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

Krasheninnikov, S. I.

The equations of motion of a dust grain with non-spherical shape in plasma are generalized by incorporating the effects associated with propeller-like features of the grain's shape. For the grain shape close to rotationally symmetric, the stability of “stationary” (in terms of variables used in the grain dynamic equations) solutions are considered. It is found that propeller-like features of the grain's shape can crucially alter stability of such “stationary” states.

Nodal domains of a non-separable problem—the right-angled isosceles triangle

NASA Astrophysics Data System (ADS)

Aronovitch, Amit; Band, Ram; Fajman, David; Gnutzmann, Sven

2012-03-01

We study the nodal set of eigenfunctions of the Laplace operator on the right-angled isosceles triangle. A local analysis of the nodal pattern provides an algorithm for computing the number νn of nodal domains for any eigenfunction. In addition, an exact recursive formula for the number of nodal domains is found to reproduce all existing data. Eventually, we use the recursion formula to analyse a large sequence of nodal counts statistically. Our analysis shows that the distribution of nodal counts for this triangular shape has a much richer structure than the known cases of regular separable shapes or completely irregular shapes. Furthermore, we demonstrate that the nodal count sequence contains information about the periodic orbits of the corresponding classical ray dynamics.

A surprising dynamical mass for V773 Tau B

DOE PAGES

Boden, Andrew F.; Torres, Guillermo; Duchene, Gaspard; ...

2012-02-10

Here, we report on new high-resolution imaging and spectroscopy on the multiple T Tauri star system V773 Tau over the 2003-2009 period. With these data we derive relative astrometry, photometry between the A and B components, and radial velocity (RV) of the A-subsystem components. Combining these new data with previously published astrometry and RVs, we update the relative A-B orbit model. This updated orbit model, the known system distance, and A-subsystem parameters yield a dynamical mass for the B component for the first time. Remarkably, the derived B dynamical mass is in the range 1.7-3.0 M⊙. This is much highermore » than previous estimates and suggests that like A, B is also a multiple stellar system. Among these data, spatially resolved spectroscopy provides new insight into the nature of the B component. Similar to A, these near-IR spectra indicate that the dominant source in B is of mid-K spectral type. If B is in fact a multiple star system as suggested by the dynamical mass estimate, the simplest assumption is that B is composed of similar ~1.2 M ⊙ pre-main-sequence stars in a close (<1 AU) binary system. This inference is supported by line-shape changes in near-IR spectroscopy of B, tentatively interpreted as changing RV among components in V773 Tau B. Relative photometry indicates that B is highly variable in the near-IR. The most likely explanation for this variability is circum-B material resulting in variable line-of-sight extinction. The distribution of this material must be significantly affected by both the putative B multiplicity and the A-B orbit.« less

The Geometric Phase of Stock Trading.

PubMed

Altafini, Claudio

2016-01-01

Geometric phases describe how in a continuous-time dynamical system the displacement of a variable (called phase variable) can be related to other variables (shape variables) undergoing a cyclic motion, according to an area rule. The aim of this paper is to show that geometric phases can exist also for discrete-time systems, and even when the cycles in shape space have zero area. A context in which this principle can be applied is stock trading. A zero-area cycle in shape space represents the type of trading operations normally carried out by high-frequency traders (entering and exiting a position on a fast time-scale), while the phase variable represents the cash balance of a trader. Under the assumption that trading impacts stock prices, even zero-area cyclic trading operations can induce geometric phases, i.e., profits or losses, without affecting the stock quote.

Evolution of the cytoskeleton

PubMed Central

Erickson, Harold P.

2009-01-01

Summary The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40−50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP. PMID:17563102

The Geometric Phase of Stock Trading

PubMed Central

2016-01-01

Geometric phases describe how in a continuous-time dynamical system the displacement of a variable (called phase variable) can be related to other variables (shape variables) undergoing a cyclic motion, according to an area rule. The aim of this paper is to show that geometric phases can exist also for discrete-time systems, and even when the cycles in shape space have zero area. A context in which this principle can be applied is stock trading. A zero-area cycle in shape space represents the type of trading operations normally carried out by high-frequency traders (entering and exiting a position on a fast time-scale), while the phase variable represents the cash balance of a trader. Under the assumption that trading impacts stock prices, even zero-area cyclic trading operations can induce geometric phases, i.e., profits or losses, without affecting the stock quote. PMID:27556642

Contour Tracking in Echocardiographic Sequences via Sparse Representation and Dictionary Learning

PubMed Central

Huang, Xiaojie; Dione, Donald P.; Compas, Colin B.; Papademetris, Xenophon; Lin, Ben A.; Bregasi, Alda; Sinusas, Albert J.; Staib, Lawrence H.; Duncan, James S.

2013-01-01

This paper presents a dynamical appearance model based on sparse representation and dictionary learning for tracking both endocardial and epicardial contours of the left ventricle in echocardiographic sequences. Instead of learning offline spatiotemporal priors from databases, we exploit the inherent spatiotemporal coherence of individual data to constraint cardiac contour estimation. The contour tracker is initialized with a manual tracing of the first frame. It employs multiscale sparse representation of local image appearance and learns online multiscale appearance dictionaries in a boosting framework as the image sequence is segmented frame-by-frame sequentially. The weights of multiscale appearance dictionaries are optimized automatically. Our region-based level set segmentation integrates a spectrum of complementary multilevel information including intensity, multiscale local appearance, and dynamical shape prediction. The approach is validated on twenty-six 4D canine echocardiographic images acquired from both healthy and post-infarct canines. The segmentation results agree well with expert manual tracings. The ejection fraction estimates also show good agreement with manual results. Advantages of our approach are demonstrated by comparisons with a conventional pure intensity model, a registration-based contour tracker, and a state-of-the-art database-dependent offline dynamical shape model. We also demonstrate the feasibility of clinical application by applying the method to four 4D human data sets. PMID:24292554

Spatiotemporal attention operator using isotropic contrast and regional homogeneity

NASA Astrophysics Data System (ADS)

Palenichka, Roman; Lakhssassi, Ahmed; Zaremba, Marek

2011-04-01

A multiscale operator for spatiotemporal isotropic attention is proposed to reliably extract attention points during image sequence analysis. Its consecutive local maxima indicate attention points as the centers of image fragments of variable size with high intensity contrast, region homogeneity, regional shape saliency, and temporal change presence. The scale-adaptive estimation of temporal change (motion) and its aggregation with the regional shape saliency contribute to the accurate determination of attention points in image sequences. Multilocation descriptors of an image sequence are extracted at the attention points in the form of a set of multidimensional descriptor vectors. A fast recursive implementation is also proposed to make the operator's computational complexity independent from the spatial scale size, which is the window size in the spatial averaging filter. Experiments on the accuracy of attention-point detection have proved the operator consistency and its high potential for multiscale feature extraction from image sequences.

Spike Train Similarity Space (SSIMS) Method Detects Effects of Obstacle Proximity and Experience on Temporal Patterning of Bat Biosonar

PubMed Central

Accomando, Alyssa W.; Vargas-Irwin, Carlos E.; Simmons, James A.

2018-01-01

Bats emit biosonar pulses in complex temporal patterns that change to accommodate dynamic surroundings. Efforts to quantify these patterns have included analyses of inter-pulse intervals, sonar sound groups, and changes in individual signal parameters such as duration or frequency. Here, the similarity in temporal structure between trains of biosonar pulses is assessed. The spike train similarity space (SSIMS) algorithm, originally designed for neural activity pattern analysis, was applied to determine which features of the environment influence temporal patterning of pulses emitted by flying big brown bats, Eptesicus fuscus. In these laboratory experiments, bats flew down a flight corridor through an obstacle array. The corridor varied in width (100, 70, or 40 cm) and shape (straight or curved). Using a relational point-process framework, SSIMS was able to discriminate between echolocation call sequences recorded from flights in each of the corridor widths. SSIMS was also able to tell the difference between pulse trains recorded during flights where corridor shape through the obstacle array matched the previous trials (fixed, or expected) as opposed to those recorded from flights with randomized corridor shape (variable, or unexpected), but only for the flight path shape in which the bats had previous training. The results show that experience influences the temporal patterns with which bats emit their echolocation calls. It is demonstrated that obstacle proximity to the bat affects call patterns more dramatically than flight path shape. PMID:29472848

Spike Train Similarity Space (SSIMS) Method Detects Effects of Obstacle Proximity and Experience on Temporal Patterning of Bat Biosonar.

PubMed

Accomando, Alyssa W; Vargas-Irwin, Carlos E; Simmons, James A

2018-01-01

Bats emit biosonar pulses in complex temporal patterns that change to accommodate dynamic surroundings. Efforts to quantify these patterns have included analyses of inter-pulse intervals, sonar sound groups, and changes in individual signal parameters such as duration or frequency. Here, the similarity in temporal structure between trains of biosonar pulses is assessed. The spike train similarity space (SSIMS) algorithm, originally designed for neural activity pattern analysis, was applied to determine which features of the environment influence temporal patterning of pulses emitted by flying big brown bats, Eptesicus fuscus . In these laboratory experiments, bats flew down a flight corridor through an obstacle array. The corridor varied in width (100, 70, or 40 cm) and shape (straight or curved). Using a relational point-process framework, SSIMS was able to discriminate between echolocation call sequences recorded from flights in each of the corridor widths. SSIMS was also able to tell the difference between pulse trains recorded during flights where corridor shape through the obstacle array matched the previous trials (fixed, or expected) as opposed to those recorded from flights with randomized corridor shape (variable, or unexpected), but only for the flight path shape in which the bats had previous training. The results show that experience influences the temporal patterns with which bats emit their echolocation calls. It is demonstrated that obstacle proximity to the bat affects call patterns more dramatically than flight path shape.

Shape Distributions of Nonlinear Dynamical Systems for Video-Based Inference.

PubMed

Venkataraman, Vinay; Turaga, Pavan

2016-12-01

This paper presents a shape-theoretic framework for dynamical analysis of nonlinear dynamical systems which appear frequently in several video-based inference tasks. Traditional approaches to dynamical modeling have included linear and nonlinear methods with their respective drawbacks. A novel approach we propose is the use of descriptors of the shape of the dynamical attractor as a feature representation of nature of dynamics. The proposed framework has two main advantages over traditional approaches: a) representation of the dynamical system is derived directly from the observational data, without any inherent assumptions, and b) the proposed features show stability under different time-series lengths where traditional dynamical invariants fail. We illustrate our idea using nonlinear dynamical models such as Lorenz and Rossler systems, where our feature representations (shape distribution) support our hypothesis that the local shape of the reconstructed phase space can be used as a discriminative feature. Our experimental analyses on these models also indicate that the proposed framework show stability for different time-series lengths, which is useful when the available number of samples are small/variable. The specific applications of interest in this paper are: 1) activity recognition using motion capture and RGBD sensors, 2) activity quality assessment for applications in stroke rehabilitation, and 3) dynamical scene classification. We provide experimental validation through action and gesture recognition experiments on motion capture and Kinect datasets. In all these scenarios, we show experimental evidence of the favorable properties of the proposed representation.

Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

PubMed Central

Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W.; Qin, Peter Z.

2014-01-01

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes. PMID:25092920

Coupling Osmolarity Dynamics within Human Tear Film on an Eye-Shaped Domain

NASA Astrophysics Data System (ADS)

Li, Longfei; Braun, R. J.; Driscoll, T. A.; Henshaw, W. D.; Banks, J. W.; King-Smith, P. E.

2013-11-01

The concentration of ions in the tear film (osmolarity) is a key variable in understanding dry eye symptoms and disease. We derived a mathematical model that couples osmolarity (treated as a single solute) and fluid dynamics within the tear film on a 2D eye-shaped domain. The model concerns the physical effects of evaporation, surface tension, viscosity, ocular surface wettability, osmolarity, osmosis and tear fluid supply and drainage. We solved the governing system of coupled nonlinear PDEs using the Overture computational framework developed at LLNL, together with a new hybrid time stepping scheme (using variable step BDF and RKC) that was added to the framework. Results of our numerical simulations show good agreement with existing 1D models (for both tear film and osmolarity dynamics) and provide new insight about the osmolarity distribution over the ocular surface during the interblink.

Learning Latent Variable and Predictive Models of Dynamical Systems

DTIC Science & Technology

2009-10-01

stable over the full 1000 frame image sequence without significant damping. C. Sam- ples drawn from a least squares synthesized sequences (top), and...LDS stabilizing algorithms, LB-1 and LB-2. Bars at every 20 timesteps denote variance in the results. CG provides the best stable short term predictions...observations. This thesis contributes (1) novel learning algorithms for existing dynamical system models that overcome significant limitations of previous

Extended q -Gaussian and q -exponential distributions from gamma random variables

NASA Astrophysics Data System (ADS)

Budini, Adrián A.

2015-05-01

The family of q -Gaussian and q -exponential probability densities fit the statistical behavior of diverse complex self-similar nonequilibrium systems. These distributions, independently of the underlying dynamics, can rigorously be obtained by maximizing Tsallis "nonextensive" entropy under appropriate constraints, as well as from superstatistical models. In this paper we provide an alternative and complementary scheme for deriving these objects. We show that q -Gaussian and q -exponential random variables can always be expressed as a function of two statistically independent gamma random variables with the same scale parameter. Their shape index determines the complexity q parameter. This result also allows us to define an extended family of asymmetric q -Gaussian and modified q -exponential densities, which reduce to the standard ones when the shape parameters are the same. Furthermore, we demonstrate that a simple change of variables always allows relating any of these distributions with a beta stochastic variable. The extended distributions are applied in the statistical description of different complex dynamics such as log-return signals in financial markets and motion of point defects in a fluid flow.

Toward dynamic magnetic resonance imaging of the vocal tract during speech production.

PubMed

Ventura, Sandra M Rua; Freitas, Diamantino Rui S; Tavares, João Manuel R S

2011-07-01

The most recent and significant magnetic resonance imaging (MRI) improvements allow for the visualization of the vocal tract during speech production, which has been revealed to be a powerful tool in dynamic speech research. However, a synchronization technique with enhanced temporal resolution is still required. The study design was transversal in nature. Throughout this work, a technique for the dynamic study of the vocal tract with MRI by using the heart's signal to synchronize and trigger the imaging-acquisition process is presented and described. The technique in question is then used in the measurement of four speech articulatory parameters to assess three different syllables (articulatory gestures) of European Portuguese Language. The acquired MR images are automatically reconstructed so as to result in a variable sequence of images (slices) of different vocal tract shapes in articulatory positions associated with Portuguese speech sounds. The knowledge obtained as a result of the proposed technique represents a direct contribution to the improvement of speech synthesis algorithms, thereby allowing for novel perceptions in coarticulation studies, in addition to providing further efficient clinical guidelines in the pursuit of more proficient speech rehabilitation processes. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Subsonic Static and Dynamic Aerodynamics of Blunt Entry Vehicles

NASA Technical Reports Server (NTRS)

Mitcheltree, Robert A.; Fremaux, Charles M.; Yates, Leslie A.

1999-01-01

The incompressible subsonic aerodynamics of four entry-vehicle shapes with variable c.g. locations are examined in the Langley 20-Foot Vertical Spin Tunnel. The shapes examined are spherically-blunted cones with half-cone angles of 30, 45, and 60 deg. The nose bluntness varies between 0.25 and 0.5 times the base diameter. The Reynolds number based on model diameter for these tests is near 500,000. Quantitative data on attitude and location are collected using a video-based data acquisition system and reduced with a six deg-of-freedom inverse method. All of the shapes examined suffered from strong dynamic instabilities which could produced limit cycles with sufficient amplitudes to overcome static stability of the configuration. Increasing cone half-angle or nose bluntness increases drag but decreases static and dynamic stability.

Linking genetic and environmental factors in amphibian disease risk

PubMed Central

Savage, Anna E; Becker, Carlos G; Zamudio, Kelly R

2015-01-01

A central question in evolutionary biology is how interactions between organisms and the environment shape genetic differentiation. The pathogen Batrachochytrium dendrobatidis (Bd) has caused variable population declines in the lowland leopard frog (Lithobates yavapaiensis); thus, disease has potentially shaped, or been shaped by, host genetic diversity. Environmental factors can also influence both amphibian immunity and Bd virulence, confounding our ability to assess the genetic effects on disease dynamics. Here, we used genetics, pathogen dynamics, and environmental data to characterize L. yavapaiensis populations, estimate migration, and determine relative contributions of genetic and environmental factors in predicting Bd dynamics. We found that the two uninfected populations belonged to a single genetic deme, whereas each infected population was genetically unique. We detected an outlier locus that deviated from neutral expectations and was significantly correlated with mortality within populations. Across populations, only environmental variables predicted infection intensity, whereas environment and genetics predicted infection prevalence, and genetic diversity alone predicted mortality. At one locality with geothermally elevated water temperatures, migration estimates revealed source–sink dynamics that have likely prevented local adaptation. We conclude that integrating genetic and environmental variation among populations provides a better understanding of Bd spatial epidemiology, generating more effective conservation management strategies for mitigating amphibian declines. PMID:26136822

Symbolic dynamics for arrhythmia identification from heart variability of rats with cardiac failures

NASA Astrophysics Data System (ADS)

Letellier, C.; Roulin, E.; Loriot, S.; Morin, J.-P.; Dionnet, F.

2004-12-01

Heart rate variability of rats is investigated using concepts from the nonlinear dynamical system theory. Among the important techniques offered, symbolic dynamics is very appealing by its power to investigate patterns which can be repeated in a time series. The present analysis was performed in six control rats and six chronic cardiac insufficient rats (myocardial infarction due to left descendent coronary artery ligation). Rats are left in clean atmosphere or exposed to atmosphere containing diluted engine emission pollutants. The evolution of the heart rate variability is then investigated with a three element symbolic dynamics which allows to distinguish extrasystoles from tachycardia or bradycardia using the symbol sequences.

The Ultrasensitivity of Living Polymers

NASA Astrophysics Data System (ADS)

O'Shaughnessy, Ben; Vavylonis, Dimitrios

2003-03-01

Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: Even a small perturbation (e.g., temperature jump) nonlinearly distorts the CLD, eliminating or massively augmenting short chains. The origin is fast relaxation of mass variables (mean chain length, monomer concentration) which perturbs CLD shape variables before these can relax via slow chain growth rate fluctuations. Viscosity relaxation predictions agree with experiments on the best-studied synthetic system, α-methylstyrene.

Microprocessor based implementation of attitude and shape control of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1984-01-01

The feasibility of off the shelf eight bit and 16 bit microprocessors to implement linear state variable feedback control laws and assessing the real time response to spacecraft dynamics is studied. The complexity of the dynamic model is described along with the appropriate software. An experimental setup of a beam, microprocessor system for implementing the control laws and the needed generalized software to implement any state variable feedback control system is included.

Universality of human microbial dynamics

NASA Astrophysics Data System (ADS)

Bashan, Amir; Gibson, Travis E.; Friedman, Jonathan; Carey, Vincent J.; Weiss, Scott T.; Hohmann, Elizabeth L.; Liu, Yang-Yu

2016-06-01

Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.

Coupled Vortex-Lattice Flight Dynamic Model with Aeroelastic Finite-Element Model of Flexible Wing Transport Aircraft with Variable Camber Continuous Trailing Edge Flap for Drag Reduction

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Ting, Eric; Nguyen, Daniel; Dao, Tung; Trinh, Khanh

2013-01-01

This paper presents a coupled vortex-lattice flight dynamic model with an aeroelastic finite-element model to predict dynamic characteristics of a flexible wing transport aircraft. The aircraft model is based on NASA Generic Transport Model (GTM) with representative mass and stiffness properties to achieve a wing tip deflection about twice that of a conventional transport aircraft (10% versus 5%). This flexible wing transport aircraft is referred to as an Elastically Shaped Aircraft Concept (ESAC) which is equipped with a Variable Camber Continuous Trailing Edge Flap (VCCTEF) system for active wing shaping control for drag reduction. A vortex-lattice aerodynamic model of the ESAC is developed and is coupled with an aeroelastic finite-element model via an automated geometry modeler. This coupled model is used to compute static and dynamic aeroelastic solutions. The deflection information from the finite-element model and the vortex-lattice model is used to compute unsteady contributions to the aerodynamic force and moment coefficients. A coupled aeroelastic-longitudinal flight dynamic model is developed by coupling the finite-element model with the rigid-body flight dynamic model of the GTM.

Musculoskeletal motion flow fields using hierarchical variable-sized block matching in ultrasonographic video sequences.

PubMed

Revell, J D; Mirmehdi, M; McNally, D S

2004-04-01

We examine tissue deformations using non-invasive dynamic musculoskeletal ultrasonograhy, and quantify its performance on controlled in vitro gold standard (groundtruth) sequences followed by clinical in vivo data. The proposed approach employs a two-dimensional variable-sized block matching algorithm with a hierarchical full search. We extend this process by refining displacements to sub-pixel accuracy. We show by application that this technique yields quantitatively reliable results.

High sensitivity of tidewater outlet glacier dynamics to shape

NASA Astrophysics Data System (ADS)

Enderlin, E. M.; Howat, I. M.; Vieli, A.

2013-02-01

Variability in tidewater outlet glacier behavior under similar external forcing has been attributed to differences in outlet shape (i.e. bed elevation and width), but this dependence has not been investigated in detail. Here we use a numerical ice flow model to show that the dynamics of tidewater outlet glaciers under external forcing are highly sensitive to width and bed topography. Our sensitivity tests indicate that for glaciers with similar discharge, the trunks of wider glaciers and those grounded over deeper basal depressions tend to be closer to flotation, so that less dynamically induced thinning results in rapid, unstable retreat following a perturbation. The lag time between the onset of the perturbation and unstable retreat varies with outlet shape, which may help explain intra-regional variability in tidewater outlet glacier behavior. Further, because the perturbation response is dependent on the thickness relative to flotation, varying the bed topography within the range of observational uncertainty can result in either stable or unstable retreat due to the same perturbation. Thus, extreme care must be taken when interpreting the future behavior of actual glacier systems using numerical ice flow models that are not accompanied by comprehensive sensitivity analyses.

High sensitivity of tidewater outlet glacier dynamics to shape

NASA Astrophysics Data System (ADS)

Enderlin, E. M.; Howat, I. M.; Vieli, A.

2013-06-01

Variability in tidewater outlet glacier behavior under similar external forcing has been attributed to differences in outlet shape (i.e., bed elevation and width), but this dependence has not been investigated in detail. Here we use a numerical ice flow model to show that the dynamics of tidewater outlet glaciers under external forcing are highly sensitive to width and bed topography. Our sensitivity tests indicate that for glaciers with similar discharge, the trunks of wider glaciers and those grounded over deeper basal depressions tend to be closer to flotation, so that less dynamically induced thinning results in rapid, unstable retreat following a perturbation. The lag time between the onset of the perturbation and unstable retreat varies with outlet shape, which may help explain intra-regional variability in tidewater outlet glacier behavior. Further, because the perturbation response is dependent on the thickness relative to flotation, varying the bed topography within the range of observational uncertainty can result in either stable or unstable retreat due to the same perturbation. Thus, extreme care must be taken when interpreting the future behavior of actual glacier systems using numerical ice flow models that are not accompanied by comprehensive sensitivity analyses.

Demographic models reveal the shape of density dependence for a specialist insect herbivore on variable host plants.

PubMed

Miller, Tom E X

2007-07-01

1. It is widely accepted that density-dependent processes play an important role in most natural populations. However, persistent challenges in our understanding of density-dependent population dynamics include evaluating the shape of the relationship between density and demographic rates (linear, concave, convex), and identifying extrinsic factors that can mediate this relationship. 2. I studied the population dynamics of the cactus bug Narnia pallidicornis on host plants (Opuntia imbricata) that varied naturally in relative reproductive effort (RRE, the proportion of meristems allocated to reproduction), an important plant quality trait. I manipulated per-plant cactus bug densities, quantified subsequent dynamics, and fit stage-structured models to the experimental data to ask if and how density influences demographic parameters. 3. In the field experiment, I found that populations with variable starting densities quickly converged upon similar growth trajectories. In the model-fitting analyses, the data strongly supported a model that defined the juvenile cactus bug retention parameter (joint probability of surviving and not dispersing) as a nonlinear decreasing function of density. The estimated shape of this relationship shifted from concave to convex with increasing host-plant RRE. 4. The results demonstrate that host-plant traits are critical sources of variation in the strength and shape of density dependence in insects, and highlight the utility of integrated experimental-theoretical approaches for identifying processes underlying patterns of change in natural populations.

Videogrammetry Using Projected Circular Targets: Proof-of-Concept Test

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Black, Jonathan T.

2003-01-01

Videogrammetry is the science of calculating 3D object coordinates as a function of time from image sequences. It expands the method of photogrammetry to multiple time steps enabling the object to be characterized dynamically. Photogrammetry achieves the greatest accuracy with high contrast, solid-colored, circular targets. The high contrast is most often effected using retro-reflective targets attached to the measurement article. Knowledge of the location of each target allows those points to be tracked in a sequence of images, thus yielding dynamic characterization of the overall object. For ultra-lightweight and inflatable gossamer structures (e.g. solar sails, inflatable antennae, sun shields, etc.) where it may be desirable to avoid physically attaching retro-targets, a high-density grid of projected circular targets - called dot projection - is a viable alternative. Over time the object changes shape or position independently of the dots. Dynamic behavior, such as deployment or vibration, can be characterized by tracking the overall 3D shape of the object instead of tracking specific object points. To develop this method, an oscillating rigid object was measured using both retroreflective targets and dot projection. This paper details these tests, compares the results, and discusses the overall accuracy of dot projection videogrammetry.

Videogrammetry Using Projected Circular Targets: Proof-of-Concept Test

NASA Technical Reports Server (NTRS)

Black, Jonathan T.; Pappa, Richard S.

2003-01-01

Videogrammetry is the science of calculating 3D object coordinates as a function of time from image sequences. It expands the method of photogrammetry to multiple time steps enabling the object to be characterized dynamically. Photogrammetry achieves the greatest accuracy with high contrast, solid-colored circular targets. The high contrast is most often effected using retro-reflective targets attached to the measurement article. Knowledge of the location of each target allows those points to be tracked in a sequence of images, thus yielding dynamic characterization of the overall object. For ultra-lightweight and inflatable gossamer structures (e.g. solar sails, inflatable antennae, sun shields, etc.) where it may be desirable to avoid physically attaching retro-targets, a high-density grid of projected circular targets - called dot projection - is a viable alternative. Over time the object changes shape or position independently of the dots. Dynamic behavior, such as deployment or vibration, can be characterized by tracking the overall 3D shape of the object instead of tracking specific object points. To develop this method, an oscillating rigid object was measured using both retro- reflective targets and dot projection. This paper details these tests, compares the results, and discusses the overall accuracy of dot projection videogrammetry.

Confounding environmental colour and distribution shape leads to underestimation of population extinction risk.

PubMed

Fowler, Mike S; Ruokolainen, Lasse

2013-01-01

The colour of environmental variability influences the size of population fluctuations when filtered through density dependent dynamics, driving extinction risk through dynamical resonance. Slow fluctuations (low frequencies) dominate in red environments, rapid fluctuations (high frequencies) in blue environments and white environments are purely random (no frequencies dominate). Two methods are commonly employed to generate the coloured spatial and/or temporal stochastic (environmental) series used in combination with population (dynamical feedback) models: autoregressive [AR(1)] and sinusoidal (1/f) models. We show that changing environmental colour from white to red with 1/f models, and from white to red or blue with AR(1) models, generates coloured environmental series that are not normally distributed at finite time-scales, potentially confounding comparison with normally distributed white noise models. Increasing variability of sample Skewness and Kurtosis and decreasing mean Kurtosis of these series alter the frequency distribution shape of the realised values of the coloured stochastic processes. These changes in distribution shape alter patterns in the probability of single and series of extreme conditions. We show that the reduced extinction risk for undercompensating (slow growing) populations in red environments previously predicted with traditional 1/f methods is an artefact of changes in the distribution shapes of the environmental series. This is demonstrated by comparison with coloured series controlled to be normally distributed using spectral mimicry. Changes in the distribution shape that arise using traditional methods lead to underestimation of extinction risk in normally distributed, red 1/f environments. AR(1) methods also underestimate extinction risks in traditionally generated red environments. This work synthesises previous results and provides further insight into the processes driving extinction risk in model populations. We must let the characteristics of known natural environmental covariates (e.g., colour and distribution shape) guide us in our choice of how to best model the impact of coloured environmental variation on population dynamics.

Distribution and predictors of wing shape and size variability in three sister species of solitary bees

PubMed Central

Prunier, Jérôme G.; Dewulf, Alexandre; Kuhlmann, Michael; Michez, Denis

2017-01-01

Morphological traits can be highly variable over time in a particular geographical area. Different selective pressures shape those traits, which is crucial in evolutionary biology. Among these traits, insect wing morphometry has already been widely used to describe phenotypic variability at the inter-specific level. On the contrary, fewer studies have focused on intra-specific wing morphometric variability. Yet, such investigations are relevant to study potential convergences of variation that could highlight micro-evolutionary processes. The recent sampling and sequencing of three solitary bees of the genus Melitta across their entire species range provides an excellent opportunity to jointly analyse genetic and morphometric variability. In the present study, we first aim to analyse the spatial distribution of the wing shape and centroid size (used as a proxy for body size) variability. Secondly, we aim to test different potential predictors of this variability at both the intra- and inter-population levels, which includes genetic variability, but also geographic locations and distances, elevation, annual mean temperature and precipitation. The comparison of spatial distribution of intra-population morphometric diversity does not reveal any convergent pattern between species, thus undermining the assumption of a potential local and selective adaptation at the population level. Regarding intra-specific wing shape differentiation, our results reveal that some tested predictors, such as geographic and genetic distances, are associated with a significant correlation for some species. However, none of these predictors are systematically identified for the three species as an important factor that could explain the intra-specific morphometric variability. As a conclusion, for the three solitary bee species and at the scale of this study, our results clearly tend to discard the assumption of the existence of a common pattern of intra-specific signal/structure within the intra-specific wing shape and body size variability. PMID:28273178

Opto-numerical procedures supporting dynamic lower limbs monitoring and their medical diagnosis

NASA Astrophysics Data System (ADS)

Witkowski, Marcin; Kujawińska, Malgorzata; Rapp, Walter; Sitnik, Robert

2006-01-01

New optical full-field shape measurement systems allow transient shape capture at rates between 15 and 30 Hz. These frequency rates are enough to monitor controlled movements used e.g. for medical examination purposes. In this paper we present a set of algorithms which may be applied for processing of data gathered by fringe projection method implemented for lower limbs shape measurement. The purpose of presented algorithms is to locate anatomical structures based on the limb shape and its deformation in time. The algorithms are based on local surface curvature calculation and analysis of curvature maps changes during the measurement sequence. One of anatomical structure of high medical interest that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. Therefore the usefulness of the algorithms developed was proven at examples of patella localization and monitoring.

Computed tear film and osmolarity dynamics on an eye-shaped domain

PubMed Central

Li, Longfei; Braun, Richard J.; Driscoll, Tobin A.; Henshaw, William D.; Banks, Jeffrey W.; King-Smith, P. Ewen

2016-01-01

The concentration of ions, or osmolarity, in the tear film is a key variable in understanding dry eye symptoms and disease. In this manuscript, we derive a mathematical model that couples osmolarity (treated as a single solute) and fluid dynamics within the tear film on a 2D eye-shaped domain. The model includes the physical effects of evaporation, surface tension, viscosity, ocular surface wettability, osmolarity, osmosis and tear fluid supply and drainage. The governing system of coupled non-linear partial differential equations is solved using the Overture computational framework, together with a hybrid time-stepping scheme, using a variable step backward differentiation formula and a Runge–Kutta–Chebyshev method that were added to the framework. The results of our numerical simulations provide new insight into the osmolarity distribution over the ocular surface during the interblink. PMID:25883248

Population dynamics of HIV-1 inferred from gene sequences.

PubMed Central

Grassly, N C; Harvey, P H; Holmes, E C

1999-01-01

A method for the estimation of population dynamic history from sequence data is described and used to investigate the past population dynamics of HIV-1 subtypes A and B. Using both gag and env gene alignments the effective population size of each subtype is estimated and found to be surprisingly small. This may be a result of the selective sweep of mutations through the population, or may indicate an important role of genetic drift in the fixation of mutations. The implications of these results for the spread of drug-resistant mutations and transmission dynamics, and also the roles of selection and recombination in shaping HIV-1 genetic diversity, are discussed. A larger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population structure. To investigate the importance of population structure a model of population subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant. PMID:9927440

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

PubMed Central

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

Seasonal dynamics of bacterioplankton community in a large, shallow, highly dynamic freshwater lake.

PubMed

Kong, Zhaoyu; Kou, Wenbo; Ma, Yantian; Yu, Haotian; Ge, Gang; Wu, Lan

2018-05-23

The spatio-temporal shifts of bacterioplankton community can mirror their transition of functional traits in aquatic ecosystem. However, our understanding of spatio-temporal variation of bacterioplankton community composition structure (BCCs) within large, shallow and highly dynamic freshwater lake is still elusive. Here we examined the seasonal and spatial variability of BCCs in the Poyang Lake by 16S rRNA gene amplicon sequencing to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of BCCs were mainly attributed to the differences between autumn and spring/winter. Higher alpha diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significant lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1 and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature and nutrient status shaped the seasonal patterns of BCCs in the Poyang Lake.

Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: proposal of three new species.

PubMed

Alvarez, Eduardo; Stchigel, Alberto M; Cano, Josep; Sutton, Deanna A; Fothergill, Annette W; Chander, Jagdish; Salas, Valentina; Rinaldi, Michael G; Guarro, Josep

2010-06-30

Apophysomyces is a monotypic genus belonging to the order Mucorales. The species Apophysomyces elegans has been reported to cause severe infections in immunocompromised and immunocompetent people. In a previous study of Alvarez et al.(3) [J Clin Microbiol 2009;47:1650-6], we demonstrated a high variability among the 5.8S rRNA gene sequences of clinical strains of A. elegans. We performed a polyphasic study based on the analysis of the sequences of the histone 3 gene, the internal transcribed spacer region of the rDNA gene, and domains D1 and D2 of the 28S rRNA gene, as well as by evaluation of some relevant morphological and physiological characteristics of a set of clinical and environmental strains of A. elegans. We have demonstrated that A. elegans is a complex of species. We propose as new species Apophysomyces ossiformis, characterised by bone-shaped sporangiospores, Apophysomyces trapeziformis, with trapezoid-shaped sporangiospores, and Apophysomyces variabilis, with variable-shaped sporangiospores. These species failed to assimilate esculin, whereas A. elegans was able to assimilate that glycoside. Amphotericin B and posaconazole are the most active in vitro drugs against Apophysomyces. Copyright 2009 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

PubMed

Andrabi, Munazah; Hutchins, Andrew Paul; Miranda-Saavedra, Diego; Kono, Hidetoshi; Nussinov, Ruth; Mizuguchi, Kenji; Ahmad, Shandar

2017-06-22

DNA shape is emerging as an important determinant of transcription factor binding beyond just the DNA sequence. The only tool for large scale DNA shape estimates, DNAshape was derived from Monte-Carlo simulations and predicts four broad and static DNA shape features, Propeller twist, Helical twist, Minor groove width and Roll. The contributions of other shape features e.g. Shift, Slide and Opening cannot be evaluated using DNAshape. Here, we report a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustive set of DNA shape features. We compared the DNAshape and DynaSeq predictions for the common features and applied both to predict the genome-wide binding sites of 1312 TFs available from protein interaction quantification (PIQ) data. The results indicate a good agreement between the two methods for the common shape features and point to advantages in using DynaSeq. Predictive models employing ensembles from individual conformational parameters revealed that base-pair opening - known to be important in strand separation - was the best predictor of transcription factor-binding sites (TFBS) followed by features employed by DNAshape. Of note, TFBS could be predicted not only from the features at the target motif sites, but also from those as far as 200 nucleotides away from the motif.

Body movement selectively shapes the neural representation of musical rhythms.

PubMed

Chemin, Baptiste; Mouraux, André; Nozaradan, Sylvie

2014-12-01

It is increasingly recognized that motor routines dynamically shape the processing of sensory inflow (e.g., when hand movements are used to feel a texture or identify an object). In the present research, we captured the shaping of auditory perception by movement in humans by taking advantage of a specific context: music. Participants listened to a repeated rhythmical sequence before and after moving their bodies to this rhythm in a specific meter. We found that the brain responses to the rhythm (as recorded with electroencephalography) after body movement were significantly enhanced at frequencies related to the meter to which the participants had moved. These results provide evidence that body movement can selectively shape the subsequent internal representation of auditory rhythms. © The Author(s) 2014.

Real-time filtering and detection of dynamics for compression of HDTV

NASA Technical Reports Server (NTRS)

Sauer, Ken D.; Bauer, Peter

1991-01-01

The preprocessing of video sequences for data compressing is discussed. The end goal associated with this is a compression system for HDTV capable of transmitting perceptually lossless sequences at under one bit per pixel. Two subtopics were emphasized to prepare the video signal for more efficient coding: (1) nonlinear filtering to remove noise and shape the signal spectrum to take advantage of insensitivities of human viewers; and (2) segmentation of each frame into temporally dynamic/static regions for conditional frame replenishment. The latter technique operates best under the assumption that the sequence can be modelled as a superposition of active foreground and static background. The considerations were restricted to monochrome data, since it was expected to use the standard luminance/chrominance decomposition, which concentrates most of the bandwidth requirements in the luminance. Similar methods may be applied to the two chrominance signals.

Measurement of inter- and intra-annual variability of landscape fire activity at a continental scale: The Australian case

Treesearch

Grant J. Williamson; Lynda D. Prior; Matt Jolly; Mark A. Cochrane; Brett P. Murphy; David M. J. S. Bowman

2016-01-01

Climate dynamics at diurnal, seasonal and inter-annual scales shape global fire activity, although difficulties of assembling reliable fire and meteorological data with sufficient spatio-temporal resolution have frustrated quantification of this variability. Using Australia as a case study, we combine data from 4760 meteorological stations with 12 years of satellite-...

MHz-Rate NO PLIF Imaging in a Mach 10 Hypersonic Wind Tunnel

NASA Technical Reports Server (NTRS)

Jiang, N.; Webster, M.; Lempert, Walter R.; Miller, J. D.; Meyer, T. R.; Danehy, Paul M.

2010-01-01

NO PLIF imaging at repetition rates as high as 1 MHz is demonstrated in the NASA Langley 31 inch Mach 10 hypersonic wind tunnel. Approximately two hundred time correlated image sequences, of between ten and twenty individual frames, were obtained over eight days of wind tunnel testing spanning two entries in March and September of 2009. The majority of the image sequences were obtained from the boundary layer of a 20 flat plate model, in which transition was induced using a variety of cylindrical and triangular shaped protuberances. The high speed image sequences captured a variety of laminar and transitional flow phenomena, ranging from mostly laminar flow, typically at lower Reynolds number and/or in the near wall region of the model, to highly transitional flow in which the temporal evolution and progression of characteristic streak instabilities and/or corkscrew-shaped vortices could be clearly identified. A series of image sequences were also obtained from a 20 compression ramp at a 10 angle of attack in which the temporal dynamics of the characteristic separated flow was captured in a time correlated manner.

Liquid behavior of cross-linked actin bundles.

PubMed

Weirich, Kimberly L; Banerjee, Shiladitya; Dasbiswas, Kinjal; Witten, Thomas A; Vaikuntanathan, Suriyanarayanan; Gardel, Margaret L

2017-02-28

The actin cytoskeleton is a critical regulator of cytoplasmic architecture and mechanics, essential in a myriad of physiological processes. Here we demonstrate a liquid phase of actin filaments in the presence of the physiological cross-linker, filamin. Filamin condenses short actin filaments into spindle-shaped droplets, or tactoids, with shape dynamics consistent with a continuum model of anisotropic liquids. We find that cross-linker density controls the droplet shape and deformation timescales, consistent with a variable interfacial tension and viscosity. Near the liquid-solid transition, cross-linked actin bundles show behaviors reminiscent of fluid threads, including capillary instabilities and contraction. These data reveal a liquid droplet phase of actin, demixed from the surrounding solution and dominated by interfacial tension. These results suggest a mechanism to control organization, morphology, and dynamics of the actin cytoskeleton.

Stabilizing detached Bridgman melt crystal growth: Model-based nonlinear feedback control

NASA Astrophysics Data System (ADS)

Yeckel, Andrew; Daoutidis, Prodromos; Derby, Jeffrey J.

2012-12-01

The dynamics and operability limits of a nonlinear-proportional-integral controller designed to stabilize detached vertical Bridgman crystal growth are studied. The manipulated variable is the pressure difference between upper and lower vapor spaces, and the controlled variable is the gap width at the triple-phase line. The controller consists of a model-based nonlinear component coupled with a standard proportional-integral controller. The nonlinear component is based on a capillary model of shape stability. Perturbations to gap width, pressure difference, wetting angle, and growth angle are studied under both shape stable and shape unstable conditions. The nonlinear-PI controller allows a wider operating range of gain than a standard PI controller used alone, is easier to tune, and eliminates solution multiplicity from closed-loop operation.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

Phytoplankton dynamics of a subtropical reservoir controlled by the complex interplay among hydrological, abiotic, and biotic variables.

PubMed

Kuo, Yi-Ming; Wu, Jiunn-Tzong

2016-12-01

This study was conducted to identify the key factors related to the spatiotemporal variations in phytoplankton abundance in a subtropical reservoir from 2006 to 2010 and to assist in developing strategies for water quality management. Dynamic factor analysis (DFA), a dimension-reduction technique, was used to identify interactions between explanatory variables (i.e., environmental variables) and abundance (biovolume) of predominant phytoplankton classes. The optimal DFA model significantly described the dynamic changes in abundances of predominant phytoplankton groups (including dinoflagellates, diatoms, and green algae) at five monitoring sites. Water temperature, electrical conductivity, water level, nutrients (total phosphorus, NO 3 -N, and NH 3 -N), macro-zooplankton, and zooplankton were the key factors affecting the dynamics of aforementioned phytoplankton. Therefore, transformations of nutrients and reactions between water quality variables and aforementioned processes altered by hydrological conditions may also control the abundance dynamics of phytoplankton, which may represent common trends in the DFA model. The meandering shape of Shihmen Reservoir and its surrounding rivers caused a complex interplay between hydrological conditions and abiotic and biotic variables, resulting in phytoplankton abundance that could not be estimated using certain variables. Additional water quality and hydrological variables at surrounding rivers and monitoring plans should be executed a few days before and after reservoir operations and heavy storm, which would assist in developing site-specific preventive strategies to control phytoplankton abundance.

OMV: A simplified mathematical model of the orbital maneuvering vehicle

NASA Technical Reports Server (NTRS)

Teoh, W.

1984-01-01

A model of the orbital maneuvering vehicle (OMV) is presented which contains several simplications. A set of hand controller signals may be used to control the motion of the OMV. Model verification is carried out using a sequence of tests. The dynamic variables generated by the model are compared, whenever possible, with the corresponding analytical variables. The results of the tests show conclusively that the present model is behaving correctly. Further, this model interfaces properly with the state vector transformation module (SVX) developed previously. Correct command sentence sequences are generated by the OMV and and SVX system, and these command sequences can be used to drive the flat floor simulation system at MSFC.

Modal analysis of a nonuniform string with end mass and variable tension

NASA Technical Reports Server (NTRS)

Rheinfurth, M. H.; Galaboff, Z. J.

1983-01-01

Modal synthesis techniques for dynamic systems containing strings describe the lateral displacements of these strings by properly chosen shape functions. An iterative algorithm is provided to calculate the natural modes of a nonuniform string and variable tension for some typical boundary conditions including one end mass. Numerical examples are given for a string in a constant and a gravity gradient force field.

The Mathematics of Psychotherapy: A Nonlinear Model of Change Dynamics.

PubMed

Schiepek, Gunter; Aas, Benjamin; Viol, Kathrin

2016-07-01

Psychotherapy is a dynamic process produced by a complex system of interacting variables. Even though there are qualitative models of such systems the link between structure and function, between network and network dynamics is still missing. The aim of this study is to realize these links. The proposed model is composed of five state variables (P: problem severity, S: success and therapeutic progress, M: motivation to change, E: emotions, I: insight and new perspectives) interconnected by 16 functions. The shape of each function is modified by four parameters (a: capability to form a trustful working alliance, c: mentalization and emotion regulation, r: behavioral resources and skills, m: self-efficacy and reward expectation). Psychologically, the parameters play the role of competencies or traits, which translate into the concept of control parameters in synergetics. The qualitative model was transferred into five coupled, deterministic, nonlinear difference equations generating the dynamics of each variable as a function of other variables. The mathematical model is able to reproduce important features of psychotherapy processes. Examples of parameter-dependent bifurcation diagrams are given. Beyond the illustrated similarities between simulated and empirical dynamics, the model has to be further developed, systematically tested by simulated experiments, and compared to empirical data.

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

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

Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanitamore » fungi. We used methods developed to interrogate both assembled and unassembled sequences, and characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.« less

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

DOE PAGES

Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.; ...

2014-06-12

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanitamore » fungi. We used methods developed to interrogate both assembled and unassembled sequences, and characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.« less

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

PubMed Central

Shigematsu, Megumi; Honda, Shozo; Loher, Phillipe; Telonis, Aristeidis G.; Rigoutsos, Isidore

2017-01-01

Abstract Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes. PMID:28108659

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

PubMed

Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

Maneuvering control and configuration adaptation of a biologically inspired morphing aircraft

NASA Astrophysics Data System (ADS)

Abdulrahim, Mujahid

Natural flight as a source of inspiration for aircraft design was prominent with early aircraft but became marginalized as aircraft became larger and faster. With recent interest in small unmanned air vehicles, biological inspiration is a possible technology to enhance mission performance of aircraft that are dimensionally similar to gliding birds. Serial wing joints, loosely modeling the avian skeletal structure, are used in the current study to allow significant reconfiguration of the wing shape. The wings are reconfigured to optimize aerodynamic performance and maneuvering metrics related to specific mission tasks. Wing shapes for each mission are determined and related to the seagulls, falcons, albatrosses, and non-migratory African swallows on which the aircraft are based. Variable wing geometry changes the vehicle dynamics, affording versatility in flight behavior but also requiring appropriate compensation to maintain stability and controllability. Time-varying compensation is in the form of a baseline controller which adapts to both the variable vehicle dynamics and to the changing mission requirements. Wing shape is adapted in flight to minimize a cost function which represents energy, temporal, and spatial efficiency. An optimal control architecture unifies the control and adaptation tasks.

Fuzzy Mixed Assembly Line Sequencing and Scheduling Optimization Model Using Multiobjective Dynamic Fuzzy GA

PubMed Central

Tahriri, Farzad; Dawal, Siti Zawiah Md; Taha, Zahari

2014-01-01

A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA) is proposed in order to solve this optimization model. In establishing the FAGA, five dynamic fuzzy parameter controllers are devised in which fuzzy expert experience controller (FEEC) is integrated with automatic learning dynamic fuzzy controller (ALDFC) technique. The enhanced algorithm dynamically adjusts the population size, number of generations, tournament candidate, crossover rate, and mutation rate compared with using fixed control parameters. The main idea is to improve the performance and effectiveness of existing GAs by dynamic adjustment and control of the five parameters. Verification and validation of the dynamic fuzzy GA are carried out by developing test-beds and testing using a multiobjective fuzzy mixed production assembly line sequencing optimization problem. The simulation results highlight that the performance and efficacy of the proposed novel optimization algorithm are more efficient than the performance of the standard genetic algorithm in mixed assembly line sequencing model. PMID:24982962

Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

NASA Astrophysics Data System (ADS)

Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

2015-09-01

Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

Dissecting genomic diversity, one cell at a time

PubMed Central

Blainey, Paul C; Quake, Stephen R

2014-01-01

Emerging technologies are bringing single-cell genome sequencing into the mainstream; this field has already yielded insights into the genetic architecture and variability between cells that highlight the dynamic nature of the genome. PMID:24524132

Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

PubMed Central

Koenig, Patrick; Lee, Chingwei V.; Walters, Benjamin T.; Janakiraman, Vasantharajan; Stinson, Jeremy; Patapoff, Thomas W.; Fuh, Germaine

2017-01-01

Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo. PMID:28057863

Origins of house mice in ecological niches created by settled hunter-gatherers in the Levant 15,000 y ago

PubMed Central

Weissbrod, Lior; Marshall, Fiona B.; Valla, François R.; Khalaily, Hamoudi; Bar-Oz, Guy; Auffray, Jean-Christophe; Vigne, Jean-Denis; Cucchi, Thomas

2017-01-01

Reductions in hunter-gatherer mobility during the Late Pleistocene influenced settlement ecologies, altered human relations with animal communities, and played a pivotal role in domestication. The influence of variability in human mobility on selection dynamics and ecological interactions in human settlements has not been extensively explored, however. This study of mice in modern African villages and changing mice molar shapes in a 200,000-y-long sequence from the Levant demonstrates competitive advantages for commensal mice in long-term settlements. Mice from African pastoral households provide a referential model for habitat partitioning among mice taxa in settlements of varying durations. The data reveal the earliest known commensal niche for house mice in long-term forager settlements 15,000 y ago. Competitive dynamics and the presence and abundance of mice continued to fluctuate with human mobility through the terminal Pleistocene. At the Natufian site of Ain Mallaha, house mice displaced less commensal wild mice during periods of heavy occupational pressure but were outcompeted when mobility increased. Changing food webs and ecological dynamics in long-term settlements allowed house mice to establish durable commensal populations that expanded with human societies. This study demonstrates the changing magnitude of cultural niche construction with varying human mobility and the extent of environmental influence before the advent of farming. PMID:28348225

Origins of house mice in ecological niches created by settled hunter-gatherers in the Levant 15,000 y ago.

PubMed

Weissbrod, Lior; Marshall, Fiona B; Valla, François R; Khalaily, Hamoudi; Bar-Oz, Guy; Auffray, Jean-Christophe; Vigne, Jean-Denis; Cucchi, Thomas

2017-04-18

Reductions in hunter-gatherer mobility during the Late Pleistocene influenced settlement ecologies, altered human relations with animal communities, and played a pivotal role in domestication. The influence of variability in human mobility on selection dynamics and ecological interactions in human settlements has not been extensively explored, however. This study of mice in modern African villages and changing mice molar shapes in a 200,000-y-long sequence from the Levant demonstrates competitive advantages for commensal mice in long-term settlements. Mice from African pastoral households provide a referential model for habitat partitioning among mice taxa in settlements of varying durations. The data reveal the earliest known commensal niche for house mice in long-term forager settlements 15,000 y ago. Competitive dynamics and the presence and abundance of mice continued to fluctuate with human mobility through the terminal Pleistocene. At the Natufian site of Ain Mallaha, house mice displaced less commensal wild mice during periods of heavy occupational pressure but were outcompeted when mobility increased. Changing food webs and ecological dynamics in long-term settlements allowed house mice to establish durable commensal populations that expanded with human societies. This study demonstrates the changing magnitude of cultural niche construction with varying human mobility and the extent of environmental influence before the advent of farming.

The impact of short term synaptic depression and stochastic vesicle dynamics on neuronal variability

PubMed Central

Reich, Steven

2014-01-01

Neuronal variability plays a central role in neural coding and impacts the dynamics of neuronal networks. Unreliability of synaptic transmission is a major source of neural variability: synaptic neurotransmitter vesicles are released probabilistically in response to presynaptic action potentials and are recovered stochastically in time. The dynamics of this process of vesicle release and recovery interacts with variability in the arrival times of presynaptic spikes to shape the variability of the postsynaptic response. We use continuous time Markov chain methods to analyze a model of short term synaptic depression with stochastic vesicle dynamics coupled with three different models of presynaptic spiking: one model in which the timing of presynaptic action potentials are modeled as a Poisson process, one in which action potentials occur more regularly than a Poisson process (sub-Poisson) and one in which action potentials occur more irregularly (super-Poisson). We use this analysis to investigate how variability in a presynaptic spike train is transformed by short term depression and stochastic vesicle dynamics to determine the variability of the postsynaptic response. We find that sub-Poisson presynaptic spiking increases the average rate at which vesicles are released, that the number of vesicles released over a time window is more variable for smaller time windows than larger time windows and that fast presynaptic spiking gives rise to Poisson-like variability of the postsynaptic response even when presynaptic spike times are non-Poisson. Our results complement and extend previously reported theoretical results and provide possible explanations for some trends observed in recorded data. PMID:23354693

Russell body inducing threshold depends on the variable domain sequences of individual human IgG clones and the cellular protein homeostasis.

PubMed

Stoops, Janelle; Byrd, Samantha; Hasegawa, Haruki

2012-10-01

Russell bodies are intracellular aggregates of immunoglobulins. Although the mechanism of Russell body biogenesis has been extensively studied by using truncated mutant heavy chains, the importance of the variable domain sequences in this process and in immunoglobulin biosynthesis remains largely unknown. Using a panel of structurally and functionally normal human immunoglobulin Gs, we show that individual immunoglobulin G clones possess distinctive Russell body inducing propensities that can surface differently under normal and abnormal cellular conditions. Russell body inducing predisposition unique to each immunoglobulin G clone was corroborated by the intrinsic physicochemical properties encoded in the heavy chain variable domain/light chain variable domain sequence combinations that define each immunoglobulin G clone. While the sequence based intrinsic factors predispose certain immunoglobulin G clones to be more prone to induce Russell bodies, extrinsic factors such as stressful cell culture conditions also play roles in unmasking Russell body propensity from immunoglobulin G clones that are normally refractory to developing Russell bodies. By taking advantage of heterologous expression systems, we dissected the roles of individual subunit chains in Russell body formation and examined the effect of non-cognate subunit chain pair co-expression on Russell body forming propensity. The results suggest that the properties embedded in the variable domain of individual light chain clones and their compatibility with the partnering heavy chain variable domain sequences underscore the efficiency of immunoglobulin G biosynthesis, the threshold for Russell body induction, and the level of immunoglobulin G secretion. We propose that an interplay between the unique properties encoded in variable domain sequences and the state of protein homeostasis determines whether an immunoglobulin G expressing cell will develop the Russell body phenotype in a dynamic cellular setting. Copyright © 2012 Elsevier B.V. All rights reserved.

Kinematic variability, fractal dynamics and local dynamic stability of treadmill walking

PubMed Central

2011-01-01

Background Motorized treadmills are widely used in research or in clinical therapy. Small kinematics, kinetics and energetics changes induced by Treadmill Walking (TW) as compared to Overground Walking (OW) have been reported in literature. The purpose of the present study was to characterize the differences between OW and TW in terms of stride-to-stride variability. Classical (Standard Deviation, SD) and non-linear (fractal dynamics, local dynamic stability) methods were used. In addition, the correlations between the different variability indexes were analyzed. Methods Twenty healthy subjects performed 10 min TW and OW in a random sequence. A triaxial accelerometer recorded trunk accelerations. Kinematic variability was computed as the average SD (MeanSD) of acceleration patterns among standardized strides. Fractal dynamics (scaling exponent α) was assessed by Detrended Fluctuation Analysis (DFA) of stride intervals. Short-term and long-term dynamic stability were estimated by computing the maximal Lyapunov exponents of acceleration signals. Results TW did not modify kinematic gait variability as compared to OW (multivariate T2, p = 0.87). Conversely, TW significantly modified fractal dynamics (t-test, p = 0.01), and both short and long term local dynamic stability (T2 p = 0.0002). No relationship was observed between variability indexes with the exception of significant negative correlation between MeanSD and dynamic stability in TW (3 × 6 canonical correlation, r = 0.94). Conclusions Treadmill induced a less correlated pattern in the stride intervals and increased gait stability, but did not modify kinematic variability in healthy subjects. This could be due to changes in perceptual information induced by treadmill walking that would affect locomotor control of the gait and hence specifically alter non-linear dependencies among consecutive strides. Consequently, the type of walking (i.e. treadmill or overground) is important to consider in each protocol design. PMID:21345241

Learning predictive statistics from temporal sequences: Dynamics and strategies

PubMed Central

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E.; Kourtzi, Zoe

2017-01-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics—that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments. PMID:28973111

Learning predictive statistics from temporal sequences: Dynamics and strategies.

PubMed

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

2017-10-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

Local contrast-enhanced MR images via high dynamic range processing.

PubMed

Chandra, Shekhar S; Engstrom, Craig; Fripp, Jurgen; Neubert, Ales; Jin, Jin; Walker, Duncan; Salvado, Olivier; Ho, Charles; Crozier, Stuart

2018-09-01

To develop a local contrast-enhancing and feature-preserving high dynamic range (HDR) image processing algorithm for multichannel and multisequence MR images of multiple body regions and tissues, and to evaluate its performance for structure visualization, bias field (correction) mitigation, and automated tissue segmentation. A multiscale-shape and detail-enhancement HDR-MRI algorithm is applied to data sets of multichannel and multisequence MR images of the brain, knee, breast, and hip. In multisequence 3T hip images, agreement between automatic cartilage segmentations and corresponding synthesized HDR-MRI series were computed for mean voxel overlap established from manual segmentations for a series of cases. Qualitative comparisons between the developed HDR-MRI and standard synthesis methods were performed on multichannel 7T brain and knee data, and multisequence 3T breast and knee data. The synthesized HDR-MRI series provided excellent enhancement of fine-scale structure from multiple scales and contrasts, while substantially reducing bias field effects in 7T brain gradient echo, T 1 and T 2 breast images and 7T knee multichannel images. Evaluation of the HDR-MRI approach on 3T hip multisequence images showed superior outcomes for automatic cartilage segmentations with respect to manual segmentation, particularly around regions with hyperintense synovial fluid, across a set of 3D sequences. The successful combination of multichannel/sequence MR images into a single-fused HDR-MR image format provided consolidated visualization of tissues within 1 omnibus image, enhanced definition of thin, complex anatomical structures in the presence of variable or hyperintense signals, and improved tissue (cartilage) segmentation outcomes. © 2018 International Society for Magnetic Resonance in Medicine.

