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Sample records for estimating spike rate

  1. State-Space Algorithms for Estimating Spike Rate Functions

    PubMed Central

    Smith, Anne C.; Scalon, Joao D.; Wirth, Sylvia; Yanike, Marianna; Suzuki, Wendy A.; Brown, Emery N.

    2010-01-01

    The accurate characterization of spike firing rates including the determination of when changes in activity occur is a fundamental issue in the analysis of neurophysiological data. Here we describe a state-space model for estimating the spike rate function that provides a maximum likelihood estimate of the spike rate, model goodness-of-fit assessments, as well as confidence intervals for the spike rate function and any other associated quantities of interest. Using simulated spike data, we first compare the performance of the state-space approach with that of Bayesian adaptive regression splines (BARS) and a simple cubic spline smoothing algorithm. We show that the state-space model is computationally efficient and comparable with other spline approaches. Our results suggest both a theoretically sound and practical approach for estimating spike rate functions that is applicable to a wide range of neurophysiological data. PMID:19911062

  2. Estimating spiking irregularities under changing environments.

    PubMed

    Miura, Keiji; Okada, Masato; Amari, Shun-Ichi

    2006-10-01

    We considered a gamma distribution of interspike intervals as a statistical model for neuronal spike generation. A gamma distribution is a natural extension of the Poisson process taking the effect of a refractory period into account. The model is specified by two parameters: a time-dependent firing rate and a shape parameter that characterizes spiking irregularities of individual neurons. Because the environment changes over time, observed data are generated from a model with a time-dependent firing rate, which is an unknown function. A statistical model with an unknown function is called a semiparametric model and is generally very difficult to solve. We used a novel method of estimating functions in information geometry to estimate the shape parameter without estimating the unknown function. We obtained an optimal estimating function analytically for the shape parameter independent of the functional form of the firing rate. This estimation is efficient without Fisher information loss and better than maximum likelihood estimation. We suggest a measure of spiking irregularity based on the estimating function, which may be useful for characterizing individual neurons in changing environments. PMID:16907630

  3. Optimal firing rate estimation

    NASA Technical Reports Server (NTRS)

    Paulin, M. G.; Hoffman, L. F.

    2001-01-01

    We define a measure for evaluating the quality of a predictive model of the behavior of a spiking neuron. This measure, information gain per spike (Is), indicates how much more information is provided by the model than if the prediction were made by specifying the neuron's average firing rate over the same time period. We apply a maximum Is criterion to optimize the performance of Gaussian smoothing filters for estimating neural firing rates. With data from bullfrog vestibular semicircular canal neurons and data from simulated integrate-and-fire neurons, the optimal bandwidth for firing rate estimation is typically similar to the average firing rate. Precise timing and average rate models are limiting cases that perform poorly. We estimate that bullfrog semicircular canal sensory neurons transmit in the order of 1 bit of stimulus-related information per spike.

  4. Estimating membrane voltage correlations from extracellular spike trains.

    PubMed

    Dorn, Jessy D; Ringach, Dario L

    2003-04-01

    The cross-correlation coefficient between neural spike trains is a commonly used tool in the study of neural interactions. Two well-known complications that arise in its interpretation are 1) modulations in the correlation coefficient may result solely from changes in the mean firing rate of the cells and 2) the mean firing rates of the neurons impose upper and lower bounds on the correlation coefficient whose absolute values differ by an order of magnitude or more. Here, we propose a model-based approach to the interpretation of spike train correlations that circumvents these problems. The basic idea of our proposal is to estimate the cross-correlation coefficient between the membrane voltages of two cells from their extracellular spike trains and use the resulting value as the degree of correlation (or association) of neural activity. This is done in the context of a model that assumes the membrane voltages of the cells have a joint normal distribution and spikes are generated by a simple thresholding operation. We show that, under these assumptions, the estimation of the correlation coefficient between the membrane voltages reduces to the calculation of a tetrachoric correlation coefficient (a measure of association in nominal data introduced by Karl Pearson) on a contingency table calculated from the spike data. Simulations of conductance-based leaky integrate-and-fire neurons indicate that, despite its simplicity, the technique yields very good estimates of the intracellular membrane voltage correlation from the extracellular spike trains in biologically realistic models. PMID:12686584

  5. Estimating nonstationary input signals from a single neuronal spike train

    NASA Astrophysics Data System (ADS)

    Kim, Hideaki; Shinomoto, Shigeru

    2012-11-01

    Neurons temporally integrate input signals, translating them into timed output spikes. Because neurons nonperiodically emit spikes, examining spike timing can reveal information about input signals, which are determined by activities in the populations of excitatory and inhibitory presynaptic neurons. Although a number of mathematical methods have been developed to estimate such input parameters as the mean and fluctuation of the input current, these techniques are based on the unrealistic assumption that presynaptic activity is constant over time. Here, we propose tracking temporal variations in input parameters with a two-step analysis method. First, nonstationary firing characteristics comprising the firing rate and non-Poisson irregularity are estimated from a spike train using a computationally feasible state-space algorithm. Then, information about the firing characteristics is converted into likely input parameters over time using a transformation formula, which was constructed by inverting the neuronal forward transformation of the input current to output spikes. By analyzing spike trains recorded in vivo, we found that neuronal input parameters are similar in the primary visual cortex V1 and middle temporal area, whereas parameters in the lateral geniculate nucleus of the thalamus were markedly different.

  6. Optimal Estimation and Rank Detection for Sparse Spiked Covariance Matrices

    PubMed Central

    Cai, Tony; Ma, Zongming; Wu, Yihong

    2014-01-01

    This paper considers a sparse spiked covariancematrix model in the high-dimensional setting and studies the minimax estimation of the covariance matrix and the principal subspace as well as the minimax rank detection. The optimal rate of convergence for estimating the spiked covariance matrix under the spectral norm is established, which requires significantly different techniques from those for estimating other structured covariance matrices such as bandable or sparse covariance matrices. We also establish the minimax rate under the spectral norm for estimating the principal subspace, the primary object of interest in principal component analysis. In addition, the optimal rate for the rank detection boundary is obtained. This result also resolves the gap in a recent paper by Berthet and Rigollet [2] where the special case of rank one is considered. PMID:26257453

  7. Asynchronous Rate Chaos in Spiking Neuronal Circuits.

    PubMed

    Harish, Omri; Hansel, David

    2015-07-01

    The brain exhibits temporally complex patterns of activity with features similar to those of chaotic systems. Theoretical studies over the last twenty years have described various computational advantages for such regimes in neuronal systems. Nevertheless, it still remains unclear whether chaos requires specific cellular properties or network architectures, or whether it is a generic property of neuronal circuits. We investigate the dynamics of networks of excitatory-inhibitory (EI) spiking neurons with random sparse connectivity operating in the regime of balance of excitation and inhibition. Combining Dynamical Mean-Field Theory with numerical simulations, we show that chaotic, asynchronous firing rate fluctuations emerge generically for sufficiently strong synapses. Two different mechanisms can lead to these chaotic fluctuations. One mechanism relies on slow I-I inhibition which gives rise to slow subthreshold voltage and rate fluctuations. The decorrelation time of these fluctuations is proportional to the time constant of the inhibition. The second mechanism relies on the recurrent E-I-E feedback loop. It requires slow excitation but the inhibition can be fast. In the corresponding dynamical regime all neurons exhibit rate fluctuations on the time scale of the excitation. Another feature of this regime is that the population-averaged firing rate is substantially smaller in the excitatory population than in the inhibitory population. This is not necessarily the case in the I-I mechanism. Finally, we discuss the neurophysiological and computational significance of our results. PMID:26230679

  8. Spike timing precision changes with spike rate adaptation in the owl's auditory space map.

    PubMed

    Keller, Clifford H; Takahashi, Terry T

    2015-10-01

    Spike rate adaptation (SRA) is a continuing change of responsiveness to ongoing stimuli, which is ubiquitous across species and levels of sensory systems. Under SRA, auditory responses to constant stimuli change over time, relaxing toward a long-term rate often over multiple timescales. With more variable stimuli, SRA causes the dependence of spike rate on sound pressure level to shift toward the mean level of recent stimulus history. A model based on subtractive adaptation (Benda J, Hennig RM. J Comput Neurosci 24: 113-136, 2008) shows that changes in spike rate and level dependence are mechanistically linked. Space-specific neurons in the barn owl's midbrain, when recorded under ketamine-diazepam anesthesia, showed these classical characteristics of SRA, while at the same time exhibiting changes in spike timing precision. Abrupt level increases of sinusoidally amplitude-modulated (SAM) noise initially led to spiking at higher rates with lower temporal precision. Spike rate and precision relaxed toward their long-term values with a time course similar to SRA, results that were also replicated by the subtractive model. Stimuli whose amplitude modulations (AMs) were not synchronous across carrier frequency evoked spikes in response to stimulus envelopes of a particular shape, characterized by the spectrotemporal receptive field (STRF). Again, abrupt stimulus level changes initially disrupted the temporal precision of spiking, which then relaxed along with SRA. We suggest that shifts in latency associated with stimulus level changes may differ between carrier frequency bands and underlie decreased spike precision. Thus SRA is manifest not simply as a change in spike rate but also as a change in the temporal precision of spiking. PMID:26269555

  9. Estimating Neuronal Information: Logarithmic Binning of Neuronal Inter-Spike Intervals.

    PubMed

    Dorval, Alan D

    2011-02-01

    Neurons communicate via the relative timing of all-or-none biophysical signals called spikes. For statistical analysis, the time between spikes can be accumulated into inter-spike interval histograms. Information theoretic measures have been estimated from these histograms to assess how information varies across organisms, neural systems, and disease conditions. Because neurons are computational units that, to the extent they process time, work not by discrete clock ticks but by the exponential decays of numerous intrinsic variables, we propose that neuronal information measures scale more naturally with the logarithm of time. For the types of inter-spike interval distributions that best describe neuronal activity, the logarithm of time enables fewer bins to capture the salient features of the distributions. Thus, discretizing the logarithm of inter-spike intervals, as compared to the inter-spike intervals themselves, yields histograms that enable more accurate entropy and information estimates for fewer bins and less data. Additionally, as distribution parameters vary, the entropy and information calculated from the logarithm of the inter-spike intervals are substantially better behaved, e.g., entropy is independent of mean rate, and information is equally affected by rate gains and divisions. Thus, when compiling neuronal data for subsequent information analysis, the logarithm of the inter-spike intervals is preferred, over the untransformed inter-spike intervals, because it yields better information estimates and is likely more similar to the construction used by nature herself. PMID:24839390

  10. Generalized analog thresholding for spike acquisition at ultralow sampling rates.

    PubMed

    He, Bryan D; Wein, Alex; Varshney, Lav R; Kusuma, Julius; Richardson, Andrew G; Srinivasan, Lakshminarayan

    2015-07-01

    Efficient spike acquisition techniques are needed to bridge the divide from creating large multielectrode arrays (MEA) to achieving whole-cortex electrophysiology. In this paper, we introduce generalized analog thresholding (gAT), which achieves millisecond temporal resolution with sampling rates as low as 10 Hz. Consider the torrent of data from a single 1,000-channel MEA, which would generate more than 3 GB/min using standard 30-kHz Nyquist sampling. Recent neural signal processing methods based on compressive sensing still require Nyquist sampling as a first step and use iterative methods to reconstruct spikes. Analog thresholding (AT) remains the best existing alternative, where spike waveforms are passed through an analog comparator and sampled at 1 kHz, with instant spike reconstruction. By generalizing AT, the new method reduces sampling rates another order of magnitude, detects more than one spike per interval, and reconstructs spike width. Unlike compressive sensing, the new method reveals a simple closed-form solution to achieve instant (noniterative) spike reconstruction. The base method is already robust to hardware nonidealities, including realistic quantization error and integration noise. Because it achieves these considerable specifications using hardware-friendly components like integrators and comparators, generalized AT could translate large-scale MEAs into implantable devices for scientific investigation and medical technology. PMID:25904712

  11. Generalized analog thresholding for spike acquisition at ultralow sampling rates

    PubMed Central

    He, Bryan D.; Wein, Alex; Varshney, Lav R.; Kusuma, Julius; Richardson, Andrew G.

    2015-01-01

    Efficient spike acquisition techniques are needed to bridge the divide from creating large multielectrode arrays (MEA) to achieving whole-cortex electrophysiology. In this paper, we introduce generalized analog thresholding (gAT), which achieves millisecond temporal resolution with sampling rates as low as 10 Hz. Consider the torrent of data from a single 1,000-channel MEA, which would generate more than 3 GB/min using standard 30-kHz Nyquist sampling. Recent neural signal processing methods based on compressive sensing still require Nyquist sampling as a first step and use iterative methods to reconstruct spikes. Analog thresholding (AT) remains the best existing alternative, where spike waveforms are passed through an analog comparator and sampled at 1 kHz, with instant spike reconstruction. By generalizing AT, the new method reduces sampling rates another order of magnitude, detects more than one spike per interval, and reconstructs spike width. Unlike compressive sensing, the new method reveals a simple closed-form solution to achieve instant (noniterative) spike reconstruction. The base method is already robust to hardware nonidealities, including realistic quantization error and integration noise. Because it achieves these considerable specifications using hardware-friendly components like integrators and comparators, generalized AT could translate large-scale MEAs into implantable devices for scientific investigation and medical technology. PMID:25904712

  12. Benchmarking Spike Rate Inference in Population Calcium Imaging.

    PubMed

    Theis, Lucas; Berens, Philipp; Froudarakis, Emmanouil; Reimer, Jacob; Román Rosón, Miroslav; Baden, Tom; Euler, Thomas; Tolias, Andreas S; Bethge, Matthias

    2016-05-01

    A fundamental challenge in calcium imaging has been to infer spike rates of neurons from the measured noisy fluorescence traces. We systematically evaluate different spike inference algorithms on a large benchmark dataset (>100,000 spikes) recorded from varying neural tissue (V1 and retina) using different calcium indicators (OGB-1 and GCaMP6). In addition, we introduce a new algorithm based on supervised learning in flexible probabilistic models and find that it performs better than other published techniques. Importantly, it outperforms other algorithms even when applied to entirely new datasets for which no simultaneously recorded data is available. Future data acquired in new experimental conditions can be used to further improve the spike prediction accuracy and generalization performance of the model. Finally, we show that comparing algorithms on artificial data is not informative about performance on real data, suggesting that benchmarking different methods with real-world datasets may greatly facilitate future algorithmic developments in neuroscience. PMID:27151639

  13. Incorporating spike-rate adaptation into a rate code in mathematical and biological neurons.

    PubMed

    Ralston, Bridget N; Flagg, Lucas Q; Faggin, Eric; Birmingham, John T

    2016-06-01

    For a slowly varying stimulus, the simplest relationship between a neuron's input and output is a rate code, in which the spike rate is a unique function of the stimulus at that instant. In the case of spike-rate adaptation, there is no unique relationship between input and output, because the spike rate at any time depends both on the instantaneous stimulus and on prior spiking (the "history"). To improve the decoding of spike trains produced by neurons that show spike-rate adaptation, we developed a simple scheme that incorporates "history" into a rate code. We utilized this rate-history code successfully to decode spike trains produced by 1) mathematical models of a neuron in which the mechanism for adaptation (IAHP) is specified, and 2) the gastropyloric receptor (GPR2), a stretch-sensitive neuron in the stomatogastric nervous system of the crab Cancer borealis, that exhibits long-lasting adaptation of unknown origin. Moreover, when we modified the spike rate either mathematically in a model system or by applying neuromodulatory agents to the experimental system, we found that changes in the rate-history code could be related to the biophysical mechanisms responsible for altering the spiking. PMID:26888106

  14. Philosophy of the Spike: Rate-Based vs. Spike-Based Theories of the Brain

    PubMed Central

    Brette, Romain

    2015-01-01

    Does the brain use a firing rate code or a spike timing code? Considering this controversial question from an epistemological perspective, I argue that progress has been hampered by its problematic phrasing. It takes the perspective of an external observer looking at whether those two observables vary with stimuli, and thereby misses the relevant question: which one has a causal role in neural activity? When rephrased in a more meaningful way, the rate-based view appears as an ad hoc methodological postulate, one that is practical but with virtually no empirical or theoretical support. PMID:26617496

  15. A memristive spiking neuron with firing rate coding

    PubMed Central

    Ignatov, Marina; Ziegler, Martin; Hansen, Mirko; Petraru, Adrian; Kohlstedt, Hermann

    2015-01-01

    Perception, decisions, and sensations are all encoded into trains of action potentials in the brain. The relation between stimulus strength and all-or-nothing spiking of neurons is widely believed to be the basis of this coding. This initiated the development of spiking neuron models; one of today's most powerful conceptual tool for the analysis and emulation of neural dynamics. The success of electronic circuit models and their physical realization within silicon field-effect transistor circuits lead to elegant technical approaches. Recently, the spectrum of electronic devices for neural computing has been extended by memristive devices, mainly used to emulate static synaptic functionality. Their capabilities for emulations of neural activity were recently demonstrated using a memristive neuristor circuit, while a memristive neuron circuit has so far been elusive. Here, a spiking neuron model is experimentally realized in a compact circuit comprising memristive and memcapacitive devices based on the strongly correlated electron material vanadium dioxide (VO2) and on the chemical electromigration cell Ag/TiO2−x/Al. The circuit can emulate dynamical spiking patterns in response to an external stimulus including adaptation, which is at the heart of firing rate coding as first observed by E.D. Adrian in 1926. PMID:26539074

  16. Behavior-related pauses in simple-spike activity of mouse Purkinje cells are linked to spike rate modulation.

    PubMed

    Cao, Ying; Maran, Selva K; Dhamala, Mukesh; Jaeger, Dieter; Heck, Detlef H

    2012-06-20

    Purkinje cells (PCs) in the mammalian cerebellum express high-frequency spontaneous activity with average spike rates between 30 and 200 Hz. Cerebellar nuclear (CN) neurons receive converging input from many PCs, resulting in a continuous barrage of inhibitory inputs. It has been hypothesized that pauses in PC activity trigger increases in CN spiking activity. A prediction derived from this hypothesis is that pauses in PC simple-spike activity represent relevant behavioral or sensory events. Here, we asked whether pauses in the simple-spike activity of PCs related to either fluid licking or respiration, play a special role in representing information about behavior. Both behaviors are widely represented in cerebellar PC simple-spike activity. We recorded PC activity in the vermis and lobus simplex of head-fixed mice while monitoring licking and respiratory behavior. Using cross-correlation and Granger causality analysis, we examined whether short interspike intervals (ISIs) had a different temporal relationship to behavior than long ISIs or pauses. Behavior-related simple-spike pauses occurred during low-rate simple-spike activity in both licking- and breathing-related PCs. Granger causality analysis revealed causal relationships between simple-spike pauses and behavior. However, the same results were obtained from an analysis of surrogate spike trains with gamma ISI distributions constructed to match rate modulations of behavior-related Purkinje cells. Our results therefore suggest that the occurrence of pauses in simple-spike activity does not represent additional information about behavioral or sensory events that goes beyond the simple-spike rate modulations. PMID:22723707

  17. Separating Spike Count Correlation from Firing Rate Correlation

    PubMed Central

    Vinci, Giuseppe; Ventura, Valérie; Smith, Matthew A.; Kass, Robert E.

    2016-01-01

    Populations of cortical neurons exhibit shared fluctuations in spiking activity over time. When measured for a pair of neurons over multiple repetitions of an identical stimulus, this phenomenon emerges as correlated trial-to-trial response variability via spike count correlation (SCC). However, spike counts can be viewed as noisy versions of firing rates, which can vary from trial to trial. From this perspective, the SCC for a pair of neurons becomes a noisy version of the corresponding firing-rate correlation (FRC). Furthermore, the magnitude of the SCC is generally smaller than that of the FRC, and is likely to be less sensitive to experimental manipulation. We provide statistical methods for disambiguating time-averaged drive from within-trial noise, thereby separating FRC from SCC. We study these methods to document their reliability, and we apply them to neurons recorded in vivo from area V4, in an alert animal. We show how the various effects we describe are reflected in the data: within-trial effects are largely negligible, while attenuation due to trial-to-trial variation dominates, and frequently produces comparisons in SCC that, because of noise, do not accurately reflect those based on the underlying FRC. PMID:26942746

  18. Separating Spike Count Correlation from Firing Rate Correlation.

    PubMed

    Vinci, Giuseppe; Ventura, Valérie; Smith, Matthew A; Kass, Robert E

    2016-05-01

    Populations of cortical neurons exhibit shared fluctuations in spiking activity over time. When measured for a pair of neurons over multiple repetitions of an identical stimulus, this phenomenon emerges as correlated trial-to-trial response variability via spike count correlation (SCC). However, spike counts can be viewed as noisy versions of firing rates, which can vary from trial to trial. From this perspective, the SCC for a pair of neurons becomes a noisy version of the corresponding firing rate correlation (FRC). Furthermore, the magnitude of the SCC is generally smaller than that of the FRC and is likely to be less sensitive to experimental manipulation. We provide statistical methods for disambiguating time-averaged drive from within-trial noise, thereby separating FRC from SCC. We study these methods to document their reliability, and we apply them to neurons recorded in vivo from area V4 in an alert animal. We show how the various effects we describe are reflected in the data: within-trial effects are largely negligible, while attenuation due to trial-to-trial variation dominates and frequently produces comparisons in SCC that, because of noise, do not accurately reflect those based on the underlying FRC. PMID:26942746

  19. How adaptation shapes spike rate oscillations in recurrent neuronal networks

    PubMed Central

    Augustin, Moritz; Ladenbauer, Josef; Obermayer, Klaus

    2012-01-01

    Neural mass signals from in-vivo recordings often show oscillations with frequencies ranging from <1 to 100 Hz. Fast rhythmic activity in the beta and gamma range can be generated by network-based mechanisms such as recurrent synaptic excitation-inhibition loops. Slower oscillations might instead depend on neuronal adaptation currents whose timescales range from tens of milliseconds to seconds. Here we investigate how the dynamics of such adaptation currents contribute to spike rate oscillations and resonance properties in recurrent networks of excitatory and inhibitory neurons. Based on a network of sparsely coupled spiking model neurons with two types of adaptation current and conductance-based synapses with heterogeneous strengths and delays we use a mean-field approach to analyze oscillatory network activity. For constant external input, we find that spike-triggered adaptation currents provide a mechanism to generate slow oscillations over a wide range of adaptation timescales as long as recurrent synaptic excitation is sufficiently strong. Faster rhythms occur when recurrent inhibition is slower than excitation and oscillation frequency increases with the strength of inhibition. Adaptation facilitates such network-based oscillations for fast synaptic inhibition and leads to decreased frequencies. For oscillatory external input, adaptation currents amplify a narrow band of frequencies and cause phase advances for low frequencies in addition to phase delays at higher frequencies. Our results therefore identify the different key roles of neuronal adaptation dynamics for rhythmogenesis and selective signal propagation in recurrent networks. PMID:23450654

  20. Estimating individual firing frequencies in a multiple spike train record.

    PubMed

    Pokora, Ondrej; Lansky, Petr

    2012-11-15

    Neuronal activity of several neurons is commonly recorded by a single electrode and then the individual spike trains are separated. If the separation is difficult or fails, then as a minimal result of the experiment, the individual firing rates are of interest. The proposed method solves the problem of their identification. This is possible under the condition that the recorded neurons are independent in their activities. The number of the neurons in the multi-unit record needs to be given (known or assumed) prior the calculation. The proposed method is based on the presence of the refractory period in neuronal firing, however, its precise value is not required. In addition to the determination of the individual firing rates the method can be used for an inference about the refractory period itself. PMID:23000722

  1. Analysis of the effects of periodic forcing in the spike rate and spike correlation's in semiconductor lasers with optical feedback

    NASA Astrophysics Data System (ADS)

    Quintero-Quiroz, C.; Sorrentino, Taciano; Torrent, M. C.; Masoller, Cristina

    2016-04-01

    We study the dynamics of semiconductor lasers with optical feedback and direct current modulation, operating in the regime of low frequency fluctuations (LFFs). In the LFF regime the laser intensity displays abrupt spikes: the intensity drops to zero and then gradually recovers. We focus on the inter-spike-intervals (ISIs) and use a method of symbolic time-series analysis, which is based on computing the probabilities of symbolic patterns. We show that the variation of the probabilities of the symbols with the modulation frequency and with the intrinsic spike rate of the laser allows to identify different regimes of noisy locking. Simulations of the Lang-Kobayashi model are in good qualitative agreement with experimental observations.

  2. Estimating temporal causal interaction between spike trains with permutation and transfer entropy.

    PubMed

    Li, Zhaohui; Li, Xiaoli

    2013-01-01

    Estimating the causal interaction between neurons is very important for better understanding the functional connectivity in neuronal networks. We propose a method called normalized permutation transfer entropy (NPTE) to evaluate the temporal causal interaction between spike trains, which quantifies the fraction of ordinal information in a neuron that has presented in another one. The performance of this method is evaluated with the spike trains generated by an Izhikevich's neuronal model. Results show that the NPTE method can effectively estimate the causal interaction between two neurons without influence of data length. Considering both the precision of time delay estimated and the robustness of information flow estimated against neuronal firing rate, the NPTE method is superior to other information theoretic method including normalized transfer entropy, symbolic transfer entropy and permutation conditional mutual information. To test the performance of NPTE on analyzing simulated biophysically realistic synapses, an Izhikevich's cortical network that based on the neuronal model is employed. It is found that the NPTE method is able to characterize mutual interactions and identify spurious causality in a network of three neurons exactly. We conclude that the proposed method can obtain more reliable comparison of interactions between different pairs of neurons and is a promising tool to uncover more details on the neural coding. PMID:23940662

  3. Estimating Temporal Causal Interaction between Spike Trains with Permutation and Transfer Entropy

    PubMed Central

    Li, Zhaohui; Li, Xiaoli

    2013-01-01

    Estimating the causal interaction between neurons is very important for better understanding the functional connectivity in neuronal networks. We propose a method called normalized permutation transfer entropy (NPTE) to evaluate the temporal causal interaction between spike trains, which quantifies the fraction of ordinal information in a neuron that has presented in another one. The performance of this method is evaluated with the spike trains generated by an Izhikevich’s neuronal model. Results show that the NPTE method can effectively estimate the causal interaction between two neurons without influence of data length. Considering both the precision of time delay estimated and the robustness of information flow estimated against neuronal firing rate, the NPTE method is superior to other information theoretic method including normalized transfer entropy, symbolic transfer entropy and permutation conditional mutual information. To test the performance of NPTE on analyzing simulated biophysically realistic synapses, an Izhikevich’s cortical network that based on the neuronal model is employed. It is found that the NPTE method is able to characterize mutual interactions and identify spurious causality in a network of three neurons exactly. We conclude that the proposed method can obtain more reliable comparison of interactions between different pairs of neurons and is a promising tool to uncover more details on the neural coding. PMID:23940662

  4. Estimating Extracellular Spike Waveforms from CA1 Pyramidal Cells with Multichannel Electrodes

    PubMed Central

    Molden, Sturla; Moldestad, Olve; Storm, Johan F.

