling wave compact accelerator having two or more pulse forming lines each with a switch for producing a short acceleration pulse along a short length of a beam tube, and a trigger mechanism for sequentially triggering the switches so that a traveling axial electric field is produced along the beam tube in synchronism with an axially traversing pulsed beam of charged particles to serially impart energy to the particle beam.

  4. Curved Folded Plate Timber Structures

    OpenAIRE

    Buri, Hans Ulrich; Stotz, Ivo; Weinand, Yves

    2011-01-01

    This work investigates the development of a Curved Origami Prototype made with timber panels. In the last fifteen years the timber industry has developed new, large size, timber panels. Composition and dimensions of these panels and the possibility of milling them with Computer Numerical Controlled machines shows great potential for folded plate structures. To generate the form of these structures we were inspired by Origami, the Japanese art of paper folding. Common paper tessellations are c...

  5. No-recoil approximation to the knock-on exchange potential in the double folding model for heavy-ion collisions

    International Nuclear Information System (INIS)

    Hagino, K.; Takehi, T.; Takigawa, N.

    2006-01-01

    We propose the no-recoil approximation, which is valid for heavy systems, for a double folding nucleus-nucleus potential. With this approximation, the nonlocal knock-on exchange contribution becomes a local form. We discuss the applicability of this approximation for elastic scattering of the 6 Li + 40 Ca system. We find that, for this and heavier systems , the no-recoil approximation works as good as another widely used local approximation that employs a local plane wave for the relative motion between the colliding nuclei. We also compare the results of the no-recoil calculations with those of the zero-range approximation often used to handle the knock-on exchange effect

  6. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    Science.gov (United States)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    In appropriate physiological milieux proteins spontaneously fold into their functional three-dimensional structures. The amino acid sequences of functional proteins contain all the information necessary to specify the folds. This remarkable observation has spawned research aimed at answering two major questions. (1) Of all the conceivable structures that a protein can adopt, why is the ensemble of native-like structures the most favorable? (2) What are the paths by which proteins manage to robustly and reproducibly fold into their native structures? Anfinsen's thermodynamic hypothesis has guided the pursuit of answers to the first question whereas Levinthal's paradox has influenced the development of models for protein folding dynamics. Decades of work have led to significant advances in the folding problem. Mean-field models have been developed to capture our current, coarse grain understanding of the driving forces for protein folding. These models are being used to predict three-dimensional protein structures from sequence and stability profiles as a function of thermodynamic and chemical perturbations. Impressive strides have also been made in the field of protein design, also known as the inverse folding problem, thereby testing our understanding of the determinants of the fold specificities of different sequences. Early work on protein folding pathways focused on the specific sequence of events that could lead to a simplification of the search process. However, unifying principles proved to be elusive. Proteins that show reversible two-state folding-unfolding transitions turned out to be a gift of natural selection. Focusing on these simple systems helped researchers to uncover general principles regarding the origins of cooperativity in protein folding thermodynamics and kinetics. On the theoretical front, concepts borrowed from polymer physics and the physics of spin glasses led to the development of a framework based on energy landscape theories. These

  7. Sequential use of the STICS crop model and of the MACRO pesticide fate model to simulate pesticides leaching in cropping systems.

    Science.gov (United States)

    Lammoglia, Sabine-Karen; Moeys, Julien; Barriuso, Enrique; Larsbo, Mats; Marín-Benito, Jesús-María; Justes, Eric; Alletto, Lionel; Ubertosi, Marjorie; Nicolardot, Bernard; Munier-Jolain, Nicolas; Mamy, Laure

    2017-03-01

    The current challenge in sustainable agriculture is to introduce new cropping systems to reduce pesticides use in order to reduce ground and surface water contamination. However, it is difficult to carry out in situ experiments to assess the environmental impacts of pesticide use for all possible combinations of climate, crop, and soils; therefore, in silico tools are necessary. The objective of this work was to assess pesticides leaching in cropping systems coupling the performances of a crop model (STICS) and of a pesticide fate model (MACRO). STICS-MACRO has the advantage of being able to simulate pesticides fate in complex cropping systems and to consider some agricultural practices such as fertilization, mulch, or crop residues management, which cannot be accounted for with MACRO. The performance of STICS-MACRO was tested, without calibration, from measurements done in two French experimental sites with contrasted soil and climate properties. The prediction of water percolation and pesticides concentrations with STICS-MACRO was satisfactory, but it varied with the pedoclimatic context. The performance of STICS-MACRO was shown to be similar or better than that of MACRO. The improvement of the simulation of crop growth allowed better estimate of crop transpiration therefore of water balance. It also allowed better estimate of pesticide interception by the crop which was found to be crucial for the prediction of pesticides concentrations in water. STICS-MACRO is a new promising tool to improve the assessment of the environmental risks of pesticides used in cropping systems.

  8. The influence of thyroarytenoid and cricothyroid muscle activation on vocal fold stiffness and eigenfrequencies

    OpenAIRE

    Yin, Jun; Zhang, Zhaoyan

    2013-01-01

    The influence of the thyroarytenoid (TA) and cricothyroid (CT) muscle activation on vocal fold stiffness and eigenfrequencies was investigated in a muscularly controlled continuum model of the vocal folds. Unlike the general understanding that vocal fold fundamental frequency was determined by vocal fold tension, this study showed that vocal fold eigenfrequencies were primarily determined by vocal fold stiffness. This study further showed that, with reference to the resting state of zero stra...

  9. Repairing the vibratory vocal fold.

    Science.gov (United States)

    Long, Jennifer L

    2018-01-01

    A vibratory vocal fold replacement would introduce a new treatment paradigm for structural vocal fold diseases such as scarring and lamina propria loss. This work implants a tissue-engineered replacement for vocal fold lamina propria and epithelium in rabbits and compares histology and function to injured controls and orthotopic transplants. Hypotheses were that the cell-based implant would engraft and control the wound response, reducing fibrosis and restoring vibration. Translational research. Rabbit adipose-derived mesenchymal stem cells (ASC) were embedded within a three-dimensional fibrin gel, forming the cell-based outer vocal fold replacement (COVR). Sixteen rabbits underwent unilateral resection of vocal fold epithelium and lamina propria, as well as reconstruction with one of three treatments: fibrin glue alone with healing by secondary intention, replantation of autologous resected vocal fold cover, or COVR implantation. After 4 weeks, larynges were examined histologically and with phonation. Fifteen rabbits survived. All tissues incorporated well after implantation. After 1 month, both graft types improved histology and vibration relative to injured controls. Extracellular matrix (ECM) of the replanted mucosa was disrupted, and ECM of the COVR implants remained immature. Immune reaction was evident when male cells were implanted into female rabbits. Best histologic and short-term vibratory outcomes were achieved with COVR implants containing male cells implanted into male rabbits. Vocal fold cover replacement with a stem cell-based tissue-engineered construct is feasible and beneficial in acute rabbit implantation. Wound-modifying behavior of the COVR implant is judged to be an important factor in preventing fibrosis. NA. Laryngoscope, 128:153-159, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  10. Folding Membrane Proteins by Deep Transfer Learning

    KAUST Repository

    Wang, Sheng

    2017-08-29

    Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here, we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-MPs and then predicts 3D structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs, and generates 3D models with root-mean-square deviation (RMSD) less than 4 and 5 Å for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation project shows that our method predicted high-resolution 3D models for two recent test MPs of 210 residues with RMSD ∼2 Å. We estimated that our method could predict correct folds for 1,345–1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at MPs.

  11. Comparing the Folding and Misfolding Energy Landscapes of Phosphoglycerate Kinase

    OpenAIRE

    Agocs, Gergely; Szabo, Bence T.; Koehler, Gottfried; Osvath, Szabolcs

    2012-01-01

    Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the prop...

  12. Ligand-promoted protein folding by biased kinetic partitioning.

    Science.gov (United States)

    Hingorani, Karan S; Metcalf, Matthew C; Deming, Derrick T; Garman, Scott C; Powers, Evan T; Gierasch, Lila M

    2017-04-01

    Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.

  13. Iterative Controller Tuning for Process with Fold Bifurcations

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted; Poulsen, Niels Kjølstad; Jørgensen, Sten Bay

    2007-01-01

    Processes involving fold bifurcation are notoriously difficult to control in the vicinity of the fold where most often optimal productivity is achieved . In cases with limited process insight a model based control synthesis is not possible. This paper uses a data driven approach with an improved...... version of iterative feedback tuning to optimizing a closed loop performance criterion, as a systematic tool for tuning process with fold bifurcations....

  14. Remarks on sequential designs in risk assessment

    International Nuclear Information System (INIS)

    Seidenfeld, T.

    1982-01-01

    The special merits of sequential designs are reviewed in light of particular challenges that attend risk assessment for human population. The kinds of ''statistical inference'' are distinguished and the problem of design which is pursued is the clash between Neyman-Pearson and Bayesian programs of sequential design. The value of sequential designs is discussed and the Neyman-Pearson vs. Bayesian sequential designs are probed in particular. Finally, warnings with sequential designs are considered, especially in relation to utilitarianism

  15. Objective Quantification of Pre-and Postphonosurgery Vocal Fold Vibratory Characteristics Using High-Speed Videoendoscopy and a Harmonic Waveform Model

    Science.gov (United States)

    Ikuma, Takeshi; Kunduk, Melda; McWhorter, Andrew J.

    2014-01-01

    Purpose: The model-based quantitative analysis of high-speed videoendoscopy (HSV) data at a low frame rate of 2,000 frames per second was assessed for its clinical adequacy. Stepwise regression was employed to evaluate the HSV parameters using harmonic models and their relationships to the Voice Handicap Index (VHI). Also, the model-based HSV…

  16. On the relationship between input parameters in two-mass vocal-fold model with acoustical coupling an signal parameters of the glottal flow

    NARCIS (Netherlands)

    van Hirtum, Annemie; Lopez, Ines; Hirschberg, Abraham; Pelorson, Xavier

    2003-01-01

    In this paper the sensitivity of the two-mass model with acoustical coupling to the model input-parameters is assessed. The model-output or the glottal volume air flow is characterised by signal-parameters in the time-domain. The influence of changing input-parameters on the signal-parameters is

  17. On the relationship between input parameters in the two-mass vocal-fold model with acoustical coupling and signal parameters of the glottal flow

    NARCIS (Netherlands)

    Hirtum, van A.; Lopez Arteaga, I.; Hirschberg, A.; Pelorson, X.

    2003-01-01

    In this paper the sensitivity of the two-mass model with acoustical coupling to the model input-parameters is assessed. The model-output or the glottal volume air flow is characterised by signal-parameters in the time-domain. The influence of changing input-parameters on the signal-parameters is

  18. Folding pathways explored with artificial potential functions

    International Nuclear Information System (INIS)

    Ulutaş, B; Bozma, I; Haliloglu, T

    2009-01-01

    This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions—originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that—motivated by work on robotic navigation—a nonlinear compositional scheme of constructing the energy model is adapted instead of an additive formulation. The artificial potential naturally gives rise to a dynamic system for the protein structure that ensures collision-free motion to an equilibrium point. In cases where the equilibrium point is the native conformation, the motion trajectory corresponds to the folding pathway. This framework is used to investigate folding in a variety of protein structures, and the results are compared with those of other approaches including experimental studies

  19. Sequential flavor symmetry breaking

    International Nuclear Information System (INIS)

    Feldmann, Thorsten; Jung, Martin; Mannel, Thomas

    2009-01-01

    The gauge sector of the standard model exhibits a flavor symmetry that allows for independent unitary transformations of the fermion multiplets. In the standard model the flavor symmetry is broken by the Yukawa couplings to the Higgs boson, and the resulting fermion masses and mixing angles show a pronounced hierarchy. In this work we connect the observed hierarchy to a sequence of intermediate effective theories, where the flavor symmetries are broken in a stepwise fashion by vacuum expectation values of suitably constructed spurion fields. We identify the possible scenarios in the quark sector and discuss some implications of this approach.

  20. Sequential flavor symmetry breaking

    Science.gov (United States)

    Feldmann, Thorsten; Jung, Martin; Mannel, Thomas

    2009-08-01

    The gauge sector of the standard model exhibits a flavor symmetry that allows for independent unitary transformations of the fermion multiplets. In the standard model the flavor symmetry is broken by the Yukawa couplings to the Higgs boson, and the resulting fermion masses and mixing angles show a pronounced hierarchy. In this work we connect the observed hierarchy to a sequence of intermediate effective theories, where the flavor symmetries are broken in a stepwise fashion by vacuum expectation values of suitably constructed spurion fields. We identify the possible scenarios in the quark sector and discuss some implications of this approach.

  1. Sequential versus simultaneous market delineation

    DEFF Research Database (Denmark)

    Haldrup, Niels; Møllgaard, Peter; Kastberg Nielsen, Claus

    2005-01-01

    and geographical markets. Using a unique data setfor prices of Norwegian and Scottish salmon, we propose a methodologyfor simultaneous market delineation and we demonstrate that comparedto a sequential approach conclusions will be reversed.JEL: C3, K21, L41, Q22Keywords: Relevant market, econometric delineation......Delineation of the relevant market forms a pivotal part of most antitrustcases. The standard approach is sequential. First the product marketis delineated, then the geographical market is defined. Demand andsupply substitution in both the product dimension and the geographicaldimension...