Biofidelic Human Activity Modeling and Simulation with Large Variability

DTIC Science & Technology

2014-11-25

A systematic approach was developed for biofidelic human activity modeling and simulation by using body scan data and motion capture data to...replicate a human activity in 3D space. Since technologies for simultaneously capturing human motion and dynamic shapes are not yet ready for practical use, a...that can replicate a human activity in 3D space with the true shape and true motion of a human. Using this approach, a model library was built to

Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution.

PubMed

Wei, Wei; Davis, Robert E; Jomantiene, Rasa; Zhao, Yan

2008-08-19

Mobile genetic elements have impacted biological evolution across all studied organisms, but evidence for a role in evolutionary emergence of an entire phylogenetic clade has not been forthcoming. We suggest that mobile element predation played a formative role in emergence of the phytoplasma clade. Phytoplasmas are cell wall-less bacteria that cause numerous diseases in plants. Phylogenetic analyses indicate that these transkingdom parasites descended from Gram-positive walled bacteria, but events giving rise to the first phytoplasma have remained unknown. Previously we discovered a unique feature of phytoplasmal genome architecture, genes clustered in sequence-variable mosaics (SVMs), and suggested that such structures formed through recurrent, targeted attacks by mobile elements. In the present study, we discovered that cryptic prophage remnants, originating from phages in the order Caudovirales, formed SVMs and comprised exceptionally large percentages of the chromosomes of 'Candidatus Phytoplasma asteris'-related strains OYM and AYWB, occupying nearly all major nonsyntenic sections, and accounting for most of the size difference between the two genomes. The clustered phage remnants formed genomic islands exhibiting distinct DNA physical signatures, such as dinucleotide relative abundance and codon position GC values. Phytoplasma strain-specific genes identified as phage morons were located in hypervariable regions within individual SVMs, indicating that prophage remnants played important roles in generating phytoplasma genetic diversity. Because no SVM-like structures could be identified in genomes of ancestral relatives including Acholeplasma spp., we hypothesize that ancient phage attacks leading to SVM formation occurred after divergence of phytoplasmas from acholeplasmas, triggering evolution of the phytoplasma clade.

Anode optimization for miniature electronic brachytherapy X-ray sources using Monte Carlo and computational fluid dynamic codes

PubMed Central

Khajeh, Masoud; Safigholi, Habib

2015-01-01

A miniature X-ray source has been optimized for electronic brachytherapy. The cooling fluid for this device is water. Unlike the radionuclide brachytherapy sources, this source is able to operate at variable voltages and currents to match the dose with the tumor depth. First, Monte Carlo (MC) optimization was performed on the tungsten target-buffer thickness layers versus energy such that the minimum X-ray attenuation occurred. Second optimization was done on the selection of the anode shape based on the Monte Carlo in water TG-43U1 anisotropy function. This optimization was carried out to get the dose anisotropy functions closer to unity at any angle from 0° to 170°. Three anode shapes including cylindrical, spherical, and conical were considered. Moreover, by Computational Fluid Dynamic (CFD) code the optimal target-buffer shape and different nozzle shapes for electronic brachytherapy were evaluated. The characterization criteria of the CFD were the minimum temperature on the anode shape, cooling water, and pressure loss from inlet to outlet. The optimal anode was conical in shape with a conical nozzle. Finally, the TG-43U1 parameters of the optimal source were compared with the literature. PMID:26966563

Analysis on the use of Multi-Sequence MRI Series for Segmentation of Abdominal Organs

NASA Astrophysics Data System (ADS)

Selver, M. A.; Selvi, E.; Kavur, E.; Dicle, O.

2015-01-01

Segmentation of abdominal organs from MRI data sets is a challenging task due to various limitations and artefacts. During the routine clinical practice, radiologists use multiple MR sequences in order to analyze different anatomical properties. These sequences have different characteristics in terms of acquisition parameters (such as contrast mechanisms and pulse sequence designs) and image properties (such as pixel spacing, slice thicknesses and dynamic range). For a complete understanding of the data, computational techniques should combine the information coming from these various MRI sequences. These sequences are not acquired in parallel but in a sequential manner (one after another). Therefore, patient movements and respiratory motions change the position and shape of the abdominal organs. In this study, the amount of these effects is measured using three different symmetric surface distance metrics performed to three dimensional data acquired from various MRI sequences. The results are compared to intra and inter observer differences and discussions on using multiple MRI sequences for segmentation and the necessities for registration are presented.

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

Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg; Dai, J., E-mail: daijing491@gmail.com; Sieradzan, A., E-mail: adams86@wp.pl

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 unresolvedmore » 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.« less

Solitons and protein folding: An In Silico experiment

NASA Astrophysics Data System (ADS)

Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

2015-10-01

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.

Multi-classification of cell deformation based on object alignment and run length statistic.

PubMed

Li, Heng; Liu, Zhiwen; An, Xing; Shi, Yonggang

2014-01-01

Cellular morphology is widely applied in digital pathology and is essential for improving our understanding of the basic physiological processes of organisms. One of the main issues of application is to develop efficient methods for cell deformation measurement. We propose an innovative indirect approach to analyze dynamic cell morphology in image sequences. The proposed approach considers both the cellular shape change and cytoplasm variation, and takes each frame in the image sequence into account. The cell deformation is measured by the minimum energy function of object alignment, which is invariant to object pose. Then an indirect analysis strategy is employed to overcome the limitation of gradual deformation by run length statistic. We demonstrate the power of the proposed approach with one application: multi-classification of cell deformation. Experimental results show that the proposed method is sensitive to the morphology variation and performs better than standard shape representation methods.

The auditory dynamic attending theory revisited: A closer look at the pitch comparison task.

PubMed

Bauer, Anna-Katharina R; Jaeger, Manuela; Thorne, Jeremy D; Bendixen, Alexandra; Debener, Stefan

2015-11-11

The dynamic attending theory as originally proposed by Jones, 1976. Psychol. Rev. 83(5), 323-355 posits that tone sequences presented at a regular rhythm entrain attentional oscillations and thereby facilitate the processing of sounds presented in phase with this rhythm. The increased interest in neural correlates of dynamic attending requires robust behavioral indicators of the phenomenon. Here we aimed to replicate and complement the most prominent experimental implementation of dynamic attending (Jones et al., 2002. Psychol. Sci. 13(4), 313-319). The paradigm uses a pitch comparison task in which two tones, the initial and the last of a longer series, have to be compared. In-between the two, distractor tones with variable pitch are presented, at a regular pace. A comparison tone presented in phase with the entrained rhythm is hypothesized to lead to better behavioral performance. Aiming for a conceptual replication, four different variations of the original paradigm were created which were followed by an exact replication attempt. Across all five experiments, only 40 of the 140 tested participants showed the hypothesized pattern of an inverted U-shaped profile in task accuracy, and the group average effects did not replicate the pattern reported by Jones et al., 2002. Psychol. Sci. 13(4), 313-319 in any of the five experiments. However, clear evidence for a relationship between musicality and overall behavioral performance was found. This study casts doubt on the suitability of the pitch comparison task for demonstrating auditory dynamic attending. We discuss alternative tasks that have been shown to support dynamic attending theory, thus lending themselves more readily to studying its neural correlates. This article is part of a Special Issue entitled SI: Prediction and Attention. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Economy, Movement Dynamics, and Muscle Activity of Human Walking at Different Speeds.

PubMed

Raffalt, P C; Guul, M K; Nielsen, A N; Puthusserypady, S; Alkjær, T

2017-03-08

The complex behaviour of human walking with respect to movement variability, economy and muscle activity is speed dependent. It is well known that a U-shaped relationship between walking speed and economy exists. However, it is an open question if the movement dynamics of joint angles and centre of mass and muscle activation strategy also exhibit a U-shaped relationship with walking speed. We investigated the dynamics of joint angle trajectories and the centre of mass accelerations at five different speeds ranging from 20 to 180% of the predicted preferred speed (based on Froude speed) in twelve healthy males. The muscle activation strategy and walking economy were also assessed. The movement dynamics was investigated using a combination of the largest Lyapunov exponent and correlation dimension. We observed an intermediate stage of the movement dynamics of the knee joint angle and the anterior-posterior and mediolateral centre of mass accelerations which coincided with the most energy-efficient walking speed. Furthermore, the dynamics of the joint angle trajectories and the muscle activation strategy was closely linked to the functional role and biomechanical constraints of the joints.

Dynamic control of nutrient-removal from industrial wastewater in a sequencing batch reactor, using common and low-cost online sensors.

PubMed

Dries, Jan

2016-01-01

On-line control of the biological treatment process is an innovative tool to cope with variable concentrations of chemical oxygen demand and nutrients in industrial wastewater. In the present study we implemented a simple dynamic control strategy for nutrient-removal in a sequencing batch reactor (SBR) treating variable tank truck cleaning wastewater. The control system was based on derived signals from two low-cost and robust sensors that are very common in activated sludge plants, i.e. oxidation reduction potential (ORP) and dissolved oxygen. The amount of wastewater fed during anoxic filling phases, and the number of filling phases in the SBR cycle, were determined by the appearance of the 'nitrate knee' in the profile of the ORP. The phase length of the subsequent aerobic phases was controlled by the oxygen uptake rate measured online in the reactor. As a result, the sludge loading rate (F/M ratio), the volume exchange rate and the SBR cycle length adapted dynamically to the activity of the activated sludge and the actual characteristics of the wastewater, without affecting the final effluent quality.

Accuracy of dynamical-decoupling-based spectroscopy of Gaussian noise

NASA Astrophysics Data System (ADS)

Szańkowski, Piotr; Cywiński, Łukasz

2018-03-01

The fundamental assumption of dynamical-decoupling-based noise spectroscopy is that the coherence decay rate of qubit (or qubits) driven with a sequence of many pulses, is well approximated by the environmental noise spectrum spanned on frequency comb defined by the sequence. Here we investigate the precise conditions under which this commonly used spectroscopic approach is quantitatively correct. To this end we focus on two representative examples of spectral densities: the long-tailed Lorentzian, and finite-ranged Gaussian—both expected to be encountered when using the qubit for nanoscale nuclear resonance imaging. We have found that, in contrast to Lorentz spectrum, for which the corrections to the standard spectroscopic formulas can easily be made negligible, the spectra with finite range are more challenging to reconstruct accurately. For Gaussian line shape of environmental spectral density, direct application of the standard dynamical-decoupling-based spectroscopy leads to erroneous attribution of long-tail behavior to the reconstructed spectrum. Fortunately, artifacts such as this, can be completely avoided with the simple extension to standard reconstruction method.

Dynamical evolution of motion perception.

PubMed

Kanai, Ryota; Sheth, Bhavin R; Shimojo, Shinsuke

2007-03-01

Motion is defined as a sequence of positional changes over time. However, in perception, spatial position and motion dynamically interact with each other. This reciprocal interaction suggests that the perception of a moving object itself may dynamically evolve following the onset of motion. Here, we show evidence that the percept of a moving object systematically changes over time. In experiments, we introduced a transient gap in the motion sequence or a brief change in some feature (e.g., color or shape) of an otherwise smoothly moving target stimulus. Observers were highly sensitive to the gap or transient change if it occurred soon after motion onset (< or =200 ms), but significantly less so if it occurred later (> or = 300 ms). Our findings suggest that the moving stimulus is initially perceived as a time series of discrete potentially isolatable frames; later failures to perceive change suggests that over time, the stimulus begins to be perceived as a single, indivisible gestalt integrated over space as well as time, which could well be the signature of an emergent stable motion percept.

Dynamics and control of DNA sequence amplification

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

Marimuthu, Karthikeyan; Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu; Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054

2014-10-28

DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reactionmore » are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.« less

Object view in spatial system dynamics: a grassland farming example

PubMed Central

Neuwirth, Christian; Hofer, Barbara; Schaumberger, Andreas

2016-01-01

Abstract Spatial system dynamics (SSD) models are typically implemented by linking stock variables to raster grids while the use of object representations of human artefacts such as buildings or ownership has been limited. This limitation is addressed by this article, which demonstrates the use of object representations in SSD. The objects are parcels of land that are attributed to grassland farms. The model simulates structural change in agriculture, i.e., change in the size of farms. The aim of the model is to reveal relations between structural change, farmland fragmentation and variable farmland quality. Results show that fragmented farms tend to become consolidated by structural change, whereas consolidated initial conditions result in a significant increase of fragmentation. Consolidation is reinforced by a dynamic land market and high transportation costs. The example demonstrates the capabilities of the object-based approach for integrating object geometries (parcel shapes) and relations between objects (distances between parcels) dynamically in SSD. PMID:28190972

Inter-level Scaffolding and Sequences of Representational Activities in Teaching a Chemical System with Graphical Simulations

NASA Astrophysics Data System (ADS)

Li, Na; Black, John B.

2016-10-01

Chemistry knowledge can be represented at macro-, micro- and symbolic levels, and learning a chemistry topic requires students to engage in multiple representational activities. This study focused on scaffolding for inter-level connection-making in learning chemistry knowledge with graphical simulations. We also tested whether different sequences of representational activities produced different student learning outcomes in learning a chemistry topic. A sample of 129 seventh graders participated in this study. In a simulation-based environment, participants completed three representational activities to learn several ideal gas law concepts. We conducted a 2 × 3 factorial design experiment. We compared two scaffolding conditions: (1) the inter- level scaffolding condition in which participants received inter-level questions and experienced the dynamic link function in the simulation-based environment and (2) the intra- level scaffolding condition in which participants received intra-level questions and did not experience the dynamic link function. We also compared three different sequences of representational activities: macro-symbolic-micro, micro-symbolic-macro and symbolic-micro-macro. For the scaffolding variable, we found that the inter- level scaffolding condition produced significantly better performance in both knowledge comprehension and application, compared to the intra- level scaffolding condition. For the sequence variable, we found that the macro-symbolic-micro sequence produced significantly better knowledge comprehension performance than the other two sequences; however, it did not benefit knowledge application performance. There was a trend that the treatment group who experienced inter- level scaffolding and the micro-symbolic-macro sequence achieved the best knowledge application performance.

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs.

PubMed

Shigematsu, Megumi; Honda, Shozo; Loher, Phillipe; Telonis, Aristeidis G; Rigoutsos, Isidore; Kirino, Yohei

2017-05-19

Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Neural-network-designed pulse sequences for robust control of singlet-triplet qubits

NASA Astrophysics Data System (ADS)

Yang, Xu-Chen; Yung, Man-Hong; Wang, Xin

2018-04-01

Composite pulses are essential for universal manipulation of singlet-triplet spin qubits. In the absence of noise, they are required to perform arbitrary single-qubit operations due to the special control constraint of a singlet-triplet qubit, while in a noisy environment, more complicated sequences have been developed to dynamically correct the error. Tailoring these sequences typically requires numerically solving a set of nonlinear equations. Here we demonstrate that these pulse sequences can be generated by a well-trained, double-layer neural network. For sequences designed for the noise-free case, the trained neural network is capable of producing almost exactly the same pulses known in the literature. For more complicated noise-correcting sequences, the neural network produces pulses with slightly different line shapes, but the robustness against noises remains comparable. These results indicate that the neural network can be a judicious and powerful alternative to existing techniques in developing pulse sequences for universal fault-tolerant quantum computation.

Automated design evolution of stereochemically randomized protein foldamers

NASA Astrophysics Data System (ADS)

Ranbhor, Ranjit; Kumar, Anil; Patel, Kirti; Ramakrishnan, Vibin; Durani, Susheel

2018-05-01

Diversification of chain stereochemistry opens up the possibilities of an ‘in principle’ increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials. To diversify protein structure stereochemically, we introduced L- and D-α-amino acids as the design alphabet. With a sequence design algorithm, we explored the usage of specific variables such as chirality and the sequence of this alphabet in independent steps. With molecular dynamics, we folded stereochemically diverse homopolypeptides and evaluated their ‘fitness’ for possible design as protein-like foldamers. We propose a fitness function to prune the most optimal fold among 1000 structures simulated with an automated repetitive simulated annealing molecular dynamics (AR-SAMD) approach. The highly scored poly-leucine fold with sequence lengths of 24 and 30 amino acids were later sequence-optimized using a Dead End Elimination cum Monte Carlo based optimization tool. This paper demonstrates a novel approach for the de novo design of protein-like foldamers.

Range and variation in landscape patch dynamics: Implications for ecosystem management

Treesearch

Robert E. Keane; Janice L. Garner; Casey Teske; Cathy Stewart; Paul Hessburg

2001-01-01

Northern Rocky Mountain landscape patterns are shaped primarily by fire and succession, and conversely, these vegetation patterns influence burning patterns and plant colonization processes. Historical range and variability (HRV) of landscape pattern can be quantified from three sources: (1) historical chronosequences, (2) spatial series, and (3) simulated...

Precipitation legacy effects on dryland ecosystem carbon fluxes: direction, magnitude and biogeochemical carryovers

USDA-ARS?s Scientific Manuscript database

The precipitation legacy effect, defined as the impact of historical precipitation (PPT) on extant ecosystem dynamics, has been recognized as an important driver in shaping the temporal variability of dryland aboveground net primary production (ANPP) and soil respiration. How the PPT legacy influenc...

Data-driven Modeling of Metal-oxide Sensors with Dynamic Bayesian Networks

NASA Astrophysics Data System (ADS)

Gosangi, Rakesh; Gutierrez-Osuna, Ricardo

2011-09-01

We present a data-driven probabilistic framework to model the transient response of MOX sensors modulated with a sequence of voltage steps. Analytical models of MOX sensors are usually built based on the physico-chemical properties of the sensing materials. Although building these models provides an insight into the sensor behavior, they also require a thorough understanding of the underlying operating principles. Here we propose a data-driven approach to characterize the dynamical relationship between sensor inputs and outputs. Namely, we use dynamic Bayesian networks (DBNs), probabilistic models that represent temporal relations between a set of random variables. We identify a set of control variables that influence the sensor responses, create a graphical representation that captures the causal relations between these variables, and finally train the model with experimental data. We validated the approach on experimental data in terms of predictive accuracy and classification performance. Our results show that DBNs can accurately predict the dynamic response of MOX sensors, as well as capture the discriminatory information present in the sensor transients.

The sequence of cortical activity inferred by response latency variability in the human ventral pathway of face processing.

PubMed

Lin, Jo-Fu Lotus; Silva-Pereyra, Juan; Chou, Chih-Che; Lin, Fa-Hsuan

2018-04-11

Variability in neuronal response latency has been typically considered caused by random noise. Previous studies of single cells and large neuronal populations have shown that the temporal variability tends to increase along the visual pathway. Inspired by these previous studies, we hypothesized that functional areas at later stages in the visual pathway of face processing would have larger variability in the response latency. To test this hypothesis, we used magnetoencephalographic data collected when subjects were presented with images of human faces. Faces are known to elicit a sequence of activity from the primary visual cortex to the fusiform gyrus. Our results revealed that the fusiform gyrus showed larger variability in the response latency compared to the calcarine fissure. Dynamic and spectral analyses of the latency variability indicated that the response latency in the fusiform gyrus was more variable than in the calcarine fissure between 70 ms and 200 ms after the stimulus onset and between 4 Hz and 40 Hz, respectively. The sequential processing of face information from the calcarine sulcus to the fusiform sulcus was more reliably detected based on sizes of the response variability than instants of the maximal response peaks. With two areas in the ventral visual pathway, we show that the variability in response latency across brain areas can be used to infer the sequence of cortical activity.

The resolved nucleus of Comet Siding Spring (C/2013 A1) in MRO HiRISE images

NASA Astrophysics Data System (ADS)

Farnham, Tony; Kelley, Michael S.; Bodewits, Dennis; Bauer, James M.

2017-10-01

Comet Siding Spring (C/2013 A1) passed within 140,000 km of Mars on 19 Oct 2014. The MRO spacecraft, in orbit around Mars, used its HiRISE camera to monitor the comet during the encounter, obtaining the first resolved images of the nucleus of a dynamically new comet.MRO observed Siding Spring from 60 hr before, to 15 hr after close approach, obtaining 122 images in three different color filters. Close approach images, with a spatial scale as small as 138 m/pix, reveal an elongated crescent that changes shape over the course of the sequence, indicating that we are seeing a ~1 km non-spherical body from different viewpoints as the comet rapidly sweeps past. To better constrain the characteristics of the nucleus, we are performing detailed analyses, including modeling of the inner coma to separate its flux contribution from that of the nucleus. In conjunction with the coma removal, we will model the nucleus as a prolate/triaxial ellipsoid and, combined with the known illumination and viewing conditions, will use the changing aspect in the images to constrain the size, shape, orientation, albedo and possibly the phase dependence of the nucleus.In addition to the close approach observations, the images before and after close approach capture the coma structure and brightness. The photometric lightcurve from these images shows variability with an 8.1 hr period, which is presumed to be the rotational modulation of the coma activity. The observed morphology changes as well, promising to provide a measure of the nucleus' spin axis orientation.We will report on the results from our analyses, and provide the first direct measurements of the nucleus of a dynamically new comet.

Relaxation estimation of RMSD in molecular dynamics immunosimulations.

PubMed

Schreiner, Wolfgang; Karch, Rudolf; Knapp, Bernhard; Ilieva, Nevena

2012-01-01

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

PubMed

Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

2018-01-23

Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Resolving coiled shapes reveals new reorientation behaviors in C. elegans

PubMed Central

Broekmans, Onno D; Rodgers, Jarlath B; Ryu, William S; Stephens, Greg J

2016-01-01

We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of 2D worm behavior. We apply our algorithm to show that visually complex, coiled sequences are a superposition of two simpler patterns: the body wave dynamics and a head-curvature pulse. We demonstrate the precise Ω-turn dynamics of an escape response and uncover a surprising new dichotomy in spontaneous, large-amplitude coils; deep reorientations occur not only through classical Ω-shaped postures but also through larger postural excitations which we label here as δ-turns. We find that omega and delta turns occur independently, suggesting a distinct triggering mechanism, and are the serpentine analog of a random left-right step. Finally, we show that omega and delta turns occur with approximately equal rates and adapt to food-free conditions on a similar timescale, a simple strategy to avoid navigational bias. DOI: http://dx.doi.org/10.7554/eLife.17227.001 PMID:27644113

Sequential associative memory with nonuniformity of the layer sizes.

PubMed

Teramae, Jun-Nosuke; Fukai, Tomoki

2007-01-01

Sequence retrieval has a fundamental importance in information processing by the brain, and has extensively been studied in neural network models. Most of the previous sequential associative memory embedded sequences of memory patterns have nearly equal sizes. It was recently shown that local cortical networks display many diverse yet repeatable precise temporal sequences of neuronal activities, termed "neuronal avalanches." Interestingly, these avalanches displayed size and lifetime distributions that obey power laws. Inspired by these experimental findings, here we consider an associative memory model of binary neurons that stores sequences of memory patterns with highly variable sizes. Our analysis includes the case where the statistics of these size variations obey the above-mentioned power laws. We study the retrieval dynamics of such memory systems by analytically deriving the equations that govern the time evolution of macroscopic order parameters. We calculate the critical sequence length beyond which the network cannot retrieve memory sequences correctly. As an application of the analysis, we show how the present variability in sequential memory patterns degrades the power-law lifetime distribution of retrieved neural activities.

HIV-1 subtype A gag variability and epitope evolution.

PubMed

Abidi, Syed Hani; Kalish, Marcia L; Abbas, Farhat; Rowland-Jones, Sarah; Ali, Syed

2014-01-01

The aim of this study was to examine the course of time-dependent evolution of HIV-1 subtype A on a global level, especially with respect to the dynamics of immunogenic HIV gag epitopes. We used a total of 1,893 HIV-1 subtype A gag sequences representing a timeline from 1985 through 2010, and 19 different countries in Africa, Europe and Asia. The phylogenetic relationship of subtype A gag and its epidemic dynamics was analysed through a Maximum Likelihood tree and Bayesian Skyline plot, genomic variability was measured in terms of G → A substitutions and Shannon entropy, and the time-dependent evolution of HIV subtype A gag epitopes was examined. Finally, to confirm observations on globally reported HIV subtype A sequences, we analysed the gag epitope data from our Kenyan, Pakistani, and Afghan cohorts, where both cohort-specific gene epitope variability and HLA restriction profiles of gag epitopes were examined. The most recent common ancestor of the HIV subtype A epidemic was estimated to be 1956 ± 1. A period of exponential growth began about 1980 and lasted for approximately 7 years, stabilized for 15 years, declined for 2-3 years, then stabilized again from about 2004. During the course of evolution, a gradual increase in genomic variability was observed that peaked in 2005-2010. We observed that the number of point mutations and novel epitopes in gag also peaked concurrently during 2005-2010. It appears that as the HIV subtype A epidemic spread globally, changing population immunogenetic pressures may have played a role in steering immune-evolution of this subtype in new directions. This trend is apparent in the genomic variability and epitope diversity of HIV-1 subtype A gag sequences.

Red Lesion Detection Using Dynamic Shape Features for Diabetic Retinopathy Screening.

PubMed

Seoud, Lama; Hurtut, Thomas; Chelbi, Jihed; Cheriet, Farida; Langlois, J M Pierre

2016-04-01

The development of an automatic telemedicine system for computer-aided screening and grading of diabetic retinopathy depends on reliable detection of retinal lesions in fundus images. In this paper, a novel method for automatic detection of both microaneurysms and hemorrhages in color fundus images is described and validated. The main contribution is a new set of shape features, called Dynamic Shape Features, that do not require precise segmentation of the regions to be classified. These features represent the evolution of the shape during image flooding and allow to discriminate between lesions and vessel segments. The method is validated per-lesion and per-image using six databases, four of which are publicly available. It proves to be robust with respect to variability in image resolution, quality and acquisition system. On the Retinopathy Online Challenge's database, the method achieves a FROC score of 0.420 which ranks it fourth. On the Messidor database, when detecting images with diabetic retinopathy, the proposed method achieves an area under the ROC curve of 0.899, comparable to the score of human experts, and it outperforms state-of-the-art approaches.

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

PubMed Central

Figuerola, Eva L. M.; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch

PubMed Central

Lu, Changrui; Smith, Angela M; Ding, Fang; Chowdhury, Anirban; Henkin, Tina M; Ke, Ailong

2012-01-01

The SMK box (SAM-III) translational riboswitches were identified in S-adenosyl-L-methionine (SAM) synthetase metK genes in members of the Lactobacillales. This riboswitch switches between two alternative conformations in response to the intracellular SAM concentration and controls metK expression at the level of translation initiation. We previously reported the crystal structure of the SAM-bound SMK box riboswitch. In this study we combined SHAPE chemical probing with mutagenesis to probe the ligand-induced conformational switching mechanism. We revealed that while the majority of the apo SMK box RNA molecules exist in an alternatively base paired (ON) conformation, a subset of them pre-organize into a SAM-bound-like (READY) conformation, which upon SAM exposure is selectively stabilized into the SAM-bound (OFF) conformation through an induced-fit mechanism. Mutagenesis showed that the ON state is only slightly more stable than the READY state, as several single-nucleotide substitutions in a hypervariable region outside the SAM-binding core can alter the folding landscape to favor the READY state. Such SMK variants display a “constitutively-OFF” behavior both in vitro and in vivo. Time-resolved and temperature-dependent SHAPE analyses revealed adaptation of the SMK box RNA to its mesothermal working environment. The latter analysis revealed that the SAM-bound SMK box RNA follows a two-step folding/unfolding process. PMID:21549712

Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers

NASA Astrophysics Data System (ADS)

Zoccarato, Luca; Pallavicini, Alberto; Cerino, Federica; Fonda Umani, Serena; Celussi, Mauro

2016-12-01

Deep-sea environments host the largest pool of microbes and represent the last largely unexplored and poorly known ecosystems on Earth. The Ross Sea is characterized by unique oceanographic dynamics and harbors several water masses deeply involved in cooling and ventilation of deep oceans. In this study the V9 region of the 18S rDNA was targeted and sequenced with the Ion Torrent high-throughput sequencing technology to unveil differences in protist communities (>2 μm) correlated with biogeochemical properties of the water masses. The analyzed samples were significantly different in terms of environmental parameters and community composition outlining significant structuring effects of temperature and salinity. Overall, Alveolata (especially Dinophyta), Stramenopiles and Excavata groups dominated mesopelagic and bathypelagic layers, and protist communities were shaped according to the biogeochemistry of the water masses (advection effect and mixing events). Newly-formed High Salinity Shelf Water (HSSW) was characterized by high relative abundance of phototrophic organisms that bloom at the surface during the austral summer. Oxygen-depleted Circumpolar Deep Water (CDW) showed higher abundance of Excavata, common bacterivores in deep water masses. At the shelf-break, Antarctic Bottom Water (AABW), formed by the entrainment of shelf waters in CDW, maintained the eukaryotic genetic signature typical of both parental water masses.

Contrast of artificial subcutaneous hematomas in MRI over time.

PubMed

Hassler, Eva Maria; Ogris, Kathrin; Petrovic, Andreas; Neumayer, Bernhard; Widek, Thomas; Yen, Kathrin; Scheurer, Eva

2015-03-01

In clinical forensic medicine, hematomas and other externally visible injuries build the basis for the reconstruction of events. However, dating of subcutaneous hematomas based on their external aspect is difficult. Magnetic resonance imaging (MRI) has proven its use in dating intracranial hemorrhage. Thus, the aim was to investigate if MRI can also be used for dating subcutaneous hematomas and to analyze an eventual influence of the hematoma shape. In 20 healthy volunteers (11 females, 9 males, aged 26.9 ± 3.8 years), 4 ml of autologous blood were injected subcutaneously in the thigh. The hematoma was scanned immediately after the injection, after 3 and 24 h and 3, 7, and 14 days using three sequences with different contrast. Data was analyzed by measuring signal intensities of the hematoma, the muscle, and the subcutaneous tissue over time, and the Michelson contrast coefficients between the tissues were calculated. In the analysis, hematoma shape was considered. Signal intensity of blood in the proton density-weighted sequence reached its maximum 3 h after the injection with a subsequent decrease, whereas the signal intensities of muscle and fatty tissue remained constant. The time course of the Michelson coefficient of blood versus muscle decreased exponentially with a change from hyperintensity to hypointensity at 116.9 h, depending on hematoma shape. In the other sequences, either variability was large or contrast coefficients stayed constant over time. The observed change of contrast of blood versus muscle permits a quick estimate of a hematoma's age. The consideration of the hematoma shape is expected to further enhance dating using MRI.

Differing Roles of Functional Movement Variability as Experience Increases in Gymnastics

PubMed Central

Busquets, Albert; Marina, Michel; Davids, Keith; Angulo-Barroso, Rosa

2016-01-01

Current theories, like Ecological Dynamics, propose that inter-trial movement variability is functional when acquiring or refining movement coordination. Here, we examined how age-based experience levels of gymnasts constrained differences in emergent movement pattern variability during task performance. Specifically, we investigated different roles of movement pattern variability when gymnasts in different age groups performed longswings on a high bar, capturing the range of experience from beginner to advanced status. We also investigated the functionality of the relationships between levels of inter-trial variability and longswing amplitude during performance. One-hundred and thirteen male gymnasts in five age groups were observed performing longswings (with three different experience levels: beginners, intermediates and advanced performers). Performance was evaluated by analysis of key events in coordination of longswing focused on the arm-trunk and trunk-thigh segmental relations. Results revealed that 10 of 18 inter-trial variability measures changed significantly as a function of increasing task experience. Four of ten variability measures conformed to a U-shaped function with age implying exploratory strategies amongst beginners and functional adaptive variability amongst advanced performers. Inter-trial variability of arm-trunk coordination variables (6 of 10) conformed to a \\-shaped curve, as values were reduced to complete the longswings. Changes in coordination variability from beginner to intermediate status were largely restrictive, with only one variability measure related to exploration. Data revealed how inter-trial movement variability in gymnastics, relative to performance outcomes, needs careful interpretation, implying different roles as task experience changes. Key points Inter-trial variability while performing longswings on a high bar was assessed in a large sample (113 participants) divided into five age groups (form beginners to advanced gymnasts). Longswing assessment allowed us to evaluate inter-trial variability in representative performance context. Coordination variability presented two different configurations across experience levels depending on the variable of interest: either a U-shaped or a L- or \\-shaped graph. Increased inter-trial variability of the functional phase events offered flexibility to adapt the longswing performance in the advanced gymnasts, while decreasing variability in arm-trunk coordination modes was critical to improve longswing and to achieve the most advanced level. In addition, the relationship between variability measures and the global performance outcome (i.e. the swing amplitude) revealed different functional roles of movement variability (exploratory or restrictive) as a function of changes in experience levels. PMID:27274664

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

PubMed

Xia, Li C; Ai, Dongmei; Cram, Jacob A; Liang, Xiaoyi; Fuhrman, Jed A; Sun, Fengzhu

2015-09-21

Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics of biological systems. However, slow permutation procedures to evaluate the statistical significance of local trend scores have limited its applications to high-throughput time series data analysis, e.g., data from the next generation sequencing technology based studies. By extending the theories for the tail probability of the range of sum of Markovian random variables, we propose formulae for approximating the statistical significance of local trend scores. Using simulations and real data, we show that the approximate p-value is close to that obtained using a large number of permutations (starting at time points >20 with no delay and >30 with delay of at most three time steps) in that the non-zero decimals of the p-values obtained by the approximation and the permutations are mostly the same when the approximate p-value is less than 0.05. In addition, the approximate p-value is slightly larger than that based on permutations making hypothesis testing based on the approximate p-value conservative. The approximation enables efficient calculation of p-values for pairwise local trend analysis, making large scale all-versus-all comparisons possible. We also propose a hybrid approach by integrating the approximation and permutations to obtain accurate p-values for significantly associated pairs. We further demonstrate its use with the analysis of the Polymouth Marine Laboratory (PML) microbial community time series from high-throughput sequencing data and found interesting organism co-occurrence dynamic patterns. The software tool is integrated into the eLSA software package that now provides accelerated local trend and similarity analysis pipelines for time series data. The package is freely available from the eLSA website: http://bitbucket.org/charade/elsa.

Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire.

PubMed

Liu, Ju; Li, Ruihua; Liu, Kun; Li, Liangliang; Zai, Xiaodong; Chi, Xiangyang; Fu, Ling; Xu, Junjie; Chen, Wei

2016-04-22

High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies. Copyright © 2016 Elsevier Inc. All rights reserved.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Missouri Ozark forest soils: perspectives and realities

Treesearch

R. David. Hammer

1997-01-01

Ozark forest soils are dynamic in space and time, and most formed in multiple parent materials. Erosion and mass movement have been variable and extensive. Soil attributes including texture, cation exchange capacity, and mineralogy are related to geologic strata and to geomorphic conditions. Soil organic carbon content is influenced by surface shape, position in...

The calculation of weakly non-spherical cavitation bubble impact on a solid

NASA Astrophysics Data System (ADS)

Aganin, A. A.; Guseva, T. S.; Kosolapova, L. A.; Khismatullina, N. A.

2016-11-01

The effect of small spheroidal non-sphericity of a cavitation bubble touching a solid at the beginning of its collapse on its impact on the solid of a copper-nickel alloy is investigated. The impact on the solid is realized by means of a high-speed liquid jet arising at collapse on the bubble surface. The shape of the jet, its velocity and pressure are calculated by the boundary element method. The spatial and temporal characteristics of the pressure pulses on the solid surface are determined by the CIP-CUP method on dynamically adaptive grids without explicitly separating the gas-liquid interface. The solid surface layer dynamics is evaluated by the Godunov method. The results are analyzed in dimensionless variables obtained with using the water hammer pressure, the time moment and the jet-solid contact area radius at which the jet begins to spread on the solid surface. It is shown that in those dimensionless variables, the dependence of the spatial and temporal characteristics of the solid surface pressure pulses on the initial bubble shape non-sphericity is relatively small. The nonsphericity also slightly influences the main qualitative features of the dynamic processes inside the solid, whereas its effect on their quantitative characteristics can be significant.

Length and sequence dependence in the association of Huntingtin protein with lipid membranes

NASA Astrophysics Data System (ADS)

Jawahery, Sudi; Nagarajan, Anu; Matysiak, Silvina

2013-03-01

There is a fundamental gap in our understanding of how aggregates of mutant Huntingtin protein (htt) with overextended polyglutamine (polyQ) sequences gain the toxic properties that cause Huntington's disease (HD). Experimental studies have shown that the most important step associated with toxicity is the binding of mutant htt aggregates to lipid membranes. Studies have also shown that flanking amino acid sequences around the polyQ sequence directly affect interactions with the lipid bilayer, and that polyQ sequences of greater than 35 glutamine repeats in htt are a characteristic of HD. The key steps that determine how flanking sequences and polyQ length affect the structure of lipid bilayers remain unknown. In this study, we use atomistic molecular dynamics simulations to study the interactions between lipid membranes of varying compositions and polyQ peptides of varying lengths and flanking sequences. We find that overextended polyQ interactions do cause deformation in model membranes, and that the flanking sequences do play a role in intensifying this deformation by altering the shape of the affected regions.

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

PubMed Central

Schreiner, Wolfgang; Karch, Rudolf; Knapp, Bernhard; Ilieva, Nevena

2012-01-01

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged. PMID:23019425

Human action classification using procrustes shape theory

NASA Astrophysics Data System (ADS)

Cho, Wanhyun; Kim, Sangkyoon; Park, Soonyoung; Lee, Myungeun

2015-02-01

In this paper, we propose new method that can classify a human action using Procrustes shape theory. First, we extract a pre-shape configuration vector of landmarks from each frame of an image sequence representing an arbitrary human action, and then we have derived the Procrustes fit vector for pre-shape configuration vector. Second, we extract a set of pre-shape vectors from tanning sample stored at database, and we compute a Procrustes mean shape vector for these preshape vectors. Third, we extract a sequence of the pre-shape vectors from input video, and we project this sequence of pre-shape vectors on the tangent space with respect to the pole taking as a sequence of mean shape vectors corresponding with a target video. And we calculate the Procrustes distance between two sequences of the projection pre-shape vectors on the tangent space and the mean shape vectors. Finally, we classify the input video into the human action class with minimum Procrustes distance. We assess a performance of the proposed method using one public dataset, namely Weizmann human action dataset. Experimental results reveal that the proposed method performs very good on this dataset.

The 1D Richards' equation in two layered soils: a Filippov approach to treat discontinuities

NASA Astrophysics Data System (ADS)

Berardi, Marco; Difonzo, Fabio; Vurro, Michele; Lopez, Luciano

2018-05-01

The infiltration process into the soil is generally modeled by the Richards' partial differential equation (PDE). In this paper a new approach for modeling the infiltration process through the interface of two different soils is proposed, where the interface is seen as a discontinuity surface defined by suitable state variables. Thus, the original 1D Richards' PDE, enriched by a particular choice of the boundary conditions, is first approximated by means of a time semidiscretization, that is by means of the transversal method of lines (TMOL). In such a way a sequence of discontinuous initial value problems, described by a sequence of second order differential systems in the space variable, is derived. Then, Filippov theory on discontinuous dynamical systems may be applied in order to study the relevant dynamics of the problem. The numerical integration of the semidiscretized differential system will be performed by using a one-step method, which employs an event driven procedure to locate the discontinuity surface and to adequately change the vector field.

Isolation and characterization of a virus infecting the freshwater algae Chrysochromulina parva

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

Mirza, S.F.; Staniewski, M.A.; Short, C.M.

Water samples from Lake Ontario, Canada were tested for lytic activity against the freshwater haptophyte algae Chrysochromulina parva. A filterable lytic agent was isolated and identified as a virus via transmission electron microscopy and molecular methods. The virus, CpV-BQ1, is icosahedral, ca. 145 nm in diameter, assembled within the cytoplasm, and has a genome size of ca. 485 kb. Sequences obtained through PCR-amplification of DNA polymerase (polB) genes clustered among sequences from the family Phycodnaviridae, whereas major capsid protein (MCP) sequences clustered among sequences from either the Phycodnaviridae or Mimiviridae. Based on quantitative molecular assays, C. parva's abundance in Lakemore » Ontario was relatively stable, yet CpV-BQ1's abundance was variable suggesting complex virus-host dynamics. This study demonstrates that CpV-BQ1 is a member of the proposed order Megavirales with characteristics of both phycodnaviruses and mimiviruses indicating that, in addition to its complex ecological dynamics, it also has a complex evolutionary history. - Highlights: • A virus infecting the algae C. parva was isolated from Lake Ontario. • Virus characteristics demonstrated that this novel virus is an NCLDV. • The virus's polB sequence suggests taxonomic affiliation with the Phycodnaviridae. • The virus's capsid protein sequences also suggest Mimiviridae ancestry. • Surveys of host and virus natural abundances revealed complex host–virus dynamics.« less

Dynamics of Variable Mass Systems

NASA Technical Reports Server (NTRS)

Eke, Fidelis O.

1998-01-01

This report presents the results of an investigation of the effects of mass loss on the attitude behavior of spinning bodies in flight. The principal goal is to determine whether there are circumstances under which the motion of variable mass systems can become unstable in the sense that their transverse angular velocities become unbounded. Obviously, results from a study of this kind would find immediate application in the aerospace field. The first part of this study features a complete and mathematically rigorous derivation of a set of equations that govern both the translational and rotational motions of general variable mass systems. The remainder of the study is then devoted to the application of the equations obtained to a systematic investigation of the effect of various mass loss scenarios on the dynamics of increasingly complex models of variable mass systems. It is found that mass loss can have a major impact on the dynamics of mechanical systems, including a possible change in the systems stability picture. Factors such as nozzle geometry, combustion chamber geometry, propellant's initial shape, size and relative mass, and propellant location can all have important influences on the system's dynamic behavior. The relative importance of these parameters on-system motion are quantified in a way that is useful for design purposes.

A Fly-Inspired Mushroom Bodies Model for Sensory-Motor Control Through Sequence and Subsequence Learning.

PubMed

Arena, Paolo; Calí, Marco; Patané, Luca; Portera, Agnese; Strauss, Roland

2016-09-01

Classification and sequence learning are relevant capabilities used by living beings to extract complex information from the environment for behavioral control. The insect world is full of examples where the presentation time of specific stimuli shapes the behavioral response. On the basis of previously developed neural models, inspired by Drosophila melanogaster, a new architecture for classification and sequence learning is here presented under the perspective of the Neural Reuse theory. Classification of relevant input stimuli is performed through resonant neurons, activated by the complex dynamics generated in a lattice of recurrent spiking neurons modeling the insect Mushroom Bodies neuropile. The network devoted to context formation is able to reconstruct the learned sequence and also to trace the subsequences present in the provided input. A sensitivity analysis to parameter variation and noise is reported. Experiments on a roving robot are reported to show the capabilities of the architecture used as a neural controller.

Alternating absorption features during attosecond-pulse propagation in a laser-controlled gaseous medium

NASA Astrophysics Data System (ADS)

Pfeiffer, Adrian N.; Bell, M. Justine; Beck, Annelise R.; Mashiko, Hiroki; Neumark, Daniel M.; Leone, Stephen R.

2013-11-01

Recording the transmitted spectrum of a weak attosecond pulse through a medium, while a strong femtosecond pulse copropagates at variable delay, probes the strong-field dynamics of atoms, molecules, and solids. Usually, the interpretation of these measurements is based on the assumption of a thin medium. Here, the propagation through a macroscopic medium of helium atoms in the region of fully allowed resonances is investigated both theoretically and experimentally. The propagation has dramatic effects on the transient spectrum even at relatively low pressures (50 mbar) and short propagation lengths (1 mm). The absorption does not evolve monotonically with the product of propagation distance and pressure, but regions with characteristics of Lorentz line shapes and characteristics of Fano line shapes alternate. Criteria are deduced to estimate whether macroscopic effects can be neglected or not in a transient absorption experiment. Furthermore, the theory in the limit of single-atom response yields a general equation for Lorentz- and Fano-type line shapes at variable pulse delay.

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.

PubMed

Volk, Jochen; Herrmann, Torsten; Wüthrich, Kurt

2008-07-01

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness.

Pairing-induced speedup of nuclear spontaneous fission

NASA Astrophysics Data System (ADS)

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; Sheikh, J. A.; Baran, A.

2014-12-01

Background: Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. Purpose: To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. Methods: We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependent pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Results: Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. Conclusions: The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. Consequently, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.

Pairing-induced speedup of nuclear spontaneous fission

DOE PAGES

Sadhukhan, Jhilam; Dobaczewski, J.; Nazarewicz, W.; ...

2014-12-22

Collective inertia is strongly influenced at the level crossing at which the quantum system changes its microscopic configuration diabatically. Pairing correlations tend to make the large-amplitude nuclear collective motion more adiabatic by reducing the effect of these configuration changes. Competition between pairing and level crossing is thus expected to have a profound impact on spontaneous fission lifetimes. To elucidate the role of nucleonic pairing on spontaneous fission, we study the dynamic fission trajectories of 264Fm and 240Pu using the state-of-the-art self-consistent framework. We employ the superfluid nuclear density functional theory with the Skyrme energy density functional SkM* and a density-dependentmore » pairing interaction. Along with shape variables, proton and neutron pairing correlations are taken as collective coordinates. The collective inertia tensor is calculated within the nonperturbative cranking approximation. The fission paths are obtained by using the least action principle in a four-dimensional collective space of shape and pairing coordinates. Pairing correlations are enhanced along the minimum-action fission path. For the symmetric fission of 264Fm, where the effect of triaxiality on the fission barrier is large, the geometry of the fission pathway in the space of the shape degrees of freedom is weakly impacted by pairing. This is not the case for 240Pu, where pairing fluctuations restore the axial symmetry of the dynamic fission trajectory. The minimum-action fission path is strongly impacted by nucleonic pairing. In some cases, the dynamical coupling between shape and pairing degrees of freedom can lead to a dramatic departure from the static picture. As a result, in the dynamical description of nuclear fission, particle-particle correlations should be considered on the same footing as those associated with shape degrees of freedom.« less

Sequence-encoded colloidal origami and microbot assemblies from patchy magnetic cubes

PubMed Central

Han, Koohee; Shields, C. Wyatt; Diwakar, Nidhi M.; Bharti, Bhuvnesh; López, Gabriel P.; Velev, Orlin D.

2017-01-01

Colloidal-scale assemblies that reconfigure on demand may serve as the next generation of soft “microbots,” artificial muscles, and other biomimetic devices. This requires the precise arrangement of particles into structures that are preprogrammed to reversibly change shape when actuated by external fields. The design and making of colloidal-scale assemblies with encoded directional particle-particle interactions remain a major challenge. We show how assemblies of metallodielectric patchy microcubes can be engineered to store energy through magnetic polarization and release it on demand by microscale reconfiguration. The dynamic pattern of folding and reconfiguration of the chain-like assemblies can be encoded in the sequence of the cube orientation. The residual polarization of the metallic facets on the microcubes leads to local interactions between the neighboring particles, which is directed by the conformational restrictions of their shape after harvesting energy from external magnetic fields. These structures can also be directionally moved, steered, and maneuvered by global forces from external magnetic fields. We illustrate these capabilities by examples of assemblies of specific sequences that can be actuated, reoriented, and spatially maneuvered to perform microscale operations such as capturing and transporting live cells, acting as prototypes of microbots, micromixers, and other active microstructures. PMID:28798960

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

PubMed

Zhang, Allen W; McPherson, Andrew; Milne, Katy; Kroeger, David R; Hamilton, Phineas T; Miranda, Alex; Funnell, Tyler; Little, Nicole; de Souza, Camila P E; Laan, Sonya; LeDoux, Stacey; Cochrane, Dawn R; Lim, Jamie L P; Yang, Winnie; Roth, Andrew; Smith, Maia A; Ho, Julie; Tse, Kane; Zeng, Thomas; Shlafman, Inna; Mayo, Michael R; Moore, Richard; Failmezger, Henrik; Heindl, Andreas; Wang, Yi Kan; Bashashati, Ali; Grewal, Diljot S; Brown, Scott D; Lai, Daniel; Wan, Adrian N C; Nielsen, Cydney B; Huebner, Curtis; Tessier-Cloutier, Basile; Anglesio, Michael S; Bouchard-Côté, Alexandre; Yuan, Yinyin; Wasserman, Wyeth W; Gilks, C Blake; Karnezis, Anthony N; Aparicio, Samuel; McAlpine, Jessica N; Huntsman, David G; Holt, Robert A; Nelson, Brad H; Shah, Sohrab P

2018-05-07

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion. Copyright © 2018 Elsevier Inc. All rights reserved.

Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers.

PubMed

Calleros, Lucía; Betancor, Laura; Iraola, Gregorio; Méndez, Alejandra; Morsella, Claudia; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Pérez, Ruben

2017-01-01

Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections. Copyright © 2016 Elsevier B.V. All rights reserved.

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

PubMed Central

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

Background The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. Methodology/Principal Findings By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. Conclusions/Significance We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses. PMID:19052647

Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.

PubMed

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.

Flexible Control of Safety Margins for Action Based on Environmental Variability.

PubMed

Hadjiosif, Alkis M; Smith, Maurice A

2015-06-17

To reduce the risk of slip, grip force (GF) control includes a safety margin above the force level ordinarily sufficient for the expected load force (LF) dynamics. The current view is that this safety margin is based on the expected LF dynamics, amounting to a static safety factor like that often used in engineering design. More efficient control could be achieved, however, if the motor system reduces the safety margin when LF variability is low and increases it when this variability is high. Here we show that this is indeed the case by demonstrating that the human motor system sizes the GF safety margin in proportion to an internal estimate of LF variability to maintain a fixed statistical confidence against slip. In contrast to current models of GF control that neglect the variability of LF dynamics, we demonstrate that GF is threefold more sensitive to the SD than the expected value of LF dynamics, in line with the maintenance of a 3-sigma confidence level. We then show that a computational model of GF control that includes a variability-driven safety margin predicts highly asymmetric GF adaptation between increases versus decreases in load. We find clear experimental evidence for this asymmetry and show that it explains previously reported differences in how rapidly GFs and manipulatory forces adapt. This model further predicts bizarre nonmonotonic shapes for GF learning curves, which are faithfully borne out in our experimental data. Our findings establish a new role for environmental variability in the control of action. Copyright © 2015 the authors 0270-6474/15/359106-16$15.00/0.

Phylogeography of Coxsackievirus A16 Reveals Global Transmission Pathways and Recent Emergence and Spread of a Recombinant Genogroup.

PubMed

Hassel, Chervin; Mirand, Audrey; Farkas, Agnes; Diedrich, Sabine; Huemer, Hartwig P; Peigue-Lafeuille, Hélène; Archimbaud, Christine; Henquell, Cécile; Bailly, Jean-Luc

2017-09-15

Coxsackievirus A16 (CV-A16; Picornaviridae ) is an enterovirus (EV) type associated with hand, foot, and mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data sampled during a prospective sentinel surveillance of HFMD in France (2010 to 2014) and phylogenetic reconstruction. A data set of 168 VP1 sequences was assembled with 416 publicly available sequences of various geographic origins. The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D. The time origins of clades B and D were assessed in 1978 (1973 to 1981) and 2004 (2001 to 2007), respectively. The shape of the global CV-A16 phylogeny indicated worldwide cocirculation of genetically distinct virus lineages over time and across geographic regions. Phylogenetic tree topologies and Bayes factor analysis indicated virus migration. Virus transportation events in clade B within Europe and Asia and between countries of the two geographic regions were assessed. The sustained transmission of clade D viruses over 4 years was analyzed at the township level in France and traced back to Peru in South America. Comparative genomics provided evidence of recombination between CV-A16 clades B and D and suggested an intertype recombinant origin for clade D. Time-resolved phylogenies and HFMD surveillance data indicated that CV-A16 persistence is sustained by continuing virus migration at different geographic scales, from community transmission to virus transportation between distant countries. The results showed a significant impact of virus movements on the epidemiological dynamics of HFMD that could have implications for disease prevention. IMPORTANCE Coxsackievirus A16 is one of the most prevalent enterovirus types in hand, foot, and mouth disease outbreaks reported in Southeast Asia. This study is based on epidemiological and viral data on HFMD caused by CV-A16 in a European country. The phylogeographic data complemented the syndromic surveillance with virus migration patterns between geographic regions in France. The results show how viral evolutionary dynamics and global virus spread interact to shape the worldwide pattern of an EV disease. CV-A16 transmission is driven by movements of infected individuals at different geographic levels: within a country (local dynamics), between neighboring countries (regional dynamics), and between distant countries (transcontinental dynamics). The results are consistent with our earlier data on EV-A71 and confirm the epidemiological interconnection of Asia and Europe with regard to EV infections. Copyright © 2017 American Society for Microbiology.

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

15N CSA tensors and 15N-1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

NASA Astrophysics Data System (ADS)

Vugmeyster, Liliya; Ostrovsky, Dmitry; Fu, Riqiang

2015-10-01

In this work, we assess the usefulness of static 15N NMR techniques for the determination of the 15N chemical shift anisotropy (CSA) tensor parameters and 15N-1H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone 15N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the 15N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the 15N CSA parameters, a more advanced approach based on the ;magic sandwich; SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the 15N-1H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

Dynamics of vector dark solitons propagation and tunneling effect in the variable coefficient coupled nonlinear Schrödinger equation.

PubMed

Musammil, N M; Porsezian, K; Subha, P A; Nithyanandan, K

2017-02-01

We investigate the dynamics of vector dark solitons propagation using variable coefficient coupled nonlinear Schrödinger (Vc-CNLS) equation. The dark soliton propagation and evolution dynamics in the inhomogeneous system are studied analytically by employing the Hirota bilinear method. It is apparent from our asymptotic analysis that the collision between the dark solitons is elastic in nature. The various inhomogeneous effects on the evolution and interaction between dark solitons are explored, with a particular emphasis on nonlinear tunneling. It is found that the tunneling of the soliton depends on a condition related to the height of the barrier and the amplitude of the soliton. The intensity of the tunneling soliton either forms a peak or a valley, thus retaining its shape after tunneling. For the case of exponential background, the soliton tends to compress after tunneling through the barrier/well. Thus, a comprehensive study of dark soliton pulse evolution and propagation dynamics in Vc-CNLS equation is presented in the paper.

Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp.

PubMed Central

Wollenberg, Amanda C.; Slough, Greg; Hoinville, Megan E.

2016-01-01

ABSTRACT Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (Galleria mellonella) larvae cadavers killed by Heterorhabditis nematodes and their Photorhabdus symbionts. We found that, although Photorhabdus strains did initially displace an Enterococcus-dominated community present in uninfected G. mellonella insect larvae, the cadaver community was not static. Twelve days postinfection, Photorhabdus shared the cadaver with Stenotrophomonas species. Consistent with this result, Stenotrophomonas strains isolated from infected cadavers were resistant to Photorhabdus-mediated toxicity in solid coculture assays. We isolated and characterized a Photorhabdus-produced antibiotic from G. mellonella cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased G. mellonella-associated Enterococcus growth, but not Stenotrophomonas growth, in vitro. Finally, we showed that the Stenotrophomonas strains described here negatively affected Photorhabdus growth in vitro. Our results add an important dimension to a broader understanding of Heterorhabditis-Photorhabdus biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a Heterorhabditis-Photorhabdus-parasitized insect cadaver. IMPORTANCE Understanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic in vitro microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers. PMID:27451445

A multiscale, hierarchical model of pulse dynamics in arid-land ecosystems

USGS Publications Warehouse

Collins, Scott L.; Belnap, Jayne; Grimm, N. B.; Rudgers, J. A.; Dahm, Clifford N.; D'Odorico, P.; Litvak, M.; Natvig, D. O.; Peters, Douglas C.; Pockman, W. T.; Sinsabaugh, R. L.; Wolf, B. O.

2014-01-01

Ecological processes in arid lands are often described by the pulse-reserve paradigm, in which rain events drive biological activity until moisture is depleted, leaving a reserve. This paradigm is frequently applied to processes stimulated by one or a few precipitation events within a growing season. Here we expand the original framework in time and space and include other pulses that interact with rainfall. This new hierarchical pulse-dynamics framework integrates space and time through pulse-driven exchanges, interactions, transitions, and transfers that occur across individual to multiple pulses extending from micro to watershed scales. Climate change will likely alter the size, frequency, and intensity of precipitation pulses in the future, and arid-land ecosystems are known to be highly sensitive to climate variability. Thus, a more comprehensive understanding of arid-land pulse dynamics is needed to determine how these ecosystems will respond to, and be shaped by, increased climate variability.

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.

PubMed

van den Broek, M; Bolat, I; Nijkamp, J F; Ramos, E; Luttik, M A H; Koopman, F; Geertman, J M; de Ridder, D; Pronk, J T; Daran, J-M

2015-09-01

Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. Copyright © 2015, van den Broek et al.

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

PubMed Central

van den Broek, M.; Bolat, I.; Nijkamp, J. F.; Ramos, E.; Luttik, M. A. H.; Koopman, F.; Geertman, J. M.; de Ridder, D.; Pronk, J. T.

2015-01-01

Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. PMID:26150454

Quantum simulation of ultrafast dynamics using trapped ultracold atoms.