    2013-01-01

    Extracellular (EC) recordings of action potentials from the intact brain are embedded in background voltage fluctuations known as the “local field potential” (LFP). In order to use EC spike recordings for studying biophysical properties of neurons, the spike waveforms must be separated from the LFP. Linear low-pass and high-pass filters are usually insufficient to separate spike waveforms from LFP, because they have overlapping frequency bands. Broad-band recordings of LFP and spikes were obtained with a 16-channel laminar electrode array (silicone probe). We developed an algorithm whereby local LFP signals from spike-containing channel were modeled using locally weighted polynomial regression analysis of adjoining channels without spikes. The modeled LFP signal was subtracted from the recording to estimate the embedded spike waveforms. We tested the method both on defined spike waveforms added to LFP recordings, and on in vivo-recorded extracellular spikes from hippocampal CA1 pyramidal cells in anaesthetized mice. We show that the algorithm can correctly extract the spike waveforms embedded in the LFP. In contrast, traditional high-pass filters failed to recover correct spike shapes, albeit produceing smaller standard errors. We found that high-pass RC or 2-pole Butterworth filters with cut-off frequencies below 12.5 Hz, are required to retrieve waveforms comparable to our method. The method was also compared to spike-triggered averages of the broad-band signal, and yielded waveforms with smaller standard errors and less distortion before and after the spike. PMID:24391714

  5. Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo

    PubMed Central

    Deneux, Thomas; Kaszas, Attila; Szalay, Gergely; Katona, Gergely; Lakner, Tamás; Grinvald, Amiram; Rózsa, Balázs; Vanzetta, Ivo

    2016-01-01

    Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo. PMID:27432255

  6. Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo.

    PubMed

    Deneux, Thomas; Kaszas, Attila; Szalay, Gergely; Katona, Gergely; Lakner, Tamás; Grinvald, Amiram; Rózsa, Balázs; Vanzetta, Ivo

    2016-01-01

    Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo. PMID:27432255

  7. Single-trial estimation of stimulus and spike-history effects on time-varying ensemble spiking activity of multiple neurons: a simulation study

    NASA Astrophysics Data System (ADS)

    Shimazaki, Hideaki

    2013-12-01

    Neurons in cortical circuits exhibit coordinated spiking activity, and can produce correlated synchronous spikes during behavior and cognition. We recently developed a method for estimating the dynamics of correlated ensemble activity by combining a model of simultaneous neuronal interactions (e.g., a spin-glass model) with a state-space method (Shimazaki et al. 2012 PLoS Comput Biol 8 e1002385). This method allows us to estimate stimulus-evoked dynamics of neuronal interactions which is reproducible in repeated trials under identical experimental conditions. However, the method may not be suitable for detecting stimulus responses if the neuronal dynamics exhibits significant variability across trials. In addition, the previous model does not include effects of past spiking activity of the neurons on the current state of ensemble activity. In this study, we develop a parametric method for simultaneously estimating the stimulus and spike-history effects on the ensemble activity from single-trial data even if the neurons exhibit dynamics that is largely unrelated to these effects. For this goal, we model ensemble neuronal activity as a latent process and include the stimulus and spike-history effects as exogenous inputs to the latent process. We develop an expectation-maximization algorithm that simultaneously achieves estimation of the latent process, stimulus responses, and spike-history effects. The proposed method is useful to analyze an interaction of internal cortical states and sensory evoked activity.

  8. A spike correction approach for variability analysis of heart rate sick infants

    NASA Astrophysics Data System (ADS)

    Govindan, R. B.; Al-Shargabi, Tareq; Metzler, Marina; Andescavage, Nickie N.; Joshi, Radhika; du Plessis, Adré

    2016-02-01

    In critical care monitoring, the heart rate (HR) offers valuable insight into the autonomic function of sick infants. However, the intensity of monitoring and clinical care such as intubation, suctioning, and venesection as well as routine movement, create a hostile environment for contamination of continuous signals. These artifacts usually present as spikes in the HR signal, which interfere with the characterization and subsequent evaluation of the HR. Post hoc spike removal is commonly required in research studies but is not feasible in clinical monitoring. We propose a two-step process to correct spikes in HR data. Step 1 comprises of two sub-steps to remove the spikes with upward deflection and downward deflection. In Step 2, we repeat Step 1, for different ɛ values and calculate root mean square (RMS) of the difference between the uncorrected HR and the corrected HR. The corrected HR that displayed either the smallest RMS value or the same RMS values for two or more ɛ values is considered optimally corrected data. We demonstrate the application of this approach to HR data collected from 5 preterm infants. We show that there is a significant difference between the spectral powers obtained for spike uncorrected and spike corrected HR.

  9. Associative Memory Neural Network with Low Temporal Spiking Rates

    NASA Astrophysics Data System (ADS)

    Amit, Daniel J.; Treves, A.

    1989-10-01

    We describe a modified attractor neural network in which neuronal dynamics takes place on a time scale of the absolute refractory period but the mean temporal firing rate of any neuron in the network is lower by an arbitrary factor that characterizes the strength of the effective inhibition. It operates by encoding information on the excitatory neurons only and assuming the inhibitory neurons to be faster and to inhibit the excitatory ones by an effective postsynaptic potential that is expressed in terms of the activity of the excitatory neurons themselves. Retrieval is identified as a nonergodic behavior of the network whose consecutive states have a significantly enhanced activity rate for the neurons that should be active in a stored pattern and a reduced activity rate for the neurons that are inactive in the memorized pattern. In contrast to the Hopfield model the network operates away from fixed points and under the strong influence of noise. As a consequence, of the neurons that should be active in a pattern, only a small fraction is active in any given time cycle and those are randomly distributed, leading to reduced temporal rates. We argue that this model brings neural network models much closer to biological reality. We present the results of detailed analysis of the model as well as simulations.

  10. Monte Carlo point process estimation of electromyographic envelopes from motor cortical spikes for brain-machine interfaces

    NASA Astrophysics Data System (ADS)

    Liao, Yuxi; She, Xiwei; Wang, Yiwen; Zhang, Shaomin; Zhang, Qiaosheng; Zheng, Xiaoxiang; Principe, Jose C.

    2015-12-01

    Objective. Representation of movement in the motor cortex (M1) has been widely studied in brain-machine interfaces (BMIs). The electromyogram (EMG) has greater bandwidth than the conventional kinematic variables (such as position, velocity), and is functionally related to the discharge of cortical neurons. As the stochastic information of EMG is derived from the explicit spike time structure, point process (PP) methods will be a good solution for decoding EMG directly from neural spike trains. Previous studies usually assume linear or exponential tuning curves between neural firing and EMG, which may not be true. Approach. In our analysis, we estimate the tuning curves in a data-driven way and find both the traditional functional-excitatory and functional-inhibitory neurons, which are widely found across a rat’s motor cortex. To accurately decode EMG envelopes from M1 neural spike trains, the Monte Carlo point process (MCPP) method is implemented based on such nonlinear tuning properties. Main results. Better reconstruction of EMG signals is shown on baseline and extreme high peaks, as our method can better preserve the nonlinearity of the neural tuning during decoding. The MCPP improves the prediction accuracy (the normalized mean squared error) 57% and 66% on average compared with the adaptive point process filter using linear and exponential tuning curves respectively, for all 112 data segments across six rats. Compared to a Wiener filter using spike rates with an optimal window size of 50 ms, MCPP decoding EMG from a point process improves the normalized mean square error (NMSE) by 59% on average. Significance. These results suggest that neural tuning is constantly changing during task execution and therefore, the use of spike timing methodologies and estimation of appropriate tuning curves needs to be undertaken for better EMG decoding in motor BMIs.

  11. Goodness-of-Fit Tests and Nonparametric Adaptive Estimation for Spike Train Analysis.

    PubMed

    Reynaud-Bouret, Patricia; Rivoirard, Vincent; Grammont, Franck; Tuleau-Malot, Christine

    2014-01-01

    When dealing with classical spike train analysis, the practitioner often performs goodness-of-fit tests to test whether the observed process is a Poisson process, for instance, or if it obeys another type of probabilistic model (Yana et al. in Biophys. J. 46(3):323-330, 1984; Brown et al. in Neural Comput. 14(2):325-346, 2002; Pouzat and Chaffiol in Technical report, http://arxiv.org/abs/arXiv:0909.2785, 2009). In doing so, there is a fundamental plug-in step, where the parameters of the supposed underlying model are estimated. The aim of this article is to show that plug-in has sometimes very undesirable effects. We propose a new method based on subsampling to deal with those plug-in issues in the case of the Kolmogorov-Smirnov test of uniformity. The method relies on the plug-in of good estimates of the underlying model that have to be consistent with a controlled rate of convergence. Some nonparametric estimates satisfying those constraints in the Poisson or in the Hawkes framework are highlighted. Moreover, they share adaptive properties that are useful from a practical point of view. We show the performance of those methods on simulated data. We also provide a complete analysis with these tools on single unit activity recorded on a monkey during a sensory-motor task.Electronic Supplementary MaterialThe online version of this article (doi:10.1186/2190-8567-4-3) contains supplementary material. PMID:24742008

  12. Goodness-of-Fit Tests and Nonparametric Adaptive Estimation for Spike Train Analysis

    PubMed Central

    2014-01-01

    When dealing with classical spike train analysis, the practitioner often performs goodness-of-fit tests to test whether the observed process is a Poisson process, for instance, or if it obeys another type of probabilistic model (Yana et al. in Biophys. J. 46(3):323–330, 1984; Brown et al. in Neural Comput. 14(2):325–346, 2002; Pouzat and Chaffiol in Technical report, http://arxiv.org/abs/arXiv:0909.2785, 2009). In doing so, there is a fundamental plug-in step, where the parameters of the supposed underlying model are estimated. The aim of this article is to show that plug-in has sometimes very undesirable effects. We propose a new method based on subsampling to deal with those plug-in issues in the case of the Kolmogorov–Smirnov test of uniformity. The method relies on the plug-in of good estimates of the underlying model that have to be consistent with a controlled rate of convergence. Some nonparametric estimates satisfying those constraints in the Poisson or in the Hawkes framework are highlighted. Moreover, they share adaptive properties that are useful from a practical point of view. We show the performance of those methods on simulated data. We also provide a complete analysis with these tools on single unit activity recorded on a monkey during a sensory-motor task. Electronic Supplementary Material The online version of this article (doi:10.1186/2190-8567-4-3) contains supplementary material. PMID:24742008

  13. PBXN-110 Burn Rate Estimate

    SciTech Connect

    Glascoe, E

    2008-08-11

    It is estimated that PBXN-110 will burn laminarly with a burn function of B = (0.6-1.3)*P{sup 1.0} (B is the burn rate in mm/s and P is pressure in MPa). This paper provides a brief discussion of how this burn behavior was estimated.

  14. Effect of marital status on death rates. Part 2: Transient mortality spikes

    NASA Astrophysics Data System (ADS)

    Richmond, Peter; Roehner, Bertrand M.

    2016-05-01

    We examine what happens in a population when it experiences an abrupt change in surrounding conditions. Several cases of such "abrupt transitions" for both physical and living social systems are analyzed from which it can be seen that all share a common pattern. First, a steep rising death rate followed by a much slower relaxation process during which the death rate decreases as a power law. This leads us to propose a general principle which can be summarized as follows: "Any abrupt change in living conditions generates a mortality spike which acts as a kind of selection process". This we term the Transient Shock conjecture. It provides a qualitative model which leads to testable predictions. For example, marriage certainly brings about a major change in personal and social conditions and according to our conjecture one would expect a mortality spike in the months following marriage. At first sight this may seem an unlikely proposition but we demonstrate (by three different methods) that even here the existence of mortality spikes is supported by solid empirical evidence.

  15. The impact of geomagnetic spikes on the production rates of cosmogenic 14C and 10Be in the Earth's atmosphere

    NASA Astrophysics Data System (ADS)

    Fournier, Alexandre; Gallet, Yves; Usoskin, Ilya; Livermore, Philip W.; Kovaltsov, Gennady A.

    2015-04-01

    We seek corroborative evidence of the geomagnetic spikes detected in the Near East ca. 980 BC and 890 BC in the records of the past production rates of the cosmogenic nuclides 14C and 10Be. Our forward modeling strategy rests on global, time-dependent, geomagnetic spike field models feeding state-of-the-art models of cosmogenic nuclide production. We find that spike models with an energy budget in line with presently inferred large-scale flow at Earth's core surface fail to produce a visible imprint in the nuclide record. Spike models able to reproduce the intensity changes reported in the Near East require an unaccountably high-magnitude core flow, yet their computed impact on cosmogenic isotope production rates remains ambiguous. No simple and unequivocal agreement is obtained between the observed and modeled nuclide records at the epochs of interest. This indicates that cosmogenic nuclides cannot immediately be used to confirm the occurrence of these two geomagnetic spikes.

  16. Particle swarm optimization algorithm based parameters estimation and control of epileptiform spikes in a neural mass model.

    PubMed

    Shan, Bonan; Wang, Jiang; Deng, Bin; Wei, Xile; Yu, Haitao; Zhang, Zhen; Li, Huiyan

    2016-07-01

    This paper proposes an epilepsy detection and closed-loop control strategy based on Particle Swarm Optimization (PSO) algorithm. The proposed strategy can effectively suppress the epileptic spikes in neural mass models, where the epileptiform spikes are recognized as the biomarkers of transitions from the normal (interictal) activity to the seizure (ictal) activity. In addition, the PSO algorithm shows capabilities of accurate estimation for the time evolution of key model parameters and practical detection for all the epileptic spikes. The estimation effects of unmeasurable parameters are improved significantly compared with unscented Kalman filter. When the estimated excitatory-inhibitory ratio exceeds a threshold value, the epileptiform spikes can be inhibited immediately by adopting the proportion-integration controller. Besides, numerical simulations are carried out to illustrate the effectiveness of the proposed method as well as the potential value for the model-based early seizure detection and closed-loop control treatment design. PMID:27475078

  17. Particle swarm optimization algorithm based parameters estimation and control of epileptiform spikes in a neural mass model

    NASA Astrophysics Data System (ADS)

    Shan, Bonan; Wang, Jiang; Deng, Bin; Wei, Xile; Yu, Haitao; Zhang, Zhen; Li, Huiyan

    2016-07-01

    This paper proposes an epilepsy detection and closed-loop control strategy based on Particle Swarm Optimization (PSO) algorithm. The proposed strategy can effectively suppress the epileptic spikes in neural mass models, where the epileptiform spikes are recognized as the biomarkers of transitions from the normal (interictal) activity to the seizure (ictal) activity. In addition, the PSO algorithm shows capabilities of accurate estimation for the time evolution of key model parameters and practical detection for all the epileptic spikes. The estimation effects of unmeasurable parameters are improved significantly compared with unscented Kalman filter. When the estimated excitatory-inhibitory ratio exceeds a threshold value, the epileptiform spikes can be inhibited immediately by adopting the proportion-integration controller. Besides, numerical simulations are carried out to illustrate the effectiveness of the proposed method as well as the potential value for the model-based early seizure detection and closed-loop control treatment design.

  18. Automatic Spike Sorting Using Tuning Information

    PubMed Central

    Ventura, Valérie

    2011-01-01

    Current spike sorting methods focus on clustering neurons’ characteristic spike waveforms. The resulting spike-sorted data are typically used to estimate how covariates of interest modulate the firing rates of neurons. However, when these covariates do modulate the firing rates, they provide information about spikes’ identities, which thus far have been ignored for the purpose of spike sorting. This letter describes a novel approach to spike sorting, which incorporates both waveform information and tuning information obtained from the modulation of firing rates. Because it efficiently uses all the available information, this spike sorter yields lower spike misclassification rates than traditional automatic spike sorters. This theoretical result is verified empirically on several examples. The proposed method does not require additional assumptions; only its implementation is different. It essentially consists of performing spike sorting and tuning estimation simultaneously rather than sequentially, as is currently done. We used an expectation-maximization maximum likelihood algorithm to implement the new spike sorter. We present the general form of this algorithm and provide a detailed implementable version under the assumptions that neurons are independent and spike according to Poisson processes. Finally, we uncover a systematic flaw of spike sorting based on waveform information only. PMID:19548802

  19. Stimulus encoding within the barn owl optic tectum using gamma oscillations vs. spike rate: a modeling approach.

    PubMed

    Patel, Mainak; Reed, Mike

    2013-01-01

    The optic tectum of the barn owl is a multimodal structure with multiple layers, with each layer topographically organized according to spatial receptive field. The response of a site to a stimulus can be measured as either spike rate or local field potential (LFP) gamma (25-90 Hz) power; within superficial layers, spike rate and gamma power spatial tuning curves are narrow and contrast-response functions rise slowly. Within deeper layers, however, spike rate tuning curves broaden and gamma power contrast-response functions sharpen. In this work, we employ a computational model to describe the inputs required to generate these transformations from superficial to deep layers and show that gamma power and spike rate can act as parallel information processing streams. PMID:23406211

  20. Effects of sodium salicylate on spontaneous and evoked spike rate in the dorsal cochlear nucleus

    PubMed Central

    Wei, Lei; Ding, Dalian; Sun, Wei; Xu-Friedman, Matthew A.; Salvi, Richard

    2010-01-01

    Spontaneous hyperactivity in the dorsal cochlear nucleus (DCN), particularly in fusiform cells, has been proposed as a neural generator of tinnitus. To determine if sodium salicylate, a reliable tinnitus inducer, could evoke hyperactivity in the DCN, we measured the spontaneous and depolarization-evoked spike rate in fusiform and cartwheel cells during salicylate superfusion. Five minute treatment with 1.4 mM salicylate suppressed spontaneous and evoked firing in fusiform cells; this decrease partially recovered after salicylate washout. Less suppression and greater recovery occurred with 3 minute treatment using 1.4 mM salicylate. In contrast, salicylate had no effect on the spontaneous or evoked firing of cartwheel cells indicating that salicylate’s suppressive effects are specific to fusiform cells. To determine if salicylate’s suppressive effects were a consequence of increased synaptic inhibition, spontaneous inhibitory post-synaptic currents (IPSC) were measured during salicylate treatment. Salicylate unexpectedly reduced IPSC thereby ruling out increased inhibition as a mechanism to explain the depressed firing rates in fusiform cells. The salicylate-induced suppression of fusiform spike rate apparently arises from unidentified changes in the cell’s intrinsic excitability. PMID:20430089

  1. Spike rate of multi-unit muscle sympathetic nerve fibers after catheter-based renal nerve ablation.

    PubMed

    Tank, Jens; Heusser, Karsten; Brinkmann, Julia; Schmidt, Bernhard M; Menne, Jan; Bauersachs, Johann; Haller, Hermann; Diedrich, André; Jordan, Jens

    2015-10-01

    Patients with treatment-resistant arterial hypertension exhibited profound reductions in single sympathetic vasoconstrictor fiber firing rates after renal nerve ablation. In contrast, integrated multi-unit muscle sympathetic nerve activity (MSNA) changed little or not at all. We hypothesized that conventional MSNA analysis may have missed single fiber discharges, thus, obscuring sympathetic inhibition after renal denervation. We studied patients with difficult-to-control arterial hypertension (age 45-74 years) before, 6 (n = 11), and 12 months (n = 8) after renal nerve ablation. Electrocardiogram, respiration, brachial, and finger arterial blood pressure (BP), as well as the MSNA and raw MSNA signals were analyzed. We detected MSNA action-potential spikes using 2 stage kurtosis wavelet denoising techniques to assess mean, median, and maximum spike rates for each beat-to-beat interval. Supine heart rate and systolic BP did not change at 6 (ΔHR: -2 ± 3 bpm; ΔSBP: 2 ± 9 mm Hg) or at 12 months (ΔHR: -1 ± 3 mm Hg, ΔSBP: -1 ± 9 mm Hg) after renal nerve ablation. Mean burst frequency and mean spike frequency at baseline were 34 ± 3 bursts per minute and 8 ± 1 spikes per second. Both measurements did not change at 6 months (-1.4 ± 3.6 bursts/minute; -0.6 ± 1.4 spikes/second) or at 12 months (-2.5 ± 4.0 bursts/minute; -2.0 ± 1.6 spikes/second) after renal nerve ablation. After renal nerve ablation, BP decreased in 3 of 11 patients. BP and MSNA spike frequency changes were not correlated (slope = -0.06; P = .369). Spike rate analysis of multi-unit MSNA neurograms further suggests that profound sympathetic inhibition is not a consistent finding after renal nerve ablation. PMID:26324745

  2. A biophysically-based neuromorphic model of spike rate- and timing-dependent plasticity.

    PubMed

    Rachmuth, Guy; Shouval, Harel Z; Bear, Mark F; Poon, Chi-Sang

    2011-12-01

    Current advances in neuromorphic engineering have made it possible to emulate complex neuronal ion channel and intracellular ionic dynamics in real time using highly compact and power-efficient complementary metal-oxide-semiconductor (CMOS) analog very-large-scale-integrated circuit technology. Recently, there has been growing interest in the neuromorphic emulation of the spike-timing-dependent plasticity (STDP) Hebbian learning rule by phenomenological modeling using CMOS, memristor or other analog devices. Here, we propose a CMOS circuit implementation of a biophysically grounded neuromorphic (iono-neuromorphic) model of synaptic plasticity that is capable of capturing both the spike rate-dependent plasticity (SRDP, of the Bienenstock-Cooper-Munro or BCM type) and STDP rules. The iono-neuromorphic model reproduces bidirectional synaptic changes with NMDA receptor-dependent and intracellular calcium-mediated long-term potentiation or long-term depression assuming retrograde endocannabinoid signaling as a second coincidence detector. Changes in excitatory or inhibitory synaptic weights are registered and stored in a nonvolatile and compact digital format analogous to the discrete insertion and removal of AMPA or GABA receptor channels. The versatile Hebbian synapse device is applicable to a variety of neuroprosthesis, brain-machine interface, neurorobotics, neuromimetic computation, machine learning, and neural-inspired adaptive control problems. PMID:22089232

  3. Solution to the inverse problem of estimating gap-junctional and inhibitory conductance in inferior olive neurons from spike trains by network model simulation.

    PubMed

    Onizuka, Miho; Hoang, Huu; Kawato, Mitsuo; Tokuda, Isao T; Schweighofer, Nicolas; Katori, Yuichi; Aihara, Kazuyuki; Lang, Eric J; Toyama, Keisuke

    2013-11-01

    The inferior olive (IO) possesses synaptic glomeruli, which contain dendritic spines from neighboring neurons and presynaptic terminals, many of which are inhibitory and GABAergic. Gap junctions between the spines electrically couple neighboring neurons whereas the GABAergic synaptic terminals are thought to act to decrease the effectiveness of this coupling. Thus, the glomeruli are thought to be important for determining the oscillatory and synchronized activity displayed by IO neurons. Indeed, the tendency to display such activity patterns is enhanced or reduced by the local administration of the GABA-A receptor blocker picrotoxin (PIX) or the gap junction blocker carbenoxolone (CBX), respectively. We studied the functional roles of the glomeruli by solving the inverse problem of estimating the inhibitory (gi) and gap-junctional conductance (gc) using an IO network model. This model was built upon a prior IO network model, in which the individual neurons consisted of soma and dendritic compartments, by adding a glomerular compartment comprising electrically coupled spines that received inhibitory synapses. The model was used in the forward mode to simulate spike data under PIX and CBX conditions for comparison with experimental data consisting of multi-electrode recordings of complex spikes from arrays of Purkinje cells (complex spikes are generated in a one-to-one manner by IO spikes and thus can substitute for directly measuring IO spike activity). The spatiotemporal firing dynamics of the experimental and simulation spike data were evaluated as feature vectors, including firing rates, local variation, auto-correlogram, cross-correlogram, and minimal distance, and were contracted onto two-dimensional principal component analysis (PCA) space. gc and gi were determined as the solution to the inverse problem such that the simulation and experimental spike data were closely matched in the PCA space. The goodness of the match was confirmed by an analysis of variance

  4. Stereopsis and 3D surface perception by spiking neurons in laminar cortical circuits: a method for converting neural rate models into spiking models.

    PubMed

    Cao, Yongqiang; Grossberg, Stephen

    2012-02-01

    A laminar cortical model of stereopsis and 3D surface perception is developed and simulated. The model shows how spiking neurons that interact in hierarchically organized laminar circuits of the visual cortex can generate analog properties of 3D visual percepts. The model describes how monocular and binocular oriented filtering interact with later stages of 3D boundary formation and surface filling-in in the LGN and cortical areas V1, V2, and V4. It proposes how interactions between layers 4, 3B, and 2/3 in V1 and V2 contribute to stereopsis, and how binocular and monocular information combine to form 3D boundary and surface representations. The model suggests how surface-to-boundary feedback from V2 thin stripes to pale stripes helps to explain how computationally complementary boundary and surface formation properties lead to a single consistent percept, eliminate redundant 3D boundaries, and trigger figure-ground perception. The model also shows how false binocular boundary matches may be eliminated by Gestalt grouping properties. In particular, the disparity filter, which helps to solve the correspondence problem by eliminating false matches, is realized using inhibitory interneurons as part of the perceptual grouping process by horizontal connections in layer 2/3 of cortical area V2. The 3D sLAMINART model simulates 3D surface percepts that are consciously seen in 18 psychophysical experiments. These percepts include contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, Panum's limiting case, the Venetian blind illusion, stereopsis with polarity-reversed stereograms, da Vinci stereopsis, and perceptual closure. The model hereby illustrates a general method of unlumping rate-based models that use the membrane equations of neurophysiology into models that use spiking neurons, and which may be embodied in VLSI chips that use spiking neurons to minimize heat production. PMID

  5. Hearing aid gain prescriptions balance restoration of auditory nerve mean-rate and spike-timing representations of speech.

    PubMed

    Dinath, Faheem; Bruce, Ian C

    2008-01-01

    Linear and nonlinear amplification schemes for hearing aids have thus far been developed and evaluated based on perceptual criteria such as speech intelligibility, sound comfort, and loudness equalization. Finding amplification schemes that optimize all of these perceptual metrics has proven difficult. Using a physiological model, Bruce et al. [1] investigated the effects of single-band gain adjustments to linear amplification prescriptions. Optimal gain adjustments for model auditory-nerve fiber responses to speech sentences from the TIMIT database were dependent on whether the error metric included the spike timing information (i.e., a time-resolution of several microseconds) or the mean firing rates (i.e., a time-resolution of several milliseconds). Results showed that positive gain adjustments are required to optimize the mean firing rate responses, whereas negative gain adjustments tend to optimize spike timing information responses. In this paper we examine the results in more depth using a similar optimization scheme applied to a synthetic vowel /E/. It is found that negative gain adjustments (i.e., below the linear gain prescriptions) minimize the spread of synchrony and deviation of the phase response to vowel formants in responses containing spike-timing information. In contrast, positive gain adjustments (i.e., above the linear gain prescriptions) normalize the distribution of mean discharge rates in the auditory nerve responses. Thus, linear amplification prescriptions appear to find a balance between restoring the spike-timing and mean-rate information in auditory-nerve responses. PMID:19163029

  6. Deoxyxylulose 5-phosphate reductoisomerase is not a rate-determining enzyme for essential oil production in spike lavender.