  2. Sequential logic analysis and synthesis

    CERN Document Server

    Cavanagh, Joseph

    2007-01-01

    Until now, there was no single resource for actual digital system design. Using both basic and advanced concepts, Sequential Logic: Analysis and Synthesis offers a thorough exposition of the analysis and synthesis of both synchronous and asynchronous sequential machines. With 25 years of experience in designing computing equipment, the author stresses the practical design of state machines. He clearly delineates each step of the structured and rigorous design principles that can be applied to practical applications. The book begins by reviewing the analysis of combinatorial logic and Boolean a

  3. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...... acceptor sites. In some cases, all the newly synthesized mutant protein was modified at the novel site while in others no modification took place. In the most interesting category of mutants, the level of glycosylation was dependent on the conditions for folding. This shows that folding and glycosylation...

  4. Thermodynamics of protein folding: a random matrix formulation.

    Science.gov (United States)

    Shukla, Pragya

    2010-10-20

    The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters, e.g. the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows, however, that the evolution of the statistical measures, e.g. Gibbs free energy, heat capacity, and entropy, is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies. © 2010 IOP Publishing Ltd

  5. Comparison of Sequential and Variational Data Assimilation

    Science.gov (United States)

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

    2017-04-01

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

  6. Wrinkles, folds, and plasticity in granular rafts

    Science.gov (United States)

    Jambon-Puillet, Etienne; Josserand, Christophe; Protière, Suzie

    2017-09-01

    We investigate the mechanical response of a compressed monolayer of large and dense particles at a liquid-fluid interface: a granular raft. Upon compression, rafts first wrinkle; then, as the confinement increases, the deformation localizes in a unique fold. This characteristic buckling pattern is usually associated with floating elastic sheets, and as a result, particle laden interfaces are often modeled as such. Here, we push this analogy to its limits by comparing quantitative measurements of the raft morphology to a theoretical continuous elastic model of the interface. We show that, although powerful to describe the wrinkle wavelength, the wrinkle-to-fold transition, and the fold shape, this elastic description does not capture the finer details of the experiment. We describe an unpredicted secondary wavelength, a compression discrepancy with the model, and a hysteretic behavior during compression cycles, all of which are a signature of the intrinsic discrete and frictional nature of granular rafts. It suggests also that these composite materials exhibit both plastic transition and jamming dynamics.

  7. Generalized infimum and sequential product of quantum effects

    International Nuclear Information System (INIS)

    Li Yuan; Sun Xiuhong; Chen Zhengli

    2007-01-01

    The quantum effects for a physical system can be described by the set E(H) of positive operators on a complex Hilbert space H that are bounded above by the identity operator I. For A, B(set-membership sign)E(H), the operation of sequential product A(convolution sign)B=A 1/2 BA 1/2 was proposed as a model for sequential quantum measurements. A nice investigation of properties of the sequential product has been carried over [Gudder, S. and Nagy, G., 'Sequential quantum measurements', J. Math. Phys. 42, 5212 (2001)]. In this note, we extend some results of this reference. In particular, a gap in the proof of Theorem 3.2 in this reference is overcome. In addition, some properties of generalized infimum A sqcap B are studied

  8. Evaluation Using Sequential Trials Methods.

    Science.gov (United States)

    Cohen, Mark E.; Ralls, Stephen A.

    1986-01-01

    Although dental school faculty as well as practitioners are interested in evaluating products and procedures used in clinical practice, research design and statistical analysis can sometimes pose problems. Sequential trials methods provide an analytical structure that is both easy to use and statistically valid. (Author/MLW)

  9. The influence of thyroarytenoid and cricothyroid muscle activation on vocal fold stiffness and eigenfrequencies

    Science.gov (United States)

    Yin, Jun; Zhang, Zhaoyan

    2013-01-01

    The influence of the thyroarytenoid (TA) and cricothyroid (CT) muscle activation on vocal fold stiffness and eigenfrequencies was investigated in a muscularly controlled continuum model of the vocal folds. Unlike the general understanding that vocal fold fundamental frequency was determined by vocal fold tension, this study showed that vocal fold eigenfrequencies were primarily determined by vocal fold stiffness. This study further showed that, with reference to the resting state of zero strain, vocal fold stiffness in both body and cover layers increased with either vocal fold elongation or shortening. As a result, whether vocal fold eigenfrequencies increased or decreased with CT/TA activation depended on how the CT/TA interaction influenced vocal fold deformation. For conditions of strong CT activation and thus an elongated vocal fold, increasing TA contraction reduced the degree of vocal fold elongation and thus reduced vocal fold eigenfrequencies. For conditions of no CT activation and thus a resting or slightly shortened vocal fold, increasing TA contraction increased the degree of vocal fold shortening and thus increased vocal fold eigenfrequencies. In the transition region of a slightly elongated vocal fold, increasing TA contraction first decreased and then increased vocal fold eigenfrequencies. PMID:23654401

  10. A Relational Account of Call-by-Value Sequentiality

    DEFF Research Database (Denmark)

    Riecke, Jon Gary; Sandholm, Anders Bo

    2002-01-01

    We construct a model for FPC, a purely functional, sequential, call-by-value language. The model is built from partial continuous functions, in the style of Plotkin, further constrained to be uniform with respect to a class of logical relations. We prove that the model is fully abstract....

  11. Dynamics in thin folded polymer films

    Science.gov (United States)

    Croll, Andrew; Rozairo, Damith

    Origami and Kirigami inspired structures depend on a complex interplay between geometry and material properties. While clearly important to the overall function, very little attention has focused on how extreme curvatures and singularities in real materials influence the overall dynamic behaviour of folded structures. In this work we use a set of three polymer thin films in order to closely examine the interaction of material and geometry. Specifically, we use polydimethylsiloxane (PDMS), polystyrene (PS) and polycarbonate (PC) thin films which we subject to loading in several model geometries of varying complexity. Depending on the material, vastly different responses are noted in our experiments; D-cones can annihilate, cut or lead to a crumpling cascade when pushed through a film. Remarkably, order can be generated with additional perturbation. Finally, the role of adhesion in complex folded structures can be addressed. AFOSR under the Young Investigator Program (FA9550-15-1-0168).

  12. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    Science.gov (United States)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  13. Deformation and kinematics of the central Kirthar Fold Belt, Pakistan

    Science.gov (United States)

    Hinsch, Ralph; Hagedorn, Peter; Asmar, Chloé; Nasim, Muhammad; Aamir Rasheed, Muhammad; Kiely, James M.

    2017-04-01

    The Kirthar Fold Belt is part of the lateral mountain belts in Pakistan linking the Himalaya orogeny with the Makran accretionary wedge. This region is deforming very oblique/nearly parallel to the regional plate motion vector. The study area is situated between the prominent Chaman strike-slip fault in the West and the un-deformed foreland (Kirthar Foredeep/Middle Indus Basin) in the East. The Kirthar Fold Belt is subdivided into several crustal blocks/units based on structural orientation and deformation style (e.g. Kallat, Khuzdar, frontal Kirthar). This study uses newly acquired and depth-migrated 2D seismic lines, surface geology observations and Google Earth assessments to construct three balanced cross sections for the frontal part of the fold belt. Further work was done in order to insure the coherency of the built cross-sections by taking a closer look at the regional context inferred from published data, simple analogue modelling, and constructed regional sketch sections. The Khuzdar area and the frontal Kirthar Fold Belt are dominated by folding. Large thrusts with major stratigraphic repetitions are not observed. Furthermore, strike-slip faults in the Khuzdar area are scarce and not observed in the frontal Kirthar Fold Belt. The regional structural elevation rises from the foreland across the Kirthar Fold Belt towards the hinterland (Khuzdar area). These observations indicate that basement-involved deformation is present at depth. The domination of folding indicates a weak decollement below the folds (soft-linked deformation). The fold pattern in the Khuzdar area is complex, whereas the large folds of the central Kirthar Fold Belt trend SSW-NNE to N-S and are best described as large detachment folds that have been slightly uplifted by basement involved transpressive deformation underneath. Towards the foreland, the deformation is apparently more hard-linked and involves fault-propagation folding and a small triangle zone in Cretaceous sediments

  14. Time scale of random sequential adsorption.

    Science.gov (United States)

    Erban, Radek; Chapman, S Jonathan

    2007-04-01

    A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) The kinetics of the chemical reaction between adsorbing molecules and the surface and (ii) geometrical constraints on the surface made by molecules which are already adsorbed. The process (i) is modeled in a diffusion-driven context, i.e., the conditional probability of adsorbing a molecule provided that the molecule hits the surface is related to the macroscopic surface reaction rate. The geometrical constraint (ii) is modeled using random sequential adsorption (RSA), which is the sequential addition of molecules at random positions on a surface; one attempt to attach a molecule is made per one RSA simulation time step. By coupling RSA with the diffusion of molecules in the solution above the surface the RSA simulation time step is related to the real physical time. The method is illustrated on a model of chemisorption of reactive polymers to a virus surface.

  15. A Bayesian sequential processor approach to spectroscopic portal system decisions

    Energy Technology Data Exchange (ETDEWEB)

    Sale, K; Candy, J; Breitfeller, E; Guidry, B; Manatt, D; Gosnell, T; Chambers, D

    2007-07-31

    The development of faster more reliable techniques to detect radioactive contraband in a portal type scenario is an extremely important problem especially in this era of constant terrorist threats. Towards this goal the development of a model-based, Bayesian sequential data processor for the detection problem is discussed. In the sequential processor each datum (detector energy deposit and pulse arrival time) is used to update the posterior probability distribution over the space of model parameters. The nature of the sequential processor approach is that a detection is produced as soon as it is statistically justified by the data rather than waiting for a fixed counting interval before any analysis is performed. In this paper the Bayesian model-based approach, physics and signal processing models and decision functions are discussed along with the first results of our research.

  16. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations : Application in the refinement of de novo models

    NARCIS (Netherlands)

    Fan, Hao; Periole, Xavier; Mark, Alan E.

    The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment,

  17. The use of paleo-thermo-barometers and coupled thermal, fluid flow and pore fluid pressure modelling for hydrocarbon and reservoir prediction in fold and thrust belts

    NARCIS (Netherlands)

    Roure, F.; Andriessen, P.A.M.; Callot, J.P.; Ferket, H.; Gonzales, E.; Guilhaumou, N.; Hardebol, N.J.; Lacombe, O.; Malandain, J.; Mougin, P.; Muska, K.; Ortuno, S.; Sassi, W.; Swennen, R.; Vilasi, N.

    2010-01-01

    Basin modelling tools are now more efficient to reconstruct palinspastic structural cross sections and compute the history of temperature, pore-fluid pressure and fluid flow circulations in complex structural settings. In many cases and especially in areas where limited erosion occurred, the use of

  18. Current Understanding and Future Directions for Vocal Fold Mechanobiology

    Science.gov (United States)

    Li, Nicole Y.K.; Heris, Hossein K.; Mongeau, Luc

    2013-01-01

    The vocal folds, which are located in the larynx, are the main organ of voice production for human communication. The vocal folds are under continuous biomechanical stress similar to other mechanically active organs, such as the heart, lungs, tendons and muscles. During speech and singing, the vocal folds oscillate at frequencies ranging from 20 Hz to 3 kHz with amplitudes of a few millimeters. The biomechanical stress associated with accumulated phonation is believed to alter vocal fold cell activity and tissue structure in many ways. Excessive phonatory stress can damage tissue structure and induce a cell-mediated inflammatory response, resulting in a pathological vocal fold lesion. On the other hand, phonatory stress is one major factor in the maturation of the vocal folds into a specialized tri-layer structure. One specific form of vocal fold oscillation, which involves low impact and large amplitude excursion, is prescribed therapeutically for patients with mild vocal fold injuries. Although biomechanical forces affect vocal fold physiology and pathology, there is little understanding of how mechanical forces regulate these processes at the cellular and molecular level. Research into vocal fold mechanobiology has burgeoned over the past several years. Vocal fold bioreactors are being developed in several laboratories to provide a biomimic environment that allows the systematic manipulation of physical and biological factors on the cells of interest in vitro. Computer models have been used to simulate the integrated response of cells and proteins as a function of phonation stress. The purpose of this paper is to review current research on the mechanobiology of the vocal folds as it relates to growth, pathogenesis and treatment as well as to propose specific research directions that will advance our understanding of this subject. PMID:24812638

  19. Force generation by titin folding.

    Science.gov (United States)

    Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

    2017-07-01

    Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

  20. Decoding restricted participation in sequential electricity markets

    Energy Technology Data Exchange (ETDEWEB)

    Knaut, Andreas; Paschmann, Martin

    2017-06-15

    Restricted participation in sequential markets may cause high price volatility and welfare losses. In this paper we therefore analyze the drivers of restricted participation in the German intraday auction which is a short-term electricity market with quarter-hourly products. Applying a fundamental electricity market model with 15-minute temporal resolution, we identify the lack of sub-hourly market coupling being the most relevant driver of restricted participation. We derive a proxy for price volatility and find that full market coupling may trigger quarter-hourly price volatility to decrease by a factor close to four.

  1. From sequential to parallel programming with patterns

    CERN Document Server

    CERN. Geneva

    2018-01-01

    To increase in both performance and efficiency, our programming models need to adapt to better exploit modern processors. The classic idioms and patterns for programming such as loops, branches or recursion are the pillars of almost every code and are well known among all programmers. These patterns all have in common that they are sequential in nature. Embracing parallel programming patterns, which allow us to program for multi- and many-core hardware in a natural way, greatly simplifies the task of designing a program that scales and performs on modern hardware, independently of the used programming language, and in a generic way.