PubMed

Senaratne, Ruwan; Rajagopal, Shankari V; Shimasaki, Toshihiko; Dotti, Peter E; Fujiwara, Kurt M; Singh, Kevin; Geiger, Zachary A; Weld, David M

2018-05-25

Ultrafast electronic dynamics are typically studied using pulsed lasers. Here we demonstrate a complementary experimental approach: quantum simulation of ultrafast dynamics using trapped ultracold atoms. Counter-intuitively, this technique emulates some of the fastest processes in atomic physics with some of the slowest, leading to a temporal magnification factor of up to 12 orders of magnitude. In these experiments, time-varying forces on neutral atoms in the ground state of a tunable optical trap emulate the electric fields of a pulsed laser acting on bound charged particles. We demonstrate the correspondence with ultrafast science by a sequence of experiments: nonlinear spectroscopy of a many-body bound state, control of the excitation spectrum by potential shaping, observation of sub-cycle unbinding dynamics during strong few-cycle pulses, and direct measurement of carrier-envelope phase dependence of the response to an ultrafast-equivalent pulse. These results establish cold-atom quantum simulation as a complementary tool for studying ultrafast dynamics.

Face processing regions are sensitive to distinct aspects of temporal sequence in facial dynamics.

PubMed

Reinl, Maren; Bartels, Andreas

2014-11-15

Facial movement conveys important information for social interactions, yet its neural processing is poorly understood. Computational models propose that shape- and temporal sequence sensitive mechanisms interact in processing dynamic faces. While face processing regions are known to respond to facial movement, their sensitivity to particular temporal sequences has barely been studied. Here we used fMRI to examine the sensitivity of human face-processing regions to two aspects of directionality in facial movement trajectories. We presented genuine movie recordings of increasing and decreasing fear expressions, each of which were played in natural or reversed frame order. This two-by-two factorial design matched low-level visual properties, static content and motion energy within each factor, emotion-direction (increasing or decreasing emotion) and timeline (natural versus artificial). The results showed sensitivity for emotion-direction in FFA, which was timeline-dependent as it only occurred within the natural frame order, and sensitivity to timeline in the STS, which was emotion-direction-dependent as it only occurred for decreased fear. The occipital face area (OFA) was sensitive to the factor timeline. These findings reveal interacting temporal sequence sensitive mechanisms that are responsive to both ecological meaning and to prototypical unfolding of facial dynamics. These mechanisms are temporally directional, provide socially relevant information regarding emotional state or naturalness of behavior, and agree with predictions from modeling and predictive coding theory. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Jitter Correction

NASA Technical Reports Server (NTRS)

Waegell, Mordecai J.; Palacios, David M.

2011-01-01

Jitter_Correct.m is a MATLAB function that automatically measures and corrects inter-frame jitter in an image sequence to a user-specified precision. In addition, the algorithm dynamically adjusts the image sample size to increase the accuracy of the measurement. The Jitter_Correct.m function takes an image sequence with unknown frame-to-frame jitter and computes the translations of each frame (column and row, in pixels) relative to a chosen reference frame with sub-pixel accuracy. The translations are measured using a Cross Correlation Fourier transformation method in which the relative phase of the two transformed images is fit to a plane. The measured translations are then used to correct the inter-frame jitter of the image sequence. The function also dynamically expands the image sample size over which the cross-correlation is measured to increase the accuracy of the measurement. This increases the robustness of the measurement to variable magnitudes of inter-frame jitter

Plant centromere organization: a dynamic structure with conserved functions.

PubMed

Ma, Jianxin; Wing, Rod A; Bennetzen, Jeffrey L; Jackson, Scott A

2007-03-01

Although the structural features of centromeres from most multicellular eukaryotes remain to be characterized, recent analyses of the complete sequences of two centromeric regions of rice, together with data from Arabidopsis thaliana and maize, have illuminated the considerable size variation and sequence divergence of plant centromeres. Despite the severe suppression of meiotic chromosomal exchange in centromeric and pericentromeric regions of rice, the centromere core shows high rates of unequal homologous recombination in the absence of chromosomal exchange, resulting in frequent and extensive DNA rearrangement. Not only is the sequence of centromeric tandem and non-tandem repeats highly variable but also the copy number, spacing, order and orientation, providing ample natural variation as the basis for selection of superior centromere performance. This review article focuses on the structural and evolutionary dynamics of plant centromere organization and the potential molecular mechanisms responsible for the rapid changes of centromeric components.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

PubMed

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Revealing glacier flow and surge dynamics from animated satellite image sequences: examples from the Karakoram

NASA Astrophysics Data System (ADS)

Paul, F.

2015-04-01

Although animated images are very popular on the Internet, they have so far found only limited use for glaciological applications. With long time-series of satellite images becoming increasingly available and glaciers being well recognized for their rapid changes and variable flow dynamics, animated sequences of multiple satellite images reveal glacier dynamics in a time-lapse mode, making the otherwise slow changes of glacier movement visible and understandable for a wide public. For this study animated image sequences were created from freely available image quick-looks of orthorectified Landsat scenes for four regions in the central Karakoram mountain range. The animations play automatically in a web-browser and might help to demonstrate glacier flow dynamics for educational purposes. The animations revealed highly complex patterns of glacier flow and surge dynamics over a 15-year time period (1998-2013). In contrast to other regions, surging glaciers in the Karakoram are often small (around 10 km2), steep, debris free, and advance for several years at comparably low annual rates (a few hundred m a-1). The advance periods of individual glaciers are generally out of phase, indicating a limited climatic control on their dynamics. On the other hand, nearly all other glaciers in the region are either stable or slightly advancing, indicating balanced or even positive mass budgets over the past few years to decades.

Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope

PubMed Central

Özen, Ayşegül; Haliloğlu, Türkan; Schiffer, Celia A.

2011-01-01

HIV-1 protease (PR) permits viral maturation by processing the Gag and Gag-Pro-Pol polyproteins. Though HIV-1 PR inhibitors (PIs) are used in combination antiviral therapy, the emergence of drug resistance has limited their efficacy. The rapid evolution of HIV-1 necessitates the consideration of drug resistance in novel drug-design strategies. Drug-resistant HIV-1 PR variants, while no longer efficiently inhibited, continue to efficiently hydrolyze the natural viral substrates. Though highly diverse in sequence, the HIV-1 PR substrates bind in a conserved three-dimensional shape we defined as the “substrate envelope”. We previously showed that resistance mutations arise where PIs protrude beyond the substrate envelope, as these regions are crucial for drug binding but not for substrate recognition. Here, we extend this model by considering the role of protein dynamics in the interaction of HIV-1 PR with its substrates. Seven molecular dynamics simulations of PR-substrate complexes were performed to estimate the conformational flexibility of substrates in their complexes. Interdependency of the substrate-protease interactions may compensate for the variations in cleavage-site sequences, and explain how a diverse set of sequences can be recognized as substrates by the same enzyme. This diversity may be essential for regulating sequential processing of substrates. We also define a dynamic substrate envelope as a more accurate representation of PR-substrate interactions. This dynamic substrate envelope, described by a probability distribution function, is a powerful tool for drug design efforts targeting ensembles of resistant HIV-1 PR variants with the aim of developing drugs that are less susceptible to resistance. PMID:21762811

DNA tetrominoes: the construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes.

PubMed

Ong, Hui San; Rahim, Mohd Syafiq; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

2015-01-01

The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.

Development of Variable Camber Continuous Trailing Edge Flap for Performance Adaptive Aeroelastic Wing

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Kaul, Upender; Lebofsky, Sonia; Ting, Eric; Chaparro, Daniel; Urnes, James

2015-01-01

This paper summarizes the recent development of an adaptive aeroelastic wing shaping control technology called variable camber continuous trailing edge flap (VCCTEF). As wing flexibility increases, aeroelastic interactions with aerodynamic forces and moments become an increasingly important consideration in aircraft design and aerodynamic performance. Furthermore, aeroelastic interactions with flight dynamics can result in issues with vehicle stability and control. The initial VCCTEF concept was developed in 2010 by NASA under a NASA Innovation Fund study entitled "Elastically Shaped Future Air Vehicle Concept," which showed that highly flexible wing aerodynamic surfaces can be elastically shaped in-flight by active control of wing twist and bending deflection in order to optimize the spanwise lift distribution for drag reduction. A collaboration between NASA and Boeing Research & Technology was subsequently funded by NASA from 2012 to 2014 to further develop the VCCTEF concept. This paper summarizes some of the key research areas conducted by NASA during the collaboration with Boeing Research and Technology. These research areas include VCCTEF design concepts, aerodynamic analysis of VCCTEF camber shapes, aerodynamic optimization of lift distribution for drag minimization, wind tunnel test results for cruise and high-lift configurations, flutter analysis and suppression control of flexible wing aircraft, and multi-objective flight control for adaptive aeroelastic wing shaping control.

Research on the Integration of Bionic Geometry Modeling and Simulation of Robot Foot Based on Characteristic Curve

NASA Astrophysics Data System (ADS)

He, G.; Zhu, H.; Xu, J.; Gao, K.; Zhu, D.

2017-09-01

The bionic research of shape is an important aspect of the research on bionic robot, and its implementation cannot be separated from the shape modeling and numerical simulation of the bionic object, which is tedious and time-consuming. In order to improve the efficiency of shape bionic design, the feet of animals living in soft soil and swamp environment are taken as bionic objects, and characteristic skeleton curve, section curve, joint rotation variable, position and other parameters are used to describe the shape and position information of bionic object’s sole, toes and flipper. The geometry modeling of the bionic object is established by using the parameterization of characteristic curves and variables. Based on this, the integration framework of parametric modeling and finite element modeling, dynamic analysis and post-processing of sinking process in soil is proposed in this paper. The examples of bionic ostrich foot and bionic duck foot are also given. The parametric modeling and integration technique can achieve rapid improved design based on bionic object, and it can also greatly improve the efficiency and quality of robot foot bionic design, and has important practical significance to improve the level of bionic design of robot foot’s shape and structure.

Interplay of lancet furrows and shape change in the horseshoe bat noseleaf.

PubMed

Gupta, Anupam K; Webster, Dane; Müller, Rolf

2015-11-01

Horseshoe bats emit biosonar pulses through the nostrils and diffract the outgoing ultrasonic pulses with baffles, so-called "noseleaves," that surround the nostrils. The noseleaves have complex static geometries and can furthermore undergo dynamic shape changes during emission of the biosonar pulses. The posterior noseleaf part, the lancet, has been shown to carry out anterior-posterior flicking motions during biosonar emissions with average lancet tip displacements of about 1 mm. Here, the acoustic effects of the interplay between the lancet furrows and shape change (lancet rotation) on the emission beam were investigated using the animated digital models obtained from the noseleaves of greater horseshoe bats (Rhinolophus ferrumequinum). It was found that forward lancet rotations increase the amount of sound energy allocated to secondary amplitude maxima (sidelobes) in the beampattern, but only in the presence of the furrows. The interaction between static and dynamic features can be readily quantified by roughness (standard deviation about local mean) of the amplitude distribution of the beampatterns. This effect goes beyond the static impact of the furrows on the width of the mainlobe. It could allow the bats to send out their pulses through a sequence of qualitatively different beampatterns.

Arabidopsis FH1 Formin Affects Cotyledon Pavement Cell Shape by Modulating Cytoskeleton Dynamics.

PubMed

Rosero, Amparo; Oulehlová, Denisa; Stillerová, Lenka; Schiebertová, Petra; Grunt, Michal; Žárský, Viktor; Cvrčková, Fatima

2016-03-01

Plant cell morphogenesis involves concerted rearrangements of microtubules and actin microfilaments. We previously reported that FH1, the main Arabidopsis thaliana housekeeping Class I membrane-anchored formin, contributes to actin dynamics and microtubule stability in rhizodermis cells. Here we examine the effects of mutations affecting FH1 (At3g25500) on cell morphogenesis and above-ground organ development in seedlings, as well as on cytoskeletal organization and dynamics, using a combination of confocal and variable angle epifluorescence microscopy with a pharmacological approach. Homozygous fh1 mutants exhibited cotyledon epinasty and had larger cotyledon pavement cells with more pronounced lobes than the wild type. The pavement cell shape alterations were enhanced by expression of the fluorescent microtubule marker GFP-microtubule-associated protein 4 (MAP4). Mutant cotyledon pavement cells exhibited reduced density and increased stability of microfilament bundles, as well as enhanced dynamics of microtubules. Analogous results were also obtained upon treatments with the formin inhibitor SMIFH2 (small molecule inhibitor of formin homology 2 domains). Pavement cell shape in wild-type (wt) and fh1 plants in some situations exhibited a differential response towards anti-cytoskeletal drugs, especially the microtubule disruptor oryzalin. Our observations indicate that FH1 participates in the control of microtubule dynamics, possibly via its effects on actin, subsequently influencing cell morphogenesis and macroscopic organ development. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Compressive sensing method for recognizing cat-eye effect targets.

PubMed

Li, Li; Li, Hui; Dang, Ersheng; Liu, Bo

2013-10-01

This paper proposes a cat-eye effect target recognition method with compressive sensing (CS) and presents a recognition method (sample processing before reconstruction based on compressed sensing, or SPCS) for image processing. In this method, the linear projections of original image sequences are applied to remove dynamic background distractions and extract cat-eye effect targets. Furthermore, the corresponding imaging mechanism for acquiring active and passive image sequences is put forward. This method uses fewer images to recognize cat-eye effect targets, reduces data storage, and translates the traditional target identification, based on original image processing, into measurement vectors processing. The experimental results show that the SPCS method is feasible and superior to the shape-frequency dual criteria method.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses.

PubMed

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-11-26

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

PubMed Central

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-01-01

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics. PMID:27898037

A Flexible Question-and-Answer Task for Measuring Speech Understanding.

PubMed

Best, Virginia; Streeter, Timothy; Roverud, Elin; Mason, Christine R; Kidd, Gerald

2016-11-24

This report introduces a new speech task based on simple questions and answers. The task differs from a traditional sentence recall task in that it involves an element of comprehension and can be implemented in an ongoing fashion. It also contains two target items (the question and the answer) that may be associated with different voices and locations to create dynamic listening scenarios. A set of 227 questions was created, covering six broad categories (days of the week, months of the year, numbers, colors, opposites, and sizes). All questions and their one-word answers were spoken by 11 female and 11 male talkers. In this study, listeners were presented with question-answer pairs and asked to indicate whether the answer was true or false. Responses were given as simple button or key presses, which are quick to make and easy to score. Two preliminary experiments are presented that illustrate different ways of implementing the basic task. In the first experiment, question-answer pairs were presented in speech-shaped noise, and performance was compared across subjects, question categories, and time, to examine the different sources of variability. In the second experiment, sequences of question-answer pairs were presented amidst competing conversations in an ongoing, spatially dynamic listening scenario. Overall, the question-and-answer task appears to be feasible and could be implemented flexibly in a number of different ways. © The Author(s) 2016.

A Flexible Question-and-Answer Task for Measuring Speech Understanding

PubMed Central

Streeter, Timothy; Roverud, Elin; Mason, Christine R.; Kidd, Gerald

2016-01-01

This report introduces a new speech task based on simple questions and answers. The task differs from a traditional sentence recall task in that it involves an element of comprehension and can be implemented in an ongoing fashion. It also contains two target items (the question and the answer) that may be associated with different voices and locations to create dynamic listening scenarios. A set of 227 questions was created, covering six broad categories (days of the week, months of the year, numbers, colors, opposites, and sizes). All questions and their one-word answers were spoken by 11 female and 11 male talkers. In this study, listeners were presented with question-answer pairs and asked to indicate whether the answer was true or false. Responses were given as simple button or key presses, which are quick to make and easy to score. Two preliminary experiments are presented that illustrate different ways of implementing the basic task. In the first experiment, question-answer pairs were presented in speech-shaped noise, and performance was compared across subjects, question categories, and time, to examine the different sources of variability. In the second experiment, sequences of question-answer pairs were presented amidst competing conversations in an ongoing, spatially dynamic listening scenario. Overall, the question-and-answer task appears to be feasible and could be implemented flexibly in a number of different ways. PMID:27888257

Prediction of RNA secondary structures: from theory to models and real molecules

NASA Astrophysics Data System (ADS)

Schuster, Peter

2006-05-01

RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA molecules can be modelled readily at the secondary structure level and allows prediction of the most stable (mfe) conformations of complexes together with suboptimal states. Cofolding algorithms are important tools for efficient and highly specific primer design in the polymerase chain reaction (PCR) and help to explain the mechanisms of small interference RNA (si-RNA) molecules in gene regulation. The evolutionary optimization of RNA structures is illustrated by the search for a target structure and mimics aptamer selection in evolutionary biotechnology. It occurs typically in steps consisting of short adaptive phases interrupted by long epochs of little or no obvious progress in optimization. During these quasi-stationary epochs the populations are essentially confined to neutral networks where they search for sequences that allow a continuation of the adaptive process. Modelling RNA evolution as a simultaneous process in sequence and shape space provides answers to questions of the optimal population size and mutation rates. Kinetic folding is a stochastic process in conformation space. Exact solutions are derived by direct simulation in the form of trajectory sampling or by solving the master equation. The exact solutions can be approximated straightforwardly by Arrhenius kinetics on barrier trees, which represent simplified versions of conformational energy landscapes. The existence of at least one sequence forming any arbitrarily chosen pair of structures is granted by the intersection theorem. Folding kinetics is the key to understanding and designing multistable RNA molecules or RNA switches. These RNAs form two or more long lived conformations, and conformational changes occur either spontaneously or are induced through binding of small molecules or other biopolymers. RNA switches are found in nature where they act as elements in genetic and metabolic regulation. The reliability of RNA secondary structure prediction is limited by the accuracy with which the empirical parameters can be determined and by principal deficiencies, for example by the lack of energy contributions resulting from tertiary interactions. In addition, native structures may be determined by folding kinetics rather than by thermodynamics. We address the first problem by considering base pair probabilities or base pairing entropies, which are derived from the partition function of conformations. A high base pair probability corresponding to a low pairing entropy is taken as an indicator of a high reliability of prediction. Pseudoknots are discussed as an example of a tertiary interaction that is highly important for RNA function. Moreover, pseudoknot formation is readily incorporated into structure prediction algorithms. Some examples of experimental data on RNA secondary structures that are readily explained using the landscape concept are presented. They deal with (i) properties of RNA molecules with random sequences, (ii) RNA molecules from restricted alphabets, (iii) existence of neutral networks, (iv) shape space covering, (v) riboswitches and (vi) evolution of non-coding RNAs as an example of evolution restricted to neutral networks.

Response properties in the adsorption-desorption model on a triangular lattice

NASA Astrophysics Data System (ADS)

Šćepanović, J. R.; Stojiljković, D.; Jakšić, Z. M.; Budinski-Petković, Lj.; Vrhovac, S. B.

2016-06-01

The out-of-equilibrium dynamical processes during the reversible random sequential adsorption (RSA) of objects of various shapes on a two-dimensional triangular lattice are studied numerically by means of Monte Carlo simulations. We focused on the influence of the order of symmetry axis of the shape on the response of the reversible RSA model to sudden perturbations of the desorption probability Pd. We provide a detailed discussion of the significance of collective events for governing the time coverage behavior of shapes with different rotational symmetries. We calculate the two-time density-density correlation function C(t ,tw) for various waiting times tw and show that longer memory of the initial state persists for the more symmetrical shapes. Our model displays nonequilibrium dynamical effects such as aging. We find that the correlation function C(t ,tw) for all objects scales as a function of single variable ln(tw) / ln(t) . We also study the short-term memory effects in two-component mixtures of extended objects and give a detailed analysis of the contribution to the densification kinetics coming from each mixture component. We observe the weakening of correlation features for the deposition processes in multicomponent systems.

Modeling and Simulation of Variable Mass, Flexible Structures

NASA Technical Reports Server (NTRS)

Tobbe, Patrick A.; Matras, Alex L.; Wilson, Heath E.

2009-01-01

The advent of the new Ares I launch vehicle has highlighted the need for advanced dynamic analysis tools for variable mass, flexible structures. This system is composed of interconnected flexible stages or components undergoing rapid mass depletion through the consumption of solid or liquid propellant. In addition to large rigid body configuration changes, the system simultaneously experiences elastic deformations. In most applications, the elastic deformations are compatible with linear strain-displacement relationships and are typically modeled using the assumed modes technique. The deformation of the system is approximated through the linear combination of the products of spatial shape functions and generalized time coordinates. Spatial shape functions are traditionally composed of normal mode shapes of the system or even constraint modes and static deformations derived from finite element models of the system. Equations of motion for systems undergoing coupled large rigid body motion and elastic deformation have previously been derived through a number of techniques [1]. However, in these derivations, the mode shapes or spatial shape functions of the system components were considered constant. But with the Ares I vehicle, the structural characteristics of the system are changing with the mass of the system. Previous approaches to solving this problem involve periodic updates to the spatial shape functions or interpolation between shape functions based on system mass or elapsed mission time. These solutions often introduce misleading or even unstable numerical transients into the system. Plus, interpolation on a shape function is not intuitive. This paper presents an approach in which the shape functions are held constant and operate on the changing mass and stiffness matrices of the vehicle components. Each vehicle stage or component finite element model is broken into dry structure and propellant models. A library of propellant models is used to describe the distribution of mass in the fuel tank or Solid Rocket Booster (SRB) case for various propellant levels. Based on the mass consumed by the liquid engine or SRB, the appropriate propellant model is coupled with the dry structure model for the stage. Then using vehicle configuration data, the integrated vehicle model is assembled and operated on by the constant system shape functions. The system mode shapes and frequencies can then be computed from the resulting generalized mass and stiffness matrices for that mass configuration. The rigid body mass properties of the vehicle are derived from the integrated vehicle model. The coupling terms between the vehicle rigid body motion and elastic deformation are also updated from the constant system shape functions and the integrated vehicle model. This approach was first used to analyze variable mass spinning beams and then prototyped into a generic dynamics simulation engine. The resulting code was tested against Crew Launch Vehicle (CLV-)class problems worked in the TREETOPS simulation package and by Wilson [2]. The Ares I System Integration Laboratory (SIL) is currently being developed at the Marshall Space Flight Center (MSFC) to test vehicle avionics hardware and software in a hardware-in-the-loop (HWIL) environment and certify that the integrated system is prepared for flight. The Ares I SIL utilizes the Ares Real-Time Environment for Modeling, Integration, and Simulation (ARTEMIS) tool to simulate the launch vehicle and stimulate avionics hardware. Due to the presence of vehicle control system filters and the thrust oscillation suppression system, which are tuned to the structural characteristics of the vehicle, ARTEMIS must incorporate accurate structural models of the Ares I launch vehicle. The ARTEMIS core dynamics simulation models the highly coupled nature of the vehicle flexible body dynamics, propellant slosh, and vehicle nozzle inertia effects combined with mass and flexible body properties that vary significant with time during the flight. All forces that act on the vehicle during flight must be simulated, including deflected engine thrust force, spatially distributed aerodynamic forces, gravity, and reaction control jet thrust forces. These forces are used to excite an integrated flexible vehicle, slosh, and nozzle dynamics model for the vehicle stack that simulates large rigid body translations and rotations along with small elastic deformations. Highly effective matrix math operations on a distributed, threaded high-performance simulation node allow ARTEMIS to retain up to 30 modes of flex for real-time simulation. Stage elements that separate from the stack during flight are propagated as independent rigid six degrees of freedom (6DOF) bodies. This paper will present the formulation of the resulting equations of motion, solutions to example problems, and describe the resulting dynamics simulation engine within ARTEMIS.

Molecular and cellular bases of adaptation to a changing environment in microorganisms.

PubMed

Bleuven, Clara; Landry, Christian R

2016-10-26

Environmental heterogeneity constitutes an evolutionary challenge for organisms. While evolutionary dynamics under variable conditions has been explored for decades, we still know relatively little about the cellular and molecular mechanisms involved. It is of paramount importance to examine these molecular bases because they may play an important role in shaping the course of evolution. In this review, we examine the diversity of adaptive mechanisms in the face of environmental changes. We exploit the recent literature on microbial systems because those have benefited the most from the recent emergence of genetic engineering and experimental evolution followed by genome sequencing. We identify four emerging trends: (i) an adaptive molecular change in a pathway often results in fitness trade-off in alternative environments but the effects are dependent on a mutation's genetic background; (ii) adaptive changes often modify transcriptional and signalling pathways; (iii) several adaptive changes may occur within the same molecular pathway but be associated with pleiotropy of different signs across environments; (iv) because of their large associated costs, macromolecular changes such as gene amplification and aneuploidy may be a rapid mechanism of adaptation in the short-term only. The course of adaptation in a variable environment, therefore, depends on the complexity of the environment but also on the molecular relationships among the genes involved and between the genes and the phenotypes under selection. © 2016 The Author(s).

Eclipse SteerTech liquid lenslet beam steering technology

NASA Astrophysics Data System (ADS)

Westfall, Raymond T.; Rogers, Stanley; Shannon, Kenneth C., III

2007-09-01

Eclipse SteerTech TM transmissive fluid state electrowetting technology has successfully demonstrated the ability to control the shape and position of a fluid lenslet. In its final form, the technology will incorporate a dual fluid lenslet approach capable of operating in extremely high acceleration environments. The beam steering system works on the principle of electro-wetting. A substrate is covered with a closely spaced array of, independently addressable, transparent, electrically conductive pixels utilizing Eclipse's proprietary EclipseTEC TM technology. By activating and deactivating selected EclipseTEC TM pixels in the proper sequence, the shape and position of fluid lenslets or arrays of lenslets can be dynamically changed at will. The position and shape of individual fluid lenslets may be accurately controlled on any flat, simply curved, or complex curved, transparent or reflective surface. The smaller the pixels the better control of the position and shape of the fluid lenslets. Information on the successful testing of the Eclipse SteerTech TM lenslet and discussion of its use in a de-centered lenslet array will be presented.

Morphable Word Clouds for Time-Varying Text Data Visualization.

PubMed

Chi, Ming-Te; Lin, Shih-Syun; Chen, Shiang-Yi; Lin, Chao-Hung; Lee, Tong-Yee

2015-12-01

A word cloud is a visual representation of a collection of text documents that uses various font sizes, colors, and spaces to arrange and depict significant words. The majority of previous studies on time-varying word clouds focuses on layout optimization and temporal trend visualization. However, they do not fully consider the spatial shapes and temporal motions of word clouds, which are important factors for attracting people's attention and are also important cues for human visual systems in capturing information from time-varying text data. This paper presents a novel method that uses rigid body dynamics to arrange multi-temporal word-tags in a specific shape sequence under various constraints. Each word-tag is regarded as a rigid body in dynamics. With the aid of geometric, aesthetic, and temporal coherence constraints, the proposed method can generate a temporally morphable word cloud that not only arranges word-tags in their corresponding shapes but also smoothly transforms the shapes of word clouds over time, thus yielding a pleasing time-varying visualization. Using the proposed frame-by-frame and morphable word clouds, people can observe the overall story of a time-varying text data from the shape transition, and people can also observe the details from the word clouds in frames. Experimental results on various data demonstrate the feasibility and flexibility of the proposed method in morphable word cloud generation. In addition, an application that uses the proposed word clouds in a simulated exhibition demonstrates the usefulness of the proposed method.

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments.

PubMed

Díaz-Muñoz, Samuel L

2017-01-01

Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus-host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus-virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus-virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus-virus interactions also increased culture coinfection with ssDNA-dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of virus-virus interactions in coinfection with implications for phage therapy, microbiome dynamics, and viral infection treatments.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

PubMed

Roux-Rouquie, M; Marilley, M

2000-09-15

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

Command Generation and Control of Momentum Exchange Electrodynamic Reboost Tethered Satellite

NASA Technical Reports Server (NTRS)

Robertson, Michael J.

2005-01-01

The research completed for this NASA Graduate Student Research Program Fellowship sought to enhance the current state-of-the-art dynamic models and control laws for Momentum Exchange Electrodynamic Reboost satellite systems by utilizing command generation, specifically Input Shaping. The precise control of tethered spacecraft with flexible appendages is extremely difficult. The complexity is magnified many times when the satellite must interact with other satellites as in a momentum exchange via a tether. The Momentum Exchange Electronic Reboost Tether (MXER) concept encapsulates all of these challenging tasks [l]. Input Shaping is a command generation technique that allows flexible spacecraft to move without inducing residual vibration [2], limit transient deflection [3] and utilize fuel-efficient actuation [4]. Input shaping is implemented by convolving a sequence of impulses, known as the input shaper, with a desired system command to produce a shaped input that is then used to drive the system. This process is demonstrated in Figure 1. The shaped command is then use to drive the system without residual vibration while meeting many other performance specifications. The completed work developed tether control algorithms for retrieval. A simple model of the tether response has been developed and command shaping was implemented to minimize unwanted dynamics. A model of a flexible electrodynamic tether has been developed to investigate the tether s response during reboost. Command shaping techniques have been developed to eliminate the tether oscillations and reduce the tether s deflection to pre-specified levels during reboost. Additionally, a model for the spin-up of a tethered system was developed. This model was used in determining the parameters for optimization the resulting angular velocity.

Diagnosing and Reconstructing Real-World Hydroclimatic Dynamics from Time Sequenced Data: The Case of Saltwater Intrusion into Coastal Wetlands in Everglades National Park

NASA Astrophysics Data System (ADS)

Huffaker, R.; Munoz-Carpena, R.

2016-12-01

There are increasing calls to audit decision-support models used for environmental policy to ensure that they correspond with the reality facing policy makers. Modelers can establish correspondence by providing empirical evidence of real-world dynamic behavior that their models skillfully simulate. We present a pre-modeling diagnostic framework—based on nonlinear dynamic analysis—for detecting and reconstructing real-world environmental dynamics from observed time-sequenced data. Phenomenological (data-driven) modeling—based on machine learning regression techniques—extracts a set of ordinary differential equations governing empirically-diagnosed system dynamics from a single time series, or from multiple time series on causally-interacting variables. We apply the framework to investigate saltwater intrusion into coastal wetlands in Everglades National Park, Florida, USA. We test the following hypotheses posed in the literature linking regional hydrologic variables with global climatic teleconnections: (1) Sea level in Florida Bay drives well level and well salinity in the coastal Everglades; (2) Atlantic Multidecadal Oscillation (AMO) drives sea level, well level and well salinity; and (3) AMO and (El Niño Southern Oscillation) ENSO bi-causally interact. The thinking is that salt water intrusion links ocean-surface salinity with salinity of inland water sources, and sea level with inland water; that AMO and ENSO share a teleconnective relationship (perhaps through the atmosphere); and that AMO and ENSO both influence inland precipitation and thus well levels. Our results support these hypotheses, and we successfully construct a parsimonious phenomenological model that reproduces diagnosed nonlinear dynamics and system interactions. We propose that reconstructed data dynamics be used, along with other expert information, as a rigorous benchmark to guide specification and testing of hydrologic decision support models corresponding with real-world behavior.

Long-term dynamics emerging in floodplains and deltas from the interactions between hydrology and society in a changing climate

NASA Astrophysics Data System (ADS)

Di Baldassarre, Giuliano; Viglione, Alberto; Yan, Kun; Brandimarte, Luigia; Blöschl, Günter

2014-05-01

Economic losses and fatalities associated to flood events have increased dramatically over the past decades. This situation might worsen in the near future because of rapid urbanization of many floodplains and deltas, along with enhancement of flood water levels as a result of human interventions, climate variability or sea level rise. To explore future dynamics, we developed a novel approach, which takes into account the dynamic nature of flood risk by an explicit treatment of the interactions and feedbacks between the hydrological and social components of flood risk (i.e. probability of flooding, and potential adverse consequences). In particular, we developed a socio-hydrological model that allows considering how the frequency and magnitude of flooding shapes the evolution of societies, while, at the same time, dynamic societies shape the frequency and magnitude of flooding. We then use this model to simulate long-term dynamics of different types of societies under hydrological change, e.g. increasing flood frequency. Based on the study of long-term dynamics of different floodplains and deltas around the world (e.g. Netherlands, Bangladesh), we identify two main typologies of flood-shaped societies: i) techno-societies, which "fight floods", and typically deal with risk by building and strengthening flood protection structures, such as levees or dikes; and ii) green-societies, which "lives with floods", and mainly cope with risk via adaptation measures, such as resettling out of flood prone areas. The outcomes of this study are relevant for the management of deltas and floodplains as they allow a comparison of long-term dynamics between diverse types of societies in terms of robustness to hydrological change.

Gesture-Controlled Interfaces for Self-Service Machines

NASA Technical Reports Server (NTRS)

Cohen, Charles J.; Beach, Glenn

2006-01-01

Gesture-controlled interfaces are software- driven systems that facilitate device control by translating visual hand and body signals into commands. Such interfaces could be especially attractive for controlling self-service machines (SSMs) for example, public information kiosks, ticket dispensers, gasoline pumps, and automated teller machines (see figure). A gesture-controlled interface would include a vision subsystem comprising one or more charge-coupled-device video cameras (at least two would be needed to acquire three-dimensional images of gestures). The output of the vision system would be processed by a pure software gesture-recognition subsystem. Then a translator subsystem would convert a sequence of recognized gestures into commands for the SSM to be controlled; these could include, for example, a command to display requested information, change control settings, or actuate a ticket- or cash-dispensing mechanism. Depending on the design and operational requirements of the SSM to be controlled, the gesture-controlled interface could be designed to respond to specific static gestures, dynamic gestures, or both. Static and dynamic gestures can include stationary or moving hand signals, arm poses or motions, and/or whole-body postures or motions. Static gestures would be recognized on the basis of their shapes; dynamic gestures would be recognized on the basis of both their shapes and their motions. Because dynamic gestures include temporal as well as spatial content, this gesture- controlled interface can extract more information from dynamic than it can from static gestures.

Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes

PubMed Central

Tiwari, Sandhya P.; Reuter, Nathalie

2016-01-01

The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design. PMID:27015412

Simultaneous Modeling of the Thermophysical and Dynamical Evolution of Saturn's Icy Satellites

NASA Astrophysics Data System (ADS)

Johnson, Torrence V.; Castillo-Rogez, J. C.; Matson, D. L.; Sotin, C.; Lunine, J. I.

2007-10-01

This poster describes the methodology we use in modeling the geophysical and dynamical evolution of the icy satellites of Saturn. For each of the model's modules we identify the relevant physical, chemical, mineralogical, and material science principals that are used. Then we present the logic of the modeling approach and its implementation. The main modules handle thermal, geological, and dynamical processes. Key parameters such as temperature, thermal conductivity, rigidity, viscosity, Young's modulus, dynamic Love number k2, and frequency-dependent dissipation factor Q(ω) are transmitted between the modules in the course of calculating an evolutionary sequence. Important initial conditions include volatile and nonvolatile compositions, formation time, rotation period and shape, orbital eccentricity and semimajor axis, and temperature and porosity profiles. The thermal module treats the thermal effects of accretion, melting of ice, differentiation and tidal dissipation. Heat transfer is by conduction only because in the cases thus far studied the criterion for convection is not met. The geological module handles the evolution of porosity, shape, and lithospheric strength. The dynamical module calculates despinning and orbital evolution. Chief outputs include the orbital evolution, the interior temperatures as a function of time and depth, and other parameters of interest such as k2, and Q(ω) as a function of time. This work was carried out at the Jet Propulsion Laboratory-California Institute of Technology, under contract to NASA.

Drag Optimization Of Light Trucks Using Computational Fluid Dynamics

DTIC Science & Technology

2003-09-01

dimensional design case 19 study on the Lockheed C-141B aircraft wing, Cosentino and Holst [Ref. 10] reduced the number of design variables from 120 to 12... case letters) 6. AUTHOR(S) 5. FUNDING NUMBERS 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Postgraduate School Monterey, CA 93943...23 B. TWO DIMENSIONAL LIGHT TRUCK SHAPE STUDIES .................. 23 1. Canopies

Structure and dynamics of Saturn's outer magnetosphere and boundary regions

NASA Technical Reports Server (NTRS)

Behannon, K. W.; Lepping, R. P.; Ness, N. F.

1983-01-01

In 1979-1981, the three USA spacecraft Pioneer 11 and Voyagers 1 and 2 discovered and explored the magnetosphere of Saturn to the limited extent possible on flyby trajectories. Considerable variation in the locations of the bow shock (BS) and magnetopause (MP) surfaces were observed in association with variable solar wind conditions and, during the Voyager 2 encounter, possible immersion in Jupiter's distant magnetic tail. The limited number of BS and MP crossings were concentrated near the subsolar region and the dawn terminator, and that fact, together with the temporal variability, makes it difficult to assess the three dimensional shape of the sunward magnetospheric boundary. The combined BS and MP crossing positions from the three spacecraft yield an average BS-to-MP stagnation point distance ratio of 1.29 +/- 0.10. This is near the 1.33 value for the Earth's magnetosphere, implying a similar sunward shape at Saturn. Study of the structure and dynamical behavior of the outer magnetosphere, both in the sunward hemisphere and the magnetotail region using combined plasma and magnetic field data, suggest that Saturn's magnetosphere is more similar to that of Earth than that of Jupiter.

Dynamics of Multistable States during Ongoing and Evoked Cortical Activity

PubMed Central

Mazzucato, Luca

2015-01-01

Single-trial analyses of ensemble activity in alert animals demonstrate that cortical circuits dynamics evolve through temporal sequences of metastable states. Metastability has been studied for its potential role in sensory coding, memory, and decision-making. Yet, very little is known about the network mechanisms responsible for its genesis. It is often assumed that the onset of state sequences is triggered by an external stimulus. Here we show that state sequences can be observed also in the absence of overt sensory stimulation. Analysis of multielectrode recordings from the gustatory cortex of alert rats revealed ongoing sequences of states, where single neurons spontaneously attain several firing rates across different states. This single-neuron multistability represents a challenge to existing spiking network models, where typically each neuron is at most bistable. We present a recurrent spiking network model that accounts for both the spontaneous generation of state sequences and the multistability in single-neuron firing rates. Each state results from the activation of neural clusters with potentiated intracluster connections, with the firing rate in each cluster depending on the number of active clusters. Simulations show that the model's ensemble activity hops among the different states, reproducing the ongoing dynamics observed in the data. When probed with external stimuli, the model predicts the quenching of single-neuron multistability into bistability and the reduction of trial-by-trial variability. Both predictions were confirmed in the data. Together, these results provide a theoretical framework that captures both ongoing and evoked network dynamics in a single mechanistic model. PMID:26019337

A Geometric Model for Specularity Prediction on Planar Surfaces with Multiple Light Sources.

PubMed

Morgand, Alexandre; Tamaazousti, Mohamed; Bartoli, Adrien

2018-05-01

Specularities are often problematic in computer vision since they impact the dynamic range of the image intensity. A natural approach would be to predict and discard them using computer graphics models. However, these models depend on parameters which are difficult to estimate (light sources, objects' material properties and camera). We present a geometric model called JOLIMAS: JOint LIght-MAterial Specularity, which predicts the shape of specularities. JOLIMAS is reconstructed from images of specularities observed on a planar surface. It implicitly includes light and material properties, which are intrinsic to specularities. This model was motivated by the observation that specularities have a conic shape on planar surfaces. The conic shape is obtained by projecting a fixed quadric on the planar surface. JOLIMAS thus predicts the specularity using a simple geometric approach with static parameters (object material and light source shape). It is adapted to indoor light sources such as light bulbs and fluorescent lamps. The prediction has been tested on synthetic and real sequences. It works in a multi-light context by reconstructing a quadric for each light source with special cases such as lights being switched on or off. We also used specularity prediction for dynamic retexturing and obtained convincing rendering results. Further results are presented as supplementary video material, which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/TVCG.2017.2677445.

Probabilistic models for neural populations that naturally capture global coupling and criticality

PubMed Central

2017-01-01

Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality. PMID:28926564

Multi-objective four-dimensional vehicle motion planning in large dynamic environments.

PubMed

Wu, Paul P-Y; Campbell, Duncan; Merz, Torsten

2011-06-01

This paper presents Multi-Step A∗ (MSA∗), a search algorithm based on A∗ for multi-objective 4-D vehicle motion planning (three spatial and one time dimensions). The research is principally motivated by the need for offline and online motion planning for autonomous unmanned aerial vehicles (UAVs). For UAVs operating in large dynamic uncertain 4-D environments, the motion plan consists of a sequence of connected linear tracks (or trajectory segments). The track angle and velocity are important parameters that are often restricted by assumptions and a grid geometry in conventional motion planners. Many existing planners also fail to incorporate multiple decision criteria and constraints such as wind, fuel, dynamic obstacles, and the rules of the air. It is shown that MSA∗ finds a cost optimal solution using variable length, angle, and velocity trajectory segments. These segments are approximated with a grid-based cell sequence that provides an inherent tolerance to uncertainty. The computational efficiency is achieved by using variable successor operators to create a multiresolution memory-efficient lattice sampling structure. The simulation studies on the UAV flight planning problem show that MSA∗ meets the time constraints of online replanning and finds paths of equivalent cost but in a quarter of the time (on average) of a vector neighborhood-based A∗.

Exploring dynamic lighting, colour and form with smart textiles

NASA Astrophysics Data System (ADS)

Cabral, I.; Silva, C.; Worbin, L.; Souto, A. P.

2017-10-01

This paper addresses an ongoing research, aiming at the development of smart textiles that transform the incident light that passes through them - light transmittance - to design dynamic light without acting upon the light source. A colour and shape change prototype was developed with the objective of studying textile changes in time; to explore temperature as a dynamic variable through electrical activation of the smart materials and conductive threads integrated in the textile substrate; and to analyse the relation between textile chromic and morphologic behaviour in interaction with light. Based on the experiments conducted, results have highlighted some considerations of the dynamic parameters involved in the behaviour of thermo-responsive textiles and demonstrated design possibilities to create interactive lighting scenarios.

Exploring viral infection using single-cell sequencing.

PubMed

Rato, Sylvie; Golumbeanu, Monica; Telenti, Amalio; Ciuffi, Angela

2017-07-15

Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Characterization of emergent synaptic topologies in noisy neural networks

NASA Astrophysics Data System (ADS)

Miller, Aaron James

Learned behaviors are one of the key contributors to an animal's ultimate survival. It is widely believed that the brain's microcircuitry undergoes structural changes when a new behavior is learned. In particular, motor learning, during which an animal learns a sequence of muscular movements, often requires precisely-timed coordination between muscles and becomes very natural once ingrained. Experiments show that neurons in the motor cortex exhibit precisely-timed spike activity when performing a learned motor behavior, and constituent stereotypical elements of the behavior can last several hundred milliseconds. The subject of this manuscript concerns how organized synaptic structures that produce stereotypical spike sequences emerge from random, dynamical networks. After a brief introduction in Chapter 1, we begin Chapter 2 by introducing a spike-timing-dependent plasticity (STDP) rule that defines how the activity of the network drives changes in network topology. The rule is then applied to idealized networks of leaky integrate-and-fire neurons (LIF). These neurons are not subjected to the variability that typically characterize neurons in vivo. In noiseless networks, synapses develop closed loops of strong connectivity that reproduce stereotypical, precisely-timed spike patterns from an initially random network. We demonstrate the characteristics of the asymptotic synaptic configuration are dependent on the statistics of the initial random network. The spike timings of the neurons simulated in Chapter 2 are generated exactly by a computationally economical, nonlinear mapping which is extended to LIF neurons injected with fluctuating current in Chapter 3. Development of an economical mapping that incorporates noise provides a practical solution to the long simulation times required to produce asymptotic synaptic topologies in networks with STDP in the presence of realistic neuronal variability. The mapping relies on generating numerical solutions to the dynamics of a LIF neuron subjected to Gaussian white noise (GWN). The system reduces to the Ornstein-Uhlenbeck first passage time problem, the solution of which we build into the mapping method of Chapter 2. We demonstrate that simulations using the stochastic mapping have reduced computation time compared to traditional Runge-Kutta methods by more than a factor of 150. In Chapter 4, we use the stochastic mapping to study the dynamics of emerging synaptic topologies in noisy networks. With the addition of membrane noise, networks with dynamical synapses can admit states in which the distribution of the synaptic weights is static under spontaneous activity, but the random connectivity between neurons is dynamical. The widely cited problem of instabilities in networks with STDP is avoided with the implementation of a synaptic decay and an activation threshold on each synapse. When such networks are presented with stimulus modeled by a focused excitatory current, chain-like networks can emerge with the addition of an axon-remodeling plasticity rule, a topological constraint on the connectivity modeling the finite resources available to each neuron. The emergent topologies are the result of an iterative stochastic process. The dynamics of the growth process suggest a strong interplay between the network topology and the spike sequences they produce during development. Namely, the existence of an embedded spike sequence alters the distribution of synaptic weights through the entire network. The roles of model parameters that affect the interplay between network structure and activity are elucidated. Finally, we propose two mathematical growth models, which are complementary, that capture the essence of the growth dynamics observed in simulations. In Chapter 5, we present an extension of the stochastic mapping that allows the possibility of neuronal cooperation. We demonstrate that synaptic topologies admitting stereotypical sequences can emerge in yet higher, biologically realistic levels of membrane potential variability when neurons cooperate to innervate shared targets. The structure that is most robust to the variability is that of a synfire chain. The principles of growth dynamics detailed in Chapter 4 are the same that sculpt the emergent synfire topologies. We conclude by discussing avenues for extensions of these results.

Beat to beat variability in cardiovascular variables: noise or music?

NASA Technical Reports Server (NTRS)

Appel, M. L.; Berger, R. D.; Saul, J. P.; Smith, J. M.; Cohen, R. J.

1989-01-01

Cardiovascular variables such as heart rate, arterial blood pressure, stroke volume and the shape of electrocardiographic complexes all fluctuate on a beat to beat basis. These fluctuations have traditionally been ignored or, at best, treated as noise to be averaged out. The variability in cardiovascular signals reflects the homeodynamic interplay between perturbations to cardiovascular function and the dynamic response of the cardiovascular regulatory systems. Modern signal processing techniques provide a means of analyzing beat to beat fluctuations in cardiovascular signals, so as to permit a quantitative, noninvasive or minimally invasive method of assessing closed loop hemodynamic regulation and cardiac electrical stability. This method promises to provide a new approach to the clinical diagnosis and management of alterations in cardiovascular regulation and stability.

Dynamic covalent chemistry enables formation of antimicrobial peptide quaternary assemblies in a completely abiotic manner

NASA Astrophysics Data System (ADS)

Reuther, James F.; Dees, Justine L.; Kolesnichenko, Igor V.; Hernandez, Erik T.; Ukraintsev, Dmitri V.; Guduru, Rusheel; Whiteley, Marvin; Anslyn, Eric V.

2018-01-01

Naturally occurring peptides and proteins often use dynamic disulfide bonds to impart defined tertiary/quaternary structures for the formation of binding pockets with uniform size and function. Although peptide synthesis and modification are well established, controlling quaternary structure formation remains a significant challenge. Here, we report the facile incorporation of aryl aldehyde and acyl hydrazide functionalities into peptide oligomers via solid-phase copper-catalysed azide-alkyne cycloaddition (SP-CuAAC) click reactions. When mixed, these complementary functional groups rapidly react in aqueous media at neutral pH to form peptide-peptide intermolecular macrocycles with highly tunable ring sizes. Moreover, sequence-specific figure-of-eight, dumbbell-shaped, zipper-like and multi-loop quaternary structures were formed selectively. Controlling the proportions of reacting peptides with mismatched numbers of complementary reactive groups results in the formation of higher-molecular-weight sequence-defined ladder polymers. This also amplified antimicrobial effectiveness in select cases. This strategy represents a general approach to the creation of complex abiotic peptide quaternary structures.

Dynamics of Laser-Driven Shock Waves in Solid Targets

NASA Astrophysics Data System (ADS)

Aglitskiy, Y.; Karasik, M.; Velikovich, A. L.; Serlin, V.; Weaver, J.; Schmitt, A. J.; Obenschain, S. P.; Grun, J.; Metzler, N.; Zalesak, S. T.; Gardner, J. H.; Oh, J.; Harding, E. C.

2009-11-01

Accurate shock timing is a key issue of both indirect- and direct-drive laser fusions. The experiments on the Nike laser at NRL presented here were made possible by improvements in the imaging capability of our monochromatic x-ray diagnostics based on Bragg reflection from spherically curved crystals. Side-on imaging implemented on Nike makes it possible to observe dynamics of the shock wave and ablation front in laser-driven solid targets. We can choose to observe a sequence of 2D images or a continuous time evolution of an image resolved in one spatial dimension. A sequence of 300 ps snapshots taken using vanadium backlighter at 5.2 keV reveals propagation of a shock wave in a solid plastic target. The shape of the shock wave reflects the intensity distribution in the Nike beam. The streak records with continuous time resolution show the x-t trajectory of a laser-driven shock wave in a 10% solid density DVB foam.

On continuous user authentication via typing behavior.

PubMed

Roth, Joseph; Liu, Xiaoming; Metaxas, Dimitris

2014-10-01

We hypothesize that an individual computer user has a unique and consistent habitual pattern of hand movements, independent of the text, while typing on a keyboard. As a result, this paper proposes a novel biometric modality named typing behavior (TB) for continuous user authentication. Given a webcam pointing toward a keyboard, we develop real-time computer vision algorithms to automatically extract hand movement patterns from the video stream. Unlike the typical continuous biometrics, such as keystroke dynamics (KD), TB provides a reliable authentication with a short delay, while avoiding explicit key-logging. We collect a video database where 63 unique subjects type static text and free text for multiple sessions. For one typing video, the hands are segmented in each frame and a unique descriptor is extracted based on the shape and position of hands, as well as their temporal dynamics in the video sequence. We propose a novel approach, named bag of multi-dimensional phrases, to match the cross-feature and cross-temporal pattern between a gallery sequence and probe sequence. The experimental results demonstrate a superior performance of TB when compared with KD, which, together with our ultrareal-time demo system, warrant further investigation of this novel vision application and biometric modality.

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

PubMed Central

2014-01-01

Background Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site’s Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site’s LPD with its rate of evolution. Results We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein’s potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant’s active conformation. We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. Conclusions We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship between LPD and evolutionary rate. Moreover, the model also accounts for the nonlinear dependence between evolutionary rate and dynamical flexibility. PMID:24716445

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

Rhythm is it: effects of dynamic body feedback on affect and attitudes

PubMed Central

Koch, Sabine C.

2014-01-01

Body feedback is the proprioceptive feedback that denominates the afferent information from position and movement of the body to the central nervous system. It is crucial in experiencing emotions, in forming attitudes and in regulating emotions and behavior. This paper investigates effects of dynamic body feedback on affect and attitudes, focusing on the impact of movement rhythms with smooth vs. sharp reversals as one basic category of movement qualities. It relates those qualities to already explored effects of approach vs. avoidance motor behavior as one basic category of movement shape. Studies 1 and 2 tested the effects of one of two basic movement qualities (smooth vs. sharp rhythms) on affect and cognition. The third study tested those movement qualities in combination with movement shape (approach vs. avoidance motor behavior) and the effects of those combinations on affect and attitudes toward initially valence-free stimuli. Results suggest that movement rhythms influence affect (studies 1 and 2), and attitudes (study 3), and moderate the impact of approach and avoidance motor behavior on attitudes (study 3). Extending static body feedback research with a dynamic account, findings indicate that movement qualities – next to movement shape – play an important role, when movement of the lived body is an independent variable. PMID:24959153

Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility.

PubMed

Kulik, Natallia; Slámová, Kristýna; Ettrich, Rüdiger; Křen, Vladimír

2015-01-28

β-N-Acetylhexosaminidase (GH20) from the filamentous fungus Talaromyces flavus, previously identified as a prominent enzyme in the biosynthesis of modified glycosides, lacks a high resolution three-dimensional structure so far. Despite of high sequence identity to previously reported Aspergillus oryzae and Penicilluim oxalicum β-N-acetylhexosaminidases, this enzyme tolerates significantly better substrate modification. Understanding of key structural features, prediction of effective mutants and potential substrate characteristics prior to their synthesis are of general interest. Computational methods including homology modeling and molecular dynamics simulations were applied to shad light on the structure-activity relationship in the enzyme. Primary sequence analysis revealed some variable regions able to influence difference in substrate affinity of hexosaminidases. Moreover, docking in combination with consequent molecular dynamics simulations of C-6 modified glycosides enabled us to identify the structural features required for accommodation and processing of these bulky substrates in the active site of hexosaminidase from T. flavus. To access the reliability of predictions on basis of the reported model, all results were confronted with available experimental data that demonstrated the principal correctness of the predictions as well as the model. The main variable regions in β-N-acetylhexosaminidases determining difference in modified substrate affinity are located close to the active site entrance and engage two loops. Differences in primary sequence and the spatial arrangement of these loops and their interplay with active site amino acids, reflected by interaction energies and dynamics, account for the different catalytic activity and substrate specificity of the various fungal and bacterial β-N-acetylhexosaminidases.

First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs.

PubMed

Clissmann, Fionn; Fiore-Donno, Anna Maria; Hoppe, Björn; Krüger, Dirk; Kahl, Tiemo; Unterseher, Martin; Schnittler, Martin

2015-06-01

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Self-similarity in nature

NASA Astrophysics Data System (ADS)

Timashev, S. F.

2000-02-01

A general phenomenological approach to the analysis of experimental temporal, spatial and energetic series for extracting truly physical non-model parameters ("passport data") is presented, which may be used to characterize and distinguish the evolution as well as the spatial and energetic structure of any open nonlinear dissipative system. This methodology is based on a postulate concerning the crucial information contained in the sequences of non-regularities of the measured dynamic variable (temporal, spatial, energetic). In accordance with this approach, multi-parametric formulas for dynamic variable power spectra as well as for structural functions of different orders are identical for every spatial-temporal-energetic level of the system under consideration. In effect, this entails the introduction of a new kind of self-similarity in Nature. An algorithm has been developed for obtaining as many "passport data" as are necessary for the characterization of a dynamic system. Applications of this approach in the analysis of various experimental series (temporal, spatial, energetic) demonstrate its potential for defining adequate phenomenological parameters of different dynamic processes and structures.

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

PubMed Central

Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe

2015-01-01

Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860

Avalanche correlations in the martensitic transition of a Cu-Zn-Al shape memory alloy: analysis of acoustic emission and calorimetry.

PubMed

Baró, Jordi; Martín-Olalla, José-María; Romero, Francisco Javier; Gallardo, María Carmen; Salje, Ekhard K H; Vives, Eduard; Planes, Antoni

2014-03-26

The existence of temporal correlations during the intermittent dynamics of a thermally driven structural phase transition is studied in a Cu-Zn-Al alloy. The sequence of avalanches is observed by means of two techniques: acoustic emission and high sensitivity calorimetry. Both methods reveal the existence of event clustering in a way that is equivalent to the Omori correlations between aftershocks in earthquakes as are commonly used in seismology.

Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo

PubMed Central

Fontaine, Bertrand; Peña, José Luis; Brette, Romain

2014-01-01

Neurons encode information in sequences of spikes, which are triggered when their membrane potential crosses a threshold. In vivo, the spiking threshold displays large variability suggesting that threshold dynamics have a profound influence on how the combined input of a neuron is encoded in the spiking. Threshold variability could be explained by adaptation to the membrane potential. However, it could also be the case that most threshold variability reflects noise and processes other than threshold adaptation. Here, we investigated threshold variation in auditory neurons responses recorded in vivo in barn owls. We found that spike threshold is quantitatively predicted by a model in which the threshold adapts, tracking the membrane potential at a short timescale. As a result, in these neurons, slow voltage fluctuations do not contribute to spiking because they are filtered by threshold adaptation. More importantly, these neurons can only respond to input spikes arriving together on a millisecond timescale. These results demonstrate that fast adaptation to the membrane potential captures spike threshold variability in vivo. PMID:24722397

Genome-wide analysis of promoter architecture in Drosophila melanogaster

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

Hoskins, Roger A.; Landolin, Jane M.; Brown, James B.

2010-10-20

Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLMRACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysismore » indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.« less

Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16-22 and Sup357-13 in AOT reverse micelles

NASA Astrophysics Data System (ADS)

Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.

2014-12-01

Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.

[B lymphocyte clonal evolution of human reactive lymph nodes revealed by lineage tree analysis].

PubMed

Tabibian-Keissar, Hilla; Schiby, Ginette; Azogui-Rosenthal, Noemie; Hazanov, Helena; Rakovsky, Aviya Shapira; Michaeli, Miri; Rosenblatt, Kinneret; Mehr, Ramit; Barshack, Iris

2013-06-01

Hypermutation and selection processes, characterizing T-dependent B cell responses taking place in germinal centers of lymph nodes, lead to B cell receptor affinity maturation. Those immune responses lead to the development of memory B cells and plasma cells that secrete high amounts of antibody molecules. The dynamics of B cell clonal evolution during affinity maturation has significant importance in infectious and autoimmune diseases, malignancies and aging. Immunoglobulin (Ig) gene mutational Lineage tree construction by comparing variable regions of Ig-gene sequences to the Ig germline gene is an interesting approach for studying B cell cLonal evolution. Lineage tree shapes and Ig gene mutations can be evaluated not only qualitatively and intuitively, but also quantitatively, and thus reveal important information related to hypermutation and selection. In this paper we describe the experimental protocols that we used for PCR amplification of Igvariable region genes from human formalin fixed paraffin embedded reactive lymph node tissues and the subsequent bioinformatical analyses of sequencing data using Ig mutational lineage trees. B cell populations of three out of four reactive Lymph node tissues were composed of several clones. Most of the Ig gene mutational lineage trees were small and narrow. Significant differences were not detected by quantification of Lineage trees. B lymphocyte clones that were detected in human reactive lymph node tissues represent major responding clones in normal polyclonal immune response. This result is in line with the polyclonal profile of B Lymphocyte populations that reside in reactive lymph node tissues.