    PubMed

    Mendoza-Poudereux, Isabel; Muñoz-Bertomeu, Jesús; Arrillaga, Isabel; Segura, Juan

    2014-11-01

    Spike lavender (Lavandula latifolia) is an economically important aromatic plant producing essential oils, whose components (mostly monoterpenes) are mainly synthesized through the plastidial methylerythritol 4-phosphate (MEP) pathway. 1-Deoxy-D-xylulose-5-phosphate (DXP) synthase (DXS), that catalyzes the first step of the MEP pathway, plays a crucial role in monoterpene precursors biosynthesis in spike lavender. To date, however, it is not known whether the DXP reductoisomerase (DXR), that catalyzes the conversion of DXP into MEP, is also a rate-limiting enzyme for the biosynthesis of monoterpenes in spike lavender. To investigate it, we generated transgenic spike lavender plants constitutively expressing the Arabidopsis thaliana DXR gene. Although two out of the seven transgenic T0 plants analyzed accumulated more essential oils than the controls, this is hardly imputable to the DXR transgene effect since a clear correlation between transcript accumulation and monoterpene production could not be established. Furthermore, these increased essential oil phenotypes were not maintained in their respective T1 progenies. Similar results were obtained when total chlorophyll and carotenoid content in both T0 transgenic plants and their progenies were analyzed. Our results then demonstrate that DXR enzyme does not play a crucial role in the synthesis of plastidial monoterpene precursors, suggesting that the control flux of the MEP pathway in spike lavender is primarily exerted by the DXS enzyme. PMID:25151124

  7. Methods for estimating neural firing rates, and their application to brain-machine interfaces.

    PubMed

    Cunningham, John P; Gilja, Vikash; Ryu, Stephen I; Shenoy, Krishna V

    2009-11-01

    Neural spike trains present analytical challenges due to their noisy, spiking nature. Many studies of neuroscientific and neural prosthetic importance rely on a smoothed, denoised estimate of a spike train's underlying firing rate. Numerous methods for estimating neural firing rates have been developed in recent years, but to date no systematic comparison has been made between them. In this study, we review both classic and current firing rate estimation techniques. We compare the advantages and drawbacks of these methods. Then, in an effort to understand their relevance to the field of neural prostheses, we also apply these estimators to experimentally gathered neural data from a prosthetic arm-reaching paradigm. Using these estimates of firing rate, we apply standard prosthetic decoding algorithms to compare the performance of the different firing rate estimators, and, perhaps surprisingly, we find minimal differences. This study serves as a review of available spike train smoothers and a first quantitative comparison of their performance for brain-machine interfaces. PMID:19349143

  8. Multiscale analysis of neural spike trains.

    PubMed

    Ramezan, Reza; Marriott, Paul; Chenouri, Shojaeddin

    2014-01-30

    This paper studies the multiscale analysis of neural spike trains, through both graphical and Poisson process approaches. We introduce the interspike interval plot, which simultaneously visualizes characteristics of neural spiking activity at different time scales. Using an inhomogeneous Poisson process framework, we discuss multiscale estimates of the intensity functions of spike trains. We also introduce the windowing effect for two multiscale methods. Using quasi-likelihood, we develop bootstrap confidence intervals for the multiscale intensity function. We provide a cross-validation scheme, to choose the tuning parameters, and study its unbiasedness. Studying the relationship between the spike rate and the stimulus signal, we observe that adjusting for the first spike latency is important in cross-validation. We show, through examples, that the correlation between spike trains and spike count variability can be multiscale phenomena. Furthermore, we address the modeling of the periodicity of the spike trains caused by a stimulus signal or by brain rhythms. Within the multiscale framework, we introduce intensity functions for spike trains with multiplicative and additive periodic components. Analyzing a dataset from the retinogeniculate synapse, we compare the fit of these models with the Bayesian adaptive regression splines method and discuss the limitations of the methodology. Computational efficiency, which is usually a challenge in the analysis of spike trains, is one of the highlights of these new models. In an example, we show that the reconstruction quality of a complex intensity function demonstrates the ability of the multiscale methodology to crack the neural code. PMID:23996238

  9. Estimating birth and death rates of zooplankton

    SciTech Connect

    Taylor, B.E.; Slatkin, M.

    1981-01-01

    Two estimates of the birth rate using an egg ratio are derived from a three-stage (eggs, juveniles, and adults) model for an exponentially growing population, and the sensitivity of these estimates to time and age-dependence of the birth and death rates and to measurement errors is explored. Tests to determine whether a population violates the assumptions of the model are suggested, and birth rate estimates which partially compensate for some departures from the model are proposed. Other methods for estimating birth and death rates based on this type of model are reviewed. Four birth rate estimates are compared using data for a population of Daphnia pulicaria, and recommendations on the use of birth and death rates based on the egg ratio are made.

  10. Least squares estimation of avian molt rates

    USGS Publications Warehouse

    Johnson, D.H.

    1989-01-01

    A straightforward least squares method of estimating the rate at which birds molt feathers is presented, suitable for birds captured more than once during the period of molt. The date of molt onset can also be estimated. The method is applied to male and female mourning doves.

  11. Estimating mutation rate: how to count mutations?

    PubMed Central

    Fu, Yun-Xin; Huai, Haying

    2003-01-01

    Mutation rate is an essential parameter in genetic research. Counting the number of mutant individuals provides information for a direct estimate of mutation rate. However, mutant individuals in the same family can share the same mutations due to premeiotic mutation events, so that the number of mutant individuals can be significantly larger than the number of mutation events observed. Since mutation rate is more closely related to the number of mutation events, whether one should count only independent mutation events or the number of mutants remains controversial. We show in this article that counting mutant individuals is a correct approach for estimating mutation rate, while counting only mutation events will result in underestimation. We also derived the variance of the mutation-rate estimate, which allows us to examine a number of important issues about the design of such experiments. The general strategy of such an experiment should be to sample as many families as possible and not to sample much more offspring per family than the reciprocal of the pairwise correlation coefficient within each family. To obtain a reasonably accurate estimate of mutation rate, the number of sampled families needs to be in the same or higher order of magnitude as the reciprocal of the mutation rate. PMID:12807798

  12. Monitoring spike train synchrony.

    PubMed

    Kreuz, Thomas; Chicharro, Daniel; Houghton, Conor; Andrzejak, Ralph G; Mormann, Florian

    2013-03-01

    Recently, the SPIKE-distance has been proposed as a parameter-free and timescale-independent measure of spike train synchrony. This measure is time resolved since it relies on instantaneous estimates of spike train dissimilarity. However, its original definition led to spuriously high instantaneous values for eventlike firing patterns. Here we present a substantial improvement of this measure that eliminates this shortcoming. The reliability gained allows us to track changes in instantaneous clustering, i.e., time-localized patterns of (dis)similarity among multiple spike trains. Additional new features include selective and triggered temporal averaging as well as the instantaneous comparison of spike train groups. In a second step, a causal SPIKE-distance is defined such that the instantaneous values of dissimilarity rely on past information only so that time-resolved spike train synchrony can be estimated in real time. We demonstrate that these methods are capable of extracting valuable information from field data by monitoring the synchrony between neuronal spike trains during an epileptic seizure. Finally, the applicability of both the regular and the real-time SPIKE-distance to continuous data is illustrated on model electroencephalographic (EEG) recordings. PMID:23221419

  13. Event-based minimum-time control of oscillatory neuron models: phase randomization, maximal spike rate increase, and desynchronization.

    PubMed

    Danzl, Per; Hespanha, João; Moehlis, Jeff

    2009-12-01

    We present an event-based feedback control method for randomizing the asymptotic phase of oscillatory neurons. Phase randomization is achieved by driving the neuron's state to its phaseless set, a point at which its phase is undefined and is extremely sensitive to background noise. We consider the biologically relevant case of a fixed magnitude constraint on the stimulus signal, and show how the control objective can be accomplished in minimum time. The control synthesis problem is addressed using the minimum-time-optimal Hamilton-Jacobi-Bellman framework, which is quite general and can be applied to any spiking neuron model in the conductance-based Hodgkin-Huxley formalism. We also use this methodology to compute a feedback control protocol for optimal spike rate increase. This framework provides a straightforward means of visualizing isochrons, without actually calculating them in the traditional way. Finally, we present an extension of the phase randomizing control scheme that is applied at the population level, to a network of globally coupled neurons that are firing in synchrony. The applied control signal desynchronizes the population in a demand-controlled way. PMID:19911192

  14. Calcium-based plasticity model explains sensitivity of synaptic changes to spike pattern, rate, and dendritic location.

    PubMed

    Graupner, Michael; Brunel, Nicolas

    2012-03-01

    Multiple stimulation protocols have been found to be effective in changing synaptic efficacy by inducing long-term potentiation or depression. In many of those protocols, increases in postsynaptic calcium concentration have been shown to play a crucial role. However, it is still unclear whether and how the dynamics of the postsynaptic calcium alone determine the outcome of synaptic plasticity. Here, we propose a calcium-based model of a synapse in which potentiation and depression are activated above calcium thresholds. We show that this model gives rise to a large diversity of spike timing-dependent plasticity curves, most of which have been observed experimentally in different systems. It accounts quantitatively for plasticity outcomes evoked by protocols involving patterns with variable spike timing and firing rate in hippocampus and neocortex. Furthermore, it allows us to predict that differences in plasticity outcomes in different studies are due to differences in parameters defining the calcium dynamics. The model provides a mechanistic understanding of how various stimulation protocols provoke specific synaptic changes through the dynamics of calcium concentration and thresholds implementing in simplified fashion protein signaling cascades, leading to long-term potentiation and long-term depression. The combination of biophysical realism and analytical tractability makes it the ideal candidate to study plasticity at the synapse, neuron, and network levels. PMID:22357758

  15. Biophysical Insights into How Spike Threshold Depends on the Rate of Membrane Potential Depolarization in Type I and Type II Neurons

    PubMed Central

    Yi, Guo-Sheng; Wang, Jiang; Tsang, Kai-Ming; Wei, Xi-Le; Deng, Bin

    2015-01-01

    Dynamic spike threshold plays a critical role in neuronal input-output relations. In many neurons, the threshold potential depends on the rate of membrane potential depolarization (dV/dt) preceding a spike. There are two basic classes of neural excitability, i.e., Type I and Type II, according to input-output properties. Although the dynamical and biophysical basis of their spike initiation has been established, the spike threshold dynamic for each cell type has not been well described. Here, we use a biophysical model to investigate how spike threshold depends on dV/dt in two types of neuron. It is observed that Type II spike threshold is more depolarized and more sensitive to dV/dt than Type I. With phase plane analysis, we show that each threshold dynamic arises from the different separatrix and K+ current kinetics. By analyzing subthreshold properties of membrane currents, we find the activation of hyperpolarizing current prior to spike initiation is a major factor that regulates the threshold dynamics. The outward K+ current in Type I neuron does not activate at the perithresholds, which makes its spike threshold insensitive to dV/dt. The Type II K+ current activates prior to spike initiation and there is a large net hyperpolarizing current at the perithresholds, which results in a depolarized threshold as well as a pronounced threshold dynamic. These predictions are further attested in several other functionally equivalent cases of neural excitability. Our study provides a fundamental description about how intrinsic biophysical properties contribute to the threshold dynamics in Type I and Type II neurons, which could decipher their significant functions in neural coding. PMID:26083350

  16. Estimated recharge rates at the Hanford Site

    SciTech Connect

    Fayer, M.J.; Walters, T.B.

    1995-02-01

    The Ground-Water Surveillance Project monitors the distribution of contaminants in ground water at the Hanford Site for the U.S. Department of Energy. A subtask called {open_quotes}Water Budget at Hanford{close_quotes} was initiated in FY 1994. The objective of this subtask was to produce a defensible map of estimated recharge rates across the Hanford Site. Methods that have been used to estimate recharge rates at the Hanford Site include measurements (of drainage, water contents, and tracers) and computer modeling. For the simulations of 12 soil-vegetation combinations, the annual rates varied from 0.05 mm/yr for the Ephrata sandy loam with bunchgrass to 85.2 mm/yr for the same soil without vegetation. Water content data from the Grass Site in the 300 Area indicated that annual rates varied from 3.0 to 143.5 mm/yr during an 8-year period. The annual volume of estimated recharge was calculated to be 8.47 {times} 10{sup 9} L for the potential future Hanford Site (i.e., the portion of the current Site bounded by Highway 240 and the Columbia River). This total volume is similar to earlier estimates of natural recharge and is 2 to 10x higher than estimates of runoff and ground-water flow from higher elevations. Not only is the volume of natural recharge significant in comparison to other ground-water inputs, the distribution of estimated recharge is highly skewed to the disturbed sandy soils (i.e., the 200 Areas, where most contaminants originate). The lack of good estimates of the means and variances of the supporting data (i.e., the soil map, the vegetation/land use map, the model parameters) translates into large uncertainties in the recharge estimates. When combined, the significant quantity of estimated recharge, its high sensitivity to disturbance, and the unquantified uncertainty of the data and model parameters suggest that the defensibility of the recharge estimates should be improved.

  17. Satellite Angular Rate Estimation From Vector Measurements

    NASA Technical Reports Server (NTRS)

    Azor, Ruth; Bar-Itzhack, Itzhack Y.; Harman, Richard R.

    1996-01-01

    This paper presents an algorithm for estimating the angular rate vector of a satellite which is based on the time derivatives of vector measurements expressed in a reference and body coordinate. The computed derivatives are fed into a spacial Kalman filter which yields an estimate of the spacecraft angular velocity. The filter, named Extended Interlaced Kalman Filter (EIKF), is an extension of the Kalman filter which, although being linear, estimates the state of a nonlinear dynamic system. It consists of two or three parallel Kalman filters whose individual estimates are fed to one another and are considered as known inputs by the other parallel filter(s). The nonlinear dynamics stem from the nonlinear differential equation that describes the rotation of a three dimensional body. Initial results, using simulated data, and real Rossi X ray Timing Explorer (RXTE) data indicate that the algorithm is efficient and robust.

  18. Consensus-Based Sorting of Neuronal Spike Waveforms

    PubMed Central

    Fournier, Julien; Mueller, Christian M.; Shein-Idelson, Mark; Hemberger, Mike

    2016-01-01

    Optimizing spike-sorting algorithms is difficult because sorted clusters can rarely be checked against independently obtained “ground truth” data. In most spike-sorting algorithms in use today, the optimality of a clustering solution is assessed relative to some assumption on the distribution of the spike shapes associated with a particular single unit (e.g., Gaussianity) and by visual inspection of the clustering solution followed by manual validation. When the spatiotemporal waveforms of spikes from different cells overlap, the decision as to whether two spikes should be assigned to the same source can be quite subjective, if it is not based on reliable quantitative measures. We propose a new approach, whereby spike clusters are identified from the most consensual partition across an ensemble of clustering solutions. Using the variability of the clustering solutions across successive iterations of the same clustering algorithm (template matching based on K-means clusters), we estimate the probability of spikes being clustered together and identify groups of spikes that are not statistically distinguishable from one another. Thus, we identify spikes that are most likely to be clustered together and therefore correspond to consistent spike clusters. This method has the potential advantage that it does not rely on any model of the spike shapes. It also provides estimates of the proportion of misclassified spikes for each of the identified clusters. We tested our algorithm on several datasets for which there exists a ground truth (simultaneous intracellular data), and show that it performs close to the optimum reached by a support vector machine trained on the ground truth. We also show that the estimated rate of misclassification matches the proportion of misclassified spikes measured from the ground truth data. PMID:27536990

  19. Consensus-Based Sorting of Neuronal Spike Waveforms.

    PubMed

    Fournier, Julien; Mueller, Christian M; Shein-Idelson, Mark; Hemberger, Mike; Laurent, Gilles

    2016-01-01

    Optimizing spike-sorting algorithms is difficult because sorted clusters can rarely be checked against independently obtained "ground truth" data. In most spike-sorting algorithms in use today, the optimality of a clustering solution is assessed relative to some assumption on the distribution of the spike shapes associated with a particular single unit (e.g., Gaussianity) and by visual inspection of the clustering solution followed by manual validation. When the spatiotemporal waveforms of spikes from different cells overlap, the decision as to whether two spikes should be assigned to the same source can be quite subjective, if it is not based on reliable quantitative measures. We propose a new approach, whereby spike clusters are identified from the most consensual partition across an ensemble of clustering solutions. Using the variability of the clustering solutions across successive iterations of the same clustering algorithm (template matching based on K-means clusters), we estimate the probability of spikes being clustered together and identify groups of spikes that are not statistically distinguishable from one another. Thus, we identify spikes that are most likely to be clustered together and therefore correspond to consistent spike clusters. This method has the potential advantage that it does not rely on any model of the spike shapes. It also provides estimates of the proportion of misclassified spikes for each of the identified clusters. We tested our algorithm on several datasets for which there exists a ground truth (simultaneous intracellular data), and show that it performs close to the optimum reached by a support vector machine trained on the ground truth. We also show that the estimated rate of misclassification matches the proportion of misclassified spikes measured from the ground truth data. PMID:27536990

  20. Estimation of hydrocarbon biodegradation rates in gasoline-contaminated sediment from measured respiration rates

    USGS Publications Warehouse

    Baker, R.J.; Baehr, A.L.; Lahvis, M.A.

    2000-01-01

    An open microcosm method for quantifying microbial respiration and estimating biodegradation rates of hydrocarbons in gasoline-contaminated sediment samples has been developed and validated. Stainless-steel bioreactors are filled with soil or sediment samples, and the vapor-phase composition (concentrations of oxygen (O2), nitrogen (N2), carbon dioxide (CO2), and selected hydrocarbons) is monitored over time. Replacement gas is added as the vapor sample is taken, and selection of the replacement gas composition facilitates real-time decision-making regarding environmental conditions within the bioreactor. This capability allows for maintenance of field conditions over time, which is not possible in closed microcosms. Reaction rates of CO2 and O2 are calculated from the vapor-phase composition time series. Rates of hydrocarbon biodegradation are either measured directly from the hydrocarbon mass balance, or estimated from CO2 and O2 reaction rates and assumed reaction stoichiometries. Open microcosm experiments using sediments spiked with toluene and p-xylene were conducted to validate the stoichiometric assumptions. Respiration rates calculated from O2 consumption and from CO2 production provide estimates of toluene and p- xylene degradation rates within about ??50% of measured values when complete mineralization stoichiometry is assumed. Measured values ranged from 851.1 to 965.1 g m-3 year-1 for toluene, and 407.2-942.3 g m-3 year-1 for p- xylene. Contaminated sediment samples from a gasoline-spill site were used in a second set of microcosm experiments. Here, reaction rates of O2 and CO2 were measured and used to estimate hydrocarbon respiration rates. Total hydrocarbon reaction rates ranged from 49.0 g m-3 year-1 in uncontaminated (background) to 1040.4 g m-3 year-1 for highly contaminated sediment, based on CO2 production data. These rate estimates were similar to those obtained independently from in situ CO2 vertical gradient and flux determinations at the

  1. Firing rate analysis using decompostion-enhanced spike triggered averaging in the quadriceps femoris.

    PubMed

    Conwit, R A; Tracy, B; Cowl, A; McHugh, M; Stashuk, D; Brown, W F; Metter, E J

    1998-10-01

    Electromyographic signals detected from the quadriceps femoris during various constant force contractions were decomposed to identify individual motor unit discharges and mean firing rates (FRs). Subject and group mean FRs were calculated for each force level. Mean FR values and FR variability increased with force. Individual, subject, and group mean FRs showed slight increases until 30% of maximum voluntary contraction and larger increases thereafter. Findings are discussed in relation to motor unit recruitment, frequency modulation, and fatigue. PMID:9736067

  2. Towards universal hybrid star formation rate estimators

    NASA Astrophysics Data System (ADS)

    Boquien, M.; Kennicutt, R.; Calzetti, D.; Dale, D.; Galametz, M.; Sauvage, M.; Croxall, K.; Draine, B.; Kirkpatrick, A.; Kumari, N.; Hunt, L.; De Looze, I.; Pellegrini, E.; Relaño, M.; Smith, J.-D.; Tabatabaei, F.

    2016-06-01

    Context. To compute the star formation rate (SFR) of galaxies from the rest-frame ultraviolet (UV), it is essential to take the obscuration by dust into account. To do so, one of the most popular methods consists in combining the UV with the emission from the dust itself in the infrared (IR). Yet, different studies have derived different estimators, showing that no such hybrid estimator is truly universal. Aims: In this paper we aim at understanding and quantifying what physical processes fundamentally drive the variations between different hybrid estimators. In so doing, we aim at deriving new universal UV+IR hybrid estimators to correct the UV for dust attenuation at local and global scales, taking the intrinsic physical properties of galaxies into account. Methods: We use the CIGALE code to model the spatially resolved far-UV to far-IR spectral energy distributions of eight nearby star-forming galaxies drawn from the KINGFISH sample. This allows us to determine their local physical properties, and in particular their UV attenuation, average SFR, average specific SFR (sSFR), and their stellar mass. We then examine how hybrid estimators depend on said properties. Results: We find that hybrid UV+IR estimators strongly depend on the stellar mass surface density (in particular at 70 μm and 100 μm) and on the sSFR (in particular at 24 μm and the total infrared). Consequently, the IR scaling coefficients for UV obscuration can vary by almost an order of magnitude: from 1.55 to 13.45 at 24 μm for instance. This result contrasts with other groups who found relatively constant coefficients with small deviations. We exploit these variations to construct a new class of adaptative hybrid estimators based on observed UV to near-IR colours and near-IR luminosity densities per unit area. We find that they can reliably be extended to entire galaxies. Conclusions: The new estimators provide better estimates of attenuation-corrected UV emission than classical hybrid estimators

  3. Effect of duration of synaptic activity on spike rate of a Hodgkin-Huxley neuron with delayed feedback

    NASA Astrophysics Data System (ADS)

    Hashemi, M.; Valizadeh, A.; Azizi, Y.

    2012-02-01

    A recurrent loop consisting of a single Hodgkin-Huxley neuron influenced by a chemical excitatory delayed synaptic feedback is considered. We show that the behavior of the system depends on the duration of the activity of the synapse, which is determined by the activation and deactivation time constants of the synapse. For the fast synapses, those for which the effect of the synaptic activity is small compared to the period of firing, depending on the delay time, spiking with single and multiple interspike intervals is possible and the average firing rate can be smaller or larger than that of the open loop neuron. For slow synapses for which the synaptic time constants are of order of the period of the firing, the self-excitation increases the firing rate for all values of the delay time. We also show that for a chain consisting of few similar oscillators, if the synapses are chosen from different time constants, the system will follow the dynamics imposed by the fastest element, which is the oscillator that receives excitations via a slow synapse. The generalization of the results to other types of relaxation oscillators is discussed and the results are compared to those of the loops with inhibitory synapses as well as with gap junctions.

  4. Quantitative Estimation of Tissue Blood Flow Rate.

    PubMed

    Tozer, Gillian M; Prise, Vivien E; Cunningham, Vincent J

    2016-01-01

    The rate of blood flow through a tissue (F) is a critical parameter for assessing the functional efficiency of a blood vessel network following angiogenesis. This chapter aims to provide the principles behind the estimation of F, how F relates to other commonly used measures of tissue perfusion, and a practical approach for estimating F in laboratory animals, using small readily diffusible and metabolically inert radio-tracers. The methods described require relatively nonspecialized equipment. However, the analytical descriptions apply equally to complementary techniques involving more sophisticated noninvasive imaging.Two techniques are described for the quantitative estimation of F based on measuring the rate of tissue uptake following intravenous administration of radioactive iodo-antipyrine (or other suitable tracer). The Tissue Equilibration Technique is the classical approach and the Indicator Fractionation Technique, which is simpler to perform, is a practical alternative in many cases. The experimental procedures and analytical methods for both techniques are given, as well as guidelines for choosing the most appropriate method. PMID:27172960

  5. A Model-Based Spike Sorting Algorithm for Removing Correlation Artifacts in Multi-Neuron Recordings

    PubMed Central

    Chichilnisky, E. J.; Simoncelli, Eero P.

    2013-01-01

    We examine the problem of estimating the spike trains of multiple neurons from voltage traces recorded on one or more extracellular electrodes. Traditional spike-sorting methods rely on thresholding or clustering of recorded signals to identify spikes. While these methods can detect a large fraction of the spikes from a recording, they generally fail to identify synchronous or near-synchronous spikes: cases in which multiple spikes overlap. Here we investigate the geometry of failures in traditional sorting algorithms, and document the prevalence of such errors in multi-electrode recordings from primate retina. We then develop a method for multi-neuron spike sorting using a model that explicitly accounts for the superposition of spike waveforms. We model the recorded voltage traces as a linear combination of spike waveforms plus a stochastic background component of correlated Gaussian noise. Combining this measurement model with a Bernoulli prior over binary spike trains yields a posterior distribution for spikes given the recorded data. We introduce a greedy algorithm to maximize this posterior that we call “binary pursuit”. The algorithm allows modest variability in spike waveforms and recovers spike times with higher precision than the voltage sampling rate. This method substantially corrects cross-correlation artifacts that arise with conventional methods, and substantially outperforms clustering methods on both real and simulated data. Finally, we develop diagnostic tools that can be used to assess errors in spike sorting in the absence of ground truth. PMID:23671583

  6. Revisiting the Estimation of Dinosaur Growth Rates

    PubMed Central

    Myhrvold, Nathan P.

    2013-01-01

    Previous growth-rate studies covering 14 dinosaur taxa, as represented by 31 data sets, are critically examined and reanalyzed by using improved statistical techniques. The examination reveals that some previously reported results cannot be replicated by using the methods originally reported; results from new methods are in many cases different, in both the quantitative rates and the qualitative nature of the growth, from results in the prior literature. Asymptotic growth curves, which have been hypothesized to be ubiquitous, are shown to provide best fits for only four of the 14 taxa. Possible reasons for non-asymptotic growth patterns are discussed; they include systematic errors in the age-estimation process and, more likely, a bias toward younger ages among the specimens analyzed. Analysis of the data sets finds that only three taxa include specimens that could be considered skeletally mature (i.e., having attained 90% of maximum body size predicted by asymptotic curve fits), and eleven taxa are quite immature, with the largest specimen having attained less than 62% of predicted asymptotic size. The three taxa that include skeletally mature specimens are included in the four taxa that are best fit by asymptotic curves. The totality of results presented here suggests that previous estimates of both maximum dinosaur growth rates and maximum dinosaur sizes have little statistical support. Suggestions for future research are presented. PMID:24358133

  7. Estimating instantaneous respiratory rate from the photoplethysmogram.

    PubMed

    Dehkordi, Parastoo; Garde, Ainara; Molavi, Behnam; Petersen, Christian L; Ansermino, J Mark; Dumont, Guy A

    2015-08-01

    The photoplethysmogram (PPG) obtained from pulse oximetry shows the local changes of blood volume in tissues. Respiration induces variation in the PPG baseline due to the variation in venous blood return during each breathing cycle. We have proposed an algorithm based on the synchrosqueezing transform (SST) to estimate instantaneous respiratory rate (IRR) from the PPG. The SST is a combination of wavelet analysis and a reallocation method which aims to sharpen the time-frequency representation of the signal and can provide an accurate estimation of instantaneous frequency. In this application, the SST was applied to the PPG and IRR was detected as the predominant ridge in the respiratory band (0.1 Hz - 1 Hz) in the SST plane. The algorithm was tested against the Capnobase benchmark dataset that contains PPG, capnography, and expert labelled reference respiratory rate from 42 subjects. The IRR estimation accuracy was assessed using the root mean square (RMS) error and Bland-Altman plot. The median RMS error was 0.39 breaths/min for all subjects which ranged from the lowest error of 0.18 breaths/min to the highest error of 13.86 breaths/min. A Bland-Altman plot showed an agreement between the IRR obtained from PPG and reference respiratory rate with a bias of -0.32 and limits agreement of -7.72 to 7.07. Extracting IRR from PPG expands the functionality of pulse oximeters and provides additional diagnostic power to this non-invasive monitoring tool. PMID:26737696

  8. A model of curved saccade trajectories: spike rate adaptation in the brainstem as the cause of deviation away.

    PubMed

    Kruijne, Wouter; Van der Stigchel, Stefan; Meeter, Martijn

    2014-03-01

    The trajectory of saccades to a target is often affected whenever there is a distractor in the visual field. Distractors can cause a saccade to deviate towards their location or away from it. The oculomotor mechanisms that produce deviation towards distractors have been thoroughly explored in behavioral, neurophysiological and computational studies. The mechanisms underlying deviation away, on the other hand, remain unclear. Behavioral findings suggest a mechanism of spatially focused, top-down inhibition in a saccade map, and deviation away has become a tool to investigate such inhibition. However, this inhibition hypothesis has little neuroanatomical or neurophysiological support, and recent findings go against it. Here, we propose that deviation away results from an unbalanced saccade drive from the brainstem, caused by spike rate adaptation in brainstem long-lead burst neurons. Adaptation to stimulation in the direction of the distractor results in an unbalanced drive away from it. An existing model of the saccade system was extended with this theory. The resulting model simulates a wide range of findings on saccade trajectories, including findings that have classically been interpreted to support inhibition views. Furthermore, the model replicated the effect of saccade latency on deviation away, but predicted this effect would be absent with large (400 ms) distractor-target onset asynchrony. This prediction was confirmed in an experiment, which demonstrates that the theory both explains classical findings on saccade trajectories and predicts new findings. PMID:24486387

  9. Robust Speech Rate Estimation for Spontaneous Speech

    PubMed Central

    Wang, Dagen; Narayanan, Shrikanth S.

