Structural network heterogeneities and network dynamics: A possible dynamical mechanism for hippocampal memory reactivation

NASA Astrophysics Data System (ADS)

Jablonski, Piotr; Poe, Gina R.; Zochowski, Michal

2007-01-01

The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.

The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

DOE PAGES

Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; ...

2017-01-06

The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from -20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV andmore » 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies.« less

The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

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

Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.

The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from -20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV andmore » 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies.« less

The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

NASA Astrophysics Data System (ADS)

Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; Shin, S. J.; Shao, L.; Kucheyev, S. O.

2017-01-01

The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from -20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10-0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV and 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies.

Environmental structure and competitive scoring advantages in team competitions.

PubMed

Merritt, Sears; Clauset, Aaron

2013-10-29

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

Environmental structure and competitive scoring advantages in team competitions

NASA Astrophysics Data System (ADS)

Merritt, Sears; Clauset, Aaron

2013-10-01

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

Bighorn sheep habitat studies, population dynamics, and population modeling in Bighorn Canyon National Recreation Area, Wyoming and Montana, 2000-2003

USGS Publications Warehouse

Singer, Francis J.; Schoenecker, Kathryn A.

2004-01-01

The bighorn sheep population of the greater Bighorn Canyon National Recreation Area (BICA) was extirpated in the 1800s, and then reintroduced in 1973. The herd increased to a peak population of about 211 animals (Kissell and others, 1996), but then declined sharply in 1995 and 1996. Causes for the decline were unknown. Numbers have remained around 100 ± 20 animals since 1998. Previous modeling efforts determined what areas were suitable bighorn sheep habitat (Gudorf and others, 1996). We tried to determine why sheep were not using areas that were modeled as suitable or acceptable habitat, and to evaluate population dynamics of the herd.

Littoral Combat Ship: Knowledge of Survivability and Lethality Capabilities Needed Prior to Making Major Funding Decisions

DTIC Science & Technology

2015-12-01

USS Port Royal hit a coral reef in order to provide an independent review of the damage the ship sustained. Our classified report discussed...explosion. Underwater explosions create a shock wave and a highly compressed gas bubble that expands and contracts. This can cause a type of vertical or...conditions also remains unknown. Due to the dynamic nature of waves , the Navy cannot rely on modeling and simulation alone to provide an accurate

77 FR 40901 - Notice of Inventory Completion: Gregg County Historical Museum, Longview, TX

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-11

... adult, one adult of unknown sex, and one juvenile of unknown sex. The human remains from Burial 6 include an occipital cranial bone fragment of one adult of unknown sex. The human remains from Burial 7 include one adult of unknown sex. No known individuals were identified. The 11 associated funerary objects...

Four chemical trends will shape the next decade's directions in Perfluoroalkyl and Polyfluoroalkyl substances research

NASA Astrophysics Data System (ADS)

Kotthoff, Matthias; Bücking, Mark

2018-04-01

Per- and polyfluoroalkyl substances (PFAS) represent a versatile group of ubiquitously occurring chemicals of increasing regulatory concern. The past years lead to an ever expanding portfolio of detected anthropogenic PFAS in numerous products encountered in daily life. Yet no clear picture of the full range of individual substance that comprise PFAS is available and this challenges analytical and engineering sciences. Authorities struggle to cope with uncertainties in managing risk of harm posed by PFAS.This is a result of an incomplete understanding of the range of compounds that they comprise in differing products. There are analytical uncertainties identifying PFAS and estimating the concentrations of the total PFAS loadindividual molecules remain unknown. There are four major trends from the chemical perspective that will shape PFAS research for the next decade. 1.Mobility: A wide and dynamic distribution of short chain PFAS due to their high polarity, persistency and volatility. 2.Substitution of regulated substances: The ban or restrictions of individual molecules will lead to a replacement with substitutes of similar concern. 3.Increase in structural diversity of existing PFAS molecules: Introduction of e.g. hydrogens and chlorine atoms instead of fluorine, as well as branching and cross-linking lead to a high versatility of unknown target molecules. 4. Unknown “Dark Matter”: The amount, identity, formation pathways, and transformation dynamics of polymers and PFAS precursors are largely unknown. These directions require optimized analytical setups, especially multi-methods, and semi-specific tools to determine PFAS-sum parameters in any relevant matrix.

Regulation of branching dynamics by axon-intrinsic asymmetries in Tyrosine Kinase Receptor signaling

PubMed Central

Zschätzsch, Marlen; Oliva, Carlos; Langen, Marion; De Geest, Natalie; Özel, Mehmet Neset; Williamson, W Ryan; Lemon, William C; Soldano, Alessia; Munck, Sebastian; Hiesinger, P Robin; Sanchez-Soriano, Natalia; Hassan, Bassem A

2014-01-01

Axonal branching allows a neuron to connect to several targets, increasing neuronal circuit complexity. While axonal branching is well described, the mechanisms that control it remain largely unknown. We find that in the Drosophila CNS branches develop through a process of excessive growth followed by pruning. In vivo high-resolution live imaging of developing brains as well as loss and gain of function experiments show that activation of Epidermal Growth Factor Receptor (EGFR) is necessary for branch dynamics and the final branching pattern. Live imaging also reveals that intrinsic asymmetry in EGFR localization regulates the balance between dynamic and static filopodia. Elimination of signaling asymmetry by either loss or gain of EGFR function results in reduced dynamics leading to excessive branch formation. In summary, we propose that the dynamic process of axon branch development is mediated by differential local distribution of signaling receptors. DOI: http://dx.doi.org/10.7554/eLife.01699.001 PMID:24755286

Spatio-Temporal Patterning in Primary Motor Cortex at Movement Onset.

PubMed

Best, Matthew D; Suminski, Aaron J; Takahashi, Kazutaka; Brown, Kevin A; Hatsopoulos, Nicholas G

2017-02-01

Voluntary movement initiation involves the engagement of large populations of motor cortical neurons around movement onset. Despite knowledge of the temporal dynamics that lead to movement, the spatial structure of these dynamics across the cortical surface remains unknown. In data from 4 rhesus macaques, we show that the timing of attenuation of beta frequency local field potential oscillations, a correlate of locally activated cortex, forms a spatial gradient across primary motor cortex (MI). We show that these spatio-temporal dynamics are recapitulated in the engagement order of ensembles of MI neurons. We demonstrate that these patterns are unique to movement onset and suggest that movement initiation requires a precise spatio-temporal sequential activation of neurons in MI. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

What kind of noise is brain noise: anomalous scaling behavior of the resting brain activity fluctuations

PubMed Central

Fraiman, Daniel; Chialvo, Dante R.

2012-01-01

The study of spontaneous fluctuations of brain activity, often referred as brain noise, is getting increasing attention in functional magnetic resonance imaging (fMRI) studies. Despite important efforts, much of the statistical properties of such fluctuations remain largely unknown. This work scrutinizes these fluctuations looking at specific statistical properties which are relevant to clarify its dynamical origins. Here, three statistical features which clearly differentiate brain data from naive expectations for random processes are uncovered: First, the variance of the fMRI mean signal as a function of the number of averaged voxels remains constant across a wide range of observed clusters sizes. Second, the anomalous behavior of the variance is originated by bursts of synchronized activity across regions, regardless of their widely different sizes. Finally, the correlation length (i.e., the length at which the correlation strength between two regions vanishes) as well as mutual information diverges with the cluster's size considered, such that arbitrarily large clusters exhibit the same collective dynamics than smaller ones. These three properties are known to be exclusive of complex systems exhibiting critical dynamics, where the spatio-temporal dynamics show these peculiar type of fluctuations. Thus, these findings are fully consistent with previous reports of brain critical dynamics, and are relevant for the interpretation of the role of fluctuations and variability in brain function in health and disease. PMID:22934058

The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering

PubMed Central

Greenway, Kyle T.; LeGresley, Eric B.; Pinto, B. Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations – the structures of which are provided to facilitate future molecular docking studies – and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed. PMID:23544106

The influence of 150-cavity binders on the dynamics of influenza A neuraminidases as revealed by molecular dynamics simulations and combined clustering.

PubMed

Greenway, Kyle T; LeGresley, Eric B; Pinto, B Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6 µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations--the structures of which are provided to facilitate future molecular docking studies--and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed.

Activity-Dependence of Synaptic Vesicle Dynamics

PubMed Central

Forte, Luca A.

2017-01-01

The proper function of synapses relies on efficient recycling of synaptic vesicles. The small size of synaptic boutons has hampered efforts to define the dynamical states of vesicles during recycling. Moreover, whether vesicle motion during recycling is regulated by neural activity remains largely unknown. We combined nanoscale-resolution tracking of individual synaptic vesicles in cultured hippocampal neurons from rats of both sexes with advanced motion analyses to demonstrate that the majority of recently endocytosed vesicles undergo sequences of transient dynamical states including epochs of directed, diffusional, and stalled motion. We observed that vesicle motion is modulated in an activity-dependent manner, with dynamical changes apparent in ∼20% of observed boutons. Within this subpopulation of boutons, 35% of observed vesicles exhibited acceleration and 65% exhibited deceleration, accompanied by corresponding changes in directed motion. Individual vesicles observed in the remaining ∼80% of boutons did not exhibit apparent dynamical changes in response to stimulation. More quantitative transient motion analyses revealed that the overall reduction of vesicle mobility, and specifically of the directed motion component, is the predominant activity-evoked change across the entire bouton population. Activity-dependent modulation of vesicle mobility may represent an important mechanism controlling vesicle availability and neurotransmitter release. SIGNIFICANCE STATEMENT Mechanisms governing synaptic vesicle dynamics during recycling remain poorly understood. Using nanoscale resolution tracking of individual synaptic vesicles in hippocampal synapses and advanced motion analysis tools we demonstrate that synaptic vesicles undergo complex sets of dynamical states that include epochs of directed, diffusive, and stalled motion. Most importantly, our analyses revealed that vesicle motion is modulated in an activity-dependent manner apparent as the reduction in overall vesicle mobility in response to stimulation. These results define the vesicle dynamical states during recycling and reveal their activity-dependent modulation. Our study thus provides fundamental new insights into the principles governing synaptic function. PMID:28954868

Conscience and Consciousness: a definition

PubMed Central

Vithoulkas, G; Muresanu, DF

2014-01-01

While consciousness has been examined extensively in its different aspects, like in philosophy, psychiatry, neurophysiology, neuroplasticity, etc., conscience though it is an equal important aspect of the human existence, which remains an unknown to a great degree as an almost transcendental aspect of the human mind. It has not been examined as thoroughly as consciousness and largely remains a “terra incognita" for its neurophysiology, brain topography, etc. Conscience and consciousness are part of a system of information that governs our experience and decision making process. The intent of this paper is to define these terms, to discuss about consciousness from both neurological and quantum physics point of view, the relationship between the dynamics of consciousness and neuroplasticity and to highlight the relationship between conscience, stress and health. PMID:24653768

Conscience and consciousness: a definition.

PubMed

Vithoulkas, G; Muresanu, D F

2014-03-15

While consciousness has been examined extensively in its different aspects, like in philosophy, psychiatry, neurophysiology, neuroplasticity, etc., conscience though it is an equal important aspect of the human existence, which remains an unknown to a great degree as an almost transcendental aspect of the human mind. It has not been examined as thoroughly as consciousness and largely remains a "terra incognita" for its neurophysiology, brain topography, etc. Conscience and consciousness are part of a system of information that governs our experience and decision making process. The intent of this paper is to define these terms, to discuss about consciousness from both neurological and quantum physics point of view, the relationship between the dynamics of consciousness and neuroplasticity and to highlight the relationship between conscience, stress and health.

Adaptation to sensory input tunes visual cortex to criticality

NASA Astrophysics Data System (ADS)

Shew, Woodrow L.; Clawson, Wesley P.; Pobst, Jeff; Karimipanah, Yahya; Wright, Nathaniel C.; Wessel, Ralf

2015-08-01

A long-standing hypothesis at the interface of physics and neuroscience is that neural networks self-organize to the critical point of a phase transition, thereby optimizing aspects of sensory information processing. This idea is partially supported by strong evidence for critical dynamics observed in the cerebral cortex, but the impact of sensory input on these dynamics is largely unknown. Thus, the foundations of this hypothesis--the self-organization process and how it manifests during strong sensory input--remain unstudied experimentally. Here we show in visual cortex and in a computational model that strong sensory input initially elicits cortical network dynamics that are not critical, but adaptive changes in the network rapidly tune the system to criticality. This conclusion is based on observations of multifaceted scaling laws predicted to occur at criticality. Our findings establish sensory adaptation as a self-organizing mechanism that maintains criticality in visual cortex during sensory information processing.

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2010-01-01

Summary The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease. PMID:20948980

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-01-01

The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease.

Dynamic functional connectivity using state-based dynamic community structure: method and application to opioid analgesia.

PubMed

Robinson, Lucy F; Atlas, Lauren Y; Wager, Tor D

2015-03-01

We present a new method, State-based Dynamic Community Structure, that detects time-dependent community structure in networks of brain regions. Most analyses of functional connectivity assume that network behavior is static in time, or differs between task conditions with known timing. Our goal is to determine whether brain network topology remains stationary over time, or if changes in network organization occur at unknown time points. Changes in network organization may be related to shifts in neurological state, such as those associated with learning, drug uptake or experimental conditions. Using a hidden Markov stochastic blockmodel, we define a time-dependent community structure. We apply this approach to data from a functional magnetic resonance imaging experiment examining how contextual factors influence drug-induced analgesia. Results reveal that networks involved in pain, working memory, and emotion show distinct profiles of time-varying connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Multi-sensor measurements of mixed-phase clouds above Greenland

NASA Astrophysics Data System (ADS)

Stillwell, Robert A.; Shupe, Matthew D.; Thayer, Jeffrey P.; Neely, Ryan R.; Turner, David D.

2018-04-01

Liquid-only and mixed-phase clouds in the Arctic strongly affect the regional surface energy and ice mass budgets, yet much remains unknown about the nature of these clouds due to the lack of intensive measurements. Lidar measurements of these clouds are challenged by very large signal dynamic range, which makes even seemingly simple tasks, such as thermodynamic phase classification, difficult. This work focuses on a set of measurements made by the Clouds Aerosol Polarization and Backscatter Lidar at Summit, Greenland and its retrieval algorithms, which use both analog and photon counting as well as orthogonal and non-orthogonal polarization retrievals to extend dynamic range and improve overall measurement quality and quantity. Presented here is an algorithm for cloud parameter retrievals that leverages enhanced dynamic range retrievals to classify mixed-phase clouds. This best guess retrieval is compared to co-located instruments for validation.

Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

PubMed

Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

2011-12-01

Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

A Bayesian nonparametric approach to dynamical noise reduction

NASA Astrophysics Data System (ADS)

Kaloudis, Konstantinos; Hatjispyros, Spyridon J.

2018-06-01

We propose a Bayesian nonparametric approach for the noise reduction of a given chaotic time series contaminated by dynamical noise, based on Markov Chain Monte Carlo methods. The underlying unknown noise process (possibly) exhibits heavy tailed behavior. We introduce the Dynamic Noise Reduction Replicator model with which we reconstruct the unknown dynamic equations and in parallel we replicate the dynamics under reduced noise level dynamical perturbations. The dynamic noise reduction procedure is demonstrated specifically in the case of polynomial maps. Simulations based on synthetic time series are presented.

Determination of power system component parameters using nonlinear dead beat estimation method

NASA Astrophysics Data System (ADS)

Kolluru, Lakshmi

Power systems are considered the most complex man-made wonders in existence today. In order to effectively supply the ever increasing demands of the consumers, power systems are required to remain stable at all times. Stability and monitoring of these complex systems are achieved by strategically placed computerized control centers. State and parameter estimation is an integral part of these facilities, as they deal with identifying the unknown states and/or parameters of the systems. Advancements in measurement technologies and the introduction of phasor measurement units (PMU) provide detailed and dynamic information of all measurements. Accurate availability of dynamic measurements provides engineers the opportunity to expand and explore various possibilities in power system dynamic analysis/control. This thesis discusses the development of a parameter determination algorithm for nonlinear power systems, using dynamic data obtained from local measurements. The proposed algorithm was developed by observing the dead beat estimator used in state space estimation of linear systems. The dead beat estimator is considered to be very effective as it is capable of obtaining the required results in a fixed number of steps. The number of steps required is related to the order of the system and the number of parameters to be estimated. The proposed algorithm uses the idea of dead beat estimator and nonlinear finite difference methods to create an algorithm which is user friendly and can determine the parameters fairly accurately and effectively. The proposed algorithm is based on a deterministic approach, which uses dynamic data and mathematical models of power system components to determine the unknown parameters. The effectiveness of the algorithm is tested by implementing it to identify the unknown parameters of a synchronous machine. MATLAB environment is used to create three test cases for dynamic analysis of the system with assumed known parameters. Faults are introduced in the virtual test systems and the dynamic data obtained in each case is analyzed and recorded. Ideally, actual measurements are to be provided to the algorithm. As the measurements are not readily available the data obtained from simulations is fed into the determination algorithm as inputs. The obtained results are then compared to the original (or assumed) values of the parameters. The results obtained suggest that the algorithm is able to determine the parameters of a synchronous machine when crisp data is available.

Collective relaxation dynamics of small-world networks

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N , average degree k , and topological randomness q . We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q , including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle function in fission yeast

PubMed Central

Gergely, Zachary R.; Crapo, Ammon; Hough, Loren E.; McIntosh, J. Richard; Betterton, Meredith D.

2016-01-01

Kinesin-8 motor proteins destabilize microtubules. Their absence during cell division is associated with disorganized mitotic chromosome movements and chromosome loss. Despite recent work studying effects of kinesin-8s on microtubule dynamics, it remains unclear whether the kinesin-8 mitotic phenotypes are consequences of their effect on microtubule dynamics, their well-established motor activity, or additional, unknown functions. To better understand the role of kinesin-8 proteins in mitosis, we studied the effects of deletion of the fission yeast kinesin-8 proteins Klp5 and Klp6 on chromosome movements and spindle length dynamics. Aberrant microtubule-driven kinetochore pushing movements and tripolar mitotic spindles occurred in cells lacking Klp5 but not Klp6. Kinesin-8–deletion strains showed large fluctuations in metaphase spindle length, suggesting a disruption of spindle length stabilization. Comparison of our results from light microscopy with a mathematical model suggests that kinesin-8–induced effects on microtubule dynamics, kinetochore attachment stability, and sliding force in the spindle can explain the aberrant chromosome movements and spindle length fluctuations seen. PMID:27146110

Collective relaxation dynamics of small-world networks.

PubMed

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N, average degree k, and topological randomness q. We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q, including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

Simultaneous live imaging of the transcription and nuclear position of specific genes

PubMed Central

Ochiai, Hiroshi; Sugawara, Takeshi; Yamamoto, Takashi

2015-01-01

The relationship between genome organization and gene expression has recently been established. However, the relationships between spatial organization, dynamics, and transcriptional regulation of the genome remain unknown. In this study, we developed a live-imaging method for simultaneous measurements of the transcriptional activity and nuclear position of endogenous genes, which we termed the ‘Real-time Observation of Localization and EXpression (ROLEX)’ system. We demonstrated that ROLEX is highly specific and does not affect the expression level of the target gene. ROLEX enabled detection of sub-genome-wide mobility changes that depended on the state of Nanog transactivation in embryonic stem cells. We believe that the ROLEX system will become a powerful tool for exploring the relationship between transcription and nuclear dynamics in living cells. PMID:26092696

Detectable close-in planets around white dwarfs through late unpacking

NASA Astrophysics Data System (ADS)

Veras, Dimitri; Gänsicke, Boris T.

2015-02-01

Although 25-50 per cent of white dwarfs (WDs) display evidence for remnant planetary systems, their orbital architectures and overall sizes remain unknown. Vibrant close-in (≃1 R⊙) circumstellar activity is detected at WDs spanning many Gyr in age, suggestive of planets further away. Here we demonstrate how systems with 4 and 10 closely packed planets that remain stable and ordered on the main sequence can become unpacked when the star evolves into a WD and experience pervasive inward planetary incursions throughout WD cooling. Our full-lifetime simulations run for the age of the Universe and adopt main-sequence stellar masses of 1.5, 2.0 and 2.5 M⊙, which correspond to the mass range occupied by the progenitors of typical present-day WDs. These results provide (i) a natural way to generate an ever-changing dynamical architecture in post-main-sequence planetary systems, (ii) an avenue for planets to achieve temporary close-in orbits that are potentially detectable by transit photometry and (iii) a dynamical explanation for how residual asteroids might pollute particularly old WDs.

Stochastic Online Learning in Dynamic Networks under Unknown Models

DTIC Science & Technology

2016-08-02

Repeated Game with Incomplete Information, IEEE International Conference on Acoustics, Speech, and Signal Processing. 20-MAR-16, Shanghai, China...in a game theoretic framework for the application of multi-seller dynamic pricing with unknown demand models. We formulated the problem as an...infinitely repeated game with incomplete information and developed a dynamic pricing strategy referred to as Competitive and Cooperative Demand Learning

Ecological networks to unravel the routes to horizontal transposon transfers.

PubMed

Venner, Samuel; Miele, Vincent; Terzian, Christophe; Biémont, Christian; Daubin, Vincent; Feschotte, Cédric; Pontier, Dominique

2017-02-01

Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.

Dynamic Modeling from Flight Data with Unknown Time Skews

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

2016-01-01

A method for estimating dynamic model parameters from flight data with unknown time skews is described and demonstrated. The method combines data reconstruction, nonlinear optimization, and equation-error parameter estimation in the frequency domain to accurately estimate both dynamic model parameters and the relative time skews in the data. Data from a nonlinear F-16 aircraft simulation with realistic noise, instrumentation errors, and arbitrary time skews were used to demonstrate the approach. The approach was further evaluated using flight data from a subscale jet transport aircraft, where the measured data were known to have relative time skews. Comparison of modeling results obtained from time-skewed and time-synchronized data showed that the method accurately estimates both dynamic model parameters and relative time skew parameters from flight data with unknown time skews.

Revealing the subfemtosecond dynamics of orbital angular momentum in nanoplasmonic vortices

NASA Astrophysics Data System (ADS)

Spektor, G.; Kilbane, D.; Mahro, A. K.; Frank, B.; Ristok, S.; Gal, L.; Kahl, P.; Podbiel, D.; Mathias, S.; Giessen, H.; Meyer zu Heringdorf, F.-J.; Orenstein, M.; Aeschlimann, M.

2017-03-01

The ability of light to carry and deliver orbital angular momentum (OAM) in the form of optical vortices has attracted much interest. The physical properties of light with a helical wavefront can be confined onto two-dimensional surfaces with subwavelength dimensions in the form of plasmonic vortices, opening avenues for thus far unknown light-matter interactions. Because of their extreme rotational velocity, the ultrafast dynamics of such vortices remained unexplored. Here we show the detailed spatiotemporal evolution of nanovortices using time-resolved two-photon photoemission electron microscopy. We observe both long- and short-range plasmonic vortices confined to deep subwavelength dimensions on the scale of 100 nanometers with nanometer spatial resolution and subfemtosecond time-step resolution. Finally, by measuring the angular velocity of the vortex, we directly extract the OAM magnitude of light.

Mitochondrial Dynamics Impacts Stem Cell Identity and Fate Decisions by Regulating a Nuclear Transcriptional Program.

PubMed

Khacho, Mireille; Clark, Alysen; Svoboda, Devon S; Azzi, Joelle; MacLaurin, Jason G; Meghaizel, Cynthia; Sesaki, Hiromi; Lagace, Diane C; Germain, Marc; Harper, Mary-Ellen; Park, David S; Slack, Ruth S

2016-08-04

Regulated mechanisms of stem cell maintenance are key to preventing stem cell depletion and aging. While mitochondrial morphology plays a fundamental role in tissue development and homeostasis, its role in stem cells remains unknown. Here, we uncover that mitochondrial dynamics regulates stem cell identity, self-renewal, and fate decisions by orchestrating a transcriptional program. Manipulation of mitochondrial structure, through OPA1 or MFN1/2 deletion, impaired neural stem cell (NSC) self-renewal, with consequent age-dependent depletion, neurogenesis defects, and cognitive impairments. Gene expression profiling revealed ectopic expression of the Notch self-renewal inhibitor Botch and premature induction of transcription factors that promote differentiation. Changes in mitochondrial dynamics regulate stem cell fate decisions by driving a physiological reactive oxygen species (ROS)-mediated process, which triggers a dual program to suppress self-renewal and promote differentiation via NRF2-mediated retrograde signaling. These findings reveal mitochondrial dynamics as an upstream regulator of essential mechanisms governing stem cell self-renewal and fate decisions through transcriptional programming. Copyright © 2016 Elsevier Inc. All rights reserved.

Boundary Control of Linear Uncertain 1-D Parabolic PDE Using Approximate Dynamic Programming.

PubMed

Talaei, Behzad; Jagannathan, Sarangapani; Singler, John

2018-04-01

This paper develops a near optimal boundary control method for distributed parameter systems governed by uncertain linear 1-D parabolic partial differential equations (PDE) by using approximate dynamic programming. A quadratic surface integral is proposed to express the optimal cost functional for the infinite-dimensional state space. Accordingly, the Hamilton-Jacobi-Bellman (HJB) equation is formulated in the infinite-dimensional domain without using any model reduction. Subsequently, a neural network identifier is developed to estimate the unknown spatially varying coefficient in PDE dynamics. Novel tuning law is proposed to guarantee the boundedness of identifier approximation error in the PDE domain. A radial basis network (RBN) is subsequently proposed to generate an approximate solution for the optimal surface kernel function online. The tuning law for near optimal RBN weights is created, such that the HJB equation error is minimized while the dynamics are identified and closed-loop system remains stable. Ultimate boundedness (UB) of the closed-loop system is verified by using the Lyapunov theory. The performance of the proposed controller is successfully confirmed by simulation on an unstable diffusion-reaction process.

Atomistic Structure and Dynamics of the Solvation Shell Formed by Organic Carbonates around Lithium Ions via Infrared Spectroscopies

NASA Astrophysics Data System (ADS)

Kuroda, Daniel; Fufler, Kristen

Lithium-ion batteries have become ubiquitous to the portable energy storage industry, but efficiency issues still remain. Currently, most technological and scientific efforts are focused on the electrodes with little attention on the electrolyte. For example, simple fundamental questions about the lithium ion solvation shell composition in commercially used electrolytes have not been answered. Using a combination of linear and non-linear IR spectroscopies and theoretical calculations, we have carried out a thorough investigation of the solvation structure and dynamics of the lithium ion in various linear and cyclic carbonates at common battery electrolyte concentrations. Our studies show that carbonates coordinate the lithium ion tetrahedrally. They also reveal that linear and cyclic carbonates have contrasting dynamics in which cyclic carbonates present the most ordered structure. Finally, our experiments demonstrate that simple structural modifications in the linear carbonates impact significantly the microscopic interactions of the system. The stark differences in the solvation structure and dynamics among different carbonates reveal previously unknown details about the molecular level picture of these systems.

Neural dynamics of reward probability coding: a Magnetoencephalographic study in humans

PubMed Central

Thomas, Julie; Vanni-Mercier, Giovanna; Dreher, Jean-Claude

2013-01-01

Prediction of future rewards and discrepancy between actual and expected outcomes (prediction error) are crucial signals for adaptive behavior. In humans, a number of fMRI studies demonstrated that reward probability modulates these two signals in a large brain network. Yet, the spatio-temporal dynamics underlying the neural coding of reward probability remains unknown. Here, using magnetoencephalography, we investigated the neural dynamics of prediction and reward prediction error computations while subjects learned to associate cues of slot machines with monetary rewards with different probabilities. We showed that event-related magnetic fields (ERFs) arising from the visual cortex coded the expected reward value 155 ms after the cue, demonstrating that reward value signals emerge early in the visual stream. Moreover, a prediction error was reflected in ERF peaking 300 ms after the rewarded outcome and showing decreasing amplitude with higher reward probability. This prediction error signal was generated in a network including the anterior and posterior cingulate cortex. These findings pinpoint the spatio-temporal characteristics underlying reward probability coding. Together, our results provide insights into the neural dynamics underlying the ability to learn probabilistic stimuli-reward contingencies. PMID:24302894

Mass properties measurement system dynamics

NASA Technical Reports Server (NTRS)

Doty, Keith L.

1993-01-01

The MPMS mechanism possess two revolute degrees-of-freedom and allows the user to measure the mass, center of gravity, and the inertia tensor of an unknown mass. The dynamics of the Mass Properties Measurement System (MPMS) from the Lagrangian approach to illustrate the dependency of the motion on the unknown parameters.

Cell fate determination dynamics in bacteria

NASA Astrophysics Data System (ADS)

Kuchina, Anna; Espinar, Lorena; Cagatay, Tolga; Garcia-Ojalvo, Jordi; Suel, Gurol

2010-03-01

The fitness of an organism depends on many processes that serve the purpose to adapt to changing environment in a robust and coordinated fashion. One example of such process is cellular fate determination. In the presence of a variety of alternative responses each cell adopting a particular fate represents a ``choice'' that must be tightly regulated to ensure the best survival strategy for the population taking into account the broad range of possible environmental challenges. We investigated this problem in the model organism B.Subtilis which under stress conditions differentiates terminally into highly resistant spores or initiates an alternative transient state of competence. The dynamics underlying cell fate choice remains largely unknown. We utilize quantitative fluorescent microscopy to track the activities of genes involved in these responses on a single-cell level. We explored the importance of temporal interactions between competing cell fates by re- engineering the differentiation programs. I will discuss how the precise dynamics of cellular ``decision-making'' governed by the corresponding biological circuits may enable cells to adjust to diverse environments and determine survival.

A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubule dynamics

PubMed Central

Geyer, Elisabeth A; Burns, Alexander; Lalonde, Beth A; Ye, Xuecheng; Piedra, Felipe-Andres; Huffaker, Tim C; Rice, Luke M

2015-01-01

Microtubule dynamic instability depends on the GTPase activity of the polymerizing αβ-tubulin subunits, which cycle through at least three distinct conformations as they move into and out of microtubules. How this conformational cycle contributes to microtubule growing, shrinking, and switching remains unknown. Here, we report that a buried mutation in αβ-tubulin yields microtubules with dramatically reduced shrinking rate and catastrophe frequency. The mutation causes these effects by suppressing a conformational change that normally occurs in response to GTP hydrolysis in the lattice, without detectably changing the conformation of unpolymerized αβ-tubulin. Thus, the mutation weakens the coupling between the conformational and GTPase cycles of αβ-tubulin. By showing that the mutation predominantly affects post-GTPase conformational and dynamic properties of microtubules, our data reveal that the strength of the allosteric response to GDP in the lattice dictates the frequency of catastrophe and the severity of rapid shrinking. DOI: http://dx.doi.org/10.7554/eLife.10113.001 PMID:26439009

A Molecular Census of Arcuate Hypothalamus and Median Eminence Cell Types

PubMed Central

Campbell, John N.; Macosko, Evan Z.; Fenselau, Henning; Pers, Tune H.; Lyubetskaya, Anna; Tenen, Danielle; Goldman, Melissa; Verstegen, Anne M.J.; Resch, Jon M.; McCarroll, Steven A.; Rosen, Evan D.; Lowell, Bradford B.; Tsai, Linus

2017-01-01

The hypothalamic arcuate-median eminence complex (Arc-ME) controls energy balance, fertility, and growth through molecularly distinct cell types, many of which remain unknown. To catalog cell types in an unbiased way, we profiled gene expression in 20,921 individual cells in and around the adult mouse Arc-ME using Drop-seq. We identify 50 transcriptionally distinct Arc-ME cell populations, including a rare tanycyte population at the Arc-ME diffusion barrier, a novel leptin-sensing neuronal population, multiple AgRP and POMC subtypes, and an orexigenic somatostatin neuronal population. We extended Drop-seq to detect dynamic expression changes across relevant physiological perturbations, revealing cell type-specific responses to energy status, including distinctly responsive subtypes of AgRP and POMC neurons. Finally, integrating our data with human GWAS data implicates two previously unknown neuronal subtypes in the genetic control of obesity. This resource will accelerate biological discovery by providing insights into molecular and cell type diversity from which function can be inferred. PMID:28166221

A chemical proteomics approach for global analysis of lysine monomethylome profiling.

PubMed

Wu, Zhixiang; Cheng, Zhongyi; Sun, Mingwei; Wan, Xuelian; Liu, Ping; He, Tieming; Tan, Minjia; Zhao, Yingming

2015-02-01

Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Profilin1 activity in cerebellar granule neurons is required for radial migration in vivo

PubMed Central

Kullmann, Jan A; Wickertsheim, Ines; Minnerup, Lara; Costell, Mercedes; Friauf, Eckhard; Rust, Marco B

2015-01-01

Neuron migration defects are an important aspect of human neuropathies. The underlying molecular mechanisms of such migration defects are largely unknown. Actin dynamics has been recognized as an important determinant of neuronal migration, and we recently found that the actin-binding protein profilin1 is relevant for radial migration of cerebellar granule neurons (CGN). As the exploited brain-specific mutants lacked profilin1 in both neurons and glial cells, it remained unknown whether profilin1 activity in CGN is relevant for CGN migration in vivo. To test this, we capitalized on a transgenic mouse line that expresses a tamoxifen-inducible Cre variant in CGN, but no other cerebellar cell type. In these profilin1 mutants, the cell density was elevated in the molecular layer, and ectopic CGN occurred. Moreover, 5-bromo-2′-deoxyuridine tracing experiments revealed impaired CGN radial migration. Hence, our data demonstrate the cell autonomous role of profilin1 activity in CGN for radial migration. PMID:25495756

Why Atens Enjoy Enhanced Accessibility for Human Space Flight

NASA Technical Reports Server (NTRS)

Barbee, Brent W.; Adamo, Daniel R.

2011-01-01

Near-Earth objects can be grouped into multiple orbit classifications, among them being the Aten group, whose members have orbits crossing Earth's with semi-major axes less than 1 astronomical unit. Atens comprise well under 10% of known near-Earth objects. This is in dramatic contrast to results from recent human space flight near-Earth object accessibility studies, where the most favorable known destinations are typically almost 50% Atens. Geocentric dynamics explain this enhanced Aten accessibility and lead to an understanding of where the most accessible near-Earth objects reside. Without a comprehensive space-based survey, however, highly accessible Atens will remain largely unknown.

Inverse dynamic substructuring using the direct hybrid assembly in the frequency domain

NASA Astrophysics Data System (ADS)

D'Ambrogio, Walter; Fregolent, Annalisa

2014-04-01

The paper deals with the identification of the dynamic behaviour of a structural subsystem, starting from the known dynamic behaviour of both the coupled system and the remaining part of the structural system (residual subsystem). This topic is also known as decoupling problem, subsystem subtraction or inverse dynamic substructuring. Whenever it is necessary to combine numerical models (e.g. FEM) and test models (e.g. FRFs), one speaks of experimental dynamic substructuring. Substructure decoupling techniques can be classified as inverse coupling or direct decoupling techniques. In inverse coupling, the equations describing the coupling problem are rearranged to isolate the unknown substructure instead of the coupled structure. On the contrary, direct decoupling consists in adding to the coupled system a fictitious subsystem that is the negative of the residual subsystem. Starting from a reduced version of the 3-field formulation (dynamic equilibrium using FRFs, compatibility and equilibrium of interface forces), a direct hybrid assembly is developed by requiring that both compatibility and equilibrium conditions are satisfied exactly, either at coupling DoFs only, or at additional internal DoFs of the residual subsystem. Equilibrium and compatibility DoFs might not be the same: this generates the so-called non-collocated approach. The technique is applied using experimental data from an assembled system made by a plate and a rigid mass.

Mind the gap: gender differences in child special health care needs.

PubMed

Leiter, Valerie; Rieker, Patricia P

2012-07-01

The gendered nature of special health care needs in childhood is an important yet understudied area. Although gendered differences in the prevalence of special health care needs have been documented, there is less knowledge about the factors which contribute to those differences. Two research questions guide this inquiry. First, is the gender gap consistent across child special health care need indicators? Second, to what extent is the gender gap in special health care needs driven by behavioral conditions? We use multiple indicators from the U.S. National Survey of Children's Health to expand our understanding about the dynamic relationship between gender and childhood health. There are clear gender differences in the prevalence of special health care needs. Boys are more likely than girls to have special health care needs overall and on the five separate components examined (medication, more care than typical, limitations, special therapies, and educational or behavioral problem). This gender gap is dynamic and varies by indicator; while behavioral conditions play a role, it remains even after controlling for behavioral conditions. The reasons for the gender differences appear to be both biological and social but much remains unknown about this pattern.

Dynamical dark matter: A new framework for dark-matter physics

NASA Astrophysics Data System (ADS)

Dienes, Keith R.; Thomas, Brooks

2013-05-01

Although much remains unknown about the dark matter of the universe, one property is normally considered sacrosanct: dark matter must be stable well beyond cosmological time scales. However, a new framework for dark-matter physics has recently been proposed which challenges this assumption. In the "dynamical dark matter" (DDM) framework, the dark sector consists of a vast ensemble of individual dark-matter components with differing masses, lifetimes, and cosmological abundances. Moreover, the usual requirement of stability is replaced by a delicate balancing between lifetimes and cosmological abundances across the ensemble as a whole. As a result, it is possible for the DDM ensemble to remain consistent with all experimental and observational bounds on dark matter while nevertheless giving rise to collective behaviors which transcend those normally associated with traditional dark-matter candidates. These include a new, non-trivial darkmatter equation of state as well as potentially distinctive signatures in collider and direct-detection experiments. In this review article, we provide a self-contained introduction to the DDM framework and summarize some of the work which has recently been done in this area. We also present an explicit model within the DDM framework, and outline a number of ideas for future investigation.

Adaptive fuzzy wavelet network control of second order multi-agent systems with unknown nonlinear dynamics.

PubMed

Taheri, Mehdi; Sheikholeslam, Farid; Najafi, Majddedin; Zekri, Maryam

2017-07-01

In this paper, consensus problem is considered for second order multi-agent systems with unknown nonlinear dynamics under undirected graphs. A novel distributed control strategy is suggested for leaderless systems based on adaptive fuzzy wavelet networks. Adaptive fuzzy wavelet networks are employed to compensate for the effect of unknown nonlinear dynamics. Moreover, the proposed method is developed for leader following systems and leader following systems with state time delays. Lyapunov functions are applied to prove uniformly ultimately bounded stability of closed loop systems and to obtain adaptive laws. Three simulation examples are presented to illustrate the effectiveness of the proposed control algorithms. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Patterns of call communication between group-housed zebra finches change during the breeding cycle.

PubMed

Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

2015-10-06

Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems.

Dynamics of selected pre-existing polybrominated diphenylethers (PBDEs) in municipal wastewater sludge under anaerobic conditions.

PubMed

Shin, Mari; Duncan, Brigitte; Seto, Peter; Falletta, Patricia; Lee, Dae-Young

2010-03-01

Despite the rapid, widespread accumulation of polybrominated diphenylethers (PBDEs) in our surroundings, their environmental fate has been largely unknown. In the present study, most common congeners (BDE 47, 99, 100, 138, 153, 154, 183 and 209) were investigated for their dynamics in municipal sewage sludge under mesophilic condition (37 degrees C). In anaerobic batch cultures, the concentrations of BDE 47, 99, 100 and 209, exhibited significant decreases (by 22-40% from their initial concentration), whereas the levels of the other congeners, BDE 138, 153, 154 and 183, remained stable during a 238-d incubation. However, in a parallel study conducted in a pilot-scale anaerobic sludge digester, loss of all eight congeners was observed. The present study indicates that certain PBDE congeners undergo a significant mass decrease under anaerobic conditions. Crown Copyright (c) 2010. Published by Elsevier Ltd. All rights reserved.

Formation of visual memories controlled by gamma power phase-locked to alpha oscillations.

PubMed

Park, Hyojin; Lee, Dong Soo; Kang, Eunjoo; Kang, Hyejin; Hahm, Jarang; Kim, June Sic; Chung, Chun Kee; Jiang, Haiteng; Gross, Joachim; Jensen, Ole

2016-06-16

Neuronal oscillations provide a window for understanding the brain dynamics that organize the flow of information from sensory to memory areas. While it has been suggested that gamma power reflects feedforward processing and alpha oscillations feedback control, it remains unknown how these oscillations dynamically interact. Magnetoencephalography (MEG) data was acquired from healthy subjects who were cued to either remember or not remember presented pictures. Our analysis revealed that in anticipation of a picture to be remembered, alpha power decreased while the cross-frequency coupling between gamma power and alpha phase increased. A measure of directionality between alpha phase and gamma power predicted individual ability to encode memory: stronger control of alpha phase over gamma power was associated with better memory. These findings demonstrate that encoding of visual information is reflected by a state determined by the interaction between alpha and gamma activity.

Dynamic nigrostriatal dopamine biases action selection

PubMed Central

Howard, Christopher D.; Li, Hao; Geddes, Claire E.; Jin, Xin

2017-01-01

Summary Dopamine is thought to play a critical role in reinforcement learning and goal-directed behavior, but its function in action selection remains largely unknown. Here, we demonstrate that nigrostriatal dopamine biases ongoing action selection. When mice were trained to dynamically switch the action selected at different time points, changes in firing rate of nigrostriatal dopamine neurons, as well as dopamine signaling in the dorsal striatum, were found to be associated with action selection. This dopamine profile is specific to behavioral choice, scalable with interval duration, and doesn’t reflect reward prediction error, timing, or value as single factors alone. Genetic deletion of NMDA receptors on dopamine or striatal neurons, or optogenetic manipulation of dopamine concentration, alters dopamine signaling and biases action selection. These results unveil a crucial role of nigrostriatal dopamine in integrating diverse information for regulating upcoming actions and have important implications for neurological disorders including Parkinson’s disease and substance dependence. PMID:28285820

Dynamical Constraints on Non-Transiting Planets at Trappist-1

NASA Astrophysics Data System (ADS)

Jontof-Hutter, Daniel; Truong, Vinh; Ford, Eric; Robertson, Paul; Terrien, Ryan

2018-04-01

The outermost of the seven known planets of Trappist-1 orbits six times closer to its host star than Mercury orbits the sun. The architecture of this system beyond 0.07 AU remains unknown. While the presence of additional planets will ultimately be determined by observations, in the meantime, some constraints can be derived from dynamical models.We will firstly look at the expected signature of additional planets at Trappist-1 on the transit times of the known planets to determine at what distances putatuve planets can be ruled out.Secondly, the remarkably compact configuration of Trappist-1 ensures that the known planets are secularly coupled, keeping their mutual inclinations very small and making their cotransiting geometry likely if Trappist-1h transits. We determine the range of masses and orbital inclinations of a putatuve outer planet that would make the observed configuration unlikely, and compare these to these constraints to those expected from radial velocity observations.

Dynamic Nigrostriatal Dopamine Biases Action Selection.

PubMed

Howard, Christopher D; Li, Hao; Geddes, Claire E; Jin, Xin

2017-03-22

Dopamine is thought to play a critical role in reinforcement learning and goal-directed behavior, but its function in action selection remains largely unknown. Here we demonstrate that nigrostriatal dopamine biases ongoing action selection. When mice were trained to dynamically switch the action selected at different time points, changes in firing rate of nigrostriatal dopamine neurons, as well as dopamine signaling in the dorsal striatum, were found to be associated with action selection. This dopamine profile is specific to behavioral choice, scalable with interval duration, and doesn't reflect reward prediction error, timing, or value as single factors alone. Genetic deletion of NMDA receptors on dopamine or striatal neurons or optogenetic manipulation of dopamine concentration alters dopamine signaling and biases action selection. These results unveil a crucial role of nigrostriatal dopamine in integrating diverse information for regulating upcoming actions, and they have important implications for neurological disorders, including Parkinson's disease and substance dependence. Copyright © 2017 Elsevier Inc. All rights reserved.

[How our subjective coherence is built? The model of cognitive dissonance].

PubMed

Naccache, Lionel; El Karoui, Imen; Salti, Moti; Chammat, Mariam; Maillet, Mathurin; Allali, Sébastien

2015-01-01

Our conscious, subjective discourse, demonstrates a temporal coherence that distinguishes it from the many unconscious cognitive representations explored by cognitive neuroscience. This subjective coherence, --particularly its dynamics--can be modified in certain psychiatric syndromes including a " dissociative state " (e.g. schizophrenia), or in several neuropsychiatric disorders (e.g. frontal lobe syndrome). The medical and environmental consequences of these changes are significant. However, the psychological and neural mechanisms of this fundamental property remain largely unknown. We explored the dynamics of subjective coherence in an experimental paradigm (the "free choice "paradigm) originating for the field of cognitive dissonance. Using a series of behavioral experiments, conducted in healthy volunteers, we have discovered a key role for the episodic memory in the preference change process when simply making a choice. These results highlight the importance of conscious memory in the construction of subjective consistency, of which the subjects do not yet seem to be the conscious agents.

Beyond static measures: A review of functional magnetic resonance spectroscopy and its potential to investigate dynamic glutamatergic abnormalities in schizophrenia.

PubMed

Jelen, Luke A; King, Sinead; Mullins, Paul G; Stone, James M

2018-05-01

Abnormalities of the glutamate system are increasingly implicated in schizophrenia but their exact nature remains unknown. Proton magnetic resonance spectroscopy ( 1 H-MRS), while fundamental in revealing glutamatergic alterations in schizophrenia, has, until recently, been significantly limited and thought to only provide static measures. Functional magnetic resonance spectroscopy (fMRS), which uses sequential scans for dynamic measurement of a range of brain metabolites in activated brain areas, has lately been applied to a variety of task or stimulus conditions, producing interesting insights into neurometabolite responses to neural activation. Here, we summarise the existing 1 H-MRS studies of brain glutamate in schizophrenia. We then present a comprehensive review of research studies that have utilised fMRS, and lastly consider how fMRS methods might further the understanding of glutamatergic abnormalities in schizophrenia.

Dynamic denitrosylation via S-nitrosoglutathione reductase regulates cardiovascular function

PubMed Central

Beigi, Farideh; Gonzalez, Daniel R.; Minhas, Khalid M.; Sun, Qi-An; Foster, Matthew W.; Khan, Shakil A.; Treuer, Adriana V.; Dulce, Raul A.; Harrison, Robert W.; Saraiva, Roberto M.; Premer, Courtney; Schulman, Ivonne Hernandez; Stamler, Jonathan S.; Hare, Joshua M.

2012-01-01

Although protein S-nitrosylation is increasingly recognized as mediating nitric oxide (NO) signaling, roles for protein denitrosylation in physiology remain unknown. Here, we show that S-nitrosoglutathione reductase (GSNOR), an enzyme that governs levels of S-nitrosylation by promoting protein denitrosylation, regulates both peripheral vascular tone and β-adrenergic agonist-stimulated cardiac contractility, previously ascribed exclusively to NO/cGMP. GSNOR-deficient mice exhibited reduced peripheral vascular tone and depressed β-adrenergic inotropic responses that were associated with impaired β-agonist–induced denitrosylation of cardiac ryanodine receptor 2 (RyR2), resulting in calcium leak. These results indicate that systemic hemodynamic responses (vascular tone and cardiac contractility), both under basal conditions and after adrenergic activation, are regulated through concerted actions of NO synthase/GSNOR and that aberrant denitrosylation impairs cardiovascular function. Our findings support the notion that dynamic S-nitrosylation/denitrosylation reactions are essential in cardiovascular regulation. PMID:22366318

Formation of visual memories controlled by gamma power phase-locked to alpha oscillations

PubMed Central

Park, Hyojin; Lee, Dong Soo; Kang, Eunjoo; Kang, Hyejin; Hahm, Jarang; Kim, June Sic; Chung, Chun Kee; Jiang, Haiteng; Gross, Joachim; Jensen, Ole

2016-01-01

Neuronal oscillations provide a window for understanding the brain dynamics that organize the flow of information from sensory to memory areas. While it has been suggested that gamma power reflects feedforward processing and alpha oscillations feedback control, it remains unknown how these oscillations dynamically interact. Magnetoencephalography (MEG) data was acquired from healthy subjects who were cued to either remember or not remember presented pictures. Our analysis revealed that in anticipation of a picture to be remembered, alpha power decreased while the cross-frequency coupling between gamma power and alpha phase increased. A measure of directionality between alpha phase and gamma power predicted individual ability to encode memory: stronger control of alpha phase over gamma power was associated with better memory. These findings demonstrate that encoding of visual information is reflected by a state determined by the interaction between alpha and gamma activity. PMID:27306959

Plant domestication slows pest evolution.

PubMed

Turcotte, Martin M; Lochab, Amaneet K; Turley, Nash E; Johnson, Marc T J

2015-09-01

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest - the green peach aphid (Myzus persicae) - growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual-based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Dissipation in microwave quantum circuits with hybrid nanowire Josephson elements

NASA Astrophysics Data System (ADS)

Mugnai, D.; Ranfagni, A.; Agresti, A.

2017-04-01

Recent experiments on hybrid Josephson junctions have made the argument a topical subject. However, a quantity which remains still unknown is the tunneling (or response) time, which is strictly connected to the role that dissipation plays in the dynamics of the complete system. A simple way for evaluating dissipation in microwave circuits, previously developed for describing the dynamics of conventional Josephson junctions, is now presented as suitable for application even to non-conventional junctions. The method is based on a stochastic model, as derived from the telegrapher's equation, and is particularly devoted to the case of junctions loaded by real transmission lines. When the load is constituted by lumped-constant circuits, a connection with the stochastic model is also maintained. The theoretical model demonstrated its ability to analyze both classically-allowed and forbidden processes, and has found a wide field of applicability, namely in all cases in which dissipative effects cannot be ignored.

Formation of visual memories controlled by gamma power phase-locked to alpha oscillations

NASA Astrophysics Data System (ADS)

Park, Hyojin; Lee, Dong Soo; Kang, Eunjoo; Kang, Hyejin; Hahm, Jarang; Kim, June Sic; Chung, Chun Kee; Jiang, Haiteng; Gross, Joachim; Jensen, Ole

2016-06-01

Neuronal oscillations provide a window for understanding the brain dynamics that organize the flow of information from sensory to memory areas. While it has been suggested that gamma power reflects feedforward processing and alpha oscillations feedback control, it remains unknown how these oscillations dynamically interact. Magnetoencephalography (MEG) data was acquired from healthy subjects who were cued to either remember or not remember presented pictures. Our analysis revealed that in anticipation of a picture to be remembered, alpha power decreased while the cross-frequency coupling between gamma power and alpha phase increased. A measure of directionality between alpha phase and gamma power predicted individual ability to encode memory: stronger control of alpha phase over gamma power was associated with better memory. These findings demonstrate that encoding of visual information is reflected by a state determined by the interaction between alpha and gamma activity.

Stimulation-Based Control of Dynamic Brain Networks

PubMed Central

Pasqualetti, Fabio; Gu, Shi; Cieslak, Matthew

2016-01-01

The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from network control theory, we uncover the relationship between regional controllability and the focal versus global impact of stimulation, and we relate these findings to differences in the underlying network architecture. Finally, by mapping brain regions to cognitive systems, we observe that the default mode system imparts large global change despite being highly constrained by structural connectivity. This work forms an important step towards the development of personalized stimulation protocols for medical treatment or performance enhancement. PMID:27611328

Unjamming and cell shape in the asthmatic airway epithelium

NASA Astrophysics Data System (ADS)

Park, Jin-Ah; Kim, Jae Hun; Bi, Dapeng; Mitchel, Jennifer A.; Qazvini, Nader Taheri; Tantisira, Kelan; Park, Chan Young; McGill, Maureen; Kim, Sae-Hoon; Gweon, Bomi; Notbohm, Jacob; Steward, Robert, Jr.; Burger, Stephanie; Randell, Scott H.; Kho, Alvin T.; Tambe, Dhananjay T.; Hardin, Corey; Shore, Stephanie A.; Israel, Elliot; Weitz, David A.; Tschumperlin, Daniel J.; Henske, Elizabeth P.; Weiss, Scott T.; Manning, M. Lisa; Butler, James P.; Drazen, Jeffrey M.; Fredberg, Jeffrey J.

2015-10-01

From coffee beans flowing in a chute to cells remodelling in a living tissue, a wide variety of close-packed collective systems--both inert and living--have the potential to jam. The collective can sometimes flow like a fluid or jam and rigidify like a solid. The unjammed-to-jammed transition remains poorly understood, however, and structural properties characterizing these phases remain unknown. Using primary human bronchial epithelial cells, we show that the jamming transition in asthma is linked to cell shape, thus establishing in that system a structural criterion for cell jamming. Surprisingly, the collapse of critical scaling predicts a counter-intuitive relationship between jamming, cell shape and cell-cell adhesive stresses that is borne out by direct experimental observations. Cell shape thus provides a rigorous structural signature for classification and investigation of bronchial epithelial layer jamming in asthma, and potentially in any process in disease or development in which epithelial dynamics play a prominent role.

Attitude determination using an adaptive multiple model filtering Scheme

NASA Technical Reports Server (NTRS)

Lam, Quang; Ray, Surendra N.

1995-01-01

Attitude determination has been considered as a permanent topic of active research and perhaps remaining as a forever-lasting interest for spacecraft system designers. Its role is to provide a reference for controls such as pointing the directional antennas or solar panels, stabilizing the spacecraft or maneuvering the spacecraft to a new orbit. Least Square Estimation (LSE) technique was utilized to provide attitude determination for the Nimbus 6 and G. Despite its poor performance (estimation accuracy consideration), LSE was considered as an effective and practical approach to meet the urgent need and requirement back in the 70's. One reason for this poor performance associated with the LSE scheme is the lack of dynamic filtering or 'compensation'. In other words, the scheme is based totally on the measurements and no attempts were made to model the dynamic equations of motion of the spacecraft. We propose an adaptive filtering approach which employs a bank of Kalman filters to perform robust attitude estimation. The proposed approach, whose architecture is depicted, is essentially based on the latest proof on the interactive multiple model design framework to handle the unknown of the system noise characteristics or statistics. The concept fundamentally employs a bank of Kalman filter or submodel, instead of using fixed values for the system noise statistics for each submodel (per operating condition) as the traditional multiple model approach does, we use an on-line dynamic system noise identifier to 'identify' the system noise level (statistics) and update the filter noise statistics using 'live' information from the sensor model. The advanced noise identifier, whose architecture is also shown, is implemented using an advanced system identifier. To insure the robust performance for the proposed advanced system identifier, it is also further reinforced by a learning system which is implemented (in the outer loop) using neural networks to identify other unknown quantities such as spacecraft dynamics parameters, gyro biases, dynamic disturbances, or environment variations.

Attitude determination using an adaptive multiple model filtering Scheme

NASA Astrophysics Data System (ADS)

Lam, Quang; Ray, Surendra N.

1995-05-01

Attitude determination has been considered as a permanent topic of active research and perhaps remaining as a forever-lasting interest for spacecraft system designers. Its role is to provide a reference for controls such as pointing the directional antennas or solar panels, stabilizing the spacecraft or maneuvering the spacecraft to a new orbit. Least Square Estimation (LSE) technique was utilized to provide attitude determination for the Nimbus 6 and G. Despite its poor performance (estimation accuracy consideration), LSE was considered as an effective and practical approach to meet the urgent need and requirement back in the 70's. One reason for this poor performance associated with the LSE scheme is the lack of dynamic filtering or 'compensation'. In other words, the scheme is based totally on the measurements and no attempts were made to model the dynamic equations of motion of the spacecraft. We propose an adaptive filtering approach which employs a bank of Kalman filters to perform robust attitude estimation. The proposed approach, whose architecture is depicted, is essentially based on the latest proof on the interactive multiple model design framework to handle the unknown of the system noise characteristics or statistics. The concept fundamentally employs a bank of Kalman filter or submodel, instead of using fixed values for the system noise statistics for each submodel (per operating condition) as the traditional multiple model approach does, we use an on-line dynamic system noise identifier to 'identify' the system noise level (statistics) and update the filter noise statistics using 'live' information from the sensor model. The advanced noise identifier, whose architecture is also shown, is implemented using an advanced system identifier. To insure the robust performance for the proposed advanced system identifier, it is also further reinforced by a learning system which is implemented (in the outer loop) using neural networks to identify other unknown quantities such as spacecraft dynamics parameters, gyro biases, dynamic disturbances, or environment variations.

Dynamic modelling and adaptive robust tracking control of a space robot with two-link flexible manipulators under unknown disturbances

NASA Astrophysics Data System (ADS)

Yang, Xinxin; Ge, Shuzhi Sam; He, Wei

2018-04-01

In this paper, both the closed-form dynamics and adaptive robust tracking control of a space robot with two-link flexible manipulators under unknown disturbances are developed. The dynamic model of the system is described with assumed modes approach and Lagrangian method. The flexible manipulators are represented as Euler-Bernoulli beams. Based on singular perturbation technique, the displacements/joint angles and flexible modes are modelled as slow and fast variables, respectively. A sliding mode control is designed for trajectories tracking of the slow subsystem under unknown but bounded disturbances, and an adaptive sliding mode control is derived for slow subsystem under unknown slowly time-varying disturbances. An optimal linear quadratic regulator method is proposed for the fast subsystem to damp out the vibrations of the flexible manipulators. Theoretical analysis validates the stability of the proposed composite controller. Numerical simulation results demonstrate the performance of the closed-loop flexible space robot system.

Epistemic and aleatory uncertainty in the study of dynamic human-water systems

NASA Astrophysics Data System (ADS)

Di Baldassarre, Giuliano; Brandimarte, Luigia; Beven, Keith

2016-04-01

Here we discuss epistemic and aleatory uncertainty in the study of dynamic human-water systems (e.g. socio-hydrology), which is one of the main topics of Panta Rhei, the current scientific decade of the International Association of Hydrological Sciences (IAHS). In particular, we identify three types of lack of understanding: (i) known unknowns, which are things we know we don't know; (ii) unknown unknowns, which are things we don't know we don't know; and (iii) wrong assumptions, things we think we know, but we actually don't know. We posit that a better understanding of human-water interactions and feedbacks can help coping with wrong assumptions and known unknowns. Moreover, being aware of the existence of unknown unknowns, and their potential capability to generate surprises or black swans, suggest the need to rely more on bottom-up approaches, based on social vulnerabilities and possibilities of failures, and less on top-down approaches, based on optimization and quantitative predictions.