Slow-fast stochastic diffusion dynamics and quasi-stationarity for diploid populations with varying size.

PubMed

Coron, Camille

2016-01-01

We are interested in the long-time behavior of a diploid population with sexual reproduction and randomly varying population size, characterized by its genotype composition at one bi-allelic locus. The population is modeled by a 3-dimensional birth-and-death process with competition, weak cooperation and Mendelian reproduction. This stochastic process is indexed by a scaling parameter K that goes to infinity, following a large population assumption. When the individual birth and natural death rates are of order K, the sequence of stochastic processes indexed by K converges toward a new slow-fast dynamics with variable population size. We indeed prove the convergence toward 0 of a fast variable giving the deviation of the population from quasi Hardy-Weinberg equilibrium, while the sequence of slow variables giving the respective numbers of occurrences of each allele converges toward a 2-dimensional diffusion process that reaches (0,0) almost surely in finite time. The population size and the proportion of a given allele converge toward a Wright-Fisher diffusion with stochastically varying population size and diploid selection. We insist on differences between haploid and diploid populations due to population size stochastic variability. Using a non trivial change of variables, we study the absorption of this diffusion and its long time behavior conditioned on non-extinction. In particular we prove that this diffusion starting from any non-trivial state and conditioned on not hitting (0,0) admits a unique quasi-stationary distribution. We give numerical approximations of this quasi-stationary behavior in three biologically relevant cases: neutrality, overdominance, and separate niches.

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

PubMed

Ma, Wenxiu; Yang, Lin; Rohs, Remo; Noble, William Stafford

2017-10-01

Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites. We describe a sequence + shape kernel that leverages DNA sequence and shape information to better understand protein-DNA binding preference and affinity. This kernel extends an existing class of k-mer based sequence kernels, based on the recently described di-mismatch kernel. Using three in vitro benchmark datasets, derived from universal protein binding microarrays (uPBMs), genomic context PBMs (gcPBMs) and SELEX-seq data, we demonstrate that incorporating DNA shape information improves our ability to predict protein-DNA binding affinity. In particular, we observe that (i) the k-spectrum + shape model performs better than the classical k-spectrum kernel, particularly for small k values; (ii) the di-mismatch kernel performs better than the k-mer kernel, for larger k; and (iii) the di-mismatch + shape kernel performs better than the di-mismatch kernel for intermediate k values. The software is available at https://bitbucket.org/wenxiu/sequence-shape.git. rohs@usc.edu or william-noble@uw.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure

NASA Astrophysics Data System (ADS)

Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander

2015-04-01

Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer parallel shortening. Mechanical model have been developed to rigorously correlate rheological properties of rock to the fold shape. A quantitative fold shape analysis combined with the folding theory allows deciphering the rock rheology. In this study, we analyse anhydrite layers embedded in the rock salt from the Upper Permian Zechstein salt formation from Dutch offshore. The anhydrite layers are common intercalation in the sequence. Their thickness varies between few millimetres up to hundred meters. The layers are strongly deformed often forming fold structures, which can be observed on a wide range of scales: in core samples, mine galleries, and also in the seismic sections. For our analysis, we select single layer fold trains. Quantitative fold shape analysis is carried out using Fold Geometry Toolbox [3], which allows deciphering the viscosity ratio between anhydrite and salt. The results indicate that anhydrite layer is ca. 10 to 30 times more viscous than the embedding salt. Further, we use the estimated rheological parameters of anhydrite in the numerical analysis of the internal salt dynamics. We solve an incompressible Stokes equation in the presence of the gravity using the finite element method solver MILAMIN [4]. We show that the presence of denser and more viscous anhydrite layers in the tectonically stable regime is insignificant for the internal stability of the salt structures. [1] Chemia, Z., Koyi, H., Schmeling, H. 2008. Numerical modelling of rise and fall of a dense layer in salt diapirs. Geophysical Journal International, 172: 798-816. [2] Muller, W.H., Briegel, U. 1978. The rheological behaviour of polycrystalline Anhydrite. Eclogae Geol. Helv, 71(2): 397-407 [3] Adamuszek M., Schmid D.W., Dabrowski M. 2011. Fold geometry toolbox - Automated determination of fold shape, shortening, and material properties, Journal of Structural Geology, 33: 1406-1416. [4] Dabrowski, M., Krotkiewski, M., and Schmid, D. W. 2008. MILAMIN: MATLAB-based finite element method solver for large problems. Geochemistry Geophysics Geosystems, 9: Q04030.

Variability sensitivity of dynamic texture based recognition in clinical CT data

NASA Astrophysics Data System (ADS)

Kwitt, Roland; Razzaque, Sharif; Lowell, Jeffrey; Aylward, Stephen

2014-03-01

Dynamic texture recognition using a database of template models has recently shown promising results for the task of localizing anatomical structures in Ultrasound video. In order to understand its clinical value, it is imperative to study the sensitivity with respect to inter-patient variability as well as sensitivity to acquisition parameters such as Ultrasound probe angle. Fully addressing patient and acquisition variability issues, however, would require a large database of clinical Ultrasound from many patients, acquired in a multitude of controlled conditions, e.g., using a tracked transducer. Since such data is not readily attainable, we advocate an alternative evaluation strategy using abdominal CT data as a surrogate. In this paper, we describe how to replicate Ultrasound variabilities by extracting subvolumes from CT and interpreting the image material as an ordered sequence of video frames. Utilizing this technique, and based on a database of abdominal CT from 45 patients, we report recognition results on an organ (kidney) recognition task, where we try to discriminate kidney subvolumes/videos from a collection of randomly sampled negative instances. We demonstrate that (1) dynamic texture recognition is relatively insensitive to inter-patient variation while (2) viewing angle variability needs to be accounted for in the template database. Since naively extending the template database to counteract variability issues can lead to impractical database sizes, we propose an alternative strategy based on automated identification of a small set of representative models.

Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

PubMed

Kijima, T E; Innan, Hideki

2013-11-01

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

PubMed

Smola, Matthew J; Rice, Greggory M; Busan, Steven; Siegfried, Nathan A; Weeks, Kevin M

2015-11-01

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.

Network structure shapes spontaneous functional connectivity dynamics.

PubMed

Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

2015-04-08

The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

Calibration of visually guided reaching is driven by error-corrective learning and internal dynamics.

PubMed

Cheng, Sen; Sabes, Philip N

2007-04-01

The sensorimotor calibration of visually guided reaching changes on a trial-to-trial basis in response to random shifts in the visual feedback of the hand. We show that a simple linear dynamical system is sufficient to model the dynamics of this adaptive process. In this model, an internal variable represents the current state of sensorimotor calibration. Changes in this state are driven by error feedback signals, which consist of the visually perceived reach error, the artificial shift in visual feedback, or both. Subjects correct for > or =20% of the error observed on each movement, despite being unaware of the visual shift. The state of adaptation is also driven by internal dynamics, consisting of a decay back to a baseline state and a "state noise" process. State noise includes any source of variability that directly affects the state of adaptation, such as variability in sensory feedback processing, the computations that drive learning, or the maintenance of the state. This noise is accumulated in the state across trials, creating temporal correlations in the sequence of reach errors. These correlations allow us to distinguish state noise from sensorimotor performance noise, which arises independently on each trial from random fluctuations in the sensorimotor pathway. We show that these two noise sources contribute comparably to the overall magnitude of movement variability. Finally, the dynamics of adaptation measured with random feedback shifts generalizes to the case of constant feedback shifts, allowing for a direct comparison of our results with more traditional blocked-exposure experiments.

Healthy older adults demonstrate generalized postural motor learning in response to variable amplitude oscillations of the support surface

PubMed Central

Van Ooteghem, Karen; Frank, James S.; Allard, Fran; Horak, Fay B

2011-01-01

Postural motor learning for dynamic balance tasks has been demonstrated in healthy older adults (Van Ooteghem et al. 2009). The purpose of this study was to investigate the type of knowledge (general or specific) obtained with balance training in this age group and to examine whether embedding perturbation regularities within a balance task masks specific learning. Two groups of older adults maintained balance on a constant frequency-variable amplitude oscillating platform. One group was trained using an embedded sequence (ES) protocol which contained the same 15-s sequence of variable amplitude oscillations in the middle of each trial. A second group was trained using a looped sequence (LS) protocol which contained a 15-s sequence repeated three times to form each trial. All trials were 45-s. Participants were not informed of any repetition. To examine learning, participants performed a retention test following a 24-h delay. LS participants also completed a transfer task. Specificity of learning was examined by comparing performance for repeated versus random sequences (ES) and training versus transfer sequences (LS). Performance was measured by deriving spatial and temporal measures of whole body centre of mass (COM), and trunk orientation. Both groups improved performance with practice as characterized by reduced COM displacement, improved COM-platform phase relationships, and decreased angular trunk motion. Improvements were also characterized by general rather than specific postural motor learning. These findings are similar to young adults (Van Ooteghem et al. 2008) and indicate that age does not influence the type of learning which occurs for balance control. PMID:20544184

Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime.

PubMed

Hung, Ivan; Wu, Gang; Gan, Zhehong

NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17 O NMR of solid NaNO 3 in which the NO 3 - ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO 3 acquired in the temperature range of 173-413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO 3 - ion jumps span eight orders of magnitude (10 2 -10 10 s -1 ) covering both transitions of the dynamic 17 O line shape. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular dynamics simulation of a needle-sphere binary mixture

NASA Astrophysics Data System (ADS)

Raghavan, Karthik

This paper investigates the dynamic behaviour of a hard needle-sphere binary system using a novel numerical technique called the Newton homotopy continuation (NHC) method. This mixture is representative of a polymer melt where both long chain molecules and monomers coexist. Since the intermolecular forces are generated from hard body interactions, the consequence of missed collisions or incorrect collision sequences have a significant bearing on the dynamic properties of the fluid. To overcome this problem, in earlier work NHC was chosen over traditional Newton-Raphson methods to solve the hard body dynamics of a needle fluid in random media composed of overlapping spheres. Furthermore, the simplicity of interactions and dynamics allows us to focus our research directly on the effects of particle shape and density on the transport behaviour of the mixture. These studies are also compared with earlier works that examined molecular chains in porous media primarily to understand the differences in molecular transport in the bulk versus porous systems.

Redesigning Task Sequences to Support Instrumental Genesis in the Use of Movable Points and Slider Bars

ERIC Educational Resources Information Center

Fahlgren, Maria

2017-01-01

This paper examines the process of instrumental genesis through which students develop their proficiency in making use of movable points and slider bars--two tools that dynamic mathematics software provides for working with variable coordinates and parameters in the field of functions. The paper analyses students' responses to task sequences…

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

PubMed

Dueck, Hannah; Khaladkar, Mugdha; Kim, Tae Kyung; Spaethling, Jennifer M; Francis, Chantal; Suresh, Sangita; Fisher, Stephen A; Seale, Patrick; Beck, Sheryl G; Bartfai, Tamas; Kuhn, Bernhard; Eberwine, James; Kim, Junhyong

2015-06-09

Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. Additionally, single-cell transcriptomics presents unique analysis challenges that need to be addressed to answer this question. We present high quality deep read-depth single-cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within-cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single-cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. Single-cell RNA-sequencing data provide a unique view of transcriptome function; however, careful analysis is required in order to use single-cell RNA-sequencing measurements for this purpose. Technical variation must be considered in single-cell RNA-sequencing studies of expression variation. For a subset of genes, biological variability within each cell type appears to be regulated in order to perform dynamic functions, rather than solely molecular noise.

Traveling wave and soliton solutions of coupled nonlinear Schrödinger equations with harmonic potential and variable coefficients.

PubMed

Zhong, Wei-Ping; Belić, Milivoj

2010-10-01

Exact traveling wave and soliton solutions, including the bright-bright and dark-dark soliton pairs, are found for the system of two coupled nonlinear Schrödinger equations with harmonic potential and variable coefficients, by employing the homogeneous balance principle and the F-expansion technique. A kind of shape-changing soliton collision is identified in the system. The collision is essentially elastic between the two solitons with opposite velocities. Our results demonstrate that the dynamics of solitons can be controlled by selecting the diffraction, nonlinearity, and gain coefficients.

A fractal approach to dynamic inference and distribution analysis

PubMed Central

van Rooij, Marieke M. J. W.; Nash, Bertha A.; Rajaraman, Srinivasan; Holden, John G.

2013-01-01

Event-distributions inform scientists about the variability and dispersion of repeated measurements. This dispersion can be understood from a complex systems perspective, and quantified in terms of fractal geometry. The key premise is that a distribution's shape reveals information about the governing dynamics of the system that gave rise to the distribution. Two categories of characteristic dynamics are distinguished: additive systems governed by component-dominant dynamics and multiplicative or interdependent systems governed by interaction-dominant dynamics. A logic by which systems governed by interaction-dominant dynamics are expected to yield mixtures of lognormal and inverse power-law samples is discussed. These mixtures are described by a so-called cocktail model of response times derived from human cognitive performances. The overarching goals of this article are twofold: First, to offer readers an introduction to this theoretical perspective and second, to offer an overview of the related statistical methods. PMID:23372552

Study of Geometric Porosity on Static Stability and Drag Using Computational Fluid Dynamics for Rigid Parachute Shapes

NASA Technical Reports Server (NTRS)

Greathouse, James S.; Schwing, Alan M.

2015-01-01

This paper explores use of computational fluid dynamics to study the e?ect of geometric porosity on static stability and drag for NASA's Multi-Purpose Crew Vehicle main parachute. Both of these aerodynamic characteristics are of interest to in parachute design, and computational methods promise designers the ability to perform detailed parametric studies and other design iterations with a level of control previously unobtainable using ground or flight testing. The approach presented here uses a canopy structural analysis code to define the inflated parachute shapes on which structured computational grids are generated. These grids are used by the computational fluid dynamics code OVERFLOW and are modeled as rigid, impermeable bodies for this analysis. Comparisons to Apollo drop test data is shown as preliminary validation of the technique. Results include several parametric sweeps through design variables in order to better understand the trade between static stability and drag. Finally, designs that maximize static stability with a minimal loss in drag are suggested for further study in subscale ground and flight testing.

Soft inclusion in a confined fluctuating active gel

NASA Astrophysics Data System (ADS)

Singh Vishen, Amit; Rupprecht, J.-F.; Shivashankar, G. V.; Prost, J.; Rao, Madan

2018-03-01

We study stochastic dynamics of a point and extended inclusion within a one-dimensional confined active viscoelastic gel. We show that the dynamics of a point inclusion can be described by a Langevin equation with a confining potential and multiplicative noise. Using a systematic adiabatic elimination over the fast variables, we arrive at an overdamped equation with a proper definition of the multiplicative noise. To highlight various features and to appeal to different biological contexts, we treat the inclusion in turn as a rigid extended element, an elastic element, and a viscoelastic (Kelvin-Voigt) element. The dynamics for the shape and position of the extended inclusion can be described by coupled Langevin equations. Deriving exact expressions for the corresponding steady-state probability distributions, we find that the active noise induces an attraction to the edges of the confining domain. In the presence of a competing centering force, we find that the shape of the probability distribution exhibits a sharp transition upon varying the amplitude of the active noise. Our results could help understanding the positioning and deformability of biological inclusions, e.g., organelles in cells, or nucleus and cells within tissues.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter

PubMed Central

Roux-Rouquie, Magali; Marilley, Monique

2000-01-01

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X.laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed. PMID:10982860

Dynamic shape transitions in the sdg boson model

NASA Astrophysics Data System (ADS)

Kuyucak, S.

The dynamic evolution of shapes in the sdg interacting boson model is investigated using the angular momentum projected mean field theory. Deformed nuclei are found to be quite stable against shape changes but transitional nuclei could exhibit dynamic shape transitions in the region L = 10-20. Conditions of existence and experimental signatures for dynamic shape transitions are discussed together with a likely candidate, 192Os.

Microbial Communities Are Well Adapted to Disturbances in Energy Input

PubMed Central

Vallino, Joseph J.

2016-01-01

ABSTRACT Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic “unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems. PMID:27822558

Evidence for photometric activity cycles in 3203 Kepler stars

NASA Astrophysics Data System (ADS)

Reinhold, Timo; Cameron, Robert H.; Gizon, Laurent

2017-07-01

Context. In recent years it has been claimed that the length of stellar activity cycles is determined by the stellar rotation rate. It has been observed that the cycle period increases with rotation period along two distinct sequences, known as the active and inactive sequences. In this picture the Sun occupies a solitary position between the two sequences. Whether the Sun might undergo a transitional evolutionary stage is currently under debate. Aims: Our goal is to measure cyclic variations of the stellar light curve amplitude and the rotation period using four years of Kepler data. Periodic changes in the light curve amplitude or the stellar rotation period are associated with an underlying activity cycle. Methods: Using a recent sample of active stars we compute the rotation period and the variability amplitude for each individual Kepler quarter and search for periodic variations of both time series. To test for periodicity in each stellar time series we consider Lomb-Scargle periodograms and use a selection based on a false alarm probability (FAP). Results: We detect amplitude periodicities in 3203 stars between 0.5 < Pcyc < 6 yr covering rotation periods between 1 < Prot < 40 days. Given our sample size of 23 601 stars and our selection criteria that the FAP is less than 5%, this number is almost three times higher than that expected from pure noise. We do not detect periodicities in the rotation period beyond those expected from noise. Our measurements reveal that the cycle period shows a weak dependence on rotation rate, slightly increasing for longer rotation periods. We further show that the shape of the variability deviates from a pure sine curve, consistent with observations of the solar cycle. The cycle shape does not show a statistically significant dependence on effective temperature. Conclusions: We detect activity cycles in more than 13% of our final sample with a FAP of 5% (calculated by randomly shuffling the measured 90-day variability measurements for each star). Our measurements do not support the existence of distinct sequences in the Prot-Pcyc plane, although there is some evidence for the inactive sequence for rotation periods between 5-25 days. Unfortunately, the total observing time is too short to draw sound conclusions on activity cycles with similar lengths to that of the solar cycle. A table containing all cycle periods and time series is only available in electronic form at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/603/A52

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis

PubMed Central

Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.

2016-01-01

SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499

A fully relativistic twisted disc around a slowly rotating Kerr black hole: derivation of dynamical equations and the shape of stationary configurations

NASA Astrophysics Data System (ADS)

Zhuravlev, V. V.; Ivanov, P. B.

2011-08-01

In this paper we derive equations describing the dynamics and stationary configurations of a twisted fully relativistic thin accretion disc around a slowly rotating black hole. We assume that the inclination angle of the disc is small and that the standard relativistic generalization of the α model of accretion discs is valid when the disc is flat. We find that similar to the case of non-relativistic twisted discs the disc dynamics and stationary shapes can be determined by a pair of equations formulated for two complex variables describing the orientation of the disc rings and velocity perturbations induced by the twist. We analyse analytically and numerically the shapes of stationary twisted configurations of accretion discs having non-zero inclinations with respect to the black hole equatorial plane at large distances r from the black hole. It is shown that the stationary configurations depend on two parameters - the viscosity parameter α and the parameter ?, where δ* is the opening angle (δ*˜h/r, where h is the disc half-thickness and r is large) of a flat disc and a is the black hole rotational parameter. When a > 0 and ? the shapes depend drastically on the value of α. When α is small the disc inclination angle oscillates with radius with amplitude and radial frequency of the oscillations dramatically increasing towards the last stable orbit, Rms. When α has a moderately small value the oscillations do not take place but the disc does not align with the equatorial plane at small radii. The disc inclination angle either is increasing towards Rms or exhibits a non-monotonic dependence on the radial coordinate. Finally, when α is sufficiently large the disc aligns with the equatorial plane at small radii. When a < 0 the disc aligns with the equatorial plane for all values of α. The results reported here may have implications for determining the structure and variability of accretion discs close to Rms as well as for modelling of emission spectra coming from different sources, which are supposed to contain black holes.

The intra-day dynamics of affect, self-esteem, tiredness, and suicidality in Major Depression.

PubMed

Crowe, Eimear; Daly, Michael; Delaney, Liam; Carroll, Susan; Malone, Kevin M

2018-02-21

Despite growing interest in the temporal dynamics of Major Depressive Disorder (MDD), we know little about the intra-day fluctuations of key symptom constructs. In a study of momentary experience, the Experience Sampling Method captured the within-day dynamics of negative affect, positive affect, self-esteem, passive suicidality, and tiredness across clinical MDD (N= 31) and healthy control groups (N= 33). Ten symptom measures were taken per day over 6 days (N= 2231 observations). Daily dynamics were modeled via intra-day time-trends, variability, and instability in symptoms. MDD participants showed significantly increased variability and instability in negative affect, positive affect, self-esteem, and suicidality. Significantly different time-trends were found in positive affect (increased diurnal variation and an inverted U-shaped pattern in MDD, compared to a positive linear trend in controls) and tiredness (decreased diurnal variation in MDD). In the MDD group only, passive suicidality displayed a negative linear trend and self-esteem displayed a quadratic inverted U trend. MDD and control participants thus showed distinct dynamic profiles in all symptoms measured. As well as the overall severity of symptoms, intra-day dynamics appear to define the experience of MDD symptoms. Copyright © 2018 Elsevier B.V. All rights reserved.

Dual gait generative models for human motion estimation from a single camera.

PubMed

Zhang, Xin; Fan, Guoliang

2010-08-01

This paper presents a general gait representation framework for video-based human motion estimation. Specifically, we want to estimate the kinematics of an unknown gait from image sequences taken by a single camera. This approach involves two generative models, called the kinematic gait generative model (KGGM) and the visual gait generative model (VGGM), which represent the kinematics and appearances of a gait by a few latent variables, respectively. The concept of gait manifold is proposed to capture the gait variability among different individuals by which KGGM and VGGM can be integrated together, so that a new gait with unknown kinematics can be inferred from gait appearances via KGGM and VGGM. Moreover, a new particle-filtering algorithm is proposed for dynamic gait estimation, which is embedded with a segmental jump-diffusion Markov Chain Monte Carlo scheme to accommodate the gait variability in a long observed sequence. The proposed algorithm is trained from the Carnegie Mellon University (CMU) Mocap data and tested on the Brown University HumanEva data with promising results.

Modeling bias and variation in the stochastic processes of small RNA sequencing

PubMed Central

Etheridge, Alton; Sakhanenko, Nikita; Galas, David

2017-01-01

Abstract The use of RNA-seq as the preferred method for the discovery and validation of small RNA biomarkers has been hindered by high quantitative variability and biased sequence counts. In this paper we develop a statistical model for sequence counts that accounts for ligase bias and stochastic variation in sequence counts. This model implies a linear quadratic relation between the mean and variance of sequence counts. Using a large number of sequencing datasets, we demonstrate how one can use the generalized additive models for location, scale and shape (GAMLSS) distributional regression framework to calculate and apply empirical correction factors for ligase bias. Bias correction could remove more than 40% of the bias for miRNAs. Empirical bias correction factors appear to be nearly constant over at least one and up to four orders of magnitude of total RNA input and independent of sample composition. Using synthetic mixes of known composition, we show that the GAMLSS approach can analyze differential expression with greater accuracy, higher sensitivity and specificity than six existing algorithms (DESeq2, edgeR, EBSeq, limma, DSS, voom) for the analysis of small RNA-seq data. PMID:28369495

Modeling the dynamics of choice.

PubMed

Baum, William M; Davison, Michael

2009-06-01

A simple linear-operator model both describes and predicts the dynamics of choice that may underlie the matching relation. We measured inter-food choice within components of a schedule that presented seven different pairs of concurrent variable-interval schedules for 12 food deliveries each with no signals indicating which pair was in force. This measure of local choice was accurately described and predicted as obtained reinforcer sequences shifted it to favor one alternative or the other. The effect of a changeover delay was reflected in one parameter, the asymptote, whereas the effect of a difference in overall rate of food delivery was reflected in the other parameter, rate of approach to the asymptote. The model takes choice as a primary dependent variable, not derived by comparison between alternatives-an approach that agrees with the molar view of behaviour.

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.

PubMed

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia , which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla ), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase ( ndh ) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci- ndhA intron, matK-5'trnK , clpP-psbB , rps8-rpl14 , trnT-trnL , 3'trnK-matK , clpP intron , psbK-trnK , trnS-psbC , and ndhF-rpl32 -that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

PubMed Central

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed. PMID:29046685

Autogenic dynamics of debris-flow fans

NASA Astrophysics Data System (ADS)

van den Berg, Wilco; de Haas, Tjalling; Braat, Lisanne; Kleinhans, Maarten

2015-04-01

Alluvial fans develop their semi-conical shape by cyclic avulsion of their geomorphologically active sector from a fixed fan apex. These cyclic avulsions have been attributed to both allogenic and autogenic forcings and processes. Autogenic dynamics have been extensively studied on fluvial fans through physical scale experiments, and are governed by cyclic alternations of aggradation by unconfined sheet flow, fanhead incision leading to channelized flow, channel backfilling and avulsion. On debris-flow fans, however, autogenic dynamics have not yet been directly observed. We experimentally created debris-flow fans under constant extrinsic forcings, and show that autogenic dynamics are a fundamental intrinsic process on debris-flow fans. We found that autogenic cycles on debris-flow fans are driven by sequences of backfilling, avulsion and channelization, similar to the cycles on fluvial fans. However, the processes that govern these sequences are unique for debris-flow fans, and differ fundamentally from the processes that govern autogenic dynamics on fluvial fans. We experimentally observed that backfilling commenced after the debris flows reached their maximum possible extent. The next debris flows then progressively became shorter, driven by feedbacks on fan morphology and flow-dynamics. The progressively decreasing debris-flow length caused in-channel sedimentation, which led to increasing channel overflow and wider debris flows. This reduced the impulse of the liquefied flow body to the flow front, which then further reduced flow velocity and runout length, and induced further in-channel sedimentation. This commenced a positive feedback wherein debris flows became increasingly short and wide, until the channel was completely filled and the apex cross-profile was plano-convex. At this point, there was no preferential transport direction by channelization, and the debris flows progressively avulsed towards the steepest, preferential, flow path. Simultaneously, the debris flows started to channelize, forced by increasingly effective concentration of the flow impulse to the flow front, which caused more effective lateral levee formation and an increasingly well-defined channel. This process continued until the debris flows reached their maximum possible extent and the cycle was reverted. Channelization occurred in the absence of erosion, in contrast with fluvial fans. Backfilling and channelization cycles were gradual and symmetric, requiring multiple debris flows to be completed. These results add debris-flow fans to the spectrum of fan-shaped aqueous systems that are affected by autogenic dynamics, now ranging from low-gradient rivers systems to steep-gradient mass-flow fans.

High-resolution clustered pinhole (131)Iodine SPECT imaging in mice.

PubMed

van der Have, Frans; Ivashchenko, Oleksandra; Goorden, Marlies C; Ramakers, Ruud M; Beekman, Freek J

2016-08-01

High-resolution pre-clinical (131)I SPECT can facilitate development of new radioiodine therapies for cancer. To this end, it is important to limit resolution-degrading effects of pinhole edge penetration by the high-energy γ-photons of iodine. Here we introduce, optimize and validate (131)I SPECT performed with a dedicated high-energy clustered multi-pinhole collimator. A SPECT-CT system (VECTor/CT) with stationary gamma-detectors was equipped with a tungsten collimator with clustered pinholes. Images were reconstructed with pixel-based OSEM, using a dedicated (131)I system matrix that models the distance- and energy-dependent resolution and sensitivity of each pinhole, as well as the intrinsic detector blurring and variable depth of interaction in the detector. The system performance was characterized with phantoms and in vivo static and dynamic (131)I-NaI scans of mice. Reconstructed image resolution reached 0.6mm, while quantitative accuracy measured with a (131)I filled syringe reaches an accuracy of +3.6±3.5% of the gold standard value. In vivo mice scans illustrated a clear shape of the thyroid and biodistribution of (131)I within the animal. Pharmacokinetics of (131)I was assessed with 15-s time frames from the sequence of dynamic images and time-activity curves of (131)I-NaI. High-resolution quantitative and fast dynamic (131)I SPECT in mice is possible by means of a high-energy collimator and optimized system modeling. This enables analysis of (131)I uptake even within small organs in mice, which can be highly valuable for development and optimization of targeted cancer therapies. Copyright © 2016 Elsevier Inc. All rights reserved.

Impact of height and shape of building roof on air quality in urban street canyons

NASA Astrophysics Data System (ADS)

Yassin, Mohamed F.

2011-09-01

A building's roof shape and roof height play an important role in determining pollutant concentrations from vehicle emissions and its complex flow patterns within urban street canyons. The impact of the roof shape and height on wind flow and dispersion of gaseous pollutants from vehicle exhaust within urban canyons were investigated numerically using a Computational Fluid Dynamics (CFD) model. Two-dimensional flow and dispersion of gaseous pollutants were analyzed using standard κ- ɛ turbulence model, which was numerically solved based on Reynolds Averaged Navier-Stokes (RANS) equations. The diffusion fields in the urban canyons were examined with three roof heights ( Z H/ H = 0.17, 0.33 and 0.5) and five roof shapes: (1) flat-shaped roof, (2) slanted-shaped roof, (3) downwind wedge-shaped roof, (4) upwind wedge-shaped roof, and (5) trapezoid-shaped roof. The numerical model was validated against the wind tunnels results in order to optimize the turbulence model. The numerical simulations agreed reasonably with the wind tunnel results. The results obtained indicated that the pollutant concentration increased as the roof height decreases. It also decreased with the slanted and trapezoid-shaped roofs but increased with the flat-shaped roof. The pollutant concentration distributions simulated in the present work, indicated that the variability of the roof shapes and roof heights of the buildings are important factors for estimating air quality within urban canyons.

A Tour Through Shape Dynamic Black Holes

NASA Astrophysics Data System (ADS)

Herczeg, Gabriel

Shape dynamics is a classical theory of gravity which agrees with general relativity in many important cases, but possesses different gauge symmetries and constraints. Rather than spacetime diffeomorphism invariance, shape dynamics takes spatial diffeomorphism invariance and spatial Weyl invariance as the fundamental gauge symmetries associated with the gravitational field. Despite these differences, shape dynamics and general relativity generically predict the same dynamics--there exist gauge-fixings of each theory that ensure agreement with the other. However, these gauge-fixing conditions are not necessarily globally well-defined and it is therefore possible to find solutions of the shape dynamics equations of motion that agree with general relativity on some open neighborhoods, but which have different global structures. In particular, the black hole solutions of the two theories disagree globally. Understanding these novel "shape dynamic black holes" is the primary goal of this thesis.

Where do these bugs come from? Phenotypic structure of Triatoma infestans populations after control interventions in the Argentine Chaco

PubMed Central

Gaspe, María Sol; Provecho, Yael Mariana; Piccinali, Romina Valeria; Gürtler/, Ricardo Esteban

2015-01-01

House re-invasion by native triatomines after insecticide-based control campaigns represents a major threat for Chagas disease vector control. We conducted a longitudinal intervention study in a rural section (Area III, 407 houses) of Pampa del Indio, northeastern Argentina, and used wing geometric morphometry to compare pre-spray and post-spray (re-infestant bugs) Triatoma infestans populations. The community-wide spraying with pyrethroids reduced the prevalence of house infestation by T. infestans from 31.9% to < 1% during a four-year follow-up, unlike our previous studies in the neighbouring Area I. Two groups of bug collection sites differing in wing shape variables before interventions (including 221 adults from 11 domiciles) were used as a reference for assigning 44 post-spray adults. Wing shape variables from post-spray, high-density bug colonies and pre-spray groups were significantly different, suggesting that re-infestant insects had an external origin. Insects from one house differed strongly in wing shape variables from all other specimens. A further comparison between insects from both areas supported the existence of independent re-infestation processes within the same district. These results point to local heterogeneities in house re-infestation dynamics and emphasise the need to expand the geographic coverage of vector surveillance and control operations to the affected region. PMID:25946158

Current problems in the dynamics and design of mechanisms and machines

NASA Astrophysics Data System (ADS)

Kestel'Man, V. N.

The papers contained in this volume deal with possible ways of improving the dynamic and structural properties of machines and mechanisms and also with problems associated with the design of aircraft equipment. Topics discussed include estimation of the stressed state of a model of an orbital film structure, a study of the operation of an aerodynamic angle transducer in flow of a hot gas, calculation of the efficiency of aircraft gear drives, and dynamic accuracy of a controlled manipulator. Papers are also presented on optimal synthesis of mechanical systems with variable properties, synthesis of mechanisms using initial kinematic chains, and using shape memory materials in the design of machines and mechanisms. (For individual items see A93-31202 to A93-31214)

Influence of environmental heterogeneity on the distribution and persistence of a subterranean rodent in a highly unstable landscape.

PubMed

Gómez Fernández, María Jimena; Boston, Emma S M; Gaggiotti, Oscar E; Kittlein, Marcelo J; Mirol, Patricia M

2016-12-01

In this study we combine information from landscape characteristics, demographic inference and species distribution modelling to identify environmental factors that shape the genetic distribution of the fossorial rodent Ctenomys. We sequenced the mtDNA control region and amplified 12 microsatellites from 27 populations distributed across the Iberá wetland ecosystem. Hierarchical Bayesian modelling was used to construct phylogenies and estimate divergence times. We developed species distribution models to determine what climatic variables and soil parameters predicted species presence by comparing the current to the historic and predicted future distribution of the species. Finally, we explore the impact of environmental variables on the genetic structure of Ctenomys based on current and past species distributions. The variables that consistently correlated with the predicted distribution of the species and explained the observed genetic differentiation among populations included the distribution of well-drained sandy soils and temperature seasonality. A core region of stable suitable habitat was identified from the Last Interglacial, which is projected to remain stable into the future. This region is also the most genetically diverse and is currently under strong anthropogenic pressure. Results reveal complex demographic dynamics, which have been in constant change in both time and space, and are likely linked to the evolution of the Paraná River. We suggest that any alteration of soil properties (climatic or anthropic) may significantly impact the availability of suitable habitat and consequently the ability of individuals to disperse. The protection of this core stable habitat is of prime importance given the increasing levels of human disturbance across this wetland system and the threat of climate change.

OPEN PROBLEM: Orbits' statistics in chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Arnold, V.

2008-07-01

This paper shows how the measurement of the stochasticity degree of a finite sequence of real numbers, published by Kolmogorov in Italian in a journal of insurances' statistics, can be usefully applied to measure the objective stochasticity degree of sequences, originating from dynamical systems theory and from number theory. Namely, whenever the value of Kolmogorov's stochasticity parameter of a given sequence of numbers is too small (or too big), one may conclude that the conjecture describing this sequence as a sample of independent values of a random variables is highly improbable. Kolmogorov used this strategy fighting (in a paper in 'Doklady', 1940) against Lysenko, who had tried to disprove the classical genetics' law of Mendel experimentally. Calculating his stochasticity parameter value for the numbers from Lysenko's experiment reports, Kolmogorov deduced, that, while these numbers were different from the exact fulfilment of Mendel's 3 : 1 law, any smaller deviation would be a manifestation of the report's number falsification. The calculation of the values of the stochasticity parameter would be useful for many other generators of pseudorandom numbers and for many other chaotically looking statistics, including even the prime numbers distribution (discussed in this paper as an example).

Transport induced by mean-eddy interaction: II. Analysis of transport processes

NASA Astrophysics Data System (ADS)

Ide, Kayo; Wiggins, Stephen

2015-03-01

We present a framework for the analysis of transport processes resulting from the mean-eddy interaction in a flow. The framework is based on the Transport Induced by the Mean-Eddy Interaction (TIME) method presented in a companion paper (Ide and Wiggins, 2014) [1]. The TIME method estimates the (Lagrangian) transport across stationary (Eulerian) boundaries defined by chosen streamlines of the mean flow. Our framework proceeds after first carrying out a sequence of preparatory steps that link the flow dynamics to the transport processes. This includes the construction of the so-called "instantaneous flux" as the Hovmöller diagram. Transport processes are studied by linking the signals of the instantaneous flux field to the dynamical variability of the flow. This linkage also reveals how the variability of the flow contributes to the transport. The spatio-temporal analysis of the flux diagram can be used to assess the efficiency of the variability in transport processes. We apply the method to the double-gyre ocean circulation model in the situation where the Rossby-wave mode dominates the dynamic variability. The spatio-temporal analysis shows that the inter-gyre transport is controlled by the circulating eddy vortices in the fast eastward jet region, whereas the basin-scale Rossby waves have very little impact.

Spatio-Temporal Dynamics of Impulse Responses to Figure Motion in Optic Flow Neurons

PubMed Central

Lee, Yu-Jen; Jönsson, H. Olof; Nordström, Karin

2015-01-01

White noise techniques have been used widely to investigate sensory systems in both vertebrates and invertebrates. White noise stimuli are powerful in their ability to rapidly generate data that help the experimenter decipher the spatio-temporal dynamics of neural and behavioral responses. One type of white noise stimuli, maximal length shift register sequences (m-sequences), have recently become particularly popular for extracting response kernels in insect motion vision. We here use such m-sequences to extract the impulse responses to figure motion in hoverfly lobula plate tangential cells (LPTCs). Figure motion is behaviorally important and many visually guided animals orient towards salient features in the surround. We show that LPTCs respond robustly to figure motion in the receptive field. The impulse response is scaled down in amplitude when the figure size is reduced, but its time course remains unaltered. However, a low contrast stimulus generates a slower response with a significantly longer time-to-peak and half-width. Impulse responses in females have a slower time-to-peak than males, but are otherwise similar. Finally we show that the shapes of the impulse response to a figure and a widefield stimulus are very similar, suggesting that the figure response could be coded by the same input as the widefield response. PMID:25955416

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server.

PubMed

Abriata, Luciano A; Bovigny, Christophe; Dal Peraro, Matteo

2016-06-17

Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting detailed analyses to positions of extremely high or low variability or dubbed important beforehand based on existing knowledge about active sites, interaction surfaces, (de)stabilizing mutations, etc. Our new webserver PsychoProt (freely available without registration at http://psychoprot.epfl.ch or at http://lucianoabriata.altervista.org/psychoprot/index.html ) helps to detect, quantify, and sequence/structure map the biophysical and biochemical traits that shape amino acid preferences throughout a protein as determined by deep-sequencing of saturated mutational libraries or from large alignments of naturally occurring variants. We exemplify how PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data. Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory. This and other differences call for caution when extrapolating results from in vitro experiments to natural scenarios in, for example, studies of protein evolution. We show through examples how PsychoProt can be a useful tool for the broad communities of structural biology and molecular evolution, particularly for studies about protein modeling, evolution and design.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

PubMed Central

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-01-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. PMID:24462600

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

PubMed

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-06-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. Copyright © 2014 Elsevier Inc. All rights reserved.

Re-accumulation Scenarios Governing Final Global Shapes of Rubble-Pile Asteroids

NASA Astrophysics Data System (ADS)

Hestroffer, Daniel; Tanga, P.; Comito, C.; Paolicchi, P.; Walsh, K.; Richardson, D. C.; Cellino, A.

2009-05-01

Asteroids, since the formation of the solar system, are known to have experienced catastrophic collisions, which---depending on the impact energy---can produce a major disruption of the parent body and possibly give birth to asteroid families or binaries [1]. We present a general study of the final shape and dynamical state of asteroids produced by the re-accumulation process following a catastrophic disruption. Starting from a cloud of massive particles (mono-disperse spheres) with given density and velocity distributions, we analyse the final shape, spin state, and angular momentum of the system from numerical integration of a N-body gravitational system (code pkdgrav [2]). The re-accumulation process itself is relatively fast, with a dynamical time corresponding to the spin-period of the final body (several hours). The final global shapes---which are described as tri-axial ellipsoids---exhibit slopes consistent with a degree of shear stress sustained by interlocking particles. We point out a few results: -the final shapes are close to those of hydrostatic equilibrium for incompressible fluids, preferably Maclaurin spheroid rather than Jacobi ellipsoids -for bodies closest to the sequence of hydrostatic equilibrium, there is a direct relation between spin, density and outer shape, suggesting that the outer surface is nearly equipotential -the evolution of the shape during the process follows a track along a gradient of potential energy, without necessarily reaching its minimum -the loose random packing of the particles implies low friction angle and hence fluid-like behaviour, which extends the results of [3]. Future steps of our analysis will include feature refinements of the model initial conditions and re-accumulation process, including impact shakings, realistic velocity distributions, and non equal-sized elementary spheres. References [1] Michel P. et al. 2001. Science 294, 1696 [2] Leinhardt Z.M. et al. 2000. Icarus 146, 133 [3] Richardson D.C. et al. 2005. Icarus 173, 349

The color of sea level: Importance of spatial variations in spectral shape for assessing the significance of trends

NASA Astrophysics Data System (ADS)

Hughes, Chris W.; Williams, Simon D. P.

2010-10-01

We investigate spatial variations in the shape of the spectrum of sea level variability based on a homogeneously sampled 12 year gridded altimeter data set. We present a method of plotting spectral information as color, focusing on periods between 2 and 24 weeks, which shows that significant spatial variations in the spectral shape exist and contain useful dynamical information. Using the Bayesian Information Criterion, we determine that, typically, a fifth-order autoregressive model is needed to capture the structure in the spectrum. Using this model, we show that statistical errors in fitted local trends range between less than 1 and more than 5 times of what would be calculated assuming "white" noise and that the time needed to detect a 1 mm/yr trend ranges between about 5 years and many decades. For global mean sea level, the statistical error reduces to 0.1 mm/yr over 12 years, with only 2 years needed to detect a 1 mm/yr trend. We find significant regional differences in trend from the global mean. The patterns of these regional differences are indicative of a sea level trend dominated by dynamical ocean processes over this period.

Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

PubMed

Watters, Kyle E; Lucks, Julius B

2016-01-01

Mapping RNA structure with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry has proven to be a versatile method for characterizing RNA structure in a variety of contexts. SHAPE reagents covalently modify RNAs in a structure-dependent manner to create adducts at the 2'-OH group of the ribose backbone at nucleotides that are structurally flexible. The positions of these adducts are detected using reverse transcriptase (RT) primer extension, which stops one nucleotide before the modification, to create a pool of cDNAs whose lengths reflect the location of SHAPE modification. Quantification of the cDNA pools is used to estimate the "reactivity" of each nucleotide in an RNA molecule to the SHAPE reagent. High reactivities indicate nucleotides that are structurally flexible, while low reactivities indicate nucleotides that are inflexible. These SHAPE reactivities can then be used to infer RNA structures by restraining RNA structure prediction algorithms. Here, we provide a state-of-the-art protocol describing how to perform in vitro RNA structure probing with SHAPE chemistry using next-generation sequencing to quantify cDNA pools and estimate reactivities (SHAPE-Seq). The use of next-generation sequencing allows for higher throughput, more consistent data analysis, and multiplexing capabilities. The technique described herein, SHAPE-Seq v2.0, uses a universal reverse transcription priming site that is ligated to the RNA after SHAPE modification. The introduced priming site allows for the structural analysis of an RNA independent of its sequence.

Aging does not affect generalized postural motor learning in response to variable amplitude oscillations of the support surface.

PubMed

Van Ooteghem, Karen; Frank, James S; Allard, Fran; Horak, Fay B

2010-08-01

Postural motor learning for dynamic balance tasks has been demonstrated in healthy older adults (Van Ooteghem et al. in Exp Brain Res 199(2):185-193, 2009). The purpose of this study was to investigate the type of knowledge (general or specific) obtained with balance training in this age group and to examine whether embedding perturbation regularities within a balance task masks specific learning. Two groups of older adults maintained balance on a translating platform that oscillated with variable amplitude and constant frequency. One group was trained using an embedded-sequence (ES) protocol which contained the same 15-s sequence of variable amplitude oscillations in the middle of each trial. A second group was trained using a looped-sequence (LS) protocol which contained a 15-s sequence repeated three times to form each trial. All trials were 45 s. Participants were not informed of any repetition. To examine learning, participants performed a retention test following a 24-h delay. LS participants also completed a transfer task. Specificity of learning was examined by comparing performance for repeated versus random sequences (ES) and training versus transfer sequences (LS). Performance was measured by deriving spatial and temporal measures of whole body center of mass (COM) and trunk orientation. Both groups improved performance with practice as characterized by reduced COM displacement, improved COM-platform phase relationships, and decreased angular trunk motion. Furthermore, improvements reflected general rather than specific postural motor learning regardless of training protocol (ES or LS). This finding is similar to young adults (Van Ooteghem et al. in Exp Brain Res 187(4):603-611, 2008) and indicates that age does not influence the type of learning which occurs for balance control.

The evolution of transcriptional regulation in eukaryotes

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics.

PubMed

de Vargas Roditi, Laura; Claassen, Manfred

2015-08-01

Novel technological developments enable single cell population profiling with respect to their spatial and molecular setup. These include single cell sequencing, flow cytometry and multiparametric imaging approaches and open unprecedented possibilities to learn about the heterogeneity, dynamics and interplay of the different cell types which constitute tissues and multicellular organisms. Statistical and dynamic systems theory approaches have been applied to quantitatively describe a variety of cellular processes, such as transcription and cell signaling. Machine learning approaches have been developed to define cell types, their mutual relationships, and differentiation hierarchies shaping heterogeneous cell populations, yielding insights into topics such as, for example, immune cell differentiation and tumor cell type composition. This combination of experimental and computational advances has opened perspectives towards learning predictive multi-scale models of heterogeneous cell populations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bubble and Drop Nonlinear Dynamics experiment

NASA Technical Reports Server (NTRS)

2003-01-01

The Bubble and Drop Nonlinear Dynamics (BDND) experiment was designed to improve understanding of how the shape and behavior of bubbles respond to ultrasound pressure. By understanding this behavior, it may be possible to counteract complications bubbles cause during materials processing on the ground. This 12-second sequence came from video downlinked from STS-94, July 5 1997, MET:3/19:15 (approximate). The BDND guest investigator was Gary Leal of the University of California, Santa Barbara. The experiment was part of the space research investigations conducted during the Microgravity Science Laboratory-1R mission (STS-94, July 1-17 1997). Advanced fluid dynamics experiments will be a part of investigations plarned for the International Space Station. (189KB JPEG, 1293 x 1460 pixels; downlinked video, higher quality not available) The MPG from which this composite was made is available at http://mix.msfc.nasa.gov/ABSTRACTS/MSFC-0300163.html.

Dynamic nuclear polarization and optimal control spatial-selective 13C MRI and MRS

NASA Astrophysics Data System (ADS)

Vinding, Mads S.; Laustsen, Christoffer; Maximov, Ivan I.; Søgaard, Lise Vejby; Ardenkjær-Larsen, Jan H.; Nielsen, Niels Chr.

2013-02-01

Aimed at 13C metabolic magnetic resonance imaging (MRI) and spectroscopy (MRS) applications, we demonstrate that dynamic nuclear polarization (DNP) may be combined with optimal control 2D spatial selection to simultaneously obtain high sensitivity and well-defined spatial restriction. This is achieved through the development of spatial-selective single-shot spiral-readout MRI and MRS experiments combined with dynamic nuclear polarization hyperpolarized [1-13C]pyruvate on a 4.7 T pre-clinical MR scanner. The method stands out from related techniques by facilitating anatomic shaped region-of-interest (ROI) single metabolite signals available for higher image resolution or single-peak spectra. The 2D spatial-selective rf pulses were designed using a novel Krotov-based optimal control approach capable of iteratively fast providing successful pulse sequences in the absence of qualified initial guesses. The technique may be important for early detection of abnormal metabolism, monitoring disease progression, and drug research.

Dynamic behaviour of coastal sedimentation in the Lions Gulf. [France

NASA Technical Reports Server (NTRS)

Guy, M. (Principal Investigator)

1974-01-01

The author has identified the following significant results. A number of ERTS-1 images covering this geographical zone were studied and compared with cartographic maps, air photographs, and thermal-IR images. Old and recent sediments leave traces in the landscape which are decoded by interpreting the shapes of the clear zones forming a network against the black background representing water and humid zones. Current sedimentation and its mechanism were investigated. It had been hoped that a regular sequence of images would make it possible to follow the dynamics of the Rhone and the coastal rivers in relation to meteorological conditions. In any event only a small number of images spread over a wide period of time were obtained, and a complete study was therefore impossible. However, in comparing some of the ERTS-1 images certain thermal-IR images and information on the flow of the Rhone provided some clarification of mechanisms associated with river dynamics.

An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy

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

Li, Hua, E-mail: huli@radonc.wustl.edu; Chen, Hsin

Purpose: For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Methods: Considering the complex H&N structures andmore » ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. Results: The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28%  ±  1.46%) and margin error (0.49  ±  0.12 mm) showed good agreement between the automatic and manual results. The comparison with three other deformable model-based segmentation methods illustrated the superior shape tracking performance of the proposed method. Large interpatient variations of swallowing frequency, swallowing duration, and upper airway cross-sectional area were observed from the testing cine image sequences. Conclusions: The proposed motion tracking method can provide accurate upper airway motion tracking results, and enable automatic and quantitative identification and analysis of in-treatment H&N upper airway motion. By integrating explicit and implicit linked-shape representations within a hierarchical model-fitting process, the proposed tracking method can process complex H&N structures and low-contrast/resolution cine MRI images. Future research will focus on the improvement of method reliability, patient motion pattern analysis for providing more information on patient-specific prediction of structure displacements, and motion effects on dosimetry for better H&N motion management in radiation therapy.« less

An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy.

PubMed

Li, Hua; Chen, Hsin-Chen; Dolly, Steven; Li, Harold; Fischer-Valuck, Benjamin; Victoria, James; Dempsey, James; Ruan, Su; Anastasio, Mark; Mazur, Thomas; Gach, Michael; Kashani, Rojano; Green, Olga; Rodriguez, Vivian; Gay, Hiram; Thorstad, Wade; Mutic, Sasa

2016-08-01

For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Considering the complex H&N structures and ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28%  ±  1.46%) and margin error (0.49  ±  0.12 mm) showed good agreement between the automatic and manual results. The comparison with three other deformable model-based segmentation methods illustrated the superior shape tracking performance of the proposed method. Large interpatient variations of swallowing frequency, swallowing duration, and upper airway cross-sectional area were observed from the testing cine image sequences. The proposed motion tracking method can provide accurate upper airway motion tracking results, and enable automatic and quantitative identification and analysis of in-treatment H&N upper airway motion. By integrating explicit and implicit linked-shape representations within a hierarchical model-fitting process, the proposed tracking method can process complex H&N structures and low-contrast/resolution cine MRI images. Future research will focus on the improvement of method reliability, patient motion pattern analysis for providing more information on patient-specific prediction of structure displacements, and motion effects on dosimetry for better H&N motion management in radiation therapy.

A study on the dependence of nuclear viscosity on temperature

NASA Astrophysics Data System (ADS)

Vardaci, E.; Di Nitto, A.; Nadtochy, P. N.; La Rana, G.; Cinausero, M.; Prete, G.; Gelli, N.; Ashaduzzaman, M.; Davide, F.; Pulcini, A.; Quero, D.; Kozulin, E. M.; Knyazheva, G. N.; Itkis, I. M.

2018-05-01

Nuclear viscosity is an irreplaceable ingredient of nuclear fission collective dynamical models. It drives the exchange of energy between the collective variables and the thermal bath of single particle degrees of freedom. Its dependence on the shape and temperature is a matter of controversy. By using systems of intermediate fissility we have demonstrated in a recent study that the viscosity parameters is larger for compact shapes, and decreases for larger deformations of the fissioning system, at variance with the conclusions of the statistical model modified to include empirically viscosity and time scales. In this contribution we propose an experimental scenario to highlight the possible dependence of the viscosity from the temperature.

Effects of state recovery on creep buckling under variable loading

NASA Technical Reports Server (NTRS)

Robinson, D. N.; Arnold, S. M.

1986-01-01

Structural alloys embody internal mechanisms that allow recovery of state with varying stress and elevated temperature, i.e., they can return to a softer state following periods of hardening. Such material behavior is known to strongly influence structural response under some important thermomechanical loadings, for example, that involving thermal ratchetting. The influence of dynamic and thermal recovery on the creep buckling of a column under variable loading is investigated. The column is taken as the idealized (Shanley) sandwich column. The constitutive model, unlike the commonly employed Norton creep model, incorporates a representation of both dynamic and thermal (state) recovery. The material parameters of the constitutive model are chosen to characterize Narloy Z, a representative copper alloy used in thrust nozzle liners of reusable rocket engines. Variable loading histories include rapid cyclic unloading/reloading sequences and intermittent reductions of load for extended periods of time; these are superimposed on a constant load. The calculated results show that state recovery significantly affects creep buckling under variable loading. Structural alloys embody internal mechanisms that allow recovery of state with varying stress and time.

Learning about evolution from sequence data

NASA Astrophysics Data System (ADS)

Dayarian, Adel; Shraiman, Boris

2012-02-01

Recent advances in sequencing and in laboratory evolution experiments have made possible to obtain quantitative data on genetic diversity of populations and on the dynamics of evolution. This dynamics is shaped by the interplay between selection acting on beneficial and deleterious mutations and recombination which reshuffles genotypes. Mounting evidence suggests that natural populations harbor extensive fitness diversity, yet most of the currently available tools for analyzing polymorphism data are based on the neutral theory. Our aim is to develop methods to analyze genomic data for populations in the presence of the above-mentioned factors. We consider different evolutionary regimes - Muller's ratchet, mutation-recombination-selection balance and positive adaption rate - and revisit a number of observables considered in the nearly-neutral theory of evolution. In particular, we examine the coalescent structure in the presence of recombination and calculate quantities such as the distribution of the coalescent times along the genome, the distribution of haplotype block sizes and the correlation between ancestors of different loci along the genome. In addition, we characterize the probability and time of fixation of mutations as a function of their fitness effect.

Not spreading in reverse: The dewetting of a liquid film into a single drop

PubMed Central

Edwards, Andrew M. J.; Ledesma-Aguilar, Rodrigo; Newton, Michael I.; Brown, Carl V.; McHale, Glen

2016-01-01

Wetting and dewetting are both fundamental modes of motion of liquids on solid surfaces. They are critically important for processes in biology, chemistry, and engineering, such as drying, coating, and lubrication. However, recent progress in wetting, which has led to new fields such as superhydrophobicity and liquid marbles, has not been matched by dewetting. A significant problem has been the inability to study the model system of a uniform film dewetting from a nonwetting surface to a single macroscopic droplet—a barrier that does not exist for the reverse wetting process of a droplet spreading into a film. We report the dewetting of a dielectrophoresis-induced film into a single equilibrium droplet. The emergent picture of the full dewetting dynamics is of an initial regime, where a liquid rim recedes at constant speed and constant dynamic contact angle, followed by a relatively short exponential relaxation of a spherical cap shape. This sharply contrasts with the reverse wetting process, where a spreading droplet follows a smooth sequence of spherical cap shapes. Complementary numerical simulations and a hydrodynamic model reveal a local dewetting mechanism driven by the equilibrium contact angle, where contact line slip dominates the dewetting dynamics. Our conclusions can be used to understand a wide variety of processes involving liquid dewetting, such as drop rebound, condensation, and evaporation. In overcoming the barrier to studying single film-to-droplet dewetting, our results provide new approaches to fluid manipulation and uses of dewetting, such as inducing films of prescribed initial shapes and slip-controlled liquid retraction. PMID:27704042

Not spreading in reverse: The dewetting of a liquid film into a single drop.

PubMed

Edwards, Andrew M J; Ledesma-Aguilar, Rodrigo; Newton, Michael I; Brown, Carl V; McHale, Glen

2016-09-01

Wetting and dewetting are both fundamental modes of motion of liquids on solid surfaces. They are critically important for processes in biology, chemistry, and engineering, such as drying, coating, and lubrication. However, recent progress in wetting, which has led to new fields such as superhydrophobicity and liquid marbles, has not been matched by dewetting. A significant problem has been the inability to study the model system of a uniform film dewetting from a nonwetting surface to a single macroscopic droplet-a barrier that does not exist for the reverse wetting process of a droplet spreading into a film. We report the dewetting of a dielectrophoresis-induced film into a single equilibrium droplet. The emergent picture of the full dewetting dynamics is of an initial regime, where a liquid rim recedes at constant speed and constant dynamic contact angle, followed by a relatively short exponential relaxation of a spherical cap shape. This sharply contrasts with the reverse wetting process, where a spreading droplet follows a smooth sequence of spherical cap shapes. Complementary numerical simulations and a hydrodynamic model reveal a local dewetting mechanism driven by the equilibrium contact angle, where contact line slip dominates the dewetting dynamics. Our conclusions can be used to understand a wide variety of processes involving liquid dewetting, such as drop rebound, condensation, and evaporation. In overcoming the barrier to studying single film-to-droplet dewetting, our results provide new approaches to fluid manipulation and uses of dewetting, such as inducing films of prescribed initial shapes and slip-controlled liquid retraction.

Discrete Adjoint-Based Design Optimization of Unsteady Turbulent Flows on Dynamic Unstructured Grids

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Diskin, Boris; Yamaleev, Nail K.