    2010-01-01

    In this paper, we propose a direct method for speech rate estimation from acoustic features without requiring any automatic speech transcription. We compare various spectral and temporal signal analysis and smoothing strategies to better characterize the underlying syllable structure to derive speech rate. The proposed algorithm extends the methods of spectral subband correlation by including temporal correlation and the use of prominent spectral subbands for improving the signal correlation essential for syllable detection. Furthermore, to address some of the practical robustness issues in previously proposed methods, we introduce some novel components into the algorithm such as the use of pitch confidence for filtering spurious syllable envelope peaks, magnifying window for tackling neighboring syllable smearing, and relative peak measure thresholds for pseudo peak rejection. We also describe an automated approach for learning algorithm parameters from data, and find the optimal settings through Monte Carlo simulations and parameter sensitivity analysis. Final experimental evaluations are conducted based on a portion of the Switchboard corpus for which manual phonetic segmentation information, and published results for direct comparison are available. The results show a correlation coefficient of 0.745 with respect to the ground truth based on manual segmentation. This result is about a 17% improvement compared to the current best single estimator and a 11% improvement over the multiestimator evaluated on the same Switchboard database. PMID:20428476

  10. Comparison of magnetoencephalographic spikes with and without concurrent electroencephalographic spikes in extratemporal epilepsy.

    PubMed

    Park, Hyeon-Mi; Nakasato, Nobukazu; Iwasaki, Masaki; Shamoto, Hiroshi; Tominaga, Teiji; Yoshimoto, Takashi

    2004-07-01

    Interictal spikes in patients with epilepsy may be detected by either electroencephalography (EEG) (E-spikes) or magnetoencephalography (MEG) (M-spikes), or both MEG and EEG (E/M-spikes). Localization and amplitude were compared between E/M-spikes and M-spikes in 7 adult patients with extratemporal epilepsy to evaluate the clinical significance of MEG spikes. MEG and EEG were simultaneously measured using a helmet-shaped MEG system with planar-type gradiometers and scalp electrodes of the international 10-20 system. Sources of E/M-spikes and M-spikes were estimated by an equivalent current dipole (ECD) model for MEG at peak latency. Each subject showed 9 to 20 (mean 13.4) E/M-spikes and 9 to 31 (mean 16.3) M-spikes. No subjects showed significant differences in the ECD locations between E/M- and M-spikes. ECD moments of the E/M-spikes were significantly larger in 2 patients and not significantly different in the other 5 patients. The similar localizations of E/M-spikes and M-spikes suggest that combination of MEG and EEG is useful to detect more interictal spikes in patients with extratemporal epilepsy. The smaller tendency of ECD amplitude of the M-spikes than E/M-spikes suggests that scalp EEG may overlook small tangential spikes due to background brain noise. Localization value of M-spikes is clinically equivalent to that of E/M-spikes. PMID:15240925

  11. Spiking the Geomagnetic Field

    NASA Astrophysics Data System (ADS)

    Constable, C.; Davies, C. J.

    2015-12-01

    Geomagnetic field intensities corresponding to virtual axial dipole moments of up to 200 ZAm2, more than twice the modern value, have been inferred from archeomagnetic measurements on artifacts dated at or shortly after 1000 BC. Anomalously high values occur in the Levant and Georgia, but not in Bulgaria. The origin of this spike is believed to lie in Earth's core: however, its spatio-temporal characteristics and the geomagnetic processes responsible for such a feature remain a mystery. We show that a localized spike in the radial magnetic field at the core-mantle boundary (CMB) must necessarily contribute to the largest scale changes in Earth's surface field, namely the dipole. Even the limiting spike of a delta function at the CMB produces a minimum surface cap size of 60 degrees for a factor of two increase in paleointensity. Combined evidence from modern satellite and millennial scale field modeling suggests that the Levantine Spike is intimately associated with a strong increase in dipole moment prior to 1000 BC and likely the product of north-westward motion of concentrated near equatorial Asian flux patches like those seen in the modern field. New archeomagnetic studies are needed to confirm this interpretation. Minimum estimates of the power dissipated by the spike are comparable to independent estimates of the dissipation associated with the entire steady state geodynamo. This suggests that geomagnetic spikes are either associated with rapid changes in magnetic energy or strong Lorentz forces.

  12. Accidental Turbulent Discharge Rate Estimation from Videos

    NASA Astrophysics Data System (ADS)

    Ibarra, Eric; Shaffer, Franklin; Savaş, Ömer

    2015-11-01

    A technique to estimate the volumetric discharge rate in accidental oil releases using high speed video streams is described. The essence of the method is similar to PIV processing, however the cross correlation is carried out on the visible features of the efflux, which are usually turbulent, opaque and immiscible. The key step in the process is to perform a pixelwise time filtering on the video stream, in which the parameters are commensurate with the scales of the large eddies. The velocity field extracted from the shell of visible features is then used to construct an approximate velocity profile within the discharge. The technique has been tested on laboratory experiments using both water and oil jets at Re ~105 . The technique is accurate to 20%, which is sufficient for initial responders to deploy adequate resources for containment. The software package requires minimal user input and is intended for deployment on an ROV in the field. Supported by DOI via NETL.

  13. Information geometry of interspike intervals in spiking neurons.

    PubMed

    Ikeda, Kazushi

    2005-12-01

    An information geometrical method is developed for characterizing or classifying neurons in cortical areas, whose spike rates fluctuate in time. Under the assumption that the interspike intervals of a spike sequence of a neuron obey a gamma process with a time-variant spike rate and a fixed shape parameter, we formulate the problem of characterization as a semiparametric statistical estimation, where the spike rate is a nuisance parameter. We derive optimal criteria from the information geometrical viewpoint when certain assumptions are added to the formulation, and we show that some existing measures, such as the coefficient of variation and the local variation, are expressed as estimators of certain functions under the same assumptions. PMID:16212769

  14. Nonparametric estimation of the rediscovery rate.

    PubMed

    Lee, Donghwan; Ganna, Andrea; Pawitan, Yudi; Lee, Woojoo

    2016-08-15

    Validation studies have been used to increase the reliability of the statistical conclusions for scientific discoveries; such studies improve the reproducibility of the findings and reduce the possibility of false positives. Here, one of the important roles of statistics is to quantify reproducibility rigorously. Two concepts were recently defined for this purpose: (i) rediscovery rate (RDR), which is the expected proportion of statistically significant findings in a study that can be replicated in the validation study and (ii) false discovery rate in the validation study (vFDR). In this paper, we aim to develop a nonparametric approach to estimate the RDR and vFDR and show an explicit link between the RDR and the FDR. Among other things, the link explains why reproducing statistically significant results even with low FDR level may be difficult. Two metabolomics datasets are considered to illustrate the application of the RDR and vFDR concepts in high-throughput data analysis. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26910365

  15. Spike sorting of synchronous spikes from local neuron ensembles.

    PubMed

    Franke, Felix; Pröpper, Robert; Alle, Henrik; Meier, Philipp; Geiger, Jörg R P; Obermayer, Klaus; Munk, Matthias H J

    2015-10-01

    Synchronous spike discharge of cortical neurons is thought to be a fingerprint of neuronal cooperativity. Because neighboring neurons are more densely connected to one another than neurons that are located further apart, near-synchronous spike discharge can be expected to be prevalent and it might provide an important basis for cortical computations. Using microelectrodes to record local groups of neurons does not allow for the reliable separation of synchronous spikes from different cells, because available spike sorting algorithms cannot correctly resolve the temporally overlapping waveforms. We show that high spike sorting performance of in vivo recordings, including overlapping spikes, can be achieved with a recently developed filter-based template matching procedure. Using tetrodes with a three-dimensional structure, we demonstrate with simulated data and ground truth in vitro data, obtained by dual intracellular recording of two neurons located next to a tetrode, that the spike sorting of synchronous spikes can be as successful as the spike sorting of nonoverlapping spikes and that the spatial information provided by multielectrodes greatly reduces the error rates. We apply the method to tetrode recordings from the prefrontal cortex of behaving primates, and we show that overlapping spikes can be identified and assigned to individual neurons to study synchronous activity in local groups of neurons. PMID:26289473

  16. 19 CFR 159.38 - Rates for estimated duties.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Rates for estimated duties. 159.38 Section 159.38... TREASURY (CONTINUED) LIQUIDATION OF DUTIES Conversion of Foreign Currency § 159.38 Rates for estimated duties. For purposes of calculating estimated duties, the port director shall use the rate or...

  17. A robust estimator of rainfall rate using differential reflectivity

    NASA Technical Reports Server (NTRS)

    Gorgucci, Eugenio; Scarchilli, Gianfranco; Chandrasekar, V.

    1994-01-01

    Conventional estimator of rainfall rate using reflectivity factor and differential reflectivity Z(sub DR) becomes unstable when the measured values of Z(sub DR) are small due to measurement errors. An alternate estimator of rainfall rate using reflectivity factor and Z(sub DR) is derived, so that this estimator is fairly robust over the full dynamic range of reflectivity factor and Z(sub DR). Simulations are used to study the error structure of this robust estimator in comparison with the conventional estimator of rainfall rate. It is shown that the alternate estimator performs better than the conventional estimator of rainfall rate at all rainfall values. In particular the largest improvement of this estimator is proved to be in light rain. The robust estimator is obtained as a direct regression of rainfall rate against reflectivity factor and Z(sub DR) instead of solving for the drop size distribution.

  18. Angular-Rate Estimation Using Quaternion Measurements

    NASA Technical Reports Server (NTRS)

    Azor, Ruth; Bar-Itzhack, Y.; Deutschmann, Julie K.; Harman, Richard R.

    1998-01-01

    In most spacecraft (SC) there is a need to know the SC angular rate. Precise angular rate is required for attitude determination, and a coarse rate is needed for attitude control damping. Classically, angular rate information is obtained from gyro measurements. These days, there is a tendency to build smaller, lighter and cheaper SC, therefore the inclination now is to do away with gyros and use other means and methods to determine the angular rate. The latter is also needed even in gyro equipped satellites when performing high rate maneuvers whose angular-rate is out of range of the on board gyros or in case of gyro failure. There are several ways to obtain the angular rate in a gyro-less SC. When the attitude is known, one can differentiate the attitude in whatever parameters it is given and use the kinematics equation that connects the derivative of the attitude with the satellite angular-rate and compute the latter. Since SC usually utilize vector measurements for attitude determination, the differentiation of the attitude introduces a considerable noise component in the computed angular-rate vector.

  19. Bias in Estimation of Misclassification Rates

    ERIC Educational Resources Information Center

    Haberman, Shelby J.

    2006-01-01

    When a simple random sample of size n is employed to establish a classification rule for prediction of a polytomous variable by an independent variable, the best achievable rate of misclassification is higher than the corresponding best achievable rate if the conditional probability distribution is known for the predicted variable given the…

  20. Estimation of transition probabilities of credit ratings

    NASA Astrophysics Data System (ADS)

    Peng, Gan Chew; Hin, Pooi Ah

    2015-12-01

    The present research is based on the quarterly credit ratings of ten companies over 15 years taken from the database of the Taiwan Economic Journal. The components in the vector mi (mi1, mi2,⋯, mi10) may first be used to denote the credit ratings of the ten companies in the i-th quarter. The vector mi+1 in the next quarter is modelled to be dependent on the vector mi via a conditional distribution which is derived from a 20-dimensional power-normal mixture distribution. The transition probability Pkl (i ,j ) for getting mi+1,j = l given that mi, j = k is then computed from the conditional distribution. It is found that the variation of the transition probability Pkl (i ,j ) as i varies is able to give indication for the possible transition of the credit rating of the j-th company in the near future.

  1. Attitude and Trajectory Determination using Magnetometers and Estimated Rates

    NASA Technical Reports Server (NTRS)

    Schierman, J. D.; Schmidt, D. K.; Deutschmann, J.

    1997-01-01

    A simultaneous attitude and orbit determination algorithm which uses magnetometer measurements and estimated attitude rates is presented. This is an extension of an algorithm which uses magnetometer and rate gyro measurements. The new algorithm is intended for gyroless spacecraft, or in the case of gyro failures/saturation. Torque control input data is used in forming the rate estimates. Simulation tests of the algorithm are presented. First, tests were performed using the 'true' rate values at each time step. This simulated using accurate gyro measurements. Then, tests were performed estimating the rates. Using estimated rates rather than 'gyro measurements' did not significantly degrade the algorithm's performance if accurate estimates of the initial rates were available. An initial Root-Sum-Square (RSS) position error of 1,400 km was reduced to an average error of approximately 100 km within the first two minutes. The RSS attitude error converged to less than 1.5 degrees within three orbits.

  2. Genotypic variation in spike fertility traits and ovary size as determinants of floret and grain survival rate in wheat.

    PubMed

    Guo, Zifeng; Slafer, Gustavo A; Schnurbusch, Thorsten

    2016-07-01

    Spike fertility traits are critical attributes for grain yield in wheat (Triticum aestivum L.). Here, we examine the genotypic variation in three important traits: maximum number of floret primordia, number of fertile florets, and number of grains. We determine their relationship in determining spike fertility in 30 genotypes grown under two contrasting conditions: field and greenhouse. The maximum number of floret primordia per spikelet (MFS), fertile florets per spikelet (FFS), and number of grains per spikelet (GS) not only exhibited large genotypic variation in both growth conditions and across all spikelet positions studied, but also displayed moderate levels of heritability. FFS was closely associated with floret survival and only weakly related to MFS. We also found that the post-anthesis process of grain set/abortion was important in determining genotypic variation in GS; an increase in GS was mainly associated with improved grain survival. Ovary size at anthesis was associated with both floret survival (pre-anthesis) and grain survival (post-anthesis), and was thus believed to 'connect' the two traits. In this work, proximal florets (i.e. the first three florets from the base of a spikelet: F1, F2, and F3) produced fertile florets and set grains in most cases. The ovary size of more distal florets (F4 and beyond) seemed to act as a decisive factor for grain setting and effectively reflected pre-anthesis floret development. In both growth conditions, GS positively correlated with ovary size of florets in the distal position (F4), suggesting that assimilates allocated to distal florets may play a critical role in regulating grain set. PMID:27279276

  3. Data-Rate Estimation for Autonomous Receiver Operation

    NASA Technical Reports Server (NTRS)

    Tkacenko, A.; Simon, M. K.

    2005-01-01

    In this article, we present a series of algorithms for estimating the data rate of a signal whose admissible data rates are integer base, integer powered multiples of a known basic data rate. These algorithms can be applied to the Electra radio currently used in the Deep Space Network (DSN), which employs data rates having the above relationship. The estimation is carried out in an autonomous setting in which very little a priori information is assumed. It is done by exploiting an elegant property of the split symbol moments estimator (SSME), which is traditionally used to estimate the signal-to-noise ratio (SNR) of the received signal. By quantizing the assumed symbol-timing error or jitter, we present an all-digital implementation of the SSME which can be used to jointly estimate the data rate, SNR, and jitter. Simulation results presented show that these joint estimation algorithms perform well, even in the low SNR regions typically encountered in the DSN.

  4. Estimated soil ingestion rates for use in risk assessment

    SciTech Connect

    LaGoy, P.K.

    1987-09-01

    Assessing the risks to human health posed by contaminants present in soil requires an estimate of likely soil ingestion rates. In the past, direct measurements of soil ingestion were not available and risk assessors were forced to estimate soil ingestion rates based on observations of mouthing behavior and measurements of soil on hands. Recently, empirical data on soil ingestion rates have become available from two sources. Although preliminary, these data can be used to derive better estimates of soil ingestion rates for use in risk assessments. Estimates of average soil ingestion rates derived in this paper range from 25 to 100 mg/day, depending on the age of the individual at risk. Maximum soil ingestion rates that are unlikely to underestimate exposure range from 100 to 500 mg. A value of 5000 mg/day is considered a reasonable estimate of a maximum single-day exposure for a child with habitual pica. 12 references.

  5. ESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?

    PubMed Central

    Wertheim, Joel O.; Sanderson, Michael J.

    2010-01-01

    The dynamics of species diversification rates are a key component of macroevolutionary patterns. Though not absolutely necessary, the use of divergence times inferred from sequence data has led to development of more powerful methods for inferring diversification rates. However, it is unclear what impact uncertainty in age estimates has on diversification rate inferences. Here we quantify these effects using both Bayesian and frequentist methodology. Through simulation, we demonstrate that adding sequence data results in more precise estimates of internal node ages, but a reasonable approximation of these node ages is often sufficient to approach the theoretical minimum variance in speciation rate estimates. We also find that even crude estimates of divergence times increase the power of tests of diversification rate differences between sister clades. Finally, because Bayesian and frequentist methods provided similar assessments of error, novel Bayesian approaches may provide a useful framework for tests of diversification rates in more complex contexts than are addressed here. PMID:21044059

  6. Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

    PubMed Central

    Ho, Simon Y.W.

    2015-01-01

    Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred. PMID:25780773

  7. Asymptotically robust variance estimation for person-time incidence rates.

    PubMed

    Scosyrev, Emil

    2016-05-01

    Person-time incidence rates are frequently used in medical research. However, standard estimation theory for this measure of event occurrence is based on the assumption of independent and identically distributed (iid) exponential event times, which implies that the hazard function remains constant over time. Under this assumption and assuming independent censoring, observed person-time incidence rate is the maximum-likelihood estimator of the constant hazard, and asymptotic variance of the log rate can be estimated consistently by the inverse of the number of events. However, in many practical applications, the assumption of constant hazard is not very plausible. In the present paper, an average rate parameter is defined as the ratio of expected event count to the expected total time at risk. This rate parameter is equal to the hazard function under constant hazard. For inference about the average rate parameter, an asymptotically robust variance estimator of the log rate is proposed. Given some very general conditions, the robust variance estimator is consistent under arbitrary iid event times, and is also consistent or asymptotically conservative when event times are independent but nonidentically distributed. In contrast, the standard maximum-likelihood estimator may become anticonservative under nonconstant hazard, producing confidence intervals with less-than-nominal asymptotic coverage. These results are derived analytically and illustrated with simulations. The two estimators are also compared in five datasets from oncology studies. PMID:26439107

  8. Distal spike initiation zone location estimation by morphological simulation of ionic current filtering demonstrated in a novel model of an identified Drosophila motoneuron.

    PubMed

    Günay, Cengiz; Sieling, Fred H; Dharmar, Logesh; Lin, Wei-Hsiang; Wolfram, Verena; Marley, Richard; Baines, Richard A; Prinz, Astrid A

    2015-05-01

    Studying ion channel currents generated distally from the recording site is difficult because of artifacts caused by poor space clamp and membrane filtering. A computational model can quantify artifact parameters for correction by simulating the currents only if their exact anatomical location is known. We propose that the same artifacts that confound current recordings can help pinpoint the source of those currents by providing a signature of the neuron's morphology. This method can improve the recording quality of currents initiated at the spike initiation zone (SIZ) that are often distal to the soma in invertebrate neurons. Drosophila being a valuable tool for characterizing ion currents, we estimated the SIZ location and quantified artifacts in an identified motoneuron, aCC/MN1-Ib, by constructing a novel multicompartmental model. Initial simulation of the measured biophysical channel properties in an isopotential Hodgkin-Huxley type neuron model partially replicated firing characteristics. Adding a second distal compartment, which contained spike-generating Na+ and K+ currents, was sufficient to simulate aCC's in vivo activity signature. Matching this signature using a reconstructed morphology predicted that the SIZ is on aCC's primary axon, 70 μm after the most distal dendritic branching point. From SIZ to soma, we observed and quantified selective morphological filtering of fast activating currents. Non-inactivating K+ currents are filtered ∼3 times less and despite their large magnitude at the soma they could be as distal as Na+ currents. The peak of transient component (NaT) of the voltage-activated Na+ current is also filtered more than the magnitude of slower persistent component (NaP), which can contribute to seizures. The corrected NaP/NaT ratio explains the previously observed discrepancy when the same channel is expressed in different cells. In summary, we used an in vivo signature to estimate ion channel location and recording artifacts, which

  9. Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron

    PubMed Central

    Günay, Cengiz; Sieling, Fred H.; Dharmar, Logesh; Lin, Wei-Hsiang; Wolfram, Verena; Marley, Richard

    2015-01-01

    Studying ion channel currents generated distally from the recording site is difficult because of artifacts caused by poor space clamp and membrane filtering. A computational model can quantify artifact parameters for correction by simulating the currents only if their exact anatomical location is known. We propose that the same artifacts that confound current recordings can help pinpoint the source of those currents by providing a signature of the neuron’s morphology. This method can improve the recording quality of currents initiated at the spike initiation zone (SIZ) that are often distal to the soma in invertebrate neurons. Drosophila being a valuable tool for characterizing ion currents, we estimated the SIZ location and quantified artifacts in an identified motoneuron, aCC/MN1-Ib, by constructing a novel multicompartmental model. Initial simulation of the measured biophysical channel properties in an isopotential Hodgkin-Huxley type neuron model partially replicated firing characteristics. Adding a second distal compartment, which contained spike-generating Na+ and K+ currents, was sufficient to simulate aCC’s in vivo activity signature. Matching this signature using a reconstructed morphology predicted that the SIZ is on aCC’s primary axon, 70 μm after the most distal dendritic branching point. From SIZ to soma, we observed and quantified selective morphological filtering of fast activating currents. Non-inactivating K+ currents are filtered ∼3 times less and despite their large magnitude at the soma they could be as distal as Na+ currents. The peak of transient component (NaT) of the voltage-activated Na+ current is also filtered more than the magnitude of slower persistent component (NaP), which can contribute to seizures. The corrected NaP/NaT ratio explains the previously observed discrepancy when the same channel is expressed in different cells. In summary, we used an in vivo signature to estimate ion channel location and recording artifacts

  10. Spike Inference from Calcium Imaging Using Sequential Monte Carlo Methods

    PubMed Central

    Vogelstein, Joshua T.; Watson, Brendon O.; Packer, Adam M.; Yuste, Rafael; Jedynak, Bruno; Paninski, Liam

    2009-01-01

    Abstract As recent advances in calcium sensing technologies facilitate simultaneously imaging action potentials in neuronal populations, complementary analytical tools must also be developed to maximize the utility of this experimental paradigm. Although the observations here are fluorescence movies, the signals of interest—spike trains and/or time varying intracellular calcium concentrations—are hidden. Inferring these hidden signals is often problematic due to noise, nonlinearities, slow imaging rate, and unknown biophysical parameters. We overcome these difficulties by developing sequential Monte Carlo methods (particle filters) based on biophysical models of spiking, calcium dynamics, and fluorescence. We show that even in simple cases, the particle filters outperform the optimal linear (i.e., Wiener) filter, both by obtaining better estimates and by providing error bars. We then relax a number of our model assumptions to incorporate nonlinear saturation of the fluorescence signal, as well external stimulus and spike history dependence (e.g., refractoriness) of the spike trains. Using both simulations and in vitro fluorescence observations, we demonstrate temporal superresolution by inferring when within a frame each spike occurs. Furthermore, the model parameters may be estimated using expectation maximization with only a very limited amount of data (e.g., ∼5–10 s or 5–40 spikes), without the requirement of any simultaneous electrophysiology or imaging experiments. PMID:19619479

  11. FRAGS: estimation of coding sequence substitution rates from fragmentary data

    PubMed Central

    Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

    2004-01-01

    Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

  12. Estimating Rain Rates from Tipping-Bucket Rain Gauge Measurements

    NASA Technical Reports Server (NTRS)

    Wang, Jianxin; Fisher, Brad L.; Wolff, David B.

    2007-01-01

    This paper describes the cubic spline based operational system for the generation of the TRMM one-minute rain rate product 2A-56 from Tipping Bucket (TB) gauge measurements. Methodological issues associated with applying the cubic spline to the TB gauge rain rate estimation are closely examined. A simulated TB gauge from a Joss-Waldvogel (JW) disdrometer is employed to evaluate effects of time scales and rain event definitions on errors of the rain rate estimation. The comparison between rain rates measured from the JW disdrometer and those estimated from the simulated TB gauge shows good overall agreement; however, the TB gauge suffers sampling problems, resulting in errors in the rain rate estimation. These errors are very sensitive to the time scale of rain rates. One-minute rain rates suffer substantial errors, especially at low rain rates. When one minute rain rates are averaged to 4-7 minute or longer time scales, the errors dramatically reduce. The rain event duration is very sensitive to the event definition but the event rain total is rather insensitive, provided that the events with less than 1 millimeter rain totals are excluded. Estimated lower rain rates are sensitive to the event definition whereas the higher rates are not. The median relative absolute errors are about 22% and 32% for 1-minute TB rain rates higher and lower than 3 mm per hour, respectively. These errors decrease to 5% and 14% when TB rain rates are used at 7-minute scale. The radar reflectivity-rainrate (Ze-R) distributions drawn from large amount of 7-minute TB rain rates and radar reflectivity data are mostly insensitive to the event definition.

  13. Inclination Dependence of Estimated Galaxy Masses and Star Formation Rates

    NASA Astrophysics Data System (ADS)

    Hernandez, Betsy; Maller, Ariyeh; McKernan, Barry; Ford, Saavik

    2016-01-01

    We examine the inclination dependence of inferred star formation rates and galaxy mass estimates in the Sloan Digital Sky Survey by combining the disk/bulge de-convolved catalog of Simard et al 2011 with stellar mass estimates catalog of Mendel et al 2014 and star formation rates measured from spectra by Brinchmann et al 2004. We know that optical star formation indicators are reddened by dust, but calculated star formation rates and stellar mass estimates should account for this. However, we find that face-on galaxies have a higher calculated average star formation rates than edge-on galaxies. We also find edge-on galaxies have ,on average, slightly smaller but similar estimated masses to face-on galaxies, suggesting that there are issues with the applied dust corrections for both models.

  14. Effect of impactor area on collision rate estimates

    SciTech Connect

    Canavan, G.H.

    1996-08-01

    Analytic and numercial estimates provide an assessment of the effect of impactor area on space debris collision rates, which is sufficiently small and insensitive to parameters of inerest that it could be neglected or corrected.

  15. Estimating the exceedance probability of rain rate by logistic regression

    NASA Technical Reports Server (NTRS)

    Chiu, Long S.; Kedem, Benjamin

    1990-01-01

    Recent studies have shown that the fraction of an area with rain intensity above a fixed threshold is highly correlated with the area-averaged rain rate. To estimate the fractional rainy area, a logistic regression model, which estimates the conditional probability that rain rate over an area exceeds a fixed threshold given the values of related covariates, is developed. The problem of dependency in the data in the estimation procedure is bypassed by the method of partial likelihood. Analyses of simulated scanning multichannel microwave radiometer and observed electrically scanning microwave radiometer data during the Global Atlantic Tropical Experiment period show that the use of logistic regression in pixel classification is superior to multiple regression in predicting whether rain rate at each pixel exceeds a given threshold, even in the presence of noisy data. The potential of the logistic regression technique in satellite rain rate estimation is discussed.

  16. Estimating the encounter rate variance in distance sampling

    USGS Publications Warehouse

    Fewster, R.M.; Buckland, S.T.; Burnham, K.P.; Borchers, D.L.; Jupp, P.E.; Laake, J.L.; Thomas, L.

    2009-01-01

    The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs. We show that a design-based variance estimator improves upon the model-based estimator of Buckland et al. (2001, Introduction to Distance Sampling. Oxford: Oxford University Press, p. 79) when transects are positioned at random. However, if populations exhibit strong spatial trends, both estimators can have substantial positive bias under systematic designs. We show that poststratification is effective in reducing this bias. ?? 2008, The International Biometric Society.