Iterative Adaptive Dynamic Programming for Solving Unknown Nonlinear Zero-Sum Game Based on Online Data.

PubMed

Zhu, Yuanheng; Zhao, Dongbin; Li, Xiangjun

2017-03-01

H ∞ control is a powerful method to solve the disturbance attenuation problems that occur in some control systems. The design of such controllers relies on solving the zero-sum game (ZSG). But in practical applications, the exact dynamics is mostly unknown. Identification of dynamics also produces errors that are detrimental to the control performance. To overcome this problem, an iterative adaptive dynamic programming algorithm is proposed in this paper to solve the continuous-time, unknown nonlinear ZSG with only online data. A model-free approach to the Hamilton-Jacobi-Isaacs equation is developed based on the policy iteration method. Control and disturbance policies and value are approximated by neural networks (NNs) under the critic-actor-disturber structure. The NN weights are solved by the least-squares method. According to the theoretical analysis, our algorithm is equivalent to a Gauss-Newton method solving an optimization problem, and it converges uniformly to the optimal solution. The online data can also be used repeatedly, which is highly efficient. Simulation results demonstrate its feasibility to solve the unknown nonlinear ZSG. When compared with other algorithms, it saves a significant amount of online measurement time.

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

Spatiotemporal dynamics of optogenetically induced and spontaneous seizure transitions in primary generalized epilepsy

PubMed Central

Truccolo, Wilson; Wang, Jing; Nurmikko, Arto V.

2014-01-01

Transitions into primary generalized epileptic seizures occur abruptly and synchronously across the brain. Their potential triggers remain unknown. We used optogenetics to causally test the hypothesis that rhythmic population bursting of excitatory neurons in a local neocortical region can rapidly trigger absence seizures. Most previous studies have been purely correlational, and it remains unclear whether epileptiform events induced by rhythmic stimulation (e.g., sensory/electrical) mimic actual spontaneous seizures, especially regarding their spatiotemporal dynamics. In this study, we used a novel combination of intracortical optogenetic stimulation and microelectrode array recordings in freely moving WAG/Rij rats, a model of absence epilepsy with a cortical focus in the somatosensory cortex (SI). We report three main findings: 1) Brief rhythmic bursting, evoked by optical stimulation of neocortical excitatory neurons at frequencies around 10 Hz, induced seizures consisting of self-sustained spike-wave discharges (SWDs) for about 10% of stimulation trials. The probability of inducing seizures was frequency-dependent, reaching a maximum at 10 Hz. 2) Local field potential power before stimulation and response amplitudes during stimulation both predicted seizure induction, demonstrating a modulatory effect of brain states and neural excitation levels. 3) Evoked responses during stimulation propagated as cortical waves, likely reaching the cortical focus, which in turn generated self-sustained SWDs after stimulation was terminated. Importantly, SWDs during induced and spontaneous seizures propagated with the same spatiotemporal dynamics. Our findings demonstrate that local rhythmic bursting of excitatory neurons in neocortex at particular frequencies, under susceptible ongoing brain states, is sufficient to trigger primary generalized seizures with stereotypical spatiotemporal dynamics. PMID:25552645

Spatial dynamics of action potentials estimated by dendritic Ca(2+) signals in insect projection neurons.

PubMed

Ogawa, Hiroto; Mitani, Ruriko

2015-11-13

The spatial dynamics of action potentials, including their propagation and the location of spike initiation zone (SIZ), are crucial for the computation of a single neuron. Compared with mammalian central neurons, the spike dynamics of invertebrate neurons remain relatively unknown. Thus, we examined the spike dynamics based on single spike-induced Ca(2+) signals in the dendrites of cricket mechanosensory projection neurons, known as giant interneurons (GIs). The Ca(2+) transients induced by a synaptically evoked single spike were larger than those induced by an antidromic spike, whereas subthreshold synaptic potentials caused no elevation of Ca(2+). These results indicate that synaptic activity enhances the dendritic Ca(2+) influx through voltage-gated Ca(2+) channels. Stimulation of the presynaptic sensory afferents ipsilateral to the recording site evoked a dendritic spike with higher amplitude than contralateral stimulation, thereby suggesting that alteration of the spike waveform resulted in synaptic enhancement of the dendritic Ca(2+) transients. The SIZ estimated from the spatial distribution of the difference in the Ca(2+) amplitude was distributed throughout the right and left dendritic branches across the primary neurite connecting them in GIs. Copyright © 2015 Elsevier Inc. All rights reserved.

Coupled dynamics of body mass and population growth in response to environmental change.

PubMed

Ozgul, Arpat; Childs, Dylan Z; Oli, Madan K; Armitage, Kenneth B; Blumstein, Daniel T; Olson, Lucretia E; Tuljapurkar, Shripad; Coulson, Tim

2010-07-22

Environmental change has altered the phenology, morphological traits and population dynamics of many species. However, the links underlying these joint responses remain largely unknown owing to a paucity of long-term data and the lack of an appropriate analytical framework. Here we investigate the link between phenotypic and demographic responses to environmental change using a new methodology and a long-term (1976-2008) data set from a hibernating mammal (the yellow-bellied marmot) inhabiting a dynamic subalpine habitat. We demonstrate how earlier emergence from hibernation and earlier weaning of young has led to a longer growing season and larger body masses before hibernation. The resulting shift in both the phenotype and the relationship between phenotype and fitness components led to a decline in adult mortality, which in turn triggered an abrupt increase in population size in recent years. Direct and trait-mediated effects of environmental change made comparable contributions to the observed marked increase in population growth. Our results help explain how a shift in phenology can cause simultaneous phenotypic and demographic changes, and highlight the need for a theory integrating ecological and evolutionary dynamics in stochastic environments.

Coupled dynamics of body mass and population growth in response to environmental change

PubMed Central

Ozgul, Arpat; Childs, Dylan Z.; Oli, Madan K.; Armitage, Kenneth B.; Blumstein, Daniel T.; Olson, Lucretia E.; Tuljapurkar, Shripad; Coulson, Tim

2017-01-01

Environmental change has altered the phenology, morphological traits and population dynamics of many species1,2. However, the links underlying these joint responses remain largely unknown due to a paucity of long-term data and the lack of an appropriate analytical framework3. Here, we investigate the link between phenotypic and demographic responses to environmental change using a novel methodology and an exceptional long-term (1976–2008) dataset from a hibernating mammal (the yellow-bellied marmot) inhabiting a dynamic subalpine habitat. We demonstrate how earlier emergence from hibernation and earlier weaning of young has led to a longer growing season and larger body masses prior to hibernation. The resulting shift in both the phenotype and the relationship between phenotype and fitness components led to a decline in adult mortality, which in turn triggered an abrupt increase in population size in recent years. Direct and trait-mediated effects of environmental change had comparable contributions to the observed dramatic increase in population growth. Our results help explain how a shift in phenology can cause simultaneous phenotypic and demographic changes, and highlight the need for a theory integrating ecological and evolutionary dynamics in stochastic environments4,5. PMID:20651690

Parameter identifiability of linear dynamical systems

NASA Technical Reports Server (NTRS)

Glover, K.; Willems, J. C.

1974-01-01

It is assumed that the system matrices of a stationary linear dynamical system were parametrized by a set of unknown parameters. The question considered here is, when can such a set of unknown parameters be identified from the observed data? Conditions for the local identifiability of a parametrization are derived in three situations: (1) when input/output observations are made, (2) when there exists an unknown feedback matrix in the system and (3) when the system is assumed to be driven by white noise and only output observations are made. Also a sufficient condition for global identifiability is derived.

UAV Trajectory Modeling Using Neural Networks

NASA Technical Reports Server (NTRS)

Xue, Min

2017-01-01

Large amount of small Unmanned Aerial Vehicles (sUAVs) are projected to operate in the near future. Potential sUAV applications include, but not limited to, search and rescue, inspection and surveillance, aerial photography and video, precision agriculture, and parcel delivery. sUAVs are expected to operate in the uncontrolled Class G airspace, which is at or below 500 feet above ground level (AGL), where many static and dynamic constraints exist, such as ground properties and terrains, restricted areas, various winds, manned helicopters, and conflict avoidance among sUAVs. How to enable safe, efficient, and massive sUAV operations at the low altitude airspace remains a great challenge. NASA's Unmanned aircraft system Traffic Management (UTM) research initiative works on establishing infrastructure and developing policies, requirement, and rules to enable safe and efficient sUAVs' operations. To achieve this goal, it is important to gain insights of future UTM traffic operations through simulations, where the accurate trajectory model plays an extremely important role. On the other hand, like what happens in current aviation development, trajectory modeling should also serve as the foundation for any advanced concepts and tools in UTM. Accurate models of sUAV dynamics and control systems are very important considering the requirement of the meter level precision in UTM operations. The vehicle dynamics are relatively easy to derive and model, however, vehicle control systems remain unknown as they are usually kept by manufactures as a part of intellectual properties. That brings challenges to trajectory modeling for sUAVs. How to model the vehicle's trajectories with unknown control system? This work proposes to use a neural network to model a vehicle's trajectory. The neural network is first trained to learn the vehicle's responses at numerous conditions. Once being fully trained, given current vehicle states, winds, and desired future trajectory, the neural network should be able to predict the vehicle's future states at next time step. A complete 4-D trajectory are then generated step by step using the trained neural network. Experiments in this work show that the neural network can approximate the sUAV's model and predict the trajectory accurately.

TLR4 signaling shapes B cell dynamics via MyD88-dependent pathways and Rac GTPases.

PubMed

Barrio, Laura; Saez de Guinoa, Julia; Carrasco, Yolanda R

2013-10-01

B cells use a plethora of TLR to recognize pathogen-derived ligands. These innate signals have an important function in the B cell adaptive immune response and modify their trafficking and tissue location. The direct role of TLR signaling on B cell dynamics nonetheless remains almost entirely unknown. In this study, we used a state-of-the-art two-dimensional model combined with real-time microscopy to study the effect of TLR4 stimulation on mouse B cell motility in response to chemokines. We show that a minimum stimulation period is necessary for TLR4 modification of B cell behavior. TLR4 stimulation increased B cell polarization, migration, and directionality; these increases were dependent on the MyD88 signaling pathway and did not require ERK or p38 MAPK activity downstream of TLR4. In addition, TLR4 stimulation enhanced Rac GTPase activity and promoted sustained Rac activation in response to chemokines. These results increase our understanding of the regulation of B cell dynamics by innate signals and the underlying molecular mechanisms.

3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

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

Zhang, Xing; Zhang, Lei; Tong, Huimin

2015-05-05

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

Ultrafast terahertz-field-driven ionic response in ferroelectric BaTiO 3

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

Chen, F.; Zhu, Y.; Liu, S.

The dynamical processes associated with electric field manipulation of the polarization in a ferroelectric remain largely unknown but fundamentally determine the speed and functionality of ferroelectric materials and devices. Here we apply subpicosecond duration, single-cycle terahertz pulses as an ultrafast electric field bias to prototypical BaTiO 3 ferroelectric thin films with the atomic-scale response probed by femtosecond x-ray-scattering techniques. We show that electric fields applied perpendicular to the ferroelectric polarization drive large-amplitude displacements of the titanium atoms along the ferroelectric polarization axis, comparable to that of the built-in displacements associated with the intrinsic polarization and incoherent across unit cells. Thismore » effect is associated with a dynamic rotation of the ferroelectric polarization switching on and then off on picosecond time scales. These transient polarization modulations are followed by long-lived vibrational heating effects driven by resonant excitation of the ferroelectric soft mode, as reflected in changes in the c-axis tetragonality. The ultrafast structural characterization described here enables a direct comparison with first-principles-based molecular-dynamics simulations, with good agreement obtained.« less

Ultrafast terahertz-field-driven ionic response in ferroelectric BaTiO 3

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

Chen, F.; Zhu, Y.; Liu, S.

The dynamical processes associated with electric field manipulation of the polarization in a ferroelectric remain largely unknown but fundamentally determine the speed and functionality of ferroelectric materials and devices. Here in this paper we apply subpicosecond duration, single-cycle terahertz pulses as an ultrafast electric field bias to prototypical BaTiO 3 ferroelectric thin films with the atomic-scale response probed by femtosecond x-ray-scattering techniques. We show that electric fields applied perpendicular to the ferroelectric polarization drive large-amplitude displacements of the titanium atoms along the ferroelectric polarization axis, comparable to that of the built-in displacements associated with the intrinsic polarization and incoherent acrossmore » unit cells. This effect is associated with a dynamic rotation of the ferroelectric polarization switching on and then off on picosecond time scales. These transient polarization modulations are followed by long-lived vibrational heating effects driven by resonant excitation of the ferroelectric soft mode, as reflected in changes in the c-axis tetragonality. The ultrafast structural characterization described here enables a direct comparison with first-principles-based molecular-dynamics simulations, with good agreement obtained.« less

Ultrafast terahertz-field-driven ionic response in ferroelectric BaTiO 3

DOE PAGES

Chen, F.; Zhu, Y.; Liu, S.; ...

2016-11-22

The dynamical processes associated with electric field manipulation of the polarization in a ferroelectric remain largely unknown but fundamentally determine the speed and functionality of ferroelectric materials and devices. Here in this paper we apply subpicosecond duration, single-cycle terahertz pulses as an ultrafast electric field bias to prototypical BaTiO 3 ferroelectric thin films with the atomic-scale response probed by femtosecond x-ray-scattering techniques. We show that electric fields applied perpendicular to the ferroelectric polarization drive large-amplitude displacements of the titanium atoms along the ferroelectric polarization axis, comparable to that of the built-in displacements associated with the intrinsic polarization and incoherent acrossmore » unit cells. This effect is associated with a dynamic rotation of the ferroelectric polarization switching on and then off on picosecond time scales. These transient polarization modulations are followed by long-lived vibrational heating effects driven by resonant excitation of the ferroelectric soft mode, as reflected in changes in the c-axis tetragonality. The ultrafast structural characterization described here enables a direct comparison with first-principles-based molecular-dynamics simulations, with good agreement obtained.« less

Direction of Amygdala-Neocortex Interaction During Dynamic Facial Expression Processing.

PubMed

Sato, Wataru; Kochiyama, Takanori; Uono, Shota; Yoshikawa, Sakiko; Toichi, Motomi

2017-03-01

Dynamic facial expressions of emotion strongly elicit multifaceted emotional, perceptual, cognitive, and motor responses. Neuroimaging studies revealed that some subcortical (e.g., amygdala) and neocortical (e.g., superior temporal sulcus and inferior frontal gyrus) brain regions and their functional interaction were involved in processing dynamic facial expressions. However, the direction of the functional interaction between the amygdala and the neocortex remains unknown. To investigate this issue, we re-analyzed functional magnetic resonance imaging (fMRI) data from 2 studies and magnetoencephalography (MEG) data from 1 study. First, a psychophysiological interaction analysis of the fMRI data confirmed the functional interaction between the amygdala and neocortical regions. Then, dynamic causal modeling analysis was used to compare models with forward, backward, or bidirectional effective connectivity between the amygdala and neocortical networks in the fMRI and MEG data. The results consistently supported the model of effective connectivity from the amygdala to the neocortex. Further increasing time-window analysis of the MEG demonstrated that this model was valid after 200 ms from the stimulus onset. These data suggest that emotional processing in the amygdala rapidly modulates some neocortical processing, such as perception, recognition, and motor mimicry, when observing dynamic facial expressions of emotion. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evolutionary dynamics under interactive diversity

NASA Astrophysics Data System (ADS)

Su, Qi; Li, Aming; Wang, Long

2017-10-01

As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

Unified sensor management in unknown dynamic clutter

NASA Astrophysics Data System (ADS)

Mahler, Ronald; El-Fallah, Adel

2010-04-01

In recent years the first author has developed a unified, computationally tractable approach to multisensor-multitarget sensor management. This approach consists of closed-loop recursion of a PHD or CPHD filter with maximization of a "natural" sensor management objective function called PENT (posterior expected number of targets). In this paper we extend this approach so that it can be used in unknown, dynamic clutter backgrounds.

Mitochondria: the next (neurode)generation

PubMed Central

Schon, Eric A.; Przedborski, Serge

2012-01-01

SUMMARY Adult-onset neurodegenerative disorders are disabling and often fatal diseases of the nervous system whose underlying mechanisms of cell death remain, in most instances, unknown. Defects in mitochondrial respiration had previously been proposed to contribute to the occurrence of many, if not all of the most common neurodegenerative disorders. However, the discovery of genes mutated in hereditary forms of these enigmatic diseases has additionally suggested defects in mitochondrial dynamics. Such disturbances can lead to changes in mitochondrial trafficking, in interorganellar communication, and in mitochondrial quality control. These new mechanisms by which mitochondria may also be linked to neurodegeneration will likely have far-reaching implications for our understanding of the pathophysiology and treatment of adult-onset neurodegenerative disorders. PMID:21689593

Role of the posterior parietal cortex in updating reaching movements to a visual target.

PubMed

Desmurget, M; Epstein, C M; Turner, R S; Prablanc, C; Alexander, G E; Grafton, S T

1999-06-01

The exact role of posterior parietal cortex (PPC) in visually directed reaching is unknown. We propose that, by building an internal representation of instantaneous hand location, PPC computes a dynamic motor error used by motor centers to correct the ongoing trajectory. With unseen right hands, five subjects pointed to visual targets that either remained stationary or moved during saccadic eye movements. Transcranial magnetic stimulation (TMS) was applied over the left PPC during target presentation. Stimulation disrupted path corrections that normally occur in response to target jumps, but had no effect on those directed at stationary targets. Furthermore, left-hand movement corrections were not blocked, ruling out visual or oculomotor effects of stimulation.

The structure and evolution of angiosperm nuclear genomes.

PubMed

Bennetzen, J L

1998-04-01

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.

Adaptive neural network output feedback control for stochastic nonlinear systems with unknown dead-zone and unmodeled dynamics.

PubMed

Tong, Shaocheng; Wang, Tong; Li, Yongming; Zhang, Huaguang

2014-06-01

This paper discusses the problem of adaptive neural network output feedback control for a class of stochastic nonlinear strict-feedback systems. The concerned systems have certain characteristics, such as unknown nonlinear uncertainties, unknown dead-zones, unmodeled dynamics and without the direct measurements of state variables. In this paper, the neural networks (NNs) are employed to approximate the unknown nonlinear uncertainties, and then by representing the dead-zone as a time-varying system with a bounded disturbance. An NN state observer is designed to estimate the unmeasured states. Based on both backstepping design technique and a stochastic small-gain theorem, a robust adaptive NN output feedback control scheme is developed. It is proved that all the variables involved in the closed-loop system are input-state-practically stable in probability, and also have robustness to the unmodeled dynamics. Meanwhile, the observer errors and the output of the system can be regulated to a small neighborhood of the origin by selecting appropriate design parameters. Simulation examples are also provided to illustrate the effectiveness of the proposed approach.

Control of Complex Dynamic Systems by Neural Networks

NASA Technical Reports Server (NTRS)

Spall, James C.; Cristion, John A.

1993-01-01

This paper considers the use of neural networks (NN's) in controlling a nonlinear, stochastic system with unknown process equations. The NN is used to model the resulting unknown control law. The approach here is based on using the output error of the system to train the NN controller without the need to construct a separate model (NN or other type) for the unknown process dynamics. To implement such a direct adaptive control approach, it is required that connection weights in the NN be estimated while the system is being controlled. As a result of the feedback of the unknown process dynamics, however, it is not possible to determine the gradient of the loss function for use in standard (back-propagation-type) weight estimation algorithms. Therefore, this paper considers the use of a new stochastic approximation algorithm for this weight estimation, which is based on a 'simultaneous perturbation' gradient approximation that only requires the system output error. It is shown that this algorithm can greatly enhance the efficiency over more standard stochastic approximation algorithms based on finite-difference gradient approximations.

Differential Colonization Dynamics of Cucurbit Hosts by Erwinia tracheiphila.

PubMed

Vrisman, Cláudio M; Deblais, Loïc; Rajashekara, Gireesh; Miller, Sally A

2016-07-01

Bacterial wilt is one of the most destructive diseases of cucurbits in the Midwestern and Northeastern United States. Although the disease has been studied since 1900, host colonization dynamics remain unclear. Cucumis- and Cucurbita-derived strains exhibit host preference for the cucurbit genus from which they were isolated. We constructed a bioluminescent strain of Erwinia tracheiphila (TedCu10-BL#9) and colonization of different cucurbit hosts was monitored. At the second-true-leaf stage, Cucumis melo plants were inoculated with TedCu10-BL#9 via wounded leaves, stems, and roots. Daily monitoring of colonization showed bioluminescent bacteria in the inoculated leaf and petiole beginning 1 day postinoculation (DPI). The bacteria spread to roots via the stem by 2 DPI, reached the plant extremities 4 DPI, and the plant wilted 6 DPI. However, Cucurbita plants inoculated with TedCu10-BL#9 did not wilt, even at 35 DPI. Bioluminescent bacteria were detected 6 DPI in the main stem of squash and pumpkin plants, which harbored approximately 10(4) and 10(1) CFU/g, respectively, of TedCu10-BL#9 without symptoms. Although significantly less systemic plant colonization was observed in nonpreferred host Cucurbita plants compared with preferred hosts, the mechanism of tolerance of Cucurbita plants to E. tracheiphila strains from Cucumis remains unknown.

Drivers of Macrofungi Community Structure Differ between Soil and Rotten-Wood Substrates in a Temperate Mountain Forest in China

PubMed Central

Chen, Yun; Svenning, Jens-Christian; Wang, Xueying; Cao, Ruofan; Yuan, Zhiliang; Ye, Yongzhong

2018-01-01

The effects of environmental and dispersal processes on macrofungi community assembly remain unclear. Further, it is not well understood if community assembly differs for different functional guilds of macrofungi, e.g., soil and rotten-wood macrofungi. In this study, using 2433 macrofungi sporocarps belonging to 217 species located within a forest dynamics plot in temperate mountain forest (China), we examined the explanatory power of topography, spatial eigenvectors (representing unknown spatial processes, e.g., dispersal), plant community, and light availability for local spatial variation in the macrofungi community through variance partitioning and partial least squares path modeling. We found spatial eigenvectors and light as the most important factors for explaining species richness and composition of macrofungi. Light was negatively correlated with species richness of macrofungi. Furthermore, species richness and composition of soil macrofungi were best explained by light, and species richness and composition of rotten-wood macrofungi were best explained by spatial eigenvectors. Woody plant community structure was not an important factor for species richness and composition of macrofungi. Our findings suggest that spatial processes, perhaps dispersal limitation, and light availability were the most important factors affecting macrofungi community in temperate deciduous broad-leaved forest. Major differences in influencing factors between soil and rotten-wood macrofungi were observed, with light as the major driver for soil macrofungi and unknown spatial processes as the major driver for rotten-wood macrofungi. These findings shed new light to the processes shaping community assembly in macrofungi in temperate deciduous broad-leaved forest and point to the potential importance of both intrinsic dynamics, such as dispersal, and external forcing, such as forest dynamics, via its effect on light availability. PMID:29410660

Navigation through unknown and dynamic open spaces using topological notions

NASA Astrophysics Data System (ADS)

Miguel-Tomé, Sergio

2018-04-01

Until now, most algorithms used for navigation have had the purpose of directing system towards one point in space. However, humans communicate tasks by specifying spatial relations among elements or places. In addition, the environments in which humans develop their activities are extremely dynamic. The only option that allows for successful navigation in dynamic and unknown environments is making real-time decisions. Therefore, robots capable of collaborating closely with human beings must be able to make decisions based on the local information registered by the sensors and interpret and express spatial relations. Furthermore, when one person is asked to perform a task in an environment, this task is communicated given a category of goals so the person does not need to be supervised. Thus, two problems appear when one wants to create multifunctional robots: how to navigate in dynamic and unknown environments using spatial relations and how to accomplish this without supervision. In this article, a new architecture to address the two cited problems is presented, called the topological qualitative navigation architecture. In previous works, a qualitative heuristic called the heuristic of topological qualitative semantics (HTQS) has been developed to establish and identify spatial relations. However, that heuristic only allows for establishing one spatial relation with a specific object. In contrast, navigation requires a temporal sequence of goals with different objects. The new architecture attains continuous generation of goals and resolves them using HTQS. Thus, the new architecture achieves autonomous navigation in dynamic or unknown open environments.

Off-Policy Integral Reinforcement Learning Method to Solve Nonlinear Continuous-Time Multiplayer Nonzero-Sum Games.

PubMed

Song, Ruizhuo; Lewis, Frank L; Wei, Qinglai

2017-03-01

This paper establishes an off-policy integral reinforcement learning (IRL) method to solve nonlinear continuous-time (CT) nonzero-sum (NZS) games with unknown system dynamics. The IRL algorithm is presented to obtain the iterative control and off-policy learning is used to allow the dynamics to be completely unknown. Off-policy IRL is designed to do policy evaluation and policy improvement in the policy iteration algorithm. Critic and action networks are used to obtain the performance index and control for each player. The gradient descent algorithm makes the update of critic and action weights simultaneously. The convergence analysis of the weights is given. The asymptotic stability of the closed-loop system and the existence of Nash equilibrium are proved. The simulation study demonstrates the effectiveness of the developed method for nonlinear CT NZS games with unknown system dynamics.

Adaptive Robust Output Feedback Control for a Marine Dynamic Positioning System Based on a High-Gain Observer.

PubMed

Du, Jialu; Hu, Xin; Liu, Hongbo; Chen, C L Philip

2015-11-01

This paper develops an adaptive robust output feedback control scheme for dynamically positioned ships with unavailable velocities and unknown dynamic parameters in an unknown time-variant disturbance environment. The controller is designed by incorporating the high-gain observer and radial basis function (RBF) neural networks in vectorial backstepping method. The high-gain observer provides the estimations of the ship position and heading as well as velocities. The RBF neural networks are employed to compensate for the uncertainties of ship dynamics. The adaptive laws incorporating a leakage term are designed to estimate the weights of RBF neural networks and the bounds of unknown time-variant environmental disturbances. In contrast to the existing results of dynamic positioning (DP) controllers, the proposed control scheme relies only on the ship position and heading measurements and does not require a priori knowledge of the ship dynamics and external disturbances. By means of Lyapunov functions, it is theoretically proved that our output feedback controller can control a ship's position and heading to the arbitrarily small neighborhood of the desired target values while guaranteeing that all signals in the closed-loop DP control system are uniformly ultimately bounded. Finally, simulations involving two ships are carried out, and simulation results demonstrate the effectiveness of the proposed control scheme.

Adaptive Actor-Critic Design-Based Integral Sliding-Mode Control for Partially Unknown Nonlinear Systems With Input Disturbances.

PubMed

Fan, Quan-Yong; Yang, Guang-Hong

2016-01-01

This paper is concerned with the problem of integral sliding-mode control for a class of nonlinear systems with input disturbances and unknown nonlinear terms through the adaptive actor-critic (AC) control method. The main objective is to design a sliding-mode control methodology based on the adaptive dynamic programming (ADP) method, so that the closed-loop system with time-varying disturbances is stable and the nearly optimal performance of the sliding-mode dynamics can be guaranteed. In the first step, a neural network (NN)-based observer and a disturbance observer are designed to approximate the unknown nonlinear terms and estimate the input disturbances, respectively. Based on the NN approximations and disturbance estimations, the discontinuous part of the sliding-mode control is constructed to eliminate the effect of the disturbances and attain the expected equivalent sliding-mode dynamics. Then, the ADP method with AC structure is presented to learn the optimal control for the sliding-mode dynamics online. Reconstructed tuning laws are developed to guarantee the stability of the sliding-mode dynamics and the convergence of the weights of critic and actor NNs. Finally, the simulation results are presented to illustrate the effectiveness of the proposed method.

Confronting the catalytic dark matter encoded by sequenced genomes

PubMed Central

Ellens, Kenneth W.; Christian, Nils; Singh, Charandeep; Satagopam, Venkata P.

2017-01-01

Abstract The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the ‘unknown enzyme problem’. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research. PMID:29059321

Patterns of call communication between group-housed zebra finches change during the breeding cycle

PubMed Central

Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

2015-01-01

Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems. DOI: http://dx.doi.org/10.7554/eLife.07770.001 PMID:26441403

Interplay between population firing stability and single neuron dynamics in hippocampal networks

PubMed Central

Slomowitz, Edden; Styr, Boaz; Vertkin, Irena; Milshtein-Parush, Hila; Nelken, Israel; Slutsky, Michael; Slutsky, Inna

2015-01-01

Neuronal circuits' ability to maintain the delicate balance between stability and flexibility in changing environments is critical for normal neuronal functioning. However, to what extent individual neurons and neuronal populations maintain internal firing properties remains largely unknown. In this study, we show that distributions of spontaneous population firing rates and synchrony are subject to accurate homeostatic control following increase of synaptic inhibition in cultured hippocampal networks. Reduction in firing rate triggered synaptic and intrinsic adaptive responses operating as global homeostatic mechanisms to maintain firing macro-stability, without achieving local homeostasis at the single-neuron level. Adaptive mechanisms, while stabilizing population firing properties, reduced short-term facilitation essential for synaptic discrimination of input patterns. Thus, invariant ongoing population dynamics emerge from intrinsically unstable activity patterns of individual neurons and synapses. The observed differences in the precision of homeostatic control at different spatial scales challenge cell-autonomous theory of network homeostasis and suggest the existence of network-wide regulation rules. DOI: http://dx.doi.org/10.7554/eLife.04378.001 PMID:25556699

Neural evidence for moral intuition and the temporal dynamics of interactions between emotional processes and moral cognition.

PubMed

Gui, Dan-Yang; Gan, Tian; Liu, Chao

2016-01-01

Behavioral and neurological studies have revealed that emotions influence moral cognition. Although moral stimuli are emotionally charged, the time course of interactions between emotions and moral judgments remains unknown. In the present study, we investigated the temporal dynamics of the interaction between emotional processes and moral cognition. The results revealed that when making moral judgments, the time course of the event-related potential (ERP) waveform was significantly different between high emotional arousal and low emotional arousal contexts. Different stages of processing were distinguished, showing distinctive interactions between emotional processes and moral reasoning. The precise time course of moral intuition and moral reasoning sheds new light on theoretical models of moral psychology. Specifically, the N1 component (interpreted as representing moral intuition) did not appear to be influenced by emotional arousal. However, the N2 component and late positive potential were strongly affected by emotional arousal; the slow wave was influenced by both emotional arousal and morality, suggesting distinct moral processing at different emotional arousal levels.

Study of the benzocaine transfer from aqueous solution to the interior of a biological membrane.

PubMed

Porasso, Rodolfo D; Bennett, W F Drew; Oliveira-Costa, S D; López Cascales, J J

2009-07-23

The precise molecular mechanism of general anesthetics remains unknown. It is therefore important to understand where molecules with anesthetic properties localize within biological membranes. We have determined the free energy profile of a benzocaine molecule (BZC) across a biological membrane using molecular dynamics simulation. We use an asymmetric phospholipid bilayer with DPPS in one leaflet of a DPPC bilayer (Lopez Cascales et al. J. Phys. Chem. B 2006, 110, 2358-2363) to model a biological bilayer. From the free energy profile, we predict the zone of actuation of a benzocaine is located in the hydrocarbon region or at the end of the lipid head, depending of the presence of charged lipids (DPPS) in the leaflet. We observe a moderate increase in the disorder of the membrane and in particular an increase in the disorder of DPPS. Static and dynamic physicochemical properties of the benzocaine, such as its dipole orientation, translational diffusion coefficient, and rotational relaxation time were measured.

Atomic Scale Dynamics of Contact Formation in the Cross-Section of InGaAs Nanowire Channels

DOE PAGES

Chen, Renjie; Jungjohann, Katherine L.; Mook, William M.; ...

2017-03-23

In the alloyed and compound contacts between metal and semiconductor transistor channels we see that they enable self-aligned gate processes which play a significant role in transistor scaling. At nanoscale dimensions and for nanowire channels, prior experiments focused on reactions along the channel length, but the early stage of reaction in their cross sections remains unknown. We report on the dynamics of the solid-state reaction between metal (Ni) and semiconductor (In 0.53Ga 0.47As), along the cross-section of nanowires that are 15 nm in width. Unlike planar structures where crystalline nickelide readily forms at conventional, low alloying temperatures, nanowires exhibit amore » solid-state amorphization step that can undergo a crystal regrowth step at elevated temperatures. Here, we capture the layer-by-layer reaction mechanism and growth rate anisotropy using in situ transmission electron microscopy (TEM). Our kinetic model depicts this new, in-plane contact formation which could pave the way for engineered nanoscale transistors.« less

The Temporal Dynamics of Arc Expression Regulate Cognitive Flexibility.

PubMed

Wall, Mark J; Collins, Dawn R; Chery, Samantha L; Allen, Zachary D; Pastuzyn, Elissa D; George, Arlene J; Nikolova, Viktoriya D; Moy, Sheryl S; Philpot, Benjamin D; Shepherd, Jason D; Müller, Jürgen; Ehlers, Michael D; Mabb, Angela M; Corrêa, Sonia A L

2018-06-27

Neuronal activity regulates the transcription and translation of the immediate-early gene Arc/Arg3.1, a key mediator of synaptic plasticity. Proteasome-dependent degradation of Arc tightly limits its temporal expression, yet the significance of this regulation remains unknown. We disrupted the temporal control of Arc degradation by creating an Arc knockin mouse (ArcKR) where the predominant Arc ubiquitination sites were mutated. ArcKR mice had intact spatial learning but showed specific deficits in selecting an optimal strategy during reversal learning. This cognitive inflexibility was coupled to changes in Arc mRNA and protein expression resulting in a reduced threshold to induce mGluR-LTD and enhanced mGluR-LTD amplitude. These findings show that the abnormal persistence of Arc protein limits the dynamic range of Arc signaling pathways specifically during reversal learning. Our work illuminates how the precise temporal control of activity-dependent molecules, such as Arc, regulates synaptic plasticity and is crucial for cognition. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells.

PubMed

Sun, Rui; Fu, Ling; Liu, Keke; Tian, Caiping; Yang, Yong; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C; Yang, Jing

2017-10-01

4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adduct to cysteine. ONE-derived adducts co-localize and exhibit crosstalk with many histone marks and redox sensitive sites. All four types of modifications derived from ONE can be reversed site-specifically in cells. Taken together, our study provides much-needed mechanistic insights into the cellular signaling and potential toxicities associated with this important lipid derived electrophile. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Cutting edge: Th17 and regulatory T cell dynamics and the regulation by IL-2 in the tumor microenvironment.

PubMed

Kryczek, Ilona; Wei, Shuang; Zou, Linhua; Altuwaijri, Saleh; Szeliga, Wojciech; Kolls, Jay; Chang, Alfred; Zou, Weiping

2007-06-01

Th17 cells play an active role in inflammation and autoimmune diseases. However, the nature and regulation of Th17 in the context of tumor immunity remain unknown. In this study, we show that parallel to regulatory T (Treg) cells, IL-17(+) CD4(+) and CD8(+) T cells are kinetically induced in multiple tumor microenvironments in mice and humans. Treg cells play a crucial role in tumor immune pathogenesis and temper immune therapeutic efficacy. IL-2 is crucial for the production and function of Treg cells. We now show that IL-2 reduces IL-17(+) T cell differentiation in the tumor microenvironment accompanied with an enhanced Treg cell compartment in vitro and in vivo. Altogether, our work demonstrates a dynamic differentiation of IL-17(+) T cells in the tumor microenvironment, reveals a novel role for IL-2 in controlling the balance between IL-17(+) and Treg cells, and provides new insight of IL-17(+) T cells in tumor immune pathology and therapy.

Acidity and hydrogen exchange dynamics of iron(II)-bound nitroxyl in aqueous solution.

PubMed

Gao, Yin; Toubaei, Abouzar; Kong, Xianqi; Wu, Gang

2014-10-20

Nitroxyl-iron(II) (HNO-Fe(II)) complexes are often unstable in aqueous solution, thus making them very difficult to study. Consequently, many fundamental chemical properties of Fe(II)-bound HNO have remained unknown. Using a comprehensive multinuclear ((1)H, (15)N, (17)O) NMR approach, the acidity of the Fe(II)-bound HNO in [Fe(CN)5(HNO)](3-) was investigated and its pK(a) value was determined to be greater than 11. Additionally, HNO undergoes rapid hydrogen exchange with water in aqueous solution and this exchange process is catalyzed by both acid and base. The hydrogen exchange dynamics for the Fe(II)-bound HNO have been characterized and the obtained benchmark values, when combined with the literature data on proteins, reveal that the rate of hydrogen exchange for the Fe(II)-bound HNO in the interior of globin proteins is reduced by a factor of 10(6). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Autonomy and Non-autonomy of Angiogenic Cell Movements Revealed by Experiment-Driven Mathematical Modeling.

PubMed

Sugihara, Kei; Nishiyama, Koichi; Fukuhara, Shigetomo; Uemura, Akiyoshi; Arima, Satoshi; Kobayashi, Ryo; Köhn-Luque, Alvaro; Mochizuki, Naoki; Suda, Toshio; Ogawa, Hisao; Kurihara, Hiroki

2015-12-01

Angiogenesis is a multicellular phenomenon driven by morphogenetic cell movements. We recently reported morphogenetic vascular endothelial cell (EC) behaviors to be dynamic and complex. However, the principal mechanisms orchestrating individual EC movements in angiogenic morphogenesis remain largely unknown. Here we present an experiment-driven mathematical model that enables us to systematically dissect cellular mechanisms in branch elongation. We found that cell-autonomous and coordinated actions governed these multicellular behaviors, and a cell-autonomous process sufficiently illustrated essential features of the morphogenetic EC dynamics at both the single-cell and cell-population levels. Through refining our model and experimental verification, we further identified a coordinated mode of tip EC behaviors regulated via a spatial relationship between tip and follower ECs, which facilitates the forward motility of tip ECs. These findings provide insights that enhance our mechanistic understanding of not only angiogenic morphogenesis, but also other types of multicellular phenomenon. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

PubMed Central

Louet, Maxime; Martinez, Jean; Floquet, Nicolas

2012-01-01

After extra-cellular stimulation of G-Protein Coupled Receptors (GPCRs), GDP/GTP exchange appears as the key, rate limiting step of the intracellular activation cycle of heterotrimeric G-proteins. Despite the availability of a large number of X-ray structures, the mechanism of GDP release out of heterotrimeric G-proteins still remains unknown at the molecular level. Starting from the available X-ray structure, extensive unconstrained/constrained molecular dynamics simulations were performed on the complete membrane-anchored Gi heterotrimer complexed to GDP, for a total simulation time overcoming 500 ns. By combining Targeted Molecular Dynamics (TMD) and free energy profiles reconstruction by umbrella sampling, our data suggest that the release of GDP was much more favored on its phosphate side. Interestingly, upon the forced extraction of GDP on this side, the whole protein encountered large, collective motions in perfect agreement with those we described previously including a domain to domain motion between the two ras-like and helical sub-domains of Gα. PMID:22829757

Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide

PubMed Central

Singh, Pradeep K.; Ghosh, Dhiman; Tewari, Debanjan; Mohite, Ganesh M.; Carvalho, Edmund; Jha, Narendra Nath; Jacob, Reeba S.; Sahay, Shruti; Banerjee, Rinti; Bera, Amal K.; Maji, Samir K.

2015-01-01

Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail. PMID:25803428

Implementing a Bayes Filter in a Neural Circuit: The Case of Unknown Stimulus Dynamics.

PubMed

Sokoloski, Sacha

2017-09-01

In order to interact intelligently with objects in the world, animals must first transform neural population responses into estimates of the dynamic, unknown stimuli that caused them. The Bayesian solution to this problem is known as a Bayes filter, which applies Bayes' rule to combine population responses with the predictions of an internal model. The internal model of the Bayes filter is based on the true stimulus dynamics, and in this note, we present a method for training a theoretical neural circuit to approximately implement a Bayes filter when the stimulus dynamics are unknown. To do this we use the inferential properties of linear probabilistic population codes to compute Bayes' rule and train a neural network to compute approximate predictions by the method of maximum likelihood. In particular, we perform stochastic gradient descent on the negative log-likelihood of the neural network parameters with a novel approximation of the gradient. We demonstrate our methods on a finite-state, a linear, and a nonlinear filtering problem and show how the hidden layer of the neural network develops tuning curves consistent with findings in experimental neuroscience.

Nonholonomic Ofject Tracking with Optical Sensors and Ofject Recognition Feedback

NASA Technical Reports Server (NTRS)

Goddard, R. E.; Hadaegh, F.

1994-01-01

Robotic controllers frequently operate under constraints. Often, the constraints are imperfectly or completely unknown. In this paper, the Lagrangian dynamics of a planar robot arm are expressed as a function of a globally unknown consraint.

A novel function of the cell polarity-regulating kinase PAR-1/MARK in dendritic spines

PubMed Central

Hayashi, Kenji; Suzuki, Atsushi; Ohno, Shigeo

2011-01-01

Dendritic spines are postsynaptic structures that receive excitatory synaptic signals from presynaptic terminals in neurons. Because the morphology of spines has been considered to be a crucial factor for the efficiency of synaptic transmission, understanding the mechanisms regulating their morphology is important for neuroscience. Actin filaments and their regulatory proteins are known to actively maintain spine morphology; recent studies have also shown an essential role of microtubules (MTs). Live imaging of the plus-ends of MTs in mature neurons revealed that MTs stochastically enter spines and mediate accumulation of p140Cap, which regulates reorganization of actin filaments. However, the molecular mechanism by which MT dynamics is controlled has remained largely unknown. A cell polarity-regulating serine/threonine kinase, partitioning-defective 1 (PAR-1), phosphorylates classical MAPs and inhibits their binding to MTs. Because the interaction of MAPs with MTs can decrease MT dynamic instability, PAR-1 is supposed to activate MT dynamics through its MAP/MT affinity-regulating kinase (MARK) activity, although there is not yet any direct evidence for this. Here, we review recent findings on the localization of PAR-1b in the dendrites of mouse hippocampal neurons, and its novel function in the maintenance of mature spine morphology by regulating MT dynamics. PMID:22545177

A novel function of the cell polarity-regulating kinase PAR-1/MARK in dendritic spines.

PubMed

Hayashi, Kenji; Suzuki, Atsushi; Ohno, Shigeo

2011-11-01

Dendritic spines are postsynaptic structures that receive excitatory synaptic signals from presynaptic terminals in neurons. Because the morphology of spines has been considered to be a crucial factor for the efficiency of synaptic transmission, understanding the mechanisms regulating their morphology is important for neuroscience. Actin filaments and their regulatory proteins are known to actively maintain spine morphology; recent studies have also shown an essential role of microtubules (MTs). Live imaging of the plus-ends of MTs in mature neurons revealed that MTs stochastically enter spines and mediate accumulation of p140Cap, which regulates reorganization of actin filaments. However, the molecular mechanism by which MT dynamics is controlled has remained largely unknown. A cell polarity-regulating serine/threonine kinase, partitioning-defective 1 (PAR-1), phosphorylates classical MAPs and inhibits their binding to MTs. Because the interaction of MAPs with MTs can decrease MT dynamic instability, PAR-1 is supposed to activate MT dynamics through its MAP/MT affinity-regulating kinase (MARK) activity, although there is not yet any direct evidence for this. Here, we review recent findings on the localization of PAR-1b in the dendrites of mouse hippocampal neurons, and its novel function in the maintenance of mature spine morphology by regulating MT dynamics.

Now You See It, Now You Don't: Characterizing Ephemeral Snowpacks in the Great Basin

NASA Astrophysics Data System (ADS)

Petersky, R. S.; Harpold, A. A.

2016-12-01

It is expected that some seasonal snowpacks (persisting all winter) will transition to ephemeral snowpacks (persisting <60 days) due to increased ablation and shifts from snow to rain as a consequence of regional warming. This transition to ephemeral snowpacks will be particularly important in the Great Basin because it receives minimal precipitation and has few high elevation mountain ranges. Consequently, increased snow ephemerality potentially threatens water resources derived from mountain snowmelt. However, the current range and extent of ephemeral snowpacks in the Great Basin remains relatively unknown and under measured. We analyzed snow cover information obtained from MODIS imagery using an object-based approach to investigate three questions: 1) How does the range and extent of ephemeral snowpacks in the Great Basin increase in warm and dry years?, 2) What topographic areas are at risk for increasing ephemerality due to changes in the climate regime? and 3) What vegetation types are common in ephemeral snow zones? We found that the extent of snow-covered area declined between a colder, wetter year (2011) and a warmer, drier year (2015) by an area roughly the size of the state of Georgia. Moreover, the proportion of ephemeral snowpack increased by 19% from the wet year to the dry year. While the ecohydrologic consequences of these results remain relatively unknown, this research could potentially aid resource managers in selecting conservation locations and strategies (i.e. fire fuel reductions, grazing allotments, and species conservation) to adapt to variable and changing snowpack dynamics.

New control concepts for uncertain water resources systems: 1. Theory

NASA Astrophysics Data System (ADS)

Georgakakos, Aris P.; Yao, Huaming

1993-06-01

A major complicating factor in water resources systems management is handling unknown inputs. Stochastic optimization provides a sound mathematical framework but requires that enough data exist to develop statistical input representations. In cases where data records are insufficient (e.g., extreme events) or atypical of future input realizations, stochastic methods are inadequate. This article presents a control approach where input variables are only expected to belong in certain sets. The objective is to determine sets of admissible control actions guaranteeing that the system will remain within desirable bounds. The solution is based on dynamic programming and derived for the case where all sets are convex polyhedra. A companion paper (Yao and Georgakakos, this issue) addresses specific applications and problems in relation to reservoir system management.

Regulation of behavioral plasticity by systemic temperature signaling in Caenorhabditis elegans.

PubMed

Sugi, Takuma; Nishida, Yukuo; Mori, Ikue

2011-06-26

Animals cope with environmental changes by altering behavioral strategy. Environmental information is generally received by sensory neurons in the neural circuit that generates behavior. However, although environmental temperature inevitably influences an animal's entire body, the mechanism of systemic temperature perception remains largely unknown. We show here that systemic temperature signaling induces a change in a memory-based behavior in C. elegans. During behavioral conditioning, non-neuronal cells as well as neuronal cells respond to cultivation temperature through a heat-shock transcription factor that drives newly identified gene expression dynamics. This systemic temperature signaling regulates thermosensory neurons non-cell-autonomously through the estrogen signaling pathway, producing thermotactic behavior. We provide a link between systemic environmental recognition and behavioral plasticity in the nervous system.

The Dynamical Structure of HR 8799's Inner Debris Disk

NASA Astrophysics Data System (ADS)

Contro, B.; Wittenmyer, Robert A.; Horner, J.; Marshall, Jonathan P.

2015-06-01

The HR 8799 system, with its four giant planets and two debris belts, has an architecture closely mirroring that of our Solar system where the inner, warm asteroid belt and outer, cool Edgeworth-Kuiper belt bracket the giant planets. As such, it is a valuable laboratory for examining exoplanetary dynamics and debris disk-exoplanet interactions. Whilst the outer debris belt of HR 8799 has been well resolved by previous observations, the spatial extent of the inner disk remains unknown. This leaves a significant question mark over both the location of the planetesimals responsible for producing the belt's visible dust and the physical properties of those grains. We have performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using UNSW Australia's Katana supercomputing facility to follow the dynamical evolution of a model inner disk comprising 300,298 particles for a period of 60 Ma. These simulations have enabled the characterisation of the extent and structure of the inner disk in detail, and will in future allow us to provide a first estimate of the small-body impact rate and water delivery prospects for possible (as-yet undetected) terrestrial planet (s) in the inner system.

The dynamical structure of the HR8799 inner debris disk

NASA Astrophysics Data System (ADS)

Wittenmyer, Robert A.; Contro de Godoy, Bruna; Horner, Jonathan; Marshall, Jonathan P.

2014-11-01

The HR 8799 system, with its four giant planets and two debris belts, has an architecture closely mirroring that of our Solar System where the inner, warm asteroid belt and outer, cool Edgeworth-Kuiper belt bracket the giant planets. As such, it is a valuable laboratory for examining exoplanet dynamics and debris disc-exoplanet interactions. Whilst the outer debris belt of HR 8799 has been well resolved by previous observations, the spatial extent of the inner disc remains unknown, leaving a question mark over both the location of the planetesimals responsible for producing the belt's visible dust and the physical properties of those grains. We have performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using University of New South Wales's Katana supercomputing facility to follow the dynamical evolution of a model inner disc comprising 250,000 particles for a period of 100 million years. These simulations will (1) characterise the extent and structure of the inner disk in detail and (2) provide the first estimate of the small-body impact rate and water delivery prospects for possible (as-yet undetected) terrestrial planet(s) in the inner system.

Camera pose estimation for augmented reality in a small indoor dynamic scene

NASA Astrophysics Data System (ADS)

Frikha, Rawia; Ejbali, Ridha; Zaied, Mourad

2017-09-01

Camera pose estimation remains a challenging task for augmented reality (AR) applications. Simultaneous localization and mapping (SLAM)-based methods are able to estimate the six degrees of freedom camera motion while constructing a map of an unknown environment. However, these methods do not provide any reference for where to insert virtual objects since they do not have any information about scene structure and may fail in cases of occlusion of three-dimensional (3-D) map points or dynamic objects. This paper presents a real-time monocular piece wise planar SLAM method using the planar scene assumption. Using planar structures in the mapping process allows rendering virtual objects in a meaningful way on the one hand and improving the precision of the camera pose and the quality of 3-D reconstruction of the environment by adding constraints on 3-D points and poses in the optimization process on the other hand. We proposed to benefit from the 3-D planes rigidity motion in the tracking process to enhance the system robustness in the case of dynamic scenes. Experimental results show that using a constrained planar scene improves our system accuracy and robustness compared with the classical SLAM systems.

Effects of iron on the lattice thermal conductivity of Earth's deep mantle and implications for mantle dynamics

NASA Astrophysics Data System (ADS)

Hsieh, Wen-Pin; Deschamps, Frédéric; Okuchi, Takuo; Lin, Jung-Fu

2018-04-01

Iron may critically influence the physical properties and thermochemical structures of Earth's lower mantle. Its effects on thermal conductivity, with possible consequences on heat transfer and mantle dynamics, however, remain largely unknown. We measured the lattice thermal conductivity of lower-mantle ferropericlase to 120 GPa using the ultrafast optical pump-probe technique in a diamond anvil cell. The thermal conductivity of ferropericlase with 56% iron significantly drops by a factor of 1.8 across the spin transition around 53 GPa, while that with 8–10% iron increases monotonically with pressure, causing an enhanced iron substitution effect in the low-spin state. Combined with bridgmanite data, modeling of our results provides a self-consistent radial profile of lower-mantle thermal conductivity, which is dominated by pressure, temperature, and iron effects, and shows a twofold increase from top to bottom of the lower mantle. Such increase in thermal conductivity may delay the cooling of the core, while its decrease with iron content may enhance the dynamics of large low shear-wave velocity provinces. Our findings further show that, if hot and strongly enriched in iron, the seismic ultralow velocity zones have exceptionally low conductivity, thus delaying their cooling.

Sizable dynamics in small pores: CO2 location and motion in the α-Mg formate metal-organic framework.

PubMed

Lu, Yuanjun; Lucier, Bryan E G; Zhang, Yue; Ren, Pengju; Zheng, Anmin; Huang, Yining

2017-02-22

Metal-organic frameworks (MOFs) are promising materials for carbon dioxide (CO 2 ) adsorption and storage; however, many details regarding CO 2 dynamics and specific adsorption site locations within MOFs remain unknown, restricting the practical uses of MOFs for CO 2 capture. The intriguing α-magnesium formate (α-Mg 3 (HCOO) 6 ) MOF can adsorb CO 2 and features a small pore size. Using an intertwined approach of 13 C solid-state NMR (SSNMR) spectroscopy, 1 H- 13 C cross-polarization SSNMR, and computational molecular dynamics (MD) simulations, new physical insights and a rich variety of information have been uncovered regarding CO 2 adsorption in this MOF, including the surprising suggestion that CO 2 motion is restricted at elevated temperatures. Guest CO 2 molecules undergo a combined localized rotational wobbling and non-localized twofold jumping between adsorption sites. MD simulations and SSNMR experiments accurately locate the CO 2 adsorption sites; the mechanism behind CO 2 adsorption is the distant interaction between the hydrogen atom of the MOF formate linker and a guest CO 2 oxygen atom, which are ca. 3.2 Å apart.

The Dynamical Structure of HR 8799's Inner Debris Disk.

PubMed

Contro, B; Wittenmyer, Robert A; Horner, J; Marshall, Jonathan P

2015-06-01

The HR 8799 system, with its four giant planets and two debris belts, has an architecture closely mirroring that of our Solar system where the inner, warm asteroid belt and outer, cool Edgeworth-Kuiper belt bracket the giant planets. As such, it is a valuable laboratory for examining exoplanetary dynamics and debris disk-exoplanet interactions. Whilst the outer debris belt of HR 8799 has been well resolved by previous observations, the spatial extent of the inner disk remains unknown. This leaves a significant question mark over both the location of the planetesimals responsible for producing the belt's visible dust and the physical properties of those grains. We have performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using UNSW Australia's Katana supercomputing facility to follow the dynamical evolution of a model inner disk comprising 300,298 particles for a period of 60 Ma. These simulations have enabled the characterisation of the extent and structure of the inner disk in detail, and will in future allow us to provide a first estimate of the small-body impact rate and water delivery prospects for possible (as-yet undetected) terrestrial planet (s) in the inner system.

Effects of iron on the lattice thermal conductivity of Earth's deep mantle and implications for mantle dynamics.

PubMed

Hsieh, Wen-Pin; Deschamps, Frédéric; Okuchi, Takuo; Lin, Jung-Fu

2018-04-17

Iron may critically influence the physical properties and thermochemical structures of Earth's lower mantle. Its effects on thermal conductivity, with possible consequences on heat transfer and mantle dynamics, however, remain largely unknown. We measured the lattice thermal conductivity of lower-mantle ferropericlase to 120 GPa using the ultrafast optical pump-probe technique in a diamond anvil cell. The thermal conductivity of ferropericlase with 56% iron significantly drops by a factor of 1.8 across the spin transition around 53 GPa, while that with 8-10% iron increases monotonically with pressure, causing an enhanced iron substitution effect in the low-spin state. Combined with bridgmanite data, modeling of our results provides a self-consistent radial profile of lower-mantle thermal conductivity, which is dominated by pressure, temperature, and iron effects, and shows a twofold increase from top to bottom of the lower mantle. Such increase in thermal conductivity may delay the cooling of the core, while its decrease with iron content may enhance the dynamics of large low shear-wave velocity provinces. Our findings further show that, if hot and strongly enriched in iron, the seismic ultralow velocity zones have exceptionally low conductivity, thus delaying their cooling.

The effect of viewing a virtual environment through a head-mounted display on balance.

PubMed

Robert, Maxime T; Ballaz, Laurent; Lemay, Martin

2016-07-01

In the next few years, several head-mounted displays (HMD) will be publicly released making virtual reality more accessible. HMD are expected to be widely popular at home for gaming but also in clinical settings, notably for training and rehabilitation. HMD can be used in both seated and standing positions; however, presently, the impact of HMD on balance remains largely unknown. It is therefore crucial to examine the impact of viewing a virtual environment through a HMD on standing balance. To compare static and dynamic balance in a virtual environment perceived through a HMD and the physical environment. The visual representation of the virtual environment was based on filmed image of the physical environment and was therefore highly similar. This is an observational study in healthy adults. No significant difference was observed between the two environments for static balance. However, dynamic balance was more perturbed in the virtual environment when compared to that of the physical environment. HMD should be used with caution because of its detrimental impact on dynamic balance. Sensorimotor conflict possibly explains the impact of HMD on balance. Copyright © 2016 Elsevier B.V. All rights reserved.

BAR Proteins PSTPIP1/2 Regulate Podosome Dynamics and the Resorption Activity of Osteoclasts

PubMed Central

Sztacho, Martin; Segeletz, Sandra; Sanchez-Fernandez, Maria Arantzazu; Czupalla, Cornelia; Niehage, Christian; Hoflack, Bernard

2016-01-01

Bone resorption in vertebrates relies on the ability of osteoclasts to assemble F-actin-rich podosomes that condense into podosomal belts, forming sealing zones. Sealing zones segregate bone-facing ruffled membranes from other membrane domains, and disassemble when osteoclasts migrate to new areas. How podosome/sealing zone dynamics is regulated remains unknown. We illustrate the essential role of the membrane scaffolding F-BAR-Proline-Serine-Threonine Phosphatase Interacting Proteins (PSTPIP) 1 and 2 in this process. Whereas PSTPIP2 regulates podosome assembly, PSTPIP1 regulates their disassembly. PSTPIP1 recruits, through its F-BAR domain, the protein tyrosine phosphatase non-receptor type 6 (PTPN6) that de-phosphophorylates the phosphatidylinositol 5-phosphatases SHIP1/2 bound to the SH3 domain of PSTPIP1. Depletion of any component of this complex prevents sealing zone disassembly and increases osteoclast activity. Thus, our results illustrate the importance of BAR domain proteins in podosome structure and dynamics, and identify a new PSTPIP1/PTPN6/SHIP1/2-dependent negative feedback mechanism that counterbalances Src and PI(3,4,5)P3 signalling to control osteoclast cell polarity and activity during bone resorption. PMID:27760174

Perception of oral food breakdown. The concept of sensory trajectory.

