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Sensitivity of ecological models to their climate drivers: statistical ensembles for forcing.

Global and regional numerical models for terrestrial ecosystem dynamics require fine spatial resolution and temporally complete historical climate fields as input variables. However, because climate observations are unevenly spaced and have incomplete records, such fields need to be estimated. In addition, uncertainty in these fields associated with their estimation are rarely assessed. Ecological models are usually driven with a geostatistical model's mean estimate (kriging) of these fields without accounting for this uncertainty, much less evaluating such errors in terms of their propagation in ecological simulations. We introduce a Bayesian statistical framework to model climate observations to create spatially uniform and temporally complete fields, taking into account correlation in time and space, spatial heterogeneity, lack of normality, and uncertainty about all these factors. A key benefit of the Bayesian model is that it generates uncertainty measures for the generated fields. To demonstrate this method, we reconstruct historical monthly precipitation fields (a driver for ecological models) on a fine resolution grid for a climatically heterogeneous region in the western United States. The main goal of this work is to evaluate the sensitivity of ecological models to the uncertainty associated with prediction of their climate drivers. To assess their numerical sensitivity to predicted input variables, we generate a set of ecological model simulations run using an ensemble of different versions of the reconstructed fields. We construct such an ensemble by sampling from the posterior predictive distribution of the climate field. We demonstrate that the estimated prediction error of the climate field can be very high. We evaluate the importance of such errors in ecological model experiments using an ensemble of historical precipitation time series in simulations of grassland biogeochemical dynamics with an ecological numerical model, Century. We show how uncertainty in predicted precipitation fields is propagated into ecological model results and that this propagation had different modes. Depending on output variable, the response of model dynamics to uncertainty in inputs ranged from uncertainty in outputs that matched that of inputs to those that were muted or that were biased, as well as uncertainty that was persistent in time after input errors dropped.

Animals↗

Electrotonically mediated oscillatory patterns in neuronal ensembles: an in vitro voltage-dependent dye-imaging study in the inferior olive.

Spatiotemporal profiles of ensemble subthreshold neuronal oscillation were studied in brainstem slices using high-speed voltage-sensitive dye imaging. After local electrical stimuli, the overall voltage profile demonstrated coherent oscillatory waves that spread over the inferior olive (IO). These oscillations were also observed in concurrently obtained intracellular recordings from IO neurons. Over the first few seconds after the stimuli, the optically recorded oscillations clustered into coherent groups comprising hundreds of neurons. Statistical analysis of the spatial profiles of these clusters revealed size fluctuation around stable core regions that were surrounded by a rim the diameter of which varied in time during the oscillation period. The neuronal ensemble oscillations were calcium derived and had an average frequency range of 1-7 Hz. This rhythmic response demonstrated a different spatiotemporal distribution in the presence of picrotoxin, which induced the merging of neuronal clusters into larger areas of coherent activity. The possibility that such clustering is a consequence of intrinsic oscillations in ensembles of coupled neurons was tested using mathematical modeling.

Action Potentials↗

[The neuronal ensembles of the brain].

The conclusion about availability of two types of neuron ensembles in the central nervous structures was made on the basis of proper experimental studies and appropriate literature data analysis. The first is presented by neurons functional cooperation (Hebbian ensembles) formed during learning process on the basis of synchronization by high-frequency oscillator activity. The second is presented by morphological-and-functional structures (Kogan's neuron ensembles) formed during neurogenesis process and genetically destined for biologically valuable patterns recognition. The control of functional state of the brain neuron networks and occurred information processes is realized by non-specific systems either restrict the neurons capability of joining in the rate of global synchronization by synchronization and desynchronization actions or form and maintain the common rhythm of activity in considerable neuron populations. The latter block single elements ability to enter into specific interactions.

Animals↗

Detecting dynamical changes within a simulated neural ensemble using a measure of representational quality.

Technological advances allowing simultaneous recording of neuronal ensembles have led to many developments in our understanding of how the brain performs neural computations. One key technique for extracting information from neural populations has been population reconstruction. While reconstruction is a powerful tool, it only provides a value and gives no indication of the quality of the representation itself. In this paper, we present a mathematically and statistically justified measure for assessing the quality of a representation in a neuronal ensemble. Using a simulated neural network, we show that this measure can distinguish between system states and identify moments of dynamical change within the system. While the examples used in this paper all derive from a standard network model, the measure itself is very general. It requires only a representational space, measured tuning curves, and neural ensembles.

Animals↗

BOLD signals correlate with ensemble unit activities in rat's somatosensory cortex.