  17. Estimating Meiotic Gene Conversion Rates From Population Genetic Data

    PubMed Central

    Gay, J.; Myers, S.; McVean, G.

    2007-01-01

    Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs ∼400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be ∼1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots. PMID:17660532

  18. Spikes in quantum trajectories

    NASA Astrophysics Data System (ADS)

    Tilloy, Antoine; Bauer, Michel; Bernard, Denis

    2015-11-01

    A quantum system subjected to a strong continuous monitoring undergoes quantum jumps. This very-well-known fact hides a neglected subtlety: sharp scale-invariant fluctuations invariably decorate the jump process, even in the limit where the measurement rate is very large. This article is devoted to the quantitative study of these remaining fluctuations, which we call spikes, and to a discussion of their physical status. We start by introducing a classical model where the origin of these fluctuations is more intuitive, and then jump to the quantum realm where their existence is less intuitive. We compute the exact distribution of the spikes for a continuously monitored qubit. We conclude by discussing their physical and operational relevance.

  19. Estimating survival rates from banding of adult and juvenile birds

    USGS Publications Warehouse

    Johnson, D.H.

    1974-01-01

    The restrictive assumptions required by most available methods for estimating survival probabilities render them unsuitable for analyzing real banding data. A model is proposed which allows survival rates and recovery rates to vary with the calendar year, and also allows juveniles to have rates different from adults. In addition to survival rates and recovery rates, the differential vulnerability factors of juveniles relative to adults are estimated. Minimum values of the variances of the estimators are also given. The new procedure is applied to sets of duck and goose data in which reasonably large numbers of adult and juvenile birds were banded. The results are shown to be generally comparable to those procured by other methods, but, in addition, insight into the extent of annual variation is gained. Combining data from adults and juveniles also increases the effective sample size, since the juveniles are assumed to enter the adult age class after surviving their initial year.

  20. Estimating the normal background rate of species extinction.

    PubMed

    De Vos, Jurriaan M; Joppa, Lucas N; Gittleman, John L; Stephens, Patrick R; Pimm, Stuart L

    2015-04-01

    A key measure of humanity's global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural

  1. Effect of survey design and catch rate estimation on total catch estimates in Chinook salmon fisheries

    USGS Publications Warehouse

    McCormick, Joshua L.; Quist, Michael C.; Schill, Daniel J.

    2012-01-01

    Roving–roving and roving–access creel surveys are the primary techniques used to obtain information on harvest of Chinook salmon Oncorhynchus tshawytscha in Idaho sport fisheries. Once interviews are conducted using roving–roving or roving–access survey designs, mean catch rate can be estimated with the ratio-of-means (ROM) estimator, the mean-of-ratios (MOR) estimator, or the MOR estimator with exclusion of short-duration (≤0.5 h) trips. Our objective was to examine the relative bias and precision of total catch estimates obtained from use of the two survey designs and three catch rate estimators for Idaho Chinook salmon fisheries. Information on angling populations was obtained by direct visual observation of portions of Chinook salmon fisheries in three Idaho river systems over an 18-d period. Based on data from the angling populations, Monte Carlo simulations were performed to evaluate the properties of the catch rate estimators and survey designs. Among the three estimators, the ROM estimator provided the most accurate and precise estimates of mean catch rate and total catch for both roving–roving and roving–access surveys. On average, the root mean square error of simulated total catch estimates was 1.42 times greater and relative bias was 160.13 times greater for roving–roving surveys than for roving–access surveys. Length-of-stay bias and nonstationary catch rates in roving–roving surveys both appeared to affect catch rate and total catch estimates. Our results suggest that use of the ROM estimator in combination with an estimate of angler effort provided the least biased and most precise estimates of total catch for both survey designs. However, roving–access surveys were more accurate than roving–roving surveys for Chinook salmon fisheries in Idaho.

  2. Firing-rate, symbolic dynamics and frequency dependence in periodically driven spiking models: a piecewise-smooth approach

    NASA Astrophysics Data System (ADS)

    Granados, Albert; Krupa, Maciej

    2015-05-01

    In this work we consider a periodically forced generic integrate-and-fire model with a unique attracting equilibrium in the subthreshold dynamics and study the dependence of the firing-rate on the frequency of the drive. In an earlier study we have obtained rigorous results on the bifurcation structure in such systems, with emphasis on the relation between the firing-rate and the rotation number of the existing periodic orbits. In this work we study how these bifurcation structures behave upon variation of the frequency of the input. This allows us to show that the dependence of the firing-rate on frequency of the drive follows a devil's staircase with non-monotonic steps and that there is an optimal response in the whole frequency domain. We also characterize certain bounded frequency windows in which the firing-rate exhibits a bell-shaped envelope with a global maximum.

  3. Estimating divergence dates and substitution rates in the Drosophila phylogeny.

    PubMed

    Obbard, Darren J; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O'Grady, Patrick M; Jiggins, Francis M

    2012-11-01

    An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will

  4. Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

    PubMed Central

    Obbard, Darren J.; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O’Grady, Patrick M.; Jiggins, Francis M.

    2012-01-01

    An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will

  5. Unbiased estimation of mutation rates under fluctuating final counts.

    PubMed

    Ycart, Bernard; Veziris, Nicolas

    2014-01-01

    Estimation methods for mutation rates (or probabilities) in Luria-Delbrück fluctuation analysis usually assume that the final number of cells remains constant from one culture to another. We show that this leads to systematically underestimate the mutation rate. Two levels of information on final numbers are considered: either the coefficient of variation has been independently estimated, or the final number of cells in each culture is known. In both cases, unbiased estimation methods are proposed. Their statistical properties are assessed both theoretically and through Monte-Carlo simulation. As an application, the data from two well known fluctuation analysis studies on Mycobacterium tuberculosis are reexamined. PMID:24988217

  6. Estimation of the Dose and Dose Rate Effectiveness Factor

    NASA Technical Reports Server (NTRS)

    Chappell, L.; Cucinotta, F. A.

    2013-01-01

    Current models to estimate radiation risk use the Life Span Study (LSS) cohort that received high doses and high dose rates of radiation. Transferring risks from these high dose rates to the low doses and dose rates received by astronauts in space is a source of uncertainty in our risk calculations. The solid cancer models recommended by BEIR VII [1], UNSCEAR [2], and Preston et al [3] is fitted adequately by a linear dose response model, which implies that low doses and dose rates would be estimated the same as high doses and dose rates. However animal and cell experiments imply there should be curvature in the dose response curve for tumor induction. Furthermore animal experiments that directly compare acute to chronic exposures show lower increases in tumor induction than acute exposures. A dose and dose rate effectiveness factor (DDREF) has been estimated and applied to transfer risks from the high doses and dose rates of the LSS cohort to low doses and dose rates such as from missions in space. The BEIR VII committee [1] combined DDREF estimates using the LSS cohort and animal experiments using Bayesian methods for their recommendation for a DDREF value of 1.5 with uncertainty. We reexamined the animal data considered by BEIR VII and included more animal data and human chromosome aberration data to improve the estimate for DDREF. Several experiments chosen by BEIR VII were deemed inappropriate for application to human risk models of solid cancer risk. Animal tumor experiments performed by Ullrich et al [4], Alpen et al [5], and Grahn et al [6] were analyzed to estimate the DDREF. Human chromosome aberration experiments performed on a sample of astronauts within NASA were also available to estimate the DDREF. The LSS cohort results reported by BEIR VII were combined with the new radiobiology results using Bayesian methods.

  7. Sexually violent predators: toward reasonable estimates of recidivism base rates.

    PubMed

    Neller, Daniel J; Petris, Giovanni

    2013-01-01

    The sexual recidivism rate of sex offenders is a controversial issue. Perhaps as controversial is the sexual recidivism rate of the select group of sex offenders who are examined pursuant to sexually violent predator (SVP) statutes. At present, reliable estimates of SVP recidivism are unavailable. We propose that reasonable estimates of SVP recidivism can be reached by considering three available pieces of data: (i) a likely recidivism rate of the general population of sex offenders; (ii) procedures typically followed by jurisdictions that civilly commit sex offenders; and (iii) classification accuracy of procedures. Although sexual recidivism rates vary across jurisdictions, the results of our analyses suggest sex offenders referred for examination pursuant to SVP statutes recidivate at substantially higher rates than typical sex offenders. Our results further suggest that sex offenders recommended for commitment as SVPs recidivate at even greater rates than SVP respondents who are not recommended for commitment. We discuss practice and policy implications of these findings. PMID:23620130

  8. Evaluation and refinement of leak-rate estimation models

    SciTech Connect

    Paul, D.D.; Ahmad, J.; Scott, P.M.; Flanigan, L.F.; Wilkowski, G.M. )

    1991-04-01

    Leak-rate estimation models are important elements in developing a leak-before-break methodology in piping integrity and safety analyses. Existing thermal-hydraulic and crack-opening-area models used in current leak-rate estimations have been incorporated into a single computer code for leak-rate estimation. The code is called SQUIRT, which stands for Seepage Quantification of Upsets In Reactor Tubes. The SQUIRT program has been validated by comparing its thermal-hydraulic predictions with the limited experimental data that have been published on two-phase flow through slits and cracks, and by comparing its crack-opening-area predictions with data from the Degraded Piping Program. In addition, leak-rate experiments were conducted to obtain validation data for a circumferential fatigue crack in a carbon steel pipe girth weld. 56 refs., 30 figs., 4 tabs.

  9. The cooling-rate effect on microwave archeointensity estimates

    NASA Astrophysics Data System (ADS)

    Poletti, Wilbor; Hartmann, Gelvam A.; Hill, Mimi J.; Biggin, Andrew J.; Trindade, Ricardo I. F.

    2013-08-01

    microwave (MW) paleointensity data on historical bricks from Northeast Brazil presented a bias toward higher fields when compared to previous cooling-rate corrected double-heating paleointensity estimates; the same relates to the previously reported values for pottery from Southwestern Pacific islands. A simple theoretical approach suggests that the MW bias in both collections is due to a cooling-rate effect on MW estimates. We then experimentally corrected the MW cooling-rate effect on Brazilian fragments, increasing the degree of consistency between the previous and new results (reducing discrepancies from 25% to 8%). Results indicate similar experimental behavior between microwave and thermal procedures despite the different ways in which the energy is transferred into the spin system. Finally, they allow cooling times of less than 90 s to be empirically estimated in most of these MW experiments highlighting the need for systematic cooling-rate corrections to be applied in similar MW paleointensity studies in the future.

  10. Bayes optimal template matching for spike sorting - combining fisher discriminant analysis with optimal filtering.

    PubMed

    Franke, Felix; Quian Quiroga, Rodrigo; Hierlemann, Andreas; Obermayer, Klaus

    2015-06-01

    Spike sorting, i.e., the separation of the firing activity of different neurons from extracellular measurements, is a crucial but often error-prone step in the analysis of neuronal responses. Usually, three different problems have to be solved: the detection of spikes in the extracellular recordings, the estimation of the number of neurons and their prototypical (template) spike waveforms, and the assignment of individual spikes to those putative neurons. If the template spike waveforms are known, template matching can be used to solve the detection and classification problem. Here, we show that for the colored Gaussian noise case the optimal template matching is given by a form of linear filtering, which can be derived via linear discriminant analysis. This provides a Bayesian interpretation for the well-known matched filter output. Moreover, with this approach it is possible to compute a spike detection threshold analytically. The method can be implemented by a linear filter bank derived from the templates, and can be used for online spike sorting of multielectrode recordings. It may also be applicable to detection and classification problems of transient signals in general. Its application significantly decreases the error rate on two publicly available spike-sorting benchmark data sets in comparison to state-of-the-art template matching procedures. Finally, we explore the possibility to resolve overlapping spikes using the template matching outputs and show that they can be resolved with high accuracy. PMID:25652689

  11. Overestimating Outcome Rates: Statistical Estimation When Reliability Is Suboptimal

    PubMed Central

    Hayward, Rodney A; Heisler, Michele; Adams, John; Dudley, R Adams; Hofer, Timothy P

    2007-01-01

    Objective To demonstrate how failure to account for measurement error in an outcome (dependent) variable can lead to significant estimation errors and to illustrate ways to recognize and avoid these errors. Data Sources Medical literature and simulation models. Study Design/Data Collection Systematic review of the published and unpublished epidemiological literature on the rate of preventable hospital deaths and statistical simulation of potential estimation errors based on data from these studies. Principal Findings Most estimates of the rate of preventable deaths in U.S. hospitals rely upon classifying cases using one to three physician reviewers (implicit review). Because this method has low to moderate reliability, estimates based on statistical methods that do not account for error in the measurement of a “preventable death” can result in significant overestimation. For example, relying on a majority rule rating with three reviewers per case (reliability ∼0.45 for the average of three reviewers) can result in a 50–100 percent overestimation compared with an estimate based upon a reliably measured outcome (e.g., by using 50 reviewers per case). However, there are statistical methods that account for measurement error that can produce much more accurate estimates of outcome rates without requiring a large number of measurements per case. Conclusion The statistical principles discussed in this case study are critically important whenever one seeks to estimate the proportion of cases belonging to specific categories (such as estimating how many patients have inadequate blood pressure control or identifying high-cost or low-quality physicians). When the true outcome rate is low ( < 20 percent), using an outcome measure that has low-to-moderate reliability will generally result in substantially overestimating the proportion of the population having the outcome unless statistical methods that adjust for measurement error are used. PMID:17610445

  12. Respiratory rate estimation during triage of children in hospitals.

    PubMed

    Shah, Syed Ahmar; Fleming, Susannah; Thompson, Matthew; Tarassenko, Lionel

    2015-01-01

    Accurate assessment of a child's health is critical for appropriate allocation of medical resources and timely delivery of healthcare in Emergency Departments. The accurate measurement of vital signs is a key step in the determination of the severity of illness and respiratory rate is currently the most difficult vital sign to measure accurately. Several previous studies have attempted to extract respiratory rate from photoplethysmogram (PPG) recordings. However, the majority have been conducted in controlled settings using PPG recordings from healthy subjects. In many studies, manual selection of clean sections of PPG recordings was undertaken before assessing the accuracy of the signal processing algorithms developed. Such selection procedures are not appropriate in clinical settings. A major limitation of AR modelling, previously applied to respiratory rate estimation, is an appropriate selection of model order. This study developed a novel algorithm that automatically estimates respiratory rate from a median spectrum constructed applying multiple AR models to processed PPG segments acquired with pulse oximetry using a finger probe. Good-quality sections were identified using a dynamic template-matching technique to assess PPG signal quality. The algorithm was validated on 205 children presenting to the Emergency Department at the John Radcliffe Hospital, Oxford, UK, with reference respiratory rates up to 50 breaths per minute estimated by paediatric nurses. At the time of writing, the authors are not aware of any other study that has validated respiratory rate estimation using data collected from over 200 children in hospitals during routine triage. PMID:26548638

  13. A Spiking Neural Network in sEMG Feature Extraction.

    PubMed

    Lobov, Sergey; Mironov, Vasiliy; Kastalskiy, Innokentiy; Kazantsev, Victor

    2015-01-01

    We have developed a novel algorithm for sEMG feature extraction and classification. It is based on a hybrid network composed of spiking and artificial neurons. The spiking neuron layer with mutual inhibition was assigned as feature extractor. We demonstrate that the classification accuracy of the proposed model could reach high values comparable with existing sEMG interface systems. Moreover, the algorithm sensibility for different sEMG collecting systems characteristics was estimated. Results showed rather equal accuracy, despite a significant sampling rate difference. The proposed algorithm was successfully tested for mobile robot control. PMID:26540060

  14. A Spiking Neural Network in sEMG Feature Extraction

    PubMed Central

    Lobov, Sergey; Mironov, Vasiliy; Kastalskiy, Innokentiy; Kazantsev, Victor

    2015-01-01

    We have developed a novel algorithm for sEMG feature extraction and classification. It is based on a hybrid network composed of spiking and artificial neurons. The spiking neuron layer with mutual inhibition was assigned as feature extractor. We demonstrate that the classification accuracy of the proposed model could reach high values comparable with existing sEMG interface systems. Moreover, the algorithm sensibility for different sEMG collecting systems characteristics was estimated. Results showed rather equal accuracy, despite a significant sampling rate difference. The proposed algorithm was successfully tested for mobile robot control. PMID:26540060

  15. A new index to estimate precipitation using cloud growing rate

    NASA Astrophysics Data System (ADS)

    Bergès, Jean Claude; Jobard, Isabelle; Roca, Rémy

    2009-04-01

    A new index assessing the cloud growing rate is described in this paper. It has been designed to be integrated in rainfall estimation procedures. As the highest precipitation rates occur in growing convective cores, integrating this information should enhance the precipitation estimations. The index computation relies on image processing methods. It is composed of two steps: first a watershed segmentation is applied and then an original heritage process is performed. This second step, which is based on a simple matrix computation, is adapted to the watershed algorithm as it mitigates the over-segmentation artefact. This cloud growing rate index is compared with a cooling index which is usually computed to help in identifying raining cells and it is demonstrated to be more efficient. Moreover a simple integration of this index in a widespread rainfall estimation method leads to an improvement of the diurnal cycle retrieval.

  16. The estimation of galactic cosmic ray penetration and dose rates

    NASA Technical Reports Server (NTRS)

    Burrell, M. O.; Wright, J. J.

    1972-01-01

    This study is concerned with approximation methods that can be readily applied to estimate the absorbed dose rate from cosmic rays in rads - tissue or rems inside simple geometries of aluminum. The present work is limited to finding the dose rate at the center of spherical shells or behind plane slabs. The dose rate is calculated at tissue-point detectors or for thin layers of tissue. This study considers cosmic-rays dose rates for both free-space and earth-orbiting missions.

  17. Automating proliferation rate estimation from Ki-67 histology images

    NASA Astrophysics Data System (ADS)

    Al-Lahham, Heba Z.; Alomari, Raja S.; Hiary, Hazem; Chaudhary, Vipin

    2012-03-01

    Breast cancer is the second cause of women death and the most diagnosed female cancer in the US. Proliferation rate estimation (PRE) is one of the prognostic indicators that guide the treatment protocols and it is clinically performed from Ki-67 histopathology images. Automating PRE substantially increases the efficiency of the pathologists. Moreover, presenting a deterministic and reproducible proliferation rate value is crucial to reduce inter-observer variability. To that end, we propose a fully automated CAD system for PRE from the Ki-67 histopathology images. This CAD system is based on a model of three steps: image pre-processing, image clustering, and nuclei segmentation and counting that are finally followed by PRE. The first step is based on customized color modification and color-space transformation. Then, image pixels are clustered by K-Means depending on the features extracted from the images derived from the first step. Finally, nuclei are segmented and counted using global thresholding, mathematical morphology and connected component analysis. Our experimental results on fifty Ki-67-stained histopathology images show a significant agreement between our CAD's automated PRE and the gold standard's one, where the latter is an average between two observers' estimates. The Paired T-Test, for the automated and manual estimates, shows ρ = 0.86, 0.45, 0.8 for the brown nuclei count, blue nuclei count, and proliferation rate, respectively. Thus, our proposed CAD system is as reliable as the pathologist estimating the proliferation rate. Yet, its estimate is reproducible.

  18. Magnetometer-Only Attitude and Rate Estimates for Spinning Spacecraft

    NASA Technical Reports Server (NTRS)

    Challa, M.; Natanson, G.; Ottenstein, N.

    2000-01-01

    A deterministic algorithm and a Kalman filter for gyroless spacecraft are used independently to estimate the three-axis attitude and rates of rapidly spinning spacecraft using only magnetometer data. In-flight data from the Wide-Field Infrared Explorer (WIRE) during its tumble, and the Fast Auroral Snapshot Explorer (FAST) during its nominal mission mode are used to show that the algorithms can successfully estimate the above in spite of the high rates. Results using simulated data are used to illustrate the importance of accurate and frequent data.

  19. Angular-Rate Estimation using Star Tracker Measurements

    NASA Technical Reports Server (NTRS)

    Azor, R.; Bar-Itzhack, Itzhack Y.; Deutschmann, Julie K.; Harman, Richard R.

    1999-01-01

    This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared, one that uses differentiated quaternion measurements to yield coarse rate measurements which are then fed into two different estimators. In the other approach the raw quaternion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear rate dependent part of the rotational dynamics equation of a rigid body into a product of an angular-rate dependent matrix and the angular-rate vector itself. This decomposition, which is not unique, enables the treatment of the nonlinear spacecraft dynamics model as a linear one and, consequently, the application of a Pseudo-Linear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the Kalman gain matrix and thus eliminates the need to propagate and update the filter covariance matrix. The replacement of the elaborate rotational dynamics by a simple first order Markov model is also examined. In this paper a special consideration is given to the problem of delayed quaternion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results of these tests are presented.

  20. Angular-Rate Estimation Using Star Tracker Measurements

    NASA Technical Reports Server (NTRS)

    Azor, R.; Bar-Itzhack, I.; Deutschmann, Julie K.; Harman, Richard R.

    1999-01-01

    This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared, one that uses differentiated quatemion measurements to yield coarse rate measurements which are then fed into two different estimators. In the other approach the raw quatemion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear rate dependent part of the rotational dynamics equation of a rigid body into a product of an angular-rate dependent matrix and the angular-rate vector itself This decomposition, which is not unique, enables the treatment of the nonlinear spacecraft dynamics model as a linear one and, consequently, the application of a Pseudo-Linear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the Kalman gain matrix and thus eliminates the need to propagate and update the filter covariance matrix. The replacement of the elaborate rotational dynamics by a simple first order Markov model is also examined. In this paper a special consideration is given to the problem of delayed quatemion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results of these tests are presented.

  1. Estimating cause-specific mortality rates using recovered carcasses.

    PubMed

    Joly, Damien O; Heisey, Dennis M; Samuel, Michael D; Ribic, Christine A; Thomas, Nancy J; Wright, Scott D; Wright, Irene E

    2009-01-01

    Stranding networks, in which carcasses are recovered and sent to diagnostic laboratories for necropsy and determination of cause of death, have been developed to monitor the health of marine mammal and bird populations. These programs typically accumulate comprehensive, long-term datasets on causes of death that can be used to identify important sources of mortality or changes in mortality patterns that lead to management actions. However, the utility of these data in determining cause-specific mortality rates has not been explored. We present a maximum likelihood-based approach that partitions total mortality rate, estimated by independent sources, into cause-specific mortality rates. We also demonstrate how variance estimates are derived for these rates. We present examples of the method using mortality data for California sea otters (Enhydra lutris nereis) and Florida manatees (Trichechus manatus latirostris). PMID:19204341

  2. Anthropogenic radionuclides for estimating rates of soil redistribution by wind

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Erosion of soil by wind and water is a degrading process that affects millions of hectares worldwide. Atmospheric testing of nuclear weapons and the resulting fallout of anthropogenic radioisotopes, particularly Cesium 137, has made possible the estimation of mean soil redistribution rates. The pe...

  3. Anthropogenic radioisotopes to estimate rates of soil redistribution by wind

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Erosion of soil by wind and water is a degrading process that affects millions of hectares worldwide. Atmospheric testing of nuclear weapons and the resulting fallout of anthropogenic radioisotopes, particularly Cesium 137, has made possible the estimation of mean soil redistribution rates. The pe...

  4. Angular-Rate Estimation Using Delayed Quaternion Measurements

    NASA Technical Reports Server (NTRS)

    Azor, R.; Bar-Itzhack, I. Y.; Harman, R. R.

    1999-01-01

    This paper presents algorithms for estimating the angular-rate vector of satellites using quaternion measurements. Two approaches are compared one that uses differentiated quaternion measurements to yield coarse rate measurements, which are then fed into two different estimators. In the other approach the raw quaternion measurements themselves are fed directly into the two estimators. The two estimators rely on the ability to decompose the non-linear part of the rotas rotational dynamics equation of a body into a product of an angular-rate dependent matrix and the angular-rate vector itself. This non unique decomposition, enables the treatment of the nonlinear spacecraft (SC) dynamics model as a linear one and, thus, the application of a PseudoLinear Kalman Filter (PSELIKA). It also enables the application of a special Kalman filter which is based on the use of the solution of the State Dependent Algebraic Riccati Equation (SDARE) in order to compute the gain matrix and thus eliminates the need to compute recursively the filter covariance matrix. The replacement of the rotational dynamics by a simple Markov model is also examined. In this paper special consideration is given to the problem of delayed quaternion measurements. Two solutions to this problem are suggested and tested. Real Rossi X-Ray Timing Explorer (RXTE) data is used to test these algorithms, and results are presented.

  5. Quantifying Spike Train Oscillations: Biases, Distortions and Solutions

    PubMed Central

    Matzner, Ayala; Bar-Gad, Izhar

    2015-01-01

    Estimation of the power spectrum is a common method for identifying oscillatory changes in neuronal activity. However, the stochastic nature of neuronal activity leads to severe biases in the estimation of these oscillations in single unit spike trains. Different biological and experimental factors cause the spike train to differentially reflect its underlying oscillatory rate function. We analyzed the effect of factors, such as the mean firing rate and the recording duration, on the detectability of oscillations and their significance, and tested these theoretical results on experimental data recorded in Parkinsonian non-human primates. The effect of these factors is dramatic, such that in some conditions, the detection of existing oscillations is impossible. Moreover, these biases impede the comparison of oscillations across brain regions, neuronal types, behavioral states and separate recordings with different underlying parameters, and lead inevitably to a gross misinterpretation of experimental results. We introduce a novel objective measure, the "modulation index", which overcomes these biases, and enables reliable detection of oscillations from spike trains and a direct estimation of the oscillation magnitude. The modulation index detects a high percentage of oscillations over a wide range of parameters, compared to classical spectral analysis methods, and enables an unbiased comparison between spike trains recorded from different neurons and using different experimental protocols. PMID:25909328

  6. Quantifying spike train oscillations: biases, distortions and solutions.

    PubMed

    Matzner, Ayala; Bar-Gad, Izhar

    2015-04-01

    Estimation of the power spectrum is a common method for identifying oscillatory changes in neuronal activity. However, the stochastic nature of neuronal activity leads to severe biases in the estimation of these oscillations in single unit spike trains. Different biological and experimental factors cause the spike train to differentially reflect its underlying oscillatory rate function. We analyzed the effect of factors, such as the mean firing rate and the recording duration, on the detectability of oscillations and their significance, and tested these theoretical results on experimental data recorded in Parkinsonian non-human primates. The effect of these factors is dramatic, such that in some conditions, the detection of existing oscillations is impossible. Moreover, these biases impede the comparison of oscillations across brain regions, neuronal types, behavioral states and separate recordings with different underlying parameters, and lead inevitably to a gross misinterpretation of experimental results. We introduce a novel objective measure, the "modulation index", which overcomes these biases, and enables reliable detection of oscillations from spike trains and a direct estimation of the oscillation magnitude. The modulation index detects a high percentage of oscillations over a wide range of parameters, compared to classical spectral analysis methods, and enables an unbiased comparison between spike trains recorded from different neurons and using different experimental protocols. PMID:25909328

  7. A Pulse Rate Estimation Algorithm Using PPG and Smartphone Camera.

    PubMed

    Siddiqui, Sarah Ali; Zhang, Yuan; Feng, Zhiquan; Kos, Anton

    2016-05-01

    The ubiquitous use and advancement in built-in smartphone sensors and the development in big data processing have been beneficial in several fields including healthcare. Among the basic vitals monitoring, pulse rate monitoring is the most important healthcare necessity. A multimedia video stream data acquired by built-in smartphone camera can be used to estimate it. In this paper, an algorithm that uses only smartphone camera as a sensor to estimate pulse rate using PhotoPlethysmograph (PPG) signals is proposed. The results obtained by the proposed algorithm are compared with the actual pulse rate and the maximum error found is 3 beats per minute. The standard deviation in percentage error and percentage accuracy is found to be 0.68 % whereas the average percentage error and percentage accuracy is found to be 1.98 % and 98.02 % respectively. PMID:27067432

  8. Estimation of Eruption Source Parameters from Plume Growth Rate

    NASA Astrophysics Data System (ADS)

    Pouget, Solene; Bursik, Marcus; Webley, Peter; Dehn, Jon; Pavalonis, Michael; Singh, Tarunraj; Singla, Puneet; Patra, Abani; Pitman, Bruce; Stefanescu, Ramona; Madankan, Reza; Morton, Donald; Jones, Matthew

    2013-04-01

    The eruption of Eyjafjallajokull, Iceland in April and May, 2010, brought to light the hazards of airborne volcanic ash and the importance of Volcanic Ash Transport and Dispersion models (VATD) to estimate the concentration of ash with time. These models require Eruption Source Parameters (ESP) as input, which typically include information about the plume height, the mass eruption rate, the duration of the eruption and the particle size distribution. However much of the time these ESP are unknown or poorly known a priori. We show that the mass eruption rate can be estimated from the downwind plume or umbrella cloud growth rate. A simple version of the continuity equation can be applied to the growth of either an umbrella cloud or the downwind plume. The continuity equation coupled with the momentum equation using only inertial and gravitational terms provides another model. Numerical modeling or scaling relationships can be used, as necessary, to provide values for unknown or unavailable parameters. Use of these models applied to data on plume geometry provided by satellite imagery allows for direct estimation of plume volumetric and mass growth with time. To test our methodology, we compared our results with five well-studied and well-characterized historical eruptions: Mount St. Helens, 1980; Pinatubo, 1991, Redoubt, 1990; Hekla, 2000 and Eyjafjallajokull, 2010. These tests show that the methodologies yield results comparable to or better than currently accepted methodologies of ESP estimation. We then applied the methodology to umbrella clouds produced by the eruptions of Okmok, 12 July 2008, and Sarychev Peak, 12 June 2009, and to the downwind plume produced by the eruptions of Hekla, 2000; Kliuchevsko'i, 1 October 1994; Kasatochi 7-8 August 2008 and Bezymianny, 1 September 2012. The new methods allow a fast, remote assessment of the mass eruption rate, even for remote volcanoes. They thus provide an additional path to estimation of the ESP and the forecasting

  9. Estimates of Biogenic Methane Production Rates in Deep Marine Sediments

    NASA Astrophysics Data System (ADS)

    Colwell, F. S.; Boyd, S.; Delwiche, M. E.; Reed, D. W.