PubMed

Lenfant, Francine; Loret, Chrystel; Pineau, Nicolas; Hartmann, Christoph; Martin, Nathalie

2009-06-01

Texture perceived in mouth largely depends on the behaviour of the food when it is broken down and transformed by the mouth elements. Texture results from a dynamic process in which texture attributes are continuously analysed by the oral sensory systems during mastication. However, the particular sequence of perceptual events that occur during oral food breakdown remains unknown. The aim of the present study is to describe the succession of perceptual events that happen in mouth during mastication and to show that for each food a texture pathway can be built. This for, we used a sensory method enabling to evaluate the dynamics of texture perceptions during food consumption: the Temporal Dominance of Sensation. On different breakfast cereals, we measured the sensation dominating at each point of the mastication process. We showed that the dynamics of appearance and disappearance of each texture sensation experienced in mouth during the eating process differed among cereals. However, some common features in this sensory trajectory were also observed for the category of products studied. Hardness, crackliness and crispness were rather perceived at the beginning of the mastication period, brittleness and lightness in the middle and stickiness at the end.

Molecular mechanism for cavitation in water under tension

PubMed Central

Menzl, Georg; Gonzalez, Miguel A.; Geiger, Philipp; Caupin, Frédéric; Abascal, José L. F.; Dellago, Christoph

2016-01-01

Despite its relevance in biology and engineering, the molecular mechanism driving cavitation in water remains unknown. Using computer simulations, we investigate the structure and dynamics of vapor bubbles emerging from metastable water at negative pressures. We find that in the early stages of cavitation, bubbles are irregularly shaped and become more spherical as they grow. Nevertheless, the free energy of bubble formation can be perfectly reproduced in the framework of classical nucleation theory (CNT) if the curvature dependence of the surface tension is taken into account. Comparison of the observed bubble dynamics to the predictions of the macroscopic Rayleigh–Plesset (RP) equation, augmented with thermal fluctuations, demonstrates that the growth of nanoscale bubbles is governed by viscous forces. Combining the dynamical prefactor determined from the RP equation with CNT based on the Kramers formalism yields an analytical expression for the cavitation rate that reproduces the simulation results very well over a wide range of pressures. Furthermore, our theoretical predictions are in excellent agreement with cavitation rates obtained from inclusion experiments. This suggests that homogeneous nucleation is observed in inclusions, whereas only heterogeneous nucleation on impurities or defects occurs in other experiments. PMID:27803329

Adaptive fuzzy dynamic surface control for the chaotic permanent magnet synchronous motor using Nussbaum gain

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

Luo, Shaohua

This paper is concerned with the problem of adaptive fuzzy dynamic surface control (DSC) for the permanent magnet synchronous motor (PMSM) system with chaotic behavior, disturbance and unknown control gain and parameters. Nussbaum gain is adopted to cope with the situation that the control gain is unknown. And the unknown items can be estimated by fuzzy logic system. The proposed controller guarantees that all the signals in the closed-loop system are bounded and the system output eventually converges to a small neighborhood of the desired reference signal. Finally, the numerical simulations indicate that the proposed scheme can suppress the chaosmore » of PMSM and show the effectiveness and robustness of the proposed method.« less

Adaptive fuzzy dynamic surface control for the chaotic permanent magnet synchronous motor using Nussbaum gain.

PubMed

Luo, Shaohua

2014-09-01

This paper is concerned with the problem of adaptive fuzzy dynamic surface control (DSC) for the permanent magnet synchronous motor (PMSM) system with chaotic behavior, disturbance and unknown control gain and parameters. Nussbaum gain is adopted to cope with the situation that the control gain is unknown. And the unknown items can be estimated by fuzzy logic system. The proposed controller guarantees that all the signals in the closed-loop system are bounded and the system output eventually converges to a small neighborhood of the desired reference signal. Finally, the numerical simulations indicate that the proposed scheme can suppress the chaos of PMSM and show the effectiveness and robustness of the proposed method.

Automated adaptive inference of phenomenological dynamical models.

PubMed

Daniels, Bryan C; Nemenman, Ilya

2015-08-21

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved.

Automated adaptive inference of phenomenological dynamical models

PubMed Central

Daniels, Bryan C.; Nemenman, Ilya

2015-01-01

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization.

PubMed

Lee, S Seirin; Tashiro, S; Awazu, A; Kobayashi, R

2017-01-01

Specific features of nuclear architecture are important for the functional organization of the nucleus, and chromatin consists of two forms, heterochromatin and euchromatin. Conventional nuclear architecture is observed when heterochromatin is enriched at nuclear periphery, and it represents the primary structure in the majority of eukaryotic cells, including the rod cells of diurnal mammals. In contrast to this, inverted nuclear architecture is observed when the heterochromatin is distributed at the center of the nucleus, which occurs in the rod cells of nocturnal mammals. The inverted architecture found in the rod cells of the adult mouse is formed through the reorganization of conventional architecture during terminal differentiation. Although a previous experimental approach has demonstrated the relationship between these two nuclear architecture types at the molecular level, the mechanisms underlying long-range reorganization processes remain unknown. The details of nuclear structures and their spatial and temporal dynamics remain to be elucidated. Therefore, a comprehensive approach, using mathematical modeling, is required, in order to address these questions. Here, we propose a new mathematical approach to the understanding of nuclear architecture dynamics using the phase-field method. We successfully recreated the process of nuclear architecture reorganization, and showed that it is robustly induced by physical features, independent of a specific genotype. Our study demonstrates the potential of phase-field method application in the life science fields.

Off-Policy Actor-Critic Structure for Optimal Control of Unknown Systems With Disturbances.

PubMed

Song, Ruizhuo; Lewis, Frank L; Wei, Qinglai; Zhang, Huaguang

2016-05-01

An optimal control method is developed for unknown continuous-time systems with unknown disturbances in this paper. The integral reinforcement learning (IRL) algorithm is presented to obtain the iterative control. Off-policy learning is used to allow the dynamics to be completely unknown. Neural networks are used to construct critic and action networks. It is shown that if there are unknown disturbances, off-policy IRL may not converge or may be biased. For reducing the influence of unknown disturbances, a disturbances compensation controller is added. It is proven that the weight errors are uniformly ultimately bounded based on Lyapunov techniques. Convergence of the Hamiltonian function is also proven. The simulation study demonstrates the effectiveness of the proposed optimal control method for unknown systems with disturbances.

Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

PubMed

Fei, Juntao; Lu, Cheng

2018-04-01

In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

Dual Rate Adaptive Control for an Industrial Heat Supply Process Using Signal Compensation Approach

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

Chai, Tianyou; Jia, Yao; Wang, Hong

The industrial heat supply process (HSP) is a highly nonlinear cascaded process which uses a steam valve opening as its control input, the steam flow-rate as its inner loop output and the supply water temperature as its outer loop output. The relationship between the heat exchange rate and the model parameters, such as steam density, entropy, and fouling correction factor and heat exchange efficiency are unknown and nonlinear. Moreover, these model parameters vary in line with steam pressure, ambient temperature and the residuals caused by the quality variations of the circulation water. When the steam pressure and the ambient temperaturemore » are of high values and are subjected to frequent external random disturbances, the supply water temperature and the steam flow-rate would interact with each other and fluctuate a lot. This is also true when the process exhibits unknown characteristic variations of the process dynamics caused by the unexpected changes of the heat exchange residuals. As a result, it is difficult to control the supply water temperature and the rates of changes of steam flow-rate well inside their targeted ranges. In this paper, a novel compensation signal based dual rate adaptive controller is developed by representing the unknown variations of dynamics as unmodeled dynamics. In the proposed controller design, such a compensation signal is constructed and added onto the control signal obtained from the linear deterministic model based feedback control design. Such a compensation signal aims at eliminating the unmodeled dynamics and the rate of changes of the currently sample unmodeled dynamics. A successful industrial application is carried out, where it has been shown that both the supply water temperature and the rate of the changes of the steam flow-rate can be controlled well inside their targeted ranges when the process is subjected to unknown variations of its dynamics.« less

Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

USDA-ARS?s Scientific Manuscript database

Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

Hebbian Wiring Plasticity Generates Efficient Network Structures for Robust Inference with Synaptic Weight Plasticity

PubMed Central

Hiratani, Naoki; Fukai, Tomoki

2016-01-01

In the adult mammalian cortex, a small fraction of spines are created and eliminated every day, and the resultant synaptic connection structure is highly nonrandom, even in local circuits. However, it remains unknown whether a particular synaptic connection structure is functionally advantageous in local circuits, and why creation and elimination of synaptic connections is necessary in addition to rich synaptic weight plasticity. To answer these questions, we studied an inference task model through theoretical and numerical analyses. We demonstrate that a robustly beneficial network structure naturally emerges by combining Hebbian-type synaptic weight plasticity and wiring plasticity. Especially in a sparsely connected network, wiring plasticity achieves reliable computation by enabling efficient information transmission. Furthermore, the proposed rule reproduces experimental observed correlation between spine dynamics and task performance. PMID:27303271

HIV-1 dynamics revisited: biphasic decay by cytotoxic T lymphocyte killing?

PubMed Central

Arnaout, R A; Nowak, M A; Wodarz, D

2000-01-01

The biphasic decay of blood viraemia in patients being treated for human immunodeficiency virus type 1 (HIV-1) infection has been explained as the decay of two distinct populations of cells: the rapid death of productively infected cells followed by the much slower elimination of a second population the identity of which remains unknown. Here we advance an alternative explanation based on the immune response against a single population of infected cells. We show that the biphasic decay can be explained simply, without invoking multiple compartments: viral load falls quickly while cytotoxic T lymphocytes (CTL) are still abundant, and more slowly as CTL disappear. We propose a method to test this idea, and develop a framework that is readily applicable to treatment of other infections. PMID:10972131

Paradox of pattern separation and adult neurogenesis: A dual role for new neurons balancing memory resolution and robustness.

PubMed

Johnston, Stephen T; Shtrahman, Matthew; Parylak, Sarah; Gonçalves, J Tiago; Gage, Fred H

2016-03-01

Hippocampal adult neurogenesis is thought to subserve pattern separation, the process by which similar patterns of neuronal inputs are transformed into distinct neuronal representations, permitting the discrimination of highly similar stimuli in hippocampus-dependent tasks. However, the mechanism by which immature adult-born dentate granule neurons cells (abDGCs) perform this function remains unknown. Two theories of abDGC function, one by which abDGCs modulate and sparsify activity in the dentate gyrus and one by which abDGCs act as autonomous coding units, are generally suggested to be mutually exclusive. This review suggests that these two mechanisms work in tandem to dynamically regulate memory resolution while avoiding memory interference and maintaining memory robustness. Copyright © 2015 Elsevier Inc. All rights reserved.

Predictive Computational Modeling of Chromatin Folding

NASA Astrophysics Data System (ADS)

di Pierro, Miichele; Zhang, Bin; Wolynes, Peter J.; Onuchic, Jose N.

In vivo, the human genome folds into well-determined and conserved three-dimensional structures. The mechanism driving the folding process remains unknown. We report a theoretical model (MiChroM) for chromatin derived by using the maximum entropy principle. The proposed model allows Molecular Dynamics simulations of the genome using as input the classification of loci into chromatin types and the presence of binding sites of loop forming protein CTCF. The model was trained to reproduce the Hi-C map of chromosome 10 of human lymphoblastoid cells. With no additional tuning the model was able to predict accurately the Hi-C maps of chromosomes 1-22 for the same cell line. Simulations show unknotted chromosomes, phase separation of chromatin types and a preference of chromatin of type A to sit at the periphery of the chromosomes.

Crystallization by Particle Attachment in Synthetic, Biogenic, and Geologic Environments

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

De Yoreo, James J.; Gilbert, Pupa U.; Sommerdijk, Nico

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. These non-classical pathways to crystallization are diverse, in contrast to classical models that consider the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle attachment processes and show that multiple pathways result from the interplay of free energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects; particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemblemore » behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems and patterns of mineralization in natural environments.« less

Dynamic parameter identification of robot arms with servo-controlled electrical motors

NASA Astrophysics Data System (ADS)

Jiang, Zhao-Hui; Senda, Hiroshi

2005-12-01

This paper addresses the issue of dynamic parameter identification of the robot manipulator with servo-controlled electrical motors. An assumption is made that all kinematical parameters, such as link lengths, are known, and only dynamic parameters containing mass, moment of inertia, and their functions need to be identified. First, we derive dynamics of the robot arm with a linear form of the unknown dynamic parameters by taking dynamic characteristics of the motor and servo unit into consideration. Then, we implement the parameter identification approach to identify the unknown parameters with respect to individual link separately. A pseudo-inverse matrix is used for formulation of the parameter identification. The optimal solution is guaranteed in a sense of least-squares of the mean errors. A Direct Drive (DD) SCARA type industrial robot arm AdeptOne is used as an application example of the parameter identification. Simulations and experiments for both open loop and close loop controls are carried out. Comparison of the results confirms the correctness and usefulness of the parameter identification and the derived dynamic model.

Differential flap dynamics in l,d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics.

PubMed

Fakhar, Zeynab; Govender, Thavendran; Maguire, Glenn E M; Lamichhane, Gyanu; Walker, Ross C; Kruger, Hendrik G; Honarparvar, Bahareh

2017-06-01

Despite the advances in tuberculosis treatment, TB is still one the most deadly infectious diseases and remains a major global health quandary. Mycobacterium tuberculosis (Mtb) is the only known mycobacterium with a high content of 3→3 crosslinks in the biosynthesis of peptidoglycan, which is negligible in most bacterial species. An Mtb lacking Ldt Mt2 leads to alteration of the colony morphology and loss of virulence which makes this enzyme an attractive target. Regardless of the vital role of Ldt Mt2 for cell wall survival, the impact of ligand binding on the dynamics of the β-hairpin flap is still unknown. Understanding the structural and dynamical behaviour of the flap regions provides clear insight into the design of the effective inhibitors against Ldt Mt2 . Carbapenems, an specific class of β-lactam family, have been shown to inactivate this enzyme. Herein a comprehensive investigation of the flap dynamics of Ldt Mt2 complex with substrate and three carbapenems namely, ertapenem, imipenem and meropenem is discussed and analyzed for the first account using 140 ns molecular dynamics simulations. The structural features (RMSD, RMSF and R g ) derived by MD trajectories were analyzed. Distance analysis, particularly tip-tip SER135-ASN167 index, identified conformational changes in terms of flap opening and closure within binding process. Principal component analysis (PCA) was employed to qualitatively understand the divergent effects of different inhibitors on the dominant motion of each residue. To probe different internal dynamics induced by ligand binding, dynamic cross-correlation marix (DCCM) analysis was used. The binding free energies of the selected complexes were assessed using MM-GBSA method and per residue free energy decomposition analysis were performed to characterize the contribution of the key residues to the total binding free energies.

76 FR 75907 - Notice of Inventory Completion: Minnesota Indian Affairs Council, Bemidji, MN

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

...''). History and Description of the Remains At an unknown date, human remains representing, at minimum, two.... SUMMARY: The Minnesota Indian Affairs Council has completed an inventory of human remains and associated... tribe that believes itself to be culturally affiliated with the human remains may contact the Minnesota...

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

PubMed Central

Bulusu, Gopalakrishnan

2014-01-01

Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. PMID:24603363

Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries.

PubMed

Rogers, Lauren A; Schindler, Daniel E; Lisi, Peter J; Holtgrieve, Gordon W; Leavitt, Peter R; Bunting, Lynda; Finney, Bruce P; Selbie, Daniel T; Chen, Guangjie; Gregory-Eaves, Irene; Lisac, Mark J; Walsh, Patrick B

2013-01-29

Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on interdecadal time scales (30- to 80-y cycles), centennial-scale variation, undetectable in modern-day catch records and survey data, has dominated salmon population dynamics over the past 500 y. Before 1900, variation in abundance was clearly not synchronous among stocks, and the only temporal signal common to lake sediment records from this region was the onset of commercial fishing in the late 1800s. Thus, historical changes in climate did not synchronize stock dynamics over centennial time scales, emphasizing that ecosystem complexity can produce a diversity of ecological responses to regional climate forcing. Our results show that marine fish populations may alternate between naturally driven periods of high and low abundance over time scales of decades to centuries and suggest that management models that assume time-invariant productivity or carrying capacity parameters may be poor representations of the biological reality in these systems.

Method to investigate temporal dynamics of ganglion and other retinal cells in the living human eye

NASA Astrophysics Data System (ADS)

Kurokawa, Kazuhiro; Liu, Zhuolin; Crowell, James; Zhang, Furu; Miller, Donald T.

2018-02-01

The inner retina is critical for visual processing, but much remains unknown about its neural circuitry and vulnerability to disease. A major bottleneck has been our inability to observe the structure and function of the cells composing these retinal layers in the living human eye. Here, we present a noninvasive method to observe both structural and functional information. Adaptive optics optical coherence tomography (AO-OCT) is used to resolve the inner retinal cells in all three dimensions and novel post processing algorithms are applied to extract structure and physiology down to the cellular level. AO-OCT captured the 3D mosaic of individual ganglion cell somas, retinal nerve fiber bundles of micron caliber, and microglial cells, all in exquisite detail. Time correlation analysis of the AO-OCT videos revealed notable temporal differences between the principal layers of the inner retina. The GC layer was more dynamic than the nerve fiber and inner plexiform layers. At the cellular level, we applied a customized correlation method to individual GCL somas, and found a mean time constant of activity of 0.57 s and spread of +/-0.1 s suggesting a range of physiological dynamics even in the same cell type. Extending our method to slower dynamics (from minutes to one year), time-lapse imaging and temporal speckle contrast revealed appendage and soma motion of resting microglial cells at the retinal surface.

Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries

PubMed Central

Rogers, Lauren A.; Schindler, Daniel E.; Lisi, Peter J.; Holtgrieve, Gordon W.; Leavitt, Peter R.; Bunting, Lynda; Finney, Bruce P.; Selbie, Daniel T.; Chen, Guangjie; Gregory-Eaves, Irene; Lisac, Mark J.; Walsh, Patrick B.

2013-01-01

Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on interdecadal time scales (30- to 80-y cycles), centennial-scale variation, undetectable in modern-day catch records and survey data, has dominated salmon population dynamics over the past 500 y. Before 1900, variation in abundance was clearly not synchronous among stocks, and the only temporal signal common to lake sediment records from this region was the onset of commercial fishing in the late 1800s. Thus, historical changes in climate did not synchronize stock dynamics over centennial time scales, emphasizing that ecosystem complexity can produce a diversity of ecological responses to regional climate forcing. Our results show that marine fish populations may alternate between naturally driven periods of high and low abundance over time scales of decades to centuries and suggest that management models that assume time-invariant productivity or carrying capacity parameters may be poor representations of the biological reality in these systems. PMID:23322737

Imidazoles and benzimidazoles as tubulin-modulators for anti-cancer therapy.

PubMed

Torres, Fernando C; García-Rubiño, M Eugenia; Lozano-López, César; Kawano, Daniel F; Eifler-Lima, Vera L; von Poser, Gilsane L; Campos, Joaquín M

2015-01-01

Imidazoles and benzimidazoles are privileged heterocyclic bioactive compounds used with success in the clinical practice of innumerous diseases. Although there are many advancements in cancer therapy, microtubules remain as one of the few macromolecular targets validated for planning active anti-cancer compounds, and the design of drugs that modulate microtubule dynamics in unknown sites of tubulin is one of the goals of the medicinal chemistry. The discussion of the role of new and commercially available imidazole and benzimidazole derivatives as tubulin modulators is scattered throughout scientific literature, and indicates that these compounds have a tubulin modulation mechanism different from that of tubulin modulators clinically available, such as paclitaxel, docetaxel, vincristine and vinblastine. In fact, recent literature indicates that these derivatives inhibit microtubule formation binding to the colchicine site, present good pharmacokinetic properties and are capable of overcoming multidrug resistance in many cell lines. The understanding of the mechanisms involved in the imidazoles/benzimidazoles modulation of microtubule dynamics is very important to develop new strategies to overcome the resistance to anti-cancer drugs and to discover new biomarkers and targets for cancer chemotherapy.

Common resting brain dynamics indicate a possible mechanism underlying zolpidem response in severe brain injury

PubMed Central

Williams, Shawniqua T; Conte, Mary M; Goldfine, Andrew M; Noirhomme, Quentin; Gosseries, Olivia; Thonnard, Marie; Beattie, Bradley; Hersh, Jennifer; Katz, Douglas I; Victor, Jonathan D; Laureys, Steven; Schiff, Nicholas D

2013-01-01

Zolpidem produces paradoxical recovery of speech, cognitive and motor functions in select subjects with severe brain injury but underlying mechanisms remain unknown. In three diverse patients with known zolpidem responses we identify a distinctive pattern of EEG dynamics that suggests a mechanistic model. In the absence of zolpidem, all subjects show a strong low frequency oscillatory peak ∼6–10 Hz in the EEG power spectrum most prominent over frontocentral regions and with high coherence (∼0.7–0.8) within and between hemispheres. Zolpidem administration sharply reduces EEG power and coherence at these low frequencies. The ∼6–10 Hz activity is proposed to arise from intrinsic membrane properties of pyramidal neurons that are passively entrained across the cortex by locally-generated spontaneous activity. Activation by zolpidem is proposed to arise from a combination of initial direct drug effects on cortical, striatal, and thalamic populations and further activation of underactive brain regions induced by restoration of cognitively-mediated behaviors. DOI: http://dx.doi.org/10.7554/eLife.01157.001 PMID:24252875

Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.

PubMed

Rhee, Ho Sung; Closser, Michael; Guo, Yuchun; Bashkirova, Elizaveta V; Tan, G Christopher; Gifford, David K; Wichterle, Hynek

2016-12-21

Generic spinal motor neuron identity is established by cooperative binding of programming transcription factors (TFs), Isl1 and Lhx3, to motor-neuron-specific enhancers. How expression of effector genes is maintained following downregulation of programming TFs in maturing neurons remains unknown. High-resolution exonuclease (ChIP-exo) mapping revealed that the majority of enhancers established by programming TFs are rapidly deactivated following Lhx3 downregulation in stem-cell-derived hypaxial motor neurons. Isl1 is released from nascent motor neuron enhancers and recruited to new enhancers bound by clusters of Onecut1 in maturing neurons. Synthetic enhancer reporter assays revealed that Isl1 operates as an integrator factor, translating the density of Lhx3 or Onecut1 binding sites into transient enhancer activity. Importantly, independent Isl1/Lhx3- and Isl1/Onecut1-bound enhancers contribute to sustained expression of motor neuron effector genes, demonstrating that outwardly stable expression of terminal effector genes in postmitotic neurons is controlled by a dynamic relay of stage-specific enhancers. Copyright © 2016 Elsevier Inc. All rights reserved.

The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET.

PubMed

Yang, Mengyi; Peng, Sijia; Sun, Ruirui; Lin, Jingdi; Wang, Nan; Chen, Chunlai

2018-01-09

Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Salt Stress–Induced Disassembly of Arabidopsis Cortical Microtubule Arrays Involves 26S Proteasome–Dependent Degradation of SPIRAL1[C][W

PubMed Central

Wang, Songhu; Kurepa, Jasmina; Hashimoto, Takashi; Smalle, Jan A.

2011-01-01

The dynamic instability of cortical microtubules (MTs) (i.e., their ability to rapidly alternate between phases of growth and shrinkage) plays an essential role in plant growth and development. In addition, recent studies have revealed a pivotal role for dynamic instability in the response to salt stress conditions. The salt stress response includes a rapid depolymerization of MTs followed by the formation of a new MT network that is believed to be better suited for surviving high salinity. Although this initial depolymerization response is essential for the adaptation to salt stress, the underlying molecular mechanism has remained largely unknown. Here, we show that the MT-associated protein SPIRAL1 (SPR1) plays a key role in salt stress–induced MT disassembly. SPR1, a microtubule stabilizing protein, is degraded by the 26S proteasome, and its degradation rate is accelerated in response to high salinity. We show that accelerated SPR1 degradation is required for a fast MT disassembly response to salt stress and for salt stress tolerance. PMID:21954463

3D General Circulation Model of the Middle Atmosphere of Jupiter

NASA Astrophysics Data System (ADS)

Zube, Nicholas Gerard; Zhang, Xi; Li, Cheng; Le, Tianhao

2017-10-01

The characteristics of Jupiter’s large-scale stratospheric circulation remain largely unknown. Detailed distributions of temperature and photochemical species have been provided by recent observations [1], but have not yet been accurately reproduced by middle atmosphere general circulation models (GCM). Jupiter’s stratosphere and upper troposphere are influenced by radiative forcing from solar insolation and infrared cooling from hydrogen and hydrocarbons, as well as waves propagating from the underlying troposphere [2]. The relative significance of radiative and mechanical forcing on stratospheric circulation is still being debated [3]. Here we present a 3D GCM of Jupiter’s atmosphere with a correlated-k radiative transfer scheme. The simulation results are compared with observations. We analyze the impact of model parameters on the stratospheric temperature distribution and dynamical features. Finally, we discuss future tracer transport and gravity wave parameterization schemes that may be able to accurately simulate the middle atmosphere dynamics of Jupiter and other giant planets.[1] Kunde et al. 2004, Science 305, 1582.[2] Zhang et al. 2013a, EGU General Assembly, EGU2013-5797-2.[3] Conrath 1990, Icarus, 83, 255-281.

Dynamic model predicting overweight, obesity, and extreme obesity prevalence trends.

PubMed

Thomas, Diana M; Weedermann, Marion; Fuemmeler, Bernard F; Martin, Corby K; Dhurandhar, Nikhil V; Bredlau, Carl; Heymsfield, Steven B; Ravussin, Eric; Bouchard, Claude

2014-02-01

Obesity prevalence in the United States appears to be leveling, but the reasons behind the plateau remain unknown. Mechanistic insights can be provided from a mathematical model. The objective of this study is to model known multiple population parameters associated with changes in body mass index (BMI) classes and to establish conditions under which obesity prevalence will plateau. A differential equation system was developed that predicts population-wide obesity prevalence trends. The model considers both social and nonsocial influences on weight gain, incorporates other known parameters affecting obesity trends, and allows for country specific population growth. The dynamic model predicts that: obesity prevalence is a function of birthrate and the probability of being born in an obesogenic environment; obesity prevalence will plateau independent of current prevention strategies; and the US prevalence of overweight, obesity, and extreme obesity will plateau by about 2030 at 28%, 32%, and 9% respectively. The US prevalence of obesity is stabilizing and will plateau, independent of current preventative strategies. This trend has important implications in accurately evaluating the impact of various anti-obesity strategies aimed at reducing obesity prevalence. Copyright © 2013 The Obesity Society.

In situ observation of shear-driven amorphization in silicon crystals.

PubMed

He, Yang; Zhong, Li; Fan, Feifei; Wang, Chongmin; Zhu, Ting; Mao, Scott X

2016-10-01

Amorphous materials are used for both structural and functional applications. An amorphous solid usually forms under driven conditions such as melt quenching, irradiation, shock loading or severe mechanical deformation. Such extreme conditions impose significant challenges on the direct observation of the amorphization process. Various experimental techniques have been used to detect how the amorphous phases form, including synchrotron X-ray diffraction, transmission electron microscopy (TEM) and Raman spectroscopy, but a dynamic, atomistic characterization has remained elusive. Here, by using in situ high-resolution TEM (HRTEM), we show the dynamic amorphization process in silicon nanocrystals during mechanical straining on the atomic scale. We find that shear-driven amorphization occurs in a dominant shear band starting with the diamond-cubic (dc) to diamond-hexagonal (dh) phase transition and then proceeds by dislocation nucleation and accumulation in the newly formed dh-Si phase. This process leads to the formation of an amorphous Si (a-Si) band, embedded with dh-Si nanodomains. The amorphization of dc-Si via an intermediate dh-Si phase is a previously unknown pathway of solid-state amorphization.

Near-Membrane Refractometry Using Supercritical Angle Fluorescence.

PubMed

Brunstein, Maia; Roy, Lopamudra; Oheim, Martin

2017-05-09

Total internal reflection fluorescence (TIRF) microscopy and its variants are key technologies for visualizing the dynamics of single molecules or organelles in live cells. Yet truly quantitative TIRF remains problematic. One unknown hampering the interpretation of evanescent-wave excited fluorescence intensities is the undetermined cell refractive index (RI). Here, we use a combination of TIRF excitation and supercritical angle fluorescence emission detection to directly measure the average RI in the "footprint" region of the cell during image acquisition. Our RI measurement is based on the determination on a back-focal plane image of the critical angle separating evanescent and far-field fluorescence emission components. We validate our method by imaging mouse embryonic fibroblasts and BON cells. By targeting various dyes and fluorescent-protein chimeras to vesicles, the plasma membrane, as well as mitochondria and the endoplasmic reticulum, we demonstrate local RI measurements with subcellular resolution on a standard TIRF microscope, with a removable Bertrand lens as the only modification. Our technique has important applications for imaging axial vesicle dynamics and the mitochondrial energy state or detecting metabolically more active cancer cells. Copyright © 2017. Published by Elsevier Inc.

Urban sprawl and fragmentation in Latin America: a dynamic quantification and characterization of spatial patterns.

PubMed

Inostroza, Luis; Baur, Rolf; Csaplovics, Elmar

2013-01-30

South America is one of the most urbanized continents in the world, where almost 84% of the total population lives in cities, more urbanized than North America (82%) and Europe (73%). Spatial dynamics, their structure, main features, land consumption rates, spatial arrangement, fragmentation degrees and comparability, remain mostly unknown for most Latin American cities. Using satellite imagery the main parameters of sprawl are quantified for 10 Latin American cities over a period of 20 years by monitoring growth patterns and identifying spatial metrics to characterize urban development and sprawling features measured with GIS tools. This quantification contributes to a better understanding of urban form in Latin America. A pervasive spatial expansion has been observed, where most of the studied cities are expanding at fast rates with falling densities trend. Although important differences in the rates of land consumption and densities exist, there is an underlying fragmentation trend towards increasing sprawl. These trends of spatial discontinuity may eventually be intensified by further economic development. Urban Sprawl/Latin America/GIS metrics/spatial development. Copyright © 2012 Elsevier Ltd. All rights reserved.

Molecular characteristics of stress overshoot for polymer melts under start-up shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Baig, Chunggi

2017-12-21

Stress overshoot is one of the most important nonlinear rheological phenomena exhibited by polymeric liquids undergoing start-up shear at sufficient flow strengths. Despite considerable previous research, the fundamental molecular characteristics underlying stress overshoot remain unknown. Here, we analyze the intrinsic molecular mechanisms behind the overshoot phenomenon using atomistic nonequilibrium molecular dynamics simulations of entangled linear polyethylene melts under shear flow. Through a detailed analysis of the transient rotational chain dynamics, we identify an intermolecular collision angular regime in the vicinity of the chain orientation angle θ ≈ 20° with respect to the flow direction. The shear stress overshoot occurs via strong intermolecular collisions between chains in the collision regime at θ = 15°-25°, corresponding to a peak strain of 2-4, which is an experimentally well-known value. The normal stress overshoot appears at approximately θ = 10°, at a corresponding peak strain roughly equivalent to twice that for the shear stress. We provide plausible answers to several basic questions regarding the stress overshoot, which may further help understand other nonlinear phenomena of polymeric systems.

Adaptive Approximation-Based Regulation Control for a Class of Uncertain Nonlinear Systems Without Feedback Linearizability.

PubMed

Wang, Ning; Sun, Jing-Chao; Han, Min; Zheng, Zhongjiu; Er, Meng Joo

2017-09-06

In this paper, for a general class of uncertain nonlinear (cascade) systems, including unknown dynamics, which are not feedback linearizable and cannot be solved by existing approaches, an innovative adaptive approximation-based regulation control (AARC) scheme is developed. Within the framework of adding a power integrator (API), by deriving adaptive laws for output weights and prediction error compensation pertaining to single-hidden-layer feedforward network (SLFN) from the Lyapunov synthesis, a series of SLFN-based approximators are explicitly constructed to exactly dominate completely unknown dynamics. By the virtue of significant advancements on the API technique, an adaptive API methodology is eventually established in combination with SLFN-based adaptive approximators, and it contributes to a recursive mechanism for the AARC scheme. As a consequence, the output regulation error can asymptotically converge to the origin, and all other signals of the closed-loop system are uniformly ultimately bounded. Simulation studies and comprehensive comparisons with backstepping- and API-based approaches demonstrate that the proposed AARC scheme achieves remarkable performance and superiority in dealing with unknown dynamics.

Online Solution of Two-Player Zero-Sum Games for Continuous-Time Nonlinear Systems With Completely Unknown Dynamics.

PubMed

Fu, Yue; Chai, Tianyou

2016-12-01

Regarding two-player zero-sum games of continuous-time nonlinear systems with completely unknown dynamics, this paper presents an online adaptive algorithm for learning the Nash equilibrium solution, i.e., the optimal policy pair. First, for known systems, the simultaneous policy updating algorithm (SPUA) is reviewed. A new analytical method to prove the convergence is presented. Then, based on the SPUA, without using a priori knowledge of any system dynamics, an online algorithm is proposed to simultaneously learn in real time either the minimal nonnegative solution of the Hamilton-Jacobi-Isaacs (HJI) equation or the generalized algebraic Riccati equation for linear systems as a special case, along with the optimal policy pair. The approximate solution to the HJI equation and the admissible policy pair is reexpressed by the approximation theorem. The unknown constants or weights of each are identified simultaneously by resorting to the recursive least square method. The convergence of the online algorithm to the optimal solutions is provided. A practical online algorithm is also developed. Simulation results illustrate the effectiveness of the proposed method.

GTSE1 tunes microtubule stability for chromosome alignment and segregation by inhibiting the microtubule depolymerase MCAK

PubMed Central

Bendre, Shweta; Hall, Conrad; Lin, Yu-Chih

2016-01-01

The dynamic regulation of microtubules (MTs) during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore MTs have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The MT depolymerase MCAK (mitotic centromere-associated kinesin) can influence CIN through its impact on MT stability, but how its potent activity is controlled in cells remains unclear. In this study, we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumors, regulates MT stability during mitosis by inhibiting MCAK MT depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning as a result of MT instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, whereas artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus, GTSE1 inhibition of MCAK activity regulates the balance of MT stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability. PMID:27881713

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.

PubMed

Bennion, Brian J; Daggett, Valerie

2004-04-27

Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.

A family of dynamic models for large-eddy simulation

NASA Technical Reports Server (NTRS)

Carati, D.; Jansen, K.; Lund, T.

1995-01-01

Since its first application, the dynamic procedure has been recognized as an effective means to compute rather than prescribe the unknown coefficients that appear in a subgrid-scale model for Large-Eddy Simulation (LES). The dynamic procedure is usually used to determine the nondimensional coefficient in the Smagorinsky (1963) model. In reality the procedure is quite general and it is not limited to the Smagorinsky model by any theoretical or practical constraints. The purpose of this note is to consider a generalized family of dynamic eddy viscosity models that do not necessarily rely on the local equilibrium assumption built into the Smagorinsky model. By invoking an inertial range assumption, it will be shown that the coefficients in the new models need not be nondimensional. This additional degree of freedom allows the use of models that are scaled on traditionally unknown quantities such as the dissipation rate. In certain cases, the dynamic models with dimensional coefficients are simpler to implement, and allow for a 30% reduction in the number of required filtering operations.

Don't break a leg: running birds from quail to ostrich prioritise leg safety and economy on uneven terrain.

PubMed

Birn-Jeffery, Aleksandra V; Hubicki, Christian M; Blum, Yvonne; Renjewski, Daniel; Hurst, Jonathan W; Daley, Monica A

2014-11-01

Cursorial ground birds are paragons of bipedal running that span a 500-fold mass range from quail to ostrich. Here we investigate the task-level control priorities of cursorial birds by analysing how they negotiate single-step obstacles that create a conflict between body stability (attenuating deviations in body motion) and consistent leg force-length dynamics (for economy and leg safety). We also test the hypothesis that control priorities shift between body stability and leg safety with increasing body size, reflecting use of active control to overcome size-related challenges. Weight-support demands lead to a shift towards straighter legs and stiffer steady gait with increasing body size, but it remains unknown whether non-steady locomotor priorities diverge with size. We found that all measured species used a consistent obstacle negotiation strategy, involving unsteady body dynamics to minimise fluctuations in leg posture and loading across multiple steps, not directly prioritising body stability. Peak leg forces remained remarkably consistent across obstacle terrain, within 0.35 body weights of level running for obstacle heights from 0.1 to 0.5 times leg length. All species used similar stance leg actuation patterns, involving asymmetric force-length trajectories and posture-dependent actuation to add or remove energy depending on landing conditions. We present a simple stance leg model that explains key features of avian bipedal locomotion, and suggests economy as a key priority on both level and uneven terrain. We suggest that running ground birds target the closely coupled priorities of economy and leg safety as the direct imperatives of control, with adequate stability achieved through appropriately tuned intrinsic dynamics. © 2014. Published by The Company of Biologists Ltd.

Computational Wear Simulation of Patellofemoral Articular Cartilage during In Vitro Testing

PubMed Central

Li, Lingmin; Patil, Shantanu; Steklov, Nick; Bae, Won; Temple-Wong, Michele; D'Lima, Darryl D.; Sah, Robert L.; Fregly, Benjamin J.

2011-01-01

Though changes in normal joint motions and loads (e.g., following anterior cruciate ligament injury) contribute to the development of knee osteoarthritis, the precise mechanism by which these changes induce osteoarthritis remains unknown. As a first step toward identifying this mechanism, this study evaluates computational wear simulations of a patellofemoral joint specimen wear tested on a knee simulator machine. A multi-body dynamic model of the specimen mounted in the simulator machine was constructed in commercial computer-aided engineering software. A custom elastic foundation contact model was used to calculate contact pressures and wear on the femoral and patellar articular surfaces using geometry created from laser scan and MR data. Two different wear simulation approaches were investigated – one that wore the surface geometries gradually over a sequence of 10 one-cycle dynamic simulations (termed the “progressive” approach), and one that wore the surface geometries abruptly using results from a single one-cycle dynamic simulation (termed the “non-progressive” approach). The progressive approach with laser scan geometry reproduced the experimentally measured wear depths and areas for both the femur and patella. The less costly non-progressive approach predicted deeper wear depths, especially on the patella, but had little influence on predicted wear areas. Use of MR data for creating the articular and subchondral bone geometry altered wear depth and area predictions by at most 13%. These results suggest that MR-derived geometry may be sufficient for simulating articular cartilage wear in vivo and that a progressive simulation approach may be needed for the patella and tibia since both remain in continuous contact with the femur. PMID:21453922

Computational wear simulation of patellofemoral articular cartilage during in vitro testing.

PubMed

Li, Lingmin; Patil, Shantanu; Steklov, Nick; Bae, Won; Temple-Wong, Michele; D'Lima, Darryl D; Sah, Robert L; Fregly, Benjamin J

2011-05-17

Though changes in normal joint motions and loads (e.g., following anterior cruciate ligament injury) contribute to the development of knee osteoarthritis, the precise mechanism by which these changes induce osteoarthritis remains unknown. As a first step toward identifying this mechanism, this study evaluates computational wear simulations of a patellofemoral joint specimen wear tested on a knee simulator machine. A multibody dynamic model of the specimen mounted in the simulator machine was constructed in commercial computer-aided engineering software. A custom elastic foundation contact model was used to calculate contact pressures and wear on the femoral and patellar articular surfaces using geometry created from laser scan and MR data. Two different wear simulation approaches were investigated--one that wore the surface geometries gradually over a sequence of 10 one-cycle dynamic simulations (termed the "progressive" approach), and one that wore the surface geometries abruptly using results from a single one-cycle dynamic simulation (termed the "non-progressive" approach). The progressive approach with laser scan geometry reproduced the experimentally measured wear depths and areas for both the femur and patella. The less costly non-progressive approach predicted deeper wear depths, especially on the patella, but had little influence on predicted wear areas. Use of MR data for creating the articular and subchondral bone geometry altered wear depth and area predictions by at most 13%. These results suggest that MR-derived geometry may be sufficient for simulating articular cartilage wear in vivo and that a progressive simulation approach may be needed for the patella and tibia since both remain in continuous contact with the femur. Copyright © 2011 Elsevier Ltd. All rights reserved.

Don't break a leg: running birds from quail to ostrich prioritise leg safety and economy on uneven terrain

PubMed Central

Birn-Jeffery, Aleksandra V.; Hubicki, Christian M.; Blum, Yvonne; Renjewski, Daniel; Hurst, Jonathan W.; Daley, Monica A.

2014-01-01

Cursorial ground birds are paragons of bipedal running that span a 500-fold mass range from quail to ostrich. Here we investigate the task-level control priorities of cursorial birds by analysing how they negotiate single-step obstacles that create a conflict between body stability (attenuating deviations in body motion) and consistent leg force–length dynamics (for economy and leg safety). We also test the hypothesis that control priorities shift between body stability and leg safety with increasing body size, reflecting use of active control to overcome size-related challenges. Weight-support demands lead to a shift towards straighter legs and stiffer steady gait with increasing body size, but it remains unknown whether non-steady locomotor priorities diverge with size. We found that all measured species used a consistent obstacle negotiation strategy, involving unsteady body dynamics to minimise fluctuations in leg posture and loading across multiple steps, not directly prioritising body stability. Peak leg forces remained remarkably consistent across obstacle terrain, within 0.35 body weights of level running for obstacle heights from 0.1 to 0.5 times leg length. All species used similar stance leg actuation patterns, involving asymmetric force–length trajectories and posture-dependent actuation to add or remove energy depending on landing conditions. We present a simple stance leg model that explains key features of avian bipedal locomotion, and suggests economy as a key priority on both level and uneven terrain. We suggest that running ground birds target the closely coupled priorities of economy and leg safety as the direct imperatives of control, with adequate stability achieved through appropriately tuned intrinsic dynamics. PMID:25355848

The Roles of Feedback and Feedforward as Humans Learn to Control Unknown Dynamic Systems.

PubMed

Zhang, Xingye; Wang, Shaoqian; Hoagg, Jesse B; Seigler, T Michael

2018-02-01

We present results from an experiment in which human subjects interact with an unknown dynamic system 40 times during a two-week period. During each interaction, subjects are asked to perform a command-following (i.e., pursuit tracking) task. Each subject's performance at that task improves from the first trial to the last trial. For each trial, we use subsystem identification to estimate each subject's feedforward (or anticipatory) control, feedback (or reactive) control, and feedback time delay. Over the 40 trials, the magnitudes of the identified feedback controllers and the identified feedback time delays do not change significantly. In contrast, the identified feedforward controllers do change significantly. By the last trial, the average identified feedforward controller approximates the inverse of the dynamic system. This observation provides evidence that a fundamental component of human learning is updating the anticipatory control until it models the inverse dynamics.

Neuromodulation to the Rescue: Compensation of Temperature-Induced Breakdown of Rhythmic Motor Patterns via Extrinsic Neuromodulatory Input

PubMed Central

Städele, Carola; Heigele, Stefanie; Stein, Wolfgang

2015-01-01

Stable rhythmic neural activity depends on the well-coordinated interplay of synaptic and cell-intrinsic conductances. Since all biophysical processes are temperature dependent, this interplay is challenged during temperature fluctuations. How the nervous system remains functional during temperature perturbations remains mostly unknown. We present a hitherto unknown mechanism of how temperature-induced changes in neural networks are compensated by changing their neuromodulatory state: activation of neuromodulatory pathways establishes a dynamic coregulation of synaptic and intrinsic conductances with opposing effects on neuronal activity when temperature changes, hence rescuing neuronal activity. Using the well-studied gastric mill pattern generator of the crab, we show that modest temperature increase can abolish rhythmic activity in isolated neural circuits due to increased leak currents in rhythm-generating neurons. Dynamic clamp-mediated addition of leak currents was sufficient to stop neuronal oscillations at low temperatures, and subtraction of additional leak currents at elevated temperatures was sufficient to rescue the rhythm. Despite the apparent sensitivity of the isolated nervous system to temperature fluctuations, the rhythm could be stabilized by activating extrinsic neuromodulatory inputs from descending projection neurons, a strategy that we indeed found to be implemented in intact animals. In the isolated nervous system, temperature compensation was achieved by stronger extrinsic neuromodulatory input from projection neurons or by augmenting projection neuron influence via bath application of the peptide cotransmitter Cancer borealis tachykinin-related peptide Ia (CabTRP Ia). CabTRP Ia activates the modulator-induced current IMI (a nonlinear voltage-gated inward current) that effectively acted as a negative leak current and counterbalanced the temperature-induced leak to rescue neuronal oscillations. Computational modelling revealed the ability of IMI to reduce detrimental leak-current influences on neuronal networks over a broad conductance range and indicated that leak and IMI are closely coregulated in the biological system to enable stable motor patterns. In conclusion, these results show that temperature compensation does not need to be implemented within the network itself but can be conditionally provided by extrinsic neuromodulatory input that counterbalances temperature-induced modifications of circuit-intrinsic properties. PMID:26417944

Protecting unknown two-qubit entangled states by nesting Uhrig's dynamical decoupling sequences

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

Mukhtar, Musawwadah; Soh, Wee Tee; Saw, Thuan Beng

2010-11-15

Future quantum technologies rely heavily on good protection of quantum entanglement against environment-induced decoherence. A recent study showed that an extension of Uhrig's dynamical decoupling (UDD) sequence can (in theory) lock an arbitrary but known two-qubit entangled state to the Nth order using a sequence of N control pulses [Mukhtar et al., Phys. Rev. A 81, 012331 (2010)]. By nesting three layers of explicitly constructed UDD sequences, here we first consider the protection of unknown two-qubit states as superposition of two known basis states, without making assumptions of the system-environment coupling. It is found that the obtained decoherence suppression canmore » be highly sensitive to the ordering of the three UDD layers and can be remarkably effective with the correct ordering. The detailed theoretical results are useful for general understanding of the nature of controlled quantum dynamics under nested UDD. As an extension of our three-layer UDD, it is finally pointed out that a completely unknown two-qubit state can be protected by nesting four layers of UDD sequences. This work indicates that when UDD is applicable (e.g., when the environment has a sharp frequency cutoff and when control pulses can be taken as instantaneous pulses), dynamical decoupling using nested UDD sequences is a powerful approach for entanglement protection.« less

Data-driven robust approximate optimal tracking control for unknown general nonlinear systems using adaptive dynamic programming method.

PubMed

Zhang, Huaguang; Cui, Lili; Zhang, Xin; Luo, Yanhong

2011-12-01

In this paper, a novel data-driven robust approximate optimal tracking control scheme is proposed for unknown general nonlinear systems by using the adaptive dynamic programming (ADP) method. In the design of the controller, only available input-output data is required instead of known system dynamics. A data-driven model is established by a recurrent neural network (NN) to reconstruct the unknown system dynamics using available input-output data. By adding a novel adjustable term related to the modeling error, the resultant modeling error is first guaranteed to converge to zero. Then, based on the obtained data-driven model, the ADP method is utilized to design the approximate optimal tracking controller, which consists of the steady-state controller and the optimal feedback controller. Further, a robustifying term is developed to compensate for the NN approximation errors introduced by implementing the ADP method. Based on Lyapunov approach, stability analysis of the closed-loop system is performed to show that the proposed controller guarantees the system state asymptotically tracking the desired trajectory. Additionally, the obtained control input is proven to be close to the optimal control input within a small bound. Finally, two numerical examples are used to demonstrate the effectiveness of the proposed control scheme.

Time-Dependent Impact of Irreversible Electroporation on Pancreas, Liver, Blood Vessels and Nerves: A Systematic Review of Experimental Studies.

PubMed

Vogel, J A; van Veldhuisen, E; Agnass, P; Crezee, J; Dijk, F; Verheij, J; van Gulik, T M; Meijerink, M R; Vroomen, L G; van Lienden, K P; Besselink, M G

2016-01-01

Irreversible electroporation (IRE) is a novel ablation technique in the treatment of unresectable cancer. The non-thermal mechanism is thought to cause mostly apoptosis compared to necrosis in thermal techniques. Both in experimental and clinical studies, a waiting time between ablation and tissue or imaging analysis to allow for cell death through apoptosis, is often reported. However, the dynamics of the IRE effect over time remain unknown. Therefore, this study aims to summarize these effects in relation to the time between treatment and evaluation. A systematic search was performed in Pubmed, Embase and the Cochrane Library for original articles using IRE on pancreas, liver or surrounding structures in animal or human studies. Data on pathology and time between IRE and evaluation were extracted. Of 2602 screened studies, 36 could be included, regarding IRE in liver (n = 24), pancreas (n = 4), blood vessels (n = 4) and nerves (n = 4) in over 440 animals (pig, rat, goat and rabbit). No eligible human studies were found. In liver and pancreas, the first signs of apoptosis and haemorrhage were observed 1-2 hours after treatment, and remained visible until 24 hours in liver and 7 days in pancreas after which the damaged tissue was replaced by fibrosis. In solitary blood vessels, the tunica media, intima and lumen remained unchanged for 24 hours. After 7 days, inflammation, fibrosis and loss of smooth muscle cells were demonstrated, which persisted until 35 days. In nerves, the median time until demonstrable histological changes was 7 days. Tissue damage after IRE is a dynamic process with remarkable time differences between tissues in animals. Whereas pancreas and liver showed the first damages after 1-2 hours, this took 24 hours in blood vessels and 7 days in nerves.

Carbon Sequestration by Perennial Energy Crops: Is the Jury Still Out?

PubMed

Agostini, Francesco; Gregory, Andrew S; Richter, Goetz M

Soil organic carbon (SOC) changes associated with land conversion to energy crops are central to the debate on bioenergy and their potential carbon neutrality. Here, the experimental evidence on SOC under perennial energy crops (PECs) is synthesised to parameterise a whole systems model and to identify uncertainties and knowledge gaps determining PECs being a sink or source of greenhouse gas (GHG). For Miscanthus and willow ( Salix spp.) and their analogues (switchgrass, poplar), we examine carbon (C) allocation to above- and belowground residue inputs, turnover rates and retention in the soil. A meta-analysis showed that studies on dry matter partitioning and C inputs to soils are plentiful, whilst data on turnover are rare and rely on few isotopic C tracer studies. Comprehensive studies on SOC dynamics and GHG emissions under PECs are limited and subsoil processes and C losses through leaching remain unknown. Data showed dynamic changes of gross C inputs and SOC stocks depending on stand age. C inputs and turnover can now be specifically parameterised in whole PEC system models, whilst dependencies on soil texture, moisture and temperature remain empirical. In conclusion, the annual net SOC storage change exceeds the minimum mitigation requirement (0.25 Mg C ha -1 year -1 ) under herbaceous and woody perennials by far (1.14 to 1.88 and 0.63 to 0.72 Mg C ha -1 year -1 , respectively). However, long-term time series of field data are needed to verify sustainable SOC enrichment, as the physical and chemical stabilities of SOC pools remain uncertain, although they are essential in defining the sustainability of C sequestration (half-life >25 years).

[Dynamic concept of oral lichen planus. The diagnosis easy at early stages may become difficult in ancient lichen planus].

PubMed

Lombardi, Tommaso; Küffer, Roger

2016-02-01

Dynamic concept of oral lichen planus. The diagnosis easy at early stages may become difficult in ancient lichen planus. Lichen planus is a chronic inflammatory dermatosis of the skin, skin appendages and mucous membranes, which frequently affects the oral mucosa. Its aetiology still remains unknown, and currently accepted pathogenesis is that of an autoimmune cell-mediated disease. To the contrary of skin lichen planus, oral lichen planus is a long-term chronic disease with dynamic evolution, in which progressive and profound changes of the clinical and histopathological aspects occur over time and under the influence of various exogenous factors. By convention, in the history of the oral lichen planus four successive stages can be distinguished without well-defined boundaries between them. These stages can be defined as an initial phase; a long intermediate phase with alternating periods of activity and quiescence, which has a gradually increasing risk of malignant transformation; a late stage which activity is traditionally diminished; and a post-lichen cicatricial stage with an absent or negligible and undetectable activity, often undiagnosed because clinically unrecognized; in this stage, the lesion does not respond to usual treatments, but retains the same risk of malignant transformation. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

NASA Astrophysics Data System (ADS)

Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

2016-11-01

K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach -conditional time-delayed correlations (CTC) - using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.

The dynamics and endocytosis of Flot1 protein in response to flg22 in Arabidopsis.

PubMed

Yu, Meng; Liu, Haijiao; Dong, Ziyi; Xiao, Jianwei; Su, Bodan; Fan, Lusheng; Komis, George; Šamaj, Jozef; Lin, Jinxing; Li, Ruili

2017-08-01

Membrane microdomains play vital roles in the process of bacterial infection. The membrane microdomain-associated protein Flot1 acts in an endocytic pathway and is required for seedling development, however, whether Flot1 is a part of host defense mechanisms remains unknown. During an analysis of callose deposition, we found that Flot1 amiRNAi mutants exhibited defects in response to flg22. Using variable-angle total internal reflection fluorescence microscopy (VA-TIRFM), structured illumination microscopy (SIM) and fluorescence cross spectroscopy (FCS), we determined that the dynamic behavior of GFP-Flot1 in Arabidopsis thaliana cotyledon epidermal cells changed significantly in plants treated with the elicitor flg22. Moreover, we found that Flot1 was constitutively recycled via an endocytic pathway and that flg22 could promote endocytosis. Importantly, targeting of Flot1 to the late endosome/vacuole for degradation increased in response to flg22 treatment; immunoblot analysis showed that when triggered by flg22, GFP-Flot1 was gradually degraded in a time-dependent manner. Taken together, these findings support the hypothesis that the changing of dynamics and oligomeric states can promote the endocytosis and degradation of Flot1 under flg22 treatment in plant cells. Copyright © 2017 Elsevier GmbH. All rights reserved.

Adaptive Control Based Harvesting Strategy for a Predator-Prey Dynamical System.

PubMed

Sen, Moitri; Simha, Ashutosh; Raha, Soumyendu

2018-04-23

This paper deals with designing a harvesting control strategy for a predator-prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory. In order to account for unknown parameters, an adaptive control strategy has been proposed in which the control law depends on an adaptive variable which tracks the unknown parameter. Further, a switching component has been incorporated to robustify the control performance against bounded disturbances. Proofs have been provided to show that the proposed adaptive control strategy ensures asymptotic stability of the dynamics at a desired operating point, as well as exact parameter learning in the disturbance-free case and learning with bounded error in the disturbance prone case. The dynamics, with uncertainty in the death rate of the predator, subjected to a bounded disturbance has been simulated with the proposed control strategy.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Cortical and thalamic contributions to response dynamics across layers of the primary somatosensory cortex during tactile discrimination

PubMed Central

Pais-Vieira, Miguel; Kunicki, Carolina; Tseng, Po-He; Martin, Joel; Lebedev, Mikhail

2015-01-01

Tactile information processing in the rodent primary somatosensory cortex (S1) is layer specific and involves modulations from both thalamocortical and cortico-cortical loops. However, the extent to which these loops influence the dynamics of the primary somatosensory cortex while animals execute tactile discrimination remains largely unknown. Here, we describe neural dynamics of S1 layers across the multiple epochs defining a tactile discrimination task. We observed that neuronal ensembles within different layers of the S1 cortex exhibited significantly distinct neurophysiological properties, which constantly changed across the behavioral states that defined a tactile discrimination. Neural dynamics present in supragranular and granular layers generally matched the patterns observed in the ventral posterior medial nucleus of the thalamus (VPM), whereas the neural dynamics recorded from infragranular layers generally matched the patterns from the posterior nucleus of the thalamus (POM). Selective inactivation of contralateral S1 specifically switched infragranular neural dynamics from POM-like to those resembling VPM neurons. Meanwhile, ipsilateral M1 inactivation profoundly modulated the firing suppression observed in infragranular layers. This latter effect was counterbalanced by contralateral S1 block. Tactile stimulus encoding was layer specific and selectively affected by M1 or contralateral S1 inactivation. Lastly, causal information transfer occurred between all neurons in all S1 layers but was maximal from infragranular to the granular layer. These results suggest that tactile information processing in the S1 of awake behaving rodents is layer specific and state dependent and that its dynamics depend on the asynchronous convergence of modulations originating from ipsilateral M1 and contralateral S1. PMID:26180115

78 FR 2433 - Notice of Inventory Completion: Fort Collins Museum of Discovery, Fort Collins, CO

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-11

... Discovery). Although specific provenience of the human remains is unknown, osteological analysis conducted by physical anthropologists and by independent forensic scientists determined that the remains are of...

Power maximization of variable-speed variable-pitch wind turbines using passive adaptive neural fault tolerant control

NASA Astrophysics Data System (ADS)

Habibi, Hamed; Rahimi Nohooji, Hamed; Howard, Ian

2017-09-01

Power maximization has always been a practical consideration in wind turbines. The question of how to address optimal power capture, especially when the system dynamics are nonlinear and the actuators are subject to unknown faults, is significant. This paper studies the control methodology for variable-speed variable-pitch wind turbines including the effects of uncertain nonlinear dynamics, system fault uncertainties, and unknown external disturbances. The nonlinear model of the wind turbine is presented, and the problem of maximizing extracted energy is formulated by designing the optimal desired states. With the known system, a model-based nonlinear controller is designed; then, to handle uncertainties, the unknown nonlinearities of the wind turbine are estimated by utilizing radial basis function neural networks. The adaptive neural fault tolerant control is designed passively to be robust on model uncertainties, disturbances including wind speed and model noises, and completely unknown actuator faults including generator torque and pitch actuator torque. The Lyapunov direct method is employed to prove that the closed-loop system is uniformly bounded. Simulation studies are performed to verify the effectiveness of the proposed method.

Terminal Sliding Mode-Based Consensus Tracking Control for Networked Uncertain Mechanical Systems on Digraphs.

PubMed

Chen, Gang; Song, Yongduan; Guan, Yanfeng

2018-03-01

This brief investigates the finite-time consensus tracking control problem for networked uncertain mechanical systems on digraphs. A new terminal sliding-mode-based cooperative control scheme is developed to guarantee that the tracking errors converge to an arbitrarily small bound around zero in finite time. All the networked systems can have different dynamics and all the dynamics are unknown. A neural network is used at each node to approximate the local unknown dynamics. The control schemes are implemented in a fully distributed manner. The proposed control method eliminates some limitations in the existing terminal sliding-mode-based consensus control methods and extends the existing analysis methods to the case of directed graphs. Simulation results on networked robot manipulators are provided to show the effectiveness of the proposed control algorithms.