2009-01-01

An adjoint-based methodology for design optimization of unsteady turbulent flows on dynamic unstructured grids is described. The implementation relies on an existing unsteady three-dimensional unstructured grid solver capable of dynamic mesh simulations and discrete adjoint capabilities previously developed for steady flows. The discrete equations for the primal and adjoint systems are presented for the backward-difference family of time-integration schemes on both static and dynamic grids. The consistency of sensitivity derivatives is established via comparisons with complex-variable computations. The current work is believed to be the first verified implementation of an adjoint-based optimization methodology for the true time-dependent formulation of the Navier-Stokes equations in a practical computational code. Large-scale shape optimizations are demonstrated for turbulent flows over a tiltrotor geometry and a simulated aeroelastic motion of a fighter jet.

Constraining properties of disintegrating exoplanets

NASA Astrophysics Data System (ADS)

Veras, D.; Carter, P. J.; Leinhardt, Z. M.; Gänsicke, B. T.

2017-09-01

Evaporating and disintegrating planets provide unique insights into chemical makeup and physical constraints. The striking variability, depth (˜10 - 60%) and shape of the photometric transit curves due to the disintegrating minor planet orbiting white dwarf WD 1145+017 has galvanised the post-main- sequence exoplanetary science community. We have performed the first tidal disruption simulations of this planetary object, and have succeeded in constraining its mass, density, eccentricity and physical nature. We illustrate how our simulations can bound these properties, and be used in the future for other exoplanetary systems.

Preliminary Results from the Application of Automated Adjoint Code Generation to CFL3D

NASA Technical Reports Server (NTRS)

Carle, Alan; Fagan, Mike; Green, Lawrence L.

1998-01-01

This report describes preliminary results obtained using an automated adjoint code generator for Fortran to augment a widely-used computational fluid dynamics flow solver to compute derivatives. These preliminary results with this augmented code suggest that, even in its infancy, the automated adjoint code generator can accurately and efficiently deliver derivatives for use in transonic Euler-based aerodynamic shape optimization problems with hundreds to thousands of independent design variables.

Isogeometric Analysis of Boundary Integral Equations

DTIC Science & Technology

2015-04-21

methods, IgA relies on Non-Uniform Rational B- splines (NURBS) [43, 46], T- splines [55, 53] or subdivision surfaces [21, 48, 51] rather than piece- wise...structural dynamics [25, 26], plates and shells [15, 16, 27, 28, 37, 22, 23], phase-field models [17, 32, 33], and shape optimization [40, 41, 45, 59...polynomials for approximating the geometry and field variables. Thus, by replacing piecewise polynomials with NURBS or T- splines , one can develop

Survivability Enhanced Run-Flat Variable Footprint Tires

DTIC Science & Technology

2010-08-17

with tire tread . By varying the thickness and geometry of the polyurethane soft layer, this unique tire -wheel assembly can generate a wide array of...carcass severely damaged/punctured, provide the same dynamic deflection as the normal pneumatic tire , and provide similar tread life. Could a tire be...be for an optimized shape. Fig 8 shows the actual process applied to a current tire . The carbon fiber was added by removing the tread , cutting

Protein denaturation in vacuo: intrinsic unfolding pathways associated with the native tertiary structure of lysozyme

NASA Astrophysics Data System (ADS)

Arteca, Gustavo A.; Tapia, O.

Using computer-simulated molecular dynamics, we study the effect of sequence mutation on the unfolding mechanism of a native fold. The system considered is the native fold of hen egg-white lysozyme, exposed to centrifugal unfolding in vacuo. This unfolding bias elicits configurational transitions that imitate the behaviour of anhydrous proteins diffusing after electrospraying from neutral-pH solutions. By changing the sequences threaded onto the native fold of lysozyme, we probe the role of disulfide bridges and the effect of a global mutation. We find that the initial denaturing steps share common characteristics for the tested sequences. Recurrent features are: (i) the presence of dumbbell conformers with significant residual secondary structure, (ii) the ubiquitous formation of hairpins and two-stranded β-sheets regardless of disulfide bridges, and (iii) an unfolding pattern where the reduction in folding complexity is highly correlated with the decrease in chain compactness. These findings appear to be intrinsic to the shape of the native fold, suggesting that similar unfolding pathways may be accessible to many protein sequences.

Faster computation of exact RNA shape probabilities.

PubMed

Janssen, Stefan; Giegerich, Robert

2010-03-01

Abstract shape analysis allows efficient computation of a representative sample of low-energy foldings of an RNA molecule. More comprehensive information is obtained by computing shape probabilities, accumulating the Boltzmann probabilities of all structures within each abstract shape. Such information is superior to free energies because it is independent of sequence length and base composition. However, up to this point, computation of shape probabilities evaluates all shapes simultaneously and comes with a computation cost which is exponential in the length of the sequence. We device an approach called RapidShapes that computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its share of Boltzmann probability. This aims at a heuristic improvement of runtime, while still computing exact probability values. Evaluating this approach and several substrategies, we find that only a small proportion of shapes have to be actually computed. For an RNA sequence of length 400, this leads, depending on the threshold, to a 10-138 fold speed-up compared with the previous complete method. Thus, probabilistic shape analysis has become feasible in medium-scale applications, such as the screening of RNA transcripts in a bacterial genome. RapidShapes is available via http://bibiserv.cebitec.uni-bielefeld.de/rnashapes

The Tc1/mariner transposable element family shapes genetic variation and gene expression in the protist Trichomonas vaginalis

PubMed Central

2014-01-01

Background Trichomonas vaginalis is the most prevalent non-viral sexually transmitted parasite. Although the protist is presumed to reproduce asexually, 60% of its haploid genome contains transposable elements (TEs), known contributors to genome variability. The availability of a draft genome sequence and our collection of >200 global isolates of T. vaginalis facilitate the study and analysis of TE population dynamics and their contribution to genomic variability in this protist. Results We present here a pilot study of a subset of class II Tc1/mariner TEs that belong to the T. vaginalis Tvmar1 family. We report the genetic structure of 19 Tvmar1 loci, their ability to encode a full-length transposase protein, and their insertion frequencies in 94 global isolates from seven regions of the world. While most of the Tvmar1 elements studied exhibited low insertion frequencies, two of the 19 loci (locus 1 and locus 9) show high insertion frequencies of 1.00 and 0.96, respectively. The genetic structuring of the global populations identified by principal component analysis (PCA) of the Tvmar1 loci is in general agreement with published data based on genotyping, showing that Tvmar1 polymorphisms are a robust indicator of T. vaginalis genetic history. Analysis of expression of 22 genes flanking 13 Tvmar1 loci indicated significantly altered expression of six of the genes next to five Tvmar1 insertions, suggesting that the insertions have functional implications for T. vaginalis gene expression. Conclusions Our study is the first in T. vaginalis to describe Tvmar1 population dynamics and its contribution to genetic variability of the parasite. We show that a majority of our studied Tvmar1 insertion loci exist at very low frequencies in the global population, and insertions are variable between geographical isolates. In addition, we observe that low frequency insertion is related to reduced or abolished expression of flanking genes. While low insertion frequencies might be expected, we identified two Tvmar1 insertion loci that are fixed across global populations. This observation indicates that Tvmar1 insertion may have differing impacts and fitness costs in the host genome and may play varying roles in the adaptive evolution of T. vaginalis. PMID:24834134

“What Women Like”: Influence of Motion and Form on Esthetic Body Perception

PubMed Central

Cazzato, Valentina; Siega, Serena; Urgesi, Cosimo

2012-01-01

Several studies have shown the distinct contribution of motion and form to the esthetic evaluation of female bodies. Here, we investigated how variations of implied motion and body size interact in the esthetic evaluation of female and male bodies in a sample of young healthy women. Participants provided attractiveness, beauty, and liking ratings for the shape and posture of virtual renderings of human bodies with variable body size and implied motion. The esthetic judgments for both shape and posture of human models were influenced by body size and implied motion, with a preference for thinner and more dynamic stimuli. Implied motion, however, attenuated the impact of extreme body size on the esthetic evaluation of body postures, while body size variations did not affect the preference for more dynamic stimuli. Results show that body form and action cues interact in esthetic perception, but the final esthetic appreciation of human bodies is predicted by a mixture of perceptual and affective evaluative components. PMID:22866044

Adaptive beam shaping by controlled thermal lensing in optical elements

NASA Astrophysics Data System (ADS)

Arain, Muzammil A.; Quetschke, Volker; Gleason, Joseph; Williams, Luke F.; Rakhmanov, Malik; Lee, Jinho; Cruz, Rachel J.; Mueller, Guido; Tanner, D. B.; Reitze, David. H.

2007-04-01

We describe an adaptive optical system for use as a tunable focusing element. The system provides adaptive beam shaping via controlled thermal lensing in the optical elements. The system is agile, remotely controllable, touch free, and vacuum compatible; it offers a wide dynamic range, aberration-free focal length tuning, and can provide both positive and negative lensing effects. Focusing is obtained through dynamic heating of an optical element by an external pump beam. The system is especially suitable for use in interferometric gravitational wave interferometers employing high laser power, allowing for in situ control of the laser modal properties and compensation for thermal lensing of the primary laser. Using CO2 laser heating of fused-silica substrates, we demonstrate a focal length variable from infinity to 4.0 m, with a slope of 0.082 diopter/W of absorbed heat. For on-axis operation, no higher-order modes are introduced by the adaptive optical element. Theoretical modeling of the induced optical path change and predicted thermal lens agrees well with measurement.

Adaptive beam shaping by controlled thermal lensing in optical elements.

PubMed

Arain, Muzammil A; Quetschke, Volker; Gleason, Joseph; Williams, Luke F; Rakhmanov, Malik; Lee, Jinho; Cruz, Rachel J; Mueller, Guido; Tanner, D B; Reitze, David H

2007-04-20

We describe an adaptive optical system for use as a tunable focusing element. The system provides adaptive beam shaping via controlled thermal lensing in the optical elements. The system is agile, remotely controllable, touch free, and vacuum compatible; it offers a wide dynamic range, aberration-free focal length tuning, and can provide both positive and negative lensing effects. Focusing is obtained through dynamic heating of an optical element by an external pump beam. The system is especially suitable for use in interferometric gravitational wave interferometers employing high laser power, allowing for in situ control of the laser modal properties and compensation for thermal lensing of the primary laser. Using CO(2) laser heating of fused-silica substrates, we demonstrate a focal length variable from infinity to 4.0 m, with a slope of 0.082 diopter/W of absorbed heat. For on-axis operation, no higher-order modes are introduced by the adaptive optical element. Theoretical modeling of the induced optical path change and predicted thermal lens agrees well with measurement.

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

PubMed Central

Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J.

2013-01-01

Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. Conclusions/Significance To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide. PMID:23805195

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region.

PubMed

Alfonso-Morales, Abdulahi; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J

2013-01-01

Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

Optimization of the working process of the axial compressor according to the criterion of efficiency

NASA Astrophysics Data System (ADS)

Baturin, O. V.; Popov, G. M.; Goryachkin, E. S.; Novikova, Yu D.

2017-01-01

The paper shows search results of the optimal shape of low pressure compressor blades of the industrial gas turbine plant using methods of computational fluid dynamics and multicriteria methods of mathematical optimization. The essence of the methods is that an increase in compressor efficiency should be achieved by increasing the degree of compression up to 2%, and reducing the air flow to 8% relative to basic engine parameters. However, the compressor design elements should be retained as maximally unchanged as possible. During the work, the calculation model of the workflow in the test compressor has been developed and verified in the NUMECA software package, the automated algorithm of the blades shape change has been also developed using a small number of variables, while maintaining its stress-strain state. It allows reducing the number of changeable variables more than twofold. As the result of this study, the option of compressor performance was found, which can increase its efficiency by 1.3% (abs.).

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

PubMed

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

PubMed Central

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D.; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem. PMID:29093705

Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of ustilago.

PubMed

Menzies, J G; Bakkeren, G; Matheson, F; Procunier, J D; Woods, S

2003-02-01

ABSTRACT In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

A procedure for damage detection and localization of framed buildings based on curvature variation

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Carlo Ponzo, Felice; Auletta, Gianluca; Iacovino, Chiara; Mossucca, Antonello; Nigro, Domenico; Nigro, Antonella

2014-05-01

Structural Health Monitoring and Damage Detection are topics of current interest in civil, mechanical and aerospace engineering. Damage Detection approach based on dynamic monitoring of structural properties over time has received a considerable attention in recent scientific literature of the last years. The basic idea arises from the observation that spectral properties, described in terms of the so-called modal parameters (eigenfrequencies, mode shapes, and modal damping), are functions of the physical properties of the structure (mass, energy dissipation mechanisms and stiffness). Structural damage exhibits its main effects in terms of stiffness and damping variation. As a consequence, a permanent dynamic monitoring system makes it possible to detect and, if suitably concentrated on the structure, to localize structural and non-structural damage occurred on the structure during a strong earthquake. In the last years many researchers are working to set-up new methodologies for Non-destructive Damage Evaluation (NDE) based on the variation of the dynamic behaviour of structures under seismic loads. Pandey et al. (1991) highlighted on the possibility to use the structural mode shapes to extract useful information for structural damage localization. In this paper a new procedure for damage detection on framed structures based on changes in modal curvature is proposed. The proposed approach is based on the use of Stockwell Transform, a special kind of integral transformation that become a powerful tool for nonlinear signal analysis and then to analyse the nonlinear behaviour of a general structure. Using this kind of approach, it is possible to use a band-variable filter (Ditommaso et al., 2012) to extract from a signal recorded on a structure (excited by an earthquake) the response related to a single mode of vibration for which the related frequency changes over time (if the structure is being damaged). İn general, by acting simultaneously in both frequency and time domain, it is possible to use the band-variable filter to extract the dynamic characteristics of a system that evolves over time. Aim of this paper is to show, through practical examples, how it is possible to identify and to localize damage on a structure comparing mode shapes and the related curvature variations over time. It is possible to demonstrate that mode curvature variation is strongly related with the damage occurred on a structure. This paper resumes the main outcomes retrieved from many numerical non linear dynamic models of reinforced concrete framed structures characterized by different geometric configurations and designed for gravity loads only. The numerical campaign was conducted using both natural and artificial accelerograms compatible with the Italian code. The main results of experimental shaking table tests carried out on a steel framed model are also showed to confirm the effectiveness of the proposed procedure. REFERENCES Ditommaso R., Mucciarelli M., Ponzo F. C. (2012). Analysis of non-stationary structural systems by using a band-variable filter. Bulletin of Earthquake Engineering. Volume 10, Number 3, pp. 895-911. DOI: 10.1007/s10518-012-9338-y. Pandey AK, Biswas M, Samman MM (1991) "Damage detection from changes in curvature mode shapes", Journal of Sound and Vibration, Vol. 145: Issue 2, pp. 321-332.

Asymmetric multiscale multifractal analysis of wind speed signals

NASA Astrophysics Data System (ADS)

Zhang, Xiaonei; Zeng, Ming; Meng, Qinghao

We develop a new method called asymmetric multiscale multifractal analysis (A-MMA) to explore the multifractality and asymmetric autocorrelations of the signals with a variable scale range. Three numerical experiments are provided to demonstrate the effectiveness of our approach. Then, the proposed method is applied to investigate multifractality and asymmetric autocorrelations of difference sequences between wind speed fluctuations with uptrends or downtrends. The results show that these sequences appear to be far more complex and contain abundant fractal dynamics information. Through analyzing the Hurst surfaces of nine difference sequences, we found that all series exhibit multifractal properties and multiscale structures. Meanwhile, the asymmetric autocorrelations are observed in all variable scale ranges and the asymmetry results are of good consistency within a certain spatial range. The sources of multifractality and asymmetry in nine difference series are further discussed using the corresponding shuffled series and surrogate series. We conclude that the multifractality of these series is due to both long-range autocorrelation and broad probability density function, but the major source of multifractality is long-range autocorrelation, and the source of asymmetry is affected by the spatial distance.

In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure.

PubMed

Chertkova, Aleksandra A; Schiffman, Joshua S; Nuzhdin, Sergey V; Kozlov, Konstantin N; Samsonova, Maria G; Gursky, Vitaly V

2017-02-07

Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. We simulate the evolution of regulatory sequences involved in Drosophila melanogaster embryo segmentation during early development. Natural selection evaluates gene expression dynamics produced by a computational model of the developmental network. We observe a dramatic decrease in the total number of transcription factor binding sites through the course of evolution. Despite a decrease in average sequence binding energies through time, the regulatory sequences tend towards organisations containing increased high affinity transcription factor binding sites. Additionally, the binding energies of separate sequence segments demonstrate ubiquitous mutual correlations through time. Fewer than 10% of initial TFBSs are maintained throughout the entire simulation, deemed 'core' sites. These sites have increased functional importance as assessed under wild-type conditions and their binding energy distributions are highly conserved. Furthermore, TFBSs within close proximity of core sites exhibit increased longevity, reflecting functional regulatory interactions with core sites. In response to elevated mutational pressure, evolution tends to sample regulatory sequence organisations with fewer, albeit on average, stronger functional transcription factor binding sites. These organisations are also shaped by the regulatory interactions among core binding sites with sites in their local vicinity.

Soliton interactions and Bäcklund transformation for a (2+1)-dimensional variable-coefficient modified Kadomtsev-Petviashvili equation in fluid dynamics

NASA Astrophysics Data System (ADS)

Xiao, Zi-Jian; Tian, Bo; Sun, Yan

2018-01-01

In this paper, we investigate a (2+1)-dimensional variable-coefficient modified Kadomtsev-Petviashvili (mKP) equation in fluid dynamics. With the binary Bell-polynomial and an auxiliary function, bilinear forms for the equation are constructed. Based on the bilinear forms, multi-soliton solutions and Bell-polynomial-type Bäcklund transformation for such an equation are obtained through the symbolic computation. Soliton interactions are presented. Based on the graphic analysis, Parametric conditions for the existence of the shock waves, elevation solitons and depression solitons are given, and it is shown that under the condition of keeping the wave vectors invariable, the change of α(t) and β(t) can lead to the change of the solitonic velocities, but the shape of each soliton remains unchanged, where α(t) and β(t) are the variable coefficients in the equation. Oblique elastic interactions can exist between the (i) two shock waves, (ii) two elevation solitons, and (iii) elevation and depression solitons. However, oblique interactions between (i) shock waves and elevation solitons, (ii) shock waves and depression solitons are inelastic.

Structural imprints in vivo decode RNA regulatory mechanisms

PubMed Central

Spitale, Robert C.; Flynn, Ryan A.; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y.; Batista, Pedro J.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.

2015-01-01

Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program1. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles view only two of four nucleotides that make up RNA2,3. Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding proteins or RNA modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression. PMID:25799993

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

PubMed Central

Chiri, Eleonora; Nauer, Philipp A.; Rainer, Edda-Marie; Zeyer, Josef

2017-01-01

ABSTRACT Glacier forefield soils can provide a substantial sink for atmospheric CH4, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH4 uptake rates ranging from −3.7 to −0.03 mg CH4 m−2 day−1. Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH4 inventories. IMPORTANCE Oxidation of methane (CH4) in well-drained, “upland” soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH4 inventories. PMID:28687652

High temporal and spatial variability of atmospheric-methane oxidation in Alpine glacier-forefield soils.

PubMed

Chiri, Eleonora; Nauer, Philipp A; Rainer, Edda-Marie; Zeyer, Josef; Schroth, Martin H

2017-07-07

Glacier-forefield soils can provide a substantial sink for atmospheric CH 4 , facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, location in different forefield landforms, and temporal fluctuations in soil-physical parameters. We assessed spatial and temporal variability of atmospheric CH 4 oxidation in an Alpine glacier forefield during the snow-free season 2013. We quantified CH 4 flux in soils of increasing age and in different landforms (sandhill, terrace, floodplain) using soil-gas-profile and static flux-chamber methods. To determine MOB abundance and community structure, we employed pmoA -gene-based quantitative PCR and targeted-amplicon sequencing. Uptake of CH 4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH 4 uptake ranging from -0.03- -3.7 mg CH 4 m -2 d -1 Floodplain and terrace soils exhibited smaller uptake and even intermittent CH 4 emissions. Linear mixed-effect models indicated that soil age and landform were dominating factors shaping CH 4 flux, followed by cumulative rainfall (weighted sum ≤ 4 d prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with Upland Soil Clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical, but differed significantly from highly variable sandhill-soil communities. We conclude that soil age and landform modulate the soil CH 4 sink strength in glacier forefields, and recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH 4 inventories. Importance Oxidation of methane (CH 4 ) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric CH 4 oxidation in mature upland soils, little is known about this important function in young, developing soils such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat.In this field-based study we investigated spatial and temporal variability of atmospheric CH 4 oxidation and associated MOB communities in Alpine glacier-forefield soils, aiming at better understanding factors that shape the sink for atmospheric CH 4 in this young soil ecosystem. The study contributes to the knowledge on the dynamics of atmospheric CH 4 oxidation in developing upland soils, and represents a further step towards the inclusion of Alpine glacier-forefield soils in global CH 4 inventories. Copyright © 2017 American Society for Microbiology.

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation.

PubMed

Zhao, Shancen; Zheng, Pingping; Dong, Shanshan; Zhan, Xiangjiang; Wu, Qi; Guo, Xiaosen; Hu, Yibo; He, Weiming; Zhang, Shanning; Fan, Wei; Zhu, Lifeng; Li, Dong; Zhang, Xuemei; Chen, Quan; Zhang, Hemin; Zhang, Zhihe; Jin, Xuelin; Zhang, Jinguo; Yang, Huanming; Wang, Jian; Wang, Jun; Wei, Fuwen

2013-01-01

The panda lineage dates back to the late Miocene and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.

Revealing glacier flow and surge dynamics from animated satellite image sequences: examples from the Karakoram

NASA Astrophysics Data System (ADS)

Paul, F.

2015-11-01

Although animated images are very popular on the internet, they have so far found only limited use for glaciological applications. With long time series of satellite images becoming increasingly available and glaciers being well recognized for their rapid changes and variable flow dynamics, animated sequences of multiple satellite images reveal glacier dynamics in a time-lapse mode, making the otherwise slow changes of glacier movement visible and understandable to the wider public. For this study, animated image sequences were created for four regions in the central Karakoram mountain range over a 25-year time period (1990-2015) from freely available image quick-looks of orthorectified Landsat scenes. The animations play automatically in a web browser and reveal highly complex patterns of glacier flow and surge dynamics that are difficult to obtain by other methods. In contrast to other regions, surging glaciers in the Karakoram are often small (10 km2 or less), steep, debris-free, and advance for several years to decades at relatively low annual rates (about 100 m a-1). These characteristics overlap with those of non-surge-type glaciers, making a clear identification difficult. However, as in other regions, the surging glaciers in the central Karakoram also show sudden increases of flow velocity and mass waves travelling down glacier. The surges of individual glaciers are generally out of phase, indicating a limited climatic control on their dynamics. On the other hand, nearly all other glaciers in the region are either stable or slightly advancing, indicating balanced or even positive mass budgets over the past few decades.

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Equation-free and variable free modeling for complex/multiscale systems. Coarse-grained computation in science and engineering using fine-grained models

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

Kevrekidis, Ioannis G.

The work explored the linking of modern developing machine learning techniques (manifold learning and in particular diffusion maps) with traditional PDE modeling/discretization/scientific computation techniques via the equation-free methodology developed by the PI. The result (in addition to several PhD degrees, two of them by CSGF Fellows) was a sequence of strong developments - in part on the algorithmic side, linking data mining with scientific computing, and in part on applications, ranging from PDE discretizations to molecular dynamics and complex network dynamics.

Nearly neutral evolution in IFNL3 gene retains the immune function to detect and clear the viral infection in HCV.

PubMed

Singh, Pratichi; Dass, J Febin Prabhu

2018-05-07

IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed. The codon evolution result suggests that nearly neutral mutation is the key pattern in shaping the IFNL3 evolution. The results were validated by subjecting the human IFNL3 protein variants to that of the native through a molecular dynamics simulation study. The molecular dynamics simulation clearly depicts the negative impact on the reported variants in human IFNL3 protein. However, these detrimental mutations (R157Q and R157W) were shown to be negatively selected in the evolutionary study of the mammals. Hence, the variation revealed a mild impact on the IFNL3 function and may be removed from the population through negative selection due to its high functional constraints. In a nutshell, our study may contribute the overall evidence in phylotyping and structural transformation that takes place in the non-synonymous substitutions of IFNL3 protein. Substantially, our obtained theoretical knowledge will lay the path to extend the experimental validation in HCV clearance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Holographic photolysis of caged neurotransmitters

PubMed Central

Lutz, Christoph; Otis, Thomas S.; DeSars, Vincent; Charpak, Serge; DiGregorio, David A.; Emiliani, Valentina

2009-01-01

Stimulation of light-sensitive chemical probes has become a powerful tool for the study of dynamic signaling processes in living tissue. Classically, this approach has been constrained by limitations of lens–based and point-scanning illumination systems. Here we describe a novel microscope configuration that incorporates a nematic liquid crystal spatial light modulator (LC-SLM) to generate holographic patterns of illumination. This microscope can produce illumination spots of variable size and number and patterns shaped to precisely match user-defined elements in a specimen. Using holographic illumination to photolyse caged glutamate in brain slices, we demonstrate that shaped excitation on segments of neuronal dendrites and simultaneous, multi-spot excitation of different dendrites enables precise spatial and rapid temporal control of glutamate receptor activation. By allowing the excitation volume shape to be tailored precisely, the holographic microscope provides an extremely flexible method for activation of various photosensitive proteins and small molecules. PMID:19160517

Dynamics of anisotropic particles under waves

NASA Astrophysics Data System (ADS)

Dibenedetto, Michelle; Ouellette, Nicholas; Koseff, Jeffrey

2017-11-01

We present results on anisotropic particles in wavy flows in order to gain insight into the transport and mixing of microplastic particles in the near-shore environment. From theory and numerical simulations, we find that the rate of alignment of the particles is not constant and depends strongly on their initial orientation; thus, variations in initial particle orientation result in dispersion of anisotropic-particle plumes. We find that this dispersion is a function of the particle's eccentricity and the ratio of the settling and wave time scales. Experiments in which non-spherical particles of various shapes are released under surface gravity waves were also performed. Our main goal is to explore the effects of particle shape under various wave scenarios. We vary the aspect ratio of the particle in our experiments while holding other variables constant. Our results demonstrate that particle shape can be important when predicting transport.

Accuracy and variability of tumor burden measurement on multi-parametric MRI

NASA Astrophysics Data System (ADS)

Salarian, Mehrnoush; Gibson, Eli; Shahedi, Maysam; Gaed, Mena; Gómez, José A.; Moussa, Madeleine; Romagnoli, Cesare; Cool, Derek W.; Bastian-Jordan, Matthew; Chin, Joseph L.; Pautler, Stephen; Bauman, Glenn S.; Ward, Aaron D.

2014-03-01

Measurement of prostate tumour volume can inform prognosis and treatment selection, including an assessment of the suitability and feasibility of focal therapy, which can potentially spare patients the deleterious side effects of radical treatment. Prostate biopsy is the clinical standard for diagnosis but provides limited information regarding tumour volume due to sparse tissue sampling. A non-invasive means for accurate determination of tumour burden could be of clinical value and an important step toward reduction of overtreatment. Multi-parametric magnetic resonance imaging (MPMRI) is showing promise for prostate cancer diagnosis. However, the accuracy and inter-observer variability of prostate tumour volume estimation based on separate expert contouring of T2-weighted (T2W), dynamic contrastenhanced (DCE), and diffusion-weighted (DW) MRI sequences acquired using an endorectal coil at 3T is currently unknown. We investigated this question using a histologic reference standard based on a highly accurate MPMRIhistology image registration and a smooth interpolation of planimetric tumour measurements on histology. Our results showed that prostate tumour volumes estimated based on MPMRI consistently overestimated histological reference tumour volumes. The variability of tumour volume estimates across the different pulse sequences exceeded interobserver variability within any sequence. Tumour volume estimates on DCE MRI provided the lowest inter-observer variability and the highest correlation with histology tumour volumes, whereas the apparent diffusion coefficient (ADC) maps provided the lowest volume estimation error. If validated on a larger data set, the observed correlations could support the development of automated prostate tumour volume segmentation algorithms as well as correction schemes for tumour burden estimation on MPMRI.

Global Weirding? - Using Very Large Ensembles and Extreme Value Theory to assess Changes in Extreme Weather Events Today

NASA Astrophysics Data System (ADS)

Otto, F. E. L.; Mitchell, D.; Sippel, S.; Black, M. T.; Dittus, A. J.; Harrington, L. J.; Mohd Saleh, N. H.

2014-12-01

A shift in the distribution of socially-relevant climate variables such as daily minimum winter temperatures and daily precipitation extremes, has been attributed to anthropogenic climate change for various mid-latitude regions. However, while there are many process-based arguments suggesting also a change in the shape of these distributions, attribution studies demonstrating this have not currently been undertaken. Here we use a very large initial condition ensemble of ~40,000 members simulating the European winter 2013/2014 using the distributed computing infrastructure under the weather@home project. Two separate scenarios are used:1. current climate conditions, and 2. a counterfactual scenario of "world that might have been" without anthropogenic forcing. Specifically focusing on extreme events, we assess how the estimated parameters of the Generalized Extreme Value (GEV) distribution vary depending on variable-type, sampling frequency (daily, monthly, …) and geographical region. We find that the location parameter changes for most variables but, depending on the region and variables, we also find significant changes in scale and shape parameters. The very large ensemble allows, furthermore, to assess whether such findings in the fitted GEV distributions are consistent with an empirical analysis of the model data, and whether the most extreme data still follow a known underlying distribution that in a small sample size might otherwise be thought of as an out-lier. The ~40,000 member ensemble is simulated using 12 different SST patterns (1 'observed', and 11 best guesses of SSTs with no anthropogenic warming). The range in SSTs, along with the corresponding changings in the NAO and high-latitude blocking inform on the dynamics governing some of these extreme events. While strong tele-connection patterns are not found in this particular experiment, the high number of simulated extreme events allows for a more thorough analysis of the dynamics than has been performed before. Therefore, combining extreme value theory with very large ensemble simulations allows us to understand the dynamics of changes in extreme events which is not possible just using the former but also shows in which cases statistics combined with smaller ensembles give as valid results as very large initial conditions.

Implementation into earthquake sequence simulations of a rate- and state-dependent friction law incorporating pressure solution creep

NASA Astrophysics Data System (ADS)

Noda, H.

2016-05-01

Pressure solution creep (PSC) is an important elementary process in rock friction at high temperatures where solubilities of rock-forming minerals are significantly large. It significantly changes the frictional resistance and enhances time-dependent strengthening. A recent microphysical model for PSC-involved friction of clay-quartz mixtures, which can explain a transition between dilatant and non-dilatant deformation (d-nd transition), was modified here and implemented in dynamic earthquake sequence simulations. The original model resulted in essentially a kind of rate- and state-dependent friction (RSF) law, but assumed a constant friction coefficient for clay resulting in zero instantaneous rate dependency in the dilatant regime. In this study, an instantaneous rate dependency for the clay friction coefficient was introduced, consistent with experiments, resulting in a friction law suitable for earthquake sequence simulations. In addition, a term for time-dependent strengthening due to PSC was added which makes the friction law logarithmically rate-weakening in the dilatant regime. The width of the zone in which clasts overlap or, equivalently, the interface porosity involved in PSC plays a role as the state variable. Such a concrete physical meaning of the state variable is a great advantage in future modelling studies incorporating other physical processes such as hydraulic effects. Earthquake sequence simulations with different pore pressure distributions demonstrated that excess pore pressure at depth causes deeper rupture propagation with smaller slip per event and a shorter recurrence interval. The simulated ruptures were arrested a few kilometres below the point of pre-seismic peak stress at the d-nd transition and did not propagate spontaneously into the region of pre-seismic non-dilatant deformation. PSC weakens the fault against slow deformation and thus such a region cannot produce a dynamic stress drop. Dynamic rupture propagation further down to brittle-plastic transition, evidenced by geological observations, would require even smaller frictional resistance at coseismic slip rate, suggesting the importance of implementation of dynamic weakening activated at coseismic slip rates for more realistic simulation of earthquake sequences. The present models produced much smaller afterslip at deeper parts of arrested ruptures than those with logarithmic RSF laws because of a more significant rate-strengthening effect due to linearly viscous PSC. Detailed investigation of afterslip would give a clue to understand the deformation mechanism which controls shear resistance of the fault in a region of arrest of earthquake ruptures.

Internally generated hippocampal sequences as a vantage point to probe future-oriented cognition.

PubMed

Pezzulo, Giovanni; Kemere, Caleb; van der Meer, Matthijs A A

2017-05-01

Information processing in the rodent hippocampus is fundamentally shaped by internally generated sequences (IGSs), expressed during two different network states: theta sequences, which repeat and reset at the ∼8 Hz theta rhythm associated with active behavior, and punctate sharp wave-ripple (SWR) sequences associated with wakeful rest or slow-wave sleep. A potpourri of diverse functional roles has been proposed for these IGSs, resulting in a fragmented conceptual landscape. Here, we advance a unitary view of IGSs, proposing that they reflect an inferential process that samples a policy from the animal's generative model, supported by hippocampus-specific priors. The same inference affords different cognitive functions when the animal is in distinct dynamical modes, associated with specific functional networks. Theta sequences arise when inference is coupled to the animal's action-perception cycle, supporting online spatial decisions, predictive processing, and episode encoding. SWR sequences arise when the animal is decoupled from the action-perception cycle and may support offline cognitive processing, such as memory consolidation, the prospective simulation of spatial trajectories, and imagination. We discuss the empirical bases of this proposal in relation to rodent studies and highlight how the proposed computational principles can shed light on the mechanisms of future-oriented cognition in humans. © 2017 New York Academy of Sciences.

Reconfigurable and responsive droplet-based compound micro-lenses.

PubMed

Nagelberg, Sara; Zarzar, Lauren D; Nicolas, Natalie; Subramanian, Kaushikaram; Kalow, Julia A; Sresht, Vishnu; Blankschtein, Daniel; Barbastathis, George; Kreysing, Moritz; Swager, Timothy M; Kolle, Mathias

2017-03-07

Micro-scale optical components play a crucial role in imaging and display technology, biosensing, beam shaping, optical switching, wavefront-analysis, and device miniaturization. Herein, we demonstrate liquid compound micro-lenses with dynamically tunable focal lengths. We employ bi-phase emulsion droplets fabricated from immiscible hydrocarbon and fluorocarbon liquids to form responsive micro-lenses that can be reconfigured to focus or scatter light, form real or virtual images, and display variable focal lengths. Experimental demonstrations of dynamic refractive control are complemented by theoretical analysis and wave-optical modelling. Additionally, we provide evidence of the micro-lenses' functionality for two potential applications-integral micro-scale imaging devices and light field display technology-thereby demonstrating both the fundamental characteristics and the promising opportunities for fluid-based dynamic refractive micro-scale compound lenses.

Reconfigurable and responsive droplet-based compound micro-lenses

PubMed Central

Nagelberg, Sara; Zarzar, Lauren D.; Nicolas, Natalie; Subramanian, Kaushikaram; Kalow, Julia A.; Sresht, Vishnu; Blankschtein, Daniel; Barbastathis, George; Kreysing, Moritz; Swager, Timothy M.; Kolle, Mathias

2017-01-01

Micro-scale optical components play a crucial role in imaging and display technology, biosensing, beam shaping, optical switching, wavefront-analysis, and device miniaturization. Herein, we demonstrate liquid compound micro-lenses with dynamically tunable focal lengths. We employ bi-phase emulsion droplets fabricated from immiscible hydrocarbon and fluorocarbon liquids to form responsive micro-lenses that can be reconfigured to focus or scatter light, form real or virtual images, and display variable focal lengths. Experimental demonstrations of dynamic refractive control are complemented by theoretical analysis and wave-optical modelling. Additionally, we provide evidence of the micro-lenses' functionality for two potential applications—integral micro-scale imaging devices and light field display technology—thereby demonstrating both the fundamental characteristics and the promising opportunities for fluid-based dynamic refractive micro-scale compound lenses. PMID:28266505

Characterizing phenological vegetation dynamics amidst extreme climate variability in Australia with MODIS VI data

NASA Astrophysics Data System (ADS)

Broich, M.; Huete, A. R.; Xuanlon, M.; Davies, K.; Restrepo-Coupe, N.; Ratana, P.

2012-12-01

Australia's climate is extremely variable with inter-annual rainfall at any given site varying by 5- or 6-fold or more, across the continent. In addition to such inter-annual variability, there can be significant intra-annual variability, especially in monsoonal Australia (e.g. the wet tropical savannas) and Mediterranean climates in SW Australia where prolonged dry seasons occur each year. This presents unique challenges to the characterization of seasonal dynamics with satellite datasets. In contrast to annual reoccurring temperature-driven phenology of northern hemisphere mid-latitudes, vegetation dynamics of the vast and dry Australian interior are poorly quantified by existing remote sensing products. For example, in the current global-based MODIS phenology product, central Australia is covered by ~30% fill values for any given year. Two challenges are specific to Australian landscapes: first, the difficulty of characterizing seasonality of rainfall-driven ecosystems in interior Australia where duration and magnitude of green-up and brown down cycles show high inter annual variability; second, modeling two phenologic layers, the trees and the grass in savannas were the trees are evergreen but the herbaceous understory varies with rainfall. Savannas cover >50% of Australia. Australia's vegetation and climate are different from other continents. A MODIS phenology product capable of characterizing vegetation dynamics across the continent is being developed in this research as part of the AusCover national expert network aiming to provide Australian biophysical remote sensing data time-series and continental-scale map products. These products aim to support the Terrestrial Ecosystem Research Network (TERN) serving ecosystem research in Australia. The MODIS land surface product for Australia first searches the entire time series of each Climate Modeling Grid pixel for low-high-low extreme point sequences. A double logistic function is then fit to each of these sequences allowing identification of growth periods with different magnitudes and durations anywhere in the time series. Results show that the highest absolute variability in peak greenness occurred in cropped areas while the highest relative variability (coefficient of variation) occurred in interior Australia particularly around Lake Eyre, the center of a closed drainage basin in the dry interior of the continent. Across the desert interior, the timing of the green-up onset and the peak greenness was correlated with the landfall of cyclones and the inland penetration and strength of the north Australian summer monsoon (represented by TRMM data). The variability of Australian land surface phenology magnitude and timing was found to be strongly correlated with the swings between La Nina and El Nino events. The information on vegetation dynamics represented here is critical for land surface, fuel accumulation, agricultural production, and permanent ecosystem change modeling in relation to climate trends. A unique research opportunity is provided by recent climate variability: in 2010 a persistent El Nino has given way to a strong two-year La Nina breaking a decade long drought that was followed by record-breaking rainfall across most of the continent and extensive flooding followed by sustained greening.

Face shape differs in phylogenetically related populations.

PubMed

Hopman, Saskia M J; Merks, Johannes H M; Suttie, Michael; Hennekam, Raoul C M; Hammond, Peter

2014-11-01

3D analysis of facial morphology has delineated facial phenotypes in many medical conditions and detected fine grained differences between typical and atypical patients to inform genotype-phenotype studies. Next-generation sequencing techniques have enabled extremely detailed genotype-phenotype correlative analysis. Such comparisons typically employ control groups matched for age, sex and ethnicity and the distinction between ethnic categories in genotype-phenotype studies has been widely debated. The phylogenetic tree based on genetic polymorphism studies divides the world population into nine subpopulations. Here we show statistically significant face shape differences between two European Caucasian populations of close phylogenetic and geographic proximity from the UK and The Netherlands. The average face shape differences between the Dutch and UK cohorts were visualised in dynamic morphs and signature heat maps, and quantified for their statistical significance using both conventional anthropometry and state of the art dense surface modelling techniques. Our results demonstrate significant differences between Dutch and UK face shape. Other studies have shown that genetic variants influence normal facial variation. Thus, face shape difference between populations could reflect underlying genetic difference. This should be taken into account in genotype-phenotype studies and we recommend that in those studies reference groups be established in the same population as the individuals who form the subject of the study.

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

PubMed

Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

2015-01-01

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software for molecular evolutionary genetics analysis to visually compare the human Forkhead box/FOX protein evolution to its binding site evolution. We also compared the DNA binding signatures of human TP53 tumor suppressor determined by two different laboratory methods (SELEX and ChIP-seq). Further analysis of the entire yeast genome, center aligned at the start codon, also revealed a distinct sequence-independent 3 bp periodic pattern in information content, present only in coding region, and perhaps indicative of the non-random organization of the genetic code. TRX-LOGOS is useful in any situation in which important information content in DNA can be better visualized at the positions of phosphate linkages (i.e. dinucleotides) where the dynamic properties of the DNA backbone functions to facilitate DNA-protein interaction.

Perceptions of variability in facial emotion influence beliefs about the stability of psychological characteristics.

PubMed

Weisbuch, Max; Grunberg, Rebecca L; Slepian, Michael L; Ambady, Nalini

2016-10-01

Beliefs about the malleability versus stability of traits (incremental vs. entity lay theories) have a profound impact on social cognition and self-regulation, shaping phenomena that range from the fundamental attribution error and group-based stereotyping to academic motivation and achievement. Less is known about the causes than the effects of these lay theories, and in the current work the authors examine the perception of facial emotion as a causal influence on lay theories. Specifically, they hypothesized that (a) within-person variability in facial emotion signals within-person variability in traits and (b) social environments replete with within-person variability in facial emotion encourage perceivers to endorse incremental lay theories. Consistent with Hypothesis 1, Study 1 participants were more likely to attribute dynamic (vs. stable) traits to a person who exhibited several different facial emotions than to a person who exhibited a single facial emotion across multiple images. Hypothesis 2 suggests that social environments support incremental lay theories to the extent that they include many people who exhibit within-person variability in facial emotion. Consistent with Hypothesis 2, participants in Studies 2-4 were more likely to endorse incremental theories of personality, intelligence, and morality after exposure to multiple individuals exhibiting within-person variability in facial emotion than after exposure to multiple individuals exhibiting a single emotion several times. Perceptions of within-person variability in facial emotion-rather than perceptions of simple diversity in facial emotion-were responsible for these effects. Discussion focuses on how social ecologies shape lay theories. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Chemical and Biological Sensor Standards Study

DTIC Science & Technology

2005-01-01

that is utilized in lieu of Bacillus anthracis in testing biological agent sensors; both are gram positive, spore forming bacteria that have similar...for a given agent dosage is as follows: C = D r 3 f B Tη4π 3 ρ See the table for the variable designation. Using Bacillus anthracis as an example...e.g., genetic similarity, aerosol dynamics, size, shape, etc.) of the agent of interest. For example, Bacillus globigii is a widely used bacterium

Solute Dynamics and Imaging in the Tear Film on an Eye-shaped Domain

NASA Astrophysics Data System (ADS)

Braun, R. J.; Li, Longfei; Henshaw, William; Driscoll, Tobin; King-Smith, P. E.

2015-11-01

The concentration of ions in the tear film (osmolarity) is a key variable in understanding dry eye symptoms and disease, yet its global distribution is not available; direct measurements are restricted to a region near the temporal canthus. It has been suggested that imaging methods that use solutes such as fluorescein can be used as a proxy for estimating the osmolarity. The concentration of fluorescein is not measured directly either but the intensity as a function of concentration and thickness of the film is well established. We derived a mathematical model that couples multiple solutes and fluid dynamics within the tear film on a 2D eye-shaped domain. The model includes the physical effects of evaporation, surface tension, viscosity, ocular surface wettability, osmolarity, osmosis, fluorescence and tear fluid supply and drainage. We solved the governing system of coupled nonlinear PDEs using the Overture computational framework developed at LLNL, together with a hybrid time stepping scheme (using variable step BDF and RKC). Results of our numerical simulations provide new insight about the osmolarity distribution and its connection with images obtained in vivo over the whole ocular surface and in local regions of tear thinning due to evaporation and other effects. This work was supported in part by NSF grants 1022706 and 1412085, and NIH grant 1R01EY021794.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

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

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors.

PubMed

Mannan, Ahmad A; Liu, Di; Zhang, Fuzhong; Oyarzún, Diego A

2017-10-20

Metabolite biosensors are central to current efforts toward precision engineering of metabolism. Although most research has focused on building new biosensors, their tunability remains poorly understood and is fundamental for their broad applicability. Here we asked how genetic modifications shape the dose-response curve of biosensors based on metabolite-responsive transcription factors. Using the lac system in Escherichia coli as a model system, we built promoter libraries with variable operator sites that reveal interdependencies between biosensor dynamic range and response threshold. We developed a phenomenological theory to quantify such design constraints in biosensors with various architectures and tunable parameters. Our theory reveals a maximal achievable dynamic range and exposes tunable parameters for orthogonal control of dynamic range and response threshold. Our work sheds light on fundamental limits of synthetic biology designs and provides quantitative guidelines for biosensor design in applications such as dynamic pathway control, strain optimization, and real-time monitoring of metabolism.

Fast T1 and T2 mapping methods: the zoomed U-FLARE sequence compared with EPI and snapshot-FLASH for abdominal imaging at 11.7 Tesla.

PubMed

Pastor, Géraldine; Jiménez-González, María; Plaza-García, Sandra; Beraza, Marta; Reese, Torsten

2017-06-01

A newly adapted zoomed ultrafast low-angle RARE (U-FLARE) sequence is described for abdominal imaging applications at 11.7 Tesla and compared with the standard echo-plannar imaging (EPI) and snapshot fast low angle shot (FLASH) methods. Ultrafast EPI and snapshot-FLASH protocols were evaluated to determine relaxation times in phantoms and in the mouse kidney in vivo. Owing to their apparent shortcomings, imaging artefacts, signal-to-noise ratio (SNR), and variability in the determination of relaxation times, these methods are compared with the newly implemented zoomed U-FLARE sequence. Snapshot-FLASH has a lower SNR when compared with the zoomed U-FLARE sequence and EPI. The variability in the measurement of relaxation times is higher in the Look-Locker sequences than in inversion recovery experiments. Respectively, the average T1 and T2 values at 11.7 Tesla are as follows: kidney cortex, 1810 and 29 ms; kidney medulla, 2100 and 25 ms; subcutaneous tumour, 2365 and 28 ms. This study demonstrates that the zoomed U-FLARE sequence yields single-shot single-slice images with good anatomical resolution and high SNR at 11.7 Tesla. Thus, it offers a viable alternative to standard protocols for mapping very fast parameters, such as T1 and T2, or dynamic processes in vivo at high field.

Early glaciation already during the Early Miocene in the Amundsen Sea, Southern Pacific: Indications from the distribution of sedimentary sequences

NASA Astrophysics Data System (ADS)

Uenzelmann-Neben, Gabriele; Gohl, Karsten

2014-09-01

The distribution and internal architecture of seismostratigraphic sequences observed on the Antarctic continental slope and rise are results of sediment transport and deposition by bottom currents and ice sheets. Analysis of seismic reflection data allows to reconstruct sediment input and sediment transport patterns and to infer past changes in climate and oceanography. We observe four seismostratigraphic units which show distinct differences in location and shape of their depocentres and which accumulated at variable sedimentation rates. We used an age-depth model based on DSDP Leg 35 Site 324 for the Plio/Pleistocene and a correlation with seismic reflection characteristics from the Ross and Bellingshausen Seas, which unfortunately has large uncertainties. For the period before 21 Ma, we interpret low energy input of detritus via a palaeo-delta originating in an area of the Amundsen Sea shelf, where a palaeo-ice stream trough (Pine Island Trough East, PITE) is located today, and deposition of this material on the continental rise under sea ice coverage. For the period 21-14.1 Ma we postulate glacial erosion for the hinterland of this part of West Antarctica, which resulted in a larger depocentre and an increase in mass transport deposits. Warming during the Mid Miocene Climatic Optimum resulted in a polythermal ice sheet and led to a higher sediment supply along a broad front but with a focus via two palaeo-ice stream troughs, PITE and Abbot Trough (AT). Most of the glaciogenic debris was transported onto the eastern Amundsen Sea rise where it was shaped into levee-drifts by a re-circulating bottom current. A reduced sediment accumulation in the deep-sea subsequent to the onset of climatic cooling after 14 Ma indicates a reduced sediment supply probably in response to a colder and drier ice sheet. A dynamic ice sheet since 4 Ma delivered material offshore mainly via AT and Pine Island Trough West (PITW). Interaction of this glaciogenic detritus with a west-setting bottom current resulted in the continued formation of levee-drifts in the eastern and central Amundsen Sea.

An Avian Basal Ganglia-Forebrain Circuit Contributes Differentially to Syllable Versus Sequence Variability of Adult Bengalese Finch Song

PubMed Central

Hampton, Cara M.; Sakata, Jon T.; Brainard, Michael S.

2009-01-01

Behavioral variability is important for motor skill learning but continues to be present and actively regulated even in well-learned behaviors. In adult songbirds, two types of song variability can persist and are modulated by social context: variability in syllable structure and variability in syllable sequencing. The degree to which the control of both types of adult variability is shared or distinct remains unknown. The output of a basal ganglia-forebrain circuit, LMAN (the lateral magnocellular nucleus of the anterior nidopallium), has been implicated in song variability. For example, in adult zebra finches, neurons in LMAN actively control the variability of syllable structure. It is unclear, however, whether LMAN contributes to variability in adult syllable sequencing because sequence variability in adult zebra finch song is minimal. In contrast, Bengalese finches retain variability in both syllable structure and syllable sequencing into adulthood. We analyzed the effects of LMAN lesions on the variability of syllable structure and sequencing and on the social modulation of these forms of variability in adult Bengalese finches. We found that lesions of LMAN significantly reduced the variability of syllable structure but not of syllable sequencing. We also found that LMAN lesions eliminated the social modulation of the variability of syllable structure but did not detect significant effects on the modulation of sequence variability. These results show that LMAN contributes differentially to syllable versus sequence variability of adult song and suggest that these forms of variability are regulated by distinct neural pathways. PMID:19357331

(abstract) Synthesis of Speaker Facial Movements to Match Selected Speech Sequences

NASA Technical Reports Server (NTRS)

Scott, Kenneth C.

1994-01-01

We are developing a system for synthesizing image sequences the simulate the facial motion of a speaker. To perform this synthesis, we are pursuing two major areas of effort. We are developing the necessary computer graphics technology to synthesize a realistic image sequence of a person speaking selected speech sequences. Next, we are developing a model that expresses the relation between spoken phonemes and face/mouth shape. A subject is video taped speaking an arbitrary text that contains expression of the full list of desired database phonemes. The subject is video taped from the front speaking normally, recording both audio and video detail simultaneously. Using the audio track, we identify the specific video frames on the tape relating to each spoken phoneme. From this range we digitize the video frame which represents the extreme of mouth motion/shape. Thus, we construct a database of images of face/mouth shape related to spoken phonemes. A selected audio speech sequence is recorded which is the basis for synthesizing a matching video sequence; the speaker need not be the same as used for constructing the database. The audio sequence is analyzed to determine the spoken phoneme sequence and the relative timing of the enunciation of those phonemes. Synthesizing an image sequence corresponding to the spoken phoneme sequence is accomplished using a graphics technique known as morphing. Image sequence keyframes necessary for this processing are based on the spoken phoneme sequence and timing. We have been successful in synthesizing the facial motion of a native English speaker for a small set of arbitrary speech segments. Our future work will focus on advancement of the face shape/phoneme model and independent control of facial features.

A model of metastable dynamics during ongoing and evoked cortical activity

NASA Astrophysics Data System (ADS)

La Camera, Giancarlo

The dynamics of simultaneously recorded spike trains in alert animals often evolve through temporal sequences of metastable states. Little is known about the network mechanisms responsible for the genesis of such sequences, or their potential role in neural coding. In the gustatory cortex of alert rates, state sequences can be observed also in the absence of overt sensory stimulation, and thus form the basis of the so-called `ongoing activity'. This activity is characterized by a partial degree of coordination among neurons, sharp transitions among states, and multi-stability of single neurons' firing rates. A recurrent spiking network model with clustered topology can account for both the spontaneous generation of state sequences and the (network-generated) multi-stability. In the model, each network state results from the activation of specific neural clusters with potentiated intra-cluster connections. A mean field solution of the model shows a large number of stable states, each characterized by a subset of simultaneously active clusters. The firing rate in each cluster during ongoing activity depends on the number of active clusters, so that the same neuron can have different firing rates depending on the state of the network. Because of dense intra-cluster connectivity and recurrent inhibition, in finite networks the stable states lose stability due to finite size effects. Simulations of the dynamics show that the model ensemble activity continuously hops among the different states, reproducing the ongoing dynamics observed in the data. Moreover, when probed with external stimuli, the model correctly predicts the quenching of single neuron multi-stability into bi-stability, the reduction of dimensionality of the population activity, the reduction of trial-to-trial variability, and a potential role for metastable states in the anticipation of expected events. Altogether, these results provide a unified mechanistic model of ongoing and evoked cortical dynamics. NSF IIS-1161852, NIDCD K25-DC013557, NIDCD R01-DC010389.

Shape dynamics and Mach's principles: Gravity from conformal geometrodynamics

NASA Astrophysics Data System (ADS)

Gryb, Sean

2012-04-01

In this PhD thesis, we develop a new approach to classical gravity starting from Mach's principles and the idea that the local shape of spatial configurations is fundamental. This new theory, "shape dynamics", is equivalent to general relativity but differs in an important respect: shape dynamics is a theory of dynamic conformal 3-geometry, not a theory of spacetime. Equivalence is achieved by trading foliation invariance for local conformal invariance (up to a global scale). After the trading, what is left is a gauge theory invariant under 3d diffeomorphisms and conformal transformations that preserve the volume of space. The local canonical constraints are linear and the constraint algebra closes with structure constants. Shape dynamics, thus, provides a novel new starting point for quantum gravity. The procedure for the trading of symmetries was inspired by a technique called "best matching". We explain best matching and its relation to Mach's principles. The key features of best matching are illustrated through finite dimensional toy models. A general picture is then established where relational theories are treated as gauge theories on configuration space. Shape dynamics is then constructed by applying best matching to conformal geometry. We then study shape dynamics in more detail by computing its Hamiltonian and Hamilton-Jacobi functional perturbatively. This thesis is intended as a pedagogical but complete introduction to shape dynamics and the Machian ideas that led to its discovery. The reader is encouraged to start with the introduction, which gives a conceptual outline and links to the relevant sections in the text for a more rigorous exposition. When full rigor is lacking, references to the literature are given. It is hoped that this thesis may provide a starting point for anyone interested in learning about shape dynamics.

Dynamic and thermal response finite element models of multi-body space structural configurations

NASA Technical Reports Server (NTRS)

Edighoffer, Harold H.

1987-01-01

Presented is structural dynamics modeling of two multibody space structural configurations. The first configuration is a generic space station model of a cylindrical habitation module, two solar array panels, radiator panel, and central connecting tube. The second is a 15-m hoop-column antenna. Discussed is the special joint elimination sequence used for these large finite element models, so that eigenvalues could be extracted. The generic space station model aided test configuration design and analysis/test data correlation. The model consisted of six finite element models, one of each substructure and one of all substructures as a system. Static analysis and tests at the substructure level fine-tuned the finite element models. The 15-m hoop-column antenna is a truss column and structural ring interconnected with tension stabilizing cables. To the cables, pretensioned mesh membrane elements were attached to form four parabolic shaped antennae, one per quadrant. Imposing thermal preloads in the cables and mesh elements produced pretension in the finite element model. Thermal preload variation in the 96 control cables was adjusted to maintain antenna shape within the required tolerance and to give pointing accuracy.

The statistical mechanics of human weight change

PubMed Central

2017-01-01

Over the past 35 years there has been a near doubling in the worldwide prevalence of obesity. Body Mass Index (BMI) distributions in high-income societies have increasingly shifted rightwards, corresponding to increases in average BMI that are due to well-studied changes in the socioeconomic environment. However, in addition to this shift, BMI distributions have also shown marked changes in their particular shape over time, exhibiting an ongoing right-skewed broadening that is not well understood. Here, we compile and analyze the largest data set so far of year-over-year BMI changes. The data confirm that, on average, heavy individuals become lighter while light individuals become heavier year-over-year, and also show that year-over-year BMI evolution is characterized by fluctuations with a magnitude that is linearly proportional to BMI. We find that the distribution of human BMIs is intrinsically dynamic—due to the short-term variability of human weight—and its shape is determined by a balance between deterministic drift towards a natural set point and diffusion resulting from random fluctuations in, e.g., diet and physical activity. We formulate a stochastic mathematical model for BMI dynamics, deriving a theoretical shape for the BMI distribution and offering a mechanism that may explain the right-skewed broadening of BMI distributions over time. An extension of the base model investigates the hypothesis that peer-to-peer social influence plays a role in BMI dynamics. While including this effect improves the fit with the data, indicating that correlations in the behavior of individuals with similar BMI may be important for BMI dynamics, testing social transmission against other plausible unmodeled effects and interpretations remains the subject of future work. Implications of our findings on the dynamics of BMI distributions for public health interventions are discussed. PMID:29253025

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

PubMed Central

Ho, Cynthia K. Y.; Raghwani, Jayna; Koekkoek, Sylvie; Liang, Richard H.; Van der Meer, Jan T. M.; Van Der Valk, Marc; De Jong, Menno; Pybus, Oliver G.

2016-01-01

ABSTRACT In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms. IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations. PMID:28077634

Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae.