  2. Quantification of fold growth of frontal antiforms in the Zagros fold and thrust belt (Kurdistan, NE Iraq)

    Science.gov (United States)

    Bretis, Bernhard; Bartl, Nikolaus; Graseman, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold and thrust belt is a seismically active orogen, where actual kinematic models based on GPS networks suggest a north-south shortening between Arabian and Eurasian in the order of 1.5-2.5 cm/yr. Most of this deformation is partitioned in south-southwest oriented folding and thrusting with northwest-southeast to north-south trending dextral strike slip faults. The Zagros fold and thrust belt is of great economic interest because it has been estimated that this area contains about 15% of the global recoverable hydrocarbons. Whereas the SE parts of the Zagros have been investigated by detailed geological studies, the NW extent being part of the Republic of Iraq have experienced considerably less attention. In this study we combine field work and remote sensing techniques in order to investigate the interaction of erosion and fold growth in the area NE of Erbil (Kurdistan, Iraq). In particular we focus on the interaction of the transient development of drainage patterns along growing antiforms, which directly reflects the kinematics of progressive fold growth. Detailed geomorphological studies of the Bana Bawi-, Permam- and Safeen fold trains show that these anticlines have not developed from subcylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification. This fold segments with length between 5 and 25 km have been detected by mapping ancient and modern river courses that initially cut the nose of growing folds and eventually got defeated leaving behind a wind gap. Fold segments, propagating in different directions force rivers to join resulting in steep gorges, which dissect the merging fold noses. Along rapidly lateral growing folds (e.g. at the SE end of the Bana Bawi Anticline) we observed "curved wind gaps", a new type of abandoned river course, where form of the wind gap mimics a formed nose of a growing antiform. The inherited curved segments of uplifted curved river courses strongly

  3. Multi-agent sequential hypothesis testing

    KAUST Repository

    Kim, Kwang-Ki K.; Shamma, Jeff S.

    2014-01-01

    incorporate costs of taking private/public measurements, costs of time-difference and disagreement in actions of agents, and costs of false declaration/choices in the sequential hypothesis testing. The corresponding sequential decision processes have well

  4. A Bayesian Theory of Sequential Causal Learning and Abstract Transfer.

    Science.gov (United States)

    Lu, Hongjing; Rojas, Randall R; Beckers, Tom; Yuille, Alan L

    2016-03-01

    Two key research issues in the field of causal learning are how people acquire causal knowledge when observing data that are presented sequentially, and the level of abstraction at which learning takes place. Does sequential causal learning solely involve the acquisition of specific cause-effect links, or do learners also acquire knowledge about abstract causal constraints? Recent empirical studies have revealed that experience with one set of causal cues can dramatically alter subsequent learning and performance with entirely different cues, suggesting that learning involves abstract transfer, and such transfer effects involve sequential presentation of distinct sets of causal cues. It has been demonstrated that pre-training (or even post-training) can modulate classic causal learning phenomena such as forward and backward blocking. To account for these effects, we propose a Bayesian theory of sequential causal learning. The theory assumes that humans are able to consider and use several alternative causal generative models, each instantiating a different causal integration rule. Model selection is used to decide which integration rule to use in a given learning environment in order to infer causal knowledge from sequential data. Detailed computer simulations demonstrate that humans rely on the abstract characteristics of outcome variables (e.g., binary vs. continuous) to select a causal integration rule, which in turn alters causal learning in a variety of blocking and overshadowing paradigms. When the nature of the outcome variable is ambiguous, humans select the model that yields the best fit with the recent environment, and then apply it to subsequent learning tasks. Based on sequential patterns of cue-outcome co-occurrence, the theory can account for a range of phenomena in sequential causal learning, including various blocking effects, primacy effects in some experimental conditions, and apparently abstract transfer of causal knowledge. Copyright © 2015

  5. Automatic synthesis of sequential control schemes

    International Nuclear Information System (INIS)

    Klein, I.

    1993-01-01

    Of all hard- and software developed for industrial control purposes, the majority is devoted to sequential, or binary valued, control and only a minor part to classical linear control. Typically, the sequential parts of the controller are invoked during startup and shut-down to bring the system into its normal operating region and into some safe standby region, respectively. Despite its importance, fairly little theoretical research has been devoted to this area, and sequential control programs are therefore still created manually without much theoretical support to obtain a systematic approach. We propose a method to create sequential control programs automatically. The main ideas is to spend some effort off-line modelling the plant, and from this model generate the control strategy, that is the plan. The plant is modelled using action structures, thereby concentrating on the actions instead of the states of the plant. In general the planning problem shows exponential complexity in the number of state variables. However, by focusing on the actions, we can identify problem classes as well as algorithms such that the planning complexity is reduced to polynomial complexity. We prove that these algorithms are sound, i.e., the generated solution will solve the stated problem, and complete, i.e., if the algorithms fail, then no solution exists. The algorithms generate a plan as a set of actions and a partial order on this set specifying the execution order. The generated plant is proven to be minimal and maximally parallel. For a larger class of problems we propose a method to split the original problem into a number of simple problems that can each be solved using one of the presented algorithms. It is also shown how a plan can be translated into a GRAFCET chart, and to illustrate these ideas we have implemented a planing tool, i.e., a system that is able to automatically create control schemes. Such a tool can of course also be used on-line if it is fast enough. This

  6. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  7. Araguaia fold belt, new geochronological data

    International Nuclear Information System (INIS)

    Lafon, J.M.; Macambira, J.B.; Macambira, M.J.B.; Moura, C.A.V.; Souza, A.C.C.

    1990-01-01

    The northern part of the Araguaia Fold Belt (AFB) outcrops in a N-S direction for about 400 km in the state of Tocantins. Dome-like structures occur in this fold belt also in a N-S direction. Both deformation and metamorphism increase from the West to the East. The basement of the AFB consist of Colmeia complex and Cantao gneiss, which crop out mainly in the core of the dome-like structures. The supracrustals rocks of the fold belt belongs to the Baixo Araguaia supergroup which is divided into the lower Estrondo group and the upper Tocantins group. Preliminary Sm-Nd data from the Colmeia complex (Grota Rica dome) gave Archean model ages of 2.8 Ga (TNd sub(DM)) while Rb-Sr data in the same rocks give an age of 2530 ± 200 Ma. In the others dome-like structures, the Rb-Sr systematics gave ages for the Colmeia a complex of 2239 ± 47 Ma (Colmeia structure) and 1972 ± 46 Ma (Lontra structure). These younger ages are believed to represent partial to total isotopic resetting of the Rb-Sr system during the Transamazonian Event. The Rb-Sr studies of the Cantao gneiss gave an age of 1774 ± 31 Ma. (author)

  8. Origami-Inspired Folding of Thick, Rigid Panels

    Science.gov (United States)

    Trease, Brian P.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Zirbel, Shannon; Howell, Larry; Lang, Robert

    2014-01-01

    To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.

  9. Robustness of the Sequential Lineup Advantage

    Science.gov (United States)

    Gronlund, Scott D.; Carlson, Curt A.; Dailey, Sarah B.; Goodsell, Charles A.

    2009-01-01

    A growing movement in the United States and around the world involves promoting the advantages of conducting an eyewitness lineup in a sequential manner. We conducted a large study (N = 2,529) that included 24 comparisons of sequential versus simultaneous lineups. A liberal statistical criterion revealed only 2 significant sequential lineup…

  10. Sequential Probability Ration Tests : Conservative and Robust

    NARCIS (Netherlands)

    Kleijnen, J.P.C.; Shi, Wen

    2017-01-01

    In practice, most computers generate simulation outputs sequentially, so it is attractive to analyze these outputs through sequential statistical methods such as sequential probability ratio tests (SPRTs). We investigate several SPRTs for choosing between two hypothesized values for the mean output

  11. Mining Emerging Sequential Patterns for Activity Recognition in Body Sensor Networks

    DEFF Research Database (Denmark)

    Gu, Tao; Wang, Liang; Chen, Hanhua

    2010-01-01

    Body Sensor Networks oer many applications in healthcare, well-being and entertainment. One of the emerging applications is recognizing activities of daily living. In this paper, we introduce a novel knowledge pattern named Emerging Sequential Pattern (ESP)|a sequential pattern that discovers...... signicant class dierences|to recognize both simple (i.e., sequential) and complex (i.e., interleaved and concurrent) activities. Based on ESPs, we build our complex activity models directly upon the sequential model to recognize both activity types. We conduct comprehensive empirical studies to evaluate...

  12. In vivo measurement of vocal fold surface resistance.

    Science.gov (United States)

    Mizuta, Masanobu; Kurita, Takashi; Dillon, Neal P; Kimball, Emily E; Garrett, C Gaelyn; Sivasankar, M Preeti; Webster, Robert J; Rousseau, Bernard

    2017-10-01

    A custom-designed probe was developed to measure vocal fold surface resistance in vivo. The purpose of this study was to demonstrate proof of concept of using vocal fold surface resistance as a proxy of functional tissue integrity after acute phonotrauma using an animal model. Prospective animal study. New Zealand White breeder rabbits received 120 minutes of airflow without vocal fold approximation (control) or 120 minutes of raised intensity phonation (experimental). The probe was inserted via laryngoscope and placed on the left vocal fold under endoscopic visualization. Vocal fold surface resistance of the middle one-third of the vocal fold was measured after 0 (baseline), 60, and 120 minutes of phonation. After the phonation procedure, the larynx was harvested and prepared for transmission electron microscopy. In the control group, vocal fold surface resistance values remained stable across time points. In the experimental group, surface resistance (X% ± Y% relative to baseline) was significantly decreased after 120 minutes of raised intensity phonation. This was associated with structural changes using transmission electron microscopy, which revealed damage to the vocal fold epithelium after phonotrauma, including disruption of the epithelium and basement membrane, dilated paracellular spaces, and alterations to epithelial microprojections. In contrast, control vocal fold specimens showed well-preserved stratified squamous epithelia. These data demonstrate the feasibility of measuring vocal fold surface resistance in vivo as a means of evaluating functional vocal fold epithelial barrier integrity. Device prototypes are in development for additional testing, validation, and for clinical applications in laryngology. NA Laryngoscope, 127:E364-E370, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  13. Making Career Decisions--A Sequential Elimination Approach.

    Science.gov (United States)

    Gati, Itamar

    1986-01-01

    Presents a model for career decision making based on the sequential elimination of occupational alternatives, an adaptation for career decisions of Tversky's (1972) elimination-by-aspects theory of choice. The expected utility approach is reviewed as a representative compensatory model for career decisions. Advantages, disadvantages, and…

  14. Sequential Computerized Mastery Tests--Three Simulation Studies

    Science.gov (United States)

    Wiberg, Marie

    2006-01-01

    A simulation study of a sequential computerized mastery test is carried out with items modeled with the 3 parameter logistic item response theory model. The examinees' responses are either identically distributed, not identically distributed, or not identically distributed together with estimation errors in the item characteristics. The…

  15. Double folded Yukawa interaction potential between two heavy ions

    International Nuclear Information System (INIS)

    Bulgac, A.; Carstoiu, F.; Dumitrescu, O.

    1980-02-01

    A simple semi-analytical formula for the heavy ion interaction potential within the double-folding model approximation is obtained. The folded interaction is assumed to be expressed in Yukawa terms or the derivatives of them. The densities used can be both experimental or theoretical (of simple ''step-wise'', ''Fermi-Saxon-Woods'' or complicated ''shell model'' structure) densities. A way of inserting the exchange terms is discussed. Numerical calculations for some colliding partners are reported. (author)

  16. Measured and modeled evidence for a two-fold increase in water use efficiency at an old-growth forest site in the Pacific Northwest

    Science.gov (United States)

    Jiang, Y.; Rastogi, B.; Kim, J. B.; Voelker, S.; Meinzer, F. C.; Still, C. J.

    2017-12-01

    Water use efficiency (WUE), the ratio of carbon uptake to transpiration, has been widely recognized as an important measure of carbon and water cycling in plants, and is used to track forest ecosystem responses to climate change and rising atmospheric CO2concentrations. In this study we used eddy covariance measurement data and Ecosystem Demography model (ED2) simulations to explore the patterns and physiological and biophysical controls of WUE at Wind River Experimental Forest, an old-growth coniferous forest in the Pacific Northwest. We characterized how observed and simulated WUE vary between wet and dry years, and explored the drivers of the differences in WUE between the wet and dry years. Through this explorative process, we evaluated the utility of various ways that WUE have been computed in literature. Measurement-based and simulated WUE at the old-growth forest increased over twofold from 1998 to 2015. The primary driver of this trend is a decreasing trend in evapotranspiration (ET). There were significant inter-annual variations. For example, during drought years, higher air temperature drove increases in early season ET, thereby depleting soil water and decreasing GPP. Lower GPP in turn resulted in lower WUE. This mechanism might drive changes in future carbon and water budgets under warming climate. Our evaluation of multiple WUE metrics demonstrates that each metric has a distinct sensitivity to climate anomalies, but also indicates a robust increasing trend of WUE. Statistical (multiple linear regression) and machine learning (Random Forest) analyses of flux measurements indicated that atmospheric CO2 concentration, air temperature and radiation were the most important predictors of WUE at monthly, daily and half-hourly time scale, respectively. In contrast, WUE mechanism was stable across all time scales in ED2 simulations: vapor pressure deficit was consistently the most important predictor of WUE at the monthly, daily and half-hourly time scales.