Realtime motion planning for a mobile robot in an unknown environment using a neurofuzzy based approach

NASA Astrophysics Data System (ADS)

Zheng, Taixiong

2005-12-01

A neuro-fuzzy network based approach for robot motion in an unknown environment was proposed. In order to control the robot motion in an unknown environment, the behavior of the robot was classified into moving to the goal and avoiding obstacles. Then, according to the dynamics of the robot and the behavior character of the robot in an unknown environment, fuzzy control rules were introduced to control the robot motion. At last, a 6-layer neuro-fuzzy network was designed to merge from what the robot sensed to robot motion control. After being trained, the network may be used for robot motion control. Simulation results show that the proposed approach is effective for robot motion control in unknown environment.

Decentralised output feedback control of Markovian jump interconnected systems with unknown interconnections

NASA Astrophysics Data System (ADS)

Li, Li-Wei; Yang, Guang-Hong

2017-07-01

The problem of decentralised output feedback control is addressed for Markovian jump interconnected systems with unknown interconnections and general transition rates (TRs) allowed to be unknown or known with uncertainties. A class of decentralised dynamic output feedback controllers are constructed, and a cyclic-small-gain condition is exploited to dispose the unknown interconnections so that the resultant closed-loop system is stochastically stable and satisfies an H∞ performance. With slack matrices to cope with the nonlinearities incurred by unknown and uncertain TRs in control synthesis, a novel controller design condition is developed in linear matrix inequality formalism. Compared with the existing works, the proposed approach leads to less conservatism. Finally, two examples are used to illustrate the effectiveness of the new results.

Rapid hyperosmotic-induced Ca 2+ responses in Arabidopsis thaliana exhibit sensory potentiation and involvement of plastidial KEA transporters

DOE PAGES

Stephan, Aaron B.; Kunz, Hans-Henning; Yang, Eric; ...

2016-08-15

How plant roots initially sense osmotic stress in an environment of dynamic water availabilities remains largely unknown. Plants can perceive water limitation imposed by soil salinity or, potentially, by drought in the form of osmotic stress. Rapid osmotic stress-induced intracellular calcium transients provide the opportunity to dissect quantitatively the sensory mechanisms that transmit osmotic stress under environmental and genetic perturbations in plants. Here, we describe a phenomenon whereby prior exposure to osmotic stress increases the sensitivity of the rapid calcium responses to subsequent stress. Furthermore, mutations in plastidial K + exchange antiporter (KEA)1/2 and KEA3 transporters were unexpectedly found tomore » reduce the rapid osmotic stress-induced calcium elevation. These findings advance the understanding of the mechanisms underlying the rapid osmotic stress response in plants.« less

Deciphering Interplay between Salmonella Invasion Effectors

PubMed Central

Koronakis, Vassilis

2008-01-01

Bacterial pathogens have evolved a specialized type III secretion system (T3SS) to translocate virulence effector proteins directly into eukaryotic target cells. Salmonellae deploy effectors that trigger localized actin reorganization to force their own entry into non-phagocytic host cells. Six effectors (SipC, SipA, SopE/2, SopB, SptP) can individually manipulate actin dynamics at the plasma membrane, which acts as a ‘signaling hub’ during Salmonella invasion. The extent of crosstalk between these spatially coincident effectors remains unknown. Here we describe trans and cis binary entry effector interplay (BENEFIT) screens that systematically examine functional associations between effectors following their delivery into the host cell. The results reveal extensive ordered synergistic and antagonistic relationships and their relative potency, and illuminate an unexpectedly sophisticated signaling network evolved through longstanding pathogen–host interaction. PMID:18389058

Interactive Social Neuroscience to Study Autism Spectrum Disorder

PubMed Central

Rolison, Max J.; Naples, Adam J.; McPartland, James C.

2015-01-01

Individuals with autism spectrum disorder (ASD) demonstrate difficulty with social interactions and relationships, but the neural mechanisms underlying these difficulties remain largely unknown. While social difficulties in ASD are most apparent in the context of interactions with other people, most neuroscience research investigating ASD have provided limited insight into the complex dynamics of these interactions. The development of novel, innovative “interactive social neuroscience” methods to study the brain in contexts with two interacting humans is a necessary advance for ASD research. Studies applying an interactive neuroscience approach to study two brains engaging with one another have revealed significant differences in neural processes during interaction compared to observation in brain regions that are implicated in the neuropathology of ASD. Interactive social neuroscience methods are crucial in clarifying the mechanisms underlying the social and communication deficits that characterize ASD. PMID:25745371

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

Dong, Chuanfei; Lingam, Manasvi; Ma, Yingjuan

We address the important question of whether the newly discovered exoplanet, Proxima Centauri b (PCb), is capable of retaining an atmosphere over long periods of time. This is done by adapting a sophisticated multi-species MHD model originally developed for Venus and Mars and computing the ion escape losses from PCb. The results suggest that the ion escape rates are about two orders of magnitude higher than the terrestrial planets of our Solar system if PCb is unmagnetized. In contrast, if the planet does have an intrinsic dipole magnetic field, the rates are lowered for certain values of the stellar windmore » dynamic pressure, but they are still higher than the observed values for our solar system’s terrestrial planets. These results must be interpreted with due caution since most of the relevant parameters for PCb remain partly or wholly unknown.« less

Structural diversity of supercoiled DNA

PubMed Central

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-01-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function. PMID:26455586

Structural diversity of supercoiled DNA

NASA Astrophysics Data System (ADS)

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-10-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

Fast Integer Ambiguity Resolution for GPS Attitude Determination

NASA Technical Reports Server (NTRS)

Lightsey, E. Glenn; Crassidis, John L.; Markley, F. Landis

1999-01-01

In this paper, a new algorithm for GPS (Global Positioning System) integer ambiguity resolution is shown. The algorithm first incorporates an instantaneous (static) integer search to significantly reduce the search space using a geometric inequality. Then a batch-type loss function is used to check the remaining integers in order to determine the optimal integer. This batch function represents the GPS sightline vectors in the body frame as the sum of two vectors, one depending on the phase measurements and the other on the unknown integers. The new algorithm has several advantages: it does not require an a-priori estimate of the vehicle's attitude; it provides an inherent integrity check using a covariance-type expression; and it can resolve the integers even when coplanar baselines exist. The performance of the new algorithm is tested on a dynamic hardware simulator.

CRYSTAL GROWTH. Crystallization by particle attachment in synthetic, biogenic, and geologic environments.

PubMed

De Yoreo, James J; Gilbert, Pupa U P A; Sommerdijk, Nico A J M; Penn, R Lee; Whitelam, Stephen; Joester, Derk; Zhang, Hengzhong; Rimer, Jeffrey D; Navrotsky, Alexandra; Banfield, Jillian F; Wallace, Adam F; Michel, F Marc; Meldrum, Fiona C; Cölfen, Helmut; Dove, Patricia M

2015-07-31

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments. Copyright © 2015, American Association for the Advancement of Science.

Interactive social neuroscience to study autism spectrum disorder.

PubMed

Rolison, Max J; Naples, Adam J; McPartland, James C

2015-03-01

Individuals with autism spectrum disorder (ASD) demonstrate difficulty with social interactions and relationships, but the neural mechanisms underlying these difficulties remain largely unknown. While social difficulties in ASD are most apparent in the context of interactions with other people, most neuroscience research investigating ASD have provided limited insight into the complex dynamics of these interactions. The development of novel, innovative "interactive social neuroscience" methods to study the brain in contexts with two interacting humans is a necessary advance for ASD research. Studies applying an interactive neuroscience approach to study two brains engaging with one another have revealed significant differences in neural processes during interaction compared to observation in brain regions that are implicated in the neuropathology of ASD. Interactive social neuroscience methods are crucial in clarifying the mechanisms underlying the social and communication deficits that characterize ASD.

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE PAGES

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

2016-12-02

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

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

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Rapid hyperosmotic-induced Ca 2+ responses in Arabidopsis thaliana exhibit sensory potentiation and involvement of plastidial KEA transporters

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

Stephan, Aaron B.; Kunz, Hans-Henning; Yang, Eric

How plant roots initially sense osmotic stress in an environment of dynamic water availabilities remains largely unknown. Plants can perceive water limitation imposed by soil salinity or, potentially, by drought in the form of osmotic stress. Rapid osmotic stress-induced intracellular calcium transients provide the opportunity to dissect quantitatively the sensory mechanisms that transmit osmotic stress under environmental and genetic perturbations in plants. Here, we describe a phenomenon whereby prior exposure to osmotic stress increases the sensitivity of the rapid calcium responses to subsequent stress. Furthermore, mutations in plastidial K + exchange antiporter (KEA)1/2 and KEA3 transporters were unexpectedly found tomore » reduce the rapid osmotic stress-induced calcium elevation. These findings advance the understanding of the mechanisms underlying the rapid osmotic stress response in plants.« less

Confinement, Desolvation, And Electrosorption Effects on the Diffusion of Ions in Nanoporous Carbon Electrodes

PubMed Central

2015-01-01

Supercapacitors are electrochemical devices which store energy by ion adsorption on the surface of a porous carbon. They are characterized by high power delivery. The use of nanoporous carbon to increase their energy density should not hinder their fast charging. However, the mechanisms for ion transport inside electrified nanopores remain largely unknown. Here we show that the diffusion is characterized by a hierarchy of time scales arising from ion confinement, solvation, and electrosorption effects. By combining electrochemistry experiments with molecular dynamics simulations, we determine the in-pore conductivities and diffusion coefficients and their variations with the applied potential. We show that the diffusion of the ions is slower by 1 order of magnitude compared to the bulk electrolyte. The desolvation of the ions occurs on much faster time scales than electrosorption. PMID:26369420

An Efficient Solution Method for Multibody Systems with Loops Using Multiple Processors

NASA Technical Reports Server (NTRS)

Ghosh, Tushar K.; Nguyen, Luong A.; Quiocho, Leslie J.

2015-01-01

This paper describes a multibody dynamics algorithm formulated for parallel implementation on multiprocessor computing platforms using the divide-and-conquer approach. The system of interest is a general topology of rigid and elastic articulated bodies with or without loops. The algorithm divides the multibody system into a number of smaller sets of bodies in chain or tree structures, called "branches" at convenient joints called "connection points", and uses an Order-N (O (N)) approach to formulate the dynamics of each branch in terms of the unknown spatial connection forces. The equations of motion for the branches, leaving the connection forces as unknowns, are implemented in separate processors in parallel for computational efficiency, and the equations for all the unknown connection forces are synthesized and solved in one or several processors. The performances of two implementations of this divide-and-conquer algorithm in multiple processors are compared with an existing method implemented on a single processor.

Adaptive neural control for dual-arm coordination of humanoid robot with unknown nonlinearities in output mechanism.

PubMed

Liu, Zhi; Chen, Ci; Zhang, Yun; Chen, C L P

2015-03-01

To achieve an excellent dual-arm coordination of the humanoid robot, it is essential to deal with the nonlinearities existing in the system dynamics. The literatures so far on the humanoid robot control have a common assumption that the problem of output hysteresis could be ignored. However, in the practical applications, the output hysteresis is widely spread; and its existing limits the motion/force performances of the robotic system. In this paper, an adaptive neural control scheme, which takes the unknown output hysteresis and computational efficiency into account, is presented and investigated. In the controller design, the prior knowledge of system dynamics is assumed to be unknown. The motion error is guaranteed to converge to a small neighborhood of the origin by Lyapunov's stability theory. Simultaneously, the internal force is kept bounded and its error can be made arbitrarily small.

Reinforcement learning for adaptive optimal control of unknown continuous-time nonlinear systems with input constraints

NASA Astrophysics Data System (ADS)

Yang, Xiong; Liu, Derong; Wang, Ding

2014-03-01

In this paper, an adaptive reinforcement learning-based solution is developed for the infinite-horizon optimal control problem of constrained-input continuous-time nonlinear systems in the presence of nonlinearities with unknown structures. Two different types of neural networks (NNs) are employed to approximate the Hamilton-Jacobi-Bellman equation. That is, an recurrent NN is constructed to identify the unknown dynamical system, and two feedforward NNs are used as the actor and the critic to approximate the optimal control and the optimal cost, respectively. Based on this framework, the action NN and the critic NN are tuned simultaneously, without the requirement for the knowledge of system drift dynamics. Moreover, by using Lyapunov's direct method, the weights of the action NN and the critic NN are guaranteed to be uniformly ultimately bounded, while keeping the closed-loop system stable. To demonstrate the effectiveness of the present approach, simulation results are illustrated.

Robot path planning algorithm based on symbolic tags in dynamic environment

NASA Astrophysics Data System (ADS)

Vokhmintsev, A.; Timchenko, M.; Melnikov, A.; Kozko, A.; Makovetskii, A.

2017-09-01

The present work will propose a new heuristic algorithms for path planning of a mobile robot in an unknown dynamic space that have theoretically approved estimates of computational complexity and are approbated for solving specific applied problems.

[Pseudomigraine with pleocytosis].

PubMed

Pariso, Gabriela S; Parisi, Virginia L; Persi, Gabriel G; Canto, Lucila; Rugilo, Carlos A; Gatto, Emilia M

2006-01-01

The syndrome of transient headache and neurological deficits with cerebrospinal fluid lymphocytosis or pseudomigraine with temporary neurological symptoms and lymphocytic pleocytosis (HaNDL) is a syndrome consisting of recurrent headaches, reversible neurological deficit, lymphocytic pleocytosis in cerebrospinal fluid (CSF), variable duration over time and spontaneous resolution. Although several etiopathogenic mechanisms have been suggested (vascular, infectous, immunological and calcium channelopthy), its etiology remains unknown. We describe a 28 year old female, with recurrent migraine with pleocytosis, confusional syndrome and transient neurological deficit. The clinical remission was achieved within two months. Although its etiology remains unknown the differential diagnosis is discussed in order to keep in mind this syndrome.

Anticipatory Neurofuzzy Control

NASA Technical Reports Server (NTRS)

Mccullough, Claire L.

1994-01-01

Technique of feedback control, called "anticipatory neurofuzzy control," developed for use in controlling flexible structures and other dynamic systems for which mathematical models of dynamics poorly known or unknown. Superior ability to act during operation to compensate for, and adapt to, errors in mathematical model of dynamics, changes in dynamics, and noise. Also offers advantage of reduced computing time. Hybrid of two older fuzzy-logic control techniques: standard fuzzy control and predictive fuzzy control.

Neuronal long-range temporal correlations and avalanche dynamics are correlated with behavioral scaling laws

PubMed Central

Palva, J. Matias; Zhigalov, Alexander; Hirvonen, Jonni; Korhonen, Onerva; Linkenkaer-Hansen, Klaus; Palva, Satu

2013-01-01

Scale-free fluctuations are ubiquitous in behavioral performance and neuronal activity. In time scales from seconds to hundreds of seconds, psychophysical dynamics and the amplitude fluctuations of neuronal oscillations are governed by power-law-form long-range temporal correlations (LRTCs). In millisecond time scales, neuronal activity comprises cascade-like neuronal avalanches that exhibit power-law size and lifetime distributions. However, it remains unknown whether these neuronal scaling laws are correlated with those characterizing behavioral performance or whether neuronal LRTCs and avalanches are related. Here, we show that the neuronal scaling laws are strongly correlated both with each other and with behavioral scaling laws. We used source reconstructed magneto- and electroencephalographic recordings to characterize the dynamics of ongoing cortical activity. We found robust power-law scaling in neuronal LRTCs and avalanches in resting-state data and during the performance of audiovisual threshold stimulus detection tasks. The LRTC scaling exponents of the behavioral performance fluctuations were correlated with those of concurrent neuronal avalanches and LRTCs in anatomically identified brain systems. The behavioral exponents also were correlated with neuronal scaling laws derived from a resting-state condition and with a similar anatomical topography. Finally, despite the difference in time scales, the scaling exponents of neuronal LRTCs and avalanches were strongly correlated during both rest and task performance. Thus, long and short time-scale neuronal dynamics are related and functionally significant at the behavioral level. These data suggest that the temporal structures of human cognitive fluctuations and behavioral variability stem from the scaling laws of individual and intrinsic brain dynamics. PMID:23401536

In situ intracellular calcium oscillations in osteocytes in intact mouse long bones under dynamic mechanical loading

PubMed Central

Jing, Da; Baik, Andrew D.; Lu, X. Lucas; Zhou, Bin; Lai, Xiaohan; Wang, Liyun; Luo, Erping; Guo, X. Edward

2014-01-01

Osteocytes have been hypothesized to be the major mechanosensors in bone. How in situ osteocytes respond to mechanical stimuli is still unclear because of technical difficulties. In vitro studies have shown that osteocytes exhibited unique calcium (Ca2+) oscillations to fluid shear. However, whether this mechanotransduction phenomenon holds for in situ osteocytes embedded within a mineralized bone matrix under dynamic loading remains unknown. Using a novel synchronized loading/imaging technique, we successfully visualized in real time and quantified Ca2+ responses in osteocytes and bone surface cells in situ under controlled dynamic loading on intact mouse tibia. The resultant fluid-induced shear stress on the osteocyte in the lacunocanalicular system (LCS) was also quantified. Osteocytes, but not surface cells, displayed repetitive Ca2+ spikes in response to dynamic loading, with spike frequency and magnitude dependent on load magnitude, tissue strain, and shear stress in the LCS. The Ca2+ oscillations were significantly reduced by endoplasmic reticulum (ER) depletion and P2 purinergic receptor (P2R)/phospholipase C (PLC) inhibition. This study provides direct evidence that osteocytes respond to in situ mechanical loading by Ca2+ oscillations, which are dependent on the P2R/PLC/inositol trisphosphate/ER pathway. This study develops a novel approach in skeletal mechanobiology and also advances our fundamental knowledge of bone mechanotransduction.—Jing, D., Baik, A. D., Lu, X. L., Zhou, B., Lai, X., Wang, L., Luo, E., Guo, X. E. In situ intracellular calcium oscillations in osteocytes in intact mouse long bones under dynamic mechanical loading. PMID:24347610

Increasing blood flow to exercising muscle attenuates systemic cardiovascular responses during dynamic exercise in humans

PubMed Central

Ichinose-Kuwahara, Tomoko; Kondo, Narihiko; Nishiyasu, Takeshi

2015-01-01

Reducing blood flow to working muscles during dynamic exercise causes metabolites to accumulate within the active muscles and evokes systemic pressor responses. Whether a similar cardiovascular response is elicited with normal blood flow to exercising muscles during dynamic exercise remains unknown, however. To address that issue, we tested whether cardiovascular responses are affected by increases in blood flow to active muscles. Thirteen healthy subjects performed dynamic plantarflexion exercise for 12 min at 20%, 40%, and 60% of peak workload (EX20, EX40, and EX60) with their lower thigh enclosed in a negative pressure box. Under control conditions, the box pressure was the same as the ambient air pressure. Under negative pressure conditions, beginning 3 min after the start of the exercise, the box pressure was decreased by 20, 45, and then 70 mmHg in stepwise fashion with 3-min step durations. During EX20, the negative pressure had no effect on blood flow or the cardiovascular responses measured. However, application of negative pressure increased blood flow to the exercising leg during EX40 and EX60. This increase in blood flow had no significant effect on systemic cardiovascular responses during EX40, but it markedly attenuated the pressor responses otherwise seen during EX60. These results demonstrate that during mild exercise, normal blood flow to exercising muscle is not a factor eliciting cardiovascular responses, whereas it elicits an important pressor effect during moderate exercise. This suggests blood flow to exercising muscle is a major determinant of cardiovascular responses during dynamic exercise at higher than moderate intensity. PMID:26377556

Urbanization Changes the Temporal Dynamics of Nutrients and Water Chemistry

NASA Astrophysics Data System (ADS)

Steele, M.; Badgley, B.

2017-12-01

Recent studies find that urban development alters the seasonal dynamics of nutrient concentrations, where the highest concentrations of nitrogen occurred during the winter in urban watersheds, rather than the summer. However, the effects of urbanization on the seasonal concentrations of other nutrients and chemical components is unknown. Therefore, to determine how urbanization changes the seasonal dynamics, once a week we measured concentrations of dissolved organic carbon (DOC), nutrients (NO3, DON, TN, PO4), base cations (Ca, Mg, Na, K), anions (F, Cl, SO4), pH, sediment, temperature, conductivity, and dissolved oxygen (DO) of nine urban, agricultural, and minimally developed watersheds in southwest Virginia, USA. We found that urbanization disrupted the seasonal dynamics of all metrics, except DON, PO4, Ca, sediment, and DO, where some shifted to high concentrations during the winter (Cl, conductivity), highs during late winter or spring (DOC, Na), a season low (TN, SO4, NO3) or high (NH4) during the summer, or remained more constant throughout the year compared to the reference watersheds (Mg, K, pH). The complex changes in seasonal dynamics coincide with a decoupling of common correlations between constituents; for example, DO and NO3 are negatively correlated in reference watersheds (NO3 increases, DO decreases), but positively correlated in urban watersheds. These results suggest that as watersheds become more intensely developed, the influence of natural drivers like temperature and vegetation become steadily overcome by the influence of urban drivers like deicing salts and wastewater leakage, which exert increasing control of seasonal water quality and aquatic habitat.

Implications of land use change on the national terrestrial carbon budget of Georgia.

PubMed

Olofsson, Pontus; Torchinava, Paata; Woodcock, Curtis E; Baccini, Alessandro; Houghton, Richard A; Ozdogan, Mutlu; Zhao, Feng; Yang, Xiaoyuan

2010-09-13

Globally, the loss of forests now contributes almost 20% of carbon dioxide emissions to the atmosphere. There is an immediate need to reduce the current rates of forest loss, and the associated release of carbon dioxide, but for many areas of the world these rates are largely unknown. The Soviet Union contained a substantial part of the world's forests and the fate of those forests and their effect on carbon dynamics remain unknown for many areas of the former Eastern Bloc. For Georgia, the political and economic transitions following independence in 1991 have been dramatic. In this paper we quantify rates of land use changes and their effect on the terrestrial carbon budget for Georgia. A carbon book-keeping model traces changes in carbon stocks using historical and current rates of land use change. Landsat satellite images acquired circa 1990 and 2000 were analyzed to detect changes in forest cover since 1990. The remote sensing analysis showed that a modest forest loss occurred, with approximately 0.8% of the forest cover having disappeared after 1990. Nevertheless, growth of Georgian forests still contribute a current national sink of about 0.3 Tg of carbon per year, which corresponds to 31% of the country anthropogenic carbon emissions. We assume that the observed forest loss is mainly a result of illegal logging, but we have not found any evidence of large-scale clear-cutting. Instead local harvesting of timber for household use is likely to be the underlying driver of the observed logging. The Georgian forests are a currently a carbon sink and will remain as such until about 2040 if the current rate of deforestation persists. Forest protection efforts, combined with economic growth, are essential for reducing the rate of deforestation and protecting the carbon sink provided by Georgian forests.

Estimation of nonlinear pilot model parameters including time delay.

NASA Technical Reports Server (NTRS)

Schiess, J. R.; Roland, V. R.; Wells, W. R.

1972-01-01

Investigation of the feasibility of using a Kalman filter estimator for the identification of unknown parameters in nonlinear dynamic systems with a time delay. The problem considered is the application of estimation theory to determine the parameters of a family of pilot models containing delayed states. In particular, the pilot-plant dynamics are described by differential-difference equations of the retarded type. The pilot delay, included as one of the unknown parameters to be determined, is kept in pure form as opposed to the Pade approximations generally used for these systems. Problem areas associated with processing real pilot response data are included in the discussion.

Robust Adaptive Dynamic Programming of Two-Player Zero-Sum Games for Continuous-Time Linear Systems.

PubMed

Fu, Yue; Fu, Jun; Chai, Tianyou

2015-12-01

In this brief, an online robust adaptive dynamic programming algorithm is proposed for two-player zero-sum games of continuous-time unknown linear systems with matched uncertainties, which are functions of system outputs and states of a completely unknown exosystem. The online algorithm is developed using the policy iteration (PI) scheme with only one iteration loop. A new analytical method is proposed for convergence proof of the PI scheme. The sufficient conditions are given to guarantee globally asymptotic stability and suboptimal property of the closed-loop system. Simulation studies are conducted to illustrate the effectiveness of the proposed method.

Graph Theory-Based Pinning Synchronization of Stochastic Complex Dynamical Networks.

PubMed

Li, Xiao-Jian; Yang, Guang-Hong

2017-02-01

This paper is concerned with the adaptive pinning synchronization problem of stochastic complex dynamical networks (CDNs). Based on algebraic graph theory and Lyapunov theory, pinning controller design conditions are derived, and the rigorous convergence analysis of synchronization errors in the probability sense is also conducted. Compared with the existing results, the topology structures of stochastic CDN are allowed to be unknown due to the use of graph theory. In particular, it is shown that the selection of nodes for pinning depends on the unknown lower bounds of coupling strengths. Finally, an example on a Chua's circuit network is given to validate the effectiveness of the theoretical results.

Chaotic Traversal (CHAT): Very Large Graphs Traversal Using Chaotic Dynamics

NASA Astrophysics Data System (ADS)

Changaival, Boonyarit; Rosalie, Martin; Danoy, Grégoire; Lavangnananda, Kittichai; Bouvry, Pascal

2017-12-01

Graph Traversal algorithms can find their applications in various fields such as routing problems, natural language processing or even database querying. The exploration can be considered as a first stepping stone into knowledge extraction from the graph which is now a popular topic. Classical solutions such as Breadth First Search (BFS) and Depth First Search (DFS) require huge amounts of memory for exploring very large graphs. In this research, we present a novel memoryless graph traversal algorithm, Chaotic Traversal (CHAT) which integrates chaotic dynamics to traverse large unknown graphs via the Lozi map and the Rössler system. To compare various dynamics effects on our algorithm, we present an original way to perform the exploration of a parameter space using a bifurcation diagram with respect to the topological structure of attractors. The resulting algorithm is an efficient and nonresource demanding algorithm, and is therefore very suitable for partial traversal of very large and/or unknown environment graphs. CHAT performance using Lozi map is proven superior than the, commonly known, Random Walk, in terms of number of nodes visited (coverage percentage) and computation time where the environment is unknown and memory usage is restricted.

Thaumarchaeal amoA and nirK Gene Abundance Patterns Reveal Spatiotemporal Dynamics of Ammonia-oxidizing Archaeal Populations in Monterey Bay, CA

NASA Astrophysics Data System (ADS)

Tolar, B. B.; Reji, L.; Smith, J. M.; Chavez, F.; Francis, C.

2016-12-01

Thaumarchaeaota are among the most abundant microorganisms on the planet, and are significant players in the global nitrogen cycle. All cultivated members of the phylum are capable of performing the first and rate-limiting step of nitrification - the aerobic oxidation of ammonia to nitrite. In marine environments, ammonia-oxidizing archaea (AOA) have been found to greatly outnumber their bacterial counterparts. However, much about their ecology remains largely unknown. Monterey Bay, a non-estuarine embayment on the central California coast, is an ideal site for studying the dynamics of natural thaumarchaeal assemblages, given the highly dynamic nature of the Bay waters with seasonal upwelling episodes and the associated steep gradients in environmental variables. In the present study, we examined thaumarchaeal population dynamics in the upper Monterey Bay water column (0-500 m) using multiple molecular markers. Following high-resolution spatiotemporal sampling (i.e., up to 10 depths sampled monthly over a period of 2 years) at two stations in the Bay, we quantified thaumarchaeal functional genes - the ammonia monooxygenase (amoA) gene and its `shallow' and `deep' marine ecotypes, and variants of the marine nitrite reductase (nirK) gene. The abundances of both genes were regressed against environmental variables to gain insights into factors shaping their spatiotemporal dynamics in the Bay. Gene abundances at both stations varied with depth and season, with winter months generally having several orders of magnitude greater abundances. Statistical analyses point to differential controls on the gene abundances, with depth and temperature potentially being the major environmental determinants of thaumarchaeal population size. Our results also highlight the importance of employing multiple marker genes to gain a more highly resolved picture of thaumarchaeal population dynamics in complex environmental systems such as the coastal ocean.

Mind wandering away from pain dynamically engages antinociceptive and default mode brain networks

PubMed Central

Kucyi, Aaron; Salomons, Tim V.; Davis, Karen D.

2013-01-01

Human minds often wander away from their immediate sensory environment. It remains unknown whether such mind wandering is unsystematic or whether it lawfully relates to an individual’s tendency to attend to salient stimuli such as pain and their associated brain structure/function. Studies of pain–cognition interactions typically examine explicit manipulation of attention rather than spontaneous mind wandering. Here we sought to better represent natural fluctuations in pain in daily life, so we assessed behavioral and neural aspects of spontaneous disengagement of attention from pain. We found that an individual’s tendency to attend to pain related to the disruptive effect of pain on his or her cognitive task performance. Next, we linked behavioral findings to neural networks with strikingly convergent evidence from functional magnetic resonance imaging during pain coupled with thought probes of mind wandering, dynamic resting state activity fluctuations, and diffusion MRI. We found that (i) pain-induced default mode network (DMN) deactivations were attenuated during mind wandering away from pain; (ii) functional connectivity fluctuations between the DMN and periaqueductal gray (PAG) dynamically tracked spontaneous attention away from pain; and (iii) across individuals, stronger PAG–DMN structural connectivity and more dynamic resting state PAG–DMN functional connectivity were associated with the tendency to mind wander away from pain. These data demonstrate that individual tendencies to mind wander away from pain, in the absence of explicit manipulation, are subserved by functional and structural connectivity within and between default mode and antinociceptive descending modulation networks. PMID:24167282

Mind wandering away from pain dynamically engages antinociceptive and default mode brain networks.

PubMed

Kucyi, Aaron; Salomons, Tim V; Davis, Karen D

2013-11-12

Human minds often wander away from their immediate sensory environment. It remains unknown whether such mind wandering is unsystematic or whether it lawfully relates to an individual's tendency to attend to salient stimuli such as pain and their associated brain structure/function. Studies of pain-cognition interactions typically examine explicit manipulation of attention rather than spontaneous mind wandering. Here we sought to better represent natural fluctuations in pain in daily life, so we assessed behavioral and neural aspects of spontaneous disengagement of attention from pain. We found that an individual's tendency to attend to pain related to the disruptive effect of pain on his or her cognitive task performance. Next, we linked behavioral findings to neural networks with strikingly convergent evidence from functional magnetic resonance imaging during pain coupled with thought probes of mind wandering, dynamic resting state activity fluctuations, and diffusion MRI. We found that (i) pain-induced default mode network (DMN) deactivations were attenuated during mind wandering away from pain; (ii) functional connectivity fluctuations between the DMN and periaqueductal gray (PAG) dynamically tracked spontaneous attention away from pain; and (iii) across individuals, stronger PAG-DMN structural connectivity and more dynamic resting state PAG-DMN functional connectivity were associated with the tendency to mind wander away from pain. These data demonstrate that individual tendencies to mind wander away from pain, in the absence of explicit manipulation, are subserved by functional and structural connectivity within and between default mode and antinociceptive descending modulation networks.

Early dynamics of the semantic priming shift

PubMed Central

Lavigne, Frédéric; Chanquoy, Lucile; Dumercy, Laurent; Vitu, Françoise

2013-01-01

Semantic processing of sequences of words requires the cognitive system to keep several word meanings simultaneously activated in working memory with limited capacity. The real- time updating of the sequence of word meanings relies on dynamic changes in the associates to the words that are activated. Protocols involving two sequential primes report a semantic priming shift from larger priming of associates to the first prime to larger priming of associates to the second prime, in a range of long SOAs (stimulus-onset asynchronies) between the second prime and the target. However, the possibility for an early semantic priming shift is still to be tested, and its dynamics as a function of association strength remain unknown. Three multiple priming experiments are proposed that cross-manipulate association strength between each of two successive primes and a target, for different values of short SOAs and prime durations. Results show an early priming shift ranging from priming of associates to the first prime only to priming of strong associates to the first prime and all of the associates to the second prime. We investigated the neural basis of the early priming shift by using a network model of spike frequency adaptive cortical neurons (e.g., Deco & Rolls, 2005), able to code different association strengths between the primes and the target. The cortical network model provides a description of the early dynamics of the priming shift in terms of pro-active and retro-active interferences within populations of excitatory neurons regulated by fast and unselective inhibitory feedback. PMID:23717346

Adaptive gait responses to awareness of an impending slip during treadmill walking.

PubMed

Yang, Feng; Kim, JaeEun; Munoz, Jose

2016-10-01

The awareness of potential slip risk has been shown to cause protective changes to human gait during overground walking. It remains unknown if such adaptations to walking pattern also exist when ambulating on a treadmill. This study sought to determine whether and to what extent individuals, when being aware of a potential slip risk during treadmill walking, could adjust their gait pattern to improve their dynamic stability against backward balance loss in response to the impending slip hazard. Fifty-four healthy young subjects (age: 23.9±4.7years) participated in this study. Subjects' gait pattern was measured under two conditions: walking on a treadmill without (or normal walking) and with (or aware walking) the awareness of the potential slip perturbation. During both walking conditions, subjects' full body kinematics were gathered by using a motion capture system. Spatial gait parameters and the dynamic gait stability against backward balance were compared between the two walking conditions. The results revealed that subjects proactively adopted a "cautious gait" during aware walking compared with the normal walking. The cautious gait, which was achieved by taking a shorter step and a more flatfoot landing, positioned the body center of mass closer to the base of support, improving participants' dynamic stability and increasing their resistance against a possible slip-related fall. The finding from this study could provide insights into the dynamic stability control when individuals anticipate potential slip risk during treadmill walking. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity

PubMed Central

Thakurela, Sudhir; Sahu, Sanjeeb Kumar; Garding, Angela; Tiwari, Vijay K.

2015-01-01

Gene regulation in mammals involves a complex interplay between promoters and distal regulatory elements that function in concert to drive precise spatiotemporal gene expression programs. However, the dynamics of the distal gene regulatory landscape and its function in the transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here, we performed a combinatorial analysis of genome-wide data sets for chromatin accessibility (FAIRE-seq) and the enhancer mark H3K27ac, revealing the highly dynamic nature of distal gene regulation during neurogenesis, which gets progressively restricted to distinct genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further find that the distal accessible and active regions serve as target sites for distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. Mature neurons respond to a sustained activity of NMDA receptors by epigenetic reprogramming at a large number of distal regulatory regions as well as dramatic reorganization of super-enhancers. Such massive remodeling of the distal regulatory landscape in turn results in a transcriptome that confers a transient loss of neuronal identity and gain of cellular plasticity. Furthermore, NMDA receptor activity also induces many novel prosurvival genes that function in neuroprotective pathways. Taken together, these findings reveal the dynamics of the distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate the transcriptome underlying neuronal development and activity. PMID:26170447

Fitting Nonlinear Ordinary Differential Equation Models with Random Effects and Unknown Initial Conditions Using the Stochastic Approximation Expectation-Maximization (SAEM) Algorithm.

PubMed

Chow, Sy-Miin; Lu, Zhaohua; Sherwood, Andrew; Zhu, Hongtu

2016-03-01

The past decade has evidenced the increased prevalence of irregularly spaced longitudinal data in social sciences. Clearly lacking, however, are modeling tools that allow researchers to fit dynamic models to irregularly spaced data, particularly data that show nonlinearity and heterogeneity in dynamical structures. We consider the issue of fitting multivariate nonlinear differential equation models with random effects and unknown initial conditions to irregularly spaced data. A stochastic approximation expectation-maximization algorithm is proposed and its performance is evaluated using a benchmark nonlinear dynamical systems model, namely, the Van der Pol oscillator equations. The empirical utility of the proposed technique is illustrated using a set of 24-h ambulatory cardiovascular data from 168 men and women. Pertinent methodological challenges and unresolved issues are discussed.

FITTING NONLINEAR ORDINARY DIFFERENTIAL EQUATION MODELS WITH RANDOM EFFECTS AND UNKNOWN INITIAL CONDITIONS USING THE STOCHASTIC APPROXIMATION EXPECTATION–MAXIMIZATION (SAEM) ALGORITHM

PubMed Central

Chow, Sy- Miin; Lu, Zhaohua; Zhu, Hongtu; Sherwood, Andrew

2014-01-01

The past decade has evidenced the increased prevalence of irregularly spaced longitudinal data in social sciences. Clearly lacking, however, are modeling tools that allow researchers to fit dynamic models to irregularly spaced data, particularly data that show nonlinearity and heterogeneity in dynamical structures. We consider the issue of fitting multivariate nonlinear differential equation models with random effects and unknown initial conditions to irregularly spaced data. A stochastic approximation expectation–maximization algorithm is proposed and its performance is evaluated using a benchmark nonlinear dynamical systems model, namely, the Van der Pol oscillator equations. The empirical utility of the proposed technique is illustrated using a set of 24-h ambulatory cardiovascular data from 168 men and women. Pertinent methodological challenges and unresolved issues are discussed. PMID:25416456

Chaotic dynamics in the (47171) Lempo triple system

NASA Astrophysics Data System (ADS)

Correia, Alexandre C. M.

2018-05-01

We investigate the dynamics of the (47171) Lempo triple system, also known by 1999 TC36. We derive a full 3D N-body model that takes into account the orbital and spin evolution of all bodies, which are assumed triaxial ellipsoids. We show that, for reasonable values of the shapes and rotational periods, the present best fitted orbital solution for the Lempo system is chaotic and unstable in short time-scales. The formation mechanism of this system is unknown, but the orbits can be stabilised when tidal dissipation is taken into account. The dynamics of the Lempo system is very rich, but depends on many parameters that are presently unknown. A better understanding of this systems thus requires more observations, which also need to be fitted with a complete model like the one presented here.

Dual adaptive dynamic control of mobile robots using neural networks.

PubMed

Bugeja, Marvin K; Fabri, Simon G; Camilleri, Liberato

2009-02-01

This paper proposes two novel dual adaptive neural control schemes for the dynamic control of nonholonomic mobile robots. The two schemes are developed in discrete time, and the robot's nonlinear dynamic functions are assumed to be unknown. Gaussian radial basis function and sigmoidal multilayer perceptron neural networks are used for function approximation. In each scheme, the unknown network parameters are estimated stochastically in real time, and no preliminary offline neural network training is used. In contrast to other adaptive techniques hitherto proposed in the literature on mobile robots, the dual control laws presented in this paper do not rely on the heuristic certainty equivalence property but account for the uncertainty in the estimates. This results in a major improvement in tracking performance, despite the plant uncertainty and unmodeled dynamics. Monte Carlo simulation and statistical hypothesis testing are used to illustrate the effectiveness of the two proposed stochastic controllers as applied to the trajectory-tracking problem of a differentially driven wheeled mobile robot.

Spatial curvilinear path following control of underactuated AUV with multiple uncertainties.

PubMed

Miao, Jianming; Wang, Shaoping; Zhao, Zhiping; Li, Yuan; Tomovic, Mileta M

2017-03-01

This paper investigates the problem of spatial curvilinear path following control of underactuated autonomous underwater vehicles (AUVs) with multiple uncertainties. Firstly, in order to design the appropriate controller, path following error dynamics model is constructed in a moving Serret-Frenet frame, and the five degrees of freedom (DOFs) dynamic model with multiple uncertainties is established. Secondly, the proposed control law is separated into kinematic controller and dynamic controller via back-stepping technique. In the case of kinematic controller, to overcome the drawback of dependence on the accurate vehicle model that are present in a number of path following control strategies described in the literature, the unknown side-slip angular velocity and attack angular velocity are treated as uncertainties. Whereas in the case of dynamic controller, the model parameters perturbations, unknown external environmental disturbances and the nonlinear hydrodynamic damping terms are treated as lumped uncertainties. Both kinematic and dynamic uncertainties are estimated and compensated by designed reduced-order linear extended state observes (LESOs). Thirdly, feedback linearization (FL) based control law is implemented for the control model using the estimates generated by reduced-order LESOs. For handling the problem of computational complexity inherent in the conventional back-stepping method, nonlinear tracking differentiators (NTDs) are applied to construct derivatives of the virtual control commands. Finally, the closed loop stability for the overall system is established. Simulation and comparative analysis demonstrate that the proposed controller exhibits enhanced performance in the presence of internal parameter variations, external unknown disturbances, unmodeled nonlinear damping terms, and measurement noises. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Forward Genetic Dissection of Biofilm Development by Fusobacterium nucleatum: Novel Functions of Cell Division Proteins FtsX and EnvC.

PubMed

Wu, Chenggang; Al Mamun, Abu Amar Mohamed; Luong, Truc Thanh; Hu, Bo; Gu, Jianhua; Lee, Ju Huck; D'Amore, Melissa; Das, Asis; Ton-That, Hung

2018-04-24

Fusobacterium nucleatum is a key member of the human oral biofilm. It is also implicated in preterm birth and colorectal cancer. To facilitate basic studies of fusobacterial virulence, we describe here a versatile transposon mutagenesis procedure and a pilot screen for mutants defective in biofilm formation. Out of 10 independent biofilm-defective mutants isolated, the affected genes included the homologs of the Escherichia coli cell division proteins FtsX and EnvC, the electron transport protein RnfA, and four proteins with unknown functions. Next, a facile new gene deletion method demonstrated that nonpolar, in-frame deletion of ftsX or envC produces viable bacteria that are highly filamentous due to defective cell division. Transmission electron and cryo-electron microscopy revealed that the Δ ftsX and Δ envC mutant cells remain joined with apparent constriction, and scanning electron microscopy (EM) uncovered a smooth cell surface without the microfolds present in wild-type cells. FtsX and EnvC proteins interact with each other as well as a common set of interacting partners, many with unknown function. Last, biofilm development is altered when cell division is blocked by MinC overproduction; however, unlike the phenotypes of Δ ftsX and Δ envC mutants, a weakly adherent biofilm is formed, and the wild-type rugged cell surface is maintained. Therefore, FtsX and EnvC may perform novel functions in Fusobacterium cell biology. This is the first report of an unbiased approach to uncover genetic determinants of fusobacterial biofilm development. It points to an intriguing link among cytokinesis, cell surface dynamics, and biofilm formation, whose molecular underpinnings remain to be elucidated. IMPORTANCE Little is known about the virulence mechanisms and associated factors in F. nucleatum , due mainly to the lack of convenient genetic tools for this organism. We employed two efficient genetic strategies to identify F. nucleatum biofilm-defective mutants, revealing FtsX and EnvC among seven biofilm-associated factors. Electron microscopy established cell division defects of the Δ ftsX and Δ envC mutants, accompanied with a smooth cell surface, unlike the microfold, rugged appearance of wild-type bacteria. Proteomic studies demonstrated that FtsX and EnvC interact with each other as well as a set of common and unique interacting proteins, many with unknown functions. Importantly, blocking cell division by MinC overproduction led to formation of a weakly adherent biofilm, without alteration of the wild-type cell surface. Thus, this work links cell division and surface dynamics to biofilm development and lays a foundation for future genetic and biochemical investigations of basic cellular processes in this clinically significant pathogen. Copyright © 2018 Wu et al.

Reproductive dynamics of Pacific sanddab, Citharichthys sordidus, off the central coast of California

NASA Astrophysics Data System (ADS)

Lefebvre, Lyndsey S.; Payne, Amber M.; Field, John C.

2016-01-01

Female Pacific sanddab were collected from the Monterey Bay, California to describe their reproductive strategy and annual reproductive cycle, as well as to estimate length at maturity, fecundity, spawning fraction (SF), and spawning interval (SI). Captive females were held to examine degradation of spawning markers and confirmed the biological spawning capabilities of the species. The reproductive season extended from May through January, as determined through macroscopic and histological examination of ovaries. Oocyte development was asynchronous, and an indeterminate fecundity pattern was displayed. Absolute and relative batch fecundity values were variable (means = 6663 eggs and 54 eggs g- 1 somatic weight, respectively) and significantly related to maternal length. During the period of highest reproductive activity, SF ranged from 0.42 to 0.98, suggesting some females were spawning on a daily basis. Monthly SF and SI were related to length, with smaller females having a truncated season and lower SF compared to larger females. Lengths at 50% (119 mm) and 95% (149 mm) maturity showed a downward shift relative to the 1940s, though the magnitude and cause of this shift remain unknown. This study highlights the importance of considering demographic shifts and size-related dynamics when modeling a stock's reproductive potential.

Offline memory reprocessing: involvement of the brain's default network in spontaneous thought processes.

PubMed

Wang, Kun; Yu, Chunshui; Xu, Lijuan; Qin, Wen; Li, Kuncheng; Xu, Lin; Jiang, Tianzi

2009-01-01

Spontaneous thought processes (STPs), also called daydreaming or mind-wandering, occur ubiquitously in daily life. However, the functional significance of STPs remains largely unknown. Using functional magnetic resonance imaging (fMRI), we first identified an STPs-network whose activity was positively correlated with the subjects' tendency of having STPs during a task-free state. The STPs-network was then found to be strongly associated with the default network, which has previously been established as being active during the task-free state. Interestingly, we found that offline reprocessing of previously memorized information further increased the activity of the STPs-network regions, although during a state with less STPs. In addition, we found that the STPs-network kept a dynamic balance between functional integration and functional separation among its component regions to execute offline memory reprocessing in STPs. These findings strengthen a view that offline memory reprocessing and STPs share the brain's default network, and thus implicate that offline memory reprocessing may be a predetermined function of STPs. This supports the perspective that memory can be consolidated and modified during STPs, and thus gives rise to a dynamic behavior dependent on both previous external and internal experiences.

Single molecule transcription factor dynamics in the syncytial Drosophila embryo

NASA Astrophysics Data System (ADS)

Darzacq, Xavier

During early development in the Drosophila embryo, cell fates are determined over the course of just 2 hours with exquisite spatio-temoral precision. One of the key regulators of this process is the transcription factor Bicoid which forms a concentration gradient across the long axis of the embryo. Although Bicoids' primary role is activation at the anterior, where concentrations are highest, it is also known to play a role in the posterior where there are only 100s of molecules per nucleus. Understanding how Bicoid can find its target at such low concentrations has remained intractable, largely due to the inability to perform single molecule imaging in the context of the developing embryo. Here we use lattice light sheet microscopy to overcome the technical barriers of sample thickness and auto-fluorescence to characterize the single molecule dynamics of Bicoid. We find that off-rates do not vary across the embryo and that instead the on-rates are modulated through the formation of clusters that enrich local concentration. This data is contrary to the current concentration dependent model of Bicoid function since local concentration within the nucleus is now a regulated parameter and suggests a previously unknown mechanism for regulation at extremely low concentrations.

Cell reprogramming modelled as transitions in a hierarchy of cell cycles

NASA Astrophysics Data System (ADS)

Hannam, Ryan; Annibale, Alessia; Kühn, Reimer

2017-10-01

We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell lineages. Although reprogramming has been demonstrated experimentally, much of the underlying processes governing cell fate decisions remain unknown. This work aims to bridge this gap by modelling cell types as a set of hierarchically related dynamical attractors representing cell cycles. Stages of the cell cycle are characterised by the configuration of gene expression levels, and reprogramming corresponds to triggering transitions between such configurations. Two mechanisms were found for reprogramming in a two level hierarchy: cycle specific perturbations and a noise induced switching. The former corresponds to a directed perturbation that induces a transition into a cycle-state of a different cell type in the potency hierarchy (mainly a stem cell) whilst the latter is a priori undirected and could be induced, e.g. by a (stochastic) change in the cellular environment. These reprogramming protocols were found to be effective in large regimes of the parameter space and make specific predictions concerning reprogramming dynamics which are broadly in line with experimental findings.

Selective Efficacy of Static and Dynamic Imagery in Different States of Physical Fatigue.

PubMed

Kanthack, Thiago Ferreira Dias; Guillot, Aymeric; Altimari, Leandro Ricardo; Nunez Nagy, Susana; Collet, Christian; Di Rienzo, Franck

2016-01-01

There is compelling evidence that motor imagery contributes to improved motor performance, and recent work showed that dynamic motor imagery (dMI) might provide additional benefits by comparison with traditional MI practice. However, the efficacy of motor imagery in different states of physical fatigue remains largely unknown, especially as imagery accuracy may be hampered by the physical fatigue states elicited by training. We investigated the effect of static motor imagery (sMI) and dMI on free-throw accuracy in 10 high-level basketball athletes, both in a non-fatigued state (Experiment 1) and immediately after an incremental running test completed until exhaustion (20 m shuttle run-test-Experiment 2). We collected perceived exhaustion and heart rate to quantify the subjective experience of fatigue and energy expenditure. We found that dMI brought better shooting performance than sMI, except when athletes were physically exhausted. These findings shed light on the conditions eliciting optimal use of sMI and dMI. In particular, considering that the current physical state affects body representation, performing dMI under fatigue may result in mismatches between actual and predicted body states.

Trophic groups and modules: two levels of group detection in food webs

PubMed Central

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-01-01

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom–top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. PMID:25878127

Dynamic Model Predicting Overweight, Obesity, and Extreme Obesity Prevalence Trends

PubMed Central

Thomas, Diana M.; Weedermann, Marion; Fuemmeler, Bernard F.; Martin, Corby K.; Dhurandhar, Nikhil V.; Bredlau, Carl; Heymsfield, Steven B.; Ravussin, Eric; Bouchard, Claude

2013-01-01

Objective Obesity prevalence in the United States (US) appears to be leveling, but the reasons behind the plateau remain unknown. Mechanistic insights can be provided from a mathematical model. The objective of this study is to model known multiple population parameters associated with changes in body mass index (BMI) classes and to establish conditions under which obesity prevalence will plateau. Design and Methods A differential equation system was developed that predicts population-wide obesity prevalence trends. The model considers both social and non-social influences on weight gain, incorporates other known parameters affecting obesity trends, and allows for country specific population growth. Results The dynamic model predicts that: obesity prevalence is a function of birth rate and the probability of being born in an obesogenic environment; obesity prevalence will plateau independent of current prevention strategies; and the US prevalence of obesity, overweight, and extreme obesity will plateau by about 2030 at 28%, 32%, and 9%, respectively. Conclusions The US prevalence of obesity is stabilizing and will plateau, independent of current preventative strategies. This trend has important implications in accurately evaluating the impact of various anti-obesity strategies aimed at reducing obesity prevalence. PMID:23804487

A strong magnetic field around the supermassive black hole at the centre of the Galaxy.

PubMed

Eatough, R P; Falcke, H; Karuppusamy, R; Lee, K J; Champion, D J; Keane, E F; Desvignes, G; Schnitzeler, D H F M; Spitler, L G; Kramer, M; Klein, B; Bassa, C; Bower, G C; Brunthaler, A; Cognard, I; Deller, A T; Demorest, P B; Freire, P C C; Kraus, A; Lyne, A G; Noutsos, A; Stappers, B; Wex, N

2013-09-19

Earth's nearest candidate supermassive black hole lies at the centre of the Milky Way. Its electromagnetic emission is thought to be powered by radiatively inefficient accretion of gas from its environment, which is a standard mode of energy supply for most galactic nuclei. X-ray measurements have already resolved a tenuous hot gas component from which the black hole can be fed. The magnetization of the gas, however, which is a crucial parameter determining the structure of the accretion flow, remains unknown. Strong magnetic fields can influence the dynamics of accretion, remove angular momentum from the infalling gas, expel matter through relativistic jets and lead to synchrotron emission such as that previously observed. Here we report multi-frequency radio measurements of a newly discovered pulsar close to the Galactic Centre and show that the pulsar's unusually large Faraday rotation (the rotation of the plane of polarization of the emission in the presence of an external magnetic field) indicates that there is a dynamically important magnetic field near the black hole. If this field is accreted down to the event horizon it provides enough magnetic flux to explain the observed emission--from radio to X-ray wavelengths--from the black hole.

A strong magnetic field around the supermassive black hole at the centre of the Galaxy

NASA Astrophysics Data System (ADS)

Eatough, R. P.; Falcke, H.; Karuppusamy, R.; Lee, K. J.; Champion, D. J.; Keane, E. F.; Desvignes, G.; Schnitzeler, D. H. F. M.; Spitler, L. G.; Kramer, M.; Klein, B.; Bassa, C.; Bower, G. C.; Brunthaler, A.; Cognard, I.; Deller, A. T.; Demorest, P. B.; Freire, P. C. C.; Kraus, A.; Lyne, A. G.; Noutsos, A.; Stappers, B.; Wex, N.

2013-09-01

Earth's nearest candidate supermassive black hole lies at the centre of the Milky Way. Its electromagnetic emission is thought to be powered by radiatively inefficient accretion of gas from its environment, which is a standard mode of energy supply for most galactic nuclei. X-ray measurements have already resolved a tenuous hot gas component from which the black hole can be fed. The magnetization of the gas, however, which is a crucial parameter determining the structure of the accretion flow, remains unknown. Strong magnetic fields can influence the dynamics of accretion, remove angular momentum from the infalling gas, expel matter through relativistic jets and lead to synchrotron emission such as that previously observed. Here we report multi-frequency radio measurements of a newly discovered pulsar close to the Galactic Centre and show that the pulsar's unusually large Faraday rotation (the rotation of the plane of polarization of the emission in the presence of an external magnetic field) indicates that there is a dynamically important magnetic field near the black hole. If this field is accreted down to the event horizon it provides enough magnetic flux to explain the observed emission--from radio to X-ray wavelengths--from the black hole.

A new structural framework for integrating replication protein A into DNA processing machinery

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

Brosey, Chris A; Yan, Chunli; Tsutakawa, Susan E

2013-01-01

By coupling the protection and organization of ssDNA with the recruitment and alignment of DNA processing factors, Replication Protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA manages to coordinate the biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA s DNA binding activity, combining small-angle x-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA s DNA-binding core. It has been long held that RPA engages ssDNA in three stages, but our data reveal that RPA undergoes two rather than threemore » transitions as it binds ssDNA. In contrast to previous models, RPA is more compact when fully engaged on 20-30 nucleotides of ssDNA than when DNA-free, and there is no evidence for significant population of a highly compacted structure in the initial 8-10 nucleotide binding mode. These results provide a new framework for understanding the integration of ssDNA into DNA processing machinery and how binding partners may manipulate RPA architecture to gain access to the substrate.« less

Coevolutionary dynamics of aspiration and strategy in spatial repeated public goods games

NASA Astrophysics Data System (ADS)

Wu, Te; Fu, Feng; Wang, Long

2018-06-01

The evolutionary dynamics remain largely unknown for spatial populations where individuals are more likely to interact repeatedly. Under this settings, individuals can make their decisions to cooperate or not based on the decisions previously adopted by others in their neighborhoods. Using repeated public goods game, we construct a spatial model and use a statistical physics approach to study the coevolutionary dynamics of aspiration and strategy. Individuals each have an aspiration towards the groups they are involved. According to the outcome of each group, individuals have assessment of whether their aspirations are satisfied. If satisfied, they cooperate next round. Otherwise, they switch to defecting. Results show threshold phenomenon for harsh collective dilemma: cooperators sticking to high levels of aspiration can prevail over defectors, while cooperators with other levels are invariably wiped out. When the collective dilemma is relaxed, cooperation is greatly facilitated by inducing a high level of diversity of aspiration. Snapshots further show the spatial patterns of how this coevolutionary process leads to the emergence of an optimal solution associated with aspiration level, whose corresponding strategy are most prevalent. This optimal solution lies in one and the highest aspiration level allowed, and depends on the intensity of the social dilemma. By removing the memory effect, our results also confirm that repeated interactions can promote cooperation, but to a limited degree.

A new structural framework for integrating replication protein A into DNA processing machinery

PubMed Central

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.

2013-01-01

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA’s DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA’s DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways. PMID:23303776

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

Effect of arm swing strategy on local dynamic stability of human gait.

PubMed

Punt, Michiel; Bruijn, Sjoerd M; Wittink, Harriet; van Dieën, Jaap H

2015-02-01

Falling causes long term disability and can even lead to death. Most falls occur during gait. Therefore improving gait stability might be beneficial for people at risk of falling. Recently arm swing has been shown to influence gait stability. However at present it remains unknown which mode of arm swing creates the most stable gait. To examine how different modes of arm swing affect gait stability. Ten healthy young male subjects volunteered for this study. All subjects walked with four different arm swing instructions at seven different gait speeds. The Xsens motion capture suit was used to capture gait kinematics. Basic gait parameters, variability and stability measures were calculated. We found an increased stability in the medio-lateral direction with excessive arm swing in comparison to normal arm swing at all gait speeds. Moreover, excessive arm swing increased stability in the anterior-posterior and vertical direction at low gait speeds. Ipsilateral and inphase arm swing did not differ compared to a normal arm swing. Excessive arm swing is a promising gait manipulation to improve local dynamic stability. For excessive arm swing in the ML direction there appears to be converging evidence. The effect of excessive arm swing on more clinically relevant groups like the more fall prone elderly or stroke survivors is worth further investigating. Excessive arm swing significantly increases local dynamic stability of human gait. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of acoustic waves on stick-slip in granular media and implications for earthquakes

USGS Publications Warehouse

Johnson, P.A.; Savage, H.; Knuth, M.; Gomberg, J.; Marone, Chris

2008-01-01

It remains unknown how the small strains induced by seismic waves can trigger earthquakes at large distances, in some cases thousands of kilometres from the triggering earthquake, with failure often occurring long after the waves have passed. Earthquake nucleation is usually observed to take place at depths of 10-20 km, and so static overburden should be large enough to inhibit triggering by seismic-wave stress perturbations. To understand the physics of dynamic triggering better, as well as the influence of dynamic stressing on earthquake recurrence, we have conducted laboratory studies of stick-slip in granular media with and without applied acoustic vibration. Glass beads were used to simulate granular fault zone material, sheared under constant normal stress, and subject to transient or continuous perturbation by acoustic waves. Here we show that small-magnitude failure events, corresponding to triggered aftershocks, occur when applied sound-wave amplitudes exceed several microstrain. These events are frequently delayed or occur as part of a cascade of small events. Vibrations also cause large slip events to be disrupted in time relative to those without wave perturbation. The effects are observed for many large-event cycles after vibrations cease, indicating a strain memory in the granular material. Dynamic stressing of tectonic faults may play a similar role in determining the complexity of earthquake recurrence. ??2007 Nature Publishing Group.

Effects of Telecoupling on Global Vegetation Dynamics

NASA Astrophysics Data System (ADS)

Viña, A.; Liu, J.