PubMed

Jeon, Junhyun; Choi, Jaeyoung; Lee, Gir-Won; Dean, Ralph A; Lee, Yong-Hwan

2013-01-01

Knowledge on mutation processes is central to interpreting genetic analysis data as well as understanding the underlying nature of almost all evolutionary phenomena. However, studies on genome-wide mutational spectrum and dynamics in fungal pathogens are scarce, hindering our understanding of their evolution and biology. Here, we explored changes in the phenotypes and genome sequences of the rice blast fungus Magnaporthe oryzae during the forced in vitro evolution by weekly transfer of cultures on artificial media. Through combination of experimental evolution with high throughput sequencing technology, we found that mutations accumulate rapidly prior to visible phenotypic changes and that both genetic drift and selection seem to contribute to shaping mutational landscape, suggesting the buffering capacity of fungal genome against mutations. Inference of mutational effects on phenotypes through the use of T-DNA insertion mutants suggested that at least some of the DNA sequence mutations are likely associated with the observed phenotypic changes. Furthermore, our data suggest oxidative damages and UV as major sources of mutation during subcultures. Taken together, our work revealed important properties of original source of variation in the genome of the rice blast fungus. We believe that these results provide not only insights into stability of pathogenicity and genome evolution in plant pathogenic fungi but also a model in which evolution of fungal pathogens in natura can be comparatively investigated.

A microcosm of musical expression: II. Quantitative analysis of pianists' dynamics in the initial measures of Chopin's Etude in E major.

PubMed

Repp, B H

1999-03-01

Patterns of expressive dynamics were measured in bars 1-5 of 115 commercially recorded performances of Chopin's Etude in E major, op. 10, No. 3. The grand average pattern (or dynamic profile) was representative of many performances and highly similar to the average dynamic profile of a group of advanced student performances, which suggests a widely shared central norm of expressive dynamics. The individual dynamic profiles were subjected to principal components analysis, which yielded Varimax-rotated components, each representing a different, nonstandard dynamic profile associated with a small subset of performances. Most performances had dynamic patterns resembling a mixture of several components, and no clustering of of performances into distinct groups was apparent. Some weak relationships of dynamic profiles with sociocultural variables were found, most notably a tendency of female pianists to exhibit a greater dynamic range in the melody. Within the melody, there were no significant relationships between expressive timing [Repp, J. Acoust. Soc. Am. 104, 1085-1100 (1998)] and expressive dynamics. These two important dimensions seemed to be controlled independently at this local level and thus offer the artist many degrees of freedom in giving a melody expressive shape.

From metadynamics to dynamics.

PubMed

Tiwary, Pratyush; Parrinello, Michele

2013-12-06

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

From Metadynamics to Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; Parrinello, Michele

2013-12-01

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

Interdisciplinary approach to exploit the tectonic memory in the continental crust of collisional belts.

NASA Astrophysics Data System (ADS)

Gosso, G.; Marotta, A. M.; Rebay, G.; Regorda, A.; Roda, M.; Spalla, M. I.; Zanoni, D.; Zucali, M.

2015-12-01

Collisional belts result by thoroughly competing thermo-mechanical disaggregation and coupling within both continental and oceanic lithospheric slices, during construction of tectono-metamorphic architectures. In multiply reworked metamorphics, tectonic units may be contoured nowadays on the base of coherent thermo-baric and structural time-sequences rather than simply relying on lithologic affinities. Sequences of equilibrium assemblages and related fabric imprints are an approach that appears as a more reliable procedure, that enables to define tectonic units as the volume of crustal slices that underwent corresponding variations during the dynamics of an active margin and takes into account a history of physical imprints. The dimensions of these tectonic units may have varied over time and must be reconstructed combining the tracers of structural and metamorphic changes of basement rocks, since such kind of tectono-metamorphic units (TMUs) is a realistic configuration of the discrete portions of orogenic crust that experienced a coherent sequence of metamorphic and textural variations. Their translational trajectories, and bulk shape changes during deformation, cannot simply be derived from the analysis of the geometries and kinematics of tectonic units, but are to be obtained by adding the reconstruction of quantitative P-T-d-t paths making full use of fossil mineral equilibria. The joint TMU field-and-laboratory definition is an investigation procedure that bears a distinct thermo-tectonic connotation, that, through modelling, offers the opportunity to test the physical compatibilities of plate-scale interconnected variables, such as density, viscosity, and heat transfer, with respect to what current interpretative geologic histories may imply. Comparison between predictions from numerical modelling and natural data obtained by this analytical approach can help to solve ambiguities on geodynamic significance of structural and thermal signatures, also as a function of tectonic rate of simulated convergent or divergent kinematics. In addition the estimate of structurally and mineral-chemically re-equilibrated volumes assists the choice of physical parameters selected to constrain numerical models.

Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae).

PubMed

Yano, C F; Bertollo, L A C; Ezaz, T; Trifonov, V; Sember, A; Liehr, T; Cioffi, M B

2017-03-01

The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15-25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.

Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance.

PubMed

Patel, Seema

2016-11-01

Despite the advent of next-generation sequencing (NGS) technologies, sophisticated data analysis and drug development efforts, bacterial drug resistance persists and is escalating in magnitude. To better control the pathogens, a thorough understanding of their genomic architecture and dynamics is vital. Bacterial genome is extremely complex, a mosaic of numerous co-operating and antagonizing components, altruistic and self-interested entities, behavior of which are predictable and conserved to some extent, yet largely dictated by an array of variables. In this regard, mobile genetic elements (MGE), DNA repair systems, post-segregation killing systems, toxin-antitoxin (TA) systems, restriction-modification (RM) systems etc. are dominant agents and horizontal gene transfer (HGT), gene redundancy, epigenetics, phase and antigenic variation etc. processes shape the genome. By illegitimate recombinations, deletions, insertions, duplications, amplifications, inversions, conversions, translocations, modification of intergenic regions and other alterations, bacterial genome is modified to tackle stressors like drugs, and host immune effectors. Over the years, thousands of studies have investigated this aspect and mammoth amount of insights have been accumulated. This review strives to distillate the existing information, formulate hypotheses and to suggest directions, that might contribute towards improved mitigation of the vicious pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantification of tumor mobility during the breathing cycle using 3D dynamic MRI

NASA Astrophysics Data System (ADS)

Schoebinger, Max; Plathow, Christian; Wolf, Ivo; Kauczor, Hans-Ulrich; Meinzer, Hans-Peter

2006-03-01

Respiration causes movement and shape changes in thoracic tumors, which has a direct influence on the radio-therapy planning process. Current methods for the estimation of tumor mobility are either two-dimensional (fluoroscopy, 2D dynamic MRI) or based on radiation (3D (+t) CT, implanted gold markers). With current advances in dynamic MRI acquisition, 3D+t image sequences of the thorax can be acquired covering the thorax over the whole breathing cycle. In this work, methods are presented for the interactive segmentation of tumors in dynamic images, the calculation of tumor trajectories, dynamic tumor volumetry and dynamic tumor rotation/deformation based on 3D dynamic MRI. For volumetry calculation, a set of 21 related partial volume correcting volumetry algorithms has been evaluated based on tumor surrogates. Conventional volumetry based on voxel counting yielded a root mean square error of 29% compared to a root mean square error of 11% achieved by the algorithm performing best among the different volumetry methods. The new workflow has been applied to a set of 26 patients. Preliminary results indicate, that 3D dynamic MRI reveals important aspects of tumor behavior during the breathing cycle. This might imply the possibility to further improve high-precision radiotherapy techniques.

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

PubMed Central

Long, Hannah K.; King, Hamish W.; Patient, Roger K.; Odom, Duncan T.; Klose, Robert J.

2016-01-01

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. PMID:27084945

An investigation of the cratering-induced motions occurring during the formation of bowl-shaped craters. [using high explosive charges as the cratering source

NASA Technical Reports Server (NTRS)

Piekutowski, A. J.

1980-01-01

The effects of the dynamic processes which occur during crater formation were examined using small hemispherical high-explosive charges detonated in a tank which had one wall constructed of a thick piece of clear plexiglas. Crater formation and the motions of numerous tracer particles installed in the cratering medium at the medium-wall interface were viewed through the wall of this quarter-space tank and recorded with high-speed cameras. Subsequent study and analysis of particle motions and events recorded on the film provide data needed to develop a time-sequence description of the formation of a bowl-shaped crater. Tables show the dimensions of craters produced in a quarter-space tank compared with dimensions of craters produced in normal half-space tanks. Crater growth rate summaries are also tabulated.

Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds.

PubMed

Chen, Rubing; Holmes, Edward C

2009-01-05

Revealing the factors that shape the genetic structure of avian influenza viruses (AIVs) in wild bird populations is essential to understanding their evolution. However, the relationship between epidemiological dynamics and patterns of genetic diversity in AIV is not well understood, especially at the continental scale. To address this question, we undertook a phylogeographic analysis of complete genome sequences of AIV sampled from wild birds in North America. In particular, we asked whether host species, geographic location or sampling time played the major role in shaping patterns of viral genetic diversity. Strikingly, our analysis revealed no strong species effect, yet a significant viral clustering by time and place of sampling, as well as the circulation of multiple viral lineages in single locations. These results suggest that AIVs can readily infect many of the bird species that share breeding/feeding areas.

Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering.

PubMed

Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel

2015-10-01

A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).

Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards.

PubMed

Mezzasalma, Valerio; Sandionigi, Anna; Guzzetti, Lorenzo; Galimberti, Andrea; Grando, Maria S; Tardaguila, Javier; Labra, Massimo

2018-01-01

Recent studies have highlighted the role of the grapevine microbiome in addressing a wide panel of features, ranging from the signature of field origin to wine quality. Although the influence of cultivar and vineyard environmental conditions in shaping the grape microbiome have already been ascertained, several aspects related to this topic, deserve to be further investigated. In this study, we selected three international diffused grapevine cultivars (Cabernet Sauvignon, Syrah, and Sauvignon Blanc) at three germplasm collections characterized by different climatic conditions [Northern Italy (NI), Italian Alps (AI), and Northern Spain (NS)]. The soil and grape microbiome was characterized by 16s rRNA High Throughput Sequencing (HTS), and the obtained results showed that all grape samples shared some bacterial taxa, regardless of sampling locality (e.g., Bacillus , Methylobacterium , Sphingomonas , and other genera belonging to Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria). However, some Operational Taxonomic Units (OTUs) could act as geographical signatures and in some cases as cultivar fingerprint. Concerning the origin of the grape microbiome, our study confirms that vineyard soil represents a primary reservoir for grape associated bacteria with almost 60% of genera shared between the soil and grape. At each locality, grapevine cultivars shared a core of bacterial genera belonging to the vineyard soil, as well as from other local biodiversity elements such as arthropods inhabiting or foraging in the vineyard. Finally, a machine learning analysis showed that it was possible to predict the geographical origin and cultivar of grape starting from its microbiome composition with a high accuracy (9 cases out of 12 tested samples). Overall, these findings open new perspectives for the development of more comprehensive and integrated research activities to test which environmental variables have an effective role in shaping the microbiome composition and dynamics of cultivated species over time and space.

The effect of two different visual presentation modalities on the narratives of mainstream grade 3 children.

PubMed

Klop, D; Engelbrecht, L

2013-12-01

This study investigated whether a dynamic visual presentation method (a soundless animated video presentation) would elicit better narratives than a static visual presentation method (a wordless picture book). Twenty mainstream grade 3 children were randomly assigned to two groups and assessed with one of the visual presentation methods. Narrative performance was measured in terms of micro- and macrostructure variables. Microstructure variables included productivity (total number of words, total number of T-units), syntactic complexity (mean length of T-unit) and lexical diversity measures (number of different words). Macrostructure variables included episodic structure in terms of goal-attempt-outcome (GAO) sequences. Both visual presentation modalities elicited narratives of similar quantity and quality in terms of the micro- and macrostructure variables that were investigated. Animation of picture stimuli did not elicit better narratives than static picture stimuli.

Benefits to decomposition rates when using digestate as compost co-feedstock: Part II - Focus on microbial community dynamics.

PubMed

Arab, Golnaz; Razaviarani, Vahid; Sheng, Zhiya; Liu, Yang; McCartney, Daryl

2017-10-01

Linkage between composting reactor performance and microbial community dynamics was investigated during co-composting of digestate and fresh feedstock (organic fraction of municipal solid waste) using 25L reactors. Previously, the relationship between composting performance and various physicochemical parameters were reported in Part I of the study (Arab and McCartney, 2017). Three digestate to fresh feedstock ratios (0, 40, and 100%; wet weight basis) were selected for analysis of microbial community dynamics. The 40% ratio was selected because it was found to perform the best (Arab and McCartney, 2017). Illumina sequencing results revealed that the reactor with a greater composting performance (higher organic matter degradation and higher heat generation; 40% ratio) was associated with higher microbial diversity. Two specific bacterial orders that might result in higher performance were Thermoactinomycetaceae and Actinomycetales with a higher sequence abundance during thermophilic composting phase and during the maturing composting phase, respectively. Galactomyces, Pichia, Chaetomium, and Acremonium were the four fungal genera that are probably also involved in higher organic matter degradation in the reactor with better performance. The redundancy analysis (RDA) biplot indicated that among the studied environmental variables, temperature, total ammonia nitrogen and nitrate concentration accounted for much of the major shifts in microbial sequence abundance during the co-composting process. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Pulsed field probe of real time magnetization dynamics in magnetic nanoparticle systems

NASA Astrophysics Data System (ADS)

Foulkes, T.; Syed, M.; Taplin, T.

2015-05-01

Magnetic nanoparticles (MNPs) are extensively used in biotechnology. These applications rely on magnetic properties that are a keen function of MNP size, distribution, and shape. Various magneto-optical techniques, including Faraday Rotation (FR), Cotton-Mouton Effect, etc., have been employed to characterize magnetic properties of MNPs. Generally, these measurements employ AC or DC fields. In this work, we describe the results from a FR setup that uses pulsed magnetic fields and an analysis technique that makes use of the entire pulse shape to investigate size distribution and shape anisotropy. The setup employs a light source, polarizing components, and a detector that are used to measure the rotation of light from a sample that is subjected to a pulsed magnetic field. This magnetic field "snapshot" is recorded alongside the intensity pulse of the sample's response. This side by side comparison yields useful information about the real time magnetization dynamics of the system being probed. The setup is highly flexible with variable control of pulse length and peak magnitude. Examining the raw data for the response of bare Fe3O4 and hybrid Au and Fe3O4 nanorods reveals interesting information about Brownian relaxation and the hydrodynamic size of these nanorods. This analysis exploits the self-referencing nature of this measurement to highlight the impact of an applied field on creating a field induced transparency for a longitudinal measurement. Possible sources for this behavior include shape anisotropy and field assisted aggregate formation.

Temporal structure of motor variability is dynamically regulated and predicts motor learning ability.

PubMed

Wu, Howard G; Miyamoto, Yohsuke R; Gonzalez Castro, Luis Nicolas; Ölveczky, Bence P; Smith, Maurice A

2014-02-01

Individual differences in motor learning ability are widely acknowledged, yet little is known about the factors that underlie them. Here we explore whether movement-to-movement variability in motor output, a ubiquitous if often unwanted characteristic of motor performance, predicts motor learning ability. Surprisingly, we found that higher levels of task-relevant motor variability predicted faster learning both across individuals and across tasks in two different paradigms, one relying on reward-based learning to shape specific arm movement trajectories and the other relying on error-based learning to adapt movements in novel physical environments. We proceeded to show that training can reshape the temporal structure of motor variability, aligning it with the trained task to improve learning. These results provide experimental support for the importance of action exploration, a key idea from reinforcement learning theory, showing that motor variability facilitates motor learning in humans and that our nervous systems actively regulate it to improve learning.

Temporal structure of motor variability is dynamically regulated and predicts motor learning ability

PubMed Central

Wu, Howard G; Miyamoto, Yohsuke R; Castro, Luis Nicolas Gonzalez; Ölveczky, Bence P; Smith, Maurice A

2015-01-01

Individual differences in motor learning ability are widely acknowledged, yet little is known about the factors that underlie them. Here we explore whether movement-to-movement variability in motor output, a ubiquitous if often unwanted characteristic of motor performance, predicts motor learning ability. Surprisingly, we found that higher levels of task-relevant motor variability predicted faster learning both across individuals and across tasks in two different paradigms, one relying on reward-based learning to shape specific arm movement trajectories and the other relying on error-based learning to adapt movements in novel physical environments. We proceeded to show that training can reshape the temporal structure of motor variability, aligning it with the trained task to improve learning. These results provide experimental support for the importance of action exploration, a key idea from reinforcement learning theory, showing that motor variability facilitates motor learning in humans and that our nervous systems actively regulate it to improve learning. PMID:24413700

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

PubMed

Sanosyan, Armen; Fayd'herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification

PubMed Central

Fayd’herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Background Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Methods Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. Results BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Conclusions Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load. PMID:28850597

Feedback tracking control for dynamic morphing of piezocomposite actuated flexible wings

NASA Astrophysics Data System (ADS)

Wang, Xiaoming; Zhou, Wenya; Wu, Zhigang

2018-03-01

Aerodynamic properties of flexible wings can be improved via shape morphing using piezocomposite materials. Dynamic shape control of flexible wings is investigated in this study by considering the interactions between structural dynamics, unsteady aerodynamics and piezo-actuations. A novel antisymmetric angle-ply bimorph configuration of piezocomposite actuators is presented to realize coupled bending-torsional shape control. The active aeroelastic model is derived using finite element method and Theodorsen unsteady aerodynamic loads. A time-varying linear quadratic Gaussian (LQG) tracking control system is designed to enhance aerodynamic lift with pre-defined trajectories. Proof-of-concept simulations of static and dynamic shape control are presented for a scaled high-aspect-ratio wing model. Vibrations of the wing and fluctuations in aerodynamic forces are caused by using the static voltages directly in dynamic shape control. The lift response has tracked the trajectories well with favorable dynamic morphing performance via feedback tracking control.

Structural analysis as an alternative to identify and determine mode of action of antimicrobial peptides: proposition of a kinetic model based on molecular dynamics studies.

PubMed

Robles-Gomez, Edson Edinho; Flores-Villegas, Mirelle Citlali; Gonzalez-Manjarrez, Alicia; Soriano-Garcia, Manuel

2013-05-01

Antimicrobial peptides (AMPs) constitute an important alternative in the search for new treatments against pathogens. We analyzed the sequence variability in cytokine and chemokine proteins to investigate whether these molecules contain a sequence useful in the development of new AMPs. Cluster analysis allowed the identification of tracts, grouped in five categories showing structure and sequence homology. The structure and function relationship among these groups, was analyzed using physicochemical parameters such as length, sequence, charge, hydrophobicity and helicity, which allowed the selection of a candidate that could constitute an AMP. This peptide comprises the C-terminal alpha-helix of chemokines CXCL4/PF-457-70. Far-UV CD spectroscopy showed that this molecule adopts a random conformation in aqueous solution and the addition of 2, 2, 2 trifluoroethanol (TFE) is required to induce a helical secondary structure. The CXCL4/PF-457-70 peptide was found to have antimicrobial activity and very limited hemolytic activity. The mechanism of action was analyzed using model kinetics and molecular dynamics. The kinetic model led to a reasonable assumption about a rate constant and regulatory step on its mechanism of action. Using molecular dynamics simulations, the structural properties the CXCL4/PF-457-70 have been examined in a membrane environment. Our results show that this peptide has a strong preference for binding to the lipid head groups, consequently, increasing the surface density and decreasing the lateral mobility of the lipids alters its functionality.

Stream Width Dynamics in a Small Headwater Catchment

NASA Astrophysics Data System (ADS)

Barefoot, E. A.; Pavelsky, T.; Allen, G. H.; Zimmer, M. A.; McGlynn, B. L.

2016-12-01

Changing streamflow conditions cause small, ephemeral and intermittent stream networks to expand and contract, while simultaneously driving widening and narrowing of streams. The resulting dynamic surface area of ephemeral streams impacts critical hydrological and biogeochemical processes, including air-water gas exchange, solute transport, and sediment transport. Despite the importance of these dynamics, to our knowledge there exists no complete study of how stream widths vary throughout an entire catchment in response to changing streamflow conditions. Here we present the first characterization of how variable hydrologic conditions impact the distribution of stream widths in a 48 ha headwater catchment in the Stony Creek Research Watershed, NC, USA. We surveyed stream widths longitudinally every 5 m on 12 occasions over a range of stream discharge from 7 L/s to 128 L/s at the catchment outlet. We hypothesize that the shape and location of the stream width distribution are driven by the action of two interrelated mechanisms, network extension and at-a-station widening, both of which increase with discharge. We observe that during very low flow conditions, network extension more significantly influences distribution location, and during high flow conditions stream widening is the dominant driver. During moderate flows, we observe an approximately 1 cm rightward shift in the distribution peak with every additional 10 L/s of increased discharge, which we attribute to a greater impact of at-a-station widening on distribution location. Aside from this small shift, the qualitative location and shape of the stream width distribution are largely invariant with changing streamflow. We suggest that the basic characteristics of stream width distributions constitute an equilibrium between the two described mechanisms across variable hydrologic conditions.

Grain Size as a Control for Melt Focusing Beneath Mid-Ocean Ridges

NASA Astrophysics Data System (ADS)

Turner, A.; Katz, R. F.; Behn, M. D.

2015-12-01

Grain size is a fundamental control on both the rheology and permeability of the mantle. These properties, in turn, affect the transport of melt beneath mid-ocean ridges. Previous models of grain size beneath ridges have considered only the single-phase problem of dynamic recrystallisation and the resultant pattern of grain-size variation [1,2]. These models have not coupled the spatially variable grain-size field to two-phase (partially molten) mechanics to investigate the implications of spatially variable grain size on melt transport. Here, we present new results from numerical models that investigate the consequences of this coupling. In our two-dimensional, two-phase model the grain-size is coupled to both the permeability and rheology. The rheology is strain-rate and grain-size dependent. For simplicity, however, the grain-size field is not computed dynamically — rather, it is imposed from a single-phase, steady-state model [1] that is based on the "wattmeter" theory [3]. Our calculations predicts that a spatially variable grain size field can promote focusing of melt towards the ridge axis. This focusing is distinct from the commonly discussed, sub-lithospheric decompaction channel [4]. Furthermore, our model predicts that the shape of the partially molten region is sensitive to rheological parameters associated with grain size. The comparison of this shape with observations [5] may help to constrain the rheology of the upper mantle beneath mid-ocean ridges. References: [1] Turner et al., Geochem. Geophys. Geosyst., 16, 925-946, 2015. [2] Behn et al., EPSL, 282, 178-189, 2009. [3] Austin and Evans, Geology, 35:343-346, 2007. [4] Sparks and Parmentier, EPSL, 105, 368-377, 1991. [5] Key et al., Nature, 495, 499-502, 2013.

A fuzzy model of superelastic shape memory alloys for vibration control in civil engineering applications

NASA Astrophysics Data System (ADS)

Ozbulut, O. E.; Mir, C.; Moroni, M. O.; Sarrazin, M.; Roschke, P. N.

2007-06-01

Two experimental test programs are conducted to collect data and simulate the dynamic behavior of CuAlBe shape memory alloy (SMA) wires. First, in order to evaluate the effect of temperature changes on superelastic SMA wires, a large number of cyclic, sinusoidal, tensile tests are performed at 1 Hz. These tests are conducted in a controlled environment at 0, 25 and 50 °C with three different strain amplitudes. Second, in order to assess the dynamic effects of the material, a series of laboratory experiments is conducted on a shake table with a scale model of a three-story structure that is stiffened with SMA wires. Data from these experiments are used to create fuzzy inference systems (FISs) that can predict hysteretic behavior of CuAlBe wire. Both fuzzy models employ a total of three input variables (strain, strain-rate, and temperature or pre-stress) and an output variable (predicted stress). Gaussian membership functions are used to fuzzify data for each of the input and output variables. Values of the initially assigned membership functions are adjusted using a neural-fuzzy procedure to more accurately predict the correct stress level in the wires. Results of the trained FISs are validated using test results from experimental records that had not been previously used in the training procedure. Finally, a set of numerical simulations is conducted to illustrate practical use of these wires in a civil engineering application. The results reveal the applicability for structural vibration control of pseudoelastic CuAlBe wire whose highly nonlinear behavior is modeled by a simple, accurate, and computationally efficient FIS.

Random bursts determine dynamics of active filaments.

PubMed

Weber, Christoph A; Suzuki, Ryo; Schaller, Volker; Aranson, Igor S; Bausch, Andreas R; Frey, Erwin

2015-08-25

Constituents of living or synthetic active matter have access to a local energy supply that serves to keep the system out of thermal equilibrium. The statistical properties of such fluctuating active systems differ from those of their equilibrium counterparts. Using the actin filament gliding assay as a model, we studied how nonthermal distributions emerge in active matter. We found that the basic mechanism involves the interplay between local and random injection of energy, acting as an analog of a thermal heat bath, and nonequilibrium energy dissipation processes associated with sudden jump-like changes in the system's dynamic variables. We show here how such a mechanism leads to a nonthermal distribution of filament curvatures with a non-Gaussian shape. The experimental curvature statistics and filament relaxation dynamics are reproduced quantitatively by stochastic computer simulations and a simple kinetic model.

Random bursts determine dynamics of active filaments

PubMed Central

Weber, Christoph A.; Suzuki, Ryo; Schaller, Volker; Aranson, Igor S.; Bausch, Andreas R.; Frey, Erwin

2015-01-01

Constituents of living or synthetic active matter have access to a local energy supply that serves to keep the system out of thermal equilibrium. The statistical properties of such fluctuating active systems differ from those of their equilibrium counterparts. Using the actin filament gliding assay as a model, we studied how nonthermal distributions emerge in active matter. We found that the basic mechanism involves the interplay between local and random injection of energy, acting as an analog of a thermal heat bath, and nonequilibrium energy dissipation processes associated with sudden jump-like changes in the system’s dynamic variables. We show here how such a mechanism leads to a nonthermal distribution of filament curvatures with a non-Gaussian shape. The experimental curvature statistics and filament relaxation dynamics are reproduced quantitatively by stochastic computer simulations and a simple kinetic model. PMID:26261319

Animation control of surface motion capture.

PubMed

Tejera, Margara; Casas, Dan; Hilton, Adrian

2013-12-01

Surface motion capture (SurfCap) of actor performance from multiple view video provides reconstruction of the natural nonrigid deformation of skin and clothing. This paper introduces techniques for interactive animation control of SurfCap sequences which allow the flexibility in editing and interactive manipulation associated with existing tools for animation from skeletal motion capture (MoCap). Laplacian mesh editing is extended using a basis model learned from SurfCap sequences to constrain the surface shape to reproduce natural deformation. Three novel approaches for animation control of SurfCap sequences, which exploit the constrained Laplacian mesh editing, are introduced: 1) space–time editing for interactive sequence manipulation; 2) skeleton-driven animation to achieve natural nonrigid surface deformation; and 3) hybrid combination of skeletal MoCap driven and SurfCap sequence to extend the range of movement. These approaches are combined with high-level parametric control of SurfCap sequences in a hybrid surface and skeleton-driven animation control framework to achieve natural surface deformation with an extended range of movement by exploiting existing MoCap archives. Evaluation of each approach and the integrated animation framework are presented on real SurfCap sequences for actors performing multiple motions with a variety of clothing styles. Results demonstrate that these techniques enable flexible control for interactive animation with the natural nonrigid surface dynamics of the captured performance and provide a powerful tool to extend current SurfCap databases by incorporating new motions from MoCap sequences.

Improved prediction of disturbed flow via hemodynamically-inspired geometric variables.

PubMed

Bijari, Payam B; Antiga, Luca; Gallo, Diego; Wasserman, Bruce A; Steinman, David A

2012-06-01

Arterial geometry has long been considered as a pragmatic alternative for inferring arterial flow disturbances, and their impact on the natural history and treatment of vascular diseases. Traditionally, definition of geometric variables is based on convenient shape descriptors, with only superficial consideration of their influence on flow and wall shear stress patterns. In the present study we demonstrate that a more studied consideration of the actual (cf. nominal) local hemodynamics can lead to substantial improvements in the prediction of disturbed flow by geometry. Starting from a well-characterized computational fluid dynamics (CFD) dataset of 50 normal carotid bifurcations, we observed that disturbed flow tended to be confined proximal to the flow divider, whereas geometric variables previously shown to be significant predictors of disturbed flow included features distal to the flow divider in their definitions. Flaring of the bifurcation leading to flow separation was redefined as the maximum relative expansion of the common carotid artery (CCA), proximal to the flow divider. The beneficial effect of primary curvature on flow inertia, via suppression of flow separation, was characterized by the in-plane tortuosity of CCA as it enters the flare region. Multiple linear regressions of these redefined geometric variables against various metrics of disturbed flow revealed R(2) values approaching 0.6, better than the roughly 0.3 achieved using the conventional shape-based variables, while maintaining their demonstrated real-world reproducibility. Such a hemodynamically-inspired approach to the definition of geometric variables may reap benefits for other applications where geometry is used as a surrogate marker of local hemodynamics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Low-noise delays from dynamic Brillouin gratings based on perfect Golomb coding of pump waves.

PubMed

Antman, Yair; Levanon, Nadav; Zadok, Avi

2012-12-15

A method for long variable all-optical delay is proposed and simulated, based on reflections from localized and stationary dynamic Brillouin gratings (DBGs). Inspired by radar methods, the DBGs are inscribed by two pumps that are comodulated by perfect Golomb codes, which reduce the off-peak reflectivity. Compared with random bit sequence coding, Golomb codes improve the optical signal-to-noise ratio (OSNR) of delayed waveforms by an order of magnitude. Simulations suggest a delay of 5  Gb/s data by 9 ns, or 45 bit durations, with an OSNR of 13 dB.

The Policy Formation Process: A Conceptual Framework for Analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Fuchs, E. F.

1972-01-01

A conceptual framework for analysis which is intended to assist both the policy analyst and the policy researcher in their empirical investigations into policy phenomena is developed. It is meant to facilitate understanding of the policy formation process by focusing attention on the basic forces shaping the main features of policy formation as a dynamic social-political-organizational process. The primary contribution of the framework lies in its capability to suggest useful ways of looking at policy formation reality. It provides the analyst and the researcher with a group of indicators which suggest where to look and what to look for when attempting to analyze and understand the mix of forces which energize, maintain, and direct the operation of strategic level policy systems. The framework also highlights interconnections, linkage, and relational patterns between and among important variables. The framework offers an integrated set of conceptual tools which facilitate understanding of and research on the complex and dynamic set of variables which interact in any major strategic level policy formation process.

Temporal-spatial distribution of American bison (Bison bison) in a tallgrass prairie fire mosaic

USGS Publications Warehouse

Schuler, K.L.; Leslie, David M.; Shaw, J.H.; Maichak, E.J.

2006-01-01

Fire and bison (Bison bison) are thought to be historically responsible for shaping prairie vegetation in North America. Interactions between temporal-spatial distributions of bison and prescribed burning protocols are important in current restoration of tallgrass prairies. We examined dynamics of bison distribution in a patch-burned tallgrass prairie in the south-central United States relative to bison group size and composition, and burn age and temporal distribution. Bison formed larger mixed groups during summer and smaller sexually segregated groups the rest of the year, and bison selected dormant-season burn patches in the 1st posture growing season most often during spring and summer. Large bison herds selecting recently burned areas resulted in seasonally variable and concentrated grazing pressure that may substantially alter site-specific vegetation. These dynamics must be considered when reintroducing bison and fire into tallgrass prairie because variable outcomes of floral richness and structural complexity are likely depending on temporal-spatial distribution of bison. ?? 2006 American Society of Mammalogists.

Design optimization of hydraulic turbine draft tube based on CFD and DOE method

NASA Astrophysics Data System (ADS)

Nam, Mun chol; Dechun, Ba; Xiangji, Yue; Mingri, Jin

2018-03-01

In order to improve performance of the hydraulic turbine draft tube in its design process, the optimization for draft tube is performed based on multi-disciplinary collaborative design optimization platform by combining the computation fluid dynamic (CFD) and the design of experiment (DOE) in this paper. The geometrical design variables are considered as the median section in the draft tube and the cross section in its exit diffuser and objective function is to maximize the pressure recovery factor (Cp). Sample matrixes required for the shape optimization of the draft tube are generated by optimal Latin hypercube (OLH) method of the DOE technique and their performances are evaluated through computational fluid dynamic (CFD) numerical simulation. Subsequently the main effect analysis and the sensitivity analysis of the geometrical parameters of the draft tube are accomplished. Then, the design optimization of the geometrical design variables is determined using the response surface method. The optimization result of the draft tube shows a marked performance improvement over the original.

A Low-Cost PC-Based Image Workstation for Dynamic Interactive Display of Three-Dimensional Anatomy

NASA Astrophysics Data System (ADS)

Barrett, William A.; Raya, Sai P.; Udupa, Jayaram K.

1989-05-01

A system for interactive definition, automated extraction, and dynamic interactive display of three-dimensional anatomy has been developed and implemented on a low-cost PC-based image workstation. An iconic display is used for staging predefined image sequences through specified increments of tilt and rotation over a solid viewing angle. Use of a fast processor facilitates rapid extraction and rendering of the anatomy into predefined image views. These views are formatted into a display matrix in a large image memory for rapid interactive selection and display of arbitrary spatially adjacent images within the viewing angle, thereby providing motion parallax depth cueing for efficient and accurate perception of true three-dimensional shape, size, structure, and spatial interrelationships of the imaged anatomy. The visual effect is that of holding and rotating the anatomy in the hand.

Impact of predator dormancy on prey-predator dynamics

NASA Astrophysics Data System (ADS)

Freire, Joana G.; Gallas, Marcia R.; Gallas, Jason A. C.

2018-05-01

The impact of predator dormancy on the population dynamics of phytoplankton-zooplankton in freshwater ecosystems is investigated using a simple model including dormancy, a strategy to avoid extinction. In addition to recently reported chaos-mediated mixed-mode oscillations, as the carrying capacity grows, we find surprisingly wide phases of nonchaos-mediated mixed-mode oscillations to be present well before the onset of chaos in the system. Nonchaos-mediated cascades display spike-adding sequences, while chaos-mediated cascades show spike-doubling. A host of braided periodic phases with exotic shapes is found embedded in a region of control parameters dominated by chaotic oscillations. We describe the organization of these complicated phases and show how they are interconnected and how their complexity unfolds as control parameters change. The novel nonchaos-mediated phases are found to be large and stable, even for low carrying capacity.

Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report

PubMed Central

2014-01-01

Background The foot provides a crucial contribution to the balance and stability of the musculoskeletal system, and accurate foot measurements are important in applications such as designing custom insoles/footwear. With better understanding of the dynamic behavior of the foot, dynamic foot reconstruction techniques are surfacing as useful ways to properly measure the shape of the foot. This paper presents a novel design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Methods Engineering and clinical tests were carried out to test the accuracy and repeatability of the system. Accuracy experiments involved imaging a planar surface from different orientations and elevations and measuring the fitting errors of the data to a plane. Repeatability experiments were done using reconstructions from 27 different subjects, where for each one both right and left feet were reconstructed in static and dynamic conditions over two different days. Results The static accuracy of the system was found to be 0.3 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.4 mm (static case) and 2.8 mm (dynamic case). Conclusion The results obtained in the experiments show positive accuracy and repeatability results when compared to current literature. The design also shows to be superior to the systems available in the literature in several factors. Further studies need to be done to quantify the reliability of the system in clinical environments. PMID:24456711

Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report.

PubMed

Thabet, Ali K; Trucco, Emanuele; Salvi, Joaquim; Wang, Weijie; Abboud, Rami J

2014-01-23

The foot provides a crucial contribution to the balance and stability of the musculoskeletal system, and accurate foot measurements are important in applications such as designing custom insoles/footwear. With better understanding of the dynamic behavior of the foot, dynamic foot reconstruction techniques are surfacing as useful ways to properly measure the shape of the foot. This paper presents a novel design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Engineering and clinical tests were carried out to test the accuracy and repeatability of the system. Accuracy experiments involved imaging a planar surface from different orientations and elevations and measuring the fitting errors of the data to a plane. Repeatability experiments were done using reconstructions from 27 different subjects, where for each one both right and left feet were reconstructed in static and dynamic conditions over two different days. The static accuracy of the system was found to be 0.3 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.4 mm (static case) and 2.8 mm (dynamic case). The results obtained in the experiments show positive accuracy and repeatability results when compared to current literature. The design also shows to be superior to the systems available in the literature in several factors. Further studies need to be done to quantify the reliability of the system in clinical environments.

On the growth and form of shoots

PubMed Central

Chelakkot, Raghunath

2017-01-01

Growing plant stems and shoots exhibit a variety of shapes that embody growth in response to various stimuli. Building on experimental observations, we provide a quantitative biophysical theory for these shapes by accounting for the inherent observed passive and active effects: (i) the active controllable growth response of the shoot in response to its orientation relative to gravity, (ii) proprioception, the shoot's growth response to its own observable current shape, and (iii) the passive elastic deflection of the shoot due to its own weight, which determines the current shape of the shoot. Our theory separates the sensed and actuated variables in a growing shoot and results in a morphospace diagram in terms of two dimensionless parameters representing a scaled local active gravitropic sensitivity, and a scaled passive elastic sag. Our computational results allow us to explain the variety of observed transient and steady morphologies with effective positive, negative and even oscillatory gravitropic behaviours, without the need for ad hoc complex spatio-temporal control strategies in terms of these parameters. More broadly, our theory is applicable to the growth of soft, floppy organs where sensing and actuation are dynamically coupled through growth processes via shape. PMID:28330990

Gesteme-free context-aware adaptation of robot behavior in human-robot cooperation.

PubMed

Nessi, Federico; Beretta, Elisa; Gatti, Cecilia; Ferrigno, Giancarlo; De Momi, Elena

2016-11-01

Cooperative robotics is receiving greater acceptance because the typical advantages provided by manipulators are combined with an intuitive usage. In particular, hands-on robotics may benefit from the adaptation of the assistant behavior with respect to the activity currently performed by the user. A fast and reliable classification of human activities is required, as well as strategies to smoothly modify the control of the manipulator. In this scenario, gesteme-based motion classification is inadequate because it needs the observation of a wide signal percentage and the definition of a rich vocabulary. In this work, a system able to recognize the user's current activity without a vocabulary of gestemes, and to accordingly adapt the manipulator's dynamic behavior is presented. An underlying stochastic model fits variations in the user's guidance forces and the resulting trajectories of the manipulator's end-effector with a set of Gaussian distribution. The high-level switching between these distributions is captured with hidden Markov models. The dynamic of the KUKA light-weight robot, a torque-controlled manipulator, is modified with respect to the classified activity using sigmoidal-shaped functions. The presented system is validated over a pool of 12 näive users in a scenario that addresses surgical targeting tasks on soft tissue. The robot's assistance is adapted in order to obtain a stiff behavior during activities that require critical accuracy constraint, and higher compliance during wide movements. Both the ability to provide the correct classification at each moment (sample accuracy) and the capability of correctly identify the correct sequence of activity (sequence accuracy) were evaluated. The proposed classifier is fast and accurate in all the experiments conducted (80% sample accuracy after the observation of ∼450ms of signal). Moreover, the ability of recognize the correct sequence of activities, without unwanted transitions is guaranteed (sequence accuracy ∼90% when computed far away from user desired transitions). Finally, the proposed activity-based adaptation of the robot's dynamic does not lead to a not smooth behavior (high smoothness, i.e. normalized jerk score <0.01). The provided system is able to dynamic assist the operator during cooperation in the presented scenario. Copyright © 2016 Elsevier B.V. All rights reserved.

Cusp/cleft auroral activity in relation to solar wind dynamic pressure, interplanetary magnetic field B(sub z) and B(sub y)

NASA Technical Reports Server (NTRS)

Sandholt, P. E.; Farrugia, C. J.; Burlaga, L. F.; Holtet, J. A.; Moen, J.; Lybekk, B.; Jacobsen, B.; Opsvik, D.; Egeland, A.; Lepping, R.

1994-01-01

Continuous optical observations of cusp/cleft auroral activities within approximately equal to 09-15 MLT and 70-76 deg magnetic latitude are studied in relation to changes in solar wind dynamic pressure and interplanetary magnetic field (IMF) variability. The observed latitudinal movements of the cusp/cleft aurora in response to IMF B(sub z) changes may be explained as an effect of a variable magnetic field intensity in the outer dayside magnetosphere associated with the changing intensity of region 1 field-aligned currents and associated closure currents. Ground magnetic signatures related to such currents were observed in the present case (January 10, 1993). Strong, isolated enhancements in solar wind dynamic pressure (Delta p/p is greater than or equal to 0.5) gave rise to equatorward shifts of the cusp/cleft aurora, characteristic auroral transients, and distinct ground magnetic signatures of enhanced convection at cleft latitudes. A sequence of auroral events of approximately equal to 5-10 min recurrence time, moving eastward along the poleward boundary of the persistent cusp/cleft aurora in the approximately equal to 10-14 MLT sector, during negative IMF B(sub z) and B(sub y) conditions, were found to be correlated with brief pulses in solar wind dynamic pressure (0.1 is less than Delta p/p is less than 0.5). Simultaneous photometer observations from Ny Alesund, Svalbard, and Danmarkshavn, Greenland, show that the events often appeared on the prenoon side (approximately equal to 10-12 MLT), before moving into the postnoon sector in the case we study here, when IMF B(sub y) is less than 0. In other cases, similar auroral event sequences have been observed to move westward in the prenoon sector, during intervals of positive B(sub y). Thus a strong prenoon/postnoon asymmetry of event occurence and motion pattern related to the IMF B(sub y) polarity is observed. We find that this category of auroral event sequence is stimulated bursts of electron precipitation that originate from magnetosheath plasma that has accessed that dayside magnetosphere in the noon or near-noon sector, possibly at high latitudes, partly governed by the IMF orientation as well as by solar wind dynamic pressure pulses.

An extension of command shaping methods for controlling residual vibration using frequency sampling

NASA Technical Reports Server (NTRS)

Singer, Neil C.; Seering, Warren P.

1992-01-01

The authors present an extension to the impulse shaping technique for commanding machines to move with reduced residual vibration. The extension, called frequency sampling, is a method for generating constraints that are used to obtain shaping sequences which minimize residual vibration in systems such as robots whose resonant frequencies change during motion. The authors present a review of impulse shaping methods, a development of the proposed extension, and a comparison of results of tests conducted on a simple model of the space shuttle robot arm. Frequency shaping provides a method for minimizing the impulse sequence duration required to give the desired insensitivity.

Avalanche criticality in thermal-driven martensitic transitions: the asymmetry of the forward and reverse transitions in shape-memory materials

NASA Astrophysics Data System (ADS)

Planes, Antoni; Vives, Eduard

2017-08-01

Martensitic transitions take place intermittently as a sequence of avalanches which are accompanied by the emission of acoustic waves. The study of this acoustic emission (AE) reveals the scale-free nature of the avalanches. In a number of shape memory materials undergoing a martensitic transition it has been found that, in spite of relatively low hysteresis, the dynamics of forward and reverse transitions are different, which may explain the fact that the AE activity is different in both forward and reverse transitions. The asymmetry could be a consequence of the fact that, while nucleation is required for the transition from the parent to martensitic phase to take place, reverse transition occurs by fast shrinkage of martensitic domains. We have analysed in detail the distribution of avalanches in cooling and heating runs in Fe-Pd and Cu-Zn-Al shape-memory alloys. In the former, the martensitic transition is weakly first order while it shows a significant first order character in the latter. We have found that in Fe-Pd the distributions are power law for the forward and reverse transitions characterized by the same critical exponents. For Cu-Zn-Al the distribution of avalanches is critical in forward transitions but exponentially damped in the reverse transition. It is suggested that this different behaviour could originate from the different dynamic mechanisms in forward and reverse transitions. This paper is dedicated to our friend Ekhard Salje in the occasion of his 70th birthday.

High Fidelity and Multiscale Algorithms for Collisional-radiative and Nonequilibrium Plasmas (Briefing Charts)

DTIC Science & Technology

2014-07-01

of models for variable conditions: – Use implicit models to eliminate constraint of sequence of fast time scales: c, ve, – Price to pay: lack...collisions: – Elastic – Bragiinski terms – Inelastic – warning! Rates depend on both T and relative velocity – Multi-fluid CR model from...merge/split for particle management, efficient sampling, inelastic collisions … – Level grouping schemes of electronic states, for dynamical coarse

Estimation of the left ventricular shape and motion with a limited number of slices

NASA Astrophysics Data System (ADS)

Robert, Anne; Schmitt, Francis J. M.; Mousseaux, Elie

1996-04-01

In this paper, we describe a method for the reconstruction of the surface of the left ventricle from a set of lacunary data (that is an incomplete, unevenly sampled and unstructured data set). Global models, because they compress the properties of a surface into a small set of parameters, have a strong regularizing power and are therefore very well suited to lacunary data. Globally deformable superquadrics are particularly attractive, because of their simplicity. This model can be fitted to the data using the Levenberg-Marquardt algorithm for non-linear optimization. However, the difficulties we experienced to get temporally consistent solutions as well as the intrinsic 4D character of the data led us to generalize the classical 3D superquadric model to 4D. We present results on a 4D sequence from the Dynamic Spatial Reconstructor of the Mayo Clinic, and on a 4D IRM sequence.

Histones: Controlling Tumor Signaling Circuitry

PubMed Central

Martins, Manoela D.; Castilho, Rogerio M.

2014-01-01

Epigenetic modifications constitute the next frontier in tumor biology research. Post-translation modification of histones dynamically influences gene expression independent of alterations to the DNA sequence. These mechanisms are often mediated by histone linkers or by proteins associated with the recruitment of DNA-binding proteins, HDAC I and II interacting proteins and transcriptional activators, coactivators or corepressors. Early evidence suggested that histones and their modifiers are involved in sophisticated processes that modulate tumor behavior and cellular phenotype. In this review, we discuss how recent discoveries about chromatin modifications, particularly histone acetylation, are shaping our knowledge of cell biology and our understanding of the molecular circuitry governing tumor progression and consider whether recent insights may extend to novel therapeutic approaches. Furthermore, we discuss the latest oncogenomic findings in Head and Neck Squamous Cell Carcinoma (HNSCC) from studies using Next Generation Sequencing (NGS) technology and highlight the impact of mutations identified in histones and their modifiers. PMID:25177526

Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping

PubMed Central

Fraley, Stephanie I.; Athamanolap, Pornpat; Masek, Billie J.; Hardick, Justin; Carroll, Karen C.; Hsieh, Yu-Hsiang; Rothman, Richard E.; Gaydos, Charlotte A.; Wang, Tza-Huei; Yang, Samuel

2016-01-01

High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization. PMID:26778280

Advanced Stirling Convertor Dynamic Test Approach and Results

NASA Technical Reports Server (NTRS)

Meer, David W.; Hill, Dennis; Ursic, Joseph

2009-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. As part of the extended operation testing of this power system, the Advanced Stirling Converters (ASC) at NASA John H. Glenn Research Center undergo a vibration test sequence intended to simulate the vibration history of an ASC used in an ASRG for a space mission. This sequence includes testing at Workmanship and Flight Acceptance levels interspersed with periods of extended operation to simulate pre and post fueling. The final step in the test sequence utilizes additional testing at Flight Acceptance levels to simulate launch. To better replicate the acceleration profile seen by an ASC incorporated into an ASRG, the input spectra used in testing the convertors was modified based on dynamic testing of the ASRG Engineering Unit ( ASRG-EU) at Lockheed Martin. This paper presents the vibration test plan for current and future ASC units, including the modified input spectra, and the results of recent tests using these spectra. The test results include data from several accelerometers mounted on the convertors as well as the piston position and output power variables.

Spatial and temporal single-cell volume estimation by a fluorescence imaging technique with application to astrocytes in primary culture

NASA Astrophysics Data System (ADS)

Khatibi, Siamak; Allansson, Louise; Gustavsson, Tomas; Blomstrand, Fredrik; Hansson, Elisabeth; Olsson, Torsten

1999-05-01

Cell volume changes are often associated with important physiological and pathological processes in the cell. These changes may be the means by which the cell interacts with its surrounding. Astroglial cells change their volume and shape under several circumstances that affect the central nervous system. Following an incidence of brain damage, such as a stroke or a traumatic brain injury, one of the first events seen is swelling of the astroglial cells. In order to study this and other similar phenomena, it is desirable to develop technical instrumentation and analysis methods capable of detecting and characterizing dynamic cell shape changes in a quantitative and robust way. We have developed a technique to monitor and to quantify the spatial and temporal volume changes in a single cell in primary culture. The technique is based on two- and three-dimensional fluorescence imaging. The temporal information is obtained from a sequence of microscope images, which are analyzed in real time. The spatial data is collected in a sequence of images from the microscope, which is automatically focused up and down through the specimen. The analysis of spatial data is performed off-line and consists of photobleaching compensation, focus restoration, filtering, segmentation and spatial volume estimation.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

PubMed

King, Andrew J; Preheim, Sarah P; Bailey, Kathryn L; Robeson, Michael S; Roy Chowdhury, Taniya; Crable, Bryan R; Hurt, Richard A; Mehlhorn, Tonia; Lowe, Kenneth A; Phelps, Tommy J; Palumbo, Anthony V; Brandt, Craig C; Brown, Steven D; Podar, Mircea; Zhang, Ping; Lancaster, W Andrew; Poole, Farris; Watson, David B; W Fields, Matthew; Chandonia, John-Marc; Alm, Eric J; Zhou, Jizhong; Adams, Michael W W; Hazen, Terry C; Arkin, Adam P; Elias, Dwayne A

2017-03-07

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

DOE PAGES

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.; ...

2017-01-23

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

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

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

Geomorphic effectiveness of long profile shape and role of inherent geological controls, Ganga River Basin, India

NASA Astrophysics Data System (ADS)

Sonam, Sonam; Jain, Vikrant

2017-04-01

River long profile is one of the fundamental geomorphic parameters which provides a platform to study interaction of geological and geomorphic processes at different time scales. Long profile shape is governed by geological processes at 10 ^ 5 - 10 ^ 6 years' time scale and it controls the modern day (10 ^ 0 - 10 ^ 1 years' time scale) fluvial processes by controlling the spatial variability of channel slope. Identification of an appropriate model for river long profile may provide a tool to analyse the quantitative relationship between basin geology, profile shape and its geomorphic effectiveness. A systematic analysis of long profiles has been carried for the Himalayan tributaries of the Ganga River basin. Long profile shape and stream power distribution pattern is derived using SRTM DEM data (90 m spatial resolution). Peak discharge data from 34 stations is used for hydrological analysis. Lithological variability and major thrusts are marked along the river long profile. The best fit of long profile is analysed for power, logarithmic and exponential function. Second order exponential function provides the best representation of long profiles. The second order exponential equation is Z = K1*exp(-β1*L) + K2*exp(-β2*L), where Z is elevation of channel long profile, L is the length, K and β are coefficients of the exponential function. K1 and K2 are the proportion of elevation change of the long profile represented by β1 (fast) and β2 (slow) decay coefficients of the river long profile. Different values of coefficients express the variability in long profile shapes and is related with the litho-tectonic variability of the study area. Channel slope of long profile is estimated taking the derivative of exponential function. Stream power distribution pattern along long profile is estimated by superimposing the discharge and long profile slope. Sensitivity analysis of stream power distribution with decay coefficients of the second order exponential equation is evaluated for a range of coefficient values. Our analysis suggests that the amplitude of stream power peak value is dependent on K1, the proportion of elevation change coming under the fast decay exponent and the location of stream power peak is dependent of the long profile decay coefficient (β1). Different long profile shapes owing to litho-tectonic variability across the Himalayas are responsible for spatial variability of stream power distribution pattern. Most of the stream power peaks lie in the Higher Himalaya. In general, eastern rivers have higher stream power in hinterland area and low stream power in the alluvial plains. This is responsible for, 1) higher erosion rate and sediment supply in hinterland of eastern rivers, 2) the incised and stable nature of channels in the western alluvial plains and 3) aggrading channels with dynamic nature in the eastern alluvial plains. Our study shows that the spatial variability of litho-units defines the coefficients of long profile function which in turn controls the position and magnitude of stream power maxima and hence the geomorphic variability in a fluvial system.

Neighbouring populations, opposite dynamics: influence of body size and environmental variation on the demography of stream-resident brown trout (Salmo trutta).

PubMed

Fernández-Chacón, Albert; Genovart, Meritxell; Álvarez, David; Cano, José M; Ojanguren, Alfredo F; Rodriguez-Muñoz, Rolando; Nicieza, Alfredo G

2015-06-01

In organisms such as fish, where body size is considered an important state variable for the study of their population dynamics, size-specific growth and survival rates can be influenced by local variation in both biotic and abiotic factors, but few studies have evaluated the complex relationships between environmental variability and size-dependent processes. We analysed a 6-year capture-recapture dataset of brown trout (Salmo trutta) collected at 3 neighbouring but heterogeneous mountain streams in northern Spain with the aim of investigating the factors shaping the dynamics of local populations. The influence of body size and water temperature on survival and individual growth was assessed under a multi-state modelling framework, an extension of classical capture-recapture models that considers the state (i.e. body size) of the individual in each capture occasion and allows us to obtain state-specific demographic rates and link them to continuous environmental variables. Individual survival and growth patterns varied over space and time, and evidence of size-dependent survival was found in all but the smallest stream. At this stream, the probability of reaching larger sizes was lower compared to the other wider and deeper streams. Water temperature variables performed better in the modelling of the highest-altitude population, explaining over a 99 % of the variability in maturation transitions and survival of large fish. The relationships between body size, temperature and fitness components found in this study highlight the utility of multi-state approaches to investigate small-scale demographic processes in heterogeneous environments, and to provide reliable ecological knowledge for management purposes.

Rise and fall of outbreak-specific clone inside endemic pulsotype of Salmonella 4,[5],12:i:-; insights from high-resolution molecular surveillance in Emilia-Romagna, Italy, 2012 to 2015.

PubMed

Morganti, Marina; Bolzoni, Luca; Scaltriti, Erika; Casadei, Gabriele; Carra, Elena; Rossi, Laura; Gherardi, Paola; Faccini, Fabio; Arrigoni, Norma; Sacchi, Anna Rita; Delledonne, Marco; Pongolini, Stefano

2018-03-01

Background and aimEpidemiology of human non-typhoid salmonellosis is characterised by recurrent emergence of new clones of the pathogen over time. Some clonal lines of Salmonella have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for Salmonella 4,[5],12:i:-, a monophasic variant of serotype Typhimurium. The same clonal behaviour is recognisable at sub-serotype level where single outbreaks or more generalised epidemics are attributable to defined clones. The aim of this study was to understand the dynamics of a clone of Salmonella 4,[5],12:i:- over a 3-year period (2012-15) in a province of Northern Italy where the clone caused a large outbreak in 2013. Furthermore, the role of candidate outbreak sources was investigated and the accuracy of multilocus variable-number tandem repeat analysis (MLVA) was evaluated. Methods: we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion. Results: The study showed the transient nature of the clone in the population, possibly as a consequence of its occasional expansion in a food-processing facility. We demonstrated that important weaknesses characterise conventional typing methods applied to clonal pathogens such as Salmonella 4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking. Conclusions : The study provided evidence for the remarkable prevention potential of whole genome sequencing used as a routine tool in systems that integrate human, food and animal surveillance.

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

PubMed Central

2011-01-01

Background The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. Results A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Conclusions Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS. PMID:21486489

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers.

PubMed

Gao, Lei; Zhou, Yuan; Wang, Zhi-Wei; Su, Ying-Juan; Wang, Ting

2011-04-13

The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.

The Frequency of Fitness Peak Shifts Is Increased at Expanding Range Margins Due to Mutation Surfing

PubMed Central

Burton, Olivia J.; Travis, Justin M. J.

2008-01-01

Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic. PMID:18505864

Are all data created equal?--Exploring some boundary conditions for a lazy intuitive statistician.

PubMed

Lindskog, Marcus; Winman, Anders

2014-01-01

The study investigated potential effects of the presentation order of numeric information on retrospective subjective judgments of descriptive statistics of this information. The studies were theoretically motivated by the assumption in the naïve sampling model of independence between temporal encoding order of data in long-term memory and retrieval probability (i.e. as implied by a "random sampling" from memory metaphor). In Experiment 1, participants experienced Arabic numbers that varied in distribution shape/variability between the first and the second half of the information sequence. Results showed no effects of order on judgments of mean, variability or distribution shape. To strengthen the interpretation of these results, Experiment 2 used a repeated judgment procedure, with an initial judgment occurring prior to the change in distribution shape of the information half-way through data presentation. The results of Experiment 2 were in line with those from Experiment 1, and in addition showed that the act of making explicit judgments did not impair accuracy of later judgments, as would be suggested by an anchoring and insufficient adjustment strategy. Overall, the results indicated that participants were very responsive to the properties of the data while at the same time being more or less immune to order effects. The results were interpreted as being in line with the naïve sampling models in which values are stored as exemplars and sampled randomly from long-term memory.

Proteomic Identification of Monoclonal Antibodies from Serum

PubMed Central

2015-01-01

Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using bottom-up analysis of serum antibodies by nanoflow liquid chromatography/high-resolution tandem mass spectrometry combined with a sample-specific antibody sequence database generated by high-throughput sequencing of individual B cell immunoglobulin variable domains (V genes). Here, we describe how intrinsic features of antibody primary structure, most notably the interspersed segments of variable and conserved amino acid sequences, generate recurring patterns in the corresponding peptide mass spectra of V gene peptides, greatly complicating the assignment of correct sequences to mass spectral data. We show that the standard method of decoy-based error modeling fails to account for the error introduced by these highly similar sequences, leading to a significant underestimation of the false discovery rate. Because of these effects, antibody-derived peptide mass spectra require increased stringency in their interpretation. The use of filters based on the mean precursor ion mass accuracy of peptide-spectrum matches is shown to be particularly effective in distinguishing between “true” and “false” identifications. These findings highlight important caveats associated with the use of standard database search and error-modeling methods with nonstandard data sets and custom sequence databases. PMID:24684310

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

PubMed

Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

2014-12-01

A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

Evaluating a robust contour tracker on echocardiographic sequences.