Evoked neural activity (ensemble single-unit activity and evoked field potential) and functional magnetic resonance imaging (fMRI) changes of the primary somatosensory cortex in response to electrical stimulation of the hind paw were studied in rats under anesthesia. The effects of stimulation frequency (ranging from 0.3 to 10 Hz) and types of anesthetics (alpha-chloralose and sodium pentobarbital) on blood oxygen level dependent (BOLD) activation and neural activation were compared. Both ensemble single-unit activity and BOLD signal changes achieved maximal activation at 3 Hz of stimulation and responses were significantly stronger under alpha-chloralose anesthesia. The maximal activation of the integral evoked potential (sigmaEP), in contrast, was the highest at 10 Hz; and the values were similar for alpha-chloralose and pentobarbital. These analyses revealed that fMRI image changes were better correlated with ensemble single-unit activity than with sigmaEP during somatosensory stimulations.

Anesthesia↗

The pathological process. II(III). Lesional sequentiality and its multifactorial determining: structure and dynamics of factor ensembles.

The dynamic and structural analysis of pathological processes points out their multifactorial determining, the importance of the intrinsic conditioning, the existence of a lesional sequentiality, exemplified by the chain of lesional sequences, morphologically different, the intersequential relations of cohesive and propelling type, and the discontinuity in the progress from one lesional sequence to another. Factor ensembles, ensuring and governing the start of the process and the transition from a lesional sequence to another, were analysed in point of structure, composition, role of substrates, dynamics of ensembles, roles played by ensemble components (cohesive, propelling role).

Animals↗

Wind-chill equations predicting whole-body heat loss for a range of typical civilian outdoor clothing ensembles.

A thermal manikin with constant skin temperature and a wind-chill tunnel with constant air temperatures and wind speeds were used to measure whole-body heat loss for seven ensembles chosen to represent the full range of civilian outdoor clothing in use for everyday, nonsporting wear. Equations fitting the data with correlation coefficients exceeding 0.99 were derived for each ensemble, and diagrams were produced with these equations to interpolate and extend the range of conditions. The conditions studied were those resulting in total heat loss from 50 to 250 W.m-2, so very little extrapolation was required. The wind-chill equivalent temperature (with reference to 2 m.s-1), based on the average value for all seven ensembles, showed good agreement on this measure. The values predicted on the basis of whole-body heat loss through clothing were shown to be much lower than those predicted from the Siple wind-chill index for unprotected skin.

Air Movements↗

[Characteristics of the ensemble organization of the human cerebral cortex from birth to 20 years of age].

When studying frontal, somatosensory and visual areas of the human cerebral cortex from birth up to 20 years of age in year-to-year intervals, it has been stated that by birth in neocortex all components of the neuron-glio-vascular ensembles are presented. They are not connected in their composition. During the first year of life the size of all types of neurons increases, long-axonal basket neurons differentiate, fasciculi of radial fibers become thick. By 3 years of life in the ensembles the neurons are definitely grouped as clusters. Sizes of spindle-like and satellite neurons increase; they distribute their axonal collaterals vertically, horizontally and in frontal-posterior direction. By 5-6 years of age the horizontal connection system becomes more complex at the expense of longitudinal growth and ramification of lateral and basal dendrites of the pyramidal neurons. In the section transversal areas occupied with cell groups increase. By 9-10 years of age the pyramidal neurons reach their greatest size. By 12-14 years of age the fibrillar component of the cortex increases considerably, inter- and intraensemble horizontal connections become more complex, the system of local connections becomes more plastic owing to development of short-axonal basket-like neurons. By 16-18 years of age the ensemble cortical organization in its main parameters of architectonics reaches the level specific for mature persons.

Adolescent↗

[Prediction of the ensembles of RNA secondary structures. Kinetic analysis of self-organization].

A new approach to the problem of prediction of secondary structures of RNA, which is based on the kinetic analysis of self-organising molecules is proposed. Structural reconstructions that take place during formation of secondary structures are described in terms of Markov process. A set of states and probability transition were defined. Monte-Carlo methods were used to describe this process. Probability distributions of various secondary structures depending on time are given. Examples of calculations for ensembles of secondary structures of some tRNAs are described. An effective method of steady-state ensemble research, which is based on a quick RESETTING of all possible variance of the secondary structures of RNAs is given. By ascribing to each of these structures the value of probabilities as a function of free energy it was possible to obtain the Boltzmann ensemble of secondary structures.

Escherichia coli↗

[Probability neuronal ensembles from the position of the theory of fuzzy sets].

The questions of organization and functioning of the probability neuronal ensembles in the cerebral central analysatory structures were regarded from the standpoints of the washed out multitudes theory. The possibility of formalization of structure of a neuronal ensemble (the washed out multitude of neurons) was shown, examples of determining the function of a neuron belonging to a neuronal ensemble were presented, the questions of transition from washed out multitudes to unwashed those were considered.

Mathematics↗

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.

Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation techniques such as simulated annealing can capture these motions by comparing them to long-time molecular dynamics (MD) trajectories. The motions are analyzed by principal component analysis and compared using inner products of eigenvectors of the respective covariance matrices. Two very different systems are studied, the beta-spectrin PH domain and the single-stranded DNA binding protein (ssDBP) from the filamentous phage Pf3. A comparison of the ensembles from NMR and MD shows significant overlap of the essential spaces, which in the case of ssDBP is extraordinarily high. The influence of variations in the specifications of distance restraints is investigated. We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility. The results suggest a modified criterion that improves conformational sampling in terms of amplitudes of correlated motion.

Computer Simulation↗

Molecular modeling of closed circular DNA thermodynamic ensembles.

Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a single minimum energy structure, rather than from a complete thermodynamic ensemble. We have investigated this question using molecular dynamics simulations on a low resolution molecular mechanics model in which each base pair is represented by three points (a plane). This allows the inclusion of sequence-dependent variations of tip, inclination, and twist. Three kinds of sequences were tested: (1) homogeneous DNA, in which all base pairs have the helicoidal parameters of an ideal, average B-DNA; (2) random sequence DNA; and (3) curved DNA. We examined the rate of convergence of various structural parameters. Convergence for most of these is slowest for homogeneous sequences, more rapid for random sequences, and most rapid for curved sequences. The most slowly converging parameter is the antipodes profile. In a plasmid with N base pairs (bp), the antipodes distance is the distance dij from base pair i to base pair j halfway around the plasmid, j = i + N/2. The antipodes profile at time tau is a plot of dij over the range i = 1, N/2. In a homogeneous plasmid, convergence requires that the antipodes profile averaged over time must be flat. Even in the small plasmids examined here, the average properties of the ensembles were found to differ from those of static equilibrium structures. These effects will be even more dramatic for larger plasmids. Further, average and dynamic properties are affected by both plasmid size and sequence.

Chemical Phenomena↗

Ionomer-coated electrodes and nanoelectrode ensembles as electrochemical environmental sensors: recent advances and prospects.

This Minireview focuses on recent advances in the use of ionomer-coated electrodes and nanoelectrode ensembles for the determination of redox ions at trace concentration level with special stress on applications for environmental monitoring. After an overview on the most recent developments of ionomer-coated electrodes, attention is directed towards their use for speciation analysis in environmental samples. In particular, some examples such as the selective determination of inorganic and metallorganic species of different toxicity and the redox state speciation of multiply charged ions are discussed. The second part of the Minireview deals with the development and electroanalytical use of a new kind of nanostructured electrode, named nanoelectrode ensembles, which are prepared by template synthesis within the pores of microporous guest membranes. Advantages, peculiarities, and limits of such devices are discussed together with perspectives for their use in electroanalytical sensing at trace and ultratrace concentration levels in environmental samples.

Electrodes↗

Dissipative particle dynamics simulations in the grand canonical ensemble: applications to polymer brushes.

We have used the dissipative particle dynamics (DPD) method in the grand canonical ensemble to study the compression of grafted polymer brushes in good solvent conditions. The force-distance profiles calculated from DPD simulations in the grand canonical ensemble are in very good agreement with the self-consistent field (SCF) theoretical models and with experimental results for two polystyrene brush layers grafted onto mica surfaces in toluene.

Journal Article↗

Surface- and resonance-enhanced micro-Raman spectroscopy of xanthene dyes: from the ensemble to single molecules.

Surface-enhanced resonance Raman scattering (SERRS) spectra of various rhodamine dyes, of pyronine G and thiopyronine adsorbed on isolated silver clusters were recorded at the ensemble level and at the single-molecule level with a high-resolution confocal laser microscope equipped with a spectrograph and a CCD-detector. Comparing single-molecule spectra with ensemble spectra, various inhomogeneous spectral features, such as line splitting, spectral wandering, spectral diffusion and abrupt spectral jumps between different metastable spectral states, are revealed positions and the relative intensities of the vibronic bands. Resonance enhancement is investigated with respect to single-molecule surface-enhanced Raman scattering (SERS) spectroscopy and is found to be responsible for approximately three orders of magnitude in sensitivity. A significant influence of the substituents on the single-molecule SERRS sensitivity is found, showing that various chemical effects are responsible for surface enhancement in addition to the electromagnetic enhancement effect.

Journal Article↗

Oriented ensembles in ultrafast electron diffraction.

Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles.

Journal Article↗

Targeting the "species gene ensemble".

The members of a given species display a normal distribution of gene expression which is here termed the species gene ensemble. This more specific designation of the 'genetic background' leads to a consideration of why gene targeting outcomes are regulated by the species gene ensemble. One consequence is the utility of the heterozygous knockout which buffers the drastic compensatory reactions of the homozygous knockout thereby revealing subtle but yet consistent alterations in hippocampally-dependent behaviors.

Animals↗

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

Journal Article↗