2016-12-01

With the ever increasing trend in telecoupling processes, such as international trade, all countries around the world are becoming more interdependent. However, the effects of this growing interdependence on vegetation (e.g., shifts in the geographic extent and distribution) remain unknown even though vegetation dynamics are crucially important for food production, carbon sequestration, provision of other ecosystem services, and biodiversity conservation. In this study we evaluate the effects of international trade on the spatio-temporal trajectories of vegetation at national and global scales, using vegetation index imagery collected over more than three decades by the Advanced Very High Resolution Radiometer (AVHRR) satellite sensor series together with concurrent national and international data on international trade (and its associated movement of people, goods, services and information). The spatio-temporal trajectories of vegetation are obtained using the scale of fluctuation technique, which is based on the decomposition of the AVHRR image time series to obtain information on its spatial dependence structure over time. Similar to the correlation length, the scale of fluctuation corresponds to the range over which fluctuations in the vegetation index are spatially correlated. Results indicate that global vegetation has changed drastically over the last three decades. These changes are not uniform across space, with hotspots in active trading countries. This study not only has direct implications for understanding global vegetation dynamics, but also sheds important insights on the complexity of human-nature interactions across telecoupled systems.

Do invasive quagga mussels alter CO2 dynamics in the Laurentian Great Lakes?

NASA Astrophysics Data System (ADS)

Lin, Peng; Guo, Laodong

2016-12-01

The Laurentian Great Lakes have experienced unprecedented ecological and environmental changes, especially after the introduction of invasive quagga mussel (Dreissena rostriformis bugensis). While impacts on ecological functions have been widely recognized, the response of carbon dynamics to invasive species remains largely unknown. We report new CO2 data showing significant increases in pCO2 (up to 800 μatm in Lake Michigan) and CO2 emission fluxes in most of the Great Lakes compared to those prior to or during the early stage of the colonization of invasive quagga mussels. The increased CO2 supersaturation is most prominent in Lakes Huron and Michigan, followed by Lakes Ontario and Erie, but no evident change was observed in Lake Superior. This trend mirrors the infestation extent of invasive quagga mussels in the Great Lakes and is consistent with the decline in primary production and increase in water clarity observed pre- and post-Dreissena introduction, revealing a close linkage between invasive species and carbon dynamics. The Great Lakes have become a significant CO2 source to the atmosphere, emitting >7.7 ± 1.0 Tg-C annually, which is higher than the organic carbon burial rate in global inland-seas and attesting to the significant role of the Laurentian Great Lakes in regional/global CO2 budget and cycling.

Earthworms are associated with subpopulations of Gammaproteobacteria irrespective of the total soil microbiota composition and stability.

PubMed

Fjøsne, Trine; Myromslien, Frøydis D; Wilson, Robert C; Rudi, Knut

2018-05-01

Soil represents one of the most complex microbial ecosystems on earth. It is well-known that invertebrates such as earthworms have a major impact on transformations of organic material in soil, while their effect on the soil microbiota remains largely unknown. The aim of our work was therefore to investigate the association of earthworms with temporal stability, composition and diversity in two soil microbiota experimental series. We found that earthworms were consistently associated with an increase in subgroups of Gammaproteobacteria, despite major differences in microbiota composition and temporal stability across the experimental series. Our results therefore suggest that earthworms can affect subpopulation dynamics in the soil microbiota, irrespective of the total microbiota composition. If the soil microbiota is comprised of independent microbiota components, this can contribute to our general understanding of the complexity of the soil microbiota.

Internal amino acid state modulates yeast taste neurons to support protein homeostasis in Drosophila

PubMed Central

Itskov, Pavel M; Baltazar, Célia; Moreira, José-Maria

2018-01-01

To optimize fitness, animals must dynamically match food choices to their current needs. For drosophilids, yeast fulfills most dietary protein and micronutrient requirements. While several yeast metabolites activate known gustatory receptor neurons (GRNs) in Drosophila melanogaster, the chemosensory channels mediating yeast feeding remain unknown. Here we identify a class of proboscis GRNs required for yeast intake. Within this class, taste peg GRNs are specifically required to sustain yeast feeding. Sensillar GRNs, however, mediate feeding initiation. Furthermore, the response of yeast GRNs, but not sweet GRNs, is enhanced following deprivation from amino acids, providing a potential basis for protein-specific appetite. Although nutritional and reproductive states synergistically increase yeast appetite, reproductive state acts independently of nutritional state, modulating processing downstream of GRNs. Together, these results suggest that different internal states act at distinct levels of a dedicated gustatory circuit to elicit nutrient-specific appetites towards a complex, ecologically relevant protein source. PMID:29393045

Tagging the neuronal entrainment to beat and meter.

PubMed

Nozaradan, Sylvie; Peretz, Isabelle; Missal, Marcus; Mouraux, André

2011-07-13

Feeling the beat and meter is fundamental to the experience of music. However, how these periodicities are represented in the brain remains largely unknown. Here, we test whether this function emerges from the entrainment of neurons resonating to the beat and meter. We recorded the electroencephalogram while participants listened to a musical beat and imagined a binary or a ternary meter on this beat (i.e., a march or a waltz). We found that the beat elicits a sustained periodic EEG response tuned to the beat frequency. Most importantly, we found that meter imagery elicits an additional frequency tuned to the corresponding metric interpretation of this beat. These results provide compelling evidence that neural entrainment to beat and meter can be captured directly in the electroencephalogram. More generally, our results suggest that music constitutes a unique context to explore entrainment phenomena in dynamic cognitive processing at the level of neural networks.

High damage tolerance of electrochemically lithiated silicon

PubMed Central

Wang, Xueju; Fan, Feifei; Wang, Jiangwei; Wang, Haoran; Tao, Siyu; Yang, Avery; Liu, Yang; Beng Chew, Huck; Mao, Scott X.; Zhu, Ting; Xia, Shuman

2015-01-01

Mechanical degradation and resultant capacity fade in high-capacity electrode materials critically hinder their use in high-performance rechargeable batteries. Despite tremendous efforts devoted to the study of the electro–chemo–mechanical behaviours of high-capacity electrode materials, their fracture properties and mechanisms remain largely unknown. Here we report a nanomechanical study on the damage tolerance of electrochemically lithiated silicon. Our in situ transmission electron microscopy experiments reveal a striking contrast of brittle fracture in pristine silicon versus ductile tensile deformation in fully lithiated silicon. Quantitative fracture toughness measurements by nanoindentation show a rapid brittle-to-ductile transition of fracture as the lithium-to-silicon molar ratio is increased to above 1.5. Molecular dynamics simulations elucidate the mechanistic underpinnings of the brittle-to-ductile transition governed by atomic bonding and lithiation-induced toughening. Our results reveal the high damage tolerance in amorphous lithium-rich silicon alloys and have important implications for the development of durable rechargeable batteries. PMID:26400671

Potential in vivo roles of nucleic acid triple-helices

PubMed Central

Buske, Fabian A

2011-01-01

The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown. There is considerable albeit circumstantial evidence for the existence of nucleic triplexes in vivo and their potential participation in a variety of biological processes including chromatin organization, DNA repair, transcriptional regulation and RNA processing has been investigated in a number of studies to date. There is also a range of possible mechanisms to regulate triplex formation through differential expression of triplex-forming RNAs, alteration of chromatin accessibility, sequence unwinding and nucleotide modifications. With the advent of next generation sequencing technology combined with targeted approaches to isolate triplexes, it is now possible to survey triplex formation with respect to their genomic context, abundance and dynamical changes during differentiation and development, which may open up new vistas in understanding genome biology and gene regulation. PMID:21525785

Spatial computation of intratumoral T cells correlates with survival of patients with pancreatic cancer.

PubMed

Carstens, Julienne L; Correa de Sampaio, Pedro; Yang, Dalu; Barua, Souptik; Wang, Huamin; Rao, Arvind; Allison, James P; LeBleu, Valerie S; Kalluri, Raghu

2017-04-27

The exact nature and dynamics of pancreatic ductal adenocarcinoma (PDAC) immune composition remains largely unknown. Desmoplasia is suggested to polarize PDAC immunity. Therefore, a comprehensive evaluation of the composition and distribution of desmoplastic elements and T-cell infiltration is necessary to delineate their roles. Here we develop a novel computational imaging technology for the simultaneous evaluation of eight distinct markers, allowing for spatial analysis of distinct populations within the same section. We report a heterogeneous population of infiltrating T lymphocytes. Spatial distribution of cytotoxic T cells in proximity to cancer cells correlates with increased overall patient survival. Collagen-I and αSMA + fibroblasts do not correlate with paucity in T-cell accumulation, suggesting that PDAC desmoplasia may not be a simple physical barrier. Further exploration of this technology may improve our understanding of how specific stromal composition could impact T-cell activity, with potential impact on the optimization of immune-modulatory therapies.

Social contagions on correlated multiplex networks

NASA Astrophysics Data System (ADS)

Wang, Wei; Cai, Meng; Zheng, Muhua

2018-06-01

The existence of interlayer degree correlations has been disclosed by abundant multiplex network analysis. However, how they impose on the dynamics of social contagions are remain largely unknown. In this paper, we propose a non-Markovian social contagion model in multiplex networks with inter-layer degree correlations to delineate the behavior spreading, and develop an edge-based compartmental (EBC) theory to describe the model. We find that multiplex networks promote the final behavior adoption size. Remarkably, it can be observed that the growth pattern of the final behavior adoption size, versus the behavioral information transmission probability, changes from discontinuous to continuous once decreasing the behavior adoption threshold in one layer. We finally unravel that the inter-layer degree correlations play a role on the final behavior adoption size but have no effects on the growth pattern, which is coincidence with our prediction by using the suggested theory.

Understanding soft glassy materials using an energy landscape approach

NASA Astrophysics Data System (ADS)

Hwang, Hyun Joo; Riggleman, Robert A.; Crocker, John C.

2016-09-01

Many seemingly different soft materials--such as soap foams, mayonnaise, toothpaste and living cells--display strikingly similar viscoelastic behaviour. A fundamental physical understanding of such soft glassy rheology and how it can manifest in such diverse materials, however, remains unknown. Here, by using a model soap foam consisting of compressible spherical bubbles, whose sizes slowly evolve and whose collective motion is simply dictated by energy minimization, we study the foam's dynamics as it corresponds to downhill motion on an energy landscape function spanning a high-dimensional configuration space. We find that these downhill paths, when viewed in this configuration space, are, surprisingly, fractal. The complex behaviour of our model, including power-law rheology and non-diffusive bubble motion and avalanches, stems directly from the fractal dimension and energy function of these paths. Our results suggest that ubiquitous soft glassy rheology may be a consequence of emergent fractal geometry in the energy landscapes of many complex fluids.

Microtubules self-repair in response to mechanical stress

PubMed Central

Schaedel, Laura; John, Karin; Gaillard, Jérémie; Nachury, Maxence V.; Blanchoin, Laurent; Théry, Manuel

2015-01-01

Microtubules - which define the shape of axons, cilia and flagella, and provide tracks for intracellular transport - can be highly bent by intracellular forces, and microtubule structure and stiffness are thought to be affected by physical constraints. Yet how microtubules tolerate the vast forces exerted on them remains unknown. Here, by using a microfluidic device, we show that microtubule stiffness decreases incrementally with each cycle of bending and release. Similar to other cases of material fatigue, the concentration of mechanical stresses on pre-existing defects in the microtubule lattice is responsible for the generation of larger damages, which further decrease microtubule stiffness. Strikingly, damaged microtubules were able to incorporate new tubulin dimers into their lattice and recover their initial stiffness. Our findings demonstrate that microtubules are ductile materials with self-healing properties, that their dynamics does not exclusively occur at their ends, and that their lattice plasticity enables the microtubules' adaptation to mechanical stresses. PMID:26343914

Neuronal pattern separation in the olfactory bulb improves odor discrimination learning

PubMed Central

Lagier, Samuel; Begnaud, Frédéric; Rodriguez, Ivan; Carleton, Alan

2015-01-01

Neuronal pattern separation is thought to enable the brain to disambiguate sensory stimuli with overlapping features thereby extracting valuable information. In the olfactory system, it remains unknown whether pattern separation acts as a driving force for sensory discrimination and the learning thereof. Here we show that overlapping odor-evoked input patterns to the mouse olfactory bulb (OB) are dynamically reformatted in the network at the timescale of a single breath, giving rise to separated patterns of activity in ensemble of output neurons (mitral/tufted cells; M/T). Strikingly, the extent of pattern separation in M/T assemblies predicts behavioral discrimination performance during the learning phase. Furthermore, exciting or inhibiting GABAergic OB interneurons, using optogenetics or pharmacogenetics, altered pattern separation and thereby odor discrimination learning in a bidirectional way. In conclusion, we propose that the OB network can act as a pattern separator facilitating olfactory stimuli distinction, a process that is sculpted by synaptic inhibition. PMID:26301325

Optimal trajectories of brain state transitions

PubMed Central

Gu, Shi; Betzel, Richard F.; Mattar, Marcelo G.; Cieslak, Matthew; Delio, Philip R.; Grafton, Scott T.; Pasqualetti, Fabio; Bassett, Danielle S.

2017-01-01

The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how white matter structure constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question by drawing on recent advances in network control theory to model the underlying mechanisms of brain state transitions as elicited by the collective control of region sets. We find that previously identified attention and executive control systems are poised to affect a broad array of state transitions that cannot easily be classified by traditional engineering-based notions of control. This theoretical versatility comes with a vulnerability to injury. In patients with mild traumatic brain injury, we observe a loss of specificity in putative control processes, suggesting greater susceptibility to neurophysiological noise. These results offer fundamental insights into the mechanisms driving brain state transitions in healthy cognition and their alteration following injury. PMID:28088484

Growth and splitting of neural sequences in songbird vocal development

PubMed Central

Okubo, Tatsuo S.; Mackevicius, Emily L.; Payne, Hannah L.; Lynch, Galen F.; Fee, Michale S.

2015-01-01

Neural sequences are a fundamental feature of brain dynamics underlying diverse behaviors, but the mechanisms by which they develop during learning remain unknown. Songbirds learn vocalizations composed of syllables; in adult birds, each syllable is produced by a different sequence of action potential bursts in the premotor cortical area HVC. Here we carried out recordings of large populations of HVC neurons in singing juvenile birds throughout learning to examine the emergence of neural sequences. Early in vocal development, HVC neurons begin producing rhythmic bursts, temporally locked to a ‘prototype’ syllable. Different neurons are active at different latencies relative to syllable onset to form a continuous sequence. Through development, as new syllables emerge from the prototype syllable, initially highly overlapping burst sequences become increasingly distinct. We propose a mechanistic model in which multiple neural sequences can emerge from the growth and splitting of a common precursor sequence. PMID:26618871

Microtubules self-repair in response to mechanical stress

NASA Astrophysics Data System (ADS)

Schaedel, Laura; John, Karin; Gaillard, Jérémie; Nachury, Maxence V.; Blanchoin, Laurent; Théry, Manuel

2015-11-01

Microtubules--which define the shape of axons, cilia and flagella, and provide tracks for intracellular transport--can be highly bent by intracellular forces, and microtubule structure and stiffness are thought to be affected by physical constraints. Yet how microtubules tolerate the vast forces exerted on them remains unknown. Here, by using a microfluidic device, we show that microtubule stiffness decreases incrementally with each cycle of bending and release. Similar to other cases of material fatigue, the concentration of mechanical stresses on pre-existing defects in the microtubule lattice is responsible for the generation of more extensive damage, which further decreases microtubule stiffness. Strikingly, damaged microtubules were able to incorporate new tubulin dimers into their lattice and recover their initial stiffness. Our findings demonstrate that microtubules are ductile materials with self-healing properties, that their dynamics does not exclusively occur at their ends, and that their lattice plasticity enables the microtubules' adaptation to mechanical stresses.

Microtubules self-repair in response to mechanical stress.

PubMed

Schaedel, Laura; John, Karin; Gaillard, Jérémie; Nachury, Maxence V; Blanchoin, Laurent; Théry, Manuel

2015-11-01

Microtubules--which define the shape of axons, cilia and flagella, and provide tracks for intracellular transport--can be highly bent by intracellular forces, and microtubule structure and stiffness are thought to be affected by physical constraints. Yet how microtubules tolerate the vast forces exerted on them remains unknown. Here, by using a microfluidic device, we show that microtubule stiffness decreases incrementally with each cycle of bending and release. Similar to other cases of material fatigue, the concentration of mechanical stresses on pre-existing defects in the microtubule lattice is responsible for the generation of more extensive damage, which further decreases microtubule stiffness. Strikingly, damaged microtubules were able to incorporate new tubulin dimers into their lattice and recover their initial stiffness. Our findings demonstrate that microtubules are ductile materials with self-healing properties, that their dynamics does not exclusively occur at their ends, and that their lattice plasticity enables the microtubules' adaptation to mechanical stresses.

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

PubMed Central

Roux, Benoît; Weare, Jonathan

2013-01-01

An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method. PMID:23464140

Structural basis of mitochondrial dysfunction in response to cytochrome c phosphorylation at tyrosine 48

PubMed Central

Moreno-Beltrán, Blas; Guerra-Castellano, Alejandra; Del Conte, Rebecca; García-Mauriño, Sofía M.; Díaz-Moreno, Sofía; González-Arzola, Katiuska; Santos-Ocaña, Carlos; Velázquez-Campoy, Adrián; De la Rosa, Miguel A.; Turano, Paola; Díaz-Moreno, Irene

2017-01-01

Regulation of mitochondrial activity allows cells to adapt to changing conditions and to control oxidative stress, and its dysfunction can lead to hypoxia-dependent pathologies such as ischemia and cancer. Although cytochrome c phosphorylation—in particular, at tyrosine 48—is a key modulator of mitochondrial signaling, its action and molecular basis remain unknown. Here we mimic phosphorylation of cytochrome c by replacing tyrosine 48 with p-carboxy-methyl-l-phenylalanine (pCMF). The NMR structure of the resulting mutant reveals significant conformational shifts and enhanced dynamics around pCMF that could explain changes observed in its functionality: The phosphomimetic mutation impairs cytochrome c diffusion between respiratory complexes, enhances hemeprotein peroxidase and reactive oxygen species scavenging activities, and hinders caspase-dependent apoptosis. Our findings provide a framework to further investigate the modulation of mitochondrial activity by phosphorylated cytochrome c and to develop novel therapeutic approaches based on its prosurvival effects. PMID:28348229

Strongly anisotropic spin relaxation in graphene-transition metal dichalcogenide heterostructures at room temperature

NASA Astrophysics Data System (ADS)

Benítez, L. Antonio; Sierra, Juan F.; Savero Torres, Williams; Arrighi, Aloïs; Bonell, Frédéric; Costache, Marius V.; Valenzuela, Sergio O.

2018-03-01

A large enhancement in the spin-orbit coupling of graphene has been predicted when interfacing it with semiconducting transition metal dichalcogenides. Signatures of such an enhancement have been reported, but the nature of the spin relaxation in these systems remains unknown. Here, we unambiguously demonstrate anisotropic spin dynamics in bilayer heterostructures comprising graphene and tungsten or molybdenum disulphide (WS2, MoS2). We observe that the spin lifetime varies over one order of magnitude depending on the spin orientation, being largest when the spins point out of the graphene plane. This indicates that the strong spin-valley coupling in the transition metal dichalcogenide is imprinted in the bilayer and felt by the propagating spins. These findings provide a rich platform to explore coupled spin-valley phenomena and offer novel spin manipulation strategies based on spin relaxation anisotropy in two-dimensional materials.

Identification of structural motifs as tunneling two-level systems in amorphous alumina at low temperatures

NASA Astrophysics Data System (ADS)

Paz, Alejandro Pérez; Lebedeva, Irina V.; Tokatly, Ilya V.; Rubio, Angel

2014-12-01

One of the most accepted models that describe the anomalous thermal behavior of amorphous materials at temperatures below 1 K relies on the quantum mechanical tunneling of atoms between two nearly equivalent potential energy wells forming a two-level system (TLS). Indirect evidence for TLSs is widely available. However, the atomistic structure of these TLSs remains an unsolved topic in the physics of amorphous materials. Here, using classical molecular dynamics, we found several hitherto unknown bistable structural motifs that may be key to understanding the anomalous thermal properties of amorphous alumina at low temperatures. We show through free energy profiles that the complex potential energy surface can be reduced to canonical TLSs. The tunnel splitting predicted from instanton theory, the number density, dipole moment, and coupling to external strain of the discovered motifs are consistent with experiments.

Emotional body-word conflict evokes enhanced n450 and slow potential.

PubMed

Ma, Jianling; Liu, Chang; Zhong, Xin; Wang, Lu; Chen, Xu

2014-01-01

Emotional conflict refers to the influence of task irrelevant affective stimuli on current task set. Previously used emotional face-word tasks have produced certain electrophysiological phenomena, such as an enhanced N450 and slow potential; however, it remains unknown whether these effects emerge in other tasks. The present study used an emotional body-word conflict task to investigate the neural dynamics of emotional conflict as reflected by response time, accuracy, and event-related potentials, which were recorded with the aim of replicating the previously observed N450 and slow potential effect. Results indicated increased response time and decreased accuracy in the incongruent condition relative to the congruent condition, indicating a robust interference effect. Furthermore, the incongruent condition evoked pronounced N450 amplitudes and a more positive slow potential, which might be associated with conflict-monitoring and conflict resolution. The present findings extend our understanding of emotional conflict to the body-word domain.

Mechanism of Cytokinetic Contractile Ring Constriction in Fission Yeast

PubMed Central

Stachowiak, Matthew R.; Laplante, Caroline; Chin, Harvey F.; Guirao, Boris; Karatekin, Erdem; Pollard, Thomas D.; O’Shaughnessy, Ben

2014-01-01

SUMMARY Cytokinesis involves constriction of a contractile actomyosin ring. The mechanisms generating ring tension and setting the constriction rate remain unknown, since the organization of the ring is poorly characterized, its tension was rarely measured, and constriction is coupled to other processes. To isolate ring mechanisms we studied fission yeast protoplasts, where constriction occurs without the cell wall. Exploiting the absence of cell wall and actin cortex, we measured ring tension and imaged ring organization, which was dynamic and disordered. Computer simulations based on the amounts and biochemical properties of the key proteins showed that they spontaneously self-organize into a tension-generating bundle. Together with rapid component turnover, the self-organization mechanism continuously reassembles and remodels the constricting ring. Ring constriction depended on cell shape, revealing that the ring operates close to conditions of isometric tension. Thus, the fission yeast ring sets its own tension, but other processes set the constriction rate. PMID:24914559

Neuronal pattern separation in the olfactory bulb improves odor discrimination learning.

PubMed

Gschwend, Olivier; Abraham, Nixon M; Lagier, Samuel; Begnaud, Frédéric; Rodriguez, Ivan; Carleton, Alan

2015-10-01

Neuronal pattern separation is thought to enable the brain to disambiguate sensory stimuli with overlapping features, thereby extracting valuable information. In the olfactory system, it remains unknown whether pattern separation acts as a driving force for sensory discrimination and the learning thereof. We found that overlapping odor-evoked input patterns to the mouse olfactory bulb (OB) were dynamically reformatted in the network on the timescale of a single breath, giving rise to separated patterns of activity in an ensemble of output neurons, mitral/tufted (M/T) cells. Notably, the extent of pattern separation in M/T assemblies predicted behavioral discrimination performance during the learning phase. Furthermore, exciting or inhibiting GABAergic OB interneurons, using optogenetics or pharmacogenetics, altered pattern separation and thereby odor discrimination learning in a bidirectional way. In conclusion, we propose that the OB network can act as a pattern separator facilitating olfactory stimulus distinction, a process that is sculpted by synaptic inhibition.

Activation of VTA GABA neurons disrupts reward consumption

PubMed Central

van Zessen, Ruud; Phillips, Jana L.; Budygin, Evgeny A.; Stuber, Garret D.

2012-01-01

The activity of Ventral Tegmental Area (VTA) dopamine (DA) neurons promotes behavioral responses to rewards and environmental stimuli that predict them. VTA GABA inputs synapse directly onto DA neurons and may regulate DA neuronal activity to alter reward-related behaviors, however, the functional consequences of selective activation of VTA GABA neurons remains unknown. Here, we show that in vivo optogenetic activation of VTA GABA neurons disrupts reward consummatory behavior, but not conditioned anticipatory behavior in response to reward-predictive cues. In addition, direct activation of VTA GABA projections to the nucleus accumbens (NAc) resulted in detectable GABA release, but did not alter reward consumption. Furthermore, optogenetic stimulation of VTA GABA neurons directly suppressed the activity and excitability of neighboring DA neurons, as well as the release of DA in the NAc, suggesting that the dynamic interplay between VTA DA and GABA neurons can control the initiation and termination of reward-related behaviors. PMID:22445345

High damage tolerance of electrochemically lithiated silicon

NASA Astrophysics Data System (ADS)

Wang, Xueju; Fan, Feifei; Wang, Jiangwei; Wang, Haoran; Tao, Siyu; Yang, Avery; Liu, Yang; Beng Chew, Huck; Mao, Scott X.; Zhu, Ting; Xia, Shuman

2015-09-01

Mechanical degradation and resultant capacity fade in high-capacity electrode materials critically hinder their use in high-performance rechargeable batteries. Despite tremendous efforts devoted to the study of the electro-chemo-mechanical behaviours of high-capacity electrode materials, their fracture properties and mechanisms remain largely unknown. Here we report a nanomechanical study on the damage tolerance of electrochemically lithiated silicon. Our in situ transmission electron microscopy experiments reveal a striking contrast of brittle fracture in pristine silicon versus ductile tensile deformation in fully lithiated silicon. Quantitative fracture toughness measurements by nanoindentation show a rapid brittle-to-ductile transition of fracture as the lithium-to-silicon molar ratio is increased to above 1.5. Molecular dynamics simulations elucidate the mechanistic underpinnings of the brittle-to-ductile transition governed by atomic bonding and lithiation-induced toughening. Our results reveal the high damage tolerance in amorphous lithium-rich silicon alloys and have important implications for the development of durable rechargeable batteries.

The rise and fall of a human recombination hot spot.

PubMed

Jeffreys, Alec J; Neumann, Rita

2009-05-01

Human meiotic crossovers mainly cluster into narrow hot spots that profoundly influence patterns of haplotype diversity and that may also affect genome instability and sequence evolution. Hot spots also seem to be ephemeral, but processes of hot-spot activation and their subsequent evolutionary dynamics remain unknown. We now analyze the life cycle of a recombination hot spot. Sperm typing revealed a polymorphic hot spot that was activated in cis by a single base change, providing evidence for a primary sequence determinant necessary, though not sufficient, to activate recombination. This activating mutation occurred roughly 70,000 y ago and has persisted to the present, most likely fortuitously through genetic drift despite its systematic elimination by biased gene conversion. Nonetheless, this self-destructive conversion will eventually lead to hot-spot extinction. These findings define a subclass of highly transient hot spots and highlight the importance of understanding hot-spot turnover and how it influences haplotype diversity.

Large-Scale Experimental Planetary Science Meets Planetary Defense: Deorbiting an Asteroidal Satellite

NASA Technical Reports Server (NTRS)

Cintala, M. J.; Durda, D. D.; Housen, K. R.

2005-01-01

Other than remote-sensing and spacecraft-derived data, the only information that exists regarding the physical and chemical properties of asteroids is that inferred through calculations, numerical simulations, extrapolation of experiments, and meteorite studies. Our understanding of the dynamics of accretion of planetesimals, collisional disruption of asteroids, and the macroscopic, shock-induced modification of the surfaces of such small objects is also, for the most part, founded on similar inferences. While considerable strides have been made in improving the state of asteroid science, too many unknowns remain to assert that we understand the parameters necessary for the more practical problem of deflecting an asteroid or asteroid pair on an Earth-intersecting trajectory. Many of these deficiencies could be reduced or eliminated by intentionally deorbiting an asteroidal satellite and monitoring the resulting collision between it and the primary asteroid, a capability that is well within the limitations of current technology.

Transfer Entropy and Transient Limits of Computation

PubMed Central

Prokopenko, Mikhail; Lizier, Joseph T.

2014-01-01

Transfer entropy is a recently introduced information-theoretic measure quantifying directed statistical coherence between spatiotemporal processes, and is widely used in diverse fields ranging from finance to neuroscience. However, its relationships to fundamental limits of computation, such as Landauer's limit, remain unknown. Here we show that in order to increase transfer entropy (predictability) by one bit, heat flow must match or exceed Landauer's limit. Importantly, we generalise Landauer's limit to bi-directional information dynamics for non-equilibrium processes, revealing that the limit applies to prediction, in addition to retrodiction (information erasure). Furthermore, the results are related to negentropy, and to Bremermann's limit and the Bekenstein bound, producing, perhaps surprisingly, lower bounds on the computational deceleration and information loss incurred during an increase in predictability about the process. The identified relationships set new computational limits in terms of fundamental physical quantities, and establish transfer entropy as a central measure connecting information theory, thermodynamics and theory of computation. PMID:24953547

Initial in Situ Measurements of Perennial Meltwater Storage in the Greenland Firn Aquifer

NASA Technical Reports Server (NTRS)

Koenig, Lora S.; Miege, Clement; Forster, Richard R.; Brucker, Ludovic

2014-01-01

A perennial storage of water in a firn aquifer was discovered in southeast Greenland in 2011. We present the first in situ measurements of the aquifer, including densities and temperatures. Water was present at depths between approx. 12 and 37m and amounted to 18.7 +/- 0.9 kg in the extracted core. The water filled the firn to capacity at approx. 35m. Measurements show the aquifer temperature remained at the melting point, representing a large heat reservoir within the firn. Using model results of liquid water extent and aquifer surface depth from radar measurements, we extend our in situ measurements to the Greenland ice sheet. The estimated water volume is 140 +/- 20 Gt, representing approx. 0.4mm of sea level rise (SLR). It is unknown if the aquifer temporary buffers SLR or contributes to SLR through drainage and/or ice dynamics.

RCC1 regulates inner centromeric composition in a Ran-independent fashion.

PubMed

Zhang, Michael Shaofei; Furuta, Maiko; Arnaoutov, Alexei; Dasso, Mary

2018-01-01

RCC1 associates to chromatin dynamically within mitosis and catalyzes Ran-GTP production. Exogenous RCC1 disrupts kinetochore structure in Xenopus egg extracts (XEEs), but the molecular basis of this disruption remains unknown. We have investigated this question, utilizing replicated chromosomes that possess paired sister kinetochores. We find that exogenous RCC1 evicts a specific subset of inner KT proteins including Shugoshin-1 (Sgo1) and the chromosome passenger complex (CPC). We generated RCC1 mutants that separate its enzymatic activity and chromatin binding. Strikingly, Sgo1 and CPC eviction depended only on RCC1's chromatin affinity but not its capacity to produce Ran-GTP. RCC1 similarly released Sgo1 and CPC from synthetic kinetochores assembled on CENP-A nucleosome arrays. Together, our findings indicate RCC1 regulates kinetochores at the metaphase-anaphase transition through Ran-GTP-independent displacement of Sgo1 and CPC.

Neural-network-observer-based optimal control for unknown nonlinear systems using adaptive dynamic programming

NASA Astrophysics Data System (ADS)

Liu, Derong; Huang, Yuzhu; Wang, Ding; Wei, Qinglai

2013-09-01

In this paper, an observer-based optimal control scheme is developed for unknown nonlinear systems using adaptive dynamic programming (ADP) algorithm. First, a neural-network (NN) observer is designed to estimate system states. Then, based on the observed states, a neuro-controller is constructed via ADP method to obtain the optimal control. In this design, two NN structures are used: a three-layer NN is used to construct the observer which can be applied to systems with higher degrees of nonlinearity and without a priori knowledge of system dynamics, and a critic NN is employed to approximate the value function. The optimal control law is computed using the critic NN and the observer NN. Uniform ultimate boundedness of the closed-loop system is guaranteed. The actor, critic, and observer structures are all implemented in real-time, continuously and simultaneously. Finally, simulation results are presented to demonstrate the effectiveness of the proposed control scheme.

Crop rotations and poultry litter impact dynamic soil chemical properties and soil biota long-term

USDA-ARS?s Scientific Manuscript database

Dynamic soil physiochemical interactions with conservation agricultural practices and soil biota are largely unknown. Therefore, this study aims to quantify long-term (12-yr) impacts of cover crops, poultry litter, crop rotations, and conservation tillage and their interactions on soil physiochemica...

Mass properties measurement system: Dynamics and statics measurements

NASA Technical Reports Server (NTRS)

Doty, Keith L.

1993-01-01

This report presents and interprets experimental data obtained from the Mass Properties Measurement System (MPMS). Statics measurements yield the center-of-gravity of an unknown mass and dynamics measurements yield its inertia matrix. Observations of the MPMS performance has lead us to specific design criteria and an understanding of MPMS limitations.

76 FR 14051 - Notice of Inventory Completion: San Francisco State University, San Francisco, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-15

..., pursuant to 25 U.S.C. 3001(2), that there is a relationship of shared group identity that can be reasonably... the Tubatulabals of Kern Valley, a non-Federally recognized Indian group. On an unknown date, human remains representing a minimum of one individual were removed from an unknown site (Ca-Ker-UNK (Lake...

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

PubMed

Bandeira, Nuno; Clauser, Karl R; Pevzner, Pavel A

2007-07-01

Despite significant advances in the identification of known proteins, the analysis of unknown proteins by MS/MS still remains a challenging open problem. Although Klaus Biemann recognized the potential of MS/MS for sequencing of unknown proteins in the 1980s, low throughput Edman degradation followed by cloning still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed the powerful shotgun DNA sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated shotgun protein sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that shotgun protein sequencing has the potential to overcome the limitations of current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins.

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements1[OPEN

PubMed Central

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; Ries, Amber; Böhmer, Maik; You, Lei; Xiao, Chuanlei; Engineer, Cawas B.; Boron, Walter F.; Schroeder, Julian I.

2015-01-01

Elevated carbon dioxide (CO2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO2-induced stomatal movements by catalytic transmission of the CO2 signal in guard cells. However, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO2-regulated stomatal movements remains unknown. Here, we express fluorescently tagged CAs in guard cells of ca1ca4 double-mutant plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO2 regulation of stomatal conductance. Mathematical modeling of cellular CO2 catalysis suggests that the dynamics of the intracellular HCO3− concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Moreover, modeling supports the notion that the intracellular HCO3− concentration dynamics in guard cells are a key mechanism in mediating CO2-regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified. PMID:26243620

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements

DOE PAGES

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; ...

2015-09-28

Elevated carbon dioxide (CO 2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO 2-induced stomatal movements by catalytic transmission of the CO 2 signal in guard cells. But, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO 2-regulated stomatal movements remains unknown. We express fluorescently tagged CAs in guard cells of ca1ca4 double-mutantmore » plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO 2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO 2 regulation of stomatal conductance. Mathematical modeling of cellular CO 2 catalysis suggests that the dynamics of the intracellular HCO 3 - concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Therefore, modeling supports the notion that the intracellular HCO 3 - concentration dynamics in guard cells are a key mechanism in mediating CO 2 -regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified.« less

Population-based incidence, treatment and survival of patients with peritoneal metastases of unknown origin.

PubMed

Thomassen, Irene; Verhoeven, Rob H A; van Gestel, Yvette R B M; van de Wouw, Agnes J; Lemmens, Valery E P P; de Hingh, Ignace H J T

2014-01-01

Until recently, peritoneal metastases (PM) were regarded as an untreatable condition, regardless of the organ of origin. Currently, promising treatment options are available for selected patients with PM from colorectal, appendiceal, ovarian or gastric carcinoma. The aim of this study was to investigate the incidence, treatment and survival of patients presenting with PM in whom the origin of PM remains unknown. Data from patients diagnosed with PM of unknown origin during 1984-2010 were extracted from the Eindhoven Cancer Registry. European age-standardised incidence rates were calculated and data on treatment and survival were analysed. In total 1051 patients were diagnosed with PM of unknown origin. In 606 patients (58%) the peritoneum was the only site of metastasis, and 445 patients also had other metastases. Chemotherapy usage has increased from 8% in the earliest period to 16% in most recent years (p=.016). Median survival was extremely poor with only 42days (95% confidence interval (CI) 39-47days) and did not change over time. Median survival of patients not receiving chemotherapy was significantly worse than of those receiving chemotherapy (36 versus 218days, p<.0001). The prognosis of PM of unknown origin is extremely poor and did not improve over time. Given the recent progress that has been achieved in selected patients presenting with PM, maximum efforts should be undertaken in order to diagnose the origin of PM as accurately as possible. Potentially effective treatment strategies should be further explored for patients in whom the organ of origin remains unknown. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modality-specific spectral dynamics in response to visual and tactile sequential shape information processing tasks: An MEG study using multivariate pattern classification analysis.

PubMed

Gohel, Bakul; Lee, Peter; Jeong, Yong

2016-08-01

Brain regions that respond to more than one sensory modality are characterized as multisensory regions. Studies on the processing of shape or object information have revealed recruitment of the lateral occipital cortex, posterior parietal cortex, and other regions regardless of input sensory modalities. However, it remains unknown whether such regions show similar (modality-invariant) or different (modality-specific) neural oscillatory dynamics, as recorded using magnetoencephalography (MEG), in response to identical shape information processing tasks delivered to different sensory modalities. Modality-invariant or modality-specific neural oscillatory dynamics indirectly suggest modality-independent or modality-dependent participation of particular brain regions, respectively. Therefore, this study investigated the modality-specificity of neural oscillatory dynamics in the form of spectral power modulation patterns in response to visual and tactile sequential shape-processing tasks that are well-matched in terms of speed and content between the sensory modalities. Task-related changes in spectral power modulation and differences in spectral power modulation between sensory modalities were investigated at source-space (voxel) level, using a multivariate pattern classification (MVPC) approach. Additionally, whole analyses were extended from the voxel level to the independent-component level to take account of signal leakage effects caused by inverse solution. The modality-specific spectral dynamics in multisensory and higher-order brain regions, such as the lateral occipital cortex, posterior parietal cortex, inferior temporal cortex, and other brain regions, showed task-related modulation in response to both sensory modalities. This suggests modality-dependency of such brain regions on the input sensory modality for sequential shape-information processing. Copyright © 2016 Elsevier B.V. All rights reserved.

GPS receiver phase biases estimable in PPP-RTK networks: dynamic characterization and impact analysis

NASA Astrophysics Data System (ADS)

Zhang, Baocheng; Liu, Teng; Yuan, Yunbin

2017-11-01

The integer ambiguity resolution enabled precise point positioning (PPP-RTK) has been proven advantageous in a wide range of applications. The realization of PPP-RTK concerns the isolation of satellite phase biases (SPBs) and other corrections from a network of Global Positioning System (GPS) reference receivers. This is generally based on Kalman filter in order to achieve real-time capability, in which proper modeling of the dynamics of various types of unknowns remains crucial. This paper seeks to gain insight into how to reasonably deal with the dynamic behavior of the estimable receiver phase biases (RPBs). Using dual-frequency GPS data collected at six colocated receivers over days 50-120 of 2015, we analyze the 30-s epoch-by-epoch estimates of L1 and wide-lane (WL) RPBs for each receiver pair. The dynamics observed in these estimates are a combined effect of three factors, namely the random measurement noise, the multipath and the ambient temperature. The first factor can be overcome by turning to a real-time filter and the second by considering the use of a sidereal filtering. The third factor has an effect only on the WL, and this effect appears to be linear. After accounting for these three factors, the low-pass-filtered, sidereal-filtered, epoch-by-epoch estimates of L1 RPBs follow a random walk process, whereas those of WL RPBs are constant over time. Properly modeling the dynamics of RPBs is vital, as it ensures the best convergence of the Kalman-filtered, between-satellite single-differenced SPB estimates to their correct values and, in turn, shortens the time-to-first-fix at user side.

Seizures as imbalanced up states: excitatory and inhibitory conductances during seizure-like events

PubMed Central

Cressman, John R.; Schiff, Steven J.

2013-01-01

Precisely timed and dynamically balanced excitatory (E) and inhibitory (I) conductances underlie the basis of neural network activity. Normal E/I balance is often shifted in epilepsy, resulting in neuronal network hyperexcitability and recurrent seizures. However, dynamics of the actual excitatory and inhibitory synaptic conductances (ge and gi, respectively) during seizures remain unknown. To study the dynamics of E and I network balance, we calculated ge and gi during the initiation, body, and termination of seizure-like events (SLEs) in the rat hippocampus in vitro. Repetitive emergent SLEs in 4-aminopyridine (100 μM) and reduced extracellular magnesium (0.6 mM) were recorded in the identified CA1 pyramidal cells (PC) and oriens-lacunosum moleculare (O-LM) interneurons. Calculated ge/gi ratio dynamics showed that the initiation stage of the SLEs was dominated by inhibition in the PCs and was more balanced in the O-LM cells. During the body of the SLEs, the balance shifted toward excitation, with ge and gi peaking in both cell types at nearly the same time. In the termination phase, PCs were again dominated by inhibition, whereas O-LM cells experienced persistent excitatory synaptic barrage. In this way, increased excitability of interneurons may play roles in both seizure initiation (Žiburkus J, Cressman JR, Barreto E, Schiff SJ. J Neurophysiol 95: 3948–3954, 2006) and in their termination. Overall, SLE stages can be characterized in PC and O-LM cells by dynamically distinct changes in the balance of ge and gi, where a temporal sequence of imbalance shifts with the changing firing patterns of the cellular subtypes comprising the hyperexcitable microcircuits. PMID:23221405

Increasing blood flow to exercising muscle attenuates systemic cardiovascular responses during dynamic exercise in humans.

PubMed

Ichinose, Masashi; Ichinose-Kuwahara, Tomoko; Kondo, Narihiko; Nishiyasu, Takeshi

2015-11-15

Reducing blood flow to working muscles during dynamic exercise causes metabolites to accumulate within the active muscles and evokes systemic pressor responses. Whether a similar cardiovascular response is elicited with normal blood flow to exercising muscles during dynamic exercise remains unknown, however. To address that issue, we tested whether cardiovascular responses are affected by increases in blood flow to active muscles. Thirteen healthy subjects performed dynamic plantarflexion exercise for 12 min at 20%, 40%, and 60% of peak workload (EX20, EX40, and EX60) with their lower thigh enclosed in a negative pressure box. Under control conditions, the box pressure was the same as the ambient air pressure. Under negative pressure conditions, beginning 3 min after the start of the exercise, the box pressure was decreased by 20, 45, and then 70 mmHg in stepwise fashion with 3-min step durations. During EX20, the negative pressure had no effect on blood flow or the cardiovascular responses measured. However, application of negative pressure increased blood flow to the exercising leg during EX40 and EX60. This increase in blood flow had no significant effect on systemic cardiovascular responses during EX40, but it markedly attenuated the pressor responses otherwise seen during EX60. These results demonstrate that during mild exercise, normal blood flow to exercising muscle is not a factor eliciting cardiovascular responses, whereas it elicits an important pressor effect during moderate exercise. This suggests blood flow to exercising muscle is a major determinant of cardiovascular responses during dynamic exercise at higher than moderate intensity. Copyright © 2015 the American Physiological Society.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

PubMed Central

Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

2016-01-01

Exportin-t (Xpot) transports mature 5′- and 3′-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes. PMID:27028637

GPS receiver phase biases estimable in PPP-RTK networks: dynamic characterization and impact analysis

NASA Astrophysics Data System (ADS)

Zhang, Baocheng; Liu, Teng; Yuan, Yunbin

2018-06-01

The integer ambiguity resolution enabled precise point positioning (PPP-RTK) has been proven advantageous in a wide range of applications. The realization of PPP-RTK concerns the isolation of satellite phase biases (SPBs) and other corrections from a network of Global Positioning System (GPS) reference receivers. This is generally based on Kalman filter in order to achieve real-time capability, in which proper modeling of the dynamics of various types of unknowns remains crucial. This paper seeks to gain insight into how to reasonably deal with the dynamic behavior of the estimable receiver phase biases (RPBs). Using dual-frequency GPS data collected at six colocated receivers over days 50-120 of 2015, we analyze the 30-s epoch-by-epoch estimates of L1 and wide-lane (WL) RPBs for each receiver pair. The dynamics observed in these estimates are a combined effect of three factors, namely the random measurement noise, the multipath and the ambient temperature. The first factor can be overcome by turning to a real-time filter and the second by considering the use of a sidereal filtering. The third factor has an effect only on the WL, and this effect appears to be linear. After accounting for these three factors, the low-pass-filtered, sidereal-filtered, epoch-by-epoch estimates of L1 RPBs follow a random walk process, whereas those of WL RPBs are constant over time. Properly modeling the dynamics of RPBs is vital, as it ensures the best convergence of the Kalman-filtered, between-satellite single-differenced SPB estimates to their correct values and, in turn, shortens the time-to-first-fix at user side.

Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks

PubMed Central

Goldberg, Mati; De Pittà, Maurizio; Volman, Vladislav; Berry, Hugues; Ben-Jacob, Eshel

2010-01-01

A new paradigm has recently emerged in brain science whereby communications between glial cells and neuron-glia interactions should be considered together with neurons and their networks to understand higher brain functions. In particular, astrocytes, the main type of glial cells in the cortex, have been shown to communicate with neurons and with each other. They are thought to form a gap-junction-coupled syncytium supporting cell-cell communication via propagating Ca2+ waves. An identified mode of propagation is based on cytoplasm-to-cytoplasm transport of inositol trisphosphate (IP3) through gap junctions that locally trigger Ca2+ pulses via IP3-dependent Ca2+-induced Ca2+ release. It is, however, currently unknown whether this intracellular route is able to support the propagation of long-distance regenerative Ca2+ waves or is restricted to short-distance signaling. Furthermore, the influence of the intracellular signaling dynamics on intercellular propagation remains to be understood. In this work, we propose a model of the gap-junctional route for intercellular Ca2+ wave propagation in astrocytes. Our model yields two major predictions. First, we show that long-distance regenerative signaling requires nonlinear coupling in the gap junctions. Second, we show that even with nonlinear gap junctions, long-distance regenerative signaling is favored when the internal Ca2+ dynamics implements frequency modulation-encoding oscillations with pulsating dynamics, while amplitude modulation-encoding dynamics tends to restrict the propagation range. As a result, spatially heterogeneous molecular properties and/or weak couplings are shown to give rise to rich spatiotemporal dynamics that support complex propagation behaviors. These results shed new light on the mechanisms implicated in the propagation of Ca2+ waves across astrocytes and the precise conditions under which glial cells may participate in information processing in the brain. PMID:20865153

Dual-Schemata Model

NASA Astrophysics Data System (ADS)

Taniguchi, Tadahiro; Sawaragi, Tetsuo

In this paper, a new machine-learning method, called Dual-Schemata model, is presented. Dual-Schemata model is a kind of self-organizational machine learning methods for an autonomous robot interacting with an unknown dynamical environment. This is based on Piaget's Schema model, that is a classical psychological model to explain memory and cognitive development of human beings. Our Dual-Schemata model is developed as a computational model of Piaget's Schema model, especially focusing on sensori-motor developing period. This developmental process is characterized by a couple of two mutually-interacting dynamics; one is a dynamics formed by assimilation and accommodation, and the other dynamics is formed by equilibration and differentiation. By these dynamics schema system enables an agent to act well in a real world. This schema's differentiation process corresponds to a symbol formation process occurring within an autonomous agent when it interacts with an unknown, dynamically changing environment. Experiment results obtained from an autonomous facial robot in which our model is embedded are presented; an autonomous facial robot becomes able to chase a ball moving in various ways without any rewards nor teaching signals from outside. Moreover, emergence of concepts on the target movements within a robot is shown and discussed in terms of fuzzy logics on set-subset inclusive relationships.

Rendezvous with connectivity preservation for multi-robot systems with an unknown leader

NASA Astrophysics Data System (ADS)

Dong, Yi

2018-02-01

This paper studies the leader-following rendezvous problem with connectivity preservation for multi-agent systems composed of uncertain multi-robot systems subject to external disturbances and an unknown leader, both of which are generated by a so-called exosystem with parametric uncertainty. By combining internal model design, potential function technique and adaptive control, two distributed control strategies are proposed to maintain the connectivity of the communication network, to achieve the asymptotic tracking of all the followers to the output of the unknown leader system, as well as to reject unknown external disturbances. It is also worth to mention that the uncertain parameters in the multi-robot systems and exosystem are further allowed to belong to unknown and unbounded sets when applying the second fully distributed control law containing a dynamic gain inspired by high-gain adaptive control or self-tuning regulator.

Vitamin and Mineral Supplements Have a Nutritionally Significant Impact on Micronutrient Intakes of Older Adults Attending Senior Centers

USDA-ARS?s Scientific Manuscript database

Background: Older adults frequently report use of vitamin and mineral (VM) supplements, though the impact of supplements on dietary adequacy remains largely unknown. Despite possible improvements in dietary intake, concern remains over potential excessive nutrient consumption from VM supplement us...

Adaptive robust control of a class of non-affine variable-speed variable-pitch wind turbines with unmodeled dynamics.

PubMed

Bagheri, Pedram; Sun, Qiao

2016-07-01

In this paper, a novel synthesis of Nussbaum-type functions, and an adaptive radial-basis function neural network is proposed to design controllers for variable-speed, variable-pitch wind turbines. Dynamic equations of the wind turbine are highly nonlinear, uncertain, and affected by unknown disturbance sources. Furthermore, the dynamic equations are non-affine with respect to the pitch angle, which is a control input. To address these problems, a Nussbaum-type function, along with a dynamic control law are adopted to resolve the non-affine nature of the equations. Moreover, an adaptive radial-basis function neural network is designed to approximate non-parametric uncertainties. Further, the closed-loop system is made robust to unknown disturbance sources, where no prior knowledge of disturbance bound is assumed in advance. Finally, the Lyapunov stability analysis is conducted to show the stability of the entire closed-loop system. In order to verify analytical results, a simulation is presented and the results are compared to both a PI and an existing adaptive controllers. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Online adaptive optimal control for continuous-time nonlinear systems with completely unknown dynamics

NASA Astrophysics Data System (ADS)

Lv, Yongfeng; Na, Jing; Yang, Qinmin; Wu, Xing; Guo, Yu

2016-01-01

An online adaptive optimal control is proposed for continuous-time nonlinear systems with completely unknown dynamics, which is achieved by developing a novel identifier-critic-based approximate dynamic programming algorithm with a dual neural network (NN) approximation structure. First, an adaptive NN identifier is designed to obviate the requirement of complete knowledge of system dynamics, and a critic NN is employed to approximate the optimal value function. Then, the optimal control law is computed based on the information from the identifier NN and the critic NN, so that the actor NN is not needed. In particular, a novel adaptive law design method with the parameter estimation error is proposed to online update the weights of both identifier NN and critic NN simultaneously, which converge to small neighbourhoods around their ideal values. The closed-loop system stability and the convergence to small vicinity around the optimal solution are all proved by means of the Lyapunov theory. The proposed adaptation algorithm is also improved to achieve finite-time convergence of the NN weights. Finally, simulation results are provided to exemplify the efficacy of the proposed methods.

Control of multi-joint arm movements for the manipulation of touch in keystroke by expert pianists

PubMed Central

2010-01-01

Background Production of a variety of finger-key touches in the piano is essential for expressive musical performance. However, it remains unknown how expert pianists control multi-joint finger and arm movements for manipulating the touch. The present study investigated differences in kinematics and kinetics of the upper-limb movements while expert pianists were depressing a key with two different touches: pressed and struck. The former starts key-depression with the finger-tip contacting the key, whereas the latter involves preparatory arm-lift before striking the key. To determine the effect of individual muscular torque (MUS) as well as non-muscular torques on joint acceleration, we performed a series of inverse and forward dynamics computations. Results The pressed touch showed smaller elbow extension velocity, and larger shoulder and finger flexion velocities during key-depression compared with the struck touch. The former touch also showed smaller elbow extension acceleration directly attributed to the shoulder MUS. In contrast, the shoulder flexion acceleration induced by elbow and wrist MUS was greater for the pressed touch than the struck touch. Towards the goal of producing the target finger-key contact dynamics, the pressed and struck touches effectively took advantage of the distal-to-proximal and proximal-to-distal inter-segmental dynamics, respectively. Furthermore, a psychoacoustic experiment confirmed that a tone elicited by the pressed touch was perceived softer than that by the struck touch. Conclusion The present findings suggest that manipulation of tone timbre depends on control of inter-segmental dynamics in piano keystroke. PMID:20630085

No novel, high penetrant gene might remain to be found in Japanese patients with unknown MODY.

PubMed

Horikawa, Yukio; Hosomichi, Kazuyoshi; Enya, Mayumi; Ishiura, Hiroyuki; Suzuki, Yutaka; Tsuji, Shoji; Sugano, Sumio; Inoue, Ituro; Takeda, Jun

2018-07-01

MODY 5 and 6 have been shown to be low-penetrant MODYs. As the genetic background of unknown MODY is assumed to be similar, a new analytical strategy is applied here to elucidate genetic predispositions to unknown MODY. We examined to find whether there are major MODY gene loci remaining to be identified using SNP linkage analysis in Japanese. Whole-exome sequencing was performed with seven families with typical MODY. Candidates for novel MODY genes were examined combined with in silico network analysis. Some peaks were found only in either parametric or non-parametric analysis; however, none of these peaks showed a LOD score greater than 3.7, which is approved to be the significance threshold of evidence for linkage. Exome sequencing revealed that three mutated genes were common among 3 families and 42 mutated genes were common in two families. Only one of these genes, MYO5A, having rare amino acid mutations p.R849Q and p.V1601G, was involved in the biological network of known MODY genes through the intermediary of the INS. Although only one promising candidate gene, MYO5A, was identified, no novel, high penetrant MODY genes might remain to be found in Japanese MODY.

Interactions between HIV-1 Neutralizing Antibodies and Model Lipid Membranes imaged with AFM

NASA Astrophysics Data System (ADS)

Zauscher, Stefan; Hardy, Gregory; Alam, Munir; Shapter, Joseph

2012-02-01

Lipid membrane interactions with rare, broadly neutralizing antibodies (NAbs), 2F5 and 4E10, play a critical role in HIV-1 neutralization. Our research is motivated by recent immunization studies that have shown that induction of antibodies that avidly bind the gp41-MPER antigen is not sufficient for neutralization. Rather, it is required that antigen designs induce polyreactive antibodies that recognize MPER antigens as well as the viral lipid membrane. However, the mechanistic details of how membrane properties influence NAb-lipid and NAb-antigen interactions remain unknown. Furthermore, it is well established that the native viral membrane is heterogeneous, representing a mosaic of lipid rafts and protein clustering. However, the size, physical properties, and dynamics of these regions are poorly characterized and their potential roles in HIV-1 neutralization are also unknown. To understand how membrane properties contribute to 2F5/4E10 membrane interactions, we have engineered biomimetic supported lipid bilayers (SLBs) and use atomic force microscopy to visualize membrane domains, antigen clustering, and antibody-membrane interactions at sub-nanometer z-resolution. Our results show that localized binding of HIV-1 antigens and NAbs occur preferentially with the most fluid membrane domain. This supports the theory that NAbs may interact with regions of low lateral lipid forces that allow antibody insertion into the bilayer.

Parametric system identification of catamaran for improving controller design

NASA Astrophysics Data System (ADS)

Timpitak, Surasak; Prempraneerach, Pradya; Pengwang, Eakkachai

2018-01-01

This paper presents an estimation of simplified dynamic model for only surge- and yaw- motions of catamaran by using system identification (SI) techniques to determine associated unknown parameters. These methods will enhance the performance of designing processes for the motion control system of Unmanned Surface Vehicle (USV). The simulation results demonstrate an effective way to solve for damping forces and to determine added masses by applying least-square and AutoRegressive Exogenous (ARX) methods. Both methods are then evaluated according to estimated parametric errors from the vehicle’s dynamic model. The ARX method, which yields better estimated accuracy, can then be applied to identify unknown parameters as well as to help improving a controller design of a real unmanned catamaran.

Time-Dependent Impact of Irreversible Electroporation on Pancreas, Liver, Blood Vessels and Nerves: A Systematic Review of Experimental Studies

PubMed Central

Agnass, P.; Crezee, J.; Dijk, F.; Verheij, J.; van Gulik, T. M.; Meijerink, M. R.; Vroomen, L. G.; van Lienden, K. P.; Besselink, M. G.

2016-01-01

Introduction Irreversible electroporation (IRE) is a novel ablation technique in the treatment of unresectable cancer. The non-thermal mechanism is thought to cause mostly apoptosis compared to necrosis in thermal techniques. Both in experimental and clinical studies, a waiting time between ablation and tissue or imaging analysis to allow for cell death through apoptosis, is often reported. However, the dynamics of the IRE effect over time remain unknown. Therefore, this study aims to summarize these effects in relation to the time between treatment and evaluation. Methods A systematic search was performed in Pubmed, Embase and the Cochrane Library for original articles using IRE on pancreas, liver or surrounding structures in animal or human studies. Data on pathology and time between IRE and evaluation were extracted. Results Of 2602 screened studies, 36 could be included, regarding IRE in liver (n = 24), pancreas (n = 4), blood vessels (n = 4) and nerves (n = 4) in over 440 animals (pig, rat, goat and rabbit). No eligible human studies were found. In liver and pancreas, the first signs of apoptosis and haemorrhage were observed 1–2 hours after treatment, and remained visible until 24 hours in liver and 7 days in pancreas after which the damaged tissue was replaced by fibrosis. In solitary blood vessels, the tunica media, intima and lumen remained unchanged for 24 hours. After 7 days, inflammation, fibrosis and loss of smooth muscle cells were demonstrated, which persisted until 35 days. In nerves, the median time until demonstrable histological changes was 7 days. Conclusions Tissue damage after IRE is a dynamic process with remarkable time differences between tissues in animals. Whereas pancreas and liver showed the first damages after 1–2 hours, this took 24 hours in blood vessels and 7 days in nerves. PMID:27870918

75 FR 52021 - Notice of Inventory Completion: New York University College of Dentistry, New York, NY

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

... University College of Dentistry, New York, NY AGENCY: National Park Service, Interior. ACTION: Notice. Notice... University College of Dentistry, New York, NY. The human remains were removed from an unknown location. This... the human remains was made by New York University College of Dentistry professional staff in...