  17. Vocal fold contact patterns based on normal modes of vibration.

    Science.gov (United States)

    Smith, Simeon L; Titze, Ingo R

    2018-05-17

    The fluid-structure interaction and energy transfer from respiratory airflow to self-sustained vocal fold oscillation continues to be a topic of interest in vocal fold research. Vocal fold vibration is driven by pressures on the vocal fold surface, which are determined by the shape of the glottis and the contact between vocal folds. Characterization of three-dimensional glottal shapes and contact patterns can lead to increased understanding of normal and abnormal physiology of the voice, as well as to development of improved vocal fold models, but a large inventory of shapes has not been directly studied previously. This study aimed to take an initial step toward characterizing vocal fold contact patterns systematically. Vocal fold motion and contact was modeled based on normal mode vibration, as it has been shown that vocal fold vibration can be almost entirely described by only the few lowest order vibrational modes. Symmetric and asymmetric combinations of the four lowest normal modes of vibration were superimposed on left and right vocal fold medial surfaces, for each of three prephonatory glottal configurations, according to a surface wave approach. Contact patterns were generated from the interaction of modal shapes at 16 normalized phases during the vibratory cycle. Eight major contact patterns were identified and characterized by the shape of the flow channel, with the following descriptors assigned: convergent, divergent, convergent-divergent, uniform, split, merged, island, and multichannel. Each of the contact patterns and its variation are described, and future work and applications are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Lexical decoder for continuous speech recognition: sequential neural network approach

    International Nuclear Information System (INIS)

    Iooss, Christine

    1991-01-01

    The work presented in this dissertation concerns the study of a connectionist architecture to treat sequential inputs. In this context, the model proposed by J.L. Elman, a recurrent multilayers network, is used. Its abilities and its limits are evaluated. Modifications are done in order to treat erroneous or noisy sequential inputs and to classify patterns. The application context of this study concerns the realisation of a lexical decoder for analytical multi-speakers continuous speech recognition. Lexical decoding is completed from lattices of phonemes which are obtained after an acoustic-phonetic decoding stage relying on a K Nearest Neighbors search technique. Test are done on sentences formed from a lexicon of 20 words. The results are obtained show the ability of the proposed connectionist model to take into account the sequentiality at the input level, to memorize the context and to treat noisy or erroneous inputs. (author) [fr

  19. Understanding ensemble protein folding at atomic detail

    International Nuclear Information System (INIS)

    Wallin, Stefan; Shakhnovich, Eugene I

    2008-01-01

    Although far from routine, simulating the folding of specific short protein chains on the computer, at a detailed atomic level, is starting to become a reality. This remarkable progress, which has been made over the last decade or so, allows a fundamental aspect of the protein folding process to be addressed, namely its statistical nature. In order to make quantitative comparisons with experimental kinetic data a complete ensemble view of folding must be achieved, with key observables averaged over the large number of microscopically different folding trajectories available to a protein chain. Here we review recent advances in atomic-level protein folding simulations and the new insight provided by them into the protein folding process. An important element in understanding ensemble folding kinetics are methods for analyzing many separate folding trajectories, and we discuss techniques developed to condense the large amount of information contained in an ensemble of trajectories into a manageable picture of the folding process. (topical review)

  20. Glycoprotein folding and quality-control mechanisms in protein-folding diseases

    Directory of Open Access Journals (Sweden)

    Sean P. Ferris

    2014-03-01

    Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

  1. Human visual system automatically encodes sequential regularities of discrete events.

    Science.gov (United States)

    Kimura, Motohiro; Schröger, Erich; Czigler, István; Ohira, Hideki

    2010-06-01

    regularities. In combination with a wide range of auditory MMN studies, the present study highlights the critical role of sensory systems in automatically encoding sequential regularities when modeling the world.

  2. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  3. Microstructure history effect during sequential thermomechanical processing

    International Nuclear Information System (INIS)

    Yassar, Reza S.; Murphy, John; Burton, Christina; Horstemeyer, Mark F.; El kadiri, Haitham; Shokuhfar, Tolou

    2008-01-01

    The key to modeling the material processing behavior is the linking of the microstructure evolution to its processing history. This paper quantifies various microstructural features of an aluminum automotive alloy that undergoes sequential thermomechanical processing which is comprised hot rolling of a 150-mm billet to a 75-mm billet, rolling to 3 mm, annealing, and then cold rolling to a 0.8-mm thickness sheet. The microstructural content was characterized by means of electron backscatter diffraction, scanning electron microscopy, and transmission electron microscopy. The results clearly demonstrate the evolution of precipitate morphologies, dislocation structures, and grain orientation distributions. These data can be used to improve material models that claim to capture the history effects of the processing materials

  4. A Sequential Multiplicative Extended Kalman Filter for Attitude Estimation Using Vector Observations

    Science.gov (United States)

    Qin, Fangjun; Jiang, Sai; Zha, Feng

    2018-01-01

    In this paper, a sequential multiplicative extended Kalman filter (SMEKF) is proposed for attitude estimation using vector observations. In the proposed SMEKF, each of the vector observations is processed sequentially to update the attitude, which can make the measurement model linearization more accurate for the next vector observation. This is the main difference to Murrell’s variation of the MEKF, which does not update the attitude estimate during the sequential procedure. Meanwhile, the covariance is updated after all the vector observations have been processed, which is used to account for the special characteristics of the reset operation necessary for the attitude update. This is the main difference to the traditional sequential EKF, which updates the state covariance at each step of the sequential procedure. The numerical simulation study demonstrates that the proposed SMEKF has more consistent and accurate performance in a wide range of initial estimate errors compared to the MEKF and its traditional sequential forms. PMID:29751538

  5. A Sequential Multiplicative Extended Kalman Filter for Attitude Estimation Using Vector Observations

    Directory of Open Access Journals (Sweden)

    Fangjun Qin

    2018-05-01

    Full Text Available In this paper, a sequential multiplicative extended Kalman filter (SMEKF is proposed for attitude estimation using vector observations. In the proposed SMEKF, each of the vector observations is processed sequentially to update the attitude, which can make the measurement model linearization more accurate for the next vector observation. This is the main difference to Murrell’s variation of the MEKF, which does not update the attitude estimate during the sequential procedure. Meanwhile, the covariance is updated after all the vector observations have been processed, which is used to account for the special characteristics of the reset operation necessary for the attitude update. This is the main difference to the traditional sequential EKF, which updates the state covariance at each step of the sequential procedure. The numerical simulation study demonstrates that the proposed SMEKF has more consistent and accurate performance in a wide range of initial estimate errors compared to the MEKF and its traditional sequential forms.

  6. Rigid Origami via Optical Programming and Deferred Self-Folding of a Two-Stage Photopolymer.

    Science.gov (United States)

    Glugla, David J; Alim, Marvin D; Byars, Keaton D; Nair, Devatha P; Bowman, Christopher N; Maute, Kurt K; McLeod, Robert R

    2016-11-02

    We demonstrate the formation of shape-programmed, glassy origami structures using a single-layer photopolymer with two mechanically distinct phases. The latent origami pattern consisting of rigid, high cross-link density panels and flexible, low cross-link density creases is fabricated using a series of photomask exposures. Strong optical absorption of the polymer formulation creates depth-wise gradients in the cross-link density of the creases, enforcing directed folding which enables programming of both mountain and valley folds within the same sheet. These multiple photomask patterns can be sequentially applied because the sheet remains flat until immersed into a photopolymerizable monomer solution that differentially swells the polymer to fold and form the origami structure. After folding, a uniform photoexposure polymerizes the absorbed solution, permanently fixing the shape of the folded structure while simultaneously increasing the modulus of the folds. This approach creates sharp folds by mimicking the stiff panels and flexible creases of paper origami while overcoming the traditional trade-off of self-actuated materials that require low modulus for folding and high modulus for mechanical robustness. Using this process, we demonstrate a waterbomb base capable of supporting 1500 times its own weight.

  7. The EC BIOCLIM Project (2000-2003), 5. Euratom Framework Programme - Modelling sequential biosphere systems under climate change for radioactive waste disposal

    International Nuclear Information System (INIS)

    Calvez, Marianne

    2002-01-01

    Marianne Calvez (ANDRA, France) presented the new EC BIOCLIM project that started in 2001. Its main objective is to provide a scientific basis and practical methodology for assessing the possible long-term impacts on the safety of radioactive waste repositories in deep formations due to climate driven changes. She explained that BIOCLIM objective is not to predict what will be the future but will correspond to an illustration of how people could use the knowledge. The BIOCLIM project will use the outcomes from the Biomass project. Where Biomass considered discrete biospheres, the BIOCLIM project will consider the evolution of climate with a focus on the European climate for three regions in the United Kingdom, France and Spain. The consortium of BIOCLIM participants consists of various experts in climate modelling and various experts and organisations in performance assessment. The intent is to build an integrated dynamic climate model that represents all the important mechanisms for long-term climate evolution. The modelling will primarily address the next 200000 years. The final outcome will be an enhancement of the state-of-the-art treatment of biosphere system change over long periods of time through the use of a number of innovative climate modelling approaches and the application of the climate model outputs in performance assessments

  8. Radiation Fibrosis of the Vocal Fold: From Man to Mouse

    Science.gov (United States)

    Johns, Michael M.; Kolachala, Vasantha; Berg, Eric; Muller, Susan; Creighton, Frances X.; Branski, Ryan C.

    2013-01-01

    Objectives To characterize fundamental late tissue effects in the human vocal fold following radiation therapy. To develop a murine model of radiation fibrosis to ultimately develop both treatment and prevention paradigms. Design Translational study using archived human and fresh murine irradiated vocal fold tissue. Methods 1) Irradiated vocal fold tissue from patients undergoing laryngectomy for loss of function from radiation fibrosis were identified from pathology archives. Histomorphometry, immunohistochemistry, and whole-genome microarray as well as real-time transcriptional analyses was performed. 2) Focused radiation to the head and neck was delivered to mice in a survival fashion. One month following radiation, vocal fold tissue was analyzed with histomorphometry, immunohistochemistry, and real-time PCR transcriptional analysis for selected markers of fibrosis. Results Human irradiated vocal folds demonstrated increased collagen transcription with increased deposition and disorganization of collagen in both the thyroarytenoid muscle and the superficial lamina propria. Fibronectin were increased in the superficial lamina propria. Laminin decreased in the thyroarytenoid muscle. Whole genome microarray analysis demonstrated increased transcription of markers for fibrosis, oxidative stress, inflammation, glycosaminoglycan production and apoptosis. Irradiated murine vocal folds demonstrated increases in collagen and fibronectin transcription and deposition in the lamina propria. Transforming growth factor (TGF)-β increased in the lamina propria. Conclusion Human irradiated vocal folds demonstrate molecular changes leading to fibrosis that underlie loss of vocal fold pliability that occurs in patients following laryngeal irradiation. Irradiated murine tissue demonstrates similar findings, and this mouse model may have utility in creating prevention and treatment strategies for vocal fold radiation fibrosis. PMID:23242839

  9. Impact of hydrodynamic interactions on protein folding rates depends on temperature

    Science.gov (United States)

    Zegarra, Fabio C.; Homouz, Dirar; Eliaz, Yossi; Gasic, Andrei G.; Cheung, Margaret S.

    2018-03-01

    We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α /β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β -barrel α -spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.

  10. Nanoscale Dewetting Transition in Protein Complex Folding

    Science.gov (United States)

    Hua, Lan; Huang, Xuhui; Liu, Pu; Zhou, Ruhong; Berne, Bruce J.

    2011-01-01

    In a previous study, a surprising drying transition was observed to take place inside the nanoscale hydrophobic channel in the tetramer of the protein melittin. The goal of this paper is to determine if there are other protein complexes capable of displaying a dewetting transition during their final stage of folding. We searched the entire protein data bank (PDB) for all possible candidates, including protein tetramers, dimers, and two-domain proteins, and then performed the molecular dynamics (MD) simulations on the top candidates identified by a simple hydrophobic scoring function based on aligned hydrophobic surface areas. Our large scale MD simulations found several more proteins, including three tetramers, six dimers, and two two-domain proteins, which display a nanoscale dewetting transition in their final stage of folding. Even though the scoring function alone is not sufficient (i.e., a high score is necessary but not sufficient) in identifying the dewetting candidates, it does provide useful insights into the features of complex interfaces needed for dewetting. All top candidates have two features in common: (1) large aligned (matched) hydrophobic areas between two corresponding surfaces, and (2) large connected hydrophobic areas on the same surface. We have also studied the effect on dewetting of different water models and different treatments of the long-range electrostatic interactions (cutoff vs PME), and found the dewetting phenomena is fairly robust. This work presents a few proteins other than melittin tetramer for further experimental studies of the role of dewetting in the end stages of protein folding. PMID:17608515

  11. Sequential series for nuclear reactions

    International Nuclear Information System (INIS)

    Izumo, Ko

    1975-01-01

    A new time-dependent treatment of nuclear reactions is given, in which the wave function of compound nucleus is expanded by a sequential series of the reaction processes. The wave functions of the sequential series form another complete set of compound nucleus at the limit Δt→0. It is pointed out that the wave function is characterized by the quantities: the number of degrees of freedom of motion n, the period of the motion (Poincare cycle) tsub(n), the delay time t sub(nμ) and the relaxation time tausub(n) to the equilibrium of compound nucleus, instead of the usual quantum number lambda, the energy eigenvalue Esub(lambda) and the total width GAMMAsub(lambda) of resonance levels, respectively. The transition matrix elements and the yields of nuclear reactions also become the functions of time given by the Fourier transform of the usual ones. The Poincare cycles of compound nuclei are compared with the observed correlations among resonance levels, which are about 10 -17 --10 -16 sec for medium and heavy nuclei and about 10 -20 sec for the intermediate resonances. (auth.)