    2004-12-01

    Much of the methane in natural gas hydrates in marine sediments is made by methanogens. Current models used to predict hydrate distribution and concentration in these sediments require estimates of microbial methane production rates. However, accurate estimates are difficult to achieve because of the bias introduced by sampling and because methanogen activities in these sediments are low and not easily detected. To derive useful methane production rates for marine sediments we have measured the methanogen biomass in samples taken from different depths in Hydrate Ridge (HR) sediments off the coast of Oregon and, separately, the minimal rates of activity for a methanogen in a laboratory reactor. For methanogen biomass, we used a polymerase chain reaction assay in real time to target the methanogen-specific mcr gene. Using this method we found that a majority of the samples collected from boreholes at HR show no evidence of methanogens (detection limit: less than 100 methanogens per g of sediment). Most of the samples with detectable numbers of methanogens were from shallow sediments (less than 10 meters below seafloor [mbsf]) although a few samples with apparently high numbers of methanogens (greater than 10,000 methanogens per g) were from as deep as 230 mbsf and were associated with notable geological features (e.g., the bottom-simulating reflector and an ash-bearing zone with high fluid movement). Laboratory studies with Methanoculleus submarinus (isolated from a hydrate zone at the Nankai Trough) maintained in a biomass recycle reactor showed that when this methanogen is merely surviving, as is likely the case in deep marine sediments, it produces approximately 0.06 fmol methane per cell per day. This is far lower than rates reported for methanogens in other environments. By combining this estimate of specific methanogenic rates and an extrapolation from the numbers of methanogens at selected depths in the sediment column at HR sites we have derived a maximum

  10. Respiratory rate estimation using respiratory sinus arrhythmia from photoplethysmography.

    PubMed

    Karlen, Walter; Brouse, Christopher J; Cooke, Erin; Ansermino, J Mark; Dumont, Guy A

    2011-01-01

    Respiratory rate (RR) is an important measurement for ambulatory care and there is high interest in its detection using unobtrusive mobile devices. For this study, we investigated the estimation of RR from a photoplethysmography (PPG) signal that originated from a pulse oximeter sensor and had a sub-optimal sampling rate. We explored the possibility of estimating RR by extracting respiratory sinus arrhythmia (RSA) from the PPG-derived heart rate variability (HRV) measurement using real-time algorithms. Data from 29 children and 13 adults undergoing general anesthesia were analyzed. We compared the RSA power derived from electrocardiography (ECG) with PPG at the reference RR derived from capnography. The power of the PPG was significantly higher than that of the ECG (182.42 ± 36.75 dB vs. 162.30 ± 43.66 dB). Further, the mean RR error for PPG was lower than ECG. Both PPG and ECG RR estimation techniques were more powerful and reliable in cases of spontaneous ventilation than when pressure controlled ventilation was used. The analysis of cases containing artifacts in the PPG revealed a significant increase in RR error, a trend that was less pronounced for controlled ventilation. These results indicate that the estimation of RR from the sub-optimally sampled PPG signal is possible and more reliable than from the ECG. PMID:22254531

  11. Learning Precise Spike Train-to-Spike Train Transformations in Multilayer Feedforward Neuronal Networks.

    PubMed

    Banerjee, Arunava

    2016-05-01

    We derive a synaptic weight update rule for learning temporally precise spike train-to-spike train transformations in multilayer feedforward networks of spiking neurons. The framework, aimed at seamlessly generalizing error backpropagation to the deterministic spiking neuron setting, is based strictly on spike timing and avoids invoking concepts pertaining to spike rates or probabilistic models of spiking. The derivation is founded on two innovations. First, an error functional is proposed that compares the spike train emitted by the output neuron of the network to the desired spike train by way of their putative impact on a virtual postsynaptic neuron. This formulation sidesteps the need for spike alignment and leads to closed-form solutions for all quantities of interest. Second, virtual assignment of weights to spikes rather than synapses enables a perturbation analysis of individual spike times and synaptic weights of the output, as well as all intermediate neurons in the network, which yields the gradients of the error functional with respect to the said entities. Learning proceeds via a gradient descent mechanism that leverages these quantities. Simulation experiments demonstrate the efficacy of the proposed learning framework. The experiments also highlight asymmetries between synapses on excitatory and inhibitory neurons. PMID:26942750

  12. The electromagnetic spike solutions

    NASA Astrophysics Data System (ADS)

    Nungesser, Ernesto; Lim, Woei Chet

    2013-12-01

    The aim of this paper is to use the existing relation between polarized electromagnetic Gowdy spacetimes and vacuum Gowdy spacetimes to find explicit solutions for electromagnetic spikes by a procedure which has been developed by one of the authors for gravitational spikes. We present new inhomogeneous solutions which we call the EME and MEM electromagnetic spike solutions.

  13. Estimating digital information throughput rates for radiology networks. A model.

    PubMed

    Cox, G G; Templeton, A W; Anderson, W H; Cook, L T; Hensley, K S; Dwyer, S J

    1986-02-01

    The design and implementation of a digital radiology image management system requires the definition, evaluation, and comparison of appropriate measures of system performance. The mean throughput rate is an important measure of the actual performance of a finished system. The mean throughput rate identifies the transmission of digital information either in bits/second or tasks/second. It is dependent on software, database management, equipment interface designs, number of users and display stations, and communications media. The mean throughput rate can document resource allocation bottlenecks within a given system. A model for estimating the mean throughput rate and its application in helping us design our radiology digital image networks is described. PMID:3957590

  14. Suicide rates, national intelligence estimates, and differential K theory.

    PubMed

    Voracek, Martin

    2009-12-01

    In a nation sample of 75 countries around the world, higher suicide rates of the total male, and female population corresponded to higher levels on the superordinate K factor from differential K theory, thought to reflect a set of mutually interrelated life history and reproductive strategy traits. Countries ranking high on suicide rates concurrently ranked high on national intelligence estimates, longevity, and affluence, whilst low on rates of births, infant mortality, HIV/AIDS, and crimes (rape, serious assault, and homicide). These findings integrate previously reported positive population-level associations between suicide rates and cognitive ability variables into the conceptual space of differential K theory. The propensity toward suicidal behavior is a positive correlate of the K superfactor. PMID:20178273

  15. Precise estimates of mutation rate and spectrum in yeast

    PubMed Central

    Zhu, Yuan O.; Siegal, Mark L.; Hall, David W.; Petrov, Dmitri A.

    2014-01-01

    Mutation is the ultimate source of genetic variation. The most direct and unbiased method of studying spontaneous mutations is via mutation accumulation (MA) lines. Until recently, MA experiments were limited by the cost of sequencing and thus provided us with small numbers of mutational events and therefore imprecise estimates of rates and patterns of mutation. We used whole-genome sequencing to identify nearly 1,000 spontaneous mutation events accumulated over ∼311,000 generations in 145 diploid MA lines of the budding yeast Saccharomyces cerevisiae. MA experiments are usually assumed to have negligible levels of selection, but even mild selection will remove strongly deleterious events. We take advantage of such patterns of selection and show that mutation classes such as indels and aneuploidies (especially monosomies) are proportionately much more likely to contribute mutations of large effect. We also provide conservative estimates of indel, aneuploidy, environment-dependent dominant lethal, and recessive lethal mutation rates. To our knowledge, for the first time in yeast MA data, we identified a sufficiently large number of single-nucleotide mutations to measure context-dependent mutation rates and were able to (i) confirm strong AT bias of mutation in yeast driven by high rate of mutations from C/G to T/A and (ii) detect a higher rate of mutation at C/G nucleotides in two specific contexts consistent with cytosine methylation in S. cerevisiae. PMID:24847077

  16. Robust efficient estimation of heart rate pulse from video

    PubMed Central

    Xu, Shuchang; Sun, Lingyun; Rohde, Gustavo Kunde

    2014-01-01

    We describe a simple but robust algorithm for estimating the heart rate pulse from video sequences containing human skin in real time. Based on a model of light interaction with human skin, we define the change of blood concentration due to arterial pulsation as a pixel quotient in log space, and successfully use the derived signal for computing the pulse heart rate. Various experiments with different cameras, different illumination condition, and different skin locations were conducted to demonstrate the effectiveness and robustness of the proposed algorithm. Examples computed with normal illumination show the algorithm is comparable with pulse oximeter devices both in accuracy and sensitivity. PMID:24761294

  17. Estimating rates of debris flow entrainment from ground vibrations

    NASA Astrophysics Data System (ADS)

    Kean, J. W.; Coe, J. A.; Coviello, V.; Smith, J. B.; McCoy, S. W.; Arattano, M.

    2015-08-01

    Debris flows generate seismic waves as they travel downslope and can become more dangerous as they entrain sediment along their path. We present field observations that show a systematic relation between the magnitude of seismic waves and the amount of erodible sediment beneath the flow. Specifically, we observe that a debris flow traveling along a channel filled initially with sediment 0.34 m thick generates about 2 orders of magnitude less spectral power than a similar-sized flow over the same channel without sediment fill. We adapt a model from fluvial seismology to explain this observation and then invert it to estimate the level of bed sediment (and rate of entrainment) beneath a passing series of surges. Our estimates compare favorably with previous direct measurements of entrainment rates at the site, suggesting the approach may be a new indirect way to obtain rare field constraints needed to test models of debris flow entrainment.

  18. Improved Versions of Common Estimators of the Recombination Rate.

    PubMed

    Gärtner, Kerstin; Futschik, Andreas

    2016-09-01

    The scaled recombination parameter [Formula: see text] is one of the key parameters, turning up frequently in population genetic models. Accurate estimates of [Formula: see text] are difficult to obtain, as recombination events do not always leave traces in the data. One of the most widely used approaches is composite likelihood. Here, we show that popular implementations of composite likelihood estimators can often be uniformly improved by optimizing the trade-off between bias and variance. The amount of possible improvement depends on parameters such as the sequence length, the sample size, and the mutation rate, and it can be considerable in some cases. It turns out that approximate Bayesian computation, with composite likelihood as a summary statistic, also leads to improved estimates, but now in terms of the posterior risk. Finally, we demonstrate a practical application on real data from Drosophila. PMID:27409412

  19. Probabilistic precipitation rate estimates with ground-based radar networks

    NASA Astrophysics Data System (ADS)

    Kirstetter, Pierre-Emmanuel; Gourley, Jonathan J.; Hong, Yang; Zhang, Jian; Moazamigoodarzi, Saber; Langston, Carrie; Arthur, Ami

    2015-03-01

    The uncertainty structure of radar quantitative precipitation estimation (QPE) is largely unknown at fine spatiotemporal scales near the radar measurement scale. By using the WSR-88D radar network and gauge data sets across the conterminous US, an investigation of this subject has been carried out within the framework of the NOAA/NSSL ground radar-based Multi-Radar Multi-Sensor (MRMS) QPE system. A new method is proposed and called PRORATE for probabilistic QPE using radar observations of rate and typology estimates. Probability distributions of precipitation rates are computed instead of deterministic values using a model quantifying the relation between radar reflectivity and the corresponding "true" precipitation. The model acknowledges the uncertainty arising from many factors operative at the radar measurement scale and from the correction algorithm. Ensembles of reflectivity-to-precipitation rate relationships accounting explicitly for precipitation typology were derived at a 5 min/1 km scale. This approach conditions probabilistic quantitative precipitation estimates (PQPE) on the precipitation rate and type. The model components were estimated on the basis of a 1 year long data sample over the CONUS. This PQPE model provides the basis for precipitation probability maps and the generation of radar precipitation ensembles. Maps of the precipitation exceedance probability for specific thresholds (e.g., precipitation return periods) are computed. Precipitation probability maps are accumulated to the hourly time scale and compare favorably to the deterministic QPE. As an essential property of precipitation, the impact of the temporal correlation on the hourly accumulation is examined. This approach to PQPE can readily apply to other systems including space-based passive and active sensor algorithms.

  20. bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis.

    PubMed

    Gillet-Markowska, Alexandre; Louvel, Guillaume; Fischer, Gilles

    2015-11-01

    Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb.upmc.fr/bzrates. PMID:26338660

  1. bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis

    PubMed Central

    Gillet-Markowska, Alexandre; Louvel, Guillaume; Fischer, Gilles

    2015-01-01

    Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb.upmc.fr/bzrates. PMID:26338660

  2. Estimated diffusion rates of inorganic gases from southeastern Colorado reservoirs

    SciTech Connect

    Nelson, J.S.; Simmons, E.C. )

    1991-08-01

    Helium, argon, and nitrogen are small, chemically unreactive molecules with relatively large effective diffusion coefficients compared to most hydrocarbons. If these gases have existed in gas fields for even the shortest geologic time spans, steady-state diffusion must be at least approximated, and the diffusional flux of these gases through a reservoir cap rock may be estimated using Fick's First Law of Diffusion. Diffusional loss represents a minimum loss rate since mass transfer along fractures and faults would be faster. Under a steady-state condition, the rate of diffusional loss most be balanced by an equal influx of the gas into the reservoir. Using a natural gas field's estimated reserves, natural gas composition, area, and the estimated flux of a given gas through the field's cap rock, the turnover time of the gas is estimated. Southeastern Colorado gas fields producing from the Morrow Formation often contain anomalously high concentrations of nitrogen (to 70%), helium (to 5%) and yield turnover times for these gases of generally less than 100,000 years. Unless the N{sub 2}, He, and Ar were emplaced within the last 100,000 years, there must be a continuing large flux of gas into these fields to balance the diffusional loss. The large fluxes of inorganic gases required to maintain their concentrations in natural gases raises questions about the age and longevity of gas fields. Extension of these calculations to light hydrocarbons implies that catagenesis is a more recent and ongoing process than is often believed.

  3. Robust estimation of fetal heart rate from US Doppler signals

    NASA Astrophysics Data System (ADS)

    Voicu, Iulian; Girault, Jean-Marc; Roussel, Catherine; Decock, Aliette; Kouame, Denis

    2010-01-01

    Introduction: In utero, Monitoring of fetal wellbeing or suffering is today an open challenge, due to the high number of clinical parameters to be considered. An automatic monitoring of fetal activity, dedicated for quantifying fetal wellbeing, becomes necessary. For this purpose and in a view to supply an alternative for the Manning test, we used an ultrasound multitransducer multigate Doppler system. One important issue (and first step in our investigation) is the accurate estimation of fetal heart rate (FHR). An estimation of the FHR is obtained by evaluating the autocorrelation function of the Doppler signals for ills and healthiness foetus. However, this estimator is not enough robust since about 20% of FHR are not detected in comparison to a reference system. These non detections are principally due to the fact that the Doppler signal generated by the fetal moving is strongly disturbed by the presence of others several Doppler sources (mother' s moving, pseudo breathing, etc.). By modifying the existing method (autocorrelation method) and by proposing new time and frequency estimators used in the audio' s domain, we reduce to 5% the probability of non-detection of the fetal heart rate. These results are really encouraging and they enable us to plan the use of automatic classification techniques in order to discriminate between healthy and in suffering foetus.

  4. Estimating Divergence Times and Substitution Rates in Rhizobia.

    PubMed

    Chriki-Adeeb, Rim; Chriki, Ali

    2016-01-01

    Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes. PMID:27168719

  5. Estimating Divergence Times and Substitution Rates in Rhizobia

    PubMed Central

    Chriki-Adeeb, Rim; Chriki, Ali

    2016-01-01

    Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth–death, birth–death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes. PMID:27168719

  6. Estimating hydraulic properties of volcanic aquifers using constant-rate and variable-rate aquifer tests

    USGS Publications Warehouse

    Rotzoll, K.; El-Kadi, A. I.; Gingerich, S.B.

    2007-01-01

    In recent years the ground-water demand of the population of the island of Maui, Hawaii, has significantly increased. To ensure prudent management of the ground-water resources, an improved understanding of ground-water flow systems is needed. At present, large-scale estimations of aquifer properties are lacking for Maui. Seven analytical methods using constant-rate and variable-rate withdrawals for single wells provide an estimate of hydraulic conductivity and transmissivity for 103 wells in central Maui. Methods based on constant-rate tests, although not widely used on Maui, offer reasonable estimates. Step-drawdown tests, which are more abundantly used than other tests, provide similar estimates as constant-rate tests. A numerical model validates the suitability of analytical solutions for step-drawdown tests and additionally provides an estimate of storage parameters. The results show that hydraulic conductivity is log-normally distributed and that for dike-free volcanic rocks it ranges over several orders of magnitude from 1 to 2,500 m/d. The arithmetic mean, geometric mean, and median values of hydraulic conductivity are respectively 520, 280, and 370 m/d for basalt and 80, 50, and 30 m/d for sediment. A geostatistical approach using ordinary kriging yields a prediction of hydraulic conductivity on a larger scale. Overall, the results are in agreement with values published for other Hawaiian islands. ?? 2007 American Water Resources Association.

  7. Ancient hyaenas highlight the old problem of estimating evolutionary rates.

    PubMed

    Shapiro, Beth; Ho, Simon Y W

    2014-02-01

    Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitochondrial DNA sequences isolated from a combination of ancient and present-day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification. PMID:24450980

  8. Can we estimate bacterial growth rates from ribosomal RNA content?

    SciTech Connect

    Kemp, P.F.

    1995-12-31

    Several studies have demonstrated a strong relationship between the quantity of RNA in bacterial cells and their growth rate under laboratory conditions. It may be possible to use this relationship to provide information on the activity of natural bacterial communities, and in particular on growth rate. However, if this approach is to provide reliably interpretable information, the relationship between RNA content and growth rate must be well-understood. In particular, a requisite of such applications is that the relationship must be universal among bacteria, or alternately that the relationship can be determined and measured for specific bacterial taxa. The RNA-growth rate relationship has not been used to evaluate bacterial growth in field studies, although RNA content has been measured in single cells and in bulk extracts of field samples taken from coastal environments. These measurements have been treated as probable indicators of bacterial activity, but have not yet been interpreted as estimators of growth rate. The primary obstacle to such interpretations is a lack of information on biological and environmental factors that affect the RNA-growth rate relationship. In this paper, the available data on the RNA-growth rate relationship in bacteria will be reviewed, including hypotheses regarding the regulation of RNA synthesis and degradation as a function of growth rate and environmental factors; i.e. the basic mechanisms for maintaining RNA content in proportion to growth rate. An assessment of the published laboratory and field data, the current status of this research area, and some of the remaining questions will be presented.

  9. Redefinition and global estimation of basal ecosystem respiration rate

    USGS Publications Warehouse

    Yuan, W.; Luo, Y.; Li, X.; Liu, S.; Yu, G.; Zhou, T.; Bahn, M.; Black, A.; Desai, A.R.; Cescatti, A.; Marcolla, B.; Jacobs, C.; Chen, J.; Aurela, M.; Bernhofer, C.; Gielen, B.; Bohrer, G.; Cook, D.R.; Dragoni, D.; Dunn, A.L.; Gianelle, D.; Grnwald, T.; Ibrom, A.; Leclerc, M.Y.; Lindroth, A.; Liu, H.; Marchesini, L.B.; Montagnani, L.; Pita, G.; Rodeghiero, M.; Rodrigues, A.; Starr, G.; Stoy, P.C.

    2011-01-01

    Basal ecosystem respiration rate (BR), the ecosystem respiration rate at a given temperature, is a common and important parameter in empirical models for quantifying ecosystem respiration (ER) globally. Numerous studies have indicated that BR varies in space. However, many empirical ER models still use a global constant BR largely due to the lack of a functional description for BR. In this study, we redefined BR to be ecosystem respiration rate at the mean annual temperature. To test the validity of this concept, we conducted a synthesis analysis using 276 site-years of eddy covariance data, from 79 research sites located at latitudes ranging from ???3S to ???70N. Results showed that mean annual ER rate closely matches ER rate at mean annual temperature. Incorporation of site-specific BR into global ER model substantially improved simulated ER compared to an invariant BR at all sites. These results confirm that ER at the mean annual temperature can be considered as BR in empirical models. A strong correlation was found between the mean annual ER and mean annual gross primary production (GPP). Consequently, GPP, which is typically more accurately modeled, can be used to estimate BR. A light use efficiency GPP model (i.e., EC-LUE) was applied to estimate global GPP, BR and ER with input data from MERRA (Modern Era Retrospective-Analysis for Research and Applications) and MODIS (Moderate resolution Imaging Spectroradiometer). The global ER was 103 Pg C yr -1, with the highest respiration rate over tropical forests and the lowest value in dry and high-latitude areas. Copyright 2011 by the American Geophysical Union.

  10. Estimation of evapotranspiration rate in irrigated lands using stable isotopes

    NASA Astrophysics Data System (ADS)

    Umirzakov, Gulomjon; Windhorst, David; Forkutsa, Irina; Brauer, Lutz; Frede, Hans-Georg

    2013-04-01

    Agriculture in the Aral Sea basin is the main consumer of water resources and due to the current agricultural management practices inefficient water usage causes huge losses of freshwater resources. There is huge potential to save water resources in order to reach a more efficient water use in irrigated areas. Therefore, research is required to reveal the mechanisms of hydrological fluxes in irrigated areas. This paper focuses on estimation of evapotranspiration which is one of the crucial components in the water balance of irrigated lands. Our main objective is to estimate the rate of evapotranspiration on irrigated lands and partitioning of evaporation into transpiration using stable isotopes measurements. Experiments has done in 2 different soil types (sandy and sandy loam) irrigated areas in Ferghana Valley (Uzbekistan). Soil samples were collected during the vegetation period. The soil water from these samples was extracted via a cryogenic extraction method and analyzed for the isotopic ratio of the water isotopes (2H and 18O) based on a laser spectroscopy method (DLT 100, Los Gatos USA). Evapotranspiration rates were estimated with Isotope Mass Balance method. The results of evapotranspiration obtained using isotope mass balance method is compared with the results of Catchment Modeling Framework -1D model results which has done in the same area and the same time.

  11. Estimation of glomerular filtration rate in cynomolgus monkeys (Macaca fascicularis).

    PubMed

    Iwama, Ryosuke; Sato, Tsubasa; Sakurai, Ken; Takasuna, Kiyoshi; Ichijo, Toshihiro; Furuhama, Kazuhisa; Satoh, Hiroshi

    2014-10-01

    To estimate the glomerular filtration rate (GFR) in cynomolgus monkeys (Macaca fascicularis), a three-blood-sample method using iodixanol was assessed in comparison with the conventional multisample strategy using inulin. Iodixanol and inulin were coadministered intravenously 40 mg I/kg and 50 mg/kg, respectively, to male monkeys, followed by blood collection 60, 90 and 120 min later. A close correlation (r=0.96) was noted between the GFR values estimated by both methods. In clinically healthy monkeys, the basal values were determined to be 3.06 ± 0.50 ml/min/kg. This is the first report, suggesting that serum clearance of iodixanol is a ready-to-use tool for a screening the GFR in monkeys, although it is necessary to perform a more longitudinal study using animals with reduced renal function. PMID:24998395

  12. Estimating Fault Slip Rates: Four Ways to Evaluate Differences Between GPS and Geologic Rates

    NASA Astrophysics Data System (ADS)

    Thatcher, W.