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microbial ecology that can play a role in animal health and productivity, but the magnitude of these changes remains unknown. The objective of this study was ...

75 FR 67999 - Notice of Inventory Completion: Anthropological Studies Center, Archaeological Collections...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-04

... occupation between A.D. 1500 and 1856. Although the exact age and identity of the individual is unknown, more... relationship of shared group identity that can be reasonably traced between the Native American human remains... January 1982, human remains representing a minimum of one individual were removed from the Diamond H...

77 FR 2082 - Notice of Inventory Completion: Minnesota Indian Affairs Council, Bemidji, MN

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-13

.... The remains were removed during construction of a building and subsequently transferred to Bemidji.... At an unknown date, human remains representing, at minimum, one individual were recovered from a road construction project on Hwy 197 in Beltrami County, MN, and transferred to the Minnesota Office of the State...

Detection of abrupt changes in dynamic systems

NASA Technical Reports Server (NTRS)

Willsky, A. S.

1984-01-01

Some of the basic ideas associated with the detection of abrupt changes in dynamic systems are presented. Multiple filter-based techniques and residual-based method and the multiple model and generalized likelihood ratio methods are considered. Issues such as the effect of unknown onset time on algorithm complexity and structure and robustness to model uncertainty are discussed.

Group prioritisation with unknown expert weights in incomplete linguistic context

NASA Astrophysics Data System (ADS)

Cheng, Dong; Cheng, Faxin; Zhou, Zhili; Wang, Juan

2017-09-01

In this paper, we study a group prioritisation problem in situations when the expert weights are completely unknown and their judgement preferences are linguistic and incomplete. Starting from the theory of relative entropy (RE) and multiplicative consistency, an optimisation model is provided for deriving an individual priority vector without estimating the missing value(s) of an incomplete linguistic preference relation. In order to address the unknown expert weights in the group aggregating process, we define two new kinds of expert weight indicators based on RE: proximity entropy weight and similarity entropy weight. Furthermore, a dynamic-adjusting algorithm (DAA) is proposed to obtain an objective expert weight vector and capture the dynamic properties involved in it. Unlike the extant literature of group prioritisation, the proposed RE approach does not require pre-allocation of expert weights and can solve incomplete preference relations. An interesting finding is that once all the experts express their preference relations, the final expert weight vector derived from the DAA is fixed irrespective of the initial settings of expert weights. Finally, an application example is conducted to validate the effectiveness and robustness of the RE approach.

ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS

PubMed Central

MIAO, HONGYU; XIA, XIAOHUA; PERELSON, ALAN S.; WU, HULIN

2011-01-01

Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice. PMID:21785515

Robust ADP Design for Continuous-Time Nonlinear Systems With Output Constraints.

PubMed

Fan, Bo; Yang, Qinmin; Tang, Xiaoyu; Sun, Youxian

2018-06-01

In this paper, a novel robust adaptive dynamic programming (RADP)-based control strategy is presented for the optimal control of a class of output-constrained continuous-time unknown nonlinear systems. Our contribution includes a step forward beyond the usual optimal control result to show that the output of the plant is always within user-defined bounds. To achieve the new results, an error transformation technique is first established to generate an equivalent nonlinear system, whose asymptotic stability guarantees both the asymptotic stability and the satisfaction of the output restriction of the original system. Furthermore, RADP algorithms are developed to solve the transformed nonlinear optimal control problem with completely unknown dynamics as well as a robust design to guarantee the stability of the closed-loop systems in the presence of unavailable internal dynamic state. Via small-gain theorem, asymptotic stability of the original and transformed nonlinear system is theoretically guaranteed. Finally, comparison results demonstrate the merits of the proposed control policy.

The importance of anabolism in microbial control over soil carbon storage

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

Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolismmore » and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.« less

Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

PubMed

Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

2015-10-01

Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Uncovering a Dynamic Feature of the Transcriptional Regulatory Network for Anterior-Posterior Patterning in the Drosophila Embryo

PubMed Central

Liu, Junbo; Ma, Jun

2013-01-01

Anterior-posterior (AP) patterning in the Drosophila embryo is dependent on the Bicoid (Bcd) morphogen gradient. However, most target genes of Bcd also require additional inputs to establish their expression domains, reflective of the operation of a cross-regulatory network and contributions of other maternal signals. This is in contrast to hunchback (hb), which has an anterior expression domain driven by an enhancer that appears to respond primarily to the Bcd input. To gain a better understanding of the regulatory logic of the AP patterning network, we perform quantitative studies that specifically investigate the dynamics of hb transcription during development. We show that Bcd-dependent hb transcription, monitored by the intron-containing nascent transcripts near the P2 promoter, is turned off quickly–on the order of a few minutes–upon entering the interphase of nuclear cycle 14A. This shutdown contrasts with earlier cycles during which active hb transcription can persist until the moment when the nucleus enters mitosis. The shutdown takes place at a time when the nuclear Bcd gradient profile in the embryo remains largely intact, suggesting that this is a process likely subject to control of a currently unknown regulatory mechanism. We suggest that this dynamic feature offers a window of opportunity for hb to faithfully interpret, and directly benefit from, Bcd gradient properties, including its scaling properties, to help craft a robust AP patterning outcome. PMID:23646132

Elastin-like Protein-Hyaluronic acid (ELP-HA) Hydrogels with Decoupled Mechanical and Biochemical cues for Cartilage Regeneration

PubMed Central

Zhu, Danqing; Wang, Huiyuan; Trinh, Pavin; Heilshorn, Sarah C.; Yang, Fan

2018-01-01

Hyaluronic acid (HA) is a major component of cartilage extracellular matrix and is an attractive material for use as 3D injectable matrices for cartilage regeneration. While previous studies have shown the promise of HA-based hydrogels to support cell-based cartilage formation, varying HA concentration generally led to simultaneous changes in both biochemical cues and stiffness. How cells respond to the change of biochemical content of HA remains largely unknown. Here we report an adaptable elastin-like protein-hyaluronic acid (ELP-HA) hydrogel platform using dynamic covalent chemistry, which allows varyiation of HA concentration without affecting matrix stiffness. ELP-HA hydrogels were created through dynamic hydrazone bonds via the reaction between hydrazine-modified ELP (ELP-HYD) and aldehyde-modified HA (HA-ALD). By tuning the stoichiometric ratio of aldehyde groups to hydrazine groups while maintaining ELP-HYD concentration constant, hydrogels with variable HA concentration (1.5%, 3%, or 5%) (w/v) were fabricated with comparable stiffness. To evaluate the effects of HA concentration on cell-based cartilage regeneration, chondrocytes were encapsulated within ELP-HA hydrogels with varying HA concentration. Increasing HA concentration led to a dose-dependent increase in cartilage-marker gene expression and enhanced sGAG deposition while minimizing undesirable fibrocartilage phenotype. The use of adaptable protein hydrogels formed via dynamic covalent chemistry may be broadly applicable as 3D scaffolds with decoupled niche properties to guide other desirable cell fates and tissue repair. PMID:28268018

Bud detachment in hydra requires activation of fibroblast growth factor receptor and a Rho-ROCK-myosin II signaling pathway to ensure formation of a basal constriction.

PubMed

Holz, Oliver; Apel, David; Steinmetz, Patrick; Lange, Ellen; Hopfenmüller, Simon; Ohler, Kerstin; Sudhop, Stefanie; Hassel, Monika

2017-07-01

Hydra propagates asexually by exporting tissue into a bud, which detaches 4 days later as a fully differentiated young polyp. Prerequisite for detachment is activation of fibroblast growth factor receptor (FGFR) signaling. The mechanism which enables constriction and tissue separation within the monolayered ecto- and endodermal epithelia is unknown. Histological sections and staining of F-actin by phalloidin revealed conspicuous cell shape changes at the bud detachment site indicating a localized generation of mechanical forces and the potential enhancement of secretory functions in ectodermal cells. By gene expression analysis and pharmacological inhibition, we identified a candidate signaling pathway through Rho, ROCK, and myosin II, which controls bud base constriction and rearrangement of the actin cytoskeleton. Specific regional myosin phosphorylation suggests a crucial role of ectodermal cells at the detachment site. Inhibition of FGFR, Rho, ROCK, or myosin II kinase activity is permissive for budding, but represses myosin phosphorylation, rearrangement of F-actin and constriction. The young polyp remains permanently connected to the parent by a broad tissue bridge. Our data suggest an essential role of FGFR and a Rho-ROCK-myosin II pathway in the control of cell shape changes required for bud detachment. Developmental Dynamics 246:502-516, 2017. © 2017 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists. © 2017 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

Elastin-like protein-hyaluronic acid (ELP-HA) hydrogels with decoupled mechanical and biochemical cues for cartilage regeneration.

PubMed

Zhu, Danqing; Wang, Huiyuan; Trinh, Pavin; Heilshorn, Sarah C; Yang, Fan

2017-05-01

Hyaluronic acid (HA) is a major component of cartilage extracellular matrix and is an attractive material for use as 3D injectable matrices for cartilage regeneration. While previous studies have shown the promise of HA-based hydrogels to support cell-based cartilage formation, varying HA concentration generally led to simultaneous changes in both biochemical cues and stiffness. How cells respond to the change of biochemical content of HA remains largely unknown. Here we report an adaptable elastin-like protein-hyaluronic acid (ELP-HA) hydrogel platform using dynamic covalent chemistry, which allows variation of HA concentration without affecting matrix stiffness. ELP-HA hydrogels were created through dynamic hydrazone bonds via the reaction between hydrazine-modified ELP (ELP-HYD) and aldehyde-modified HA (HA-ALD). By tuning the stoichiometric ratio of aldehyde groups to hydrazine groups while maintaining ELP-HYD concentration constant, hydrogels with variable HA concentration (1.5%, 3%, or 5%) (w/v) were fabricated with comparable stiffness. To evaluate the effects of HA concentration on cell-based cartilage regeneration, chondrocytes were encapsulated within ELP-HA hydrogels with varying HA concentration. Increasing HA concentration led to a dose-dependent increase in cartilage-marker gene expression and enhanced sGAG deposition while minimizing undesirable fibrocartilage phenotype. The use of adaptable protein hydrogels formed via dynamic covalent chemistry may be broadly applicable as 3D scaffolds with decoupled niche properties to guide other desirable cell fates and tissue repair. Copyright © 2017 Elsevier Ltd. All rights reserved.

The diatom Phaeodactylum tricornutum adjusts nonphotochemical fluorescence quenching capacity in response to dynamic light via fine-tuned Lhcx and xanthophyll cycle pigment synthesis.

PubMed

Lepetit, Bernard; Gélin, Gautier; Lepetit, Mariana; Sturm, Sabine; Vugrinec, Sascha; Rogato, Alessandra; Kroth, Peter G; Falciatore, Angela; Lavaud, Johann

2017-04-01

Diatoms contain a highly flexible capacity to dissipate excessively absorbed light by nonphotochemical fluorescence quenching (NPQ) based on the light-induced conversion of diadinoxanthin (Dd) into diatoxanthin (Dt) and the presence of Lhcx proteins. Their NPQ fine regulation on the molecular level upon a shift to dynamic light conditions is unknown. We investigated the regulation of Dd + Dt amount, Lhcx gene and protein synthesis and NPQ capacity in the diatom Phaeodactylum tricornutum after a change from continuous low light to 3 d of sine (SL) or fluctuating (FL) light conditions. Four P. tricornutum strains with different NPQ capacities due to different expression of Lhcx1 were included. All strains responded to dynamic light comparably, independently of initial NPQ capacity. During SL, NPQ capacity was strongly enhanced due to a gradual increase of Lhcx2 and Dd + Dt amount. During FL, cells enhanced their NPQ capacity on the first day due to increased Dd + Dt, Lhcx2 and Lhcx3; already by the second day light acclimation was accomplished. While quenching efficiency of Dt was strongly lowered during SL conditions, it remained high throughout the whole FL exposure. Our results highlight a more balanced and cost-effective photoacclimation strategy of P. tricornutum under FL than under SL conditions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A neural coding scheme reproducing foraging trajectories

NASA Astrophysics Data System (ADS)

Gutiérrez, Esther D.; Cabrera, Juan Luis

2015-12-01

The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series.

Distributed Synchronization Control of Multiagent Systems With Unknown Nonlinearities.

PubMed

Su, Shize; Lin, Zongli; Garcia, Alfredo

2016-01-01

This paper revisits the distributed adaptive control problem for synchronization of multiagent systems where the dynamics of the agents are nonlinear, nonidentical, unknown, and subject to external disturbances. Two communication topologies, represented, respectively, by a fixed strongly-connected directed graph and by a switching connected undirected graph, are considered. Under both of these communication topologies, we use distributed neural networks to approximate the uncertain dynamics. Decentralized adaptive control protocols are then constructed to solve the cooperative tracker problem, the problem of synchronization of all follower agents to a leader agent. In particular, we show that, under the proposed decentralized control protocols, the synchronization errors are ultimately bounded, and their ultimate bounds can be reduced arbitrarily by choosing the control parameter appropriately. Simulation study verifies the effectiveness of our proposed protocols.

Adaptive Fuzzy Control Design for Stochastic Nonlinear Switched Systems With Arbitrary Switchings and Unmodeled Dynamics.

PubMed

Li, Yongming; Sui, Shuai; Tong, Shaocheng

2017-02-01

This paper deals with the problem of adaptive fuzzy output feedback control for a class of stochastic nonlinear switched systems. The controlled system in this paper possesses unmeasured states, completely unknown nonlinear system functions, unmodeled dynamics, and arbitrary switchings. A state observer which does not depend on the switching signal is constructed to tackle the unmeasured states. Fuzzy logic systems are employed to identify the completely unknown nonlinear system functions. Based on the common Lyapunov stability theory and stochastic small-gain theorem, a new robust adaptive fuzzy backstepping stabilization control strategy is developed. The stability of the closed-loop system on input-state-practically stable in probability is proved. The simulation results are given to verify the efficiency of the proposed fuzzy adaptive control scheme.

An accessible method for implementing hierarchical models with spatio-temporal abundance data

USGS Publications Warehouse

Ross, Beth E.; Hooten, Melvin B.; Koons, David N.

2012-01-01

A common goal in ecology and wildlife management is to determine the causes of variation in population dynamics over long periods of time and across large spatial scales. Many assumptions must nevertheless be overcome to make appropriate inference about spatio-temporal variation in population dynamics, such as autocorrelation among data points, excess zeros, and observation error in count data. To address these issues, many scientists and statisticians have recommended the use of Bayesian hierarchical models. Unfortunately, hierarchical statistical models remain somewhat difficult to use because of the necessary quantitative background needed to implement them, or because of the computational demands of using Markov Chain Monte Carlo algorithms to estimate parameters. Fortunately, new tools have recently been developed that make it more feasible for wildlife biologists to fit sophisticated hierarchical Bayesian models (i.e., Integrated Nested Laplace Approximation, ‘INLA’). We present a case study using two important game species in North America, the lesser and greater scaup, to demonstrate how INLA can be used to estimate the parameters in a hierarchical model that decouples observation error from process variation, and accounts for unknown sources of excess zeros as well as spatial and temporal dependence in the data. Ultimately, our goal was to make unbiased inference about spatial variation in population trends over time.

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

PubMed Central

Fan, Zhaosheng; Liang, Chao

2015-01-01

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We find that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as “microbial biosynthesis acceleration” (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups. PMID:25849864

Dynamic modeling and Super-Twisting Sliding Mode Control for Tethered Space Robot

NASA Astrophysics Data System (ADS)

Zhao, Yakun; Huang, Panfeng; Zhang, Fan

2018-02-01

Recent years, tethered space capturing systems have been considered as one of the most promising solutions for active space debris removal due to the increasing threat of space debris to spacecraft and astronauts. In this paper, one of the tethered space capturing systems, Tethered Space Robot (TSR), is investigated. TSR includes a space platform, a space tether, and a gripper as the terminal device. Based on the assumptions that the platform and the gripper are point masses and the tether is rigid, inextensible and remaining straight, the dynamic model of TSR is presented, in which the disturbances from space environment is considered. According to the previous study, the in-plane and out-of-plane angles of the tether oscillate periodically although the tether is released to the desired length. A super-twisting adaptive sliding mode control scheme is designed for TSR to eliminate the vibration of the tether to assure a successful capture in station-keeping phase. Both uncontrolled and controlled situations are simulated. The simulation results show that the proposed controller is effective. Additionally, after comparing with normal sliding mode control algorithm, it is verified that the proposed control scheme can avoid the chattering of normal sliding mode control and is robust for unknown boundary perturbations.

The head-regeneration transcriptome of the planarian Schmidtea mediterranea.

PubMed

Sandmann, Thomas; Vogg, Matthias C; Owlarn, Suthira; Boutros, Michael; Bartscherer, Kerstin

2011-08-16

Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

DOE PAGES

Fan, Zhaosheng; Liang, Chao

2015-04-02

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We findmore » that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as ‘‘microbial biosynthesis acceleration’’ (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups.« less

Processive motions of MreB micro-filaments coordinate cell wall growth

NASA Astrophysics Data System (ADS)

Garner, Ethan

2012-02-01

Rod-shaped bacteria elongate by the action of cell-wall synthesis complexes linked to underlying dynamic MreB filaments, but how these proteins function to allow continued elongation as a rod remains unknown. To understand how the movement of these filaments relates to cell wall synthesis, we characterized the dynamics of MreB and the cell wall elongation machinery using high-resolution particle tracking in Bacillus subtilis. We found that both MreB and the elongation machinery move in linear paths across the cell, moving at similar rates (˜20nm / second) and angles to the cell body, suggesting they function as single complexes. These proteins move circumferentially around the cell, principally perpendicular to its length. We find that the motions of these complexes are independent, as they can pause and reverse,and also as nearby complexes move independently in both directions across one surface of the cell. Inhibition of cell wall synthesis with antibiotics or depletions in the cell wall synthesis machinery blocked MreB movement, suggesting that the cell wall synthetic machinery is the motor in this system. We propose that bacteria elongate by the uncoordinated, circumferential movements of synthetic complexes that span the plasma membrane and insert radial hoops of new peptidoglycan during their transit.

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

PubMed

Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

2016-12-13

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

High-Dimensional Brain: A Tool for Encoding and Rapid Learning of Memories by Single Neurons.

PubMed

Tyukin, Ivan; Gorban, Alexander N; Calvo, Carlos; Makarova, Julia; Makarov, Valeri A

2018-03-19

Codifying memories is one of the fundamental problems of modern Neuroscience. The functional mechanisms behind this phenomenon remain largely unknown. Experimental evidence suggests that some of the memory functions are performed by stratified brain structures such as the hippocampus. In this particular case, single neurons in the CA1 region receive a highly multidimensional input from the CA3 area, which is a hub for information processing. We thus assess the implication of the abundance of neuronal signalling routes converging onto single cells on the information processing. We show that single neurons can selectively detect and learn arbitrary information items, given that they operate in high dimensions. The argument is based on stochastic separation theorems and the concentration of measure phenomena. We demonstrate that a simple enough functional neuronal model is capable of explaining: (i) the extreme selectivity of single neurons to the information content, (ii) simultaneous separation of several uncorrelated stimuli or informational items from a large set, and (iii) dynamic learning of new items by associating them with already "known" ones. These results constitute a basis for organization of complex memories in ensembles of single neurons. Moreover, they show that no a priori assumptions on the structural organization of neuronal ensembles are necessary for explaining basic concepts of static and dynamic memories.

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

PubMed Central

2011-01-01

Background Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. Results To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Conclusions Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians. PMID:21846378

Trophic groups and modules: two levels of group detection in food webs.

PubMed

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-05-06

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom-top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Actin Turnover-Mediated Gravity Response in Maize Root Apices

PubMed Central

Mancuso, Stefano; Barlow, Peter W; Volkmann, Dieter

2006-01-01

The dynamic actin cytoskeleton has been proposed to be linked to gravity sensing in plants but the mechanistic understanding of these processes remains unknown. We have performed detailed pharmacological analyses of the role of the dynamic actin cytoskeleton in gravibending of maize (Zea mays) root apices. Depolymerization of actin filaments with two drugs having different mode of their actions, cytochalasin D and latrunculin B, stimulated root gravibending. By contrast, drug-induced stimulation of actin polymerization and inhibition of actin turnover, using two different agents phalloidin and jasplakinolide, compromised the root gravibending. Importantly, all these actin drugs inhibited root growth to similar extents suggesting that high actin turnover is essential for the gravity-related growth responses rather than for the general growth process. Both latrunculin B and cytochalasin D treatments inhibited root growth but restored gravibending of the decapped root apices, indicating that there is a strong potential for effective actin-mediated gravity sensing outside the cap. This elusive gravity sensing outside the root cap is dependent not only on the high rate of actin turnover but also on weakening of myosin activities, as general inhibition of myosin ATPases induced stimulation of gravibending of the decapped root apices. Collectively, these data provide evidence for the actin turnover-mediated gravity sensing outside the root cap. PMID:19521476

MiniFluo fluorescence sensor, advances in FDOM Ocean Measurements

NASA Astrophysics Data System (ADS)

Cyr, Frédéric; Tedetti, Marc; Goutx, Madeleine

2017-04-01

As part of the European project "Next generation Low-Cost Multifunctional Web Enabled Ocean Sensor Systems Empowering Marine, Maritime and Fisheries Management (NeXOS)", we developed the MiniFluo, a glider-compatible optical sensor for measurements of fluorescent dissolved organic matter (FDOM). In situ applications of the MiniFluo are presented here. The configuration used targets both natural (Tryptophan) and an anthropogenic (Phenanthrene) DOM fluorophores. Observations from three glider campaigns in the NW Mediterranean (Fall 2015 and Spring and Summer 2016) are presented. It is shown that the use of the Minifluo highlights new features of DOM dynamics in the region. For example, the Tryptophan (an amino-acid traditionally used as a tracer for waste waters) is found here closely related to open sea Chl-a fluorescence. Differences between Chl-a and Tryptophan fluorescence also give subtle information on seasonal changes in ecosystem structure and DOM release that could not be observed with traditional glider measurements. The study also highlights the presence of phenanthrene (an anthropogenic polycyclic aromatic hydrocarbon (PAH) in the surface and sub-surface waters of the Mediterranean. Implications of these finding will be put in the context of both the Mediterranean Sea DOM dynamics and also the ocean carbon cycle, from which the Dissolved Organic Carbon pool remains qualitatively unknown.

New concepts in anaerobic digestion processes: recent advances and biological aspects.

PubMed

Castellano-Hinojosa, Antonio; Armato, Caterina; Pozo, Clementina; González-Martínez, Alejandro; González-López, Jesús

2018-06-01

Waste treatment and the simultaneous production of energy have gained great interest in the world. In the last decades, scientific efforts have focused largely on improving and developing sustainable bioprocess solutions for energy recovery from challenging waste. Anaerobic digestion (AD) has been developed as a low-cost organic waste treatment technology with a simple setup and relatively limited investment and operating costs. Different technologies such as one-stage and two-stage AD have been developed. The viability and performance of these technologies have been extensively reported, showing the supremacy of two-stage AD in terms of overall energy recovery from biomass under different substrates, temperatures, and pH conditions. However, a comprehensive review of the advantages and disadvantages of these technologies is still lacking. Since microbial ecology is critical to developing successful AD, many studies have shown the structure and dynamics of archaeal and bacterial communities in this type of system. However, the role of Eukarya groups remains largely unknown to date. In this review, we provide a comprehensive review of the role, abundance, dynamics, and structure of archaeal, bacterial, and eukaryal communities during the AD process. The information provided could help researchers to select the adequate operational parameters to obtain the best performance and biogas production results.

The effects of reputational and social knowledge on cooperation

PubMed Central

Gallo, Edoardo; Yan, Chang

2015-01-01

The emergence and sustenance of cooperative behavior is fundamental for a society to thrive. Recent experimental studies have shown that cooperation increases in dynamic networks in which subjects can choose their partners. However, these studies did not vary reputational knowledge, or what subjects know about other’s past actions, which has long been recognized as an important factor in supporting cooperation. They also did not give subjects access to global social knowledge, or information on who is connected to whom in the group. As a result, it remained unknown how reputational and social knowledge foster cooperative behavior in dynamic networks both independently and by complementing each other. In an experimental setting, we show that global reputational knowledge is crucial to sustaining a high level of cooperation and welfare. Cooperation is associated with the emergence of dense and clustered networks with highly cooperative hubs. Global social knowledge has no effect on the aggregate level of cooperation. A community analysis shows that the addition of global social knowledge to global reputational knowledge affects the distribution of cooperative activity: cooperators form a separate community that achieves a higher cooperation level than the community of defectors. Members of the community of cooperators achieve a higher payoff from interactions within the community than members of the less cooperative community. PMID:25775544

Aldolase sequesters WASP and affects WASP/Arp2/3-stimulated actin dynamics.

PubMed

Ritterson Lew, Carolyn; Tolan, Dean R

2013-08-01

In addition to its roles in sugar metabolism, fructose-1,6-bisphosphate aldolase (aldolase) has been implicated in cellular functions independent from these roles, termed "moonlighting functions." These moonlighting functions likely involve the known aldolase-actin interaction, as many proteins with which aldolase interacts are involved in actin-dependent processes. Specifically, aldolase interacts both in vitro and in cells with Wiskott-Aldrich Syndrome Protein (WASP), a protein involved in controlling actin dynamics, yet the function of this interaction remains unknown. Here, the effect of aldolase on WASP-dependent processes in vitro and in cells is investigated. Aldolase inhibits WASP/Arp2/3-dependent actin polymerization in vitro. In cells, knockdown of aldolase results in a decreased rate of cell motility and cell spreading, two WASP-dependent processes. Expression of exogenous aldolase rescues these defects. Whether these effects of aldolase on WASP-dependent processes were due to aldolase catalysis or moonlighting functions is tested using aldolase variants defective in either catalytic or actin-binding activity. While the actin-binding deficient aldolase variant is unable to inhibit actin polymerization in vitro and is unable to rescue cell motility defects in cells, the catalytically inactive aldolase is able to perform these functions, providing evidence that aldolase moonlighting plays a role in WASP-mediated processes. Copyright © 2013 Wiley Periodicals, Inc.

Regularized Semiparametric Estimation for Ordinary Differential Equations

PubMed Central

Li, Yun; Zhu, Ji; Wang, Naisyin

2015-01-01

Ordinary differential equations (ODEs) are widely used in modeling dynamic systems and have ample applications in the fields of physics, engineering, economics and biological sciences. The ODE parameters often possess physiological meanings and can help scientists gain better understanding of the system. One key interest is thus to well estimate these parameters. Ideally, constant parameters are preferred due to their easy interpretation. In reality, however, constant parameters can be too restrictive such that even after incorporating error terms, there could still be unknown sources of disturbance that lead to poor agreement between observed data and the estimated ODE system. In this paper, we address this issue and accommodate short-term interferences by allowing parameters to vary with time. We propose a new regularized estimation procedure on the time-varying parameters of an ODE system so that these parameters could change with time during transitions but remain constants within stable stages. We found, through simulation studies, that the proposed method performs well and tends to have less variation in comparison to the non-regularized approach. On the theoretical front, we derive finite-sample estimation error bounds for the proposed method. Applications of the proposed method to modeling the hare-lynx relationship and the measles incidence dynamic in Ontario, Canada lead to satisfactory and meaningful results. PMID:26392639

Storage Thresholds for Relative Sea Level Signals in the Stratigraphic Record

NASA Astrophysics Data System (ADS)

Li, Q.; Yu, L.; Straub, K. M.

2015-12-01

Many argue that the tug of Relative Sea Level (RSL) change represents the most important allogenic forcing affecting deltas and is the primary control on stratigraphic architecture of deltas. However, the range of amplitudes and periodicities of RSL cycles stored in stratigraphy remains unknown. Here we use a suite of physical experiments to show that RSL cycles with magnitudes and periodicities less than the spatial and temporal scales of deltaic internal (autogenic) dynamics cannot confidently be extracted from the physical stratigraphic record. Additional analysis of deltaic morphodynamics also suggest no significant differences between an experiment with constant boundary conditions (control experiment) and an experiment with small magnitude and short periodicity RSL cycles, relative to the autogenic dynamics. Significant differences in the aspect ratio of channel bodies and deposit sand fractions do exists between our control experiment and those experiments with either large magnitudes or long periodicities RSL cycles. Using a compilation of data from major river delta systems, we show that our predicted thresholds for RSL signal storage often overlap with the magnitudes and periodicities of commonly discussed drivers of global sea level. This theory defines quantitative limits on the range of paleo-RSL information that can be extracted from the stratigraphic record, which could aid stratigraphic prediction and the inversion of stratigraphy for paleo- deltaic response to climate change.

Profiling the dynamic expression of checkpoint molecules on cytokine-induced killer cells from non-small-cell lung cancer patients.

PubMed

Zhang, Lin; Wang, Jian; Wei, Feng; Wang, Kaiyuan; Sun, Qian; Yang, Fan; Jin, Hao; Zheng, Yu; Zhao, Hua; Wang, Limei; Yu, Wenwen; Zhang, Xiying; An, Yang; Yang, Lili; Zhang, Xinwei; Ren, Xiubao

2016-07-12

Immune checkpoints associate with dysfunctional T cells, which have a reduced ability to clear pathogens or cancer cells. T-cell checkpoint blockade may improve patient survival. However, checkpoint molecules on cytokine-induced killer (CIK) cell, a non-specific adoptive immunotherapy, remain unknown. In present study, we detected the dynamic expression of eight major checkpoint molecules (CTLA-4, PD-1, PD-L1, TIM- 3, CEACAM-1, LAG-3, TIGIT and BTLA) on CIK cells from NSCLC patients. The majority of these molecules, except BTLA, were sharply elevated during the early stage of CIK cell culture. Thereafter, PD-1 and TIGIT expressions decreased gradually towards the initial level (day 0). Moreover, CTLA-4 faded away during the later stage of CIK culture. LAG-3 expression decreased but was still significantly higher than the initial level. Of note, PD-L1 remained stably upregulated during CIK culture compared with PD-1, indicating that PD-L1 might act as an inhibitory molecule on CIK cells instead of PD-1. Furthermore, TIM-3 and CEACAM1 were strongly expressed simultaneously during long-term CIK culture and showed a significant and mutually positive correlation. BTLA displayed a distinct pattern, and its expression gradually decreased throughout the CIK culture. These observations suggested that CIK cells might be partly exhausted before clinical transfusion, characterized by the high expression of PD-L1, LAG-3, TIM- 3, and CEACAM-1 and the low expression of TIGIT, BTLA, PD-1, and CTLA-4 compared with initial culture. Our results imply that implementing combined treatment on CIK cells before transfusion via antibodies targeting PD-L1, LAG-3, TIM-3, and CEACAM-1 might improve the efficiency of CIK therapy for NSCLC patients.

Inexplicable or Simply Unexplained? The Management of Maize Seed in Mexico

PubMed Central

Dyer, George A.; López-Feldman, Alejandro

2013-01-01

Farmer management of plant germplasm pre-dates crop domestication, but humans’ role in crop evolution and diversity remains largely undocumented and often contested. Seemingly inexplicable practices observed throughout agricultural history, such as exchanging or replacing seed, continue to structure crop populations across the developing world. Seed management practices can be construed as events in the life history of crops and management data used to model crop demography, but this requires suitable quantitative data. As a prerequisite to addressing the causes and implications of maize seed management, we describe its patterns of variation across Mexico by drawing from the literature and new analysis. We find that rates of seed replacement, introduction and diffusion differ significantly across regions and altitudinal zones, but interactions among explanatory factors can obscure patterns of variation. The type, source, geographic origin and ownership of seed help explain observed rates. Yet, controlling for the characteristics of germplasm barely reduces interregional differences vastly exceeding variation across elevations. With few exceptions, monotonic altitudinal trends are absent. Causal relationships between management practices and the physical environment could determine farmers’ wellbeing and crop conservation in the face of climate change. Scarce and inconsistent data on management nevertheless could prevent an understanding of these relationships. Current conceptions on the management and dynamics of maize diversity are founded on a patchwork of observations in surprisingly few and dissimilar environments. Our estimates of management practices should shed light on differences in maize population dynamics across Mexico. Consistency with previous studies spanning over a decade suggests that common sets of forces are present within large areas, but causal associations remain unknown. The next step in explaining crop diversity should address variation in seed management across space and time simultaneously while identifying farmers’ values and motivations as underlying forces. PMID:23840847

Inexplicable or simply unexplained? The management of maize seed in Mexico.

PubMed

Dyer, George A; López-Feldman, Alejandro

2013-01-01

Farmer management of plant germplasm pre-dates crop domestication, but humans' role in crop evolution and diversity remains largely undocumented and often contested. Seemingly inexplicable practices observed throughout agricultural history, such as exchanging or replacing seed, continue to structure crop populations across the developing world. Seed management practices can be construed as events in the life history of crops and management data used to model crop demography, but this requires suitable quantitative data. As a prerequisite to addressing the causes and implications of maize seed management, we describe its patterns of variation across Mexico by drawing from the literature and new analysis. We find that rates of seed replacement, introduction and diffusion differ significantly across regions and altitudinal zones, but interactions among explanatory factors can obscure patterns of variation. The type, source, geographic origin and ownership of seed help explain observed rates. Yet, controlling for the characteristics of germplasm barely reduces interregional differences vastly exceeding variation across elevations. With few exceptions, monotonic altitudinal trends are absent. Causal relationships between management practices and the physical environment could determine farmers' wellbeing and crop conservation in the face of climate change. Scarce and inconsistent data on management nevertheless could prevent an understanding of these relationships. Current conceptions on the management and dynamics of maize diversity are founded on a patchwork of observations in surprisingly few and dissimilar environments. Our estimates of management practices should shed light on differences in maize population dynamics across Mexico. Consistency with previous studies spanning over a decade suggests that common sets of forces are present within large areas, but causal associations remain unknown. The next step in explaining crop diversity should address variation in seed management across space and time simultaneously while identifying farmers' values and motivations as underlying forces.

Distributed Containment Control for Multiple Unknown Second-Order Nonlinear Systems With Application to Networked Lagrangian Systems.

PubMed

Mei, Jie; Ren, Wei; Li, Bing; Ma, Guangfu

2015-09-01

In this paper, we consider the distributed containment control problem for multiagent systems with unknown nonlinear dynamics. More specifically, we focus on multiple second-order nonlinear systems and networked Lagrangian systems. We first study the distributed containment control problem for multiple second-order nonlinear systems with multiple dynamic leaders in the presence of unknown nonlinearities and external disturbances under a general directed graph that characterizes the interaction among the leaders and the followers. A distributed adaptive control algorithm with an adaptive gain design based on the approximation capability of neural networks is proposed. We present a necessary and sufficient condition on the directed graph such that the containment error can be reduced as small as desired. As a byproduct, the leaderless consensus problem is solved with asymptotical convergence. Because relative velocity measurements between neighbors are generally more difficult to obtain than relative position measurements, we then propose a distributed containment control algorithm without using neighbors' velocity information. A two-step Lyapunov-based method is used to study the convergence of the closed-loop system. Next, we apply the ideas to deal with the containment control problem for networked unknown Lagrangian systems under a general directed graph. All the proposed algorithms are distributed and can be implemented using only local measurements in the absence of communication. Finally, simulation examples are provided to show the effectiveness of the proposed control algorithms.

Perioperative Embolization Load and S-100β Do Not Predict Cognitive Outcome after Carotid Revascularization.

PubMed

Plessers, Maarten; Van Herzeele, Isabelle; Hemelsoet, Dimitri; Vingerhoets, Guy; Vermassen, Frank

2016-10-01

Cognitive changes after carotid revascularization have been reported in 10-20% of patients. The etiology of cognitive impairments remains largely unknown. This study evaluates the predictive value of S-100β serum values and perioperative microembolization on cognition after carotid revascularization. Forty-six patients with significant carotid stenosis underwent carotid endarterectomy (CEA, n = 26), transfemoral carotid artery stenting with distal protection (CASdp, n = 10), or transcervical carotid stenting with dynamic flow reversal (CASfr, n = 10). Twenty-six matched vascular patients without carotid stenosis were recruited as controls. All patients underwent comprehensive cognitive testing on the day before and 1 month after carotid revascularization. S-100β analysis was performed in 31 cases pre-, peri-, and 2, 6, and 24 hr after carotid surgery, and in 25 patients transcranial Doppler monitoring was done during surgery. In the 3 treatment groups similar transient increases in S-100β values were observed. CASdp was associated with a higher embolic load than CEA and CASfr, while CEA was also associated with less microembolization than CASfr. Cognitive improvement or deterioration could not be predicted by S-100β or perioperative embolic load for any of the investigated cognitive domains. Cognitive deterioration could not be predicted using perioperative embolic load and S-100β changes. A similar inverted u-curve of the S-100β levels was observed in the 3 groups and may be caused by impairment in the blood-brain barrier during intervention, and not due to cerebral infarction. Distal protection CAS is associated with a higher embolic load than transcervical CAS using dynamic flow reversal and CEA, but the long-term impact of this higher embolic load is yet unknown. Perfusion-related measures seem promising in their ability to predict cognitive decline. Copyright © 2016 Elsevier Inc. All rights reserved.

77 FR 2084 - Notice of Inventory Completion: Minnesota Indian Affairs Council, Bemidji, MN

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-13

... individual were removed from site 21-AN-1, Howard Lake, Anoka County, MN, by unknown person(s) and attached... Woodland Tradition. In 1950, L.A. Wilford of the University of Minnesota excavated human remains... the University of Minnesota. In 1999, the human remains were transferred to the MIAC (H355). No known...

Should nevirapine be used to prevent mother-to-child transmission of HIV among women of unknown serostatus?

PubMed Central

Sint, Tin Tin; Dabis, François; Kamenga, Claude; Shaffer, Nathan; de Zoysa, Isabelle F.

2005-01-01

At present, HIV testing and counselling during pregnancy represent the key entry point for women to learn their serostatus and for them to access, if they are HIV-positive, specific interventions to reduce mother-to-child transmission (MTCT) of HIV. However, the provision and uptake of testing and counselling services are inadequate, and many pregnant women in countries most affected by the HIV/AIDS epidemic remain unaware of their HIV status. The offer of single-dose nevirapine prophylaxis to women whose HIV status is unknown at the time of delivery has been proposed to circumvent these problems in high-prevalence settings. The potential advantages and disadvantages of three different programme approaches are considered: targeted programmes in which antiretroviral drugs are offered only to women who are known to be HIV-positive; combined programmes in which nevirapine prophylaxis is offered to women whose serostatus remains unknown at the time of delivery despite targeted programme inputs; and universal nevirapine prophylaxis programmes in which HIV testing and counselling are not available and all pregnant women, regardless of their serostatus, are offered nevirapine prophylaxis. PMID:15798847

Cytoprotective signaling by activated protein C requires protease-activated receptor-3 in podocytes

PubMed Central

Madhusudhan, Thati; Wang, Hongjie; Straub, Beate K.; Gröne, Elisabeth; Zhou, Qianxing; Shahzad, Khurrum; Müller-Krebs, Sandra; Schwenger, Vedat; Gerlitz, Bruce; Grinnell, Brian W.; Griffin, John H.; Reiser, Jochen; Gröne, Hermann-Josef; Esmon, Charles T.; Nawroth, Peter P.

2012-01-01

The cytoprotective effects of activated protein C (aPC) are well established. In contrast, the receptors and signaling mechanism through which aPC conveys cytoprotection in various cell types remain incompletely defined. Thus, within the renal glomeruli, aPC preserves endothelial cells via a protease-activated receptor-1 (PAR-1) and endothelial protein C receptor-dependent mechanism. Conversely, the signaling mechanism through which aPC protects podocytes remains unknown. While exploring the latter, we identified a novel aPC/PAR-dependent cytoprotective signaling mechanism. In podocytes, aPC inhibits apoptosis through proteolytic activation of PAR-3 independent of endothelial protein C receptor. PAR-3 is not signaling competent itself as it requires aPCinduced heterodimerization with PAR-2 (human podocytes) or PAR-1 (mouse podocytes). This cytoprotective signaling mechanism depends on caveolin-1 dephosphorylation. In vivo aPC protects against lipopolysaccharide-induced podocyte injury and proteinuria. Genetic deletion of PAR-3 impairs the nephroprotective effect of aPC, demonstrating the crucial role of PAR-3 for aPC-dependent podocyte protection. This novel, aPC-mediated interaction of PARs demonstrates the plasticity and cell-specificity of cytoprotective aPC signaling. The evidence of specific, dynamic signaling complexes underlying aPC-mediated cytoprotection may allow the design of cell type specific targeted therapies. PMID:22117049

Molecular Imaging of Inflammation in Atherosclerosis

PubMed Central

Wildgruber, Moritz; Swirski, Filip K.; Zernecke, Alma

2013-01-01

Acute rupture of vulnerable plaques frequently leads to myocardial infarction and stroke. Within the last decades, several cellular and molecular players have been identified that promote atherosclerotic lesion formation, maturation and plaque rupture. It is now widely recognized that inflammation of the vessel wall and distinct leukocyte subsets are involved throughout all phases of atherosclerotic lesion development. The mechanisms that render a stable plaque unstable and prone to rupture, however, remain unknown and the identification of the vulnerable plaque remains a major challenge in cardiovascular medicine. Imaging technologies used in the clinic offer minimal information about the underlying biology and potential risk for rupture. New imaging technologies are therefore being developed, and in the preclinical setting have enabled new and dynamic insights into the vessel wall for a better understanding of this complex disease. Molecular imaging has the potential to track biological processes, such as the activity of cellular and molecular biomarkers in vivo and over time. Similarly, novel imaging technologies specifically detect effects of therapies that aim to stabilize vulnerable plaques and silence vascular inflammation. Here we will review the potential of established and new molecular imaging technologies in the setting of atherosclerosis, and discuss the cumbersome steps required for translating molecular imaging approaches into the clinic. PMID:24312156

Anterior prefrontal cortex contributes to action selection through tracking of recent reward trends

PubMed Central

Kovach, Christopher K.; Daw, Nathaniel; Rudrauf, David; Tranel, Daniel; O’Doherty, John P.; Adolphs, Ralph

2012-01-01

The functions of prefrontal cortex remain enigmatic, especially so for its anterior sectors, putatively ranging from planning to self-initiated behavior, social cognition, task-switching and memory. A predominant current theory regarding the most anterior sector, frontopolar cortex (FPC), is that it is involved in exploring alternate courses of action, but the detailed causal mechanisms remain unknown. Here we investigated this issue using the lesion method together with a novel model-based analysis. Eight patients with anterior prefrontal brain lesions including the FPC performed a 4-armed bandit task known from neuroimaging studies to activate FPC. Model-based analyses of learning demonstrated a selective deficit in the ability to extrapolate the most recent trend, despite an intact general ability to learn from past rewards. Whereas both brain-damaged and healthy controls used comparisons between the two most recent choice outcomes to infer trends that influenced their decision about the next choice, the group with anterior prefrontal lesions showed a complete absence of this component and instead based their choice entirely on the cumulative reward history. Given that the FPC is thought to be the most evolutionarily recent expansion of primate prefrontal cortex, we suggest that its function may reflect uniquely human adaptations to select and update models of reward contingency in dynamic environments. PMID:22723683

Handling qualities of large flexible control-configured aircraft

NASA Technical Reports Server (NTRS)

Swaim, R. L.

1979-01-01

The approach to an analytical study of flexible airplane longitudinal handling qualities was to parametrically vary the natural frequencies of two symmetric elastic modes to induce mode interactions with the rigid body dynamics. Since the structure of the pilot model was unknown for such dynamic interactions, the optimal control pilot modeling method is being applied and used in conjunction with pilot rating method.

Disturbance rejection control for vibration suppression of piezoelectric laminated thin-walled structures

NASA Astrophysics Data System (ADS)

Zhang, S. Q.; Li, H. N.; Schmidt, R.; Müller, P. C.

2014-02-01

Thin-walled piezoelectric integrated smart structures are easily excited to vibrate by unknown disturbances. In order to design and simulate a control strategy, firstly, an electro-mechanically coupled dynamic finite element (FE) model of smart structures is developed based on first-order shear deformation (FOSD) hypothesis. Linear piezoelectric constitutive equations and the assumption of constant electric field through the thickness are considered. Based on the dynamic FE model, a disturbance rejection (DR) control with proportional-integral (PI) observer using step functions as the fictitious model of disturbances is developed for vibration suppression of smart structures. In order to achieve a better dynamic behavior of the fictitious model of disturbances, the PI observer is extended to generalized proportional-integral (GPI) observer, in which sine or polynomial functions can be used to represent disturbances resulting in better dynamics. Therefore the disturbances can be estimated either by PI or GPI observer, and then the estimated signals are fed back to the controller. The DR control is validated by various kinds of unknown disturbances, and compared with linear-quadratic regulator (LQR) control. The results illustrate that the vibrations are better suppressed by the proposed DR control.

Variational Bayesian identification and prediction of stochastic nonlinear dynamic causal models.

PubMed

Daunizeau, J; Friston, K J; Kiebel, S J

2009-11-01

In this paper, we describe a general variational Bayesian approach for approximate inference on nonlinear stochastic dynamic models. This scheme extends established approximate inference on hidden-states to cover: (i) nonlinear evolution and observation functions, (ii) unknown parameters and (precision) hyperparameters and (iii) model comparison and prediction under uncertainty. Model identification or inversion entails the estimation of the marginal likelihood or evidence of a model. This difficult integration problem can be finessed by optimising a free-energy bound on the evidence using results from variational calculus. This yields a deterministic update scheme that optimises an approximation to the posterior density on the unknown model variables. We derive such a variational Bayesian scheme in the context of nonlinear stochastic dynamic hierarchical models, for both model identification and time-series prediction. The computational complexity of the scheme is comparable to that of an extended Kalman filter, which is critical when inverting high dimensional models or long time-series. Using Monte-Carlo simulations, we assess the estimation efficiency of this variational Bayesian approach using three stochastic variants of chaotic dynamic systems. We also demonstrate the model comparison capabilities of the method, its self-consistency and its predictive power.

The Information Available to a Moving Observer on Shape with Unknown, Isotropic BRDFs.

PubMed

Chandraker, Manmohan

2016-07-01

Psychophysical studies show motion cues inform about shape even with unknown reflectance. Recent works in computer vision have considered shape recovery for an object of unknown BRDF using light source or object motions. This paper proposes a theory that addresses the remaining problem of determining shape from the (small or differential) motion of the camera, for unknown isotropic BRDFs. Our theory derives a differential stereo relation that relates camera motion to surface depth, which generalizes traditional Lambertian assumptions. Under orthographic projection, we show differential stereo may not determine shape for general BRDFs, but suffices to yield an invariant for several restricted (still unknown) BRDFs exhibited by common materials. For the perspective case, we show that differential stereo yields the surface depth for unknown isotropic BRDF and unknown directional lighting, while additional constraints are obtained with restrictions on the BRDF or lighting. The limits imposed by our theory are intrinsic to the shape recovery problem and independent of choice of reconstruction method. We also illustrate trends shared by theories on shape from differential motion of light source, object or camera, to relate the hardness of surface reconstruction to the complexity of imaging setup.

Implications of land use change on the national terrestrial carbon budget of Georgia

PubMed Central

2010-01-01

Background Globally, the loss of forests now contributes almost 20% of carbon dioxide emissions to the atmosphere. There is an immediate need to reduce the current rates of forest loss, and the associated release of carbon dioxide, but for many areas of the world these rates are largely unknown. The Soviet Union contained a substantial part of the world's forests and the fate of those forests and their effect on carbon dynamics remain unknown for many areas of the former Eastern Bloc. For Georgia, the political and economic transitions following independence in 1991 have been dramatic. In this paper we quantify rates of land use changes and their effect on the terrestrial carbon budget for Georgia. A carbon book-keeping model traces changes in carbon stocks using historical and current rates of land use change. Landsat satellite images acquired circa 1990 and 2000 were analyzed to detect changes in forest cover since 1990. Results The remote sensing analysis showed that a modest forest loss occurred, with approximately 0.8% of the forest cover having disappeared after 1990. Nevertheless, growth of Georgian forests still contribute a current national sink of about 0.3 Tg of carbon per year, which corresponds to 31% of the country anthropogenic carbon emissions. Conclusions We assume that the observed forest loss is mainly a result of illegal logging, but we have not found any evidence of large-scale clear-cutting. Instead local harvesting of timber for household use is likely to be the underlying driver of the observed logging. The Georgian forests are a currently a carbon sink and will remain as such until about 2040 if the current rate of deforestation persists. Forest protection efforts, combined with economic growth, are essential for reducing the rate of deforestation and protecting the carbon sink provided by Georgian forests. PMID:20836865

Intrathecal immunoglobulin synthesis in patients with symptomatic epilepsy and epilepsy of unknown etiology ('cryptogenic').

PubMed

Fauser, S; Soellner, C; Bien, C G; Tumani, H

2017-09-01

To compare the frequency of intrathecal immunoglobulin (Ig) synthesis in patients with symptomatic epilepsy and epilepsy of unknown etiology ('cryptogenic'). Patients with epileptic (n = 301) and non-epileptic (n = 10) seizures were retrospectively screened for autochthonous intrathecal Ig synthesis and oligoclonal bands (OCBs) in the cerebrospinal fluid. Intrathecal IgG/OCBs were detected in 8% of patients with epilepsies of unknown etiology, 5% of patients with first seizures of unknown cause and 0-4% of patients with epilepsy due to brain tumors, cerebrovascular disease or other etiologies. Intrathecal IgG/OCBs were not seen in patients with psychogenic seizures. Identical OCBs in serum and cerebrospinal fluid were more common in all patient groups (10-40% depending on underlying etiology). Intrathecal IgG synthesis/OCBs were observed slightly more frequently in patients with 'cryptogenic' epilepsy and with first seizures of unknown etiology than in other patient groups. However, this remained an infrequent finding and thus we could not confirm humoral immunity as a leading disease mechanism in patients with epilepsy in general or with unknown etiology in particular. © 2017 EAN.

Mobile robot dynamic path planning based on improved genetic algorithm

NASA Astrophysics Data System (ADS)

Wang, Yong; Zhou, Heng; Wang, Ying

2017-08-01

In dynamic unknown environment, the dynamic path planning of mobile robots is a difficult problem. In this paper, a dynamic path planning method based on genetic algorithm is proposed, and a reward value model is designed to estimate the probability of dynamic obstacles on the path, and the reward value function is applied to the genetic algorithm. Unique coding techniques reduce the computational complexity of the algorithm. The fitness function of the genetic algorithm fully considers three factors: the security of the path, the shortest distance of the path and the reward value of the path. The simulation results show that the proposed genetic algorithm is efficient in all kinds of complex dynamic environments.

Adaptive super-twisting observer for estimation of random road excitation profile in automotive suspension systems.

PubMed

Rath, J J; Veluvolu, K C; Defoort, M

2014-01-01

The estimation of road excitation profile is important for evaluation of vehicle stability and vehicle suspension performance for autonomous vehicle control systems. In this work, the nonlinear dynamics of the active automotive system that is excited by the unknown road excitation profile are considered for modeling. To address the issue of estimation of road profile, we develop an adaptive supertwisting observer for state and unknown road profile estimation. Under Lipschitz conditions for the nonlinear functions, the convergence of the estimation error is proven. Simulation results with Ford Fiesta MK2 demonstrate the effectiveness of the proposed observer for state and unknown input estimation for nonlinear active suspension system.

Adaptive Super-Twisting Observer for Estimation of Random Road Excitation Profile in Automotive Suspension Systems

PubMed Central

Rath, J. J.; Veluvolu, K. C.; Defoort, M.

2014-01-01

The estimation of road excitation profile is important for evaluation of vehicle stability and vehicle suspension performance for autonomous vehicle control systems. In this work, the nonlinear dynamics of the active automotive system that is excited by the unknown road excitation profile are considered for modeling. To address the issue of estimation of road profile, we develop an adaptive supertwisting observer for state and unknown road profile estimation. Under Lipschitz conditions for the nonlinear functions, the convergence of the estimation error is proven. Simulation results with Ford Fiesta MK2 demonstrate the effectiveness of the proposed observer for state and unknown input estimation for nonlinear active suspension system. PMID:24683321

Residual perception of biological motion in cortical blindness.

PubMed

Ruffieux, Nicolas; Ramon, Meike; Lao, Junpeng; Colombo, Françoise; Stacchi, Lisa; Borruat, François-Xavier; Accolla, Ettore; Annoni, Jean-Marie; Caldara, Roberto

2016-12-01

From birth, the human visual system shows a remarkable sensitivity for perceiving biological motion. This visual ability relies on a distributed network of brain regions and can be preserved even after damage of high-level ventral visual areas. However, it remains unknown whether this critical biological skill can withstand the loss of vision following bilateral striate damage. To address this question, we tested the categorization of human and animal biological motion in BC, a rare case of cortical blindness after anoxia-induced bilateral striate damage. The severity of his impairment, encompassing various aspects of vision (i.e., color, shape, face, and object recognition) and causing blind-like behavior, contrasts with a residual ability to process motion. We presented BC with static or dynamic point-light displays (PLDs) of human or animal walkers. These stimuli were presented either individually, or in pairs in two alternative forced choice (2AFC) tasks. When confronted with individual PLDs, the patient was unable to categorize the stimuli, irrespective of whether they were static or dynamic. In the 2AFC task, BC exhibited appropriate eye movements towards diagnostic information, but performed at chance level with static PLDs, in stark contrast to his ability to efficiently categorize dynamic biological agents. This striking ability to categorize biological motion provided top-down information is important for at least two reasons. Firstly, it emphasizes the importance of assessing patients' (visual) abilities across a range of task constraints, which can reveal potential residual abilities that may in turn represent a key feature for patient rehabilitation. Finally, our findings reinforce the view that the neural network processing biological motion can efficiently operate despite severely impaired low-level vision, positing our natural predisposition for processing dynamicity in biological agents as a robust feature of human vision. Copyright © 2016 Elsevier Ltd. All rights reserved.

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

PubMed Central

Rodriguez-Fernandez, Maria; Egea, Jose A; Banga, Julio R

2006-01-01

Background We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. Results We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown) structure (i.e. black-box models). In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned) successful methods. Conclusion Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously used for these benchmark problems. PMID:17081289

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.

PubMed

Rodriguez-Fernandez, Maria; Egea, Jose A; Banga, Julio R

2006-11-02

We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown) structure (i.e. black-box models). In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned) successful methods. Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously used for these benchmark problems.

Ice formation on kaolinite: Insights from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

2016-12-01

The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

Kinetic measures of restabilisation during volitional stepping reveal age-related alterations in the control of mediolateral dynamic stability.

PubMed

Singer, Jonathan C; McIlroy, William E; Prentice, Stephen D

2014-11-07

Research examining age-related changes in dynamic stability during stepping has recognised the importance of the restabilisation phase, subsequent to foot-contact. While regulation of the net ground reaction force (GRFnet) line of action is believed to influence dynamic stability during steady-state locomotion, such control during restabilisation remains unknown. This work explored the origins of age-related decline in mediolateral dynamic stability by examining the line of action of GRFnet relative to the centre of mass (COM) during restabilisation following voluntary stepping. Healthy younger and older adults (n=20 per group) performed three single-step tasks (varying speed and step placement), altering the challenge to stability control. Age-related differences in magnitude and intertrial variability of the angle of divergence of GRFnet line of action relative to the COM were quantified, along with the peak mediolateral and vertical GRFnet components. The angle of divergence was further examined at discrete points during restabilisation, to uncover events of potential importance to stability control. Older adults exhibited a reduced angle of divergence throughout restabilisation. Temporal and spatial constraints on stepping increased the magnitude and intertrial variability of the angle of divergence, although not differentially among the older adults. Analysis of the time-varying angle of divergence revealed age-related reductions in magnitude, with increases in timing and intertrial timing variability during the later phase of restabilisation. This work further supports the idea that age-related challenges in lateral stability control emerge during restabilisation. Age-related alterations during the later phase of restabilisation may signify challenges with reactive control. Copyright © 2014 Elsevier Ltd. All rights reserved.

Adaptive Neural Output Feedback Control for Nonstrict-Feedback Stochastic Nonlinear Systems With Unknown Backlash-Like Hysteresis and Unknown Control Directions.

PubMed

Yu, Zhaoxu; Li, Shugang; Yu, Zhaosheng; Li, Fangfei

2018-04-01

This paper investigates the problem of output feedback adaptive stabilization for a class of nonstrict-feedback stochastic nonlinear systems with both unknown backlashlike hysteresis and unknown control directions. A new linear state transformation is applied to the original system, and then, control design for the new system becomes feasible. By combining the neural network's (NN's) parameterization, variable separation technique, and Nussbaum gain function method, an input-driven observer-based adaptive NN control scheme, which involves only one parameter to be updated, is developed for such systems. All closed-loop signals are bounded in probability and the error signals remain semiglobally bounded in the fourth moment (or mean square). Finally, the effectiveness and the applicability of the proposed control design are verified by two simulation examples.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Estimating Topology of Discrete Dynamical Networks

NASA Astrophysics Data System (ADS)

Guo, Shu-Juan; Fu, Xin-Chu

2010-07-01

In this paper, by applying Lasalle's invariance principle and some results about the trace of a matrix, we propose a method for estimating the topological structure of a discrete dynamical network based on the dynamical evolution of the network. The network concerned can be directed or undirected, weighted or unweighted, and the local dynamics of each node can be nonidentical. The connections among the nodes can be all unknown or partially known. Finally, two examples, including a Hénon map and a central network, are illustrated to verify the theoretical results.