  12. Dynamics of Folds in the Plane

    Science.gov (United States)

    Krylov, Nikolai A.; Rogers, Edwin L.

    2011-01-01

    Take a strip of paper and fold a crease intersecting the long edges, creating two angles. Choose one edge and consider the angle with the crease. Fold the opposite edge along the crease, creating a new crease that bisects the angle. Fold again, this time using the newly created crease and the initial edge, creating a new angle along the chosen…

  13. Modelling and sequential simulation of multi-tubular metallic membrane and techno-economics of a hydrogen production process employing thin-layer membrane reactor

    KAUST Repository

    Shafiee, Alireza; Arab, Mobin; Lai, Zhiping; Liu, Zongwen; Abbas, Ali

    2016-01-01

    reforming hydrogen production plant. A techno-economic analysis is then conducted using the validated model for a plant producing 300 TPD of hydrogen. The plant utilises a thin (2.5 μm) defect-free and selective layer (Pd75Ag25 alloy) membrane reactor

  14. A novel folding blade of wind turbine rotor for effective power control

    International Nuclear Information System (INIS)

    Xie, Wei; Zeng, Pan; Lei, Liping

    2015-01-01

    Highlights: • A novel folding blade for wind turbine power control is proposed. • Wind tunnel experiments were conducted to analyze folding blade validity. • Folding blade is valid to control wind turbine power output. • Compared to pitch control, thrust was reduced by fold control in power regulation. • Optimum fold angles were found for wind turbine start up and aerodynamic brake. - Abstract: A concept of novel folding blade of horizontal axis wind turbine is proposed in current study. The folding blade comprises a stall regulated root blade section and a folding tip blade section with the fold axis inclined relative to blade span. By folding blade, lift force generated on the tip blade section changes and the moment arm also shortens, which leads to variations of power output. The blade folding actuation mechanism with servo motor and worm-gear reducer was designed. Wind turbine rotor control scheme and servo system with double feedback loops for blade fold angle control were proposed. In this study, a small folding blade model was tested in a wind tunnel to analyze its performance. The blade model performance was estimated in terms of rotation torque coefficient and thrust coefficient. Wind tunnel experiments were also conducted for pitch control using the same blade model in order to make a direct comparison. The power control, start up and aerodynamic brake performance of the folding blade were analyzed. According to the wind tunnel experiment results, fold angle magnitude significantly affected blade aerodynamic performance and the thrust characteristic together with the rotation torque characteristic of folding blade were revealed. The experiment results demonstrated that the folding blade was valid to control power output and had advantages in reducing thrust with maximum reduction of 51.1% compared to pitch control. Optimum fold angles of 55° and 90° were also found for start up and aerodynamic brake, respectively

  15. Unraveling metamaterial properties in zigzag-base folded sheets.

    Science.gov (United States)

    Eidini, Maryam; Paulino, Glaucio H

    2015-09-01

    Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one-degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson's ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson's ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials.

  16. Monitoring sequential electron transfer with EPR

    International Nuclear Information System (INIS)

    Thurnauer, M.C.; Feezel, L.L.; Snyder, S.W.; Tang, J.; Norris, J.R.; Morris, A.L.; Rustandi, R.R.

    1989-01-01

    A completely general model which treats electron spin polarization (ESP) found in a system in which radical pairs with different magnetic interactions are formed sequentially has been described. This treatment has been applied specifically to the ESP found in the bacterial reaction center. Test cases show clearly how parameters such as structure, lifetime, and magnetic interactions within the successive radical pairs affect the ESP, and demonstrate that previous treatments of this problem have been incomplete. The photosynthetic bacterial reaction center protein is an ideal system for testing the general model of ESP. The radical pair which exhibits ESP, P 870 + Q - (P 870 + is the oxidized, primary electron donor, a bacteriochlorophyll special pair and Q - is the reduced, primary quinone acceptor) is formed via sequential electron transport through the intermediary radical pair P 870 + I - (I - is the reduced, intermediary electron acceptor, a bacteriopheophytin). In addition, it is possible to experimentally vary most of the important parameters, such as the lifetime of the intermediary radical pair and the magnetic interactions in each pair. It has been shown how selective isotopic substitution ( 1 H or 2 H) on P 870 , I and Q affects the ESP of the EPR spectrum of P 870 + Q - , observed at two different microwave frequencies, in Fe 2+ -depleted bacterial reaction centers of Rhodobacter sphaeroides R26. Thus, the relative magnitudes of the magnetic properties (nuclear hyperfine and g-factor differences) which influence ESP development were varied. The results support the general model of ESP in that they suggest that the P 870 + Q - radical pair interactions are the dominant source of ESP production in 2 H bacterial reaction centers

  17. Long-term dynamic and pseudo-state modeling of complete partial nitrification process at high nitrogen loading rates in a sequential batch reactor (SBR).

    Science.gov (United States)

    Soliman, Moomen; Eldyasti, Ahmed

    2017-06-01

    Recently, partial nitrification has been adopted widely either for the nitrite shunt process or intermediate nitrite generation step for the Anammox process. However, partial nitrification has been hindered by the complexity of maintaining stable nitrite accumulation at high nitrogen loading rates (NLR) which affect the feasibility of the process for high nitrogen content wastewater. Thus, the operational data of a lab scale SBR performing complete partial nitrification as a first step of nitrite shunt process at NLRs of 0.3-1.2kg/(m 3 d) have been used to calibrate and validate a process model developed using BioWin® in order to describe the long-term dynamic behavior of the SBR. Moreover, an identifiability analysis step has been introduced to the calibration protocol to eliminate the needs of the respirometric analysis for SBR models. The calibrated model was able to predict accurately the daily effluent ammonia, nitrate, nitrite, alkalinity concentrations and pH during all different operational conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Sequential lineup presentation: Patterns and policy

    OpenAIRE

    Lindsay, R C L; Mansour, Jamal K; Beaudry, J L; Leach, A-M; Bertrand, M I

    2009-01-01

    Sequential lineups were offered as an alternative to the traditional simultaneous lineup. Sequential lineups reduce incorrect lineup selections; however, the accompanying loss of correct identifications has resulted in controversy regarding adoption of the technique. We discuss the procedure and research relevant to (1) the pattern of results found using sequential versus simultaneous lineups; (2) reasons (theory) for differences in witness responses; (3) two methodological issues; and (4) im...

  19. Biased lineups: sequential presentation reduces the problem.

    Science.gov (United States)

    Lindsay, R C; Lea, J A; Nosworthy, G J; Fulford, J A; Hector, J; LeVan, V; Seabrook, C

    1991-12-01

    Biased lineups have been shown to increase significantly false, but not correct, identification rates (Lindsay, Wallbridge, & Drennan, 1987; Lindsay & Wells, 1980; Malpass & Devine, 1981). Lindsay and Wells (1985) found that sequential lineup presentation reduced false identification rates, presumably by reducing reliance on relative judgment processes. Five staged-crime experiments were conducted to examine the effect of lineup biases and sequential presentation on eyewitness recognition accuracy. Sequential lineup presentation significantly reduced false identification rates from fair lineups as well as from lineups biased with regard to foil similarity, instructions, or witness attire, and from lineups biased in all of these ways. The results support recommendations that police present lineups sequentially.

  20. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  1. Adipose-Derived Mesenchymal Stem Cells in the Regeneration of Vocal Folds: A Study on a Chronic Vocal Fold Scar

    Directory of Open Access Journals (Sweden)

    Angelou Valerie

    2016-01-01

    Full Text Available Background. The aim of the study was to assess the histological effects of autologous infusion of adipose-derived stem cells (ADSC on a chronic vocal fold scar in a rabbit model as compared to an untreated scar as well as in injection of hyaluronic acid. Study Design. Animal experiment. Method. We used 74 New Zealand rabbits. Sixteen of them were used as control/normal group. We created a bilateral vocal fold wound in the remaining 58 rabbits. After 18 months we separated our population into three groups. The first group served as control/scarred group. The second one was injected with hyaluronic acid in the vocal folds, and the third received an autologous adipose-derived stem cell infusion in the scarred vocal folds (ADSC group. We measured the variation of thickness of the lamina propria of the vocal folds and analyzed histopathologic changes in each group after three months. Results. The thickness of the lamina propria was significantly reduced in the group that received the ADSC injection, as compared to the normal/scarred group. The collagen deposition, the hyaluronic acid, the elastin levels, and the organization of elastic fibers tend to return to normal after the injection of ADSC. Conclusions. Autologous injection of adipose-derived stem cells on a vocal fold chronic scar enhanced the healing of the vocal folds and the reduction of the scar tissue, even when compared to other treatments.

  2. Adipose-Derived Mesenchymal Stem Cells in the Regeneration of Vocal Folds: A Study on a Chronic Vocal Fold Scar

    Science.gov (United States)

    Vassiliki, Kalodimou; Irini, Messini; Nikolaos, Psychalakis; Karampela, Eleftheria; Apostolos, Papalois

    2016-01-01

    Background. The aim of the study was to assess the histological effects of autologous infusion of adipose-derived stem cells (ADSC) on a chronic vocal fold scar in a rabbit model as compared to an untreated scar as well as in injection of hyaluronic acid. Study Design. Animal experiment. Method. We used 74 New Zealand rabbits. Sixteen of them were used as control/normal group. We created a bilateral vocal fold wound in the remaining 58 rabbits. After 18 months we separated our population into three groups. The first group served as control/scarred group. The second one was injected with hyaluronic acid in the vocal folds, and the third received an autologous adipose-derived stem cell infusion in the scarred vocal folds (ADSC group). We measured the variation of thickness of the lamina propria of the vocal folds and analyzed histopathologic changes in each group after three months. Results. The thickness of the lamina propria was significantly reduced in the group that received the ADSC injection, as compared to the normal/scarred group. The collagen deposition, the hyaluronic acid, the elastin levels, and the organization of elastic fibers tend to return to normal after the injection of ADSC. Conclusions. Autologous injection of adipose-derived stem cells on a vocal fold chronic scar enhanced the healing of the vocal folds and the reduction of the scar tissue, even when compared to other treatments. PMID:26933440

  3. Multiplicity distributions and multiplicity correlations in sequential, off-equilibrium fragmentation process

    International Nuclear Information System (INIS)

    Botet, R.

    1996-01-01

    A new kinetic fragmentation model, the Fragmentation - Inactivation -Binary (FIB) model is described where a dissipative process stops randomly the sequential, conservative and off-equilibrium fragmentation process. (K.A.)

  4. Sequential simulation approach to modeling of multi-seam coal deposits with an application to the assessment of a Louisiana lignite

    Science.gov (United States)

    Olea, Ricardo A.; Luppens, James A.

    2012-01-01

    There are multiple ways to characterize uncertainty in the assessment of coal resources, but not all of them are equally satisfactory. Increasingly, the tendency is toward borrowing from the statistical tools developed in the last 50 years for the quantitative assessment of other mineral commodities. Here, we briefly review the most recent of such methods and formulate a procedure for the systematic assessment of multi-seam coal deposits taking into account several geological factors, such as fluctuations in thickness, erosion, oxidation, and bed boundaries. A lignite deposit explored in three stages is used for validating models based on comparing a first set of drill holes against data from infill and development drilling. Results were fully consistent with reality, providing a variety of maps, histograms, and scatterplots characterizing the deposit and associated uncertainty in the assessments. The geostatistical approach was particularly informative in providing a probability distribution modeling deposit wide uncertainty about total resources and a cumulative distribution of coal tonnage as a function of local uncertainty.

  5. Folding two dimensional crystals by swift heavy ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ochedowski, Oliver; Bukowska, Hanna [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Freire Soler, Victor M. [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Departament de Fisica Aplicada i Optica, Universitat de Barcelona, E08028 Barcelona (Spain); Brökers, Lara [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Ban-d' Etat, Brigitte; Lebius, Henning [CIMAP (CEA-CNRS-ENSICAEN-UCBN), 14070 Caen Cedex 5 (France); Schleberger, Marika, E-mail: marika.schleberger@uni-due.de [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany)

    2014-12-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS{sub 2} and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS{sub 2} does not.

  6. Folding two dimensional crystals by swift heavy ion irradiation

    International Nuclear Information System (INIS)

    Ochedowski, Oliver; Bukowska, Hanna; Freire Soler, Victor M.; Brökers, Lara; Ban-d'Etat, Brigitte; Lebius, Henning; Schleberger, Marika

    2014-01-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS 2 and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS 2 does not

  7. Immediate Sequential Bilateral Cataract Surgery

    DEFF Research Database (Denmark)

    Kessel, Line; Andresen, Jens; Erngaard, Ditte

    2015-01-01

    The aim of the present systematic review was to examine the benefits and harms associated with immediate sequential bilateral cataract surgery (ISBCS) with specific emphasis on the rate of complications, postoperative anisometropia, and subjective visual function in order to formulate evidence......-based national Danish guidelines for cataract surgery. A systematic literature review in PubMed, Embase, and Cochrane central databases identified three randomized controlled trials that compared outcome in patients randomized to ISBCS or bilateral cataract surgery on two different dates. Meta-analyses were...... performed using the Cochrane Review Manager software. The quality of the evidence was assessed using the GRADE method (Grading of Recommendation, Assessment, Development, and Evaluation). We did not find any difference in the risk of complications or visual outcome in patients randomized to ISBCS or surgery...