PubMed

Jacob, G; Noble, J A; Mulet-Parada, M; Blake, A

1999-03-01

In this paper we present an evaluation of a robust visual image tracker on echocardiographic image sequences. We show how the tracking framework can be customized to define an appropriate shape space that describes heart shape deformations that can be learnt from a training data set. We also investigate energy-based temporal boundary enhancement methods to improve image feature measurement. Results are presented demonstrating real-time tracking on real normal heart motion data sequences and abnormal synthesized and real heart motion data sequences. We conclude by discussing some of our current research efforts.

Temporal variability in stage-discharge relationships

NASA Astrophysics Data System (ADS)

Guerrero, José-Luis; Westerberg, Ida K.; Halldin, Sven; Xu, Chong-Yu; Lundin, Lars-Christer

2012-06-01

SummaryAlthough discharge estimations are central for water management and hydropower, there are few studies on the variability and uncertainty of their basis; deriving discharge from stage heights through the use of a rating curve that depends on riverbed geometry. A large fraction of the world's river-discharge stations are presumably located in alluvial channels where riverbed characteristics may change over time because of erosion and sedimentation. This study was conducted to analyse and quantify the dynamic relationship between stage and discharge and to determine to what degree currently used methods are able to account for such variability. The study was carried out for six hydrometric stations in the upper Choluteca River basin, Honduras, where a set of unusually frequent stage-discharge data are available. The temporal variability and the uncertainty of the rating curve and its parameters were analysed through a Monte Carlo (MC) analysis on a moving window of data using the Generalised Likelihood Uncertainty Estimation (GLUE) methodology. Acceptable ranges for the values of the rating-curve parameters were determined from riverbed surveys at the six stations, and the sampling space was constrained according to those ranges, using three-dimensional alpha shapes. Temporal variability was analysed in three ways: (i) with annually updated rating curves (simulating Honduran practices), (ii) a rating curve for each time window, and (iii) a smoothed, continuous dynamic rating curve derived from the MC analysis. The temporal variability of the rating parameters translated into a high rating-curve variability. The variability could turn out as increasing or decreasing trends and/or cyclic behaviour. There was a tendency at all stations to a seasonal variability. The discharge at a given stage could vary by a factor of two or more. The quotient in discharge volumes estimated from dynamic and static rating curves varied between 0.5 and 1.5. The difference between discharge volumes derived from static and dynamic curves was largest for sub-daily ratings but stayed large also for monthly and yearly totals. The relative uncertainty was largest for low flows but it was considerable also for intermediate and large flows. The standard procedure of adjusting rating curves when calculated and observed discharge differ by more than 5% would have required continuously updated rating curves at the studied locations. We believe that these findings can be applicable to many other discharge stations around the globe.

Blue large-amplitude pulsators as a new class of variable stars

NASA Astrophysics Data System (ADS)

Pietrukowicz, Paweł; Dziembowski, Wojciech A.; Latour, Marilyn; Angeloni, Rodolfo; Poleski, Radosław; di Mille, Francesco; Soszyński, Igor; Udalski, Andrzej; Szymański, Michał K.; Wyrzykowski, Łukasz; Kozłowski, Szymon; Skowron, Jan; Skowron, Dorota; Mróz, Przemek; Pawlak, Michał; Ulaczyk, Krzysztof

2017-08-01

Regular intrinsic brightness variations observed in many stars are caused by pulsations. These pulsations provide information on the global and structural parameters of the star. The pulsation periods range from seconds to years, depending on the compactness of the star and properties of the matter that forms its outer layers. Here, we report the discovery of more than a dozen previously unknown short-period variable stars: blue large-amplitude pulsators. These objects show very regular brightness variations with periods in the range of 20-40 min and amplitudes of 0.2-0.4 mag in the optical passbands. The phased light curves have a characteristic sawtooth shape, similar to the shape of classical Cepheids and RR Lyrae-type stars pulsating in the fundamental mode. The objects are significantly bluer than main-sequence stars observed in the same fields, which indicates that all of them are hot stars. Follow-up spectroscopy confirms a high surface temperature of about 30,000 K. Temperature and colour changes over the cycle prove the pulsational nature of the variables. However, large-amplitude pulsations at such short periods are not observed in any known type of stars, including hot objects. Long-term photometric observations show that the variable stars are very stable over time. Derived rates of period change are of the order of 10-7 per year and, in most cases, they are positive. According to pulsation theory, such large-amplitude oscillations may occur in evolved low-mass stars that have inflated helium-enriched envelopes. The evolutionary path that could lead to such stellar configurations remains unknown.

Deck and Cable Dynamic Testing of a Single-span Bridge Using Radar Interferometry and Videometry Measurements

NASA Astrophysics Data System (ADS)

Piniotis, George; Gikas, Vassilis; Mpimis, Thanassis; Perakis, Harris

2016-03-01

This paper presents the dynamic testing of a roadway, single-span, cable-stayed bridge for a sequence of static load and ambient vibration monitoring scenarios. Deck movements were captured along both sideways of the bridge using a Digital Image Correlation (DIC) and a Ground-based Microwave Interfererometer (GBMI) system. Cable vibrations were measured at a single point location on each of the six cables using the GBMI technique. Dynamic testing involves three types of analyses; firstly, vibration analysis and modal parameter estimation (i. e., natural frequencies and modal shapes) of the deck using the combined DIC and GBMI measurements. Secondly, dynamic testing of the cables is performed through vibration analysis and experimental computation of their tension forces. Thirdly, the mechanism of cable-deck dynamic interaction is studied through their Power Spectra Density (PSD) and the Short Time Fourier Transform (STFT) analyses. Thereby, the global (deck and cable) and local (either deck or cable) bridge modes are identified, serving a concrete benchmark of the current state of the bridge for studying the evolution of its structural performance in the future. The level of synergy and complementarity between the GBMI and DIC techniques for bridge monitoring is also examined and assessed.

The writer independent online handwriting recognition system frog on hand and cluster generative statistical dynamic time warping.

PubMed

Bahlmann, Claus; Burkhardt, Hans

2004-03-01

In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.

Robust dynamics in minimal hybrid models of genetic networks

PubMed Central

Perkins, Theodore J.; Wilds, Roy; Glass, Leon

2010-01-01

Many gene-regulatory networks necessarily display robust dynamics that are insensitive to noise and stable under evolution. We propose that a class of hybrid systems can be used to relate the structure of these networks to their dynamics and provide insight into the origin of robustness. In these systems, the genes are represented by logical functions, and the controlling transcription factor protein molecules are real variables, which are produced and destroyed. As the transcription factor concentrations cross thresholds, they control the production of other transcription factors. We discuss mathematical analysis of these systems and show how the concepts of robustness and minimality can be used to generate putative logical organizations based on observed symbolic sequences. We apply the methods to control of the cell cycle in yeast. PMID:20921006

Robust dynamics in minimal hybrid models of genetic networks.

PubMed

Perkins, Theodore J; Wilds, Roy; Glass, Leon

2010-11-13

Many gene-regulatory networks necessarily display robust dynamics that are insensitive to noise and stable under evolution. We propose that a class of hybrid systems can be used to relate the structure of these networks to their dynamics and provide insight into the origin of robustness. In these systems, the genes are represented by logical functions, and the controlling transcription factor protein molecules are real variables, which are produced and destroyed. As the transcription factor concentrations cross thresholds, they control the production of other transcription factors. We discuss mathematical analysis of these systems and show how the concepts of robustness and minimality can be used to generate putative logical organizations based on observed symbolic sequences. We apply the methods to control of the cell cycle in yeast.

Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection

USGS Publications Warehouse

Miller, John J; Eackles, Michael S.; Stauffer, Jay R; King, Timothy L.

2015-01-01

We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.

Gender differences in foot shape: a study of Chinese young adults.

PubMed

Hong, Youlian; Wang, Lin; Xu, Dong Qing; Li, Jing Xian

2011-06-01

One important extrinsic factor that causes foot deformity and pain in women is footwear. Women's sports shoes are designed as smaller versions of men's shoes. Based on this, the current study aims to identify foot shape in 1,236 Chinese young adult men and 1,085 Chinese young adult women. Three-dimensional foot shape data were collected through video filming. Nineteen foot shape variables were measured, including girth (4 variables), length (4 variables), width (3 variables), height (7 variables), and angle (1 variable). A comparison of foot measures within the range of the common foot length (FL) categories indicates that women showed significantly smaller values of foot measures in width, height, and girth than men. Three foot types were classified, and distributions of different foot shapes within the same FL were found between women and men. Foot width, medial ball length, ball angle, and instep height showed significant differences among foot types in the same FL for both genders. There were differences in the foot shape between Chinese young women and men, which should be considered in the design of Chinese young adults' sports shoes.

3-D ballistic transport of ellipsoidal volcanic projectiles considering horizontal wind field and variable shape-dependent drag coefficients

NASA Astrophysics Data System (ADS)

Bertin, Daniel

2017-02-01

An innovative 3-D numerical model for the dynamics of volcanic ballistic projectiles is presented here. The model focuses on ellipsoidal particles and improves previous approaches by considering horizontal wind field, virtual mass forces, and drag forces subjected to variable shape-dependent drag coefficients. Modeling suggests that the projectile's launch velocity and ejection angle are first-order parameters influencing ballistic trajectories. The projectile's density and minor radius are second-order factors, whereas both intermediate and major radii of the projectile are of third order. Comparing output parameters, assuming different input data, highlights the importance of considering a horizontal wind field and variable shape-dependent drag coefficients in ballistic modeling, which suggests that they should be included in every ballistic model. On the other hand, virtual mass forces should be discarded since they almost do not contribute to ballistic trajectories. Simulation results were used to constrain some crucial input parameters (launch velocity, ejection angle, wind speed, and wind azimuth) of the block that formed the biggest and most distal ballistic impact crater during the 1984-1993 eruptive cycle of Lascar volcano, Northern Chile. Subsequently, up to 106 simulations were performed, whereas nine ejection parameters were defined by a Latin-hypercube sampling approach. Simulation results were summarized as a quantitative probabilistic hazard map for ballistic projectiles. Transects were also done in order to depict aerial hazard zones based on the same probabilistic procedure. Both maps combined can be used as a hazard prevention tool for ground and aerial transits nearby unresting volcanoes.

[Study on sequence characterized amplified region (SCAR) markers of Cornus officinalis].

PubMed

Chen, Suiqing; Lu, Xiaolei; Wang, Lili

2011-05-01

To establish sequence characterized amplified region markers of Cornus officinalis and provide a scientific basis for molecular identification of C. officinalis. The random primer was screened through RAPD to obtain specific RAPD marker bands. The RAPD marker bands were separated, extracted, cloned and sequenced. Both ends of the sequence of RAPD marker bands were determined. A pair of specific primers was designed for conventional PCR reaction, and SCAR marker was acquired. Four pairs of primers were designed based on the sequence of RAPD marker bands. The DNA of the seven varieties of C. officinalis was amplified by using YST38 and YST43 primer. The results showed that seven varieties of C. officinalis were able to produce a single PCR product. It was an effective way to identify C. officinalis. The varieties with cylindrical and long-pear shape fruits amplified by YST38 showed a specific band, which could be used as the evidence of variety identification. Seven varieties of C. oficinalis were amplified by using primer YST39. But the size of band of the variety with spindly shape fruit (35,0400 bp) was about 300 bp, which was shorter than those of the variety with the other shape fruits of C. officinalis (650-700 bp). The variety with the spindly shape fruit could be identified through this difference. The primer YST92 could produce a fragment from 600-700 bp in the varieties with cylindrical and long-pear shape fruits, a fragment from 200-300 bp in the varieties with oval and short-cylindrical shape fruits and had no fragment in the varieties with long cylindrical, elliptic and short-pear shape fruits, which could be used to select the different shapes of C. officinalis. SCAR mark is established and can be used as the basis for breeding and distinguishing the verieties of C. officinalis.

Single step optimization of manipulator maneuvers with variable structure control

NASA Technical Reports Server (NTRS)

Chen, N.; Dwyer, T. A. W., III

1987-01-01

One step ahead optimization has been recently proposed for spacecraft attitude maneuvers as well as for robot manipulator maneuvers. Such a technique yields a discrete time control algorithm implementable as a sequence of state-dependent, quadratic programming problems for acceleration optimization. Its sensitivity to model accuracy, for the required inversion of the system dynamics, is shown in this paper to be alleviated by a fast variable structure control correction, acting between the sampling intervals of the slow one step ahead discrete time acceleration command generation algorithm. The slow and fast looping concept chosen follows that recently proposed for optimal aiming strategies with variable structure control. Accelerations required by the VSC correction are reserved during the slow one step ahead command generation so that the ability to overshoot the sliding surface is guaranteed.

77 FR 25587 - Anchorage Regulations; Wells, ME

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-01

... anchorage areas were out of sequence and formed an hourglass shaped anchorage. This direct final rule corrects the sequence of the coordinates so that the anchorage area forms a box-like shaped anchorage...), U.S. Department of Transportation, West Building Ground Floor, Room W12-140, 1200 New Jersey Avenue...

Geometric constraints during epithelial jamming

NASA Astrophysics Data System (ADS)

Atia, Lior; Bi, Dapeng; Sharma, Yasha; Mitchel, Jennifer A.; Gweon, Bomi; Koehler, Stephan A.; DeCamp, Stephen J.; Lan, Bo; Kim, Jae Hun; Hirsch, Rebecca; Pegoraro, Adrian F.; Lee, Kyu Ha; Starr, Jacqueline R.; Weitz, David A.; Martin, Adam C.; Park, Jin-Ah; Butler, James P.; Fredberg, Jeffrey J.

2018-06-01

As an injury heals, an embryo develops or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively whereas variability of shape from cell to cell is regarded most often as biological noise. But where do cell shape and its variability come from? Here we report that cell shape and shape variability are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern processes as diverse as maturation of the pseudostratified bronchial epithelial layer cultured from non-asthmatic or asthmatic donors, and formation of the ventral furrow in the Drosophila embryo. Across these and other epithelial systems, shape variability collapses to a family of distributions that is common to all. That distribution, in turn, is accounted for by a mechanistic theory of cell-cell interaction, showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings suggest a connection between jamming and geometry that spans living organisms and inert jammed systems, and thus transcends system details. Although molecular events are needed for any complete theory of cell shape and cell packing, observations point to the hypothesis that jamming behaviour at larger scales of organization sets overriding geometric constraints.

Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output.

PubMed

Nochomovitz, Yigal D; Li, Hao

2006-03-14

Deciphering the design principles for regulatory networks is fundamental to an understanding of biological systems. We have explored the mapping from the space of network topologies to the space of dynamical phenotypes for small networks. Using exhaustive enumeration of a simple model of three- and four-node networks, we demonstrate that certain dynamical phenotypes can be generated by an atypically broad spectrum of network topologies. Such dynamical outputs are highly designable, much like certain protein structures can be designed by an unusually broad spectrum of sequences. The network topologies that encode a highly designable dynamical phenotype possess two classes of connections: a fully conserved core of dedicated connections that encodes the stable dynamical phenotype and a partially conserved set of variable connections that controls the transient dynamical flow. By comparing the topologies and dynamics of the three- and four-node network ensembles, we observe a large number of instances of the phenomenon of "mutational buffering," whereby addition of a fourth node suppresses phenotypic variation amongst a set of three-node networks.

Automated regional analysis of B-mode ultrasound images of skeletal muscle movement

PubMed Central

Darby, John; Costen, Nicholas; Loram, Ian D.

2012-01-01

To understand the functional significance of skeletal muscle anatomy, a method of quantifying local shape changes in different tissue structures during dynamic tasks is required. Taking advantage of the good spatial and temporal resolution of B-mode ultrasound imaging, we describe a method of automatically segmenting images into fascicle and aponeurosis regions and tracking movement of features, independently, in localized portions of each tissue. Ultrasound images (25 Hz) of the medial gastrocnemius muscle were collected from eight participants during ankle joint rotation (2° and 20°), isometric contractions (1, 5, and 50 Nm), and deep knee bends. A Kanade-Lucas-Tomasi feature tracker was used to identify and track any distinctive and persistent features within the image sequences. A velocity field representation of local movement was then found and subdivided between fascicle and aponeurosis regions using segmentations from a multiresolution active shape model (ASM). Movement in each region was quantified by interpolating the effect of the fields on a set of probes. ASM segmentation results were compared with hand-labeled data, while aponeurosis and fascicle movement were compared with results from a previously documented cross-correlation approach. ASM provided good image segmentations (<1 mm average error), with fully automatic initialization possible in sequences from seven participants. Feature tracking provided similar length change results to the cross-correlation approach for small movements, while outperforming it in larger movements. The proposed method provides the potential to distinguish between active and passive changes in muscle shape and model strain distributions during different movements/conditions and quantify nonhomogeneous strain along aponeuroses. PMID:22033532

Resilience, Integrity and Ecosystem Dynamics: Bridging Ecosystem Theory and Management

NASA Astrophysics Data System (ADS)

Müller, Felix; Burkhard, Benjamin; Kroll, Franziska

In this paper different approaches to elucidate ecosystem dynamics are described, illustrated and interrelated. Ecosystem development is distinguished into two separate sequences, a complexifying phase which is characterized by orientor optimization and a destruction based phase which follows disturbances. The two developmental pathways are integrated in a modified illustration of the "adaptive cycle". Based on these fundamentals, the recent definitions of resilience, adaptability and vulnerability are discussed and a modified comprehension is proposed. Thereafter, two case studies about wetland dynamics are presented to demonstrate both, the consequences of disturbance and the potential of ecosystem recovery. In both examples ecosystem integrity is used as a key indicator variable. Based on the presented results the relativity and the normative loading of resilience quantification is worked out. The paper ends with the suggestion that the features of adaptability could be used as an integrative guideline for the analysis of ecosystem dynamics and as a well-suited concept for ecosystem management.

Macrocyclic molecular rotors with bridged steroidal frameworks.

PubMed

Czajkowska-Szczykowska, Dorota; Rodríguez-Molina, Braulio; Magaña-Vergara, Nancy E; Santillan, Rosa; Morzycki, Jacek W; Garcia-Garibay, Miguel A

2012-11-16

In this work, we describe the synthesis and solid-state dynamics of isomeric molecular rotors 7E and 7Z, consisting of two androstane steroidal frameworks linked by the D rings by triple bonds at their C17 positions to a 1,4-phenylene rotator. They are also linked by the A rings by an alkenyl diester bridge to restrict the conformational flexibility of the molecules and reduce the number of potential crystalline arrays. The analysis of the resulting molecular structures and packing motifs offered insights of the internal dynamics that were later elucidated by means of line shape analyses of the spectral features obtained through variable-temperature solid-state (13)C NMR; such analysis revealed rotations in the solid state occurring at kilohertz frequency at room temperature.

Crawling and turning in a minimal reaction-diffusion cell motility model: Coupling cell shape and biochemistry

NASA Astrophysics Data System (ADS)

Camley, Brian A.; Zhao, Yanxiang; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan

2017-01-01

We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis1[W

PubMed Central

Windsor, Aaron J.; Schranz, M. Eric; Formanová, Nataša; Gebauer-Jung, Steffi; Bishop, John G.; Schnabelrauch, Domenica; Kroymann, Juergen; Mitchell-Olds, Thomas

2006-01-01

Comparative genomics provides insight into the evolutionary dynamics that shape discrete sequences as well as whole genomes. To advance comparative genomics within the Brassicaceae, we have end sequenced 23,136 medium-sized insert clones from Boechera stricta, a wild relative of Arabidopsis (Arabidopsis thaliana). A significant proportion of these sequences, 18,797, are nonredundant and display highly significant similarity (BLASTn e-value ≤ 10−30) to low copy number Arabidopsis genomic regions, including more than 9,000 annotated coding sequences. We have used this dataset to identify orthologous gene pairs in the two species and to perform a global comparison of DNA regions 5′ to annotated coding regions. On average, the 500 nucleotides upstream to coding sequences display 71.4% identity between the two species. In a similar analysis, 61.4% identity was observed between 5′ noncoding sequences of Brassica oleracea and Arabidopsis, indicating that regulatory regions are not as diverged among these lineages as previously anticipated. By mapping the B. stricta end sequences onto the Arabidopsis genome, we have identified nearly 2,000 conserved blocks of microsynteny (bracketing 26% of the Arabidopsis genome). A comparison of fully sequenced B. stricta inserts to their homologous Arabidopsis genomic regions indicates that indel polymorphisms >5 kb contribute substantially to the genome size difference observed between the two species. Further, we demonstrate that microsynteny inferred from end-sequence data can be applied to the rapid identification and cloning of genomic regions of interest from nonmodel species. These results suggest that among diploid relatives of Arabidopsis, small- to medium-scale shotgun sequencing approaches can provide rapid and cost-effective benefits to evolutionary and/or functional comparative genomic frameworks. PMID:16607030

On the viewing angle dependence of blazar variability

NASA Astrophysics Data System (ADS)

Eldar, Avigdor; Levinson, Amir

2000-05-01

Internal shocks propagating through an ambient radiation field are subject to a radiative drag that, under certain conditions, can significantly affect their dynamics, and consequently the evolution of the beaming cone of emission produced behind the shocks. The resultant change of the Doppler factor combined with opacity effects leads to a strong dependence on the viewing angle of the variability pattern produced by such systems; specifically, the shape of the light curves and the characteristics of correlated emission. One implication is that objects oriented at relatively large viewing angles to the observer should exhibit a higher level of activity at high synchrotron frequencies (above the self-absorption frequency), and also at gamma-ray energies below the threshold energy of pair production, than at lower (radio/millimetre) frequencies.

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Learning to be different: Acquired skills, social learning, frequency dependence, and environmental variation can cause behaviourally mediated foraging specializations

USGS Publications Warehouse

Tinker, M.T.; Mangel, M.; Estes, J.A.

2009-01-01

Question: How does the ability to improve foraging skills by learning, and to transfer that learned knowledge, affect the development of intra-population foraging specializations? Features of the model: We use both a state-dependent life-history model implemented by stochastic dynamic programming (SDPM) and an individual-based model (IBM) to capture the dynamic nature of behavioural preferences in feeding. Variables in the SDPM include energy reserves, skill levels, energy and handling time per single prey item, metabolic rate, the rates at which skills are learned and forgotten, the effect of skills on handling time, and the relationship between energy reserves and fitness. Additional variables in the IBM include the probability of successful weaning, the logistic dynamics of the prey species with stochastic recruitment, the intensity of top-down control of prey by predators, the mean and variance in skill levels of new recruits, and the extent to which learned Information can be transmitted via matrilineal social learning. Key range of variables: We explore the effects of approaching the time horizon in the SDPM, changing the extent to which skills can improve with experience, increasing the rates of learning or forgetting of skills, changing whether the learning curve is constant, accelerating (T-shaped) or decelerating ('r'-shaped), changing both mean and maximum possible energy reserves, changing metabolic costs of foraging, and changing the rate of encounter with prey. Conclusions: The model results show that the following factors increase the degree of prey specialization observed in a predator population: (1) Experience handling a prey type can substantially improve foraging skills for that prey. (2) There is limited ability to retain complex learned skills for multiple prey types. (3) The learning curve for acquiring new foraging skills is accelerating, or J-shaped. (4) The metabolic costs of foraging are high relative to available energy reserves. (5) Offspring can learn foraging skills from their mothers (matrilineal social learning). (6) Food abundance is limited, such that average individual energy reserves are low Additionally, the following factors increase the likelihood of alternative specializations co-occurring in a predator population: (1) The predator exerts effective top-down control of prey abundance, resulting in frequency-dependent dynamics. (2) There is stochastic Variation in prey population dynamics, but this Variation is neither too extreme in magnitude nor too 'slow' with respect to the time required for an individual forager to learn new foraging skills. For a given predator population, we deduce that the degree of specialization will be highest for those prey types requiring complex capture or handling skills, while prey species that are both profitable and easy to capture and handle will be included in the diet of all individuals. Frequency-dependent benefits of selecting alternative prey types, combined with the ability of foragers to improve their foraging skills by learning, and transmit learned skills to offspring, can result in behaviourally mediated foraging specialization, and also lead to the co-existence of alternative specializations. The extent of such specialization is predicted to be a variable trait, increasing in locations or years when intra-specific competition is high relative to inter-specific competition. ?? 2009 M. Tim Tinker.

Stock discrimination of spottedtail goby ( Synechogobius ommaturus) in the Yellow Sea by analysis of otolith shape

NASA Astrophysics Data System (ADS)

Wang, Yingjun; Ye, Zhenjiang; Liu, Qun; Cao, Liang

2011-01-01

Otolith shape is species specific and is an ideal marker of fish population affiliation. In this study, otolith shape of spottedtail goby Synechogobius ommaturus is used to identify stocks in different spawning locations in the Yellow Sea. The main objectives of this study are to explore the potential existence of local stocks of spottedtail goby in the Yellow Sea by analysis of otolith shape, and to investigate ambient impacts on otolith shape. Spottedtail goby was sampled in five locations in the Yellow Sea in 2007 and 2008. Otoliths are described using variables correlated to size (otolith area, perimeter, length, width, and weight) and shape (rectangularity, circularity, and 20 Fourier harmonics). Only standardized otolith variables are used so that the effect of otolith size on the shape variables could be eliminated. There is no significant difference among variables of sex, year, and side (left and right). However, the otolith shapes of the spring stocks and the autumn stocks differ significantly. Otolith shape differences are greater among locations than between years. Correct classification rate of spottedtail goby with the otolith shape at different sampling locations range from 29.7%-77.4%.

Visual variability affects early verb learning.

PubMed

Twomey, Katherine E; Lush, Lauren; Pearce, Ruth; Horst, Jessica S

2014-09-01

Research demonstrates that within-category visual variability facilitates noun learning; however, the effect of visual variability on verb learning is unknown. We habituated 24-month-old children to a novel verb paired with an animated star-shaped actor. Across multiple trials, children saw either a single action from an action category (identical actions condition, for example, travelling while repeatedly changing into a circle shape) or multiple actions from that action category (variable actions condition, for example, travelling while changing into a circle shape, then a square shape, then a triangle shape). Four test trials followed habituation. One paired the habituated verb with a new action from the habituated category (e.g., 'dacking' + pentagon shape) and one with a completely novel action (e.g., 'dacking' + leg movement). The others paired a new verb with a new same-category action (e.g., 'keefing' + pentagon shape), or a completely novel category action (e.g., 'keefing' + leg movement). Although all children discriminated novel verb/action pairs, children in the identical actions condition discriminated trials that included the completely novel verb, while children in the variable actions condition discriminated the out-of-category action. These data suggest that - as in noun learning - visual variability affects verb learning and children's ability to form action categories. © 2014 The British Psychological Society.

Changes in the neural control of a complex motor sequence during learning

PubMed Central

Otchy, Timothy M.; Goldberg, Jesse H.; Aronov, Dmitriy; Fee, Michale S.

2011-01-01

The acquisition of complex motor sequences often proceeds through trial-and-error learning, requiring the deliberate exploration of motor actions and the concomitant evaluation of the resulting performance. Songbirds learn their song in this manner, producing highly variable vocalizations as juveniles. As the song improves, vocal variability is gradually reduced until it is all but eliminated in adult birds. In the present study we examine how the motor program underlying such a complex motor behavior evolves during learning by recording from the robust nucleus of the arcopallium (RA), a motor cortex analog brain region. In young birds, neurons in RA exhibited highly variable firing patterns that throughout development became more precise, sparse, and bursty. We further explored how the developing motor program in RA is shaped by its two main inputs: LMAN, the output nucleus of a basal ganglia-forebrain circuit, and HVC, a premotor nucleus. Pharmacological inactivation of LMAN during singing made the song-aligned firing patterns of RA neurons adultlike in their stereotypy without dramatically affecting the spike statistics or the overall firing patterns. Removing the input from HVC, on the other hand, resulted in a complete loss of stereotypy of both the song and the underlying motor program. Thus our results show that a basal ganglia-forebrain circuit drives motor exploration required for trial-and-error learning by adding variability to the developing motor program. As learning proceeds and the motor circuits mature, the relative contribution of LMAN is reduced, allowing the premotor input from HVC to drive an increasingly stereotyped song. PMID:21543758

Dynamic Analysis of Large In-Space Deployable Membrane Antennas

NASA Technical Reports Server (NTRS)

Fang, Houfei; Yang, Bingen; Ding, Hongli; Hah, John; Quijano, Ubaldo; Huang, John

2006-01-01

This paper presents a vibration analysis of an eight-meter diameter membrane reflectarray antenna, which is composed of a thin membrane and a deployable frame. This analysis process has two main steps. In the first step, a two-variable-parameter (2-VP) membrane model is developed to determine the in-plane stress distribution of the membrane due to pre-tensioning, which eventually yields the differential stiffness of the membrane. In the second step, the obtained differential stiffness is incorporated in a dynamic equation governing the transverse vibration of the membrane-frame assembly. This dynamic equation is then solved by a semi-analytical method, called the Distributed Transfer Function Method (DTFM), which produces the natural frequencies and mode shapes of the antenna. The combination of the 2-VP model and the DTFM provides an accurate prediction of the in-plane stress distribution and modes of vibration for the antenna.

A weak Hamiltonian finite element method for optimal control problems

NASA Technical Reports Server (NTRS)

Hodges, Dewey H.; Bless, Robert R.

1989-01-01

A temporal finite element method based on a mixed form of the Hamiltonian weak principle is developed for dynamics and optimal control problems. The mixed form of Hamilton's weak principle contains both displacements and momenta as primary variables that are expanded in terms of nodal values and simple polynomial shape functions. Unlike other forms of Hamilton's principle, however, time derivatives of the momenta and displacements do not appear therein; instead, only the virtual momenta and virtual displacements are differentiated with respect to time. Based on the duality that is observed to exist between the mixed form of Hamilton's weak principle and variational principles governing classical optimal control problems, a temporal finite element formulation of the latter can be developed in a rather straightforward manner. Several well-known problems in dynamics and optimal control are illustrated. The example dynamics problem involves a time-marching problem. As optimal control examples, elementary trajectory optimization problems are treated.

A weak Hamiltonian finite element method for optimal control problems

NASA Technical Reports Server (NTRS)

Hodges, Dewey H.; Bless, Robert R.

1990-01-01

A temporal finite element method based on a mixed form of the Hamiltonian weak principle is developed for dynamics and optimal control problems. The mixed form of Hamilton's weak principle contains both displacements and momenta as primary variables that are expanded in terms of nodal values and simple polynomial shape functions. Unlike other forms of Hamilton's principle, however, time derivatives of the momenta and displacements do not appear therein; instead, only the virtual momenta and virtual displacements are differentiated with respect to time. Based on the duality that is observed to exist between the mixed form of Hamilton's weak principle and variational principles governing classical optimal control problems, a temporal finite element formulation of the latter can be developed in a rather straightforward manner. Several well-known problems in dynamics and optimal control are illustrated. The example dynamics problem involves a time-marching problem. As optimal control examples, elementary trajectory optimization problems are treated.

Weak Hamiltonian finite element method for optimal control problems

NASA Technical Reports Server (NTRS)

Hodges, Dewey H.; Bless, Robert R.

1991-01-01

A temporal finite element method based on a mixed form of the Hamiltonian weak principle is developed for dynamics and optimal control problems. The mixed form of Hamilton's weak principle contains both displacements and momenta as primary variables that are expanded in terms of nodal values and simple polynomial shape functions. Unlike other forms of Hamilton's principle, however, time derivatives of the momenta and displacements do not appear therein; instead, only the virtual momenta and virtual displacements are differentiated with respect to time. Based on the duality that is observed to exist between the mixed form of Hamilton's weak principle and variational principles governing classical optimal control problems, a temporal finite element formulation of the latter can be developed in a rather straightforward manner. Several well-known problems in dynamics and optimal control are illustrated. The example dynamics problem involves a time-marching problem. As optimal control examples, elementary trajectory optimization problems are treated.

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB

PubMed Central

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey

2014-01-01

The assembly of protein filaments drives many cellular processes, from nucleoid segregation, growth, and division in single cells to muscle contraction in animals. In eukaryotes, shape and motility are regulated through cycles of polymerization and depolymerization of actin cytoskeletal networks. In bacteria, the actin homolog MreB forms filaments that coordinate the cell-wall synthesis machinery to regulate rod-shaped growth and contribute to cellular stiffness through unknown mechanisms. Like actin, MreB is an ATPase and requires ATP to polymerize, and polymerization promotes nucleotide hydrolysis. However, it is unclear whether other similarities exist between MreB and actin because the two proteins share low sequence identity and have distinct cellular roles. Here, we use all-atom molecular dynamics simulations to reveal surprising parallels between MreB and actin structural dynamics. We observe that MreB exhibits actin-like polymerization-dependent structural changes, wherein polymerization induces flattening of MreB subunits, which restructures the nucleotide-binding pocket to favor hydrolysis. MreB filaments exhibited nucleotide-dependent intersubunit bending, with hydrolyzed polymers favoring a straighter conformation. We use steered simulations to demonstrate a coupling between intersubunit bending and the degree of flattening of each subunit, suggesting cooperative bending along a filament. Taken together, our results provide molecular-scale insight into the diversity of structural states of MreB and the relationships among polymerization, hydrolysis, and filament properties, which may be applicable to other members of the broad actin family. PMID:24550504

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB.

PubMed

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey

2014-03-04

The assembly of protein filaments drives many cellular processes, from nucleoid segregation, growth, and division in single cells to muscle contraction in animals. In eukaryotes, shape and motility are regulated through cycles of polymerization and depolymerization of actin cytoskeletal networks. In bacteria, the actin homolog MreB forms filaments that coordinate the cell-wall synthesis machinery to regulate rod-shaped growth and contribute to cellular stiffness through unknown mechanisms. Like actin, MreB is an ATPase and requires ATP to polymerize, and polymerization promotes nucleotide hydrolysis. However, it is unclear whether other similarities exist between MreB and actin because the two proteins share low sequence identity and have distinct cellular roles. Here, we use all-atom molecular dynamics simulations to reveal surprising parallels between MreB and actin structural dynamics. We observe that MreB exhibits actin-like polymerization-dependent structural changes, wherein polymerization induces flattening of MreB subunits, which restructures the nucleotide-binding pocket to favor hydrolysis. MreB filaments exhibited nucleotide-dependent intersubunit bending, with hydrolyzed polymers favoring a straighter conformation. We use steered simulations to demonstrate a coupling between intersubunit bending and the degree of flattening of each subunit, suggesting cooperative bending along a filament. Taken together, our results provide molecular-scale insight into the diversity of structural states of MreB and the relationships among polymerization, hydrolysis, and filament properties, which may be applicable to other members of the broad actin family.

Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

PubMed

Kachhap, Sangita; Singh, Balvinder

2015-01-01

In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

Two stochastic models useful in petroleum exploration

NASA Technical Reports Server (NTRS)

Kaufman, G. M.; Bradley, P. G.

1972-01-01

A model of the petroleum exploration process that tests empirically the hypothesis that at an early stage in the exploration of a basin, the process behaves like sampling without replacement is proposed along with a model of the spatial distribution of petroleum reserviors that conforms to observed facts. In developing the model of discovery, the following topics are discussed: probabilitistic proportionality, likelihood function, and maximum likelihood estimation. In addition, the spatial model is described, which is defined as a stochastic process generating values of a sequence or random variables in a way that simulates the frequency distribution of areal extent, the geographic location, and shape of oil deposits

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

PubMed

Long, Hannah K; King, Hamish W; Patient, Roger K; Odom, Duncan T; Klose, Robert J

2016-08-19

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamic Human Body Modeling Using a Single RGB Camera.

PubMed

Zhu, Haiyu; Yu, Yao; Zhou, Yu; Du, Sidan

2016-03-18

In this paper, we present a novel automatic pipeline to build personalized parametric models of dynamic people using a single RGB camera. Compared to previous approaches that use monocular RGB images, our system can model a 3D human body automatically and incrementally, taking advantage of human motion. Based on coarse 2D and 3D poses estimated from image sequences, we first perform a kinematic classification of human body parts to refine the poses and obtain reconstructed body parts. Next, a personalized parametric human model is generated by driving a general template to fit the body parts and calculating the non-rigid deformation. Experimental results show that our shape estimation method achieves comparable accuracy with reconstructed models using depth cameras, yet requires neither user interaction nor any dedicated devices, leading to the feasibility of using this method on widely available smart phones.

Dynamic Human Body Modeling Using a Single RGB Camera

PubMed Central

Zhu, Haiyu; Yu, Yao; Zhou, Yu; Du, Sidan

2016-01-01

In this paper, we present a novel automatic pipeline to build personalized parametric models of dynamic people using a single RGB camera. Compared to previous approaches that use monocular RGB images, our system can model a 3D human body automatically and incrementally, taking advantage of human motion. Based on coarse 2D and 3D poses estimated from image sequences, we first perform a kinematic classification of human body parts to refine the poses and obtain reconstructed body parts. Next, a personalized parametric human model is generated by driving a general template to fit the body parts and calculating the non-rigid deformation. Experimental results show that our shape estimation method achieves comparable accuracy with reconstructed models using depth cameras, yet requires neither user interaction nor any dedicated devices, leading to the feasibility of using this method on widely available smart phones. PMID:26999159

Bubbles Responding to Ultrasound Pressure

NASA Technical Reports Server (NTRS)

2003-01-01

The Bubble and Drop Nonlinear Dynamics (BDND) experiment was designed to improve understanding of how the shape and behavior of bubbles respond to ultrasound pressure. By understanding this behavior, it may be possible to counteract complications bubbles cause during materials processing on the ground. This 12-second sequence came from video downlinked from STS-94, July 5 1997, MET:3/19:15 (approximate). The BDND guest investigator was Gary Leal of the University of California, Santa Barbara. The experiment was part of the space research investigations conducted during the Microgravity Science Laboratory-1R mission (STS-94, July 1-17 1997). Advanced fluid dynamics experiments will be a part of investigations plarned for the International Space Station. (435KB, 13-second MPEG, screen 160 x 120 pixels; downlinked video, higher quality not available) A still JPG composite of this movie is available at http://mix.msfc.nasa.gov/ABSTRACTS/MSFC-0300162.html.

Thermal runaway and microwave heating in thin cylindrical domains

NASA Astrophysics Data System (ADS)

Ward, Michael J.

2002-04-01

The behaviour of the solution to two nonlinear heating problems in a thin cylinder of revolution of variable cross-sectional area is analysed using asymptotic and numerical methods. The first problem is to calculate the fold point, corresponding to the onset of thermal runaway, for a steady-state nonlinear elliptic equation that arises in combustion theory. In the limit of thin cylindrical domains, it is shown that the onset of thermal runaway can be delayed when a circular cylindrical domain is perturbed into a dumbell shape. Numerical values for the fold point for different domain shapes are obtained asymptotically and numerically. The second problem that is analysed is a nonlinear parabolic equation modelling the microwave heating of a ceramic cylinder by a known electric field. The basic model in a thin circular cylindrical domain was analysed in Booty & Kriegsmann (Meth. Appl. Anal. 4 (1994) p. 403). Their analysis is extended to treat thin cylindrical domains of variable cross-section. It is shown that the steady-state and dynamic behaviours of localized regions of high temperature, called hot-spots, depend on a competition between the maxima of the electric field and the maximum deformation of the circular cylinder. For a dumbell-shaped region it is shown that two disconnected hot-spot regions can occur. Depending on the parameters in the model, these regions, ultimately, either merge as time increases or else remain as disconnected regions for all time.

Phenotypic models of evolution and development: geometry as destiny.

PubMed

François, Paul; Siggia, Eric D

2012-12-01

Quantitative models of development that consider all relevant genes typically are difficult to fit to embryonic data alone and have many redundant parameters. Computational evolution supplies models of phenotype with relatively few variables and parameters that allows the patterning dynamics to be reduced to a geometrical picture for how the state of a cell moves. The clock and wavefront model, that defines the phenotype of somitogenesis, can be represented as a sequence of two discrete dynamical transitions (bifurcations). The expression-time to space map for Hox genes and the posterior dominance rule are phenotypes that naturally follow from computational evolution without considering the genetics of Hox regulation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Outflow-Induced Dynamical and Radiative Instability in Stellar Envelopes with an Application to Luminous Blue Variables and Wolf-Rayet Stars

NASA Technical Reports Server (NTRS)

Stothers, Richard B.; Hansen, James E. (Technical Monitor)

2002-01-01

Theoretical models of the remnants of massive stars in a very hot, post-red-supergiant phase display no obvious instability if standard assumptions are made. However, the brightest observed classical luminous blue variables (LBVs) may well belong to such a phase. A simple time-dependent theory of moving stellar envelopes is developed in order to treat deep hydrodynamical disturbances caused by surface mass loss and to test the moving envelopes for dynamical instability. In the case of steady-state outflow, the theory reduces to the equivalent of the Castor, Abbott, and Klein formulation for optically thick winds at distances well above the sonic point. The time-dependent version indicates that the brightest and hottest LBVs are both dynamically and radiatively unstable, as a result of the substantial lowering of the generalized Eddington luminosity limit by the mass-loss acceleration. It is suggested that dynamical instability, by triggering secular cycles of mass loss, is primarily what differentiates LBVs from the purely radiatively unstable Wolf-Rayet stars. Furthermore, when accurate main-sequence mass-loss rates are used to calculate the evolutionary tracks, the predicted surface hydrogen and nitrogen abundances of the blue remnants agree much better with observations of the brightest LBVs than before.

Looking for a precursor of spontaneous Sleep Slow Oscillations in human sleep: The role of the sigma activity

PubMed Central

Allegrini, Paolo; Bedini, Remo; Bergamasco, Massimo; Laurino, Marco; Sebastiani, Laura; Gemignani, Angelo

2016-01-01

Sleep Slow Oscillations (SSOs), paradigmatic EEG markers of cortical bistability (alternation between cellular downstates and upstates), and sleep spindles, paradigmatic EEG markers of thalamic rhythm, are two hallmarks of sleeping brain. Selective thalamic lesions are reportedly associated to reductions of spindle activity and its spectrum ~14 Hz (sigma), and to alterations of SSO features. This apparent, parallel behavior suggests that thalamo-cortical entrainment favors cortical bistability. Here we investigate temporally-causal associations between thalamic sigma activity and shape, topology, and dynamics of SSOs. We recorded sleep EEG and studied whether spatio-temporal variability of SSO amplitude, negative slope (synchronization in downstate falling) and detection rate are driven by cortical-sigma-activity expression (12–18 Hz), in 3 consecutive 1 s-EEG-epochs preceding each SSO event (Baselines). We analyzed: (i) spatial variability, comparing maps of baseline sigma power and of SSO features, averaged over the first sleep cycle; (ii) event-by-event shape variability, computing for each electrode correlations between baseline sigma power and amplitude/slope of related SSOs; (iii) event-by-event spreading variability, comparing baseline sigma power in electrodes showing an SSO event with the homologous ones, spared by the event. The scalp distribution of baseline sigma power mirrored those of SSO amplitude and slope; event-by-event variability in baseline sigma power was associated with that in SSO amplitude in fronto-central areas; within each SSO event, electrodes involved in cortical bistability presented higher baseline sigma activity than those free of SSO. In conclusion, spatio-temporal variability of thalamocortical entrainment, measured by background sigma activity, is a reliable estimate of the cortical proneness to bistability. PMID:26003553

Analysis of mitochondrial DNA in Bolivian llama, alpaca and vicuna populations: a contribution to the phylogeny of the South American camelids.

PubMed

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Saavedra, V; Chiri, R; Latorre, E; Arranz, J J

2013-04-01

The objectives of this work were to assess the mtDNA diversity of Bolivian South American camelid (SAC) populations and to shed light on the evolutionary relationships between the Bolivian camelids and other populations of SACs. We have analysed two different mtDNA regions: the complete coding region of the MT-CYB gene and 513 bp of the D-loop region. The populations sampled included Bolivian llamas, alpacas and vicunas, and Chilean guanacos. High levels of genetic diversity were observed in the studied populations. In general, MT-CYB was more variable than D-loop. On a species level, the vicunas showed the lowest genetic variability, followed by the guanacos, alpacas and llamas. Phylogenetic analyses performed by including additional available mtDNA sequences from the studied species confirmed the existence of the two monophyletic clades previously described by other authors for guanacos (G) and vicunas (V). Significant levels of mtDNA hybridization were found in the domestic species. Our sequence analyses revealed significant sequence divergence within clade G, and some of the Bolivian llamas grouped with the majority of the southern guanacos. This finding supports the existence of more than the one llama domestication centre in South America previously suggested on the basis of archaeozoological evidence. Additionally, analysis of D-loop sequences revealed two new matrilineal lineages that are distinct from the previously reported G and V clades. The results presented here represent the first report on the population structure and genetic variability of Bolivian camelids and may help to elucidate the complex and dynamic domestication process of SAC populations. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Statistical Analyses of Brain Surfaces Using Gaussian Random Fields on 2-D Manifolds

PubMed Central

Staib, Lawrence H.; Xu, Dongrong; Zhu, Hongtu; Peterson, Bradley S.

2008-01-01

Interest in the morphometric analysis of the brain and its subregions has recently intensified because growth or degeneration of the brain in health or illness affects not only the volume but also the shape of cortical and subcortical brain regions, and new image processing techniques permit detection of small and highly localized perturbations in shape or localized volume, with remarkable precision. An appropriate statistical representation of the shape of a brain region is essential, however, for detecting, localizing, and interpreting variability in its surface contour and for identifying differences in volume of the underlying tissue that produce that variability across individuals and groups of individuals. Our statistical representation of the shape of a brain region is defined by a reference region for that region and by a Gaussian random field (GRF) that is defined across the entire surface of the region. We first select a reference region from a set of segmented brain images of healthy individuals. The GRF is then estimated as the signed Euclidean distances between points on the surface of the reference region and the corresponding points on the corresponding region in images of brains that have been coregistered to the reference. Correspondences between points on these surfaces are defined through deformations of each region of a brain into the coordinate space of the reference region using the principles of fluid dynamics. The warped, coregistered region of each subject is then unwarped into its native space, simultaneously bringing into that space the map of corresponding points that was established when the surfaces of the subject and reference regions were tightly coregistered. The proposed statistical description of the shape of surface contours makes no assumptions, other than smoothness, about the shape of the region or its GRF. The description also allows for the detection and localization of statistically significant differences in the shapes of the surfaces across groups of subjects at both a fine and coarse scale. We demonstrate the effectiveness of these statistical methods by applying them to study differences in shape of the amygdala and hippocampus in a large sample of normal subjects and in subjects with attention deficit/hyperactivity disorder (ADHD). PMID:17243583

The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea.

PubMed

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2016-01-01

The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata , and Porites lutea , were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria , and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata , both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris - and Gluconacetobacter diazotrophicus -affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea . The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.

The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea

PubMed Central

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D.; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2016-01-01

The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont. PMID:27920768

Molecular Epidemiology and Genetic Variation of Pathogenic Vibrio parahaemolyticus in Peru

PubMed Central

Gavilan, Ronnie G.; Zamudio, Maria L.; Martinez-Urtaza, Jaime

2013-01-01

Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale. The epidemiological significance of V. parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected in the region, changing the epidemic dynamics of this pathogen in Peru. With the aim to assess the impact of the arrival of the pandemic clone on local populations of pathogenic V. parahaemolyticus in Peru, we investigated the population genetics and genomic variation in a complete collection of non-pandemic strains recovered from clinical sources in Peru during the pre- and post-emergence periods of the pandemic clone. A total of 56 clinical strains isolated in Peru during the period 1994 to 2007, 13 strains from Chile and 20 strains from Asia were characterized by Multilocus Sequence Typing (MLST) and checked for the presence of Variable Genomic Regions (VGRs). The emergence of O3:K6 cases in Peru implied a drastic disruption of the seasonal dynamics of infections and a shift in the serotype dominance of pathogenic V. parahaemolyticus. After the arrival of the pandemic clone, a great diversity of serovars not previously reported was detected in the country, which supports the introduction of additional populations cohabitating with the pandemic group. Moreover, the presence of genomic regions characteristic of the pandemic clone in other non-pandemic strains may represent early evidence of genetic transfer from the introduced population to the local communities. Finally, the results of this study stress the importance of population admixture, horizontal genetic transfer and homologous recombination as major events shaping the structure and diversity of pathogenic V. parahaemolyticus. PMID:23696906

Taxonomy of Penicillium section Citrina

PubMed Central

Houbraken, J.; Frisvad, J.C.; Samson, R.A.

2011-01-01

Species of Penicillium section Citrina have a worldwide distribution and occur commonly in soils. The section is here delimited using a combination of phenotypic characters and sequences of the nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA (ITS) and partial RPB2 sequences. Species assigned to section Citrina share the production of symmetrically biverticillate conidiophores, flask shaped phialides (7.0–9.0 μm long) and relatively small conidia (2.0–3.0 μm diam). Some species can produce greyish-brown coloured cleistothecia containing flanged ascospores. In the present study, more than 250 isolates presumably belonging to section Citrina were examined using a combined analysis of phenotypic and physiological characters, extrolite profiles and ITS, β-tubulin and/or calmodulin sequences. Section Citrina includes 39 species, and 17 of those are described here as new. The most important phenotypic characters for distinguishing species are growth rates and colony reverse colours on the agar media CYA, MEA and YES; shape, size and ornamentation of conidia and the production of sclerotia or cleistothecia. Temperature-growth profiles were made for all examined species and are a valuable character characters for species identification. Species centered around P. citrinum generally have a higher maximum growth temperature (33–36 °C) than species related to P. westlingii (27–33 °C). Extrolite patterns and partial calmodulin and β-tubulin sequences can be used for sequence based identification and resolved all species. In contrast, ITS sequences were less variable and only 55 % of the species could be unambiguously identified with this locus. Taxonomic novelties: Penicillium argentinense Houbraken, Frisvad & Samson, P. atrofulvum Houbraken, Frisvad & Samson, P. aurantiacobrunneum Houbraken, Frisvad & Samson, P. cairnsense Houbraken, Frisvad & Samson, P. christenseniae Houbraken, Frisvad & Samson, P. copticola Houbraken, Frisvad & Samson, P. cosmopolitanum Houbraken, Frisvad & Samson, P. neomiczynskii Cole, Houbraken, Frisvad & Samson, P. nothofagi Houbraken, Frisvad & Samson, P. pancosmium Houbraken, Frisvad & Samson, P. pasqualense Houbraken, Frisvad & Samson, P. quebecense Seifert, Houbraken, Frisvad & Samson, P. raphiae Houbraken, Frisvad & Samson, P. terrigenum Seifert, Houbraken, Frisvad & Samson, P. ubiquetum Houbraken, Frisvad & Samson, P. vancouverense Houbraken, Frisvad & Samson, P. wellingtonense Cole, Houbraken, Frisvad & Samson. PMID:22308046

Reconfigurable and Reprocessable Thermoset Shape Memory Polymer with Synergetic Triple Dynamic Covalent Bonds.

PubMed

Wang, Yongwei; Pan, Yi; Zheng, Zhaohui; Ding, Xiaobin

2018-04-20

Degradable shape memory polymers (SMPs), especially for polyurethane-based SMPs, have shown great potential for biomedical applications. How to reasonably fabricate SMPs with the ideal combination of degradability, shape reconfigurability, and reprocessability is a critical issue and remains a challenge for medical disposable materials. Herein, a shape memory poly(urethane-urea) with synergetic triple dynamic covalent bonds is reported via embedding polycaprolactone unit into poly(urethane-urea) with the hindered urea dynamic bond. The single polymer network is biodegradable, thermadapt, and reprocessable, without sacrificing the outstanding shape memory performance. Such a shape memory network with plasticity and reprocessability is expected to have significant and positive impact on the medical device industry. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Topology optimization of pressure adaptive honeycomb for a morphing flap

NASA Astrophysics Data System (ADS)

Vos, Roelof; Scheepstra, Jan; Barrett, Ron

2011-03-01

The paper begins with a brief historical overview of pressure adaptive materials and structures. By examining avian anatomy, it is seen that pressure-adaptive structures have been used successfully in the Natural world to hold structural positions for extended periods of time and yet allow for dynamic shape changes from one flight state to the next. More modern pneumatic actuators, including FAA certified autopilot servoactuators are frequently used by aircraft around the world. Pneumatic artificial muscles (PAM) show good promise as aircraft actuators, but follow the traditional model of load concentration and distribution commonly found in aircraft. A new system is proposed which leaves distributed loads distributed and manipulates structures through a distributed actuator. By using Pressure Adaptive Honeycomb (PAH), it is shown that large structural deformations in excess of 50% strains can be achieved while maintaining full structural integrity and enabling secondary flight control mechanisms like flaps. The successful implementation of pressure-adaptive honeycomb in the trailing edge of a wing section sparked the motivation for subsequent research into the optimal topology of the pressure adaptive honeycomb within the trailing edge of a morphing flap. As an input for the optimization two known shapes are required: a desired shape in cruise configuration and a desired shape in landing configuration. In addition, the boundary conditions and load cases (including aerodynamic loads and internal pressure loads) should be specified for each condition. Finally, a set of six design variables is specified relating to the honeycomb and upper skin topology of the morphing flap. A finite-element model of the pressure-adaptive honeycomb structure is developed specifically tailored to generate fast but reliable results for a given combination of external loading, input variables, and boundary conditions. Based on two bench tests it is shown that this model correlates well to experimental results. The optimization process finds the skin and honeycomb topology that minimizes the error between the acquired shape and the desired shape in each configuration.

Coastal Ocean Variability Off the Coast of Taiwan in Response toTyphoon Morakot: River Forcing, Atmospheric Forcing, and Cold Dome Dynamics

DTIC Science & Technology

2014-09-01

very short time period and in this research, we model and study the effects of this rainfall on Taiwan?s coastal oceans as a result of river discharge...model and study the effects of this rainfall on Taiwan’s coastal oceans as a result of river discharge. We do this through the use of a river discharge... Effects of Footprint Shape on the Bulk Mixing Model . . . . . . . . . 57 4.2 Effects of the Horizontal Extent of the Bulk Mixing Model . . . . . . 59

The conformation of the monomethyl ethers of methyl beta-lactoside in D2O and Me2SO-d6 solutions.

PubMed

Fernández, P; Jiménez-Barbero, J

1993-10-04

The solution conformations of all the possible monomethyl ethers of methyl beta-lactoside have been analysed using molecular mechanics and dynamics calculations and nuclear magnetic resonance data (variable temperature and NOE experiments). The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low-energy region with phi = -100 +/- 40 degrees and psi = -135 +/- 35 degrees, which is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides.

Dynamic and structural control utilizing smart materials and structures

NASA Technical Reports Server (NTRS)

Rogers, C. A.; Robertshaw, H. H.

1989-01-01

An account is given of several novel 'smart material' structural control concepts that are currently under development. The thrust of these investigations is the evolution of intelligent materials and structures superceding the recently defined variable-geometry trusses and shape memory alloy-reinforced composites; the substances envisioned will be able to autonomously evaluate emergent environmental conditions and adapt to them, and even change their operational objectives. While until now the primary objective of the developmental efforts presently discussed has been materials that mimic biological functions, entirely novel concepts may be formulated in due course.

Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles.

PubMed

Guo, Sijin; Li, Hui; Ma, Mengshi; Fu, Jian; Dong, Yizhou; Guo, Peixuan

2017-12-15

RNA molecules have emerged as promising therapeutics. Like all other drugs, the safety profile and immune response are important criteria for drug evaluation. However, the literature on RNA immunogenicity has been controversial. Here, we used the approach of RNA nanotechnology to demonstrate that the immune response of RNA nanoparticles is size, shape, and sequence dependent. RNA triangle, square, pentagon, and tetrahedron with same shape but different sizes, or same size but different shapes were used as models to investigate the immune response. The levels of pro-inflammatory cytokines induced by these RNA nanoarchitectures were assessed in macrophage-like cells and animals. It was found that RNA polygons without extension at the vertexes were immune inert. However, when single-stranded RNA with a specific sequence was extended from the vertexes of RNA polygons, strong immune responses were detected. These immunostimulations are sequence specific, because some other extended sequences induced little or no immune response. Additionally, larger-size RNA square induced stronger cytokine secretion. 3D RNA tetrahedron showed stronger immunostimulation than planar RNA triangle. These results suggest that the immunogenicity of RNA nanoparticles is tunable to produce either a minimal immune response that can serve as safe therapeutic vectors, or a strong immune response for cancer immunotherapy or vaccine adjuvants. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Some Causes of the Variable Shape of Flocks of Birds

PubMed Central

Hemelrijk, Charlotte K.; Hildenbrandt, Hanno

2011-01-01

Flocks of birds are highly variable in shape in all contexts (while travelling, avoiding predation, wheeling above the roost). Particularly amazing in this respect are the aerial displays of huge flocks of starlings (Sturnus vulgaris) above the sleeping site at dawn. The causes of this variability are hardly known, however. Here we hypothesise that variability of shape increases when there are larger local differences in movement behaviour in the flock. We investigate this hypothesis with the help of a model of the self-organisation of travelling groups, called StarDisplay, since such a model has also increased our understanding of what causes the oblong shape of schools of fish. The flocking patterns in the model prove to resemble those of real birds, in particular of starlings and rock doves. As to shape, we measure the relative proportions of the flock in several ways, which either depend on the direction of movement or do not. We confirm that flock shape is usually more variable when local differences in movement in the flock are larger. This happens when a) flock size is larger, b) interacting partners are fewer, c) the flock turnings are stronger, and d) individuals roll into the turn. In contrast to our expectations, when variability of speed in the flock is higher, flock shape and the positions of members in the flock are more static. We explain this and indicate the adaptive value of low variability of speed and spatial restriction of interaction and develop testable hypotheses. PMID:21829627

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

PubMed

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

Collective decision dynamics in the presence of external drivers

NASA Astrophysics Data System (ADS)

Bassett, Danielle S.; Alderson, David L.; Carlson, Jean M.