Lack of evidence for meteorological effects on infradian dynamics of testosterone

NASA Astrophysics Data System (ADS)

Celec, Peter; Smreková, Lucia; Ostatníková, Daniela; Čabajová, Zlata; Hodosy, Július; Kúdela, Matúš

2009-09-01

Climatic factors are known to influence the endocrine system. Previous studies have shown that circannual seasonal variations of testosterone might be partly explained by changes in air temperature. Whether infradian variations are affected by meteorological factors is unknown. To analyze possible effects of meteorological parameters on infradian variations of salivary testosterone levels in both sexes, daily salivary testosterone levels were measured during 1 month in 14 men and 17 women. A correlation analysis between hormonal levels and selected meteorological parameters was performed. The results indicate that high testosterone levels are loosely associated with cold, sunny and dry weather in both sexes. However, only the correlations between testosterone and air temperature (men) and actual cloudiness (women) were statistically significant ( p < 0,05). Although some correlations reached the level of statistical significance, the effects of selected meteorological parameters on salivary testosterone levels remain unclear. Further longer-term studies concentrating on air temperature, cloudiness and average relative humidity in relation to the sex hormone axis are needed.

Sleep contributes to dendritic spine formation and elimination in the developing mouse somatosensory cortex

PubMed Central

Yang, Guang; Gan, Wen-Biao

2012-01-01

Sleep is maximal during early postnatal life when rapid and extensive synapse remodeling occurs. It remains unknown whether and how sleep affects synapse development and plasticity. Using transcranial two-photon microscopy, we examined the formation and elimination of fluorescently-labeled dendritic spines and filopodia of layer 5 pyramidal neurons in the barrel cortex of 3-week old mice during wakefulness and sleep. We observed high turnover of dendritic protrusions over 2 hours in both wake and sleep states. The formation rate of dendritic spines or filopodia over 2 hours was comparable between the two states. The elimination rate of dendritic spines or filopodia was lower during 2-hour wakefulness than during 2-hour sleep. Similar results were observed on dendritic protrusion dynamics over 12-hour light/dark cycle when mice spent more time asleep or awake. The substantial remodeling of dendritic protrusions during the sleep state supports the notion that sleep plays an important role in the development and plasticity of synaptic connections in the mouse cortex. PMID:22058046

Mental simulation of routes during navigation involves adaptive temporal compression

PubMed Central

Arnold, Aiden E.G.F.; Iaria, Giuseppe; Ekstrom, Arne D.

2016-01-01

Mental simulation is a hallmark feature of human cognition, allowing features from memories to be flexibly used during prospection. While past studies demonstrate the preservation of real-world features such as size and distance during mental simulation, their temporal dynamics remains unknown. Here, we compare mental simulations to navigation of routes in a large-scale spatial environment to test the hypothesis that such simulations are temporally compressed in an adaptive manner. Our results show that simulations occurred at 2.39x the speed it took to navigate a route, increasing in compression (3.57x) for slower movement speeds. Participant self-reports of vividness and spatial coherence of simulations also correlated strongly with simulation duration, providing an important link between subjective experiences of simulated events and how spatial representations are combined during prospection. These findings suggest that simulation of spatial events involve adaptive temporal mechanisms, mediated partly by the fidelity of memories used to generate the simulation. PMID:27568586

Low-intensity electric fields induce two distinct response components in neocortical neuronal populations

PubMed Central

Xu, Weifeng; Wolff, Brian S.

2014-01-01

Low-intensity alternating electric fields applied to the scalp are capable of modulating cortical activity and brain functions, but the underlying mechanisms remain largely unknown. Here, we report two distinct components of voltage-sensitive dye signals induced by low-intensity, alternating electric fields in rodent cortical slices: a “passive component,” which corresponds to membrane potential changes directly induced by the electric field; and an “active component,” which is a widespread depolarization that is dependent on excitatory synaptic transmission. The passive component is stationary, with amplitude and phase accurately reflecting the cortical cytoarchitecture. In contrast, the active component is initiated from a local “hot spot” of activity and spreads to a large population as a propagating wave with rich local dynamics. The propagation of the active component may play a role in modulating large-scale cortical activity by spreading a low level of excitation from a small initiation point to a vast neuronal population. PMID:25122710

Backbone hydration determines the folding signature of amino acid residues.

PubMed

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-08

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Control of Systems With Slow Actuators Using Time Scale Separation

NASA Technical Reports Server (NTRS)

Stepanyan, Vehram; Nguyen, Nhan

2009-01-01

This paper addresses the problem of controlling a nonlinear plant with a slow actuator using singular perturbation method. For the known plant-actuator cascaded system the proposed scheme achieves tracking of a given reference model with considerably less control demand than would otherwise result when using conventional design techniques. This is the consequence of excluding the small parameter from the actuator dynamics via time scale separation. The resulting tracking error is within the order of this small parameter. For the unknown system the adaptive counterpart is developed based on the prediction model, which is driven towards the reference model by the control design. It is proven that the prediction model tracks the reference model with an error proportional to the small parameter, while the prediction error converges to zero. The resulting closed-loop system with all prediction models and adaptive laws remains stable. The benefits of the approach are demonstrated in simulation studies and compared to conventional control approaches.

FAR and NEAR Target Dynamic Visual Acuity: A Functional Assessment of Canal and Otolith Performance

NASA Technical Reports Server (NTRS)

Peters, Brian T.; Brady, Rachel A.; Landsness, Eric C.; Black, F. Owen; Bloomberg, Jacob J.

2004-01-01

Upon their return to earth, astronauts experience the effects of vestibular adaptation to microgravity. The postflight changes in vestibular information processing can affect postural and locomotor stability and may lead to oscillopsia during activities of daily living. However, it is likely that time spent in microgravity affects canal and otolith function differently. As a result, the isolated rotational stimuli used in traditional tests of canal function may fail to identify vestibular deficits after spaceflight. Also, the functional consequences of deficits that are identified often remain unknown. In a gaze control task, the relative contributions of the canal and otolith organs are modulated with viewing distance. The ability to stabilize gaze during a perturbation, on visual targets placed at different distances from the head may therefore provide independent insight into the function of this systems. Our goal was to develop a functional measure of gaze control that can also offer independent information about the function of the canal and otolith organs.

Understanding Phase-Change Memory Alloys from a Chemical Perspective

NASA Astrophysics Data System (ADS)

Kolobov, A. V.; Fons, P.; Tominaga, J.

2015-09-01

Phase-change memories (PCM) are associated with reversible ultra-fast low-energy crystal-to-amorphous switching in GeTe-based alloys co-existing with the high stability of the two phases at ambient temperature, a unique property that has been recently explained by the high fragility of the glass-forming liquid phase, where the activation barrier for crystallisation drastically increases as the temperature decreases from the glass-transition to room temperature. At the same time the atomistic dynamics of the phase-change process and the associated changes in the nature of bonding have remained unknown. In this work we demonstrate that key to this behavior is the formation of transient three-center bonds in the excited state that is enabled due to the presence of lone-pair electrons. Our findings additionally reveal previously ignored fundamental similarities between the mechanisms of reversible photoinduced structural changes in chalcogenide glasses and phase-change alloys and offer new insights into the development of efficient PCM materials.

Understanding Phase-Change Memory Alloys from a Chemical Perspective.

PubMed

Kolobov, A V; Fons, P; Tominaga, J

2015-09-01

Phase-change memories (PCM) are associated with reversible ultra-fast low-energy crystal-to-amorphous switching in GeTe-based alloys co-existing with the high stability of the two phases at ambient temperature, a unique property that has been recently explained by the high fragility of the glass-forming liquid phase, where the activation barrier for crystallisation drastically increases as the temperature decreases from the glass-transition to room temperature. At the same time the atomistic dynamics of the phase-change process and the associated changes in the nature of bonding have remained unknown. In this work we demonstrate that key to this behavior is the formation of transient three-center bonds in the excited state that is enabled due to the presence of lone-pair electrons. Our findings additionally reveal previously ignored fundamental similarities between the mechanisms of reversible photoinduced structural changes in chalcogenide glasses and phase-change alloys and offer new insights into the development of efficient PCM materials.

Activity-dependent switch of GABAergic inhibition into glutamatergic excitation in astrocyte-neuron networks.

PubMed

Perea, Gertrudis; Gómez, Ricardo; Mederos, Sara; Covelo, Ana; Ballesteros, Jesús J; Schlosser, Laura; Hernández-Vivanco, Alicia; Martín-Fernández, Mario; Quintana, Ruth; Rayan, Abdelrahman; Díez, Adolfo; Fuenzalida, Marco; Agarwal, Amit; Bergles, Dwight E; Bettler, Bernhard; Manahan-Vaughan, Denise; Martín, Eduardo D; Kirchhoff, Frank; Araque, Alfonso

2016-12-24

Interneurons are critical for proper neural network function and can activate Ca 2+ signaling in astrocytes. However, the impact of the interneuron-astrocyte signaling into neuronal network operation remains unknown. Using the simplest hippocampal Astrocyte-Neuron network, i.e., GABAergic interneuron, pyramidal neuron, single CA3-CA1 glutamatergic synapse, and astrocytes, we found that interneuron-astrocyte signaling dynamically affected excitatory neurotransmission in an activity- and time-dependent manner, and determined the sign (inhibition vs potentiation) of the GABA-mediated effects. While synaptic inhibition was mediated by GABA A receptors, potentiation involved astrocyte GABA B receptors, astrocytic glutamate release, and presynaptic metabotropic glutamate receptors. Using conditional astrocyte-specific GABA B receptor ( Gabbr1 ) knockout mice, we confirmed the glial source of the interneuron-induced potentiation, and demonstrated the involvement of astrocytes in hippocampal theta and gamma oscillations in vivo. Therefore, astrocytes decode interneuron activity and transform inhibitory into excitatory signals, contributing to the emergence of novel network properties resulting from the interneuron-astrocyte interplay.

Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland.

PubMed

Lilja, Anna M; Rodilla, Veronica; Huyghe, Mathilde; Hannezo, Edouard; Landragin, Camille; Renaud, Olivier; Leroy, Olivier; Rulands, Steffen; Simons, Benjamin D; Fre, Silvia

2018-06-01

Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.

Phylogenetic characterization of hantaviruses from wild rodents and hantavirus pulmonary syndrome cases in the state of Parana (southern Brazil).

PubMed

Raboni, Sonia Mara; Hoffmann, Federico G; Oliveira, Renata C; Teixeira, Bernardo R; Bonvicino, Cibele R; Stella, Vanessa; Carstensen, Suzana; Bordignon, Juliano; D'Andrea, Paulo S; Lemos, Elba R S; Duarte Dos Santos, Claudia Nunes

2009-09-01

Over 1,100 cases of hantavirus pulmonary syndrome (HPS) have occurred in Brazil since 1993, but little is known about Brazilian hantaviruses, and many of their rodent hosts remain unknown. The Araucaria hantavirus (ARAUV) was described recently from HPS patients from Paraná, in southern Brazil, but its host could not be identified. In this study, rodents were captured from regions with high HPS prevalence to address this issue. ARAUV RNA was detected in three distantly related rodent species: Oligoryzomys nigripes, Oxymycterus judex and Akodon montensis. Furthermore, a specimen of A. montensis was infected with a Jaborá-like virus, implying that A. montensis can be infected by at least two different hantaviruses. The presence of the same hantavirus strain in three different rodent species and the co-circulation of two different strains in the same rodent species highlight the potential for genomic reassortment, which could have an impact on hantavirus transmission dynamics in nature and on human epidemiology.

Membrane Driven Spatial Organization of GPCRs

NASA Astrophysics Data System (ADS)

Mondal, Sayan; Johnston, Jennifer M.; Wang, Hao; Khelashvili, George; Filizola, Marta; Weinstein, Harel

2013-10-01

Spatial organization of G-protein coupled receptors (GPCRs) into dimers and higher order oligomers has been demonstrated in vitro and in vivo. The pharmacological readout was shown to depend on the specific interfaces, but why particular regions of the GPCR structure are involved, and how ligand-determined states change them remains unknown. Here we show why protein-membrane hydrophobic matching is attained upon oligomerization at specific interfaces from an analysis of coarse-grained molecular dynamics simulations of the spontaneous diffusion-interaction of the prototypical beta2-adrenergic (β2AR) receptors in a POPC lipid bilayer. The energy penalty from mismatch is significantly reduced in the spontaneously emerging oligomeric arrays, making the spatial organization of the GPCRs dependent on the pattern of mismatch in the monomer. This mismatch pattern is very different for β2AR compared to the highly homologous and structurally similar β1AR, consonant with experimentally observed oligomerization patterns of β2AR and β1AR. The results provide a mechanistic understanding of the structural context of oligomerization.

Generation Mechanism of Alternans in Luo-Rudy Model

NASA Astrophysics Data System (ADS)

Kitajima, Hiroyuki; Ioka, Eri; Yazawa, Toru

Electrical alternans is the alternating amplitude from beat to beat in the action potential of the cardiac cell. It has been associated with ventricular arrhythmias in many clinical studies; however, its dynamical mechanisms remain unknown. The reason is that we do not have realistic network models of the heart system. Recently, Yazawa clarified the network structure of the heart and the central nerve system in the crustacean heart. In this study, we construct a simple model of the heart system based on Yazawa’s experimental data. Using this model, we clarify that two parameters (the conductance of sodium ions and free concentration of potassium ions in the extracellular compartment) play the key roles of generating alternans. In particular, we clarify that the inactivation gate of the time-independent potassium channel is the most important parameter. Moreover, interaction between the membrane potential and potassium ionic currents is significant for generating alternate rhythms. This result indicates that if the muscle cell has problems such as channelopathies, there is great risk of generating alternans.

Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity

PubMed Central

Bhattacharyya, Sanchari; Bershtein, Shimon; Yan, Jin; Argun, Tijda; Gilson, Amy I; Trauger, Sunia A; Shakhnovich, Eugene I

2016-01-01

Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization – molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between ‘E. coli’s self’ and ‘foreign’ proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness. DOI: http://dx.doi.org/10.7554/eLife.20309.001 PMID:27938662

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.

Primitive chain network simulations for entangled DNA solutions

NASA Astrophysics Data System (ADS)

Masubuchi, Yuichi; Furuichi, Kenji; Horio, Kazushi; Uneyama, Takashi; Watanabe, Hiroshi; Ianniruberto, Giovanni; Greco, Francesco; Marrucci, Giuseppe

2009-09-01

Molecular theories for polymer rheology are based on conformational dynamics of the polymeric chain. Hence, measurements directly related to molecular conformations appear more appealing than indirect ones obtained from rheology. In this study, primitive chain network simulations are compared to experimental data of entangled DNA solutions [Teixeira et al., Macromolecules 40, 2461 (2007)]. In addition to rheological comparisons of both linear and nonlinear viscoelasticities, a molecular extension measure obtained by Teixeira et al. through fluorescent microscopy is compared to simulations, in terms of both averages and distributions. The influence of flow on conformational distributions has never been simulated for the case of entangled polymers, and how DNA molecular individualism extends to the entangled regime is not known. The linear viscoelastic response and the viscosity growth curve in the nonlinear regime are found in good agreement with data for various DNA concentrations. Conversely, the molecular extension measure shows significant departures, even under equilibrium conditions. The reason for such discrepancies remains unknown.

Nucleation and growth of a bacterial functional amyloid at single fiber resolution

PubMed Central

Feuillie, Cécile; Jonckheere, Wim; Valotteau, Claire; Dufrêne, Yves F.; Remaut, Han

2017-01-01

Curli are functional amyloids produced by proteobacteria like Escherichia coli, as part of the extracellular matrix that holds cells together into biofilms. The molecular events during curli nucleation and fiber extension remain largely unknown. Combining observations from curli amyloidogenesis in bulk solutions with real-time in situ nanoscopic imaging at the single fiber level, we show that curli display polar growth, and detect two kinetic regimes of fiber elongation. Single fibers exhibit stop-and-go dynamics characterized by bursts of steady-state growth alternated with periods of stagnation. At high subunit concentrations fibers show constant, unperturbed burst growth. Curli follow a one-step nucleation process, where monomers contemporaneously fold and oligomerize into minimal fiber units that have growth characteristics identical to the mature fibrils. Kinetic data and interaction studies of curli fibrillation in the presence of the natural inhibitor CsgC show the inhibitor binds curli fibers and predominantly acts at the level of fiber elongation. PMID:28628096

Strategy evolution driven by switching probabilities in structured multi-agent systems

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Chen, Zengqiang; Li, Zhiqi

2017-10-01

Evolutionary mechanism driving the commonly seen cooperation among unrelated individuals is puzzling. Related models for evolutionary games on graphs traditionally assume that players imitate their successful neighbours with higher benefits. Notably, an implicit assumption here is that players are always able to acquire the required pay-off information. To relax this restrictive assumption, a contact-based model has been proposed, where switching probabilities between strategies drive the strategy evolution. However, the explicit and quantified relation between a player's switching probability for her strategies and the number of her neighbours remains unknown. This is especially a key point in heterogeneously structured system, where players may differ in the numbers of their neighbours. Focusing on this, here we present an augmented model by introducing an attenuation coefficient and evaluate its influence on the evolution dynamics. Results show that the individual influence on others is negatively correlated with the contact numbers specified by the network topologies. Results further provide the conditions under which the coexisting strategies can be calculated analytically.

Learning shapes the aversion and reward responses of lateral habenula neurons

PubMed Central

Wang, Daqing; Li, Yi; Feng, Qiru; Guo, Qingchun; Zhou, Jingfeng; Luo, Minmin

2017-01-01

The lateral habenula (LHb) is believed to encode negative motivational values. It remains unknown how LHb neurons respond to various stressors and how learning shapes their responses. Here, we used fiber-photometry and electrophysiology to track LHb neuronal activity in freely-behaving mice. Bitterness, pain, and social attack by aggressors intensively excite LHb neurons. Aversive Pavlovian conditioning induced activation by the aversion-predicting cue in a few trials. The experience of social defeat also conditioned excitatory responses to previously neutral social stimuli. In contrast, fiber photometry and single-unit recordings revealed that sucrose reward inhibited LHb neurons and often produced excitatory rebound. It required prolonged conditioning and high reward probability to induce inhibition by reward-predicting cues. Therefore, LHb neurons can bidirectionally process a diverse array of aversive and reward signals. Importantly, their responses are dynamically shaped by learning, suggesting that the LHb participates in experience-dependent selection of behavioral responses to stressors and rewards. DOI: http://dx.doi.org/10.7554/eLife.23045.001 PMID:28561735

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors

NASA Astrophysics Data System (ADS)

Ortega, Davi R.; Yang, Chen; Ames, Peter; Baudry, Jerome; Parkinson, John S.; Zhulin, Igor B.

2013-12-01

Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a signal-dependent manner. A highly conserved residue, Phe396, appears to serve as the conformational switch, because flipping of the stacked aromatic rings of an interacting F396-F396‧ pair in the receptor homodimer takes place concomitantly with the signal-related conformational changes. We suggest that interacting aromatic residues, which are common stabilizers of protein tertiary structure, might serve as rotameric molecular switches in other biological processes as well.

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

PubMed Central

Wirth, Thierry; Hildebrand, Falk; Allix-Béguec, Caroline; Wölbeling, Florian; Kubica, Tanja; Kremer, Kristin; van Soolingen, Dick; Rüsch-Gerdes, Sabine; Locht, Camille; Brisse, Sylvain; Meyer, Axel

2008-01-01

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of “modern” human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations. PMID:18802459

Janus effect of antifreeze proteins on ice nucleation.

PubMed

Liu, Kai; Wang, Chunlei; Ma, Ji; Shi, Guosheng; Yao, Xi; Fang, Haiping; Song, Yanlin; Wang, Jianjun

2016-12-20

The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non-ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation.

Janus effect of antifreeze proteins on ice nucleation

PubMed Central

Liu, Kai; Wang, Chunlei; Ma, Ji; Shi, Guosheng; Yao, Xi; Fang, Haiping; Song, Yanlin; Wang, Jianjun

2016-01-01

The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non–ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation. PMID:27930318

Endophilin B1

PubMed Central

Cheung, Zelda H

2009-01-01

Endophilin B1 is a member of the endophilin family that is localized predominantly to intracellular membranes. Also known as Bax-interacting factor-1 (Bif-1), this protein has been observed to regulate the membrane dynamics of various intracellular compartments, such as the control of mitochondrial morphology and autophagosome formation in fibroblast. Endophilin B1 is expressed in the brain, but its functions in neurons had remained unknown. Recently, we have observed a novel role of endophilin B1 in neurons where it controls the trafficking of TrkA, cognate receptor for the prototypic neurotrophin nerve growth factor (NGF). Knock-down of endophilin B1 expression induces precocious targeting of NGF/TrkA to late endosomes and lysosomes, thereby leading to reduced TrkA levels. This is accompanied by marked attenuation of NGF-induced gene transcription and neurite outgrowth. Our observations suggest that endophilin B1 regulates TrkA level and downstream functions by controlling the movement of TrkA to late endosomes/lysosomes, possibly acting at the level of early endosomes. PMID:19704909

Ergothioneine maintains redox and bioenergetic homeostasis essential for drug susceptibility and virulence of Mycobacterium tuberculosis

PubMed Central

Saini, Vikram; Cumming, Bridgette M.; Guidry, Loni; Lamprecht, Dirk; Adamson, John H.; Reddy, Vineel P.; Chinta, Krishna C.; Mazorodzo, James; Glasgow, Joel N.; Richard-Greenblatt, Melissa; Gomez-Velasco, Anaximandro; Bach, Horacio; Av-Gay, Yossef; Eoh, Hyungjin; Rhee, Kyu; Steyn, Adrie J.C.

2016-01-01

SUMMARY The mechanisms by which Mycobacterium tuberculosis (Mtb) maintains metabolic equilibrium to survive during infection and upon exposure to antimycobacterial drugs are poorly characterized. Ergothioneine (EGT) and mycothiol (MSH) are the major redox buffers present in Mtb, but the contribution of EGT to Mtb redox homeostasis and virulence remains unknown. We report that Mtb WhiB3, a 4Fe-4S redox sensor protein, regulates EGT production and maintains bioenergetic homeostasis. We show that central carbon metabolism and lipid precursors regulate EGT production and that EGT modulates drug sensitivity. Notably, EGT and MSH are both essential for redox and bioenergetic homeostasis. Transcriptomic analyses of EGT and MSH mutants indicate overlapping, but distinct functions of EGT and MSH. Lastly, we show that EGT is critical for Mtb survival in both macrophages and mice. This study has uncovered a dynamic balance between Mtb redox and bioenergetic homeostasis, which critically influences Mtb drug susceptibility and pathogenicity. PMID:26774486

A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.

PubMed

Bartlett, Thomas M; Bratton, Benjamin P; Duvshani, Amit; Miguel, Amanda; Sheng, Ying; Martin, Nicholas R; Nguyen, Jeffrey P; Persat, Alexandre; Desmarais, Samantha M; VanNieuwenhze, Michael S; Huang, Kerwyn Casey; Zhu, Jun; Shaevitz, Joshua W; Gitai, Zemer

2017-01-12

Pathogenic Vibrio cholerae remains a major human health concern. V. cholerae has a characteristic curved rod morphology, with a longer outer face and a shorter inner face. The mechanism and function of this curvature were previously unknown. Here, we identify and characterize CrvA, the first curvature determinant in V. cholerae. CrvA self-assembles into filaments at the inner face of cell curvature. Unlike traditional cytoskeletons, CrvA localizes to the periplasm and thus can be considered a periskeletal element. To quantify how curvature forms, we developed QuASAR (quantitative analysis of sacculus architecture remodeling), which measures subcellular peptidoglycan dynamics. QuASAR reveals that CrvA asymmetrically patterns peptidoglycan insertion rather than removal, causing more material insertions into the outer face than the inner face. Furthermore, crvA is quorum regulated, and CrvA-dependent curvature increases at high cell density. Finally, we demonstrate that CrvA promotes motility in hydrogels and confers an advantage in host colonization and pathogenesis. Copyright © 2017 Elsevier Inc. All rights reserved.

The subcortical maternal complex controls symmetric division of mouse zygotes by regulating F-actin dynamics.

PubMed

Yu, Xing-Jiang; Yi, Zhaohong; Gao, Zheng; Qin, Dandan; Zhai, Yanhua; Chen, Xue; Ou-Yang, Yingchun; Wang, Zhen-Bo; Zheng, Ping; Zhu, Min-Sheng; Wang, Haibin; Sun, Qing-Yuan; Dean, Jurrien; Li, Lei

2014-09-11

Maternal effect genes play critical roles in early embryogenesis of model organisms where they have been intensively investigated. However, their molecular function in mammals remains largely unknown. Recently, we identified a subcortical maternal complex (SCMC) that contains four proteins encoded by maternal effect genes (Mater, Filia, Floped and Tle6). Here we report that TLE6, similar to FLOPED and MATER, stabilizes the SCMC and is necessary for cleavage beyond the two-cell stage of development. We document that the SCMC is required for formation of the cytoplasmic F-actin meshwork that controls the central position of the spindle and ensures symmetric division of mouse zygotes. We further demonstrate that the SCMC controls formation of the actin cytoskeleton specifically via Cofilin, a key regulator of F-actin assembly. Our results provide molecular insight into the physiological function of TLE6, its interaction with the SCMC and their roles in the symmetric division of the zygote in early mouse development.

Dynamic, cell type-specific roles for GABAergic interneurons in a mouse model of optogenetically inducible seizures

PubMed Central

Khoshkhoo, Sattar; Vogt, Daniel; Sohal, Vikaas S.

2016-01-01

SUMMARY GABAergic interneurons play critical roles in seizures, but it remains unknown whether these vary across interneuron subtypes or evolve during a seizure. This uncertainty stems from the unpredictable timing of seizures in most models, which limits neuronal imaging or manipulations around the seizure onset. Here, we describe a mouse model for optogenetic seizure induction. Combining this with calcium imaging, we find that seizure onset rapidly recruits parvalbumin (PV), somatostatin (SOM), and vasoactive intestinal peptitde (VIP)-expressing interneurons, whereas excitatory neurons are recruited several seconds later. Optogenetically inhibiting VIP interneurons consistently increased seizure threshold and reduced seizure duration. Inhibiting PV+ and SOM+ interneurons had mixed effects on seizure initiation, but consistently reduced seizure duration. Thus, while their roles may evolve during seizures, PV+ and SOM+ interneurons ultimately help maintain ongoing seizures. These results show how an optogenetically-induced seizure model can be leveraged to pinpoint a new target for seizure control: VIP interneurons. PMID:28041880

High damage tolerance of electrochemically lithiated silicon

DOE PAGES

Wang, Xueju; Fan, Feifei; Wang, Jiangwei; ...

2015-09-24

Mechanical degradation and resultant capacity fade in high-capacity electrode materials critically hinder their use in high-performance rechargeable batteries. Despite tremendous efforts devoted to the study of the electro–chemo–mechanical behaviours of high-capacity electrode materials, their fracture properties and mechanisms remain largely unknown. In this paper, we report a nanomechanical study on the damage tolerance of electrochemically lithiated silicon. Our in situ transmission electron microscopy experiments reveal a striking contrast of brittle fracture in pristine silicon versus ductile tensile deformation in fully lithiated silicon. Quantitative fracture toughness measurements by nanoindentation show a rapid brittle-to-ductile transition of fracture as the lithium-to-silicon molar ratiomore » is increased to above 1.5. Molecular dynamics simulations elucidate the mechanistic underpinnings of the brittle-to-ductile transition governed by atomic bonding and lithiation-induced toughening. Finally, our results reveal the high damage tolerance in amorphous lithium-rich silicon alloys and have important implications for the development of durable rechargeable batteries.« less

Concerted actions of distinct nonmuscle myosin II isoforms drive intracellular membrane remodeling in live animals

PubMed Central

Milberg, Oleg; Shitara, Akiko; Ebrahim, Seham; Tora, Muhibullah; Tran, Duy T.; Chen, Yun; Conti, Mary Anne; Ten Hagen, Kelly G.

2017-01-01

Membrane remodeling plays a fundamental role during a variety of biological events. However, the dynamics and the molecular mechanisms regulating this process within cells in mammalian tissues in situ remain largely unknown. In this study, we use intravital subcellular microscopy in live mice to study the role of the actomyosin cytoskeleton in driving the remodeling of membranes of large secretory granules, which are integrated into the plasma membrane during regulated exocytosis. We show that two isoforms of nonmuscle myosin II, NMIIA and NMIIB, control distinct steps of the integration process. Furthermore, we find that F-actin is not essential for the recruitment of NMII to the secretory granules but plays a key role in the assembly and activation of NMII into contractile filaments. Our data support a dual role for the actomyosin cytoskeleton in providing the mechanical forces required to remodel the lipid bilayer and serving as a scaffold to recruit key regulatory molecules. PMID:28600434

Multiple-scale neuroendocrine signals connect brain and pituitary hormone rhythms

PubMed Central

Romanò, Nicola; Guillou, Anne; Martin, Agnès O; Mollard, Patrice

2017-01-01

Small assemblies of hypothalamic “parvocellular” neurons release their neuroendocrine signals at the median eminence (ME) to control long-lasting pituitary hormone rhythms essential for homeostasis. How such rapid hypothalamic neurotransmission leads to slowly evolving hormonal signals remains unknown. Here, we show that the temporal organization of dopamine (DA) release events in freely behaving animals relies on a set of characteristic features that are adapted to the dynamic dopaminergic control of pituitary prolactin secretion, a key reproductive hormone. First, locally generated DA release signals are organized over more than four orders of magnitude (0.001 Hz–10 Hz). Second, these DA events are finely tuned within and between frequency domains as building blocks that recur over days to weeks. Third, an integration time window is detected across the ME and consists of high-frequency DA discharges that are coordinated within the minutes range. Thus, a hierarchical combination of time-scaled neuroendocrine signals displays local–global integration to connect brain–pituitary rhythms and pace hormone secretion. PMID:28193889

Functional hierarchy underlies preferential connectivity disturbances in schizophrenia.

PubMed

Yang, Genevieve J; Murray, John D; Wang, Xiao-Jing; Glahn, David C; Pearlson, Godfrey D; Repovs, Grega; Krystal, John H; Anticevic, Alan

2016-01-12

Schizophrenia may involve an elevated excitation/inhibition (E/I) ratio in cortical microcircuits. It remains unknown how this regulatory disturbance maps onto neuroimaging findings. To address this issue, we implemented E/I perturbations within a neural model of large-scale functional connectivity, which predicted hyperconnectivity following E/I elevation. To test predictions, we examined resting-state functional MRI in 161 schizophrenia patients and 164 healthy subjects. As predicted, patients exhibited elevated functional connectivity that correlated with symptom levels, and was most prominent in association cortices, such as the fronto-parietal control network. This pattern was absent in patients with bipolar disorder (n = 73). To account for the pattern observed in schizophrenia, we integrated neurobiologically plausible, hierarchical differences in association vs. sensory recurrent neuronal dynamics into our model. This in silico architecture revealed preferential vulnerability of association networks to E/I imbalance, which we verified empirically. Reported effects implicate widespread microcircuit E/I imbalance as a parsimonious mechanism for emergent inhomogeneous dysconnectivity in schizophrenia.

Functional hierarchy underlies preferential connectivity disturbances in schizophrenia

PubMed Central

Yang, Genevieve J.; Murray, John D.; Wang, Xiao-Jing; Glahn, David C.; Pearlson, Godfrey D.; Repovs, Grega; Krystal, John H.; Anticevic, Alan

2016-01-01

Schizophrenia may involve an elevated excitation/inhibition (E/I) ratio in cortical microcircuits. It remains unknown how this regulatory disturbance maps onto neuroimaging findings. To address this issue, we implemented E/I perturbations within a neural model of large-scale functional connectivity, which predicted hyperconnectivity following E/I elevation. To test predictions, we examined resting-state functional MRI in 161 schizophrenia patients and 164 healthy subjects. As predicted, patients exhibited elevated functional connectivity that correlated with symptom levels, and was most prominent in association cortices, such as the fronto-parietal control network. This pattern was absent in patients with bipolar disorder (n = 73). To account for the pattern observed in schizophrenia, we integrated neurobiologically plausible, hierarchical differences in association vs. sensory recurrent neuronal dynamics into our model. This in silico architecture revealed preferential vulnerability of association networks to E/I imbalance, which we verified empirically. Reported effects implicate widespread microcircuit E/I imbalance as a parsimonious mechanism for emergent inhomogeneous dysconnectivity in schizophrenia. PMID:26699491

Actin–microtubule coordination at growing microtubule ends

PubMed Central

López, Magdalena Preciado; Huber, Florian; Grigoriev, Ilya; Steinmetz, Michel O.; Akhmanova, Anna; Koenderink, Gijsje H.; Dogterom, Marileen

2014-01-01

To power dynamic processes in cells, the actin and microtubule cytoskeletons organize into complex structures. Although it is known that cytoskeletal coordination is vital for cell function, the mechanisms by which cross-linking proteins coordinate actin and microtubule activities remain poorly understood. In particular, it is unknown how the distinct mechanical properties of different actin architectures modulate the outcome of actin–microtubule interactions. To address this question, we engineered the protein TipAct, which links growing microtubule ends via end-binding proteins to actin filaments. We show that growing microtubules can be captured and guided by stiff actin bundles, leading to global actin–microtubule alignment. Conversely, growing microtubule ends can transport, stretch and bundle individual actin filaments, thereby globally defining actin filament organization. Our results provide a physical basis to understand actin–microtubule cross-talk, and reveal that a simple cross-linker can enable a mechanical feedback between actin and microtubule organization that is relevant to diverse biological contexts. PMID:25159196

Discovery of A New Retrograde Trans-Neptunian Object: Hint of A Common Orbital Plane for Low Semi-Major Axis, High Inclination TNOs and Centaurs

NASA Astrophysics Data System (ADS)

Chen, Ying-Tung; Lin, Hsing-Wen; Holman, Matthew J.; Payne, Matthew John; Fraser, Wesley Cristopher; Lacerda, Pedro; Ip, Wing-Huen; Pan-STARRS 1 Builders

2016-10-01

The origin of high inclination objects beyond Jupiter, including trans-Neptunian objects (TNOs) and Centaurs, remains uncertain. We report the discovery of a retrograde TNO, which we nickname "Niku", detected by the Pan-STARRS 1 Outer Solar System Survey. The numerical integrations show that the orbital dynamics of Niku are very similar to those of 2008 KV42 (Drac), with a half-life of ~ 500 Myr and analogous orbital evolution. Comparing similar high inclination members announced by the Minor-Planet Center (q > 10 AU, a < 100 AU and i > 60), we find these objects exhibit a surprising clustering of ascending node, populating a common orbital plane. The statistical significance of 3.8-sigma suggests it is unlikely to be coincidental. An unknown mechanism is required to explain the observed clustering. This discovery may provide a pathway to investigating a possible reservoir of high-inclination objects.

Neuronal differentiation modulates the dystrophin Dp71d binding to the nuclear matrix

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

Rodriguez-Munoz, Rafael; Villarreal-Silva, Marcela; Gonzalez-Ramirez, Ricardo

The function of dystrophin Dp71 in neuronal cells remains unknown. To approach this issue, we have selected the PC12 neuronal cell line. These cells express both a Dp71f cytoplasmic variant and a Dp71d nuclear isoform. In this study, we demonstrated by electron and confocal microscopy analyses of in situ nuclear matrices and Western blotting evaluation of cell extracts that Dp71d associates with the nuclear matrix. Interestingly, this binding is modulated during NGF-induced neuronal differentiation of PC12 cells with a twofold increment in the differentiated cells, compared to control cells. Also, distribution of Dp71d along the periphery of the nuclear matrixmore » observed in the undifferentiated cells is replaced by intense fluorescent foci localized in Center of the nucleoskeletal structure. In summary, we revealed that Dp71d is a dynamic component of nuclear matrix that might participate in the nuclear modeling occurring during neuronal differentiation.« less

Spondylitis Association of America

MedlinePlus

... Spondyloarthritis affects more people than Multiple Sclerosis (MS), Rheumatoid Arthritis, and Autism, yet it remains relatively unknown. MS (400,000) Rheumatoid Arthritis (1.3million) Autism (1.5million) Spondyloarthritis (2.7million) ...

Distributed Adaptive Neural Network Output Tracking of Leader-Following High-Order Stochastic Nonlinear Multiagent Systems With Unknown Dead-Zone Input.

PubMed

Hua, Changchun; Zhang, Liuliu; Guan, Xinping

2017-01-01

This paper studies the problem of distributed output tracking consensus control for a class of high-order stochastic nonlinear multiagent systems with unknown nonlinear dead-zone under a directed graph topology. The adaptive neural networks are used to approximate the unknown nonlinear functions and a new inequality is used to deal with the completely unknown dead-zone input. Then, we design the controllers based on backstepping method and the dynamic surface control technique. It is strictly proved that the resulting closed-loop system is stable in probability in the sense of semiglobally uniform ultimate boundedness and the tracking errors between the leader and the followers approach to a small residual set based on Lyapunov stability theory. Finally, two simulation examples are presented to show the effectiveness and the advantages of the proposed techniques.

The restoration of a maxillary central incisor fracture with the original crown fragment using a glass fiber-reinforced post: a clinical report.

PubMed

Durkan, Rukiye Kaplan; Ozel, M Birol; Celik, Davut; Bağiş, Bora

2008-12-01

This report describes an esthetic, conservative, and economical alternative restoration technique for a fractured central incisor using the patient's own tooth crown piece and a bondable reinforcement glass fiber. Although the long-term durability of this adhesive post core restoration remains unknown, it remains successful after 1 year.

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets (CPP) using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem has been extensively studied, but remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microflora that can affect animal health and productivity, but the majority of these changes remain unknown. The objective of ...

A neural coding scheme reproducing foraging trajectories

PubMed Central

Gutiérrez, Esther D.; Cabrera, Juan Luis

2015-01-01

The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series. PMID:26648311

Nonlinear adaptive control system design with asymptotically stable parameter estimation error

NASA Astrophysics Data System (ADS)

Mishkov, Rumen; Darmonski, Stanislav

2018-01-01

The paper presents a new general method for nonlinear adaptive system design with asymptotic stability of the parameter estimation error. The advantages of the approach include asymptotic unknown parameter estimation without persistent excitation and capability to directly control the estimates transient response time. The method proposed modifies the basic parameter estimation dynamics designed via a known nonlinear adaptive control approach. The modification is based on the generalised prediction error, a priori constraints with a hierarchical parameter projection algorithm, and the stable data accumulation concepts. The data accumulation principle is the main tool for achieving asymptotic unknown parameter estimation. It relies on the parametric identifiability system property introduced. Necessary and sufficient conditions for exponential stability of the data accumulation dynamics are derived. The approach is applied in a nonlinear adaptive speed tracking vector control of a three-phase induction motor.

Dynamic Multitasking Countermeasures to Improve Sustained Attention

DTIC Science & Technology

2013-07-12

Apr-2012 31-Dec-2012 Approved for Public Release; Distribution Unlimited Final Report: Dynamic multitasking countermeasures to improve sustained...ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 vigilance, multitasking REPORT DOCUMENTATION PAGE 11. SPONSOR... multitasking countermeasures to improve sustained attention while driving Report Title The unknown at the outset of this work was if high cognitive load

Complete Mechanism of Hemithioindigo Motor Rotation.

PubMed

Wilcken, Roland; Schildhauer, Monika; Rott, Florian; Huber, Ludwig Alexander; Guentner, Manuel; Thumser, Stefan; Hoffmann, Kerstin; Oesterling, Sven; de Vivie-Riedle, Regina; Riedle, Eberhard; Dube, Henry

2018-04-18

Hemithioindigo-based molecular motors are powered by nondamaging visible light and provide very fast directional rotations at ambient conditions. Their ground state energy profile has been probed in detail, but the crucial excited state processes are completely unknown so far. In addition, very fast processes in the ground state are also still elusive to date and thus knowledge of the whole operational mechanism remains to a large extent in the dark. In this work we elucidate the complete light-driven rotation mechanism by a combination of multiscale broadband transient absorption measurements covering a time scale from fs to ms in conjunction with a high level theoretical description of the excited state. In addition to a full description of the excited state dynamics in the various time regimes, we also provide the first experimental evidence for the elusive fourth intermediate ground state of the original HTI motor. The fate of this intermediate also is followed directly proving complete unidirectionality for both 180° rotation steps. At the same time, we uncover the hitherto unknown involvement of an unproductive triplet state pathway, which slightly diminishes the quantum yield of the E to Z photoisomerization. A rate model analysis shows that increasing the speed of motor rotation is most effectively done by increasing the photoisomerization quantum yields instead of barrier reduction for the thermal ratcheting steps. Our findings are of crucial importance for improved future designs of any light-driven molecular motor in general to yield better efficiencies and applicability.

Isolated growth hormone deficiency (GHD) in childhood and adolescence: recent advances.

PubMed

Alatzoglou, Kyriaki S; Webb, Emma Alice; Le Tissier, Paul; Dattani, Mehul T

2014-06-01

The diagnosis of GH deficiency (GHD) in childhood is a multistep process involving clinical history, examination with detailed auxology, biochemical testing, and pituitary imaging, with an increasing contribution from genetics in patients with congenital GHD. Our increasing understanding of the factors involved in the development of somatotropes and the dynamic function of the somatotrope network may explain, at least in part, the development and progression of childhood GHD in different age groups. With respect to the genetic etiology of isolated GHD (IGHD), mutations in known genes such as those encoding GH (GH1), GHRH receptor (GHRHR), or transcription factors involved in pituitary development, are identified in a relatively small percentage of patients suggesting the involvement of other, yet unidentified, factors. Genome-wide association studies point toward an increasing number of genes involved in the control of growth, but their role in the etiology of IGHD remains unknown. Despite the many years of research in the area of GHD, there are still controversies on the etiology, diagnosis, and management of IGHD in children. Recent data suggest that childhood IGHD may have a wider impact on the health and neurodevelopment of children, but it is yet unknown to what extent treatment with recombinant human GH can reverse this effect. Finally, the safety of recombinant human GH is currently the subject of much debate and research, and it is clear that long-term controlled studies are needed to clarify the consequences of childhood IGHD and the long-term safety of its treatment.

Flightless and post-molt survival and movements of female mallards molting in Klamath Basin

USGS Publications Warehouse

Fleskes, Joseph P.; Mauser, David M.; Yee, Julie L.; Blehert, David S.; Yarris, Gregory S.

2010-01-01

Flightless and post-molt survival and movements were studied during August-May, 2001-2002, 2002- 2003 and 2006-2007 for 181 adult female Mallards (Anas platyrhynchos). Birds were radiotagged just before or early in their flightless period on four wetlands that differed in size on Klamath Basin (KB) National Wildlife Refuge complex. Flightless survival varied among years but was higher on two larger than two smaller wetlands; 30-day survival ranged from 11% (SE = 6.5%) on a small wetland in 2006 to 93% (SE = 6.5%) on a large wetland in 2001, and averaged 76.8% (SE = 6.1%). Most flightless mortality was from avian botulism (64%) and predation (26%). Of the 81 radiotagged Mallards that did not die in KB, 80% moved to the Central Valley of California (CVCA) before 31 January, 16% wintered in unknown areas, and 4% remained in KB through 31 January. Mallards departed KB 21 August-13 January (average: 11 Nov 2001, 25 Oct 2002, 19 Nov 2006). Post-molt survival during August-March in KB (20.7%, SE = 6.3%) was lower than in CVCA during this (62.9%, SE = 10.1%) and an earlier study. Survival in KB was consistently high only for females that molted in large permanent marshes, and although the impact of poor survival of molting females on Mallard population dynamics is unknown, KB water management plans should be developed that maintain these habitats.

Nonlinear Dynamics of Complex Coevolutionary Systems in Historical Times

NASA Astrophysics Data System (ADS)

Perdigão, Rui A. P.

2016-04-01

A new theoretical paradigm for statistical-dynamical modeling of complex coevolutionary systems is introduced, with the aim to provide historical geoscientists with a practical tool to analyse historical data and its underlying phenomenology. Historical data is assumed to represent the history of dynamical processes of physical and socio-economic nature. If processes and their governing laws are well understood, they are often treated with traditional dynamical equations: deterministic approach. If the governing laws are unknown or impracticable, the process is often treated as if being random (even if it is not): statistical approach. Although single eventful details - such as the exact spatiotemporal structure of a particular hydro-meteorological incident - may often be elusive to a detailed analysis, the overall dynamics exhibit group properties summarized by a simple set of categories or dynamical regimes at multiple scales - from local short-lived convection patterns to large-scale hydro-climatic regimes. The overwhelming microscale complexity is thus conveniently wrapped into a manageable group entity, such as a statistical distribution. In a stationary setting whereby the distribution is assumed to be invariant, alternating regimes are approachable as dynamical intermittence. For instance, in the context of bimodal climatic oscillations such as NAO and ENSO, each mode corresponds to a dynamical regime or phase. However, given external forcings or longer-term internal variability and multiscale coevolution, the structural properties of the system may change. These changes in the dynamical structure bring about a new distribution and associated regimes. The modes of yesteryear may no longer exist as such in the new structural order of the system. In this context, aside from regime intermittence, the system exhibits structural regime change. New oscillations may emerge whilst others fade into the annals of history, e.g. particular climate fluctuations during the Little Ice Age. Traditional theories of stochastic processes and dynamical systems are grounded on the existence of so-called dynamical invariants; properties that remain unchanged as the dynamics unfold, assuming structural invariance and ergodicity of the underlying system. However, such theories are no longer optimal when trying to understand and model long-term historical records of coevolutionary systems. A new paradigm is thus needed. Therefore, we introduce a new class of dynamical systems that reinvent themselves as the dynamics unfold. Rather than only changing variables and parameters under a rigid framework, the governing laws are malleable themselves. The novel formulation captures and explains the coevolutionary dynamics of multiscale hydroclimatic systems, bringing along a physically sound understanding of their regimes, transitions and extremes over a long-term history.

Decentralized adaptive neural control for high-order interconnected stochastic nonlinear time-delay systems with unknown system dynamics.

PubMed

Si, Wenjie; Dong, Xunde; Yang, Feifei

2018-03-01

This paper is concerned with the problem of decentralized adaptive backstepping state-feedback control for uncertain high-order large-scale stochastic nonlinear time-delay systems. For the control design of high-order large-scale nonlinear systems, only one adaptive parameter is constructed to overcome the over-parameterization, and neural networks are employed to cope with the difficulties raised by completely unknown system dynamics and stochastic disturbances. And then, the appropriate Lyapunov-Krasovskii functional and the property of hyperbolic tangent functions are used to deal with the unknown unmatched time-delay interactions of high-order large-scale systems for the first time. At last, on the basis of Lyapunov stability theory, the decentralized adaptive neural controller was developed, and it decreases the number of learning parameters. The actual controller can be designed so as to ensure that all the signals in the closed-loop system are semi-globally uniformly ultimately bounded (SGUUB) and the tracking error converges in the small neighborhood of zero. The simulation example is used to further show the validity of the design method. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transitions in Prognostic Awareness Among Terminally Ill Cancer Patients in Their Last 6 Months of Life Examined by Multi-State Markov Modeling.

PubMed

Hsiu Chen, Chen; Wen, Fur-Hsing; Hou, Ming-Mo; Hsieh, Chia-Hsun; Chou, Wen-Chi; Chen, Jen-Shi; Chang, Wen-Cheng; Tang, Siew Tzuh

2017-09-01

Developing accurate prognostic awareness, a cornerstone of preference-based end-of-life (EOL) care decision-making, is a dynamic process involving more prognostic-awareness states than knowing or not knowing. Understanding the transition probabilities and time spent in each prognostic-awareness state can help clinicians identify trigger points for facilitating transitions toward accurate prognostic awareness. We examined transition probabilities in distinct prognostic-awareness states between consecutive time points in 247 cancer patients' last 6 months and estimated the time spent in each state. Prognostic awareness was categorized into four states: (a) unknown and not wanting to know, state 1; (b) unknown but wanting to know, state 2; (c) inaccurate awareness, state 3; and (d) accurate awareness, state 4. Transitional probabilities were examined by multistate Markov modeling. Initially, 59.5% of patients had accurate prognostic awareness, whereas the probabilities of being in states 1-3 were 8.1%, 17.4%, and 15.0%, respectively. Patients' prognostic awareness generally remained unchanged (probabilities of remaining in the same state: 45.5%-92.9%). If prognostic awareness changed, it tended to shift toward higher prognostic-awareness states (probabilities of shifting to state 4 were 23.2%-36.6% for patients initially in states 1-3, followed by probabilities of shifting to state 3 for those in states 1 and 2 [9.8%-10.1%]). Patients were estimated to spend 1.29, 0.42, 0.68, and 3.61 months in states 1-4, respectively, in their last 6 months. Terminally ill cancer patients' prognostic awareness generally remained unchanged, with a tendency to become more aware of their prognosis. Health care professionals should facilitate patients' transitions toward accurate prognostic awareness in a timely manner to promote preference-based EOL decisions. Terminally ill Taiwanese cancer patients' prognostic awareness generally remained stable, with a tendency toward developing higher states of awareness. Health care professionals should appropriately assess patients' readiness for prognostic information and respect patients' reluctance to confront their poor prognosis if they are not ready to know, but sensitively coach them to cultivate their accurate prognostic awareness, provide desired and understandable prognostic information for those who are ready to know, and give direct and honest prognostic information to clarify any misunderstandings for those with inaccurate awareness, thus ensuring that they develop accurate and realistic prognostic knowledge in time to make end-of-life care decisions. © AlphaMed Press 2017.

IMPLICIT DUAL CONTROL BASED ON PARTICLE FILTERING AND FORWARD DYNAMIC PROGRAMMING.

PubMed

Bayard, David S; Schumitzky, Alan

2010-03-01

This paper develops a sampling-based approach to implicit dual control. Implicit dual control methods synthesize stochastic control policies by systematically approximating the stochastic dynamic programming equations of Bellman, in contrast to explicit dual control methods that artificially induce probing into the control law by modifying the cost function to include a term that rewards learning. The proposed implicit dual control approach is novel in that it combines a particle filter with a policy-iteration method for forward dynamic programming. The integration of the two methods provides a complete sampling-based approach to the problem. Implementation of the approach is simplified by making use of a specific architecture denoted as an H-block. Practical suggestions are given for reducing computational loads within the H-block for real-time applications. As an example, the method is applied to the control of a stochastic pendulum model having unknown mass, length, initial position and velocity, and unknown sign of its dc gain. Simulation results indicate that active controllers based on the described method can systematically improve closed-loop performance with respect to other more common stochastic control approaches.

Observer-based distributed adaptive fault-tolerant containment control of multi-agent systems with general linear dynamics.

PubMed

Ye, Dan; Chen, Mengmeng; Li, Kui

2017-11-01

In this paper, we consider the distributed containment control problem of multi-agent systems with actuator bias faults based on observer method. The objective is to drive the followers into the convex hull spanned by the dynamic leaders, where the input is unknown but bounded. By constructing an observer to estimate the states and bias faults, an effective distributed adaptive fault-tolerant controller is developed. Different from the traditional method, an auxiliary controller gain is designed to deal with the unknown inputs and bias faults together. Moreover, the coupling gain can be adjusted online through the adaptive mechanism without using the global information. Furthermore, the proposed control protocol can guarantee that all the signals of the closed-loop systems are bounded and all the followers converge to the convex hull with bounded residual errors formed by the dynamic leaders. Finally, a decoupled linearized longitudinal motion model of the F-18 aircraft is used to demonstrate the effectiveness. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Probabilistic Multi-Person Tracking Using Dynamic Bayes Networks

NASA Astrophysics Data System (ADS)

Klinger, T.; Rottensteiner, F.; Heipke, C.

2015-08-01

Tracking-by-detection is a widely used practice in recent tracking systems. These usually rely on independent single frame detections that are handled as observations in a recursive estimation framework. If these observations are imprecise the generated trajectory is prone to be updated towards a wrong position. In contrary to existing methods our novel approach uses a Dynamic Bayes Network in which the state vector of a recursive Bayes filter, as well as the location of the tracked object in the image are modelled as unknowns. These unknowns are estimated in a probabilistic framework taking into account a dynamic model, and a state-of-the-art pedestrian detector and classifier. The classifier is based on the Random Forest-algorithm and is capable of being trained incrementally so that new training samples can be incorporated at runtime. This allows the classifier to adapt to the changing appearance of a target and to unlearn outdated features. The approach is evaluated on a publicly available benchmark. The results confirm that our approach is well suited for tracking pedestrians over long distances while at the same time achieving comparatively good geometric accuracy.

Self-expressive Dictionary Learning for Dynamic 3D Reconstruction.

PubMed

Zheng, Enliang; Ji, Dinghuang; Dunn, Enrique; Frahm, Jan-Michael

2017-08-22

We target the problem of sparse 3D reconstruction of dynamic objects observed by multiple unsynchronized video cameras with unknown temporal overlap. To this end, we develop a framework to recover the unknown structure without sequencing information across video sequences. Our proposed compressed sensing framework poses the estimation of 3D structure as the problem of dictionary learning, where the dictionary is defined as an aggregation of the temporally varying 3D structures. Given the smooth motion of dynamic objects, we observe any element in the dictionary can be well approximated by a sparse linear combination of other elements in the same dictionary (i.e. self-expression). Our formulation optimizes a biconvex cost function that leverages a compressed sensing formulation and enforces both structural dependency coherence across video streams, as well as motion smoothness across estimates from common video sources. We further analyze the reconstructability of our approach under different capture scenarios, and its comparison and relation to existing methods. Experimental results on large amounts of synthetic data as well as real imagery demonstrate the effectiveness of our approach.

Frontal Lobe Seizures

MedlinePlus

... cause of frontal lobe epilepsy remains unknown. Complications Status epilepticus. Frontal lobe seizures tend to occur in clusters and may provoke a dangerous condition called status epilepticus — in which seizure activity lasts much longer than ...

Metagenomic ventures into outer sequence space.

PubMed

Dutilh, Bas E

Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as "unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as "biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.

Known knowns, known unknowns and unknown unknowns in prokaryotic transposition.

PubMed

Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael

2017-08-01

Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple Ab R . Copyright © 2017 Elsevier Ltd. All rights reserved.

Prescribed performance distributed consensus control for nonlinear multi-agent systems with unknown dead-zone input

NASA Astrophysics Data System (ADS)

Cui, Guozeng; Xu, Shengyuan; Ma, Qian; Li, Yongmin; Zhang, Zhengqiang

2018-05-01

In this paper, the problem of prescribed performance distributed output consensus for higher-order non-affine nonlinear multi-agent systems with unknown dead-zone input is investigated. Fuzzy logical systems are utilised to identify the unknown nonlinearities. By introducing prescribed performance, the transient and steady performance of synchronisation errors are guaranteed. Based on Lyapunov stability theory and the dynamic surface control technique, a new distributed consensus algorithm for non-affine nonlinear multi-agent systems is proposed, which ensures cooperatively uniformly ultimately boundedness of all signals in the closed-loop systems and enables the output of each follower to synchronise with the leader within predefined bounded error. Finally, simulation examples are provided to demonstrate the effectiveness of the proposed control scheme.

Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

NASA Astrophysics Data System (ADS)

Cui, Jie; Li, Zhiying; Krems, Roman V.

2015-10-01

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A-H to make predictions of the dynamical properties for another molecule related to A-H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A-X. We assume that the effect of the -H →-X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can be used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C6H5CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C6H6 collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C6H5CN with He.

Increased clinical anticipation with maternal transmission in benign adult familial myoclonus epilepsy in Japan.

PubMed

Hitomi, Takefumi; Kobayashi, Katsuya; Jingami, Naoto; Nakagawa, Tomokazu; Imamura, Hisaji; Matsumoto, Riki; Kondo, Takayuki; Chin, Kazuo; Takahashi, Ryosuke; Ikeda, Akio

2013-12-01

We recently reported clinical anticipation in Japanese families with benign adult familial myoclonus epilepsy (BAFME). However, it remains unknown whether clinical anticipation is predominantly associated with paternal or maternal transmission. We investigated the relationship between gender of the transmitting parent and clinical anticipation in nine BAFME families. Clinical anticipation regarding either cortical tremor or generalised seizures was observed in all 12 parent/child pairs (8 mother/child pairs and 4 father/child pairs). Moreover, a higher degree of clinical anticipation was associated with maternal transmission than with paternal transmission (p=0.03). Although a causative gene for BAFME still remains unknown, our finding suggests that BAFME and diseases with unstable expanding repeats, including those in non-coding regions, might share a similar molecular mechanism because such diseases often show clinical anticipation with maternal transmission.

Mycobacterium ulcerans Ecological Dynamics and Its Association with Freshwater Ecosystems and Aquatic Communities: Results from a 12-Month Environmental Survey in Cameroon

PubMed Central

Garchitorena, Andrés; Roche, Benjamin; Kamgang, Roger; Ossomba, Joachim; Babonneau, Jérémie; Landier, Jordi; Fontanet, Arnaud; Flahault, Antoine

2014-01-01

Background Mycobacterium ulcerans (MU) is the agent responsible for Buruli Ulcer (BU), an emerging skin disease with dramatic socioeconomic and health outcomes, especially in rural settings. BU emergence and distribution is linked to aquatic ecosystems in tropical and subtropical countries, especially to swampy and flooded areas. Aquatic animal organisms are likely to play a role either as host reservoirs or vectors of the bacilli. However, information on MU ecological dynamics, both in space and time, is dramatically lacking. As a result, the ecology of the disease agent, and consequently its mode of transmission, remains largely unknown, which jeopardizes public health attempts for its control. The objective of this study was to gain insight on MU environmental distribution and colonization of aquatic organisms through time. Methodology/Principal Findings Longitudinal sampling of 32 communities of aquatic macro-invertebrates and vertebrates was conducted from different environments in two BU endemic regions in Cameroon during 12 months. As a result, 238,496 individuals were classified and MU presence was assessed by qPCR in 3,084 sample-pools containing these aquatic organisms. Our study showed a broad distribution of MU in all ecosystems and taxonomic groups, with important regional differences in its occurrence. Colonization dynamics fluctuated along the year, with the highest peaks in August and October. The large variations observed in the colonization dynamics of different taxonomic groups and aquatic ecosystems suggest that the trends shown here are the result of complex ecological processes that need further investigation. Conclusion/Perspectives This is the largest field study on MU ecology to date, providing the first detailed description of its spatio-temporal dynamics in different aquatic ecosystems within BU endemic regions. We argue that coupling this data with fine-scale epidemiological data through statistical and mathematical models will provide a major step forward in the understanding of MU ecology and mode of transmission. PMID:24831924

Controls on Water Storage, Mixing and Release in a Nested Catchment Set-up with Clean and Mixed Physiographic Characteristics

NASA Astrophysics Data System (ADS)

Pfister, L.; McDonnell, J.; Hissler, C.; Martínez-Carreras, N.; Klaus, J.