  8. Some physical approaches to protein folding

    Science.gov (United States)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    To understand how a protein folds is a problem which has important biological implications. In this article, we would like to present a physics-oriented point of view, which is twofold. First of all, we introduce simple statistical mechanics models which display, in the thermodynamic limit, folding and related transitions. These models can be divided into (i) crude spin glass-like models (with their Mattis analogs), where one may look for possible correlations between the chain self-interactions and the folded structure, (ii) glass-like models, where one emphasizes the geometrical competition between one- or two-dimensional local order (mimicking α helix or β sheet structures), and the requirement of global compactness. Both models are too simple to predict the spatial organization of a realistic protein, but are useful for the physicist and should have some feedback in other glassy systems (glasses, collapsed polymers .... ). These remarks lead us to the second physical approach, namely a new Monte-Carlo method, where one grows the protein atom-by-atom (or residue-by-residue), using a standard form (CHARMM .... ) for the total energy. A detailed comparison with other Monte-Carlo schemes, or Molecular Dynamics calculations, is then possible; we will sketch such a comparison for poly-alanines. Our twofold approach illustrates some of the difficulties one encounters in the protein folding problem, in particular those associated with the existence of a large number of metastable states. Le repliement des protéines est un problème qui a de nombreuses implications biologiques. Dans cet article, nous présentons, de deux façons différentes, un point de vue de physicien. Nous introduisons tout d'abord des modèles simples de mécanique statistique qui exhibent, à la limite thermodynamique, des transitions de repliement. Ces modèles peuvent être divisés en (i) verres de spin (éventuellement à la Mattis), où l'on peut chercher des corrélations entre les

  9. RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.

    Science.gov (United States)

    Horesh, Yair; Wexler, Ydo; Lebenthal, Ilana; Ziv-Ukelson, Michal; Unger, Ron

    2009-03-04

    Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L free energy (MFE) for the folding of each of the L-sized substrings of S. The consecutive windows folding problem can be naively solved in O(NL3) by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL2) solution for this problem has been described. Here, we describe and implement an O(NLpsi(L)) engine for the consecutive windows folding problem, where psi(L) is shown to converge to O(1) under the assumption of a standard probabilistic polymer folding model, yielding an O(L) speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5') folding bias, i.e. that the minimal free energy (MFE) of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome. The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.

  10. 'Sequential' Boron Neutron Capture Therapy (BNCT): A Novel Approach to BNCT for the Treatment of Oral Cancer in the Hamster Cheek Pouch Model

    International Nuclear Information System (INIS)

    Molinari, Ana J.; Pozzi, Emiliano C.C.; Hughes, Andrea Monti; Heber, Elisa M.; Garabalino, Marcela A.; Thorp, Silvia I.; Miller, Marcelo; Itoiz, Maria E.; Aromando, Romina F.; Nigg, David W.; Quintana, Jorge; Santa Cruz, Gustavo A.; Trivillin, Veronica A.; Schwint, Amanda E.

    2011-01-01

    In the present study we evaluated the therapeutic effect and/or potential radiotoxicity of the novel 'Tandem' Boron Neutron Capture Therapy (T-BNCT) for the treatment of oral cancer in the hamster cheek pouch model at RA-3 Nuclear Reactor. Two groups of animals were treated with 'Tandem BNCT', i.e. BNCT mediated by boronophenylalanine (BPA) followed by BNCT mediated by sodium decahydrodecaborate (GB-10) either 24 h (T-24h-BNCT) or 48 h (T-48h-BNCT) later. A total tumor dose-matched single application of BNCT mediated by BPA and GB-10 administered jointly ((BPA + GB-10)-BNCT) was administered to an additional group of animals. At 28 days post-treatment, T-24h-BNCT and T-48h-BNCT induced, respectively, overall tumor control (OTC) of 95% and 91%, with no statistically significant differences between protocols. Tumor response for the single application of (BPA + GB-10)-BNCT was 75%, significantly lower than for T-BNCT. The T-BNCT protocols and (BPA + GB-10)-BNCT induced reversible mucositis in dose-limiting precancerous tissue around treated tumors, reaching Grade 3/4 mucositis in 47% and 60% of the animals respectively. No normal tissue radiotoxicity was associated to tumor control for any of the protocols. 'Tandem' BNCT enhances tumor control in oral cancer and reduces or, at worst, does not increase, mucositis in dose-limiting precancerous tissue.

  11. Comparative Study of Compensatory Liver Regeneration in a Rat Model: Portal Vein Ligation Only versus Sequential Ligation of the Portal Vein and Hepatic Artery

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Soo Young [Dept. of Pathology, Dongnam Institute of Radiological and Medical Sciences, Busan (Korea, Republic of); Jeon, Gyeong Sik [Dept. of Radiology, CHA Bundang Medical Center, College of Medicine, CHA University, Seongnam (Korea, Republic of); Lee, Byung Mo [Dept. of Surgery, Seoul Paik Hospital, Inje University College of Medicine, Seoul (Korea, Republic of)

    2013-04-15

    To compare the volume change and the regenerative capacity between portal vein ligation (embolization) (PVL) and heterochronous PVL with hepatic artery ligation (HAL) in a rodent model. The animals were separated into three groups: group I, ligation of the left lateral and median portal vein branches; group II, completion of PVL, followed by ligation of the same branches of the hepatic artery after 48 h; control group, laparotomy without ligation was performed. Five rats from each group were sacrificed on 1, 3, 5, and 7 days after the operation. Volume change measurement, liver function tests and immunohistochemical analysis were performed. The volume of the nonligated lobe between groups I and II was not significantly different by day 5 and day 7. Mean alanine aminotransferase and total bilirubin levels were significantly higher in group II, while the albumin level was higher in group I. Both c-kit- and MIB-5-positive cells used in the activity detection of regeneration were more prevalent in group I on day 1, 3, and 5, with statistical significance. There was no operation related mortality. PVL alone is safe and effective in compensatory liver regeneration. Performing both PVL and HAL does not confer any additional benefits.

  12. Asymmetric hindwing foldings in rove beetles.

    Science.gov (United States)

    Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

    2014-11-18

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

  13. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  14. Vocal Fold Vibratory Changes Following Surgical Intervention.

    Science.gov (United States)

    Chen, Wenli; Woo, Peak; Murry, Thomas

    2016-03-01

    High-speed videoendoscopy (HSV) captures direct cycle-to-cycle visualization of vocal fold movement in real time. This ultrafast recording rate is capable of visualizing the vibratory motion of the vocal folds in severely disordered phonation and provides a direct method for examining vibratory changes after vocal fold surgery. The purpose of this study was to examine the vibratory motion before and after surgical intervention. HSV was captured from two subjects with identifiable midvocal fold benign lesions and six subjects with highly aperiodic vocal fold vibration before and after phonosurgery. Digital kymography (DKG) was used to extract high-speed kymographic vocal fold images sampled at the midmembranous, anterior 1/3, and posterior 1/3 region. Spectral analysis was subsequently applied to the DKG to quantify the cycle-to-cycle movements of the left and the right vocal fold, expressed as a spectrum. Before intervention, the vibratory spectrum consisted of decreased and flat-like spectral peaks with robust power asymmetry. After intervention, increases in spectral power and decreases in power symmetry were noted. Spectral power increases were most remarkable in the midmembranous region of the vocal fold. Surgical modification resulted in improved lateral excursion of the vocal folds, vibratory function, and perceptual measures of Voice Handicap Index-10. These changes in vibratory behavior trended toward normal vocal fold vibration. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  15. The sequential structure of brain activation predicts skill.

    Science.gov (United States)

    Anderson, John R; Bothell, Daniel; Fincham, Jon M; Moon, Jungaa

    2016-01-29

    In an fMRI study, participants were trained to play a complex video game. They were scanned early and then again after substantial practice. While better players showed greater activation in one region (right dorsal striatum) their relative skill was better diagnosed by considering the sequential structure of whole brain activation. Using a cognitive model that played this game, we extracted a characterization of the mental states that are involved in playing a game and the statistical structure of the transitions among these states. There was a strong correspondence between this measure of sequential structure and the skill of different players. Using multi-voxel pattern analysis, it was possible to recognize, with relatively high accuracy, the cognitive states participants were in during particular scans. We used the sequential structure of these activation-recognized states to predict the skill of individual players. These findings indicate that important features about information-processing strategies can be identified from a model-based analysis of the sequential structure of brain activation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. On the origin of reproducible sequential activity in neural circuits

    Science.gov (United States)

    Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

    2004-12-01

    Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

  17. A folded plate clamped along one side only

    Science.gov (United States)

    Nazarov, Serguei A.; Slutskij, Andrey S.

    2017-12-01

    An asymptotic model of a folded thin elastic plate is posed on two plane domains and contains transmission conditions at the common line segment of their boundaries. These conditions become non-local and inhomogeneous if only one side of the plate is fixed. Solvability and smoothness results and error estimates for the model are derived. xml:lang="fr"

  18. The sequential trauma score - a new instrument for the sequential mortality prediction in major trauma*

    Directory of Open Access Journals (Sweden)

    Huber-Wagner S

    2010-05-01

    Full Text Available Abstract Background There are several well established scores for the assessment of the prognosis of major trauma patients that all have in common that they can be calculated at the earliest during intensive care unit stay. We intended to develop a sequential trauma score (STS that allows prognosis at several early stages based on the information that is available at a particular time. Study design In a retrospective, multicenter study using data derived from the Trauma Registry of the German Trauma Society (2002-2006, we identified the most relevant prognostic factors from the patients basic data (P, prehospital phase (A, early (B1, and late (B2 trauma room phase. Univariate and logistic regression models as well as score quality criteria and the explanatory power have been calculated. Results A total of 2,354 patients with complete data were identified. From the patients basic data (P, logistic regression showed that age was a significant predictor of survival (AUCmodel p, area under the curve = 0.63. Logistic regression of the prehospital data (A showed that blood pressure, pulse rate, Glasgow coma scale (GCS, and anisocoria were significant predictors (AUCmodel A = 0.76; AUCmodel P + A = 0.82. Logistic regression of the early trauma room phase (B1 showed that peripheral oxygen saturation, GCS, anisocoria, base excess, and thromboplastin time to be significant predictors of survival (AUCmodel B1 = 0.78; AUCmodel P +A + B1 = 0.85. Multivariate analysis of the late trauma room phase (B2 detected cardiac massage, abbreviated injury score (AIS of the head ≥ 3, the maximum AIS, the need for transfusion or massive blood transfusion, to be the most important predictors (AUCmodel B2 = 0.84; AUCfinal model P + A + B1 + B2 = 0.90. The explanatory power - a tool for the assessment of the relative impact of each segment to mortality - is 25% for P, 7% for A, 17% for B1 and 51% for B2. A spreadsheet for the easy calculation of the sequential trauma

  19. Trial Sequential Methods for Meta-Analysis

    Science.gov (United States)

    Kulinskaya, Elena; Wood, John

    2014-01-01

    Statistical methods for sequential meta-analysis have applications also for the design of new trials. Existing methods are based on group sequential methods developed for single trials and start with the calculation of a required information size. This works satisfactorily within the framework of fixed effects meta-analysis, but conceptual…

  20. Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI.

    Directory of Open Access Journals (Sweden)

    Benjamin P Kleinstiver

    Full Text Available Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic elements by introducing double-strand breaks or nicks at defined locations. Of the major families of homing endonucleases, the modular GIY-YIG endonucleases are least understood in terms of mechanism. The GIY-YIG homing endonuclease I-BmoI generates a double-strand break by sequential nicking reactions during which the single active site of the GIY-YIG nuclease domain must undergo a substantial reorganization. Here, we show that divalent metal ion plays a significant role in regulating the two independent nicking reactions by I-BmoI. Rate constant determination for each nicking reaction revealed that limiting divalent metal ion has a greater impact on the second strand than the first strand nicking reaction. We also show that substrate mutations within the I-BmoI cleavage site can modulate the first strand nicking reaction over a 314-fold range. Additionally, in-gel DNA footprinting with mutant substrates and modeling of an I-BmoI-substrate complex suggest that amino acid contacts to a critical GC-2 base pair are required to induce a bottom-strand distortion that likely directs conformational changes for reaction progress. Collectively, our data implies mechanistic roles for divalent metal ion and substrate bases, suggesting that divalent metal ion facilitates the re-positioning of the GIY-YIG nuclease domain between sequential nicking reactions.

  1. Sequential lineup laps and eyewitness accuracy.

    Science.gov (United States)

    Steblay, Nancy K; Dietrich, Hannah L; Ryan, Shannon L; Raczynski, Jeanette L; James, Kali A

    2011-08-01

    Police practice of double-blind sequential lineups prompts a question about the efficacy of repeated viewings (laps) of the sequential lineup. Two laboratory experiments confirmed the presence of a sequential lap effect: an increase in witness lineup picks from first to second lap, when the culprit was a stranger. The second lap produced more errors than correct identifications. In Experiment 2, lineup diagnosticity was significantly higher for sequential lineup procedures that employed a single versus double laps. Witnesses who elected to view a second lap made significantly more errors than witnesses who chose to stop after one lap or those who were required to view two laps. Witnesses with prior exposure to the culprit did not exhibit a sequential lap effect.

  2. Multi-agent sequential hypothesis testing

    KAUST Repository

    Kim, Kwang-Ki K.