    2008-12-01

    Block modeling of GPS velocity fields worldwide is providing hundreds of new decadal fault slip rate estimates that can be compared with independent Holocene (10 ka) to late Quaternary (125 ka) rates obtained by geological methods. A compilation of over 40 available GPS/geologic comparisons shows general agreement but a subset of apparently significant outliers. Some of these outliers have been discussed previously and attributed either to a temporal change in slip rate or systematic error in one of the estimates. I suggest 4 criteria for assessing the differing rates. First: Is there even-handed evaluation of random and systematic errors? 'Random error' is sometimes subjectively estimated and its statistical properties may be unknown or idealized. Differences between equally likely block models introduces a systematic error into GPS rate estimates that is difficult to assess and seldom discussed. Difficulties in constraining the true initiation date of offset of geomorphic markers by faulting can introduce uncertainties much larger than quoted random errors. Second: Are rate estimates obtained by more than one geodetic or geologic method? For example, agreement between GPS and InSAR slip rate estimates on the Altyn Tagh and Haiyuan faults of Tibet make the geodetic estimates more reliable. Similarly, dating of multiple offset markers of differing age across these faults supports the consistency of the geologic rate estimates. Third: Is proposed rate change mechanism consistent with examples of changes in style and rate of deformation preserved in the geologic record? For example, temporal evolution of the multi-stranded San Andreas system during the past 5-10 Ma (Powell and Weldon 1992; Graymer et al. 2002) indicates activation and deactivation of different faults within the system accompanied by consequent changes in fault slip rate and/or creation of new crustal blocks. Similarly, reactivation of Cenozoic normal faults as thrusts indicates a late Cenozoic change

  13. Simple estimates of vehicle-induced resuspension rates.

    PubMed

    Escrig, A; Amato, F; Pandolfi, M; Monfort, E; Querol, X; Celades, I; Sanfélix, V; Alastuey, A; Orza, J A G

    2011-10-01

    Road dust emissions are considered to be a major source of airborne particulate matter (PM). This is particularly true for industrial environments, where there are high resuspension rates of deposited dust. The calculation of roads as PM emission sources has mostly focused on the consequences of this emission, viz. the increase in PM concentrations. That approach addresses the atmospheric transport of the emitted dust, and not its primary origin. In contrast, this paper examines the causes of the emission. The study is based on mass conservation of the dust deposited on the road surface. On the basis of this premise, estimates of emission rates were calculated from experimental data obtained in a road in a ceramic industrial area. PMID:21763062

  14. Interictal spikes and epileptic seizures: their relationship and underlying rhythmicity.

    PubMed

    Karoly, Philippa J; Freestone, Dean R; Boston, Ray; Grayden, David B; Himes, David; Leyde, Kent; Seneviratne, Udaya; Berkovic, Samuel; O'Brien, Terence; Cook, Mark J

    2016-04-01

    We report on a quantitative analysis of electrocorticography data from a study that acquired continuous ambulatory recordings in humans over extended periods of time. The objectives were to examine patterns of seizures and spontaneous interictal spikes, their relationship to each other, and the nature of periodic variation. The recorded data were originally acquired for the purpose of seizure prediction, and were subsequently analysed in further detail. A detection algorithm identified potential seizure activity and a template matched filter was used to locate spikes. Seizure events were confirmed manually and classified as either clinically correlated, electroencephalographically identical but not clinically correlated, or subclinical. We found that spike rate was significantly altered prior to seizure in 9 out of 15 subjects. Increased pre-ictal spike rate was linked to improved predictability; however, spike rate was also shown to decrease before seizure (in 6 out of the 9 subjects). The probability distribution of spikes and seizures were notably similar, i.e. at times of high seizure likelihood the probability of epileptic spiking also increased. Both spikes and seizures showed clear evidence of circadian regulation and, for some subjects, there were also longer term patterns visible over weeks to months. Patterns of spike and seizure occurrence were highly subject-specific. The pre-ictal decrease in spike rate is not consistent with spikes promoting seizures. However, the fact that spikes and seizures demonstrate similar probability distributions suggests they are not wholly independent processes. It is possible spikes actively inhibit seizures, or that a decreased spike rate is a secondary symptom of the brain approaching seizure. If spike rate is modulated by common regulatory factors as seizures then spikes may be useful biomarkers of cortical excitability.media-1vid110.1093/brain/aww019_video_abstractaww019_video_abstract. PMID:26912639

  15. Optimized support vector regression for drilling rate of penetration estimation

    NASA Astrophysics Data System (ADS)

    Bodaghi, Asadollah; Ansari, Hamid Reza; Gholami, Mahsa

    2015-12-01

    In the petroleum industry, drilling optimization involves the selection of operating conditions for achieving the desired depth with the minimum expenditure while requirements of personal safety, environment protection, adequate information of penetrated formations and productivity are fulfilled. Since drilling optimization is highly dependent on the rate of penetration (ROP), estimation of this parameter is of great importance during well planning. In this research, a novel approach called `optimized support vector regression' is employed for making a formulation between input variables and ROP. Algorithms used for optimizing the support vector regression are the genetic algorithm (GA) and the cuckoo search algorithm (CS). Optimization implementation improved the support vector regression performance by virtue of selecting proper values for its parameters. In order to evaluate the ability of optimization algorithms in enhancing SVR performance, their results were compared to the hybrid of pattern search and grid search (HPG) which is conventionally employed for optimizing SVR. The results demonstrated that the CS algorithm achieved further improvement on prediction accuracy of SVR compared to the GA and HPG as well. Moreover, the predictive model derived from back propagation neural network (BPNN), which is the traditional approach for estimating ROP, is selected for comparisons with CSSVR. The comparative results revealed the superiority of CSSVR. This study inferred that CSSVR is a viable option for precise estimation of ROP.

  16. Heart rate and estimated energy expenditure during ballroom dancing.

    PubMed Central

    Blanksby, B A; Reidy, P W

    1988-01-01

    Ten competitive ballroom dance couples performed simulated competitive sequences of Modern and Latin American dance. Heart rate was telemetered during the dance sequences and related to direct measures of oxygen uptake and heart rate obtained while walking on a treadmill. Linear regression was employed to estimate gross and net energy expenditures of the dance sequences. A multivariate analysis of variance with repeated measures on the dance factor was applied to the data to test for interaction and main effects on the sex and dance factors. Overall mean heart rate values for the Modern dance sequence were 170 beats.min-1 and 173 beats.min-1 for males and females respectively. During the Latin American sequence mean overall heart rate for males was 168 beats.min-1 and 177 beats.min-1 for females. Predicted mean gross values of oxygen consumption for the males were 42.8 +/- 5.7 ml.kg-1 min-1 and 42.8 +/- 6.9 ml.kg-1 min-1 for the Modern and Latin American sequences respectively. Corresponding gross estimates of oxygen consumption for the females were 34.7 +/- 3.8 ml.kg-1 min-1 and 36.1 +/- 4.1 ml.kg-1 min-1. Males were estimated to expand 54.1 +/- 8.1 kJ.min-1 of energy during the Modern sequence and 54.0 +/- 9.6 kJ.min-1 during the Latin American sequence, while predicted energy expenditure for females was 34.7 +/- 3.8 kJ.min-1 and 36.1 +/- 4.1 kJ.min-1 for Modern and Latin American dance respectively. The results suggested that both males and females were dancing at greater than 80% of their maximum oxygen consumption. A significant difference between males and females was observed for predicted gross and net values of oxygen consumption (in L.min-1 and ml.kg-1 min-1). PMID:3167503

  17. Heart rate and estimated energy expenditure during ballroom dancing.

    PubMed

    Blanksby, B A; Reidy, P W

    1988-06-01

    Ten competitive ballroom dance couples performed simulated competitive sequences of Modern and Latin American dance. Heart rate was telemetered during the dance sequences and related to direct measures of oxygen uptake and heart rate obtained while walking on a treadmill. Linear regression was employed to estimate gross and net energy expenditures of the dance sequences. A multivariate analysis of variance with repeated measures on the dance factor was applied to the data to test for interaction and main effects on the sex and dance factors. Overall mean heart rate values for the Modern dance sequence were 170 beats.min-1 and 173 beats.min-1 for males and females respectively. During the Latin American sequence mean overall heart rate for males was 168 beats.min-1 and 177 beats.min-1 for females. Predicted mean gross values of oxygen consumption for the males were 42.8 +/- 5.7 ml.kg-1 min-1 and 42.8 +/- 6.9 ml.kg-1 min-1 for the Modern and Latin American sequences respectively. Corresponding gross estimates of oxygen consumption for the females were 34.7 +/- 3.8 ml.kg-1 min-1 and 36.1 +/- 4.1 ml.kg-1 min-1. Males were estimated to expand 54.1 +/- 8.1 kJ.min-1 of energy during the Modern sequence and 54.0 +/- 9.6 kJ.min-1 during the Latin American sequence, while predicted energy expenditure for females was 34.7 +/- 3.8 kJ.min-1 and 36.1 +/- 4.1 kJ.min-1 for Modern and Latin American dance respectively. The results suggested that both males and females were dancing at greater than 80% of their maximum oxygen consumption. A significant difference between males and females was observed for predicted gross and net values of oxygen consumption (in L.min-1 and ml.kg-1 min-1). PMID:3167503

  18. Attitude/attitude-rate estimation from GPS differential phase measurements using integrated-rate parameters

    NASA Technical Reports Server (NTRS)

    Oshman, Yaakov; Markley, Landis

    1998-01-01

    A sequential filtering algorithm is presented for attitude and attitude-rate estimation from Global Positioning System (GPS) differential carrier phase measurements. A third-order, minimal-parameter method for solving the attitude matrix kinematic equation is used to parameterize the filter's state, which renders the resulting estimator computationally efficient. Borrowing from tracking theory concepts, the angular acceleration is modeled as an exponentially autocorrelated stochastic process, thus avoiding the use of the uncertain spacecraft dynamic model. The new formulation facilitates the use of aiding vector observations in a unified filtering algorithm, which can enhance the method's robustness and accuracy. Numerical examples are used to demonstrate the performance of the method.

  19. Estimation of the diffusion-limited rate of microtubule assembly.

    PubMed Central

    Odde, D J

    1997-01-01

    Microtubule assembly is a complex process with individual microtubules alternating stochastically between extended periods of assembly and disassembly, a phenomenon known as dynamic instability. Since the discovery of dynamic instability, molecular models of assembly have generally assumed that tubulin incorporation into the microtubule lattice is primarily reaction-limited. Recently this assumption has been challenged and the importance of diffusion in microtubule assembly dynamics asserted on the basis of scaling arguments, with tubulin gradients predicted to extend over length scales exceeding a cell diameter, approximately 50 microns. To assess whether individual microtubules in vivo assemble at diffusion-limited rates and to predict the theoretical upper limit on the assembly rate, a steady-state mean-field model for the concentration of tubulin about a growing microtubule tip was developed. Using published parameter values for microtubule assembly in vivo (growth rate = 7 microns/min, diffusivity = 6 x 10(-12) m2/s, tubulin concentration = 10 microM), the model predicted that the tubulin concentration at the microtubule tip was approximately 89% of the concentration far from the tip, indicating that microtubule self-assembly is not diffusion-limited. Furthermore, the gradients extended less than approximately 50 nm (the equivalent of about two microtubule diameters) from the microtubule tip, a distance much less than a cell diameter. In addition, a general relation was developed to predict the diffusion-limited assembly rate from the diffusivity and bulk tubulin concentration. Using this relation, it was estimated that the maximum theoretical assembly rate is approximately 65 microns/min, above which tubulin can no longer diffuse rapidly enough to support faster growth. Images FIGURE 1 PMID:9199774

  20. Estimation of adjusted rate differences using additive negative binomial regression.

    PubMed

    Donoghoe, Mark W; Marschner, Ian C

    2016-08-15

    Rate differences are an important effect measure in biostatistics and provide an alternative perspective to rate ratios. When the data are event counts observed during an exposure period, adjusted rate differences may be estimated using an identity-link Poisson generalised linear model, also known as additive Poisson regression. A problem with this approach is that the assumption of equality of mean and variance rarely holds in real data, which often show overdispersion. An additive negative binomial model is the natural alternative to account for this; however, standard model-fitting methods are often unable to cope with the constrained parameter space arising from the non-negativity restrictions of the additive model. In this paper, we propose a novel solution to this problem using a variant of the expectation-conditional maximisation-either algorithm. Our method provides a reliable way to fit an additive negative binomial regression model and also permits flexible generalisations using semi-parametric regression functions. We illustrate the method using a placebo-controlled clinical trial of fenofibrate treatment in patients with type II diabetes, where the outcome is the number of laser therapy courses administered to treat diabetic retinopathy. An R package is available that implements the proposed method. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27073156

  1. Rainfall Estimation Over Tropical Oceans. 1; Area Average Rain Rate

    NASA Technical Reports Server (NTRS)

    Cuddapah, Prabhakara; Cadeddu, Maria; Meneghini, R.; Short, David A.; Yoo, Jung-Moon; Dalu, G.; Schols, J. L.; Weinman, J. A.

    1997-01-01

    Multichannel dual polarization microwave radiometer SSM/I observations over oceans do not contain sufficient information to differentiate quantitatively the rain from other hydrometeors on a scale comparable to the radiometer field of view (approx. 30 km). For this reason we have developed a method to retrieve average rain rate over a mesoscale grid box of approx. 300 x 300 sq km area over the TOGA COARE region where simultaneous radiometer and radar observations are available for four months (Nov. 92 to Feb. 93). The rain area in the grid box, inferred from the scattering depression due to hydrometeors in the 85 Ghz brightness temperature, constitutes a key parameter in this method. Then the spectral and polarization information contained in all the channels of the SSM/I is utilized to deduce a second parameter. This is the ratio S/E of scattering index S, and emission index E calculated from the SSM/I data. The rain rate retrieved from this method over the mesoscale area can reproduce the radar observed rain rate with a correlation coefficient of about 0.85. Furthermore monthly total rainfall estimated from this method over that area has an average error of about 15%.

  2. Estimation of heart rate and heart rate variability from pulse oximeter recordings using localized model fitting.

    PubMed

    Wadehn, Federico; Carnal, David; Loeliger, Hans-Andrea

    2015-08-01

    Heart rate variability is one of the key parameters for assessing the health status of a subject's cardiovascular system. This paper presents a local model fitting algorithm used for finding single heart beats in photoplethysmogram recordings. The local fit of exponentially decaying cosines of frequencies within the physiological range is used to detect the presence of a heart beat. Using 42 subjects from the CapnoBase database, the average heart rate error was 0.16 BPM and the standard deviation of the absolute estimation error was 0.24 BPM. PMID:26737125

  3. The Second Spiking Threshold: Dynamics of Laminar Network Spiking in the Visual Cortex

    PubMed Central

    Forsberg, Lars E.; Bonde, Lars H.; Harvey, Michael A.; Roland, Per E.

    2016-01-01

    Most neurons have a threshold separating the silent non-spiking state and the state of producing temporal sequences of spikes. But neurons in vivo also have a second threshold, found recently in granular layer neurons of the primary visual cortex, separating spontaneous ongoing spiking from visually evoked spiking driven by sharp transients. Here we examine whether this second threshold exists outside the granular layer and examine details of transitions between spiking states in ferrets exposed to moving objects. We found the second threshold, separating spiking states evoked by stationary and moving visual stimuli from the spontaneous ongoing spiking state, in all layers and zones of areas 17 and 18 indicating that the second threshold is a property of the network. Spontaneous and evoked spiking, thus can easily be distinguished. In addition, the trajectories of spontaneous ongoing states were slow, frequently changing direction. In single trials, sharp as well as smooth and slow transients transform the trajectories to be outward directed, fast and crossing the threshold to become evoked. Although the speeds of the evolution of the evoked states differ, the same domain of the state space is explored indicating uniformity of the evoked states. All evoked states return to the spontaneous evoked spiking state as in a typical mono-stable dynamical system. In single trials, neither the original spiking rates, nor the temporal evolution in state space could distinguish simple visual scenes. PMID:27582693

  4. The Second Spiking Threshold: Dynamics of Laminar Network Spiking in the Visual Cortex.

    PubMed

    Forsberg, Lars E; Bonde, Lars H; Harvey, Michael A; Roland, Per E

    2016-01-01

    Most neurons have a threshold separating the silent non-spiking state and the state of producing temporal sequences of spikes. But neurons in vivo also have a second threshold, found recently in granular layer neurons of the primary visual cortex, separating spontaneous ongoing spiking from visually evoked spiking driven by sharp transients. Here we examine whether this second threshold exists outside the granular layer and examine details of transitions between spiking states in ferrets exposed to moving objects. We found the second threshold, separating spiking states evoked by stationary and moving visual stimuli from the spontaneous ongoing spiking state, in all layers and zones of areas 17 and 18 indicating that the second threshold is a property of the network. Spontaneous and evoked spiking, thus can easily be distinguished. In addition, the trajectories of spontaneous ongoing states were slow, frequently changing direction. In single trials, sharp as well as smooth and slow transients transform the trajectories to be outward directed, fast and crossing the threshold to become evoked. Although the speeds of the evolution of the evoked states differ, the same domain of the state space is explored indicating uniformity of the evoked states. All evoked states return to the spontaneous evoked spiking state as in a typical mono-stable dynamical system. In single trials, neither the original spiking rates, nor the temporal evolution in state space could distinguish simple visual scenes. PMID:27582693

  5. Estimating rates of authigenic carbonate precipitation in modern marine sediments

    NASA Astrophysics Data System (ADS)

    Mitnick, E. H.; Lammers, L. N.; DePaolo, D. J.

    2015-12-01

    The formation of authigenic carbonate (AC) in marine sediments provides a plausible explanation for large, long-lasting marine δ13C excursions that does not require extreme swings in atmospheric O2 or CO2. AC precipitation during diagenesis is driven by alkalinity production during anaerobic organic matter oxidation and is coupled to sulfate reduction. To evaluate the extent to which this process contributes to global carbon cycling, we need to relate AC production to the geochemical and geomicrobiological processes and ocean chemical conditions that control it. We present a method to estimate modern rates of AC precipitation using an inversion approach based on the diffusion-advection-reaction equation and sediment pore fluid chemistry profiles as a function of depth. SEM images and semi-quantitative elemental map analyses provide further constraints. Our initial focus is on ODP sites 807 and 1082. We sum the diffusive, advective, and reactive terms that describe changes in pore fluid Ca and Mg concentrations due to precipitation of secondary carbonate. We calculate the advective and diffusive terms from the first and second derivatives of the Ca and Mg pore fluid concentrations using a spline fit to the data. Assuming steady-state behavior we derive net AC precipitation rates of up to 8 x 10-4 mmol m-2 y-1 for Site 807 and 0.6 mmol m-2 y-1 for Site 1082. Site 1082 sediments contain pyrite, which increases in amount down-section towards the estimated peak carbonate precipitation rate, consistent with sulfate-reduction-induced AC precipitation. However, the presence of gypsum and barite throughout the sediment column implies incomplete sulfate reduction and merits further investigation of the biogeochemical reactions controlling authigenesis. Further adjustments to our method could account for the small but non-negligible fraction of groundmass with a CaSO4 signature. Our estimates demonstrate that AC formation may represent a sizeable flux in the modern global

  6. Estimating cougar predation rates from GPS location clusters

    USGS Publications Warehouse

    Anderson, C.R., Jr.; Lindzey, F.G.

    2003-01-01

    We examined cougar (Puma concolor) predation from Global Positioning System (GPS) location clusters (???2 locations within 200 m on the same or consecutive nights) of 11 cougars during September-May, 1999-2001. Location success of GPS averaged 2.4-5.0 of 6 location attempts/night/cougar. We surveyed potential predation sites during summer-fall 2000 and summer 2001 to identify prey composition (n = 74; 3-388 days post predation) and record predation-site variables (n = 97; 3-270 days post predation). We developed a model to estimate probability that a cougar killed a large mammal from data collected at GPS location clusters where the probability of predation increased with number of nights (defined as locations at 2200, 0200, or 0500 hr) of cougar presence within a 200-m radius (P < 0.001). Mean estimated cougar predation rates for large mammals were 7.3 days/kill for subadult females (1-2.5 yr; n = 3, 90% CI: 6.3 to 9.9), 7.0 days/kill for adult females (n = 2, 90% CI: 5.8 to 10.8), 5.4 days/kill for family groups (females with young; n = 3, 90% CI: 4.5 to 8.4), 9.5 days/kill for a subadult male (1-2.5 yr; n = 1, 90% CI: 6.9 to 16.4), and 7.8 days/kill for adult males (n = 2, 90% CI: 6.8 to 10.7). We may have slightly overestimated cougar predation rates due to our inability to separate scavenging from predation. We detected 45 deer (Odocoileus spp.), 15 elk (Cervus elaphus), 6 pronghorn (Antilocapra americana), 2 livestock, 1 moose (Alces alces), and 6 small mammals at cougar predation sites. Comparisons between cougar sexes suggested that females selected mule deer and males selected elk (P < 0.001). Cougars averaged 3.0 nights on pronghorn carcasses, 3.4 nights on deer carcasses, and 6.0 nights on elk carcasses. Most cougar predation (81.7%) occurred between 1901-0500 hr and peaked from 2201-0200 hr (31.7%). Applying GPS technology to identify predation rates and prey selection will allow managers to efficiently estimate the ability of an area's prey base to

  7. Inference of neuronal network spike dynamics and topology from calcium imaging data

    PubMed Central

    Lütcke, Henry; Gerhard, Felipe; Zenke, Friedemann; Gerstner, Wulfram; Helmchen, Fritjof

    2013-01-01

    Two-photon calcium imaging enables functional analysis of neuronal circuits by inferring action potential (AP) occurrence (“spike trains”) from cellular fluorescence signals. It remains unclear how experimental parameters such as signal-to-noise ratio (SNR) and acquisition rate affect spike inference and whether additional information about network structure can be extracted. Here we present a simulation framework for quantitatively assessing how well spike dynamics and network topology can be inferred from noisy calcium imaging data. For simulated AP-evoked calcium transients in neocortical pyramidal cells, we analyzed the quality of spike inference as a function of SNR and data acquisition rate using a recently introduced peeling algorithm. Given experimentally attainable values of SNR and acquisition rate, neural spike trains could be reconstructed accurately and with up to millisecond precision. We then applied statistical neuronal network models to explore how remaining uncertainties in spike inference affect estimates of network connectivity and topological features of network organization. We define the experimental conditions suitable for inferring whether the network has a scale-free structure and determine how well hub neurons can be identified. Our findings provide a benchmark for future calcium imaging studies that aim to reliably infer neuronal network properties. PMID:24399936

  8. Groundwater recharge rate and zone structure estimation using PSOLVER algorithm.

    PubMed

    Ayvaz, M Tamer; Elçi, Alper

    2014-01-01

    The quantification of groundwater recharge is an important but challenging task in groundwater flow modeling because recharge varies spatially and temporally. The goal of this study is to present an innovative methodology to estimate groundwater recharge rates and zone structures for regional groundwater flow models. Here, the unknown recharge field is partitioned into a number of zones using Voronoi Tessellation (VT). The identified zone structure with the recharge rates is associated through a simulation-optimization model that couples MODFLOW-2000 and the hybrid PSOLVER optimization algorithm. Applicability of this procedure is tested on a previously developed groundwater flow model of the Tahtalı Watershed. Successive zone structure solutions are obtained in an additive manner and penalty functions are used in the procedure to obtain realistic and plausible solutions. One of these functions constrains the optimization by forcing the sum of recharge rates for the grid cells that coincide with the Tahtalı Watershed area to be equal to the areal recharge rate determined in the previous modeling by a separate precipitation-runoff model. As a result, a six-zone structure is selected as the best zone structure that represents the areal recharge distribution. Comparison to results of a previous model for the same study area reveals that the proposed procedure significantly improves model performance with respect to calibration statistics. The proposed identification procedure can be thought of as an effective way to determine the recharge zone structure for groundwater flow models, in particular for situations where tangible information about groundwater recharge distribution does not exist. PMID:23746002

  9. Estimates of Lava Eruption Rates at Alba Patera, Mars

    NASA Technical Reports Server (NTRS)

    Baloga, S. M.; Pieri, D. C.

    1985-01-01

    The Martian volcanic complex Alba Patera exhibits a suite of well-defined, long and relatively narrow lava flows qualitatively resembling those found in Hawaii. Even without any information on the duration of the Martian flows, eruption rates (total volume discharge/duration of the extrusion) estimates are implied by the physical dimensions of the flows and the likely conjecture that Stephan-Boltzmann radiation is the dominating thermal loss mechanism. The ten flows in this analysis emanate radially from the central vent and were recently measured in length, plan areas, and average thicknesses by shadow measurement techniques. The dimensions of interest are shown. Although perhaps morphologically congruent to certain Hawaiian flows, the dramatically expanded physical dimensions of the Martian flows argues for some markedly distinct differences in lava flow composition for eruption characteristics.

  10. Gambling disorder: estimated prevalence rates and risk factors in Macao.

    PubMed

    Wu, Anise M S; Lai, Mark H C; Tong, Kwok-Kit

    2014-12-01

    An excessive, problematic gambling pattern has been regarded as a mental disorder in the Diagnostic and Statistical Manual for Mental Disorders (DSM) for more than 3 decades (American Psychiatric Association [APA], 1980). In this study, its latest prevalence in Macao (one of very few cities with legalized gambling in China and the Far East) was estimated with 2 major changes in the diagnostic criteria, suggested by the 5th edition of DSM (APA, 2013): (a) removing the "Illegal Act" criterion, and (b) lowering the threshold for diagnosis. A random, representative sample of 1,018 Macao residents was surveyed with a phone poll design in January 2013. After the 2 changes were adopted, the present study showed that the estimated prevalence rate of gambling disorder was 2.1% of the Macao adult population. Moreover, the present findings also provided empirical support to the application of these 2 recommended changes when assessing symptoms of gambling disorder among Chinese community adults. Personal risk factors of gambling disorder, namely being male, having low education, a preference for casino gambling, as well as high materialism, were identified. PMID:25134026

  11. Analyzing multiple spike trains with nonparametric Granger causality.

    PubMed

    Nedungadi, Aatira G; Rangarajan, Govindan; Jain, Neeraj; Ding, Mingzhou

    2009-08-01

    Simultaneous recordings of spike trains from multiple single neurons are becoming commonplace. Understanding the interaction patterns among these spike trains remains a key research area. A question of interest is the evaluation of information flow between neurons through the analysis of whether one spike train exerts causal influence on another. For continuous-valued time series data, Granger causality has proven an effective method for this purpose. However, the basis for Granger causality estimation is autoregressive data modeling, which is not directly applicable to spike trains. Various filtering options distort the properties of spike trains as point processes. Here we propose a new nonparametric approach to estimate Granger causality directly from the Fourier transforms of spike train data. We validate the method on synthetic spike trains generated by model networks of neurons with known connectivity patterns and then apply it to neurons simultaneously recorded from the thalamus and the primary somatosensory cortex of a squirrel monkey undergoing tactile stimulation. PMID:19137420

  12. Prospective Coding by Spiking Neurons

    PubMed Central

    Brea, Johanni; Gaál, Alexisz Tamás; Senn, Walter

    2016-01-01

    Animals learn to make predictions, such as associating the sound of a bell with upcoming feeding or predicting a movement that a motor command is eliciting. How predictions are realized on the neuronal level and what plasticity rule underlies their learning is not well understood. Here we propose a biologically plausible synaptic plasticity rule to learn predictions on a single neuron level on a timescale of seconds. The learning rule allows a spiking two-compartment neuron to match its current firing rate to its own expected future discounted firing rate. For instance, if an originally neutral event is repeatedly followed by an event that elevates the firing rate of a neuron, the originally neutral event will eventually also elevate the neuron’s firing rate. The plasticity rule is a form of spike timing dependent plasticity in which a presynaptic spike followed by a postsynaptic spike leads to potentiation. Even if the plasticity window has a width of 20 milliseconds, associations on the time scale of seconds can be learned. We illustrate prospective coding with three examples: learning to predict a time varying input, learning to predict the next stimulus in a delayed paired-associate task and learning with a recurrent network to reproduce a temporally compressed version of a sequence. We discuss the potential role of the learning mechanism in classical trace conditioning. In the special case that the signal to be predicted encodes reward, the neuron learns to predict the discounted future reward and learning is closely related to the temporal difference learning algorithm TD(λ). PMID:27341100

  13. Energy Detection Based Estimation of Channel Occupancy Rate with Adaptive Noise Estimation

    NASA Astrophysics Data System (ADS)

    Lehtomäki, Janne J.; Vuohtoniemi, Risto; Umebayashi, Kenta; Mäkelä, Juha-Pekka

    Recently, there has been growing interest in opportunistically utilizing the 2.4GHz ISM-band. Numerous spectrum occupancy measurements covering the ISM-band have been performed to analyze the spectrum usage. However, in these campaigns the verification of the correctness of the obtained occupancy values for the highly dynamic ISM-band has not been presented. In this paper, we propose and verify channel occupancy rate (COR) estimation utilizing energy detection mechanism with a novel adaptive energy detection threshold setting method. The results are compared with the true reference COR values. Several different types of verification measurements showed that our setup can estimate the COR values of 802.11 traffic well, with negligible overestimation. The results from real-time real-life measurements also confirm that the proposed adaptive threshold setting method enables accurate thresholds even in the situations where multiple interferers are present in the received signal.

  14. Program CONTRAST--A general program for the analysis of several survival or recovery rate estimates

    USGS Publications Warehouse

    Hines, J.E.; Sauer, J.R.

    1989-01-01

    This manual describes the use of program CONTRAST, which implements a generalized procedure for the comparison of several rate estimates. This method can be used to test both simple and composite hypotheses about rate estimates, and we discuss its application to multiple comparisons of survival rate estimates. Several examples of the use of program CONTRAST are presented. Program CONTRAST will run on IBM-cimpatible computers, and requires estimates of the rates to be tested, along with associated variance and covariance estimates.