2015-12-01

With catchment water storage being only rarely determined, storage dynamics remain largely unknown to date. However, storage bears considerable potential for catchment inter-comparison exercises, as well as it is likely to have an important role in regulating catchment functions. Catchment comparisons across a wide range of environments and scales will help to increase our understanding of relationships between storage dynamics and catchment processes. With respect to the potential of catchment storage for bringing new momentum to catchment classification and catchment processes understanding we currently investigate spatial and temporal variability of dynamic storage in a nested catchment set-up (16 catchments) of the Alzette River basin (Luxembourg, Europe), covering a wide range of geological settings, catchment areas, contrasted landuse, and hydro-meteorological and tracer series. We define catchment storage as the total amount of water stored in a control volume, delimited by the catchment's topographical boundaries and depth of saturated and unsaturated zones. Complementary storage assessments (via input-output dynamics of natural tracers, geographical sounding, groundwater level measurements, soil moisture measurements, hydrometry) are carried out for comparison purposes. In our nested catchment set-up we have (1) assessed dependencies between geology, catchment permeability and winter runoff coefficients, (2) calculated water balance derived catchment storage and mixing potential and quantified how dynamic storage differs between catchments and scales, and (3) examined how stream baseflow dD (as a proxy for baseflow transit time) and integrated flow measures (like the flow duration curve) relate to bedrock geology. Catchments with higher bedrock permeability exhibited larger storage capacities and eventually lower average winter runoff coefficients. Over a time-span of 11 years, all catchments re-produced the same winter runoff coefficients year after year, regardless of their bedrock geology, permeability and winter season storage filling ratios. Ultimately, catchment organisation in our area of interest (i.e. geology, permeability, flowpath length) appeared to have a strong control on winter runoff coefficients, catchment storage and subsequently baseflow dD.

Comparative Effects of Different Balance-Training-Progression Styles on Postural Control and Ankle Force Production: A Randomized Controlled Trial.

PubMed

Cuğ, Mutlu; Duncan, Ashley; Wikstrom, Erik

2016-02-01

Despite the effectiveness of balance training, the exact parameters needed to maximize the benefits of such programs remain unknown. One such factor is how individuals should progress to higher levels of task difficulty within a balance-training program. Yet no investigators have directly compared different balance-training-progression styles. To compare an error-based progression (ie, advance when proficient at a task) with a repetition-based progression (ie, advance after a set amount of repetitions) style during a balance-training program in healthy individuals. Randomized controlled trial. Research laboratory. A total of 28 (16 women, 12 men) physically healthy young adults (age = 21.57 ± 3.95 years, height = 171.60 ± 11.03 cm, weight = 72.96 ± 16.18 kg, body mass index = 24.53 ± 3.7). All participants completed 12 supervised balance-training sessions over 4 weeks. Each session consisted of a combination of dynamic unstable-surface tasks that incorporated a BOSU ball and lasted about 30 minutes. Static balance from an instrumented force plate, dynamic balance as measured via the Star Excursion Balance Test, and ankle force production in all 4 cardinal planes of motion as measured with a handheld dynamometer before and after the intervention. Selected static postural-control outcomes, dynamic postural control, and ankle force production in all planes of motion improved (P < .05). However, no differences between the progression styles were observed (P > .05) for any of the outcome measures. A 4-week balance-training program consisting of dynamic unstable-surface exercises on a BOSU ball improved dynamic postural control and ankle force production in healthy young adults. These results suggest that an error-based balance-training program is comparable with but not superior to a repetition-based balance-training program in improving postural control and ankle force production in healthy young adults.

Observer-based robust finite time H∞ sliding mode control for Markovian switching systems with mode-dependent time-varying delay and incomplete transition rate.

PubMed

Gao, Lijun; Jiang, Xiaoxiao; Wang, Dandan

2016-03-01

This paper investigates the problem of robust finite time H∞ sliding mode control for a class of Markovian switching systems. The system is subjected to the mode-dependent time-varying delay, partly unknown transition rate and unmeasurable state. The main difficulty is that, a sliding mode surface cannot be designed based on the unknown transition rate and unmeasurable state directly. To overcome this obstacle, the set of modes is firstly divided into two subsets standing for known transition rate subset and unknown one, based on which a state observer is established. A component robust finite-time sliding mode controller is also designed to cope with the effect of partially unknown transition rate. It is illustrated that the reachability, finite-time stability, finite-time boundedness, finite-time H∞ state feedback stabilization of sliding mode dynamics can be ensured despite the unknown transition rate. Finally, the simulation results verify the effectiveness of robust finite time control problem. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Active vibration control for piezoelectricity cantilever beam: an adaptive feedforward control method

NASA Astrophysics Data System (ADS)

Zhu, Qiao; Yue, Jun-Zhou; Liu, Wei-Qun; Wang, Xu-Dong; Chen, Jun; Hu, Guang-Di

2017-04-01

This work is focused on the active vibration control of piezoelectric cantilever beam, where an adaptive feedforward controller (AFC) is utilized to reject the vibration with unknown multiple frequencies. First, the experiment setup and its mathematical model are introduced. Due to that the channel between the disturbance and the vibration output is unknown in practice, a concept of equivalent input disturbance (EID) is employed to put an equivalent disturbance into the input channel. In this situation, the vibration control can be achieved by setting the control input be the identified EID. Then, for the EID with known multiple frequencies, the AFC is introduced to perfectly reject the vibration but is sensitive to the frequencies. In order to accurately identify the unknown frequencies of EID in presence of the random disturbances and un-modeled nonlinear dynamics, the time-frequency-analysis (TFA) method is employed to precisely identify the unknown frequencies. Consequently, a TFA-based AFC algorithm is proposed to the active vibration control with unknown frequencies. Finally, four cases are given to illustrate the efficiency of the proposed TFA-based AFC algorithm by experiment.

Enhanced litter input rather than changes in litter chemistry drive soil carbon and nitrogen cycles under elevated CO2: a microcosm study

Treesearch

Lingli Lui; John S. King; Fitzgerald L. Booker; Christian P. Giardina; H. Lee Allen; Shuijin Hu

2009-01-01

Elevated CO2 has been shown to stimulate plant productivity and change litter chemistry. These changes in substrate availability may then alter soil microbial processes and possibly lead to feedback effects on N availability. However, the strength of this feedback, and even its direction, remains unknown. Further, uncertainty remains whether...

Dynamic Failure of Materials: A Review

DTIC Science & Technology

2010-08-01

stress states . It is currently unknown how well the current trend of multi-scale modeling will impact dynamic failure; however... stress can exist in the necked region after a neck is formed due to the nonuniformity of the necked region. This triaxial stress state is extremely...7 into 8, the effective stress intensity factor (Keff) can be determined in terms of the stress intensity factor (K). Because the onset of

Factors influencing the spatial and temporal dynamics of engelmann spruce mortality during a spruce beetle outbreak on the Markagunt Plateau, Utah

Treesearch

R. Justin DeRose; James N. Long

2012-01-01

Host conditions are known to influence spruce beetle population levels, but whether they influence the spatial and temporal patterns of beetle-caused mortality during an outbreak is unknown. Using dendrochronological techniques, we quantified the spatiotemporal dynamics of a modern (late 1980s through the early 2000s) spruce beetle outbreak in Engelmann spruce on the...

Individual differences and time-varying features of modular brain architecture.

PubMed

Liao, Xuhong; Cao, Miao; Xia, Mingrui; He, Yong

2017-05-15

Recent studies have suggested that human brain functional networks are topologically organized into functionally specialized but inter-connected modules to facilitate efficient information processing and highly flexible cognitive function. However, these studies have mainly focused on group-level network modularity analyses using "static" functional connectivity approaches. How these extraordinary modular brain structures vary across individuals and spontaneously reconfigure over time remain largely unknown. Here, we employed multiband resting-state functional MRI data (N=105) from the Human Connectome Project and a graph-based modularity analysis to systematically investigate individual variability and dynamic properties in modular brain networks. We showed that the modular structures of brain networks dramatically vary across individuals, with higher modular variability primarily in the association cortex (e.g., fronto-parietal and attention systems) and lower variability in the primary systems. Moreover, brain regions spontaneously changed their module affiliations on a temporal scale of seconds, which cannot be simply attributable to head motion and sampling error. Interestingly, the spatial pattern of intra-subject dynamic modular variability largely overlapped with that of inter-subject modular variability, both of which were highly reproducible across repeated scanning sessions. Finally, the regions with remarkable individual/temporal modular variability were closely associated with network connectors and the number of cognitive components, suggesting a potential contribution to information integration and flexible cognitive function. Collectively, our findings highlight individual modular variability and the notable dynamic characteristics in large-scale brain networks, which enhance our understanding of the neural substrates underlying individual differences in a variety of cognition and behaviors. Copyright © 2017 Elsevier Inc. All rights reserved.

Fast vesicle transport is required for the slow axonal transport of synapsin.

PubMed

Tang, Yong; Scott, David; Das, Utpal; Gitler, Daniel; Ganguly, Archan; Roy, Subhojit

2013-09-25

Although it is known that cytosolic/soluble proteins synthesized in cell bodies are transported at much lower overall velocities than vesicles in fast axonal transport, the fundamental basis for this slow movement is unknown. Recently, we found that cytosolic proteins in axons of mouse cultured neurons are conveyed in a manner that superficially resembles diffusion, but with a slow anterograde bias that is energy- and motor-dependent (Scott et al., 2011). Here we show that slow axonal transport of synapsin, a prototypical member of this rate class, is dependent upon fast vesicle transport. Despite the distinct overall dynamics of slow and fast transport, experimentally induced and intrinsic variations in vesicle transport have analogous effects on slow transport of synapsin as well. Dynamic cotransport of vesicles and synapsin particles is also seen in axons, consistent with a model where higher-order assemblies of synapsin are conveyed by transient and probabilistic associations with vesicles moving in fast axonal transport. We posit that such dynamic associations generate the slow overall anterogradely biased flow of the population ("dynamic-recruitment model"). Our studies uncover the underlying kinetic basis for a classic cytosolic/soluble protein moving in slow axonal transport and reveal previously unknown links between slow and fast transport, offering a clearer conceptual picture of this curious phenomenon.

Global dynamics and diffusion in triaxial galactic models

NASA Astrophysics Data System (ADS)

Papaphilippou, Y.

We apply the Frequency Map Analysis method to the 3--dimensional logarithmic galactic potential in order to clarify the dynamical behaviour of triaxial power--law galactic models. All the fine dynamical details are displayed in the complete frequency map, a direct representation of the system's Arnol'd web. The influence of resonant lines and the extent of the chaotic zones are directly associated with the physical space of the system. Some new results related with the diffusion of galactic orbits are also discussed. This approach reveals many unknown dynamical features of triaxial galactic potentials and provides strong indications that chaos should be an innate characteristic of triaxial configurations.

Let's stay together? Intrinsic and extrinsic factors involved in pair bond dissolution in a recolonizing wolf population.

PubMed

Milleret, Cyril; Wabakken, Petter; Liberg, Olof; Åkesson, Mikael; Flagstad, Øystein; Andreassen, Harry Peter; Sand, Håkan

2017-01-01

For socially monogamous species, breeder bond dissolution has important consequences for population dynamics, but the extent to which extrinsic or intrinsic population factors causes pair dissolution remain poorly understood, especially among carnivores. Using an extensive life-history data set, a survival analysis and competing risks framework, we examined the fate of 153 different wolf (Canis lupus) pairs in the recolonizing Scandinavian wolf population, during 14 winters of snow tracking and DNA monitoring. Wolf pair dissolution was generally linked to a mortality event and was strongly affected by extrinsic (i.e. anthropogenic) causes. No divorce was observed, and among the pair dissolution where causes have been identified, death of one or both wolves was always involved. Median time from pair formation to pair dissolution was three consecutive winters (i.e. approximately 2 years). Pair dissolution was mostly human-related, primarily caused by legal control actions (36·7%), verified poaching (9·2%) and traffic-related causes (2·1%). Intrinsic factors, such as disease and age, accounted for only 7·7% of pair dissolutions. The remaining 44·3% of dissolution events were from unknown causes, but we argue that a large portion could be explained by an additional source of human-caused mortality, cryptic poaching. Extrinsic population factors, such as variables describing the geographical location of the pair, had a stronger effect on risk of pair dissolution compared to anthropogenic landscape characteristics. Population intrinsic factors, such as the inbreeding coefficient of the male pair member, had a negative effect on pair bond duration. The mechanism behind this result remains unknown, but might be explained by lower survival of inbred males or more complex inbreeding effects mediated by behaviour. Our study provides quantitative estimates of breeder bond duration in a social carnivore and highlights the effect of extrinsic (i.e. anthropogenic) and intrinsic factors (i.e. inbreeding) involved in wolf pair bond duration. Unlike the effects of intrinsic and extrinsic factors that are commonly reported on individual survival or population growth, here we provide quantitative estimates of their potential effect on the social unit of the population, the wolf pair. © 2016 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Effective grouping for energy and performance: Construction of adaptive, sustainable, and maintainable data storage

NASA Astrophysics Data System (ADS)

Essary, David S.

The performance gap between processors and storage systems has been increasingly critical over the years. Yet the performance disparity remains, and further, storage energy consumption is rapidly becoming a new critical problem. While smarter caching and predictive techniques do much to alleviate this disparity, the problem persists, and data storage remains a growing contributor to latency and energy consumption. Attempts have been made at data layout maintenance, or intelligent physical placement of data, yet in practice, basic heuristics remain predominant. Problems that early studies sought to solve via layout strategies were proven to be NP-Hard, and data layout maintenance today remains more art than science. With unknown potential and a domain inherently full of uncertainty, layout maintenance persists as an area largely untapped by modern systems. But uncertainty in workloads does not imply randomness; access patterns have exhibited repeatable, stable behavior. Predictive information can be gathered, analyzed, and exploited to improve data layouts. Our goal is a dynamic, robust, sustainable predictive engine, aimed at improving existing layouts by replicating data at the storage device level. We present a comprehensive discussion of the design and construction of such a predictive engine, including workload evaluation, where we present and evaluate classical workloads as well as our own highly detailed traces collected over an extended period. We demonstrate significant gains through an initial static grouping mechanism, and compare against an optimal grouping method of our own construction, and further show significant improvement over competing techniques. We also explore and illustrate the challenges faced when moving from static to dynamic (i.e. online) grouping, and provide motivation and solutions for addressing these challenges. These challenges include metadata storage, appropriate predictive collocation, online performance, and physical placement. We reduced the metadata needed by several orders of magnitude, reducing the required volume from more than 14% of total storage down to less than 1/2%. We also demonstrate how our collocation strategies outperform competing techniques. Finally, we present our complete model and evaluate a prototype implementation against real hardware. This model was demonstrated to be capable of reducing device-level accesses by up to 65%. Keywords: computer systems, collocation, data management, file systems, grouping, metadata, modeling and prediction, operating systems, performance, power, secondary storage.

Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs.

PubMed

Yoon, Nara; Vander Velde, Robert; Marusyk, Andriy; Scott, Jacob G

2018-05-07

Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown. To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups, [Formula: see text] and [Formula: see text], each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics. Specifically, based on a system of ordinary differential equations for [Formula: see text] and [Formula: see text], we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point, T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e., [Formula: see text]-long for DrugA and [Formula: see text]-long for DrugB with [Formula: see text] and [Formula: see text]). We prove that the optimal duration of the initial stage, in which the first drug is administered, T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition. We further analyzed the relationship between population makeup, [Formula: see text], and the effect of each drug. We determine a critical ratio, which we term [Formula: see text], at which the two drugs are equally effective. As the first stage of the optimal strategy is applied, [Formula: see text] changes monotonically to [Formula: see text] and then, during the second stage, remains at [Formula: see text] thereafter. Beyond our analytic results, we explored an individual-based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.

Spacecraft Orbit Anomaly Representation Using Thrust-Fourier-Coefficients with Orbit Determination Toolbox

NASA Astrophysics Data System (ADS)

Ko, H.; Scheeres, D.

2014-09-01

Representing spacecraft orbit anomalies between two separate states is a challenging but an important problem in achieving space situational awareness for an active spacecraft. Incorporation of such a capability could play an essential role in analyzing satellite behaviors as well as trajectory estimation of the space object. A general way to deal with the anomaly problem is to add an estimated perturbing acceleration such as dynamic model compensation (DMC) into an orbit determination process based on pre- and post-anomaly tracking data. It is a time-consuming numerical process to find valid coefficients to compensate for unknown dynamics for the anomaly. Even if the orbit determination filter with DMC can crudely estimate an unknown acceleration, this approach does not consider any fundamental element of the unknown dynamics for a given anomaly. In this paper, a new way of representing a spacecraft anomaly using an interpolation technique with the Thrust-Fourier-Coefficients (TFCs) is introduced and several anomaly cases are studied using this interpolation method. It provides a very efficient way of reconstructing the fundamental elements of the dynamics for a given spacecraft anomaly. Any maneuver performed by a satellite transitioning between two arbitrary orbital states can be represented as an equivalent maneuver using an interpolation technique with the TFCs. Given unconnected orbit states between two epochs due to a spacecraft anomaly, it is possible to obtain a unique control law using the TFCs that is able to generate the desired secular behavior for the given orbital changes. This interpolation technique can capture the fundamental elements of combined unmodeled anomaly events. The interpolated orbit trajectory, using the TFCs compensating for a given anomaly, can be used to improve the quality of orbit fits through the anomaly period and therefore help to obtain a good orbit determination solution after the anomaly. Orbit Determination Toolbox (ODTBX) is modified to adapt this technique in order to verify the performance of this interpolation approach. Spacecraft anomaly cases are based on either single or multiple low or high thrust maneuvers and the unknown thrust accelerations are recovered and compared with the true thrust acceleration. The advantage of this approach is to easily append TFCs and its dynamics to the pre-built ODTBX, which enables us to blend post-anomaly tracking data to improve the performance of the interpolation representation in the absence of detailed information about a maneuver. It allows us to improve space situational awareness in the areas of uncertainty propagation, anomaly characterization and track correlation.

Online matching with queueing dynamics.

DOT National Transportation Integrated Search

2016-12-01

We consider a variant of the multiarmed bandit problem where jobs queue for service, and service rates of different servers may be unknown. We study algorithms that minimize queue-regret: the (expected) difference between the queue-lengths obtained b...

Output-Feedback Control of Unknown Linear Discrete-Time Systems With Stochastic Measurement and Process Noise via Approximate Dynamic Programming.

PubMed

Wang, Jun-Sheng; Yang, Guang-Hong

2017-07-25

This paper studies the optimal output-feedback control problem for unknown linear discrete-time systems with stochastic measurement and process noise. A dithered Bellman equation with the innovation covariance matrix is constructed via the expectation operator given in the form of a finite summation. On this basis, an output-feedback-based approximate dynamic programming method is developed, where the terms depending on the innovation covariance matrix are available with the aid of the innovation covariance matrix identified beforehand. Therefore, by iterating the Bellman equation, the resulting value function can converge to the optimal one in the presence of the aforementioned noise, and the nearly optimal control laws are delivered. To show the effectiveness and the advantages of the proposed approach, a simulation example and a velocity control experiment on a dc machine are employed.

A Novel Extreme Learning Control Framework of Unmanned Surface Vehicles.

PubMed

Wang, Ning; Sun, Jing-Chao; Er, Meng Joo; Liu, Yan-Cheng

2016-05-01

In this paper, an extreme learning control (ELC) framework using the single-hidden-layer feedforward network (SLFN) with random hidden nodes for tracking an unmanned surface vehicle suffering from unknown dynamics and external disturbances is proposed. By combining tracking errors with derivatives, an error surface and transformed states are defined to encapsulate unknown dynamics and disturbances into a lumped vector field of transformed states. The lumped nonlinearity is further identified accurately by an extreme-learning-machine-based SLFN approximator which does not require a priori system knowledge nor tuning input weights. Only output weights of the SLFN need to be updated by adaptive projection-based laws derived from the Lyapunov approach. Moreover, an error compensator is incorporated to suppress approximation residuals, and thereby contributing to the robustness and global asymptotic stability of the closed-loop ELC system. Simulation studies and comprehensive comparisons demonstrate that the ELC framework achieves high accuracy in both tracking and approximation.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

PubMed Central

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

2015-01-01

Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

Mechanistic Comparison of "Nearly Missed" Versus "On-Target" Rotor Ablation.

PubMed

Yamazaki, Masatoshi; Avula, Uma Mahesh R; Berenfeld, Omer; Kalifa, Jérôme

2015-08-01

This study used advanced optical mapping techniques to examine atrial fibrillation (AF) dynamics before and after 2 distinct electrogram-based ablation strategies: complex fractionated atrial electrograms (CFAEs) and DFmax/rotor ablation. Among the electrogram analytical features proposed to unravel the atrial regions that perpetuate AF, CFAEs, highest dominant frequency sites (DFmax), and, more recently, phase analysis-enabled rotor mapping have received the largest attention. Still, the mechanisms by which these approaches modulate AF dynamics and lead to AF termination are unknown. In Langendorff-perfused sheep hearts, AF was maintained by the continuous perfusion of acetylcholine and high-resolution endocardial-epicardial optical videos were recorded from the left atrial free wall and the posterior left atrium. Then, DFmax/rotor regions (n = 7), or CFAE regions harboring the highest wavebreak density (HWD) (n = 5), were targeted with a 4F ablation catheter (5 to 15 W, 30 to 60 s/point). Thereafter, we examined the changes in AF dynamics and whether AF terminated. DFmax/rotor point ablation resulted in a significant decrease in DFmax values. In 2 animals AF terminated, whereas in the remaining 5 animals the post-ablation DFmax domain remained in the vicinity of its pre-ablation location. However, after HWD/CFAEs density ablation, DFmax values did not change, AF did not terminate, and post-ablation DFmax domains relocated from the left atrial free wall to the pulmonary vein-posterior left atrium region. In another group of hearts (n = 12), we observed that upon a progressive increase in acetylcholine concentration-mimicking the acute electrophysiological changes occurring after ablation-3-dimensional rotors drifted from one atrial region to another along large gradients of myocardial thickness. "On-target" DFmax/rotor ablation leads to the annihilation of the fibrillation-driving rotor. This translates into large decreases in AF frequency or AF termination. In contrast, "nearly missed" HWD/CFAEs ablation spares the fibrillation-driving rotor, and set the stage for rotor drift along large myocardial thickness gradients. Copyright © 2015 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Parkinson's Disease

MedlinePlus

... in sexual desire or performance. Prevention Because the cause of Parkinson's is unknown, proven ways to prevent the disease also remain a mystery. However, some research has shown that caffeine — which is found in coffee, tea and cola — ...

Correlates of Unknown HIV Status Among MSM Participating in the 2014 American Men's Internet Survey (AMIS).

PubMed

Traynor, S M; Brincks, A M; Feaster, D J

2017-08-29

Increasing serostatus awareness is a key HIV prevention strategy. Despite expanded testing efforts, some men who have sex with men (MSM) remain unaware of their HIV status. This study explored demographic characteristics, sexual identity, sexual role, and behavioral factors associated with unknown HIV status among MSM in the United States. Data from 9170 MSM in the 2014 American Men's Internet Survey were analyzed using logistic regression to identify correlates of unknown HIV status. Young age, race, low education, rural residence, and lack of recent healthcare visits were significantly associated with unknown HIV status. In addition, nondisclosure of one's sexual orientation (OR = 3.70, 95% CI 2.99-4.59) and a self-identified sexual role as "bottom" (OR = 1.45, 95% CI 1.24-1.70) were predictors of unknown HIV status. Post-hoc analysis showed HIV-negative MSM not tested in the last year had fewer self-reported risk behaviors than recent testers, suggesting that repeat testing among MSM may be aligned with individual risk.

Description of a Method to Obtain Complete One-Year Follow-Up in the Society of Thoracic Surgeons/American College of Cardiology Transcatheter Valve Therapy Registry.

PubMed

Wooley, Jordan; Neatherlin, Holly; Mahoney, Cecile; Squiers, John J; Tabachnick, Deborah; Suresh, Mitta; Huff, Eleanor; Basra, Sukhdeep S; DiMaio, J Michael; Brown, David L; Mack, Michael J; Holper, Elizabeth M

2018-03-15

The Centers for Medicare and Medicaid Services National Coverage Determination requires centers performing transcatheter aortic valve implantation (TAVI) to report clinical outcomes up to 1 year. Many sites encounter challenges in obtaining complete 1-year follow-up. We report our process to address this challenge. A multidisciplinary process involving clinical personnel, data and quality managers, and research coordinators was initiated to collect TAVI data at baseline, 30 days, and 1 year. This process included (1) planned clinical follow-up of all patients at 30 days and 1 year; (2) query of health-care system-wide integrated data warehouse (IDW) to ascertain last date of clinical contact within the system for all patients; (3) online obituary search, cross-referencing for unique patient identifiers to determine if mortality occurred in remaining unknown patients; and (4) phone calls to remaining unknown patients or patients' families. Between January 2012 and December 2016, 744 patients underwent TAVI. All 744 patients were eligible for 30-day follow-up and 546 were eligible for 1-year follow-up. At routine clinical follow-up of 22 of 744 (3%) patients at 30 days and 180 of 546 (33%) patients at 1 year had unknown survival status. The integrated data warehouse query confirmed status-alive for an additional 1 of 22 patients at 30 days (55%) and 91 of 180 patients at 1 year (51%). Obituaries were identified for 23 of 180 additional patients at 1 year (13%). Phone contact identified the remaining unknown patients at 30 days and 1 year, resulting in 100% known survival status for patients at 30 days (744 of 744) and at 1 year (546 of 546). In conclusion, using a comprehensive approach, we were able to determine survival status in 100% of patients who underwent TAVI. Copyright © 2017 Elsevier Inc. All rights reserved.

Convergent structural responses of tropical forests to diverse disturbance regimes.

PubMed

Kellner, James R; Asner, Gregory P

2009-09-01

Size frequency distributions of canopy gaps are a hallmark of forest dynamics. But it remains unknown whether legacies of forest disturbance are influencing vertical size structure of landscapes, or space-filling in the canopy volume. We used data from LiDAR remote sensing to quantify distributions of canopy height and sizes of 434,501 canopy gaps in five tropical rain forest landscapes in Costa Rica and Hawaii. The sites represented a wide range of variation in structure and natural disturbance history, from canopy gap dynamics in lowland Costa Rica and Hawaii, to stages and types of stand-level dieback on upland Mauna Kea and Kohala volcanoes. Large differences in vertical canopy structure characterized these five tropical rain forest landscapes, some of which were related to known disturbance events. Although there were quantitative differences in the values of scaling exponents within and among sites, size frequency distributions of canopy gaps followed power laws at all sites and in all canopy height classes. Scaling relationships in gap size at different heights in the canopy were qualitatively similar at all sites, revealing a remarkable similarity despite clearly defined differences in species composition and modes of prevailing disturbance. These findings indicate that power-law gap-size frequency distributions are ubiquitous features of these five tropical rain forest landscapes, and suggest that mechanisms of forest disturbance may be secondary to other processes in determining vertical and horizontal size structure in canopies.

Possible stimuli for strength and power adaptation : acute metabolic responses.

PubMed

Crewther, Blair; Cronin, John; Keogh, Justin

2006-01-01

The metabolic response to resistance exercise, in particular lactic acid or lactate, has a marked influence upon the muscular environment, which may enhance the training stimulus (e.g. motor unit activation, hormones or muscle damage) and thereby contribute to strength and power adaptation. Hypertrophy schemes have resulted in greater lactate responses (%) than neuronal and dynamic power schemes, suggesting possible metabolic-mediated changes in muscle growth. Factors such as age, sex, training experience and nutrition may also influence the lactate responses to resistance exercise and thereafter, muscular adaptation. Although the importance of the mechanical and hormonal stimulus to strength and power adaptation is well recognised, the contribution of the metabolic stimulus is largely unknown. Relatively few studies for example, have examined metabolic change across neuronal and dynamic power schemes, and not withstanding the fact that those mechanisms underpinning muscular adaptation, in relation to the metabolic stimulus, remain highly speculative. Inconsistent findings and methodological limitations within research (e.g. programme design, sampling period, number of samples) make interpretation further difficult. We contend that strength and power research needs to investigate those metabolic mechanisms likely to contribute to weight-training adaptation. Further research is also needed to examine the metabolic responses to different loading schemes, as well as interactions across age, sex and training status, so our understanding of how to optimise strength and power development is improved.

A translational platform for prototyping closed-loop neuromodulation systems

PubMed Central

Afshar, Pedram; Khambhati, Ankit; Stanslaski, Scott; Carlson, David; Jensen, Randy; Linde, Dave; Dani, Siddharth; Lazarewicz, Maciej; Cong, Peng; Giftakis, Jon; Stypulkowski, Paul; Denison, Tim

2013-01-01

While modulating neural activity through stimulation is an effective treatment for neurological diseases such as Parkinson's disease and essential tremor, an opportunity for improving neuromodulation therapy remains in automatically adjusting therapy to continuously optimize patient outcomes. Practical issues associated with achieving this include the paucity of human data related to disease states, poorly validated estimators of patient state, and unknown dynamic mappings of optimal stimulation parameters based on estimated states. To overcome these challenges, we present an investigational platform including: an implanted sensing and stimulation device to collect data and run automated closed-loop algorithms; an external tool to prototype classifier and control-policy algorithms; and real-time telemetry to update the implanted device firmware and monitor its state. The prototyping system was demonstrated in a chronic large animal model studying hippocampal dynamics. We used the platform to find biomarkers of the observed states and transfer functions of different stimulation amplitudes. Data showed that moderate levels of stimulation suppress hippocampal beta activity, while high levels of stimulation produce seizure-like after-discharge activity. The biomarker and transfer function observations were mapped into classifier and control-policy algorithms, which were downloaded to the implanted device to continuously titrate stimulation amplitude for the desired network effect. The platform is designed to be a flexible prototyping tool and could be used to develop improved mechanistic models and automated closed-loop systems for a variety of neurological disorders. PMID:23346048

Atomic-scale investigation of the interactions between tetrabromobisphenol A, tetrabromobisphenol S and bovine trypsin by spectroscopies and molecular dynamics simulations.

PubMed

Ding, Keke; Zhang, Huanxin; Wang, Haifei; Lv, Xuan; Pan, Liumeng; Zhang, Wenjing; Zhuang, Shulin

2015-12-15

Tetrabromobisphenol A (TBBPA) and its replacement alternative tetrabromobisphenol S (TBBPS) are used widely as brominated flame retardants (BFRs). However, the potential risk of their effects on bovine trypsin remains largely unknown. We investigated the effects of TBBPA and TBBPS to bovine trypsin by the fluorescence spectroscopy, circular dichroism and molecular dynamics (MD) simulations. They statically quenched the intrinsic fluorescence of bovine trypsin in a concentration-dependent mode and caused slight red-shifted fluorescence. The short and long fluorescence lifetime decay components of bovine trypsin were both affected, partly due to the disturbed microenvironmental changes of Trp215. The β-sheet content of bovine trypsin was significantly reduced from 82.4% to 75.7% and 76.6% by TBBPA and TBBPS, respectively, possibly impairing the physiological function of bovine trypsin. TBBPA and TBBPS bind at the 8-anilinonaphthalene-1-sulfonate (ANS) binding site with an association constant of 1.09×10(4) M(-1) and 2.41×10(4) M(-1) at 298 K, respectively. MD simulations revealed that van der Waals interactions and hydrogen bond interactions are dominant for TBBPA, whereas electrostatic interactions are critical for TBBPS. Our in vitro and in silico studies are beneficial to the understanding of risk assessment and future design of environmental benign BFRs. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation.

PubMed

Kachhap, Sangita; Priyadarshini, Pragya; Singh, Balvinder

2017-05-01

Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.

Local thermal injury elicits immediate dynamic behavioural responses by corneal Langerhans cells

PubMed Central

Ward, Brant R; Jester, James V; Nishibu, Akiko; Vishwanath, Mridula; Shalhevet, David; Kumamoto, Tadashi; Petroll, W Matthew; Cavanagh, H Dwight; Takashima, Akira

2007-01-01

Langerhans cells (LCs) represent a special subset of immature dendritic cells (DCs) that reside in epithelial tissues at the environmental interfaces. Although dynamic interactions of mature DCs with T cells have been visualized in lymph nodes, the cellular behaviours linked with the surveillance of tissues for pathogenic signals, an important function of immature DCs, remain unknown. To visualize LCs in situ, bone marrow cells from C57BL/6 mice expressing the enhanced green fluorescent protein (EGFP) transgene were transplanted into syngeneic wild-type recipients. Motile activities of EGFP+ corneal LCs in intact organ cultures were then recorded by time lapse two-photon microscopy. At baseline, corneal LCs exhibited a unique motion, termed dendrite surveillance extension and retraction cycling habitude (dSEARCH), characterized by rhythmic extension and retraction of their dendritic processes through intercellular spaces between epithelial cells. Upon pinpoint injury produced by infrared laser, LCs showed augmented dSEARCH and amoeba-like lateral movement. Interleukin (IL)-1 receptor antagonist completely abrogated both injury-associated changes, suggesting roles for IL-1. In the absence of injury, exogenous IL-1 caused a transient increase in dSEARCH without provoking lateral migration, whereas tumour necrosis factor-α induced both changes. Our results demonstrate rapid cytokine-mediated behavioural responses by LCs to local tissue injury, providing new insights into the biology of LCs. PMID:17250587

Molecular insight into the counteraction of trehalose on urea-induced protein denaturation using molecular dynamics simulation.

PubMed

Zhang, Na; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2012-06-21

Considerable experimental evidence indicates that trehalose can counteract the denaturing effects of urea on proteins. However, its molecular mechanism remains unknown due to the limitations of current experimental techniques. Herein, molecular dynamics simulations were performed to investigate the counteracting effects of trehalose against urea-induced denaturation of chymotrypsin inhibitor 2. The simulations indicate that the protein unfolds in 8 mol/L urea, but at the same condition the protein retains its native structure in the ternary solution of 8 mol/L urea and 1 mol/L trehalose. It is confirmed that the preferential exclusion of trehalose from the protein surface is the origin of its counteracting effects. It is found that trehalose binds urea via hydrogen bonds, so urea molecules are also expelled from the protein surface along with the preferential exclusion of trehalose. The exclusion of urea from the protein surface leads to the alleviation of the Lennard-Jones interactions between urea and the hydrophobic side chains of the protein in the ternary solution. In contrast, the electrostatic interactions between urea and the protein change little in the presence of trehalose because the decrease in the electrostatic interactions between urea and the protein backbone is canceled by the increase in the electrostatic interactions between urea and the charged side chains of the protein. The results have provided molecular explanations for the counteraction of urea-induced protein denaturation by trehalose.

Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

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

Martin-Garcia, Fernando; Mendieta-Moreno, Jesus Ignacio; Mendieta, Jesus

2012-03-30

Highlights: Black-Right-Pointing-Pointer Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. Black-Right-Pointing-Pointer HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. Black-Right-Pointing-Pointer HRS domains of F protein form three single {alpha}-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmentalmore » pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from {beta}-sheet conformation to an elongated coil and then spontaneously to an {alpha}-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.« less

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1.

PubMed

Duan, Juan; Hu, Chuncai; Guo, Jiafan; Guo, Lianxian; Sun, Jia; Zhao, Zuguo

2018-02-28

The mechanism of substrate hydrolysis of New Delhi metallo-β-lactamase 1 (NDM-1) has been reported, but the process in which NDM-1 captures and transports the substrate into its active center remains unknown. In this study, we investigated the process of the substrate entry into the NDM-1 activity center through long unguided molecular dynamics simulations using meropenem as the substrate. A total of 550 individual simulations were performed, each of which for 200 ns, and 110 of them showed enzyme-substrate binding events. The results reveal three categories of relatively persistent and noteworthy enzyme-substrate binding configurations, which we call configurations A, B, and C. We performed binding free energy calculations of the enzyme-substrate complexes of different configurations using the molecular mechanics Poisson-Boltzmann surface area method. The role of each residue of the active site in binding the substrate was investigated using energy decomposition analysis. The simulated trajectories provide a continuous atomic-level view of the entire binding process, revealing potentially valuable regions where the enzyme and the substrate interact persistently and five possible pathways of the substrate entering into the active center, which were validated using well-tempered metadynamics. These findings provide important insights into the binding mechanism of meropenem to NDM-1, which may provide new prospects for the design of novel metallo-β-lactamase inhibitors and enzyme-resistant antibiotics.

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals.

PubMed

Rath, Soumya Lipsa; Liu, Huihui; Okazaki, Susumu; Shinoda, Wataru

2018-02-26

Around 270 million individuals currently live with hepatitis B virus (HBV) infection. Heteroaryldihydropyrimidines (HAPs) are a family of antivirals that target the HBV capsid protein and induce aberrant self-assembly. The capsids formed resemble the native capsid structure but are unable to propagate the virus progeny because of a lack of RNA/DNA. Under normal conditions, self-assembly is initiated by the viral genome. The mode of action of HAPs, however, remains largely unknown. In this work, using molecular dynamics simulations, we attempted to understand the action of HAP by comparing the dynamics of capsid proteins with and without HAPs. We found that the inhibitor is more stable in higher oligomers. It retains its stability in the hexamer throughout 1 μs of simulation. Our results also show that the inhibitor might help in stabilizing the C-terminus, the HBc 149-183 arginine-rich domain of the capsid protein. The C-termini of dimers interact with each other, assisted by the HAP inhibitor. During capsid assembly, the termini are supposed to directly interact with the viral genome, thereby suggesting that the viral genome might work in a similar way to stabilize the capsid protein. Our results may help in understanding the underlying molecular mechanism of HBV capsid self-assembly, which should be crucial for exploring new drug targets and structure-based drug design.

Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study.

PubMed

Telesco, Shannon E; Radhakrishnan, Ravi

2009-03-18

HER2 (ErbB2/Neu) is a receptor tyrosine kinase belonging to the epidermal growth factor receptor (EGFR)/ErbB family and is overexpressed in 20-30% of human breast cancers. Although several crystal structures of ErbB kinases have been solved, the precise mechanism of HER2 activation remains unknown, and it has been suggested that HER2 is unique in its requirement for phosphorylation of Y877, a key tyrosine residue located in the activation loop. To elucidate mechanistic details of kinase domain regulation, we performed molecular dynamics simulations of a homology-modeled HER2 kinase structure in active and inactive conformations. Principal component analysis of the atomistic fluctuations reveals a tight coupling between the activation loop and catalytic loop that may contribute to alignment of residues required for catalysis in the active kinase. The free energy perturbation method is also employed to predict a role for phosphorylated Y877 in stabilizing the kinase conformations. Finally, simulation results are presented for a HER2/EGFR heterodimer and reveal that the dimeric interface induces a rearrangement of the alphaC helix toward the active conformation. Elucidation of the molecular regulatory mechanisms in HER2 will help establish structure-function relationships in the wild-type kinase, as well as predict mutations with a propensity for constitutive activation in HER2-mediated cancers.

A translational platform for prototyping closed-loop neuromodulation systems.

PubMed

Afshar, Pedram; Khambhati, Ankit; Stanslaski, Scott; Carlson, David; Jensen, Randy; Linde, Dave; Dani, Siddharth; Lazarewicz, Maciej; Cong, Peng; Giftakis, Jon; Stypulkowski, Paul; Denison, Tim

2012-01-01

While modulating neural activity through stimulation is an effective treatment for neurological diseases such as Parkinson's disease and essential tremor, an opportunity for improving neuromodulation therapy remains in automatically adjusting therapy to continuously optimize patient outcomes. Practical issues associated with achieving this include the paucity of human data related to disease states, poorly validated estimators of patient state, and unknown dynamic mappings of optimal stimulation parameters based on estimated states. To overcome these challenges, we present an investigational platform including: an implanted sensing and stimulation device to collect data and run automated closed-loop algorithms; an external tool to prototype classifier and control-policy algorithms; and real-time telemetry to update the implanted device firmware and monitor its state. The prototyping system was demonstrated in a chronic large animal model studying hippocampal dynamics. We used the platform to find biomarkers of the observed states and transfer functions of different stimulation amplitudes. Data showed that moderate levels of stimulation suppress hippocampal beta activity, while high levels of stimulation produce seizure-like after-discharge activity. The biomarker and transfer function observations were mapped into classifier and control-policy algorithms, which were downloaded to the implanted device to continuously titrate stimulation amplitude for the desired network effect. The platform is designed to be a flexible prototyping tool and could be used to develop improved mechanistic models and automated closed-loop systems for a variety of neurological disorders.

Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations.

PubMed

Sprenger, K G; Prakash, Arushi; Drobny, Gary; Pfaendtner, Jim

2018-01-23

Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

NASA Astrophysics Data System (ADS)

Taylor, Bradford P.; Penington, Catherine J.; Weitz, Joshua S.

2016-12-01

Multiple virus particles can infect a target host cell. Such multiple infections (MIs) have significant and varied ecological and evolutionary consequences for both virus and host populations. Yet, the in situ rates and drivers of MIs in virus-microbe systems remain largely unknown. Here, we develop an individual-based model (IBM) of virus-microbe dynamics to probe how spatial interactions drive the frequency and nature of MIs. In our IBMs, we identify increasingly spatially correlated clusters of viruses given sufficient decreases in viral movement. We also identify increasingly spatially correlated clusters of viruses and clusters of hosts given sufficient increases in viral infectivity. The emergence of clusters is associated with an increase in multiply infected hosts as compared to expectations from an analogous mean field model. We also observe long-tails in the distribution of the multiplicity of infection in contrast to mean field expectations that such events are exponentially rare. We show that increases in both the frequency and severity of MIs occur when viruses invade a cluster of uninfected microbes. We contend that population-scale enhancement of MI arises from an aggregate of invasion dynamics over a distribution of microbe cluster sizes. Our work highlights the need to consider spatially explicit interactions as a potentially key driver underlying the ecology and evolution of virus-microbe communities.

A new structural framework for integrating replication protein A into DNA processing machinery

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

Brosey, Chris; Yan, Chunli; Tsutakawa, Susan

2013-01-17

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamicmore » on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.« less

Functional and evolutionary trade-offs co-occur between two consolidated memory phases in Drosophila melanogaster

PubMed Central

Lagasse, Fabrice; Moreno, Celine; Preat, Thomas; Mery, Frederic

2012-01-01

Memory is a complex and dynamic process that is composed of different phases. Its evolution under natural selection probably depends on a balance between fitness benefits and costs. In Drosophila, two separate forms of consolidated memory phases can be generated experimentally: anaesthesia-resistant memory (ARM) and long-term memory (LTM). In recent years, several studies have focused on the differences between these long-lasting memory types and have found that, at the functional level, ARM and LTM are antagonistic. How this functional relationship will affect their evolutionary dynamics remains unknown. We selected for flies with either improved ARM or improved LTM over several generations, and found that flies selected specifically for improvement of one consolidated memory phase show reduced performance in the other memory phase. We also found that improved LTM was linked to decreased longevity in male flies but not in females. Conversely, males with improved ARM had increased longevity. We found no correlation between either improved ARM or LTM and other phenotypic traits. This is, to our knowledge, the first evidence of a symmetrical evolutionary trade-off between two memory phases for the same learning task. Such trade-offs may have an important impact on the evolution of cognitive capacities. On a neural level, these results support the hypothesis that mechanisms underlying these forms of consolidated memory are, to some degree, antagonistic. PMID:22859595

DNA methylation dynamics during early plant life.

PubMed

Bouyer, Daniel; Kramdi, Amira; Kassam, Mohamed; Heese, Maren; Schnittger, Arp; Roudier, François; Colot, Vincent

2017-09-25

Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10-20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis.

A new method for parameter estimation in nonlinear dynamical equations

NASA Astrophysics Data System (ADS)

Wang, Liu; He, Wen-Ping; Liao, Le-Jian; Wan, Shi-Quan; He, Tao

2015-01-01

Parameter estimation is an important scientific problem in various fields such as chaos control, chaos synchronization and other mathematical models. In this paper, a new method for parameter estimation in nonlinear dynamical equations is proposed based on evolutionary modelling (EM). This will be achieved by utilizing the following characteristics of EM which includes self-organizing, adaptive and self-learning features which are inspired by biological natural selection, and mutation and genetic inheritance. The performance of the new method is demonstrated by using various numerical tests on the classic chaos model—Lorenz equation (Lorenz 1963). The results indicate that the new method can be used for fast and effective parameter estimation irrespective of whether partial parameters or all parameters are unknown in the Lorenz equation. Moreover, the new method has a good convergence rate. Noises are inevitable in observational data. The influence of observational noises on the performance of the presented method has been investigated. The results indicate that the strong noises, such as signal noise ratio (SNR) of 10 dB, have a larger influence on parameter estimation than the relatively weak noises. However, it is found that the precision of the parameter estimation remains acceptable for the relatively weak noises, e.g. SNR is 20 or 30 dB. It indicates that the presented method also has some anti-noise performance.

Adaptive control of an exoskeleton robot with uncertainties on kinematics and dynamics.

PubMed

Brahmi, Brahim; Saad, Maarouf; Ochoa-Luna, Cristobal; Rahman, Mohammad H

2017-07-01

In this paper, we propose a new adaptive control technique based on nonlinear sliding mode control (JSTDE) taking into account kinematics and dynamics uncertainties. This approach is applied to an exoskeleton robot with uncertain kinematics and dynamics. The adaptation design is based on Time Delay Estimation (TDE). The proposed strategy does not necessitate the well-defined dynamic and kinematic models of the system robot. The updated laws are designed using Lyapunov-function to solve the adaptation problem systematically, proving the close loop stability and ensuring the convergence asymptotically of the outputs tracking errors. Experiments results show the effectiveness and feasibility of JSTDE technique to deal with the variation of the unknown nonlinear dynamics and kinematics of the exoskeleton model.

Dynamic metrology and data processing for precision freeform optics fabrication and testing

NASA Astrophysics Data System (ADS)

Aftab, Maham; Trumper, Isaac; Huang, Lei; Choi, Heejoo; Zhao, Wenchuan; Graves, Logan; Oh, Chang Jin; Kim, Dae Wook

2017-06-01

Dynamic metrology holds the key to overcoming several challenging limitations of conventional optical metrology, especially with regards to precision freeform optical elements. We present two dynamic metrology systems: 1) adaptive interferometric null testing; and 2) instantaneous phase shifting deflectometry, along with an overview of a gradient data processing and surface reconstruction technique. The adaptive null testing method, utilizing a deformable mirror, adopts a stochastic parallel gradient descent search algorithm in order to dynamically create a null testing condition for unknown freeform optics. The single-shot deflectometry system implemented on an iPhone uses a multiplexed display pattern to enable dynamic measurements of time-varying optical components or optics in vibration. Experimental data, measurement accuracy / precision, and data processing algorithms are discussed.

Adaptive governance of riverine and wetland ecosystem goods and services

EPA Science Inventory

Adaptive governance and adaptive management have developed over the past quarter century in response to institutional and organizational failures, and unforeseen changes in natural resource dynamics. Adaptive governance provides a context for managing known and unknown consequenc...

Entropic Lattice Boltzmann Methods

DTIC Science & Technology

2001-12-10

model of fluid dynamics in one dimension, first considered by Renda et al. in 1997 [14]. Here the geometric picture involves a four dimensional polytope...convention of including constant terms in an extra column of the matrix, using the device of appending 1 to the column vector of unknowns. In general, there...we apply the entropic lattice Boltzmann method to a simple five-velocity model of fluid dynamics in one dimension, first considered by Renda et al

Neighboring extremals of dynamic optimization problems with path equality constraints

NASA Technical Reports Server (NTRS)

Lee, A. Y.

1988-01-01

Neighboring extremals of dynamic optimization problems with path equality constraints and with an unknown parameter vector are considered in this paper. With some simplifications, the problem is reduced to solving a linear, time-varying two-point boundary-value problem with integral path equality constraints. A modified backward sweep method is used to solve this problem. Two example problems are solved to illustrate the validity and usefulness of the solution technique.

A Case Study in Transnational Crime: Ukraine and Modern Slavery

DTIC Science & Technology

2007-06-01

remained unable to appropriate resources or plan efficiently. The full extent of the decline remains unknown, because statistics were manipulated to hide...information is estimated to average 1 hour per response, including the time for reviewing instruction, searching existing data sources, gathering and...maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of

Kit fox population trends at the Naval Petroleum Reserves in California

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

Kato, T.T.; Scrivner, J.H.; Warrick, G.

The San Joaquin kit fox was listed as an endangered subspecies following passage of the Endangered Species Protection Act of 1966, and further classified as rare under the California Endangered Species Act of 1970. The San Joaquin kit fox occurs on the Naval Petroleum Reserves in California administered by the Department of Energy (DOE). A long term kit fox population monitoring program was initiated as part of DOE's mitigation strategy to comply with the Endangered Species Act. In addition to monitoring kit fox populations, the program includes assessments of kit fox prey density and assessments of predator abundance. The objectivesmore » of this study were to: describe the long term changes in the kit fox population on the Reserves and assess the roles of coyotes and lagomorphs in kit fox population dynamics. When the fox population on NPR-1 declined between 1980 and 1984, it appeared to have been negatively impacted by a declining prey base (lagomorphs) and an increasing coyote population. Declining lagomorph densities may have been a more important factor because as coyote numbers declined between 1985 and 1990, the kit fox population remained stable. The fox population on NPR-2 remained at a higher and more stable level than the population on NPR-1. The factors determining the higher densities and greater stability of the fox population on NPR-2 are unknown.« less

Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH.

PubMed

Camp, Emma F; Smith, David J; Evenhuis, Chris; Enochs, Ian; Manzello, Derek; Woodcock, Stephen; Suggett, David J

2016-05-25

Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50-100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals (Acropora palmata and Porites astreoides) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats. © 2016 The Author(s).

Wildfire Effects on In-stream Nutrient Processing and Hydrologic Transport

NASA Astrophysics Data System (ADS)

Rhea, A.; Covino, T. P.; Rhoades, C.; Fegel, T.

2017-12-01

In many forests throughout the Western U.S., drought, climate change, and growing fuel loads are contributing to increased fire frequency and severity. Wildfires can influence watershed nutrient retention as they fundamentally alter the biological composition and physical structure in upland landscapes, riparian corridors, and stream channels. While numerous studies have documented substantial short-term increases in stream nutrient concentrations and export (particularly reactive nitrogen, N) following forest fires, the long-term implications for watershed nutrient cycling remain unclear. For example, recent work indicates that nitrate concentrations and export can remain elevated for a decade or more following wildfire, yet the controls on these processes are unknown. In this research, we use empirical observations from nutrient tracer injections, nutrient diffusing substrates, and continuous water quality monitoring to isolate biological and physical controls on nutrient export across a burn-severity gradient. Tracer results demonstrate substantial stream-groundwater exchange, but little biological nutrient uptake in burned streams. This in part explains patterns of elevated nutrient export. Paired nutrient diffusing substrate experiments allow us to further investigate shifts in N, phosphorus, and carbon limitation that may suppress post-fire stream nutrient uptake. By isolating the mechanisms that reduce the capacity of fire-affected streams to retain and transform nutrient inputs, we can better predict dynamics in post-fire water quality and help prioritize upland and riparian restoration.

Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH

PubMed Central

Smith, David J.; Evenhuis, Chris; Enochs, Ian; Manzello, Derek; Woodcock, Stephen; Suggett, David J.

2016-01-01

Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50–100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals (Acropora palmata and Porites astreoides) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats. PMID:27194698

Towards high-speed autonomous navigation of unknown environments

NASA Astrophysics Data System (ADS)

Richter, Charles; Roy, Nicholas

2015-05-01

In this paper, we summarize recent research enabling high-speed navigation in unknown environments for dynamic robots that perceive the world through onboard sensors. Many existing solutions to this problem guarantee safety by making the conservative assumption that any unknown portion of the map may contain an obstacle, and therefore constrain planned motions to lie entirely within known free space. In this work, we observe that safety constraints may significantly limit performance and that faster navigation is possible if the planner reasons about collision with unobserved obstacles probabilistically. Our overall approach is to use machine learning to approximate the expected costs of collision using the current state of the map and the planned trajectory. Our contribution is to demonstrate fast but safe planning using a learned function to predict future collision probabilities.

Modeling of load lifting process with unknown center of gravity position

NASA Astrophysics Data System (ADS)

Kamanin, Y. N.; Zhukov, M. I.; Panichkin, A. V.; Redelin, R. A.

2018-03-01

The article proposes a new type of lifting beams that allows one to lift loads where the position of the center of gravity is unknown beforehand. The benefit of implementing this type of traverse is confirmed by the high demand for this product from the industrial enterprises and lack of their availability on the market. In conducted studies, the main kinematic and dynamic dependencies of the load lifting process with an unknown position of the center of gravity were described allowing for design and verification calculations of the traverse with flexible slings and an adjustable bail to be carried out. The obtained results can be useful to engineers and employees of enterprises engaged in the design and manufacturing of the lifting equipment and scientists doing research in “Carrying and lifting machines”.

Associations of endothelial function and air temperature in diabetic subjects

EPA Science Inventory

Background and Objective: Epidemiological studies consistently show that air temperature is associated with changes in cardiovascular morbidity and mortality. However, the biological mechanisms underlying the association remain largely unknown. As one index of endothelial functio...

Irreversible temperature gating in trpv1 sheds light on channel activation

PubMed Central

Sánchez-Moreno, Ana; Guevara-Hernández, Eduardo; Contreras-Cervera, Ricardo; Rangel-Yescas, Gisela; Ladrón-de-Guevara, Ernesto; Rosenbaum, Tamara

2018-01-01

Temperature-activated TRP channels or thermoTRPs are among the only proteins that can directly convert temperature changes into changes in channel open probability. In spite of a wealth of functional and structural information, the mechanism of temperature activation remains unknown. We have carefully characterized the repeated activation of TRPV1 by thermal stimuli and discovered a previously unknown inactivation process, which is irreversible. We propose that this form of gating in TRPV1 channels is a consequence of the heat absorption process that leads to channel opening. PMID:29869983

On position/force tracking control problem of cooperative robot manipulators using adaptive fuzzy backstepping approach.

PubMed

Baigzadehnoe, Barmak; Rahmani, Zahra; Khosravi, Alireza; Rezaie, Behrooz

2017-09-01

In this paper, the position and force tracking control problem of cooperative robot manipulator system handling a common rigid object with unknown dynamical models and unknown external disturbances is investigated. The universal approximation properties of fuzzy logic systems are employed to estimate the unknown system dynamics. On the other hand, by defining new state variables based on the integral and differential of position and orientation errors of the grasped object, the error system of coordinated robot manipulators is constructed. Subsequently by defining the appropriate change of coordinates and using the backstepping design strategy, an adaptive fuzzy backstepping position tracking control scheme is proposed for multi-robot manipulator systems. By utilizing the properties of internal forces, extra terms are also added to the control signals to consider the force tracking problem. Moreover, it is shown that the proposed adaptive fuzzy backstepping position/force control approach ensures all the signals of the closed loop system uniformly ultimately bounded and tracking errors of both positions and forces can converge to small desired values by proper selection of the design parameters. Finally, the theoretic achievements are tested on the two three-link planar robot manipulators cooperatively handling a common object to illustrate the effectiveness of the proposed approach. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407

Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

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

Cui, Jie; Krems, Roman V.; Li, Zhiying

2015-10-21

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A–H to make predictions of the dynamical properties for another molecule related to A–H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A–X. We assume that the effect of the −H →−X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can bemore » used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C{sub 6}H{sub 5}CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C{sub 6}H{sub 6} collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C{sub 6}H{sub 5}CN with He.« less

Cine CT technique for dynamic airway studies

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

Ell, S.R.; Jolles, H.; Keyes, W.D.

1985-07-01

The advent of cine CT scanning with its 50-msec data acquisition time promises a much wider range of dynamic CT studies. The authors describe a method for dynamic evaluation of the extrathoracic airway, which they believe has considerable potential application in nonfixed upper-airway disease, such as sleep apnea and stridor of unknown cause. Conventional CT is limited in such studies by long data acquisition time and can be used to study only prolonged maneuvers such as phonation. Fluoroscopy and digital subtraction studies are limited by relatively high radiation dose and inability to image all wall motions simultaneously.

Analysis of in vitro and in vivo function of total knee replacements using dynamic contact models

NASA Astrophysics Data System (ADS)

Zhao, Dong

Despite the high incidence of osteoarthritis in human knee joint, its causes remain unknown. Total knee replacement (TKR) has been shown clinically to be effective in restoring the knee function. However, wear of ultra-high molecular weight polyethylene has limited the longevity of TKRs. To address these important issues, it is necessary to investigate the in vitro and in vivo function of total knee replacements using dynamic contact models. A multibody dynamic model of an AMTI knee simulator was developed. Incorporating a wear prediction model into the contact model based on elastic foundation theory enables the contact surface to take into account creep and wear during the dynamic simulation. Comparisons of the predicted damage depth, area, and volume lost with worn retrievals from a physical machine were made to validate the model. In vivo tibial force distributions during dynamic and high flexion activities were investigated using the dynamic contact model. In vivo medial and lateral contact forces experienced by a well-aligned instrumented knee implant, as well as upper and lower bounds on contact pressures for a variety of activities were studied. For all activities, the predicted medial and lateral contact forces were insensitive to the selected material model. For this patient, the load split during the mid-stance phase of gait and during stair is more equal than anticipated. The external knee adduction torque has been proposed as a surrogate measure for medial compartment load during gait. However, a direct link between these two quantities has not been demonstrated using in vivo measurement of medial compartment load. In vivo data collected from a subject with an instrumented knee implant were analyzed to evaluate this link. The subject performed five different overground gait motions (normal, fast, slow, wide, and toe out) while instrumented implant, video motion, and ground reaction data were simultaneously collected. The high correlation coefficient results support the hypothesis that the knee adduction torque is highly correlated with medial compartment contact force and medial to total force ratio during gait.