    2014-12-15

    This paper considers multi-agent sequential hypothesis testing and presents a framework for strategic learning in sequential games with explicit consideration of both temporal and spatial coordination. The associated Bayes risk functions explicitly incorporate costs of taking private/public measurements, costs of time-difference and disagreement in actions of agents, and costs of false declaration/choices in the sequential hypothesis testing. The corresponding sequential decision processes have well-defined value functions with respect to (a) the belief states for the case of conditional independent private noisy measurements that are also assumed to be independent identically distributed over time, and (b) the information states for the case of correlated private noisy measurements. A sequential investment game of strategic coordination and delay is also discussed as an application of the proposed strategic learning rules.

  3. Sequential Product of Quantum Effects: An Overview

    Science.gov (United States)

    Gudder, Stan

    2010-12-01

    This article presents an overview for the theory of sequential products of quantum effects. We first summarize some of the highlights of this relatively recent field of investigation and then provide some new results. We begin by discussing sequential effect algebras which are effect algebras endowed with a sequential product satisfying certain basic conditions. We then consider sequential products of (discrete) quantum measurements. We next treat transition effect matrices (TEMs) and their associated sequential product. A TEM is a matrix whose entries are effects and whose rows form quantum measurements. We show that TEMs can be employed for the study of quantum Markov chains. Finally, we prove some new results concerning TEMs and vector densities.

  4. The nature of folded states of globular proteins.

    Science.gov (United States)

    Honeycutt, J D; Thirumalai, D

    1992-06-01

    We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

  5. Adaptive Origami for Efficiently Folded Structures

    Science.gov (United States)

    2016-02-01

    heating. Although a large fold angle at a high temperature is desirable in order to extrapolate the origami geometry toward closure, more emphasis is...AFRL-RQ-WP-TR-2016-0020 ADAPTIVE ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES James J. Joo and Greg Reich Design and Analysis Branch... ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES 5a. CONTRACT NUMBER In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) James J

  6. Vocal fold paralysis secondary to phonotrauma.

    Science.gov (United States)

    Klein, Travis A L; Gaziano, Joy E; Ridley, Marion B

    2014-01-01

    A unique case of acute onset vocal fold paralysis secondary to phonotrauma is presented. The cause was forceful vocalization by a drill instructor on a firearm range. Imaging studies revealed extensive intralaryngeal and retropharyngeal hemorrhage. Laryngoscopy showed a complete left vocal fold paralysis. Relative voice rest was recommended, and the patient regained normal vocal fold mobility and function after approximately 12 weeks. Copyright © 2014 The Voice Foundation. All rights reserved.

  7. Spherical images and inextensible curved folding

    Science.gov (United States)

    Seffen, Keith A.

    2018-02-01

    In their study, Duncan and Duncan [Proc. R. Soc. London A 383, 191 (1982), 10.1098/rspa.1982.0126] calculate the shape of an inextensible surface folded in two about a general curve. They find the analytical relationships between pairs of generators linked across the fold curve, the shape of the original path, and the fold angle variation along it. They present two special cases of generator layouts for which the fold angle is uniform or the folded curve remains planar, for simplifying practical folding in sheet-metal processes. We verify their special cases by a graphical treatment according to a method of Gauss. We replace the fold curve by a piecewise linear path, which connects vertices of intersecting pairs of hinge lines. Inspired by the d-cone analysis by Farmer and Calladine [Int. J. Mech. Sci. 47, 509 (2005), 10.1016/j.ijmecsci.2005.02.013], we construct the spherical images for developable folding of successive vertices: the operating conditions of the special cases in Duncan and Duncan are then revealed straightforwardly by the geometric relationships between the images. Our approach may be used to synthesize folding patterns for novel deployable and shape-changing surfaces without need of complex calculation.

  8. A folding algorithm for extended RNA secondary structures.

    Science.gov (United States)

    Höner zu Siederdissen, Christian; Bernhart, Stephan H; Stadler, Peter F; Hofacker, Ivo L

    2011-07-01

    RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

  9. Multilevel sequential Monte Carlo samplers

    KAUST Repository

    Beskos, Alexandros; Jasra, Ajay; Law, Kody; Tempone, Raul; Zhou, Yan

    2016-01-01

    In this article we consider the approximation of expectations w.r.t. probability distributions associated to the solution of partial differential equations (PDEs); this scenario appears routinely in Bayesian inverse problems. In practice, one often has to solve the associated PDE numerically, using, for instance finite element methods which depend on the step-size level . hL. In addition, the expectation cannot be computed analytically and one often resorts to Monte Carlo methods. In the context of this problem, it is known that the introduction of the multilevel Monte Carlo (MLMC) method can reduce the amount of computational effort to estimate expectations, for a given level of error. This is achieved via a telescoping identity associated to a Monte Carlo approximation of a sequence of probability distributions with discretization levels . ∞>h0>h1⋯>hL. In many practical problems of interest, one cannot achieve an i.i.d. sampling of the associated sequence and a sequential Monte Carlo (SMC) version of the MLMC method is introduced to deal with this problem. It is shown that under appropriate assumptions, the attractive property of a reduction of the amount of computational effort to estimate expectations, for a given level of error, can be maintained within the SMC context. That is, relative to exact sampling and Monte Carlo for the distribution at the finest level . hL. The approach is numerically illustrated on a Bayesian inverse problem. © 2016 Elsevier B.V.

  10. Multilevel sequential Monte Carlo samplers

    KAUST Repository

    Beskos, Alexandros

    2016-08-29

    In this article we consider the approximation of expectations w.r.t. probability distributions associated to the solution of partial differential equations (PDEs); this scenario appears routinely in Bayesian inverse problems. In practice, one often has to solve the associated PDE numerically, using, for instance finite element methods which depend on the step-size level . hL. In addition, the expectation cannot be computed analytically and one often resorts to Monte Carlo methods. In the context of this problem, it is known that the introduction of the multilevel Monte Carlo (MLMC) method can reduce the amount of computational effort to estimate expectations, for a given level of error. This is achieved via a telescoping identity associated to a Monte Carlo approximation of a sequence of probability distributions with discretization levels . ∞>h0>h1⋯>hL. In many practical problems of interest, one cannot achieve an i.i.d. sampling of the associated sequence and a sequential Monte Carlo (SMC) version of the MLMC method is introduced to deal with this problem. It is shown that under appropriate assumptions, the attractive property of a reduction of the amount of computational effort to estimate expectations, for a given level of error, can be maintained within the SMC context. That is, relative to exact sampling and Monte Carlo for the distribution at the finest level . hL. The approach is numerically illustrated on a Bayesian inverse problem. © 2016 Elsevier B.V.

  11. Sequential Scintigraphy in Renal Transplantation

    Energy Technology Data Exchange (ETDEWEB)

    Winkel, K. zum; Harbst, H.; Schenck, P.; Franz, H. E.; Ritz, E.; Roehl, L.; Ziegler, M.; Ammann, W.; Maier-Borst, W. [Institut Fuer Nuklearmedizin, Deutsches Krebsforschungszentrum, Heidelberg, Federal Republic of Germany (Germany)

    1969-05-15

    Based on experience gained from more than 1600 patients with proved or suspected kidney diseases and on results on extended studies with dogs, sequential scintigraphy was performed after renal transplantation in dogs. After intravenous injection of 500 {mu}Ci. {sup 131}I-Hippuran scintiphotos were taken during the first minute with an exposure time of 15 sec each and thereafter with an exposure of 2 min up to at least 16 min.. Several examinations were evaluated digitally. 26 examinations were performed on 11 dogs with homotransplanted kidneys. Immediately after transplantation the renal function was almost normal arid the bladder was filled in due time. At the beginning of rejection the initial uptake of radioactive Hippuran was reduced. The intrarenal transport became delayed; probably the renal extraction rate decreased. Corresponding to the development of an oedema in the transplant the uptake area increased in size. In cases of thrombosis of the main artery there was no evidence of any uptake of radioactivity in the transplant. Similar results were obtained in 41 examinations on 15 persons. Patients with postoperative anuria due to acute tubular necrosis showed still some uptake of radioactivity contrary to those with thrombosis of the renal artery, where no uptake was found. In cases of rejection the most frequent signs were a reduced initial uptake and a delayed intrarenal transport of radioactive Hippuran. Infarction could be detected by a reduced uptake in distinct areas of the transplant. (author)

  12. Sequential provisional implant prosthodontics therapy.

    Science.gov (United States)

    Zinner, Ira D; Markovits, Stanley; Jansen, Curtis E; Reid, Patrick E; Schnader, Yale E; Shapiro, Herbert J

    2012-01-01

    The fabrication and long-term use of first- and second-stage provisional implant prostheses is critical to create a favorable prognosis for function and esthetics of a fixed-implant supported prosthesis. The fixed metal and acrylic resin cemented first-stage prosthesis, as reviewed in Part I, is needed for prevention of adjacent and opposing tooth movement, pressure on the implant site as well as protection to avoid micromovement of the freshly placed implant body. The second-stage prosthesis, reviewed in Part II, should be used following implant uncovering and abutment installation. The patient wears this provisional prosthesis until maturation of the bone and healing of soft tissues. The second-stage provisional prosthesis is also a fail-safe mechanism for possible early implant failures and also can be used with late failures and/or for the necessity to repair the definitive prosthesis. In addition, the screw-retained provisional prosthesis is used if and when an implant requires removal or other implants are to be placed as in a sequential approach. The creation and use of both first- and second-stage provisional prostheses involve a restorative dentist, dental technician, surgeon, and patient to work as a team. If the dentist alone cannot do diagnosis and treatment planning, surgery, and laboratory techniques, he or she needs help by employing the expertise of a surgeon and a laboratory technician. This team approach is essential for optimum results.

  13. Social Influences in Sequential Decision Making.

    Directory of Open Access Journals (Sweden)

    Markus Schöbel

    Full Text Available People often make decisions in a social environment. The present work examines social influence on people's decisions in a sequential decision-making situation. In the first experimental study, we implemented an information cascade paradigm, illustrating that people infer information from decisions of others and use this information to make their own decisions. We followed a cognitive modeling approach to elicit the weight people give to social as compared to private individual information. The proposed social influence model shows that participants overweight their own private information relative to social information, contrary to the normative Bayesian account. In our second study, we embedded the abstract decision problem of Study 1 in a medical decision-making problem. We examined whether in a medical situation people also take others' authority into account in addition to the information that their decisions convey. The social influence model illustrates that people weight social information differentially according to the authority of other decision makers. The influence of authority was strongest when an authority's decision contrasted with private information. Both studies illustrate how the social environment provides sources of information that people integrate differently for their decisions.

  14. Social Influences in Sequential Decision Making

    Science.gov (United States)

    Schöbel, Markus; Rieskamp, Jörg; Huber, Rafael

    2016-01-01

    People often make decisions in a social environment. The present work examines social influence on people’s decisions in a sequential decision-making situation. In the first experimental study, we implemented an information cascade paradigm, illustrating that people infer information from decisions of others and use this information to make their own decisions. We followed a cognitive modeling approach to elicit the weight people give to social as compared to private individual information. The proposed social influence model shows that participants overweight their own private information relative to social information, contrary to the normative Bayesian account. In our second study, we embedded the abstract decision problem of Study 1 in a medical decision-making problem. We examined whether in a medical situation people also take others’ authority into account in addition to the information that their decisions convey. The social influence model illustrates that people weight social information differentially according to the authority of other decision makers. The influence of authority was strongest when an authority's decision contrasted with private information. Both studies illustrate how the social environment provides sources of information that people integrate differently for their decisions. PMID:26784448

  15. Sequential experimental design based generalised ANOVA

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Souvik, E-mail: csouvik41@gmail.com; Chowdhury, Rajib, E-mail: rajibfce@iitr.ac.in

    2016-07-15

    Over the last decade, surrogate modelling technique has gained wide popularity in the field of uncertainty quantification, optimization, model exploration and sensitivity analysis. This approach relies on experimental design to generate training points and regression/interpolation for generating the surrogate. In this work, it is argued that conventional experimental design may render a surrogate model inefficient. In order to address this issue, this paper presents a novel distribution adaptive sequential experimental design (DA-SED). The proposed DA-SED has been coupled with a variant of generalised analysis of variance (G-ANOVA), developed by representing the component function using the generalised polynomial chaos expansion. Moreover, generalised analytical expressions for calculating the first two statistical moments of the response, which are utilized in predicting the probability of failure, have also been developed. The proposed approach has been utilized in predicting probability of failure of three structural mechanics problems. It is observed that the proposed approach yields accurate and computationally efficient estimate of the failure probability.

  16. Social Influences in Sequential Decision Making.

    Science.gov (United States)

    Schöbel, Markus; Rieskamp, Jörg; Huber, Rafael

    2016-01-01

    People often make decisions in a social environment. The present work examines social influence on people's decisions in a sequential decision-making situation. In the first experimental study, we implemented an information cascade paradigm, illustrating that people infer information from decisions of others and use this information to make their own decisions. We followed a cognitive modeling approach to elicit the weight people give to social as compared to private individual information. The proposed social influence model shows that participants overweight their own private information relative to social information, contrary to the normative Bayesian account. In our second study, we embedded the abstract decision problem of Study 1 in a medical decision-making problem. We examined whether in a medical situation people also take others' authority into account in addition to the information that their decisions convey. The social influence model illustrates that people weight social information differentially according to the authority of other decision makers. The influence of authority was strongest when an authority's decision contrasted with private information. Both studies illustrate how the social environment provides sources of information that people integrate differently for their decisions.

  17. A path-level exact parallelization strategy for sequential simulation

    Science.gov (United States)

    Peredo, Oscar F.; Baeza, Daniel; Ortiz, Julián M.; Herrero, José R.