  15. Estimation of desmosponge (Porifera, Demospongiae) larval settlement rates from short-term recruitment rates: Preliminary experiments

    NASA Astrophysics Data System (ADS)

    Zea, Sven

    1992-09-01

    During a study of the spatial and temporal patterns of desmosponge (Porifera, Demospongiae) recruitment on rocky and coral reef habitats of Santa Marta, Colombian Caribbean Sea, preliminary attempts were made to estimate actual settlement rates from short-term (1 to a few days) recruitment censuses. Short-term recruitment rates on black, acrylic plastic plates attached to open, non-cryptic substratum by anchor screws were low and variable (0 5 recruits/plate in 1 2 days, sets of n=5 10 plates), but reflected the depth and seasonal trends found using mid-term (1 to a few months) censusing intervals. Moreover, mortality of recruits during 1 2 day intervals was low (0 12%). Thus, short-term censusing intervals can be used to estimate actual settlement rates. To be able to make statistical comparisons, however, it is necessary to increase the number of recruits per census by pooling data of n plates per set, and to have more than one set per site or treatment.

  16. Vibration (?) spikes during natural rain events

    NASA Technical Reports Server (NTRS)

    Short, David A.

    1994-01-01

    Limited analysis of optical rain gauge (ORG) data from shipboard and ground based sensors has shown the existence of spikes, possibly attributable to sensor vibration, while rain is occurring. An extreme example of this behavior was noted aboard the PRC#5 on the evening of December 24, 1992 as the ship began repositioning during a rain event in the TOGA/COARE IFA. The spikes are readily evident in the one-second resolution data, but may be indistinguishable from natural rain rate fluctuations in subsampled or averaged data. Such spikes result in increased rainfall totals.

  17. Using minute ventilation for ambulatory estimation of additional heart rate.

    PubMed

    Wilhelm, F H; Roth, W T

    1998-09-01

    Both physical activity and emotion produce physiological activation. The emotional component of heart rate (HR) can be estimated as the additional HR (aHR) above that predicted by O2 consumption. Our innovation was to substitute minute ventilation (V) for O2 consumption, calculating aHR from individual relations between V and HR during an exercise test. We physiologically monitored 28 flight phobics and 15 non-anxious controls while walking (leaving the hospital, entering a plane), and during a commercial flight. Raw HR did not differ between phobics and controls when leaving the hospital (118/114 bpm) or entering the plane (117/110 bpm). However, although aHR was not different when leaving the hospital (7.0/8.6 bpm), it was significantly greater when entering the plane (17.5/9.9 bpm), accurately reflecting the increased subjective anxiety of the phobics. V was not higher in phobics than controls during any condition, suggesting an absence of hyperventilation in the phobics. The results demonstrate the utility of our method for analyzing HR in people whose stress occurs when they are physically active. PMID:9792490

  18. Macroscopic Description for Networks of Spiking Neurons

    NASA Astrophysics Data System (ADS)

    Montbrió, Ernest; Pazó, Diego; Roxin, Alex

    2015-04-01

    A major goal of neuroscience, statistical physics, and nonlinear dynamics is to understand how brain function arises from the collective dynamics of networks of spiking neurons. This challenge has been chiefly addressed through large-scale numerical simulations. Alternatively, researchers have formulated mean-field theories to gain insight into macroscopic states of large neuronal networks in terms of the collective firing activity of the neurons, or the firing rate. However, these theories have not succeeded in establishing an exact correspondence between the firing rate of the network and the underlying microscopic state of the spiking neurons. This has largely constrained the range of applicability of such macroscopic descriptions, particularly when trying to describe neuronal synchronization. Here, we provide the derivation of a set of exact macroscopic equations for a network of spiking neurons. Our results reveal that the spike generation mechanism of individual neurons introduces an effective coupling between two biophysically relevant macroscopic quantities, the firing rate and the mean membrane potential, which together govern the evolution of the neuronal network. The resulting equations exactly describe all possible macroscopic dynamical states of the network, including states of synchronous spiking activity. Finally, we show that the firing-rate description is related, via a conformal map, to a low-dimensional description in terms of the Kuramoto order parameter, called Ott-Antonsen theory. We anticipate that our results will be an important tool in investigating how large networks of spiking neurons self-organize in time to process and encode information in the brain.

  19. Temporal spike pattern learning

    NASA Astrophysics Data System (ADS)

    Talathi, Sachin S.; Abarbanel, Henry D. I.; Ditto, William L.

    2008-09-01

    Sensory systems pass information about an animal’s environment to higher nervous system units through sequences of action potentials. When these action potentials have essentially equivalent wave forms, all information is contained in the interspike intervals (ISIs) of the spike sequence. How do neural circuits recognize and read these ISI sequences? We address this issue of temporal sequence learning by a neuronal system utilizing spike timing dependent plasticity (STDP). We present a general architecture of neural circuitry that can perform the task of ISI recognition. The essential ingredients of this neural circuit, which we refer to as “interspike interval recognition unit” (IRU) are (i) a spike selection unit, the function of which is to selectively distribute input spikes to downstream IRU circuitry; (ii) a time-delay unit that can be tuned by STDP; and (iii) a detection unit, which is the output of the IRU and a spike from which indicates successful ISI recognition by the IRU. We present two distinct configurations for the time-delay circuit within the IRU using excitatory and inhibitory synapses, respectively, to produce a delayed output spike at time t0+τ(R) in response to the input spike received at time t0 . R is the tunable parameter of the time-delay circuit that controls the timing of the delayed output spike. We discuss the forms of STDP rules for excitatory and inhibitory synapses, respectively, that allow for modulation of R for the IRU to perform its task of ISI recognition. We then present two specific implementations for the IRU circuitry, derived from the general architecture that can both learn the ISIs of a training sequence and then recognize the same ISI sequence when it is presented on subsequent occasions.

  20. Temporal spike pattern learning.

    PubMed

    Talathi, Sachin S; Abarbanel, Henry D I; Ditto, William L

    2008-09-01

    Sensory systems pass information about an animal's environment to higher nervous system units through sequences of action potentials. When these action potentials have essentially equivalent wave forms, all information is contained in the interspike intervals (ISIs) of the spike sequence. How do neural circuits recognize and read these ISI sequences? We address this issue of temporal sequence learning by a neuronal system utilizing spike timing dependent plasticity (STDP). We present a general architecture of neural circuitry that can perform the task of ISI recognition. The essential ingredients of this neural circuit, which we refer to as "interspike interval recognition unit" (IRU) are (i) a spike selection unit, the function of which is to selectively distribute input spikes to downstream IRU circuitry; (ii) a time-delay unit that can be tuned by STDP; and (iii) a detection unit, which is the output of the IRU and a spike from which indicates successful ISI recognition by the IRU. We present two distinct configurations for the time-delay circuit within the IRU using excitatory and inhibitory synapses, respectively, to produce a delayed output spike at time t_{0}+tau(R) in response to the input spike received at time t_{0} . R is the tunable parameter of the time-delay circuit that controls the timing of the delayed output spike. We discuss the forms of STDP rules for excitatory and inhibitory synapses, respectively, that allow for modulation of R for the IRU to perform its task of ISI recognition. We then present two specific implementations for the IRU circuitry, derived from the general architecture that can both learn the ISIs of a training sequence and then recognize the same ISI sequence when it is presented on subsequent occasions. PMID:18851076

  1. Measuring multiple spike train synchrony.

    PubMed

    Kreuz, Thomas; Chicharro, Daniel; Andrzejak, Ralph G; Haas, Julie S; Abarbanel, Henry D I

    2009-10-15

    Measures of multiple spike train synchrony are essential in order to study issues such as spike timing reliability, network synchronization, and neuronal coding. These measures can broadly be divided in multivariate measures and averages over bivariate measures. One of the most recent bivariate approaches, the ISI-distance, employs the ratio of instantaneous interspike intervals (ISIs). In this study we propose two extensions of the ISI-distance, the straightforward averaged bivariate ISI-distance and the multivariate ISI-diversity based on the coefficient of variation. Like the original measure these extensions combine many properties desirable in applications to real data. In particular, they are parameter-free, time scale independent, and easy to visualize in a time-resolved manner, as we illustrate with in vitro recordings from a cortical neuron. Using a simulated network of Hindemarsh-Rose neurons as a controlled configuration we compare the performance of our methods in distinguishing different levels of multi-neuron spike train synchrony to the performance of six other previously published measures. We show and explain why the averaged bivariate measures perform better than the multivariate ones and why the multivariate ISI-diversity is the best performer among the multivariate methods. Finally, in a comparison against standard methods that rely on moving window estimates, we use single-unit monkey data to demonstrate the advantages of the instantaneous nature of our methods. PMID:19591867

  2. Estimating mental fatigue based on electroencephalogram and heart rate variability

    NASA Astrophysics Data System (ADS)

    Zhang, Chong; Yu, Xiaolin

    2010-01-01

    The effects of long term mental arithmetic task on psychology are investigated by subjective self-reporting measures and action performance test. Based on electroencephalogram (EEG) and heart rate variability (HRV), the impacts of prolonged cognitive activity on central nervous system and autonomic nervous system are observed and analyzed. Wavelet packet parameters of EEG and power spectral indices of HRV are combined to estimate the change of mental fatigue. Then wavelet packet parameters of EEG which change significantly are extracted as the features of brain activity in different mental fatigue state, support vector machine (SVM) algorithm is applied to differentiate two mental fatigue states. The experimental results show that long term mental arithmetic task induces the mental fatigue. The wavelet packet parameters of EEG and power spectral indices of HRV are strongly correlated with mental fatigue. The predominant activity of autonomic nervous system of subjects turns to the sympathetic activity from parasympathetic activity after the task. Moreover, the slow waves of EEG increase, the fast waves of EEG and the degree of disorder of brain decrease compared with the pre-task. The SVM algorithm can effectively differentiate two mental fatigue states, which achieves the maximum classification accuracy (91%). The SVM algorithm could be a promising tool for the evaluation of mental fatigue. Fatigue, especially mental fatigue, is a common phenomenon in modern life, is a persistent occupational hazard for professional. Mental fatigue is usually accompanied with a sense of weariness, reduced alertness, and reduced mental performance, which would lead the accidents in life, decrease productivity in workplace and harm the health. Therefore, the evaluation of mental fatigue is important for the occupational risk protection, productivity, and occupational health.

  3. State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data

    PubMed Central

    Shimazaki, Hideaki; Amari, Shun-ichi; Brown, Emery N.; Grün, Sonja

    2012-01-01

    Precise spike coordination between the spiking activities of multiple neurons is suggested as an indication of coordinated network activity in active cell assemblies. Spike correlation analysis aims to identify such cooperative network activity by detecting excess spike synchrony in simultaneously recorded multiple neural spike sequences. Cooperative activity is expected to organize dynamically during behavior and cognition; therefore currently available analysis techniques must be extended to enable the estimation of multiple time-varying spike interactions between neurons simultaneously. In particular, new methods must take advantage of the simultaneous observations of multiple neurons by addressing their higher-order dependencies, which cannot be revealed by pairwise analyses alone. In this paper, we develop a method for estimating time-varying spike interactions by means of a state-space analysis. Discretized parallel spike sequences are modeled as multi-variate binary processes using a log-linear model that provides a well-defined measure of higher-order spike correlation in an information geometry framework. We construct a recursive Bayesian filter/smoother for the extraction of spike interaction parameters. This method can simultaneously estimate the dynamic pairwise spike interactions of multiple single neurons, thereby extending the Ising/spin-glass model analysis of multiple neural spike train data to a nonstationary analysis. Furthermore, the method can estimate dynamic higher-order spike interactions. To validate the inclusion of the higher-order terms in the model, we construct an approximation method to assess the goodness-of-fit to spike data. In addition, we formulate a test method for the presence of higher-order spike correlation even in nonstationary spike data, e.g., data from awake behaving animals. The utility of the proposed methods is tested using simulated spike data with known underlying correlation dynamics. Finally, we apply the methods

  4. State-space analysis of time-varying higher-order spike correlation for multiple neural spike train data.

    PubMed

    Shimazaki, Hideaki; Amari, Shun-Ichi; Brown, Emery N; Grün, Sonja

    2012-01-01

    Precise spike coordination between the spiking activities of multiple neurons is suggested as an indication of coordinated network activity in active cell assemblies. Spike correlation analysis aims to identify such cooperative network activity by detecting excess spike synchrony in simultaneously recorded multiple neural spike sequences. Cooperative activity is expected to organize dynamically during behavior and cognition; therefore currently available analysis techniques must be extended to enable the estimation of multiple time-varying spike interactions between neurons simultaneously. In particular, new methods must take advantage of the simultaneous observations of multiple neurons by addressing their higher-order dependencies, which cannot be revealed by pairwise analyses alone. In this paper, we develop a method for estimating time-varying spike interactions by means of a state-space analysis. Discretized parallel spike sequences are modeled as multi-variate binary processes using a log-linear model that provides a well-defined measure of higher-order spike correlation in an information geometry framework. We construct a recursive Bayesian filter/smoother for the extraction of spike interaction parameters. This method can simultaneously estimate the dynamic pairwise spike interactions of multiple single neurons, thereby extending the Ising/spin-glass model analysis of multiple neural spike train data to a nonstationary analysis. Furthermore, the method can estimate dynamic higher-order spike interactions. To validate the inclusion of the higher-order terms in the model, we construct an approximation method to assess the goodness-of-fit to spike data. In addition, we formulate a test method for the presence of higher-order spike correlation even in nonstationary spike data, e.g., data from awake behaving animals. The utility of the proposed methods is tested using simulated spike data with known underlying correlation dynamics. Finally, we apply the methods

  5. Rate control algorithm based on frame complexity estimation for MVC

    NASA Astrophysics Data System (ADS)

    Yan, Tao; An, Ping; Shen, Liquan; Zhang, Zhaoyang

    2010-07-01

    Rate control has not been well studied for multi-view video coding (MVC). In this paper, we propose an efficient rate control algorithm for MVC by improving the quadratic rate-distortion (R-D) model, which reasonably allocate bit-rate among views based on correlation analysis. The proposed algorithm consists of four levels for rate bits control more accurately, of which the frame layer allocates bits according to frame complexity and temporal activity. Extensive experiments show that the proposed algorithm can efficiently implement bit allocation and rate control according to coding parameters.

  6. ESTIMATION OF PHOSPHATE ESTER HYDROLYSIS RATE CONSTANTS. I. ALKALINE HYDROLYSIS

    EPA Science Inventory

    SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to allow the calculation of alkaline hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition state...

  7. ESTIMATION OF PHOSPHATE ESTER HYDROLYSIS RATE CONSTANTS - ALKALINE HYDROLYSIS

    EPA Science Inventory

    SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to allow the calculation of alkaline hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition state...

  8. An Overview of Bayesian Methods for Neural Spike Train Analysis

    PubMed Central

    2013-01-01

    Neural spike train analysis is an important task in computational neuroscience which aims to understand neural mechanisms and gain insights into neural circuits. With the advancement of multielectrode recording and imaging technologies, it has become increasingly demanding to develop statistical tools for analyzing large neuronal ensemble spike activity. Here we present a tutorial overview of Bayesian methods and their representative applications in neural spike train analysis, at both single neuron and population levels. On the theoretical side, we focus on various approximate Bayesian inference techniques as applied to latent state and parameter estimation. On the application side, the topics include spike sorting, tuning curve estimation, neural encoding and decoding, deconvolution of spike trains from calcium imaging signals, and inference of neuronal functional connectivity and synchrony. Some research challenges and opportunities for neural spike train analysis are discussed. PMID:24348527

  9. Millisecond solar radio spikes observed at 1420 MHz

    NASA Astrophysics Data System (ADS)

    Dabrowski, B. P.; Kus, A. J.

    We present results from observations of narrowband solar millisecond radio spikes at 1420 MHz. Observing data were collected between February 2000 and December 2001 with the 15-m radio telescope at the Centre for Astronomy Nicolaus Copernicus University in Torun, Poland, equipped with a radio spectrograph that covered the 1352-1490 MHz frequency band. The radio spectrograph has 3 MHz frequency resolution and 80 microsecond time resolution. We analyzed the individual radio spike duration, bandwidth and rate of frequency drift. A part of the observed spikes showed well-outlined subtle structures. On dynamic radio spectrograms of the investigated events we notice complex structures formed by numerous individual spikes known as chains of spikes and distinctly different structure of columns. Positions of active regions connected with radio spikes emission were investigated. It turns out that most of them are located near the center of the solar disk, suggesting strong beaming of the spikes emission.

  10. Incorporating a Time Horizon in Rate-of-Return Estimations: Discounted Cash Flow Model in Electric Transmission Rate Cases

    SciTech Connect

    Chatterjee, Bishu; Sharp, Peter A.

    2006-07-15

    Electric transmission and other rate cases use a form of the discounted cash flow model with a single long-term growth rate to estimate rates of return on equity. It cannot incorporate information about the appropriate time horizon for which analysts' estimates of earnings growth have predictive powers. Only a non-constant growth model can explicitly recognize the importance of the time horizon in an ROE calculation. (author)

  11. Improved estimates of environmental copper release rates from antifouling products.

    PubMed

    Finnie, Alistair A

    2006-01-01

    The US Navy Dome method for measuring copper release rates from antifouling paint in-service on ships' hulls can be considered to be the most reliable indicator of environmental release rates. In this paper, the relationship between the apparent copper release rate and the environmental release rate is established for a number of antifouling coating types using data from a variety of available laboratory, field and calculation methods. Apart from a modified Dome method using panels, all laboratory, field and calculation methods significantly overestimate the environmental release rate of copper from antifouling coatings. The difference is greatest for self-polishing copolymer antifoulings (SPCs) and smallest for certain erodible/ablative antifoulings, where the ASTM/ISO standard and the CEPE calculation method are seen to typically overestimate environmental release rates by factors of about 10 and 4, respectively. Where ASTM/ISO or CEPE copper release rate data are used for environmental risk assessment or regulatory purposes, it is proposed that the release rate values should be divided by a correction factor to enable more reliable generic environmental risk assessments to be made. Using a conservative approach based on a realistic worst case and accounting for experimental uncertainty in the data that are currently available, proposed default correction factors for use with all paint types are 5.4 for the ASTM/ISO method and 2.9 for the CEPE calculation method. Further work is required to expand this data-set and refine the correction factors through correlation of laboratory measured and calculated copper release rates with the direct in situ environmental release rate for different antifouling paints under a range of environmental conditions. PMID:17110352

  12. Estimation of alga growth stage and lipid content growth rate

    NASA Technical Reports Server (NTRS)

    Embaye, Tsegereda N. (Inventor); Trent, Jonathan D. (Inventor)

    2012-01-01

    Method and system for estimating a growth stage of an alga in an ambient fluid. Measured light beam absorption or reflection values through or from the alga and through an ambient fluid, in each of two or more wavelength sub-ranges, are compared with reference light beam absorption values for corresponding wavelength sub-ranges for in each alga growth stage to determine (1) which alga growth stage, if any, is more likely and (2) whether estimated lipid content of the alga is increasing or has peaked. Alga growth is preferably terminated when lipid content has approximately reached a maximum value.

  13. Estimation of leakage rates through flexible membrane liners

    SciTech Connect

    Murray, G.B.; McBean, E.A.; Sykes, J.F.

    1995-12-31

    Leakage rate calculations for both low-permeability soil liners and composite liners using flexible membrane liners (FMLs) overlying low-permeability soil are developed. Latin-Hypercube simulations with uncertainty assigned to the soil liner hydraulic conductivity value and the spatial frequency of FML holes are used to examine the variability in the liner leakage rats. The low-permeability soil hydraulic conductivity is the parameter with the greatest effect on landfill liner leakages rates. Composite liners have a significant impact on reducing leakage rates through the landfill liner.

  14. Using genetic data to estimate diffusion rates in heterogeneous landscapes.

    PubMed

    Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

    2016-08-01

    Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation. PMID:26707856

  15. Neuronal Spike Trains and Stochastic Point Processes

    PubMed Central

    Perkel, Donald H.; Gerstein, George L.; Moore, George P.

    1967-01-01

    In a growing class of neurophysiological experiments, the train of impulses (“spikes”) produced by a nerve cell is subjected to statistical treatment involving the time intervals between spikes. The statistical techniques available for the analysis of single spike trains are described and related to the underlying mathematical theory, that of stochastic point processes, i.e., of stochastic processes whose realizations may be described as series of point events occurring in time, separated by random intervals. For single stationary spike trains, several orders of complexity of statistical treatment are described; the major distinction is that between statistical measures that depend in an essential way on the serial order of interspike intervals and those that are order-independent. The interrelations among the several types of calculations are shown, and an attempt is made to ameliorate the current nomenclatural confusion in this field. Applications, interpretations, and potential difficulties of the statistical techniques are discussed, with special reference to types of spike trains encountered experimentally. Next, the related types of analysis are described for experiments which involve repeated presentations of a brief, isolated stimulus. Finally, the effects of nonstationarity, e.g. long-term changes in firing rate, on the various statistical measures are discussed. Several commonly observed patterns of spike activity are shown to be differentially sensitive to such changes. A companion paper covers the analysis of simultaneously observed spike trains. PMID:4292791

  16. ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS

    EPA Science Inventory

    SPARC chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid esters from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external...

  17. SEE Rate Estimation: Model Complexity and Data Requirements

    NASA Technical Reports Server (NTRS)

    Ladbury, Ray

    2008-01-01

    Statistical Methods outlined in [Ladbury, TNS20071 can be generalized for Monte Carlo Rate Calculation Methods Two Monte Carlo Approaches: a) Rate based on vendor-supplied (or reverse-engineered) model SEE testing and statistical analysis performed to validate model; b) Rate calculated based on model fit to SEE data Statistical analysis very similar to case for CREME96. Information Theory allows simultaneous consideration of multiple models with different complexities: a) Model with lowest AIC usually has greatest predictive power; b) Model averaging using AIC weights may give better performance if several models have similar good performance; and c) Rates can be bounded for a given confidence level over multiple models, as well as over the parameter space of a model.

  18. Curve Fitting of the Corporate Recovery Rates: The Comparison of Beta Distribution Estimation and Kernel Density Estimation

    PubMed Central

    Chen, Rongda; Wang, Ze

    2013-01-01

    Recovery rate is essential to the estimation of the portfolio’s loss and economic capital. Neglecting the randomness of the distribution of recovery rate may underestimate the risk. The study introduces two kinds of models of distribution, Beta distribution estimation and kernel density distribution estimation, to simulate the distribution of recovery rates of corporate loans and bonds. As is known, models based on Beta distribution are common in daily usage, such as CreditMetrics by J.P. Morgan, Portfolio Manager by KMV and Losscalc by Moody’s. However, it has a fatal defect that it can’t fit the bimodal or multimodal distributions such as recovery rates of corporate loans and bonds as Moody’s new data show. In order to overcome this flaw, the kernel density estimation is introduced and we compare the simulation results by histogram, Beta distribution estimation and kernel density estimation to reach the conclusion that the Gaussian kernel density distribution really better imitates the distribution of the bimodal or multimodal data samples of corporate loans and bonds. Finally, a Chi-square test of the Gaussian kernel density estimation proves that it can fit the curve of recovery rates of loans and bonds. So using the kernel density distribution to precisely delineate the bimodal recovery rates of bonds is optimal in credit risk management. PMID:23874558

  19. Curve fitting of the corporate recovery rates: the comparison of Beta distribution estimation and kernel density estimation.

    PubMed

    Chen, Rongda; Wang, Ze

    2013-01-01

    Recovery rate is essential to the estimation of the portfolio's loss and economic capital. Neglecting the randomness of the distribution of recovery rate may underestimate the risk. The study introduces two kinds of models of distribution, Beta distribution estimation and kernel density distribution estimation, to simulate the distribution of recovery rates of corporate loans and bonds. As is known, models based on Beta distribution are common in daily usage, such as CreditMetrics by J.P. Morgan, Portfolio Manager by KMV and Losscalc by Moody's. However, it has a fatal defect that it can't fit the bimodal or multimodal distributions such as recovery rates of corporate loans and bonds as Moody's new data show. In order to overcome this flaw, the kernel density estimation is introduced and we compare the simulation results by histogram, Beta distribution estimation and kernel density estimation to reach the conclusion that the Gaussian kernel density distribution really better imitates the distribution of the bimodal or multimodal data samples of corporate loans and bonds. Finally, a Chi-square test of the Gaussian kernel density estimation proves that it can fit the curve of recovery rates of loans and bonds. So using the kernel density distribution to precisely delineate the bimodal recovery rates of bonds is optimal in credit risk management. PMID:23874558

  20. Capture-recapture analysis for estimating manatee reproductive rates

    USGS Publications Warehouse

    Kendall, W.L.; Langtimm, C.A.; Beck, C.A.; Runge, M.C.

    2004-01-01

    Modeling the life history of the endangered Florida manatee (Trichechus manatus latirostris) is an important step toward understanding its population dynamics and predicting its response to management actions. We developed a multi-state mark-resighting model for data collected under Pollock's robust design. This model estimates breeding probability conditional on a female's breeding state in the previous year; assumes sighting probability depends on breeding state; and corrects for misclassification of a cow with first-year calf, by estimating conditional sighting probability for the calf. The model is also appropriate for estimating survival and unconditional breeding probabilities when the study area is closed to temporary emigration across years. We applied this model to photo-identification data for the Northwest and Atlantic Coast populations of manatees, for years 1982?2000. With rare exceptions, manatees do not reproduce in two consecutive years. For those without a first-year calf in the previous year, the best-fitting model included constant probabilities of producing a calf for the Northwest (0.43, SE = 0.057) and Atlantic (0.38, SE = 0.045) populations. The approach we present to adjust for misclassification of breeding state could be applicable to a large number of marine mammal populations.

  1. On Estimation of GPS-based Indonesian Strain Rate Map

    NASA Astrophysics Data System (ADS)

    Susilo, Susilo; Abidin, Hasanuddin Z.; Meilano, Irwan; Sapiie, Benyamin; Wijanarto, Antonius B.

    2016-04-01

    Using the GPS-derived rates at survey mode (sGPS) stations and continuous GPS stations across Indonesian region, covering the 22 years period from 1993 to 2014, the linear deformation velocities with an accuracy of about 2 to 3 mm/year level are derived. These velocities are corrected to the coseismic and postseismic deformation caused by significant earthquakes in that period. In this study, we use this GPS velocities field to construct a crustal strain rate map without including the physical model yet. An interpolation method was used to compute the velocity model. By differentiation of the continuous velocity model, we derive the strain rate map of Indonesia. At present, our result is only the magnitude of the strain rate. The Indonesian strain rate map is very important for studying the deformation characteristics in the region and to establish a deformation (velocity) model for supporting the implementation of the Indonesian Geospatial Reference System 2013 (IGRS 2013). This is a new semi-dynamic geocentric datum of Indonesia, which uses the global ITRF2008 reference frame, with a reference epoch of 1 January 2012. A deformation (velocity) model is required to transform coordinates from an observation epoch to or from this reference epoch.

  2. Estimation of the nucleation rate by differential scanning calorimetry

    NASA Technical Reports Server (NTRS)

    Kelton, Kenneth F.

    1992-01-01

    A realistic computer model is presented for calculating the time-dependent volume fraction transformed during the devitrification of glasses, assuming the classical theory of nucleation and continuous growth. Time- and cluster-dependent nucleation rates are calculated by modeling directly the evolving cluster distribution. Statistical overlap in the volume fraction transformed is taken into account using the standard Johnson-Mehl-Avrami formalism. Devitrification behavior under isothermal and nonisothermal conditions is described. The model is used to demonstrate that the recent suggestion by Ray and Day (1990) that nonisothermal DSC studies can be used to determine the temperature for the peak nucleation rate, is qualitatively correct for lithium disilicate, the glass investigated.

  3. Comparison of electrodialytic removal of Cu from spiked kaolinite, spiked soil and industrially polluted soil.

    PubMed

    