2012-09-01

We develop a sequence of models describing information transmission and decision dynamics for a network of individual agents subject to multiple sources of influence. Our general framework is set in the context of an impending natural disaster, where individuals, represented by nodes on the network, must decide whether or not to evacuate. Sources of influence include a one-to-many externally driven global broadcast as well as pairwise interactions, across links in the network, in which agents transmit either continuous opinions or binary actions. We consider both uniform and variable threshold rules on the individual opinion as baseline models for decision making. Our results indicate that (1) social networks lead to clustering and cohesive action among individuals, (2) binary information introduces high temporal variability and stagnation, and (3) information transmission over the network can either facilitate or hinder action adoption, depending on the influence of the global broadcast relative to the social network. Our framework highlights the essential role of local interactions between agents in predicting collective behavior of the population as a whole.

How many Coccolithovirus genotypes does it take to terminate an Emiliania huxleyi bloom?

PubMed

Highfield, Andrea; Evans, Claire; Walne, Anthony; Miller, Peter I; Schroeder, Declan C

2014-10-01

Giant viruses are known to be significant mortality agents of phytoplankton, often being implicated in the terminations of large Emiliania huxleyi blooms. We have previously shown the high temporal variability of E. huxleyi-infecting coccolithoviruses (EhVs) within a Norwegian fjord mesocosm. In the current study we investigated EhV dynamics within a naturally-occurring E. huxleyi bloom in the Western English Channel. Using denaturing gradient gel electrophoresis and marker gene sequencing, we uncovered a spatially highly dynamic Coccolithovirus population that was associated with a genetically stable E. huxleyi population as revealed by the major capsid protein gene (mcp) and coccolith morphology motif (CMM), respectively. Coccolithoviruses within the bloom were found to be variable with depth and unique virus populations were detected at different stations sampled indicating a complex network of EhV-host infections. This ultimately will have significant implications to the internal structure and longevity of ecologically important E. huxleyi blooms. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

PubMed Central

Volz, Erik M.; Koopman, James S.; Ward, Melissa J.; Brown, Andrew Leigh; Frost, Simon D. W.

2012-01-01

Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences, particularly among recently HIV-infected individuals, which have been used to argue for a high transmission rate during acute infection. Using a large set of HIV-1 subtype B pol sequences collected from men who have sex with men, we demonstrate that virus from recent infections tend to be phylogenetically clustered at a greater rate than virus from patients with chronic infection (‘excess clustering’) and also tend to cluster with other recent HIV infections rather than chronic, established infections (‘excess co-clustering’), consistent with previous reports. To determine the role that a higher infectivity during acute infection may play in excess clustering and co-clustering, we developed a simple model of HIV infection that incorporates an early period of intensified transmission, and explicitly considers the dynamics of phylogenetic clusters alongside the dynamics of acute and chronic infected cases. We explored the potential for clustering statistics to be used for inference of acute stage transmission rates and found that no single statistic explains very much variance in parameters controlling acute stage transmission rates. We demonstrate that high transmission rates during the acute stage is not the main cause of excess clustering of virus from patients with early/acute infection compared to chronic infection, which may simply reflect the shorter time since transmission in acute infection. Higher transmission during acute infection can result in excess co-clustering of sequences, while the extent of clustering observed is most sensitive to the fraction of infections sampled. PMID:22761556

The neural dynamics of song syntax in songbirds

NASA Astrophysics Data System (ADS)

Jin, Dezhe

2010-03-01

Songbird is ``the hydrogen atom'' of the neuroscience of complex, learned vocalizations such as human speech. Songs of Bengalese finch consist of sequences of syllables. While syllables are temporally stereotypical, syllable sequences can vary and follow complex, probabilistic syntactic rules, which are rudimentarily similar to grammars in human language. Songbird brain is accessible to experimental probes, and is understood well enough to construct biologically constrained, predictive computational models. In this talk, I will discuss the structure and dynamics of neural networks underlying the stereotypy of the birdsong syllables and the flexibility of syllable sequences. Recent experiments and computational models suggest that a syllable is encoded in a chain network of projection neurons in premotor nucleus HVC (proper name). Precisely timed spikes propagate along the chain, driving vocalization of the syllable through downstream nuclei. Through a computational model, I show that that variable syllable sequences can be generated through spike propagations in a network in HVC in which the syllable-encoding chain networks are connected into a branching chain pattern. The neurons mutually inhibit each other through the inhibitory HVC interneurons, and are driven by external inputs from nuclei upstream of HVC. At a branching point that connects the final group of a chain to the first groups of several chains, the spike activity selects one branch to continue the propagation. The selection is probabilistic, and is due to the winner-take-all mechanism mediated by the inhibition and noise. The model predicts that the syllable sequences statistically follow partially observable Markov models. Experimental results supporting this and other predictions of the model will be presented. We suggest that the syntax of birdsong syllable sequences is embedded in the connection patterns of HVC projection neurons.

The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus.

PubMed

Valdazo-González, Begoña; Kim, Jan T; Soubeyrand, Samuel; Wadsworth, Jemma; Knowles, Nick J; Haydon, Daniel T; King, Donald P

2015-06-01

Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Design of a dynamic sonar emitter inspired by hipposiderid bats.

PubMed

Yang, Luhui; Yu, Allison; Mueller, Rolf

2018-06-19

The ultrasonic emission in the biosonar systems of bats such as the Old World leaf-nosed bats (family Hipposideridae) and the related horseshoe bats (family Rhinolophidae) is characterized by a unique dynamics where baffle shapes ("noseleaves") deform while diffracting the outgoing wave packets. As of now, nothing comparable to this dynamics has been used in any related engineering application (e.g., sonar or radar). Prior work with simple concave baffle shapes has demonstrated an impact of the dynamics on the emission characteristics, but it has remained unclear if this was simply due to the change in aperture size or also influenced by geometrical shape detail. Hence, it has also remained unclear if the time-variant effects reported so far could be further enhanced through different static and dynamic geometries. To address this issue, we have created a dynamic emission baffle with biomimetic shape detail modeled after Pratt's roundleaf bats (\\textit{Hipposideros pratti}). The impact of this shape's dynamic deformation on the time-variant emission characteristics was evaluated by virtue of the gradient magnitude and the entropy in the gradient orientation. The results have shown that the dynamics resulted in much larger gradients in a signal representation that changed jointly over direction and time. © 2018 IOP Publishing Ltd.

Advances in single-cell RNA sequencing and its applications in cancer research.

PubMed

Zhu, Sibo; Qing, Tao; Zheng, Yuanting; Jin, Li; Shi, Leming

2017-08-08

Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years' development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection. One appealing area of single-cell RNA-seq is cancer research, and it is regarded as a promising way to enhance prognosis and provide more precise target therapy by identifying druggable subclones. Indeed, progresses have been made regarding solid tumor analysis to reveal intratumoral heterogeneity, correlations between signaling pathways, stemness, drug resistance, and tumor architecture shaping the microenvironment. Furthermore, through investigation into circulating tumor cells, many genes have been shown to promote a propensity toward stemness and the epithelial-mesenchymal transition, to enhance anchoring and adhesion, and to be involved in mechanisms of anoikis resistance and drug resistance. This review focuses on advances and progresses of single-cell RNA-seq with regard to the following aspects: 1. Methodologies of single-cell RNA-seq 2. Single-cell isolation techniques 3. Single-cell RNA-seq in solid tumor research 4. Single-cell RNA-seq in circulating tumor cell research 5.

Advances in single-cell RNA sequencing and its applications in cancer research

PubMed Central

Zhu, Sibo; Qing, Tao; Zheng, Yuanting; Jin, Li; Shi, Leming

2017-01-01

Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years’ development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection. One appealing area of single-cell RNA-seq is cancer research, and it is regarded as a promising way to enhance prognosis and provide more precise target therapy by identifying druggable subclones. Indeed, progresses have been made regarding solid tumor analysis to reveal intratumoral heterogeneity, correlations between signaling pathways, stemness, drug resistance, and tumor architecture shaping the microenvironment. Furthermore, through investigation into circulating tumor cells, many genes have been shown to promote a propensity toward stemness and the epithelial-mesenchymal transition, to enhance anchoring and adhesion, and to be involved in mechanisms of anoikis resistance and drug resistance. This review focuses on advances and progresses of single-cell RNA-seq with regard to the following aspects: 1. Methodologies of single-cell RNA-seq 2. Single-cell isolation techniques 3. Single-cell RNA-seq in solid tumor research 4. Single-cell RNA-seq in circulating tumor cell research 5. Perspectives PMID:28881849

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Dynamics of shaping ultrashort optical dissipative solitary pulses in the actively mode-locked semiconductor laser with an external long-haul single-mode fiber cavity

NASA Astrophysics Data System (ADS)

Shcherbakov, Alexandre S.; Moreno Zarate, Pedro

2010-02-01

We describe the conditions of shaping regular trains of optical dissipative solitary pulses, excited by multi-pulse sequences of periodic modulating signals, in the actively mode-locked semiconductor laser heterostructure with an external long-haul single-mode silicon fiber exhibiting square-law dispersion, cubic Kerr nonlinearity, and linear optical losses. The presented model for the analysis includes three principal contributions associated with the modulated gain, optical losses, as well as linear and nonlinear phase shifts. In fact, the trains of optical dissipative solitary pulses appear within simultaneous presenting and a balance of mutually compensating interactions between the second-order dispersion and cubic-law Kerr nonlinearity as well as between active medium gain and linear optical losses in the combined cavity. Within such a model, a contribution of the nonlinear Ginzburg-Landau operator to shaping the parameters of optical dissipative solitary pulses is described via exploiting an approximate variational procedure involving the technique of trial functions. Finally, the results of the illustrating proof-of-principle experiments are briefly presented and discussed in terms of optical dissipative solitary pulses.

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

PubMed Central

Mavrodi, Dmitri V.; Mavrodi, Olga V.; Elbourne, Liam D. H.; Tetu, Sasha; Bonsall, Robert F.; Parejko, James; Yang, Mingming; Paulsen, Ian T.; Weller, David M.; Thomashow, Linda S.

2018-01-01

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome. PMID:29619036

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

PubMed Central

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-01-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40–60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats. PMID:28072418

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

PubMed

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-05-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

A Neural Dynamic Architecture for Reaching and Grasping Integrates Perception and Movement Generation and Enables On-Line Updating.

PubMed

Knips, Guido; Zibner, Stephan K U; Reimann, Hendrik; Schöner, Gregor

2017-01-01

Reaching for objects and grasping them is a fundamental skill for any autonomous robot that interacts with its environment. Although this skill seems trivial to adults, who effortlessly pick up even objects they have never seen before, it is hard for other animals, for human infants, and for most autonomous robots. Any time during movement preparation and execution, human reaching movement are updated if the visual scene changes (with a delay of about 100 ms). The capability for online updating highlights how tightly perception, movement planning, and movement generation are integrated in humans. Here, we report on an effort to reproduce this tight integration in a neural dynamic process model of reaching and grasping that covers the complete path from visual perception to movement generation within a unified modeling framework, Dynamic Field Theory. All requisite processes are realized as time-continuous dynamical systems that model the evolution in time of neural population activation. Population level neural processes bring about the attentional selection of objects, the estimation of object shape and pose, and the mapping of pose parameters to suitable movement parameters. Once a target object has been selected, its pose parameters couple into the neural dynamics of movement generation so that changes of pose are propagated through the architecture to update the performed movement online. Implementing the neural architecture on an anthropomorphic robot arm equipped with a Kinect sensor, we evaluate the model by grasping wooden objects. Their size, shape, and pose are estimated from a neural model of scene perception that is based on feature fields. The sequential organization of a reach and grasp act emerges from a sequence of dynamic instabilities within a neural dynamics of behavioral organization, that effectively switches the neural controllers from one phase of the action to the next. Trajectory formation itself is driven by a dynamical systems version of the potential field approach. We highlight the emergent capacity for online updating by showing that a shift or rotation of the object during the reaching phase leads to the online adaptation of the movement plan and successful completion of the grasp.

A Neural Dynamic Architecture for Reaching and Grasping Integrates Perception and Movement Generation and Enables On-Line Updating

PubMed Central

Knips, Guido; Zibner, Stephan K. U.; Reimann, Hendrik; Schöner, Gregor

2017-01-01

Reaching for objects and grasping them is a fundamental skill for any autonomous robot that interacts with its environment. Although this skill seems trivial to adults, who effortlessly pick up even objects they have never seen before, it is hard for other animals, for human infants, and for most autonomous robots. Any time during movement preparation and execution, human reaching movement are updated if the visual scene changes (with a delay of about 100 ms). The capability for online updating highlights how tightly perception, movement planning, and movement generation are integrated in humans. Here, we report on an effort to reproduce this tight integration in a neural dynamic process model of reaching and grasping that covers the complete path from visual perception to movement generation within a unified modeling framework, Dynamic Field Theory. All requisite processes are realized as time-continuous dynamical systems that model the evolution in time of neural population activation. Population level neural processes bring about the attentional selection of objects, the estimation of object shape and pose, and the mapping of pose parameters to suitable movement parameters. Once a target object has been selected, its pose parameters couple into the neural dynamics of movement generation so that changes of pose are propagated through the architecture to update the performed movement online. Implementing the neural architecture on an anthropomorphic robot arm equipped with a Kinect sensor, we evaluate the model by grasping wooden objects. Their size, shape, and pose are estimated from a neural model of scene perception that is based on feature fields. The sequential organization of a reach and grasp act emerges from a sequence of dynamic instabilities within a neural dynamics of behavioral organization, that effectively switches the neural controllers from one phase of the action to the next. Trajectory formation itself is driven by a dynamical systems version of the potential field approach. We highlight the emergent capacity for online updating by showing that a shift or rotation of the object during the reaching phase leads to the online adaptation of the movement plan and successful completion of the grasp. PMID:28303100

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

PubMed Central

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-01-01

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

PubMed

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea

PubMed Central

Rieck, Angelika; Herlemann, Daniel P. R.; Jürgens, Klaus; Grossart, Hans-Peter

2015-01-01

Many studies on bacterial community composition (BCC) do not distinguish between particle-associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16 S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. “Shannon and Simpson indices” showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently. PMID:26648911

Diversity and dynamics of the Vibrio community in well water used for drinking in Guinea-Bissau (West Africa).

PubMed

Machado, A; Bordalo, A A

2014-09-01

Bacteria of the genus Vibrio are ubiquitous in aquatic environments and can be found either in culturable or in a viable but nonculturable (VBNC) state. The genus comprises many pathogenic species accountable for water and food-borne diseases that prove to be fatal, especially in developing countries, as in Guinea-Bissau (West Africa), where cholera is endemic. In order to ascertain the abundance and structure of Vibrio spp. community in well waters that serve as the sole source of water for the population, quantitative polymerase chain reaction (qPCR), PCR-denaturant gradient gel electrophoresis (DGGE), and cloning approaches were used. Results suggest that Vibrio spp. were present throughout the year in acidic, freshwater wells with a seasonal community composition shift. Vibrio spp. abundance was in accordance with the abundance found in coastal environments. Sequences closely related to pathogenic Vibrio species were retrieved from well water revealing exposure of the population to such pathogens. pH, ammonium, and turbidity, regulated by the rain pattern, seem to be the variables that contributed mostly to the shaping and selection of the Vibrio spp. community. These results reinforce the evidence for water monitoring with culture-independent methods and the clear need to create/recover water infrastructures and a proper water resources management in West African countries with similar environmental conditions.

Advanced Stirling Convertor Dynamic Test Approach and Results

NASA Technical Reports Server (NTRS)

Meer, David W.; Hill, Dennis; Ursic, Joseph J.

2010-01-01

The U.S. Department of Energy (DOE), Lockheed Martin Corporation (LM), and NASA Glenn Research Center (GRC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. As part of the extended operation testing of this power system, the Advanced Stirling Convertors (ASC) at NASA GRC undergo a vibration test sequence intended to simulate the vibration history that an ASC would experience when used in an ASRG for a space mission. This sequence includes testing at workmanship and flight acceptance levels interspersed with periods of extended operation to simulate prefueling and post fueling. The final step in the test sequence utilizes additional testing at flight acceptance levels to simulate launch. To better replicate the acceleration profile seen by an ASC incorporated into an ASRG, the input spectra used in testing the convertors was modified based on dynamic testing of the ASRG Engineering Unit (ASRG EU) at LM. This paper outlines the overall test approach, summarizes the test results from the ASRG EU, describes the incorporation of those results into the test approach, and presents the results of applying the test approach to the ASC-1 #3 and #4 convertors. The test results include data from several accelerometers mounted on the convertors as well as the piston position and output power variables.

Recapitulating phylogenies using k-mers: from trees to networks.

PubMed

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Learning of Chunking Sequences in Cognition and Behavior

PubMed Central

Rabinovich, Mikhail

2015-01-01

We often learn and recall long sequences in smaller segments, such as a phone number 858 534 22 30 memorized as four segments. Behavioral experiments suggest that humans and some animals employ this strategy of breaking down cognitive or behavioral sequences into chunks in a wide variety of tasks, but the dynamical principles of how this is achieved remains unknown. Here, we study the temporal dynamics of chunking for learning cognitive sequences in a chunking representation using a dynamical model of competing modes arranged to evoke hierarchical Winnerless Competition (WLC) dynamics. Sequential memory is represented as trajectories along a chain of metastable fixed points at each level of the hierarchy, and bistable Hebbian dynamics enables the learning of such trajectories in an unsupervised fashion. Using computer simulations, we demonstrate the learning of a chunking representation of sequences and their robust recall. During learning, the dynamics associates a set of modes to each information-carrying item in the sequence and encodes their relative order. During recall, hierarchical WLC guarantees the robustness of the sequence order when the sequence is not too long. The resulting patterns of activities share several features observed in behavioral experiments, such as the pauses between boundaries of chunks, their size and their duration. Failures in learning chunking sequences provide new insights into the dynamical causes of neurological disorders such as Parkinson’s disease and Schizophrenia. PMID:26584306

A Skilful Marine Sclerochronological Network Based Reconstruction of North Atlantic Subpolar Gyre Dynamics

NASA Astrophysics Data System (ADS)

Reynolds, D.; Hall, I. R.; Slater, S. M.; Scourse, J. D.; Wanamaker, A. D.; Halloran, P. R.; Garry, F. K.

2017-12-01

Spatial network analyses of precisely dated, and annually resolved, tree-ring proxy records have facilitated robust reconstructions of past atmospheric climate variability and the associated mechanisms and forcings that drive it. In contrast, a lack of similarly dated marine archives has constrained the use of such techniques in the marine realm, despite the potential for developing a more robust understanding of the role basin scale ocean dynamics play in the global climate system. Here we show that a spatial network of marine molluscan sclerochronological oxygen isotope (δ18Oshell) series spanning the North Atlantic region provides a skilful reconstruction of basin scale North Atlantic sea surface temperatures (SSTs). Our analyses demonstrate that the composite marine series (referred to as δ18Oproxy_PC1) is significantly sensitive to inter-annual variability in North Atlantic SSTs (R=-0.61 P<0.01) and surface air temperatures (SATs; R=-0.67, P<0.01) over the 20th century. Subpolar gyre (SPG) SSTs dominates variability in the δ18Oproxy_PC1 series at sub-centennial frequencies (R=-0.51, P<0.01). Comparison of the δ18Oproxy_PC1 series against variability in the strength of the European Slope Current and maximum North Atlantic meridional overturning circulation derived from numeric climate models (CMIP5), indicates that variability in the SPG region, associated with the strength of the surface currents of the North Atlantic, are playing a significant role in shaping the multi-decadal scale SST variability over the industrial era. These analyses demonstrate that spatial networks developed from sclerochronological archives can provide powerful baseline archives of past ocean variability that can facilitate the development of a quantitative understanding for the role the oceans play in the global climate systems and constraining uncertainties in numeric climate models.

The Complete Nucleotide Sequence of the Human Immunoglobulin Heavy Chain Variable Region Locus

PubMed Central

Matsuda, Fumihiko; Ishii, Kazuo; Bourvagnet, Patrice; Kuma, Kei-ichi; Hayashida, Hidenori; Miyata, Takashi; Honjo, Tasuku

1998-01-01

The complete nucleotide sequence of the 957-kb DNA of the human immunoglobulin heavy chain variable (VH) region locus was determined and 43 novel VH segments were identified. The region contains 123 VH segments classifiable into seven different families, of which 79 are pseudogenes. Of the 44 VH segments with an open reading frame, 39 are expressed as heavy chain proteins and 1 as mRNA, while the remaining 4 are not found in immunoglobulin cDNAs. Combinatorial diversity of VH region was calculated to be ∼6,000. Conservation of the promoter and recombination signal sequences was observed to be higher in functional VH segments than in pseudogenes. Phylogenetic analysis of 114 VH segments clearly showed clustering of the VH segments of each family. However, an independent branch in the tree contained a single VH, V4-44.1P, sharing similar levels of homology to human VH families and to those of other vertebrates. Comparison between different copies of homologous units that appear repeatedly across the locus clearly demonstrates that dynamic DNA reorganization of the locus took place at least eight times between 133 and 10 million years ago. One nonimmunoglobulin gene of unknown function was identified in the intergenic region. PMID:9841928

Mining the human gut microbiota for effector strains that shape the immune system

PubMed Central

Ahern, Philip P.; Faith, Jeremiah J.; Gordon, Jeffrey I.

2014-01-01

Summary The gut microbiota co-develops with the immune system beginning at birth. Mining the microbiota for bacterial strains responsible for shaping the structure and dynamic operations of the innate and adaptive arms of the immune system represents a formidable combinatorial problem but one that needs to be overcome to advance mechanistic understanding of microbial community-immune system co-regulation, and in order to develop new diagnostic and therapeutic approaches that promote health. Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice. Clonally-arrayed sequenced collections of bacterial strains are constructed from representative donor microbiota. If the collection transmits phenotypes, effector strains are identified by testing randomly generated subsets with overlapping membership in individually-housed germ-free animals. Detailed mechanistic studies of effector strain-host interactions can then be performed. PMID:24950201

Biophysical Aspects of Spindle Evolution

NASA Astrophysics Data System (ADS)

Farhadifar, Reza; Baer, Charlie; Needleman, Daniel

2011-03-01

The continual propagation of genetic material from one generation to the next is one of the most basic characteristics of all organisms. In eukaryotes, DNA is segregated into the two daughter cells by a highly dynamic, self-organizing structure called the mitotic spindle. Mitotic spindles can show remarkable variability between tissues and organisms, but there is currently little understanding of the biophysical and evolutionary basis of this diversity. We are studying how spontaneous mutations modify cell division during nematode development. By comparing the mutational variation - the raw material of evolution - with the variation present in nature, we are investigating how the mitotic spindle is shaped over the course of evolution. This combination of quantitative genetics and cellular biophysics gives insight into how the structure and dynamics of the spindle is formed through selection, drift, and biophysical constraints.

Timing the start of division in E. coli: a single-cell study

NASA Astrophysics Data System (ADS)

Reshes, G.; Vanounou, S.; Fishov, I.; Feingold, M.

2008-12-01

We monitor the shape dynamics of individual E. coli cells using time-lapse microscopy together with accurate image analysis. This allows measuring the dynamics of single-cell parameters throughout the cell cycle. In previous work, we have used this approach to characterize the main features of single-cell morphogenesis between successive divisions. Here, we focus on the behavior of the parameters that are related to cell division and study their variation over a population of 30 cells. In particular, we show that the single-cell data for the constriction width dynamics collapse onto a unique curve following appropriate rescaling of the corresponding variables. This suggests the presence of an underlying time scale that determines the rate at which the cell cycle advances in each individual cell. For the case of cell length dynamics a similar rescaling of variables emphasizes the presence of a breakpoint in the growth rate at the time when division starts, τc. We also find that the τc of individual cells is correlated with their generation time, τg, and inversely correlated with the corresponding length at birth, L0. Moreover, the extent of the T-period, τg - τc, is apparently independent of τg. The relations between τc, τg and L0 indicate possible compensation mechanisms that maintain cell length variability at about 10%. Similar behavior was observed for both fast-growing cells in a rich medium (LB) and for slower growth in a minimal medium (M9-glucose). To reveal the molecular mechanisms that lead to the observed organization of the cell cycle, we should further extend our approach to monitor the formation of the divisome.

Measurement of inter- and intra-annual variability of landscape fire activity at a continental scale: the Australian case

NASA Astrophysics Data System (ADS)

Williamson, Grant J.; Prior, Lynda D.; Jolly, W. Matt; Cochrane, Mark A.; Murphy, Brett P.; Bowman, David M. J. S.

2016-03-01

Climate dynamics at diurnal, seasonal and inter-annual scales shape global fire activity, although difficulties of assembling reliable fire and meteorological data with sufficient spatio-temporal resolution have frustrated quantification of this variability. Using Australia as a case study, we combine data from 4760 meteorological stations with 12 years of satellite-derived active fire detections to determine day and night time fire activity, fire season start and end dates, and inter-annual variability, across 61 objectively defined climate regions in three climate zones (monsoon tropics, arid and temperate). We show that geographic patterns of landscape burning (onset and duration) are related to fire weather, resulting in a latitudinal gradient from the monsoon tropics in winter, through the arid zone in all seasons except winter, and then to the temperate zone in summer and autumn. Peak fire activity precedes maximum lightning activity by several months in all regions, signalling the importance of human ignitions in shaping fire seasons. We determined median daily McArthur forest fire danger index (FFDI50) for days and nights when fires were detected: FFDI50 varied substantially between climate zones, reflecting effects of fire management in the temperate zone, fuel limitation in the arid zone and abundance of flammable grasses in the monsoon tropical zone. We found correlations between the proportion of days when FFDI exceeds FFDI50 and the Southern Oscillation index across the arid zone during spring and summer, and Indian Ocean dipole mode index across south-eastern Australia during summer. Our study demonstrates that Australia has a long fire weather season with high inter-annual variability relative to all other continents, making it difficult to detect long term trends. It also provides a way of establishing robust baselines to track changes to fire seasons, and supports a previous conceptual model highlighting multi-temporal scale effects of climate in shaping continental-scale pyrogeography.

Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences.

PubMed

Wang, Cheng-Long; Ding, Meng-Qi; Zou, Chen-Yan; Zhu, Xue-Mei; Tang, Yu; Zhou, Mei-Liang; Shao, Ji-Rong

2017-07-26

Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis. After morphological analysis, the main difference among these buckwheat were height, leaf shape, seeds and flower type. F. luojishanense was distinguishable from the cultivated species easily. Although the F. dibotrys and two cultivated species has some similarity, they different in habit and component contents. The cp genome of F. dibotrys was 159,320 bp while the F. luojishanense was 159,265 bp. 48 and 61 SSRs were found in F. dibotrys and F. luojishanense respectively. Meanwhile, 10 highly variable regions among these buckwheat species were located precisely. The phylogenetic relationships among four Fagopyrum species based on complete cp genomes was showed. The results suggested that F. dibotrys is more closely related to Fagopyrum tataricum. These data provided valuable genetic information for Fagopyrum species identification, taxonomy, phylogenetic study and molecular breeding.

Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Debroas, Didier

2007-09-01

Small eukaryotes (0.2-5 microm) in hyper-eutrophic conditions were described using terminal restriction fragment length polymorphism and cloning-sequencing, and were related to environmental variables both by an experimental approach and by a temporal field study. In situ analysis showed marked temporal variations in the dominant terminal restriction fragments (T-RFs), which were related to environmental variables such as nutrient concentrations and metazooplankton composition. To monitor the responses of the small-eukaryote community to top-down (absence or presence of planktivorous fish) and bottom-up (low or high nitrogen and phosphorus addition) effects, a cross-classified design mesocosm experiment was used. Depending on the type of treatment, we recorded changes in the diversity of T-RFs, as well as modifications in phylogenetic composition. Centroheliozoa and Cryptophyta were found in all types of treatment, whereas Chlorophyta were specific to enclosures receiving high nutrient loadings, and were associated either with LKM11 and 'environmental sequences'. Cercozoa and Fungi were not detected in enclosures receiving high nutrient loadings and fishes. Our results showed that resources and top-down factors are both clearly involved in shaping the structure of small eukaryotes, not only autotrophs but also heterotrophs, via complex interactions and trophic cascades within a microbial loop, notably in response to nutrient loading.

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; González, Angélica L; Doebeli, Michael; Farjalla, Vinicius F

2017-08-01

Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Construction of multiple trade-offs to obtain arbitrary singularities of adaptive dynamics.

PubMed

Kisdi, Éva

2015-04-01

Evolutionary singularities are central to the adaptive dynamics of evolving traits. The evolutionary singularities are strongly affected by the shape of any trade-off functions a model assumes, yet the trade-off functions are often chosen in an ad hoc manner, which may unjustifiably constrain the evolutionary dynamics exhibited by the model. To avoid this problem, critical function analysis has been used to find a trade-off function that yields a certain evolutionary singularity such as an evolutionary branching point. Here I extend this method to multiple trade-offs parameterized with a scalar strategy. I show that the trade-off functions can be chosen such that an arbitrary point in the viability domain of the trait space is a singularity of an arbitrary type, provided (next to certain non-degeneracy conditions) that the model has at least two environmental feedback variables and at least as many trade-offs as feedback variables. The proof is constructive, i.e., it provides an algorithm to find trade-off functions that yield the desired singularity. I illustrate the construction of trade-offs with an example where the virulence of a pathogen evolves in a small ecosystem of a host, its pathogen, a predator that attacks the host and an alternative prey of the predator.

Dynamic Analysis for a Geared Turbofan Engine with Variable Area Fan Nozzle

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Thomas, George L.

2017-01-01

Aggressive design goals have been set for future aero-propulsion systems with regards to fuel economy, noise, and emissions. To meet these challenging goals, advanced propulsion concepts are being explored and current operating margins are being re-evaluated to find additional concessions that can be made. One advanced propulsion concept being evaluated is a geared turbofan with a variable area fan nozzle (VAFN), developed by NASA. This engine features a small core, a fan driven by the low pressure turbine through a reduction gearbox, and a shape memory alloy (SMA)-actuated VAFN. The VAFN is designed to allow both a small exit area for efficient operation at cruise, while being able to open wider at high power conditions to reduce backpressure on the fan and ensure a safe level of stall margin is maintained. The VAFN is actuated via a SMA-based system instead of a conventional system to decrease overall weight of the system, however, SMA-based actuators respond relatively slowly, which introduces dynamic issues that are investigated in this work. This paper describes both a control system designed specifically for issues associated with SMAs, and dynamic analysis of the geared turbofan VAFN with the SMA actuators. Also, some future recommendations are provided for this type of propulsion system.

Data compression of discrete sequence: A tree based approach using dynamic programming

NASA Technical Reports Server (NTRS)

Shivaram, Gurusrasad; Seetharaman, Guna; Rao, T. R. N.

1994-01-01

A dynamic programming based approach for data compression of a ID sequence is presented. The compression of an input sequence of size N to that of a smaller size k is achieved by dividing the input sequence into k subsequences and replacing the subsequences by their respective average values. The partitioning of the input sequence is carried with the intention of reducing the mean squared error in the reconstructed sequence. The complexity involved in finding the partitions which would result in such an optimal compressed sequence is reduced by using the dynamic programming approach, which is presented.

Measurement of Size-dependent Dynamic Shape Factors of Quartz Particles in Two Flow Regimes

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

Alexander, Jennifer M.; Bell, David M.; Imre, D.

2016-08-02

Understanding and modeling the behavior of quartz dust particles, commonly found in the atmosphere, requires knowledge of many relevant particles properties, including particle shape. This study uses a single particle mass spectrometer, a differential mobility analyzer, and an aerosol particle mass analyzer to measure quartz aerosol particles mobility, aerodynamic, and volume equivalent diameters, mass, composition, effective density, and dynamic shape factor as a function of particle size, in both the free molecular and transition flow regimes. The results clearly demonstrate that dynamic shape factors can vary significantly as a function of particle size. For the quartz samples studied here, themore » dynamic shape factors increase with size, indicating that larger particles are significantly more aspherical than smaller particles. In addition, dynamic shape factors measured in the free-molecular (χv) and transition (χt) flow regimes can be significantly different, and these differences vary with the size of the quartz particles. For quartz, χv of small (d < 200 nm) particles is 1.25, while χv of larger particles (d ~ 440 nm) is 1.6, with a continuously increasing trend with particle size. In contrast χt, of small particles starts at 1.1 increasing slowly to 1.34 for 550 nm diameter particles. The multidimensional particle characterization approach used here goes beyond determination of average properties for each size, to provide additional information about how the particle dynamic shape factor may vary even for particles with the same mass and volume equivalent diameter.« less

Estimating nonrigid motion from inconsistent intensity with robust shape features

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

Liu, Wenyang; Ruan, Dan, E-mail: druan@mednet.ucla.edu; Department of Radiation Oncology, University of California, Los Angeles, California 90095

2013-12-15

Purpose: To develop a nonrigid motion estimation method that is robust to heterogeneous intensity inconsistencies amongst the image pairs or image sequence. Methods: Intensity and contrast variations, as in dynamic contrast enhanced magnetic resonance imaging, present a considerable challenge to registration methods based on general discrepancy metrics. In this study, the authors propose and validate a novel method that is robust to such variations by utilizing shape features. The geometry of interest (GOI) is represented with a flexible zero level set, segmented via well-behaved regularized optimization. The optimization energy drives the zero level set to high image gradient regions, andmore » regularizes it with area and curvature priors. The resulting shape exhibits high consistency even in the presence of intensity or contrast variations. Subsequently, a multiscale nonrigid registration is performed to seek a regular deformation field that minimizes shape discrepancy in the vicinity of GOIs. Results: To establish the working principle, realistic 2D and 3D images were subject to simulated nonrigid motion and synthetic intensity variations, so as to enable quantitative evaluation of registration performance. The proposed method was benchmarked against three alternative registration approaches, specifically, optical flow, B-spline based mutual information, and multimodality demons. When intensity consistency was satisfied, all methods had comparable registration accuracy for the GOIs. When intensities among registration pairs were inconsistent, however, the proposed method yielded pronounced improvement in registration accuracy, with an approximate fivefold reduction in mean absolute error (MAE = 2.25 mm, SD = 0.98 mm), compared to optical flow (MAE = 9.23 mm, SD = 5.36 mm), B-spline based mutual information (MAE = 9.57 mm, SD = 8.74 mm) and mutimodality demons (MAE = 10.07 mm, SD = 4.03 mm). Applying the proposed method on a real MR image sequence also provided qualitatively appealing results, demonstrating good feasibility and applicability of the proposed method. Conclusions: The authors have developed a novel method to estimate the nonrigid motion of GOIs in the presence of spatial intensity and contrast variations, taking advantage of robust shape features. Quantitative analysis and qualitative evaluation demonstrated good promise of the proposed method. Further clinical assessment and validation is being performed.« less

Estimating nonrigid motion from inconsistent intensity with robust shape features.

PubMed

Liu, Wenyang; Ruan, Dan

2013-12-01

To develop a nonrigid motion estimation method that is robust to heterogeneous intensity inconsistencies amongst the image pairs or image sequence. Intensity and contrast variations, as in dynamic contrast enhanced magnetic resonance imaging, present a considerable challenge to registration methods based on general discrepancy metrics. In this study, the authors propose and validate a novel method that is robust to such variations by utilizing shape features. The geometry of interest (GOI) is represented with a flexible zero level set, segmented via well-behaved regularized optimization. The optimization energy drives the zero level set to high image gradient regions, and regularizes it with area and curvature priors. The resulting shape exhibits high consistency even in the presence of intensity or contrast variations. Subsequently, a multiscale nonrigid registration is performed to seek a regular deformation field that minimizes shape discrepancy in the vicinity of GOIs. To establish the working principle, realistic 2D and 3D images were subject to simulated nonrigid motion and synthetic intensity variations, so as to enable quantitative evaluation of registration performance. The proposed method was benchmarked against three alternative registration approaches, specifically, optical flow, B-spline based mutual information, and multimodality demons. When intensity consistency was satisfied, all methods had comparable registration accuracy for the GOIs. When intensities among registration pairs were inconsistent, however, the proposed method yielded pronounced improvement in registration accuracy, with an approximate fivefold reduction in mean absolute error (MAE = 2.25 mm, SD = 0.98 mm), compared to optical flow (MAE = 9.23 mm, SD = 5.36 mm), B-spline based mutual information (MAE = 9.57 mm, SD = 8.74 mm) and mutimodality demons (MAE = 10.07 mm, SD = 4.03 mm). Applying the proposed method on a real MR image sequence also provided qualitatively appealing results, demonstrating good feasibility and applicability of the proposed method. The authors have developed a novel method to estimate the nonrigid motion of GOIs in the presence of spatial intensity and contrast variations, taking advantage of robust shape features. Quantitative analysis and qualitative evaluation demonstrated good promise of the proposed method. Further clinical assessment and validation is being performed.

DNA sequence-directed shape change of photopatterned hydrogels via high-degree swelling

NASA Astrophysics Data System (ADS)

Cangialosi, Angelo; Yoon, ChangKyu; Liu, Jiayu; Huang, Qi; Guo, Jingkai; Nguyen, Thao D.; Gracias, David H.; Schulman, Rebecca

2017-09-01

Shape-changing hydrogels that can bend, twist, or actuate in response to external stimuli are critical to soft robots, programmable matter, and smart medicine. Shape change in hydrogels has been induced by global cues, including temperature, light, or pH. Here we demonstrate that specific DNA molecules can induce 100-fold volumetric hydrogel expansion by successive extension of cross-links. We photopattern up to centimeter-sized gels containing multiple domains that undergo different shape changes in response to different DNA sequences. Experiments and simulations suggest a simple design rule for controlled shape change. Because DNA molecules can be coupled to molecular sensors, amplifiers, and logic circuits, this strategy introduces the possibility of building soft devices that respond to diverse biochemical inputs and autonomously implement chemical control programs.

Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae.

PubMed

Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

2014-12-01

Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

Metabolic interactions and dynamics in microbial communities

NASA Astrophysics Data System (ADS)

Segre', Daniel

Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines.

PubMed

Zomer, Aldert; Otsuka, Nao; Hiramatsu, Yukihiro; Kamachi, Kazunari; Nishimura, Naoko; Ozaki, Takao; Poolman, Jan; Geurtsen, Jeroen

2018-05-17

Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982-2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008-2013. The genome sequences afforded insight into B. pertussis genome variability and population dynamics in Japan, and revealed that the B. pertussis population in Japan was characterized by two major clades that divided more than 40 years ago. The pertactin gene was disrupted in about 20 % of the 149 NIID isolates, by either a deletion within the signal sequence (ΔSS) or the insertion of IS element IS481 (prn :: IS481). Phylogeny suggests that the parent clones for these isolates originated in Japan. Divergence dating traced the first generation of the pertactin-deficient mutants in Japan to around 1990, and indicated that strains containing the alternative pertactin allele prn2 may have appeared in Japan around 1974. Molecular clock data suggested that observed fluctuations in B. pertussis population size may have coincided with changes in vaccine usage in the country. The continuing failure to eradicate the disease warrants an exploration of novel vaccine compositions.

Dynamic laser beam shaping for material processing using hybrid holograms

NASA Astrophysics Data System (ADS)

Liu, Dun; Wang, Yutao; Zhai, Zhongsheng; Fang, Zheng; Tao, Qing; Perrie, Walter; Edwarson, Stuart P.; Dearden, Geoff

2018-06-01

A high quality, dynamic laser beam shaping method is demonstrated by displaying a series of hybrid holograms onto a spatial light modulator (SLM), while each one of the holograms consists of a binary grating and a geometric mask. A diffraction effect around the shaped beam has been significantly reduced. Beam profiles of arbitrary shape, such as square, ring, triangle, pentagon and hexagon, can be conveniently obtained by loading the corresponding holograms on the SLM. The shaped beam can be reconstructed in the range of 0.5 mm at the image plane. Ablation on a polished stainless steel sample at the image plane are consistent with the beam shape at the diffraction near-field. The ±1st order and higher order beams can be completely removed when the grating period is smaller than 160 μm. The local energy ratio of the shaped beam observed by the CCD camera is up to 77.67%. Dynamic processing at 25 Hz using different shapes has also been achieved.

Demonstration of Automatically-Generated Adjoint Code for Use in Aerodynamic Shape Optimization

NASA Technical Reports Server (NTRS)

Green, Lawrence; Carle, Alan; Fagan, Mike

1999-01-01

Gradient-based optimization requires accurate derivatives of the objective function and constraints. These gradients may have previously been obtained by manual differentiation of analysis codes, symbolic manipulators, finite-difference approximations, or existing automatic differentiation (AD) tools such as ADIFOR (Automatic Differentiation in FORTRAN). Each of these methods has certain deficiencies, particularly when applied to complex, coupled analyses with many design variables. Recently, a new AD tool called ADJIFOR (Automatic Adjoint Generation in FORTRAN), based upon ADIFOR, was developed and demonstrated. Whereas ADIFOR implements forward-mode (direct) differentiation throughout an analysis program to obtain exact derivatives via the chain rule of calculus, ADJIFOR implements the reverse-mode counterpart of the chain rule to obtain exact adjoint form derivatives from FORTRAN code. Automatically-generated adjoint versions of the widely-used CFL3D computational fluid dynamics (CFD) code and an algebraic wing grid generation code were obtained with just a few hours processing time using the ADJIFOR tool. The codes were verified for accuracy and were shown to compute the exact gradient of the wing lift-to-drag ratio, with respect to any number of shape parameters, in about the time required for 7 to 20 function evaluations. The codes have now been executed on various computers with typical memory and disk space for problems with up to 129 x 65 x 33 grid points, and for hundreds to thousands of independent variables. These adjoint codes are now used in a gradient-based aerodynamic shape optimization problem for a swept, tapered wing. For each design iteration, the optimization package constructs an approximate, linear optimization problem, based upon the current objective function, constraints, and gradient values. The optimizer subroutines are called within a design loop employing the approximate linear problem until an optimum shape is found, the design loop limit is reached, or no further design improvement is possible due to active design variable bounds and/or constraints. The resulting shape parameters are then used by the grid generation code to define a new wing surface and computational grid. The lift-to-drag ratio and its gradient are computed for the new design by the automatically-generated adjoint codes. Several optimization iterations may be required to find an optimum wing shape. Results from two sample cases will be discussed. The reader should note that this work primarily represents a demonstration of use of automatically- generated adjoint code within an aerodynamic shape optimization. As such, little significance is placed upon the actual optimization results, relative to the method for obtaining the results.

Casting Control of Floating-films into Ribbon-shape Structure by modified Dynamic FTM

NASA Astrophysics Data System (ADS)

Tripathi, A.; Pandey, M.; Nagamatsu, S.; Pandey, S. S.; Hayase, S.; Takashima, W.

2017-11-01

We have developed a new method to obtain Ribbon-shaped floating films via dynamic casting of floating-film and transfer method (dynamic-FTM). Dynamic-FTM is a unique method to prepare oriented thin-film of conjugated polymers (CPs) which is quick and easy. This method has several advantages as compared to the other conventional casting procedure to prepare oriented CP films. In the conventional dynamic FTM appearance of large scale circular orientation poses difficulty not only for practical applications but also hinders the detailed analysis of the orientation mechanism. In this present work, pros and cons of this newly proposed ribbon-shaped floating-film have been discussed in detail from those of the conventional floating-film prepared by dynamic-FTM.

Equilibrium figures inside the dark-matter ring and the shapes of elliptical galaxies

NASA Astrophysics Data System (ADS)

Kondratyev, B. P.; Trubitsyna, N. G.; Kireeva, E. N.

We solve the general problem of the theory of equilibrium figures and analyze two classes of liquid rotating gravitating figures residing inside a gravitating ring or torus. These figures form families of sequences of generalized oblate spheroids and triaxial ellipsoids, which at the lower limit of the tidal parameter α = 0 have the form of the Maclaurin spheroids and the Jacobi ellipsoids. In intermediate cases 0 < α ≤ αmax each new sequence of axisymmetric equilibrium figures has two non-rotating boundary spheroids. At the upper limit αmax/(π Gρ ) = 0.1867 the sequence degenerates into a single non-rotating spheroid with the eccentricity {e cr} ≈ 0.96 corresponding to the flattening limit of elliptical galaxies (E7). We also perform a detailed study of the sequences of generalized triaxial ellipsoids and find bifurcation points of triaxial ellipsoids in the sequences of generalized spheroids. We use this method to explain the shapes of E-galaxies. According to observations, very slowly rotating oblate E-type galaxies are known that have the shapes, which, because of instability, cannot be supported by velocity dispersion anisotropy exclusively. The hypothesis of a massive dark-matter outer ring requires no extreme anisotropy of pressure; it not only explains the shape of these elliptical galaxies, but also sheds new light on the riddle of the ellipticity limit (E7) of elliptical galaxies.

Test versus analysis: A discussion of methods

NASA Technical Reports Server (NTRS)

Butler, T. G.

1986-01-01

Some techniques for comparing structural vibration data determined from test and analysis are discussed. Orthogonality is a general category of one group, correlation is a second, synthesis is a third and matrix improvement is a fourth. Advantages and short-comings of the methods are explored with suggestions as to how they can complement one another. The purpose for comparing vibration data from test and analysis for a given structure is to find out whether each is representing the dynamic properties of the structure in the same way. Specifically, whether: mode shapes are alike; the frequencies of the modes are alike; modes appear in the same frequency sequence; and if they are not alike, how to judge which to believe.

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

The challenges of modelling antibody repertoire dynamics in HIV infection

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

Luo, Shishi; Perelson, Alan S.

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

The challenges of modelling antibody repertoire dynamics in HIV infection

DOE PAGES

Luo, Shishi; Perelson, Alan S.

2015-07-20

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences

PubMed Central

Sheinman, Michael; Ramisch, Anna; Massip, Florian; Arndt, Peter F.

2016-01-01

Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf’s law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes. PMID:27488939

Accretion dynamics in pre-main sequence binaries

NASA Astrophysics Data System (ADS)

Tofflemire, B.; Mathieu, R.; Herczeg, G.; Ardila, D.; Akeson, R.; Ciardi, D.; Johns-Krull, C.

Binary stars are a common outcome of star formation. Orbital resonances, especially in short-period systems, are capable of reshaping the distribution and flows of circumstellar material. Simulations of the binary-disk interaction predict a dynamically cleared gap around the central binary, accompanied by periodic ``pulsed'' accretion events that are driven by orbital motion. To place observational constraints on the binary-disk interaction, we have conducted a long-term monitoring program tracing the time-variable accretion behavior of 9 short-period binaries. In this proceeding we present two results from our campaign: 1) the detection of periodic pulsed accretion events in DQ Tau and TWA 3A, and 2) evidence that the TWA 3A primary is the dominant accretor in the system.

Tactical Determinants of Setting Zone in Elite Men'S Volleyball

PubMed Central

Afonso, Jose; Esteves, Francisca; Araújo, Rui; Thomas, Luke; Mesquita, Isabel

2012-01-01

The interactions between two opposing teams lead to the emergence of unique game patterns. In volleyball, attack efficacy emerges as the strongest predictor of the final result and thus it becomes of foremost importance to understand which game patterns afford the attaining of higher attack efficacies. These rely on the quality of the setting action. In turn, the serve and the serve reception constrain the setter's actions and the attacker's efficacy. Therefore, the purpose of this study was to examine predictors of the setting zone in elite-level men's volleyball. Thirty-one matches of the 2007 World Cup were analyzed, in total 5117 rallies. The dependent variable was the setting zone, and the independent variables were the server player, serve type, serve direction, serve depth, reception zone, receiver player and reception type. Multinomial logistic regression was applied, in order to obtain the estimated likelihood of occurrence of the dependent variable, based on the values of the independent variables (p < 0.05). Only the serve direction showed not to be predictive of the setting zone. Concerning the remaining variables, the tennis jump serve, serves from the middle-player, deep serves, reception near the endline or sidelines, reception by the zone 4 attackers when in defensive zone, and low reception all proved to impair the quality of reception, demanding the setter to play more often in the not acceptable setting zone. Results suggest that, at this level, practice of serve-reception should preferably cover the deep tennis jump serve, and attempt to afford the libero more opportunities to receive. By focusing on the variables with the most predictive power, performers may better allocate their attention towards the most pertinent cues at each moment. Knowledge of these interactive models provides valuable insights into the dynamics of the action sequences, affording coaches important information and guidance. Key pointsA set of key variables interact and allow predicting the setting zone, an important variable in determining attack efficacy in high-level men's volleyball.The tennis jump serve, deep serves, receptions near the endline or sidelines, serves from the middle-players, receptions by the zone 4 attackers when in defensive zone, and low reception enhance the utilization of non-ideal setting zones.By focusing on the variables with the most predictive power, performers may better allocate their attention towards the most pertinent cues at each moment.Knowledge of these interactive models provides valuable insights into the dynamics of the action sequences, affording coaches important information and guidance. PMID:24149123

A monograph of Otidea (Pyronemataceae, Pezizomycetes).

PubMed

Olariaga, I; Van Vooren, N; Carbone, M; Hansen, K

2015-12-01

The easily recognised genus Otidea is subjected to numerous problems in species identification. A number of old names have undergone various interpretations, materials from different continents have not been compared and misidentifications occur commonly. In this context, Otidea is monographed, based on our multiple gene phylogenies assessing species boundaries and comparative morphological characters (see Hansen & Olariaga 2015). All names combined in or synonymised with Otidea are dealt with. Thirty-three species are treated, with full descriptions and colour illustrations provided for 25 of these. Five new species are described, viz. O. borealis, O. brunneoparva, O. oregonensis, O. pseudoleporina and O. subformicarum. Otidea cantharella var. minor and O. onotica var. brevispora are elevated to species rank. Otideopsis kaushalii is combined in the genus Otidea. A key to the species of Otidea is given. An LSU dataset containing 167 sequences (with 44 newly generated in this study) is analysed to place collections and determine whether the named Otidea sequences in GenBank were identified correctly. Fourty-nine new ITS sequences were generated in this study. The ITS region is too variable to align across Otidea, but had low intraspecific variation and it aided in species identifications. Thirty type collections were studied, and ITS and LSU sequences are provided for 12 of these. A neotype is designated for O. cantharella and epitypes for O. concinna, O. leporina and O. onotica, along with several lectotypifications. The apothecial colour and shape, and spore characters are important for species identification. We conclude that to distinguish closely related or morphologically similar species, a combination of additional features are needed, i.e. the shape of the paraphyses, ectal excipulum structure, types of ectal excipulum resinous exudates and their reactions in Melzer's reagent and KOH, tomentum and basal mycelium colours and exudates. The KOH reaction of excipular resinous exudates and basal mycelium are introduced as novel taxonomic characters.

Sequence information signal processor for local and global string comparisons

DOEpatents

Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

1997-01-01

A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Rupture directivity of microseismic events recorded during hydraulic fracture stimulations.

NASA Astrophysics Data System (ADS)

Urbancic, T.; Smith-Boughner, L.; Baig, A.; Viegas, G.

2016-12-01

We model the dynamics of a complex rupture sequence with four sub-events. These events were recorded during hydraulic fracture stimulations in a gas-bearing shale formation. With force-balance accelerometers, 4.5Hz and 15Hz instruments recording the failure history, we study the directivity of the entire rupture sequence and each sub-event. Two models are considered: unilateral and bi-lateral failures of penny shaped cracks. From the seismic moment tensors of these sub-events, we consider different potential failure planes and rupture directions. Using numerical wave-propagation codes, we generate synthetic rupture sequences with both unilateral and bi-lateral ruptures. These are compared to the four sub-events to determine the directionality of the observed failures and the sensitivity of our recording bandwidth and geometry to distinguishing between different rupture processes. The frequency of unilateral and bilateral rupture processes throughout the fracture stimulation is estimated by comparing the directivity characteristics of the modeled sub-events to other high-quality microseismic events recorded during the same stimulation program. Understanding the failure processes of these microseismic events can provide great insight into the changes in the rock mass responsible for these complex rupture processes.

Representation and visualization of variability in a 3D anatomical atlas using the kidney as an example

NASA Astrophysics Data System (ADS)

Hacker, Silke; Handels, Heinz

2006-03-01

Computer-based 3D atlases allow an interactive exploration of the human body. However, in most cases such 3D atlases are derived from one single individual, and therefore do not regard the variability of anatomical structures concerning their shape and size. Since the geometric variability across humans plays an important role in many medical applications, our goal is to develop a framework of an anatomical atlas for representation and visualization of the variability of selected anatomical structures. The basis of the project presented is the VOXEL-MAN atlas of inner organs that was created from the Visible Human data set. For modeling anatomical shapes and their variability we utilize "m-reps" which allow a compact representation of anatomical objects on the basis of their skeletons. As an example we used a statistical model of the kidney that is based on 48 different variants. With the integration of a shape description into the VOXEL-MAN atlas it is now possible to query and visualize different shape variations of an organ, e.g. by specifying a person's age or gender. In addition to the representation of individual shape variants, the average shape of a population can be displayed. Besides a surface representation, a volume-based representation of the kidney's shape variants is also possible. It results from the deformation of the reference kidney of the volume-based model using the m-rep shape description. In this way a realistic visualization of the shape variants becomes possible, as well as the visualization of the organ's internal structures.

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

PubMed Central

Little, Damon P.

2011-01-01

For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types. PMID:21857897

Evidence for two attentional components in visual working memory.

PubMed

Allen, Richard J; Baddeley, Alan D; Hitch, Graham J

2014-11-01

How does executive attentional control contribute to memory for sequences of visual objects, and what does this reveal about storage and processing in working memory? Three experiments examined the impact of a concurrent executive load (backward counting) on memory for sequences of individually presented visual objects. Experiments 1 and 2 found disruptive concurrent load effects of equivalent magnitude on memory for shapes, colors, and colored shape conjunctions (as measured by single-probe recognition). These effects were present only for Items 1 and 2 in a 3-item sequence; the final item was always impervious to this disruption. This pattern of findings was precisely replicated in Experiment 3 when using a cued verbal recall measure of shape-color binding, with error analysis providing additional insights concerning attention-related loss of early-sequence items. These findings indicate an important role for executive processes in maintaining representations of earlier encountered stimuli in an active form alongside privileged storage of the most recent stimulus. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Taxonomic and Biological Characterization of Steinernema rarum Found in the Southeastern United States

PubMed Central

Nguyen, Khuong B.; Shapiro-Ilan, David I.; Fuxa, James R.; Wood, Bruce W.; Bertolotti, Maria A.; Adams, Byron J.

2006-01-01

Two Steinernema isolates found in Louisiana and Mississippi were later identified as isolates of S. rarum. DNA sequences of ITS regions of the United States isolates are identical with sequences of Argentinean S. rarum strains Samiento and Noetinger and differ by two bases from the Arroyo Cabral isolate from Córdoba, Argentina. SEM observations revealed several new structures in the isolates from the US: female face views have a hexagonal-star perioral disc and eye-shaped lips; some females do not have cephalic papillae; lateral fields of infective juveniles are variable; there are two openings observed close to the posterior edge of the cloaca. Virulence of the US isolates to Anthonomus grandis, Diaprepes abbreviatus, Solenopsis invicta, Coptotermes formosanus, Agrotis ipsilon, Spodoptera frugiperda, and Trichoplusia ni and reproductive potential were evaluated in comparison with other heterorhabditid and steinernematid nematodes. Results such as particularly high virulence to S. frugiperda indicate that the biocontrol potential of the new S. rarum strains merits further study. PMID:19259427

Extremophiles in Household Water Heaters

NASA Astrophysics Data System (ADS)

Wilpiszeski, R.; House, C. H.

2016-12-01

A significant fraction of Earth's microbial diversity comes from species living in extreme environments, but natural extreme environments can be difficult to access. Manmade systems like household water heaters serve as an effective proxy for thermophilic environments that are otherwise difficult to sample directly. As such, we are investigating the biogeography, taxonomic distribution, and evolution of thermophiles growing in domestic water heaters. Citizen scientists collected hot tap water culture- and filter- samples from 101 homes across the United States. We recovered a single species of thermophilic heterotroph from culture samples inoculated from water heaters across the United States, Thermus scotoductus. Whole-genome sequencing was conducted to better understand the distribution and evolution of this single species. We have also sequenced hyper-variable regions of the 16S rRNA gene from whole-community filter samples to identify the broad diversity and distribution of microbial cells captured from each water heater. These results shed light on the processes that shape thermophilic populations and genomes at a spatial resolution that is difficult to access in naturally occurring extreme ecosystems.

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile.

PubMed

Issotta, Francisco; Galleguillos, Pedro A; Moya-Beltrán, Ana; Davis-Belmar, Carol S; Rautenbach, George; Covarrubias, Paulo C; Acosta, Mauricio; Ossandon, Francisco J; Contador, Yasna; Holmes, David S; Marín-Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, Cecilia

2016-01-01

Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.