    2018-01-01

    Sequential Simulation is a well known method in geostatistical modelling. Following the Bayesian approach for simulation of conditionally dependent random events, Sequential Indicator Simulation (SIS) method draws simulated values for K categories (categorical case) or classes defined by K different thresholds (continuous case). Similarly, Sequential Gaussian Simulation (SGS) method draws simulated values from a multivariate Gaussian field. In this work, a path-level approach to parallelize SIS and SGS methods is presented. A first stage of re-arrangement of the simulation path is performed, followed by a second stage of parallel simulation for non-conflicting nodes. A key advantage of the proposed parallelization method is to generate identical realizations as with the original non-parallelized methods. Case studies are presented using two sequential simulation codes from GSLIB: SISIM and SGSIM. Execution time and speedup results are shown for large-scale domains, with many categories and maximum kriging neighbours in each case, achieving high speedup results in the best scenarios using 16 threads of execution in a single machine.

  18. Guiding the folding pathway of DNA origami.

    Science.gov (United States)

    Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

    2015-09-03

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  19. RNA folding kinetics using Monte Carlo and Gillespie algorithms.

    Science.gov (United States)

    Clote, Peter; Bayegan, Amir H

    2018-04-01

    RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

  20. Losing a dime with a satisfied mind: positive affect predicts less search in sequential decision making.

    Science.gov (United States)

    von Helversen, Bettina; Mata, Rui

    2012-12-01

    We investigated the contribution of cognitive ability and affect to age differences in sequential decision making by asking younger and older adults to shop for items in a computerized sequential decision-making task. Older adults performed poorly compared to younger adults partly due to searching too few options. An analysis of the decision process with a formal model suggested that older adults set lower thresholds for accepting an option than younger participants. Further analyses suggested that positive affect, but not fluid abilities, was related to search in the sequential decision task. A second study that manipulated affect in younger adults supported the causal role of affect: Increased positive affect lowered the initial threshold for accepting an attractive option. In sum, our results suggest that positive affect is a key factor determining search in sequential decision making. Consequently, increased positive affect in older age may contribute to poorer sequential decisions by leading to insufficient search. 2013 APA, all rights reserved

  1. Exploring the Spatial-Temporal Disparities of Urban Land Use Economic Efficiency in China and Its Influencing Factors under Environmental Constraints Based on a Sequential Slacks-Based Model

    Directory of Open Access Journals (Sweden)

    Hualin Xie

    2015-07-01

    Full Text Available Using a sequential slack-based measure (SSBM model, this paper analyzes the spatiotemporal disparities of urban land use economic efficiency (ULUEE under environmental constraints, and its influencing factors in 270 cities across China from 2003–2012. The main results are as follows: (1 The average ULUEE for Chinese cities is only 0.411, and out of the 270 cities, only six cities are always efficient in urban land use in the study period. Most cities have a lot of room to improve the economic output of secondary and tertiary industries, as well as environmental protection work; (2 The eastern region of China enjoys the highest ULUEE, followed by the western and central regions. Super-scale cities show the best performance of all four city scales, followed by large-scale, small-scale and medium-scale cities. Cities with relatively developed economies and less pollutant discharge always have better ULUEE; (3 The results of slack variables analysis show that most cities have problems such as the labor surplus, over-development, excessive pollutant discharge, economic output shortage, and unreasonable use of funds is the most serious one; (4 The regression results of the influencing factors show that improvements of the per capita GDP and land use intensity are helpful to raise ULUEE. The urbanization rate and the proportion of foreign enterprises’ output account for the total output in the secondary and tertiary industries only have the same effect in some regions and city scales. The land management policy and land leasing policy have negative impact on the ULUEE in all the three regions and four city scales; (5 Some targeted policy goals are proposed, including the reduction of surplus labor, and pay more attention to environmental protection. Most importantly, effective implementation of land management policies from the central government, and stopping blind leasing of land to make up the local government’s financial deficit would be very

  2. Advances in sequential data assimilation and numerical weather forecasting: An Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic ensemble square root filters, and a test of a new time stepping scheme in an atmospheric model

    Science.gov (United States)

    Amezcua, Javier

    This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn't represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion

  3. Sequential ensemble-based optimal design for parameter estimation: SEQUENTIAL ENSEMBLE-BASED OPTIMAL DESIGN

    Energy Technology Data Exchange (ETDEWEB)

    Man, Jun [Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou China; Zhang, Jiangjiang [Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou China; Li, Weixuan [Pacific Northwest National Laboratory, Richland Washington USA; Zeng, Lingzao [Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou China; Wu, Laosheng [Department of Environmental Sciences, University of California, Riverside California USA

    2016-10-01

    The ensemble Kalman filter (EnKF) has been widely used in parameter estimation for hydrological models. The focus of most previous studies was to develop more efficient analysis (estimation) algorithms. On the other hand, it is intuitively understandable that a well-designed sampling (data-collection) strategy should provide more informative measurements and subsequently improve the parameter estimation. In this work, a Sequential Ensemble-based Optimal Design (SEOD) method, coupled with EnKF, information theory and sequential optimal design, is proposed to improve the performance of parameter estimation. Based on the first-order and second-order statistics, different information metrics including the Shannon entropy difference (SD), degrees of freedom for signal (DFS) and relative entropy (RE) are used to design the optimal sampling strategy, respectively. The effectiveness of the proposed method is illustrated by synthetic one-dimensional and two-dimensional unsaturated flow case studies. It is shown that the designed sampling strategies can provide more accurate parameter estimation and state prediction compared with conventional sampling strategies. Optimal sampling designs based on various information metrics perform similarly in our cases. The effect of ensemble size on the optimal design is also investigated. Overall, larger ensemble size improves the parameter estimation and convergence of optimal sampling strategy. Although the proposed method is applied to unsaturated flow problems in this study, it can be equally applied in any other hydrological problems.

  4. Intermediates and the folding of proteins L and G

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  5. Monadic Maps and Folds for Arbitrary Datatypes

    NARCIS (Netherlands)

    Fokkinga, M.M.

    Each datatype constructor comes equiped not only with a so-called map and fold (catamorphism), as is widely known, but, under some condition, also with a kind of map and fold that are related to an arbitrary given monad. This result follows from the preservation of initiality under lifting

  6. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed; Yan, Dong-Ming

    2017-01-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order

  7. Merging monads and folds for functional programming

    NARCIS (Netherlands)

    Meijer, E.; Jeuring, J.T.

    1995-01-01

    These notes discuss the simultaneous use of generalised fold operators and monads to structure functional programs. Generalised fold operators structure programs after the decomposition of the value they consume. Monads structure programs after the computation of the value they produce. Our programs

  8. Theoretical study of the folded waveguide

    International Nuclear Information System (INIS)

    Chen, G.L.; Owens, T.L.; Whealton, J.H.

    1988-01-01

    We have applied a three-dimensional (3-D) algorithm for solving Maxwell's equations to the analysis of foleded waveguides used for fusion plasma heating at the ion cyclotron resonance frequency. A rigorous analysis of the magnetic field structure in the folded waveguide is presented. The results are compared to experimenntal measurements. Optimum conditions for the folded waveguide are discussed. 6 refs., 10 figs

  9. Experimental investigation into the mechanism of folding

    NARCIS (Netherlands)

    Kuenen, Ph.H.; Sitter, de L.U.

    1938-01-01

    The investigation of geological structures due to folding led de Sitter to form an opinion on the mechanical problems involved (Bibl. 7). His principal contention is that in simple cases the relative movements of particles with respect to eachother during deformation leading to a fold, have been

  10. A comparison of RNA folding measures

    Directory of Open Access Journals (Sweden)

    Gardner Paul P

    2005-10-01

    Full Text Available Abstract Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score and the other to see if the sequence has a unique fold (the average base-pair distance, D.

  11. Graph-representation of oxidative folding pathways

    Directory of Open Access Journals (Sweden)

    Kaján László

    2005-01-01

    Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

  12. [Clinical analysis of vocal fold firbrous mass].

    Science.gov (United States)

    Chen, Hao; Sun, Jing Wu; Wan, Guang Lun; Hu, Yan Ming

    2018-03-01

    To explore the character of laryngoscopy finding, voice, and therapy of vocal fold fibrous mass. Clinical data, morphology, voice character, surgery and pathology of 15 cases with vocal fold fibrous mass were analyzed. The morbidity of vocal fold fibrous mass might be related to overuse of voice and laryngopharyngeal reflex. Laryngoscopy revealed shuttle line appearance, smoothness and decreased mucosal wave of vocal fold. These patients were invalid for voice training and might be improved by surgery, but recovery is slow. The morbidity of vocal fold fibrous mass might be related to overuse of voice and laryngopharyngeal reflex. Conservative treatment is ineffective for this disease, and surgery might improve. Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.

  13. Sarcoidosis Presenting as Bilateral Vocal Fold Immobility.

    Science.gov (United States)

    Hintze, Justin M; Gnagi, Sharon H; Lott, David G

    2018-05-01

    Bilateral true vocal fold paralysis is rarely attributable to inflammatory diseases. Sarcoidosis is a rare but important etiology of bilateral true vocal fold paralysis by compressive lymphadenopathy, granulomatous infiltration, and neural involvement. We describe the first reported case of sarcoidosis presenting as bilateral vocal fold immobility caused by direct fixation by granulomatous infiltration severe enough to necessitate tracheostomy insertion. In addition, we discuss the presentation, the pathophysiology, and the treatment of this disease with a review of the literature of previously reported cases of sarcoidosis-related vocal fold immobility. Sarcoidosis should therefore be an important consideration for the otolaryngologist's differential diagnosis of true vocal fold immobility. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  14. Microvascular lesions of the true vocal fold.

    Science.gov (United States)

    Postma, G N; Courey, M S; Ossoff, R H

    1998-06-01

    Microvascular lesions, also called varices or capillary ectasias, in contrast to vocal fold polyps with telangiectatic vessels, are relatively small lesions arising from the microcirculation of the vocal fold. Varices are most commonly seen in female professional vocalists and may be secondary to repetitive trauma, hormonal variations, or repeated inflammation. Microvascular lesions may either be asymptomatic or cause frank dysphonia by interrupting the normal vibratory pattern, mass, or closure of the vocal folds. They may also lead to vocal fold hemorrhage, scarring, or polyp formation. Laryngovideostroboscopy is the key in determining the functional significance of vocal fold varices. Management of patients with a varix includes medical therapy, speech therapy, and occasionally surgical vaporization. Indications for surgery are recurrent hemorrhage, enlargement of the varix, development of a mass in conjunction with the varix or hemorrhage, and unacceptable dysphonia after maximal medical and speech therapy due to a functionally significant varix.

  15. Tradable permit allocations and sequential choice

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, Ian A. [Centre for Economic Research, ETH Zuerich, Zurichbergstrasse 18, 8092 Zuerich (Switzerland)

    2011-01-15

    This paper investigates initial allocation choices in an international tradable pollution permit market. For two sovereign governments, we compare allocation choices that are either simultaneously or sequentially announced. We show sequential allocation announcements result in higher (lower) aggregate emissions when announcements are strategic substitutes (complements). Whether allocation announcements are strategic substitutes or complements depends on the relationship between the follower's damage function and governments' abatement costs. When the marginal damage function is relatively steep (flat), allocation announcements are strategic substitutes (complements). For quadratic abatement costs and damages, sequential announcements provide a higher level of aggregate emissions. (author)

  16. Sequential Generalized Transforms on Function Space

    Directory of Open Access Journals (Sweden)

    Jae Gil Choi

    2013-01-01

    Full Text Available We define two sequential transforms on a function space Ca,b[0,T] induced by generalized Brownian motion process. We then establish the existence of the sequential transforms for functionals in a Banach algebra of functionals on Ca,b[0,T]. We also establish that any one of these transforms acts like an inverse transform of the other transform. Finally, we give some remarks about certain relations between our sequential transforms and other well-known transforms on Ca,b[0,T].

  17. Sequential method for the assessment of innovations in computer assisted industrial processes

    International Nuclear Information System (INIS)

    Suarez Antola R.

    1995-01-01

    A sequential method for the assessment of innovations in industrial processes is proposed, using suitable combinations of mathematical modelling and numerical simulation of dynamics. Some advantages and limitations of the proposed method are discussed. tabs

  18. Delayed Collapse of Wooden Folding Stairs

    Science.gov (United States)

    Krentowski, Janusz; Chyzy, Tadeusz

    2017-10-01

    During operation of folding stairs, a fastener joining the ladder hanger with the frame was torn off. A person using the stairs sustained serious injury. In several dozen other locations similar accidents were observed. As a result of inspections, some threaded parts of the screws were found in the gaps between the wooden elements of the stairs’ flaps. In the construction a hatch made of wooden strips is attached to an external frame by means of metal hangers. Laboratory strength tests were conducted on three samples made of wooden elements identical to the ones used in the damaged stairs. Due to complex load distribution mechanism acting on the base of the structure, a three-dimensional FEM model was created. An original software was used for calculations. Five computational model variants were considered. As a result of the numerical analyses, it was unquestionably shown that faulty connections were the cause of the destruction of the stairs. The weakest link in the load transmission chain were found to have been the screws connecting the hatch board with the hangers.

  19. Energy Landscapes of Folding Chromosomes

    Science.gov (United States)

    Zhang, Bin

    The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

  20. Solitons and protein folding: An In Silico experiment

    International Nuclear Information System (INIS)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-01-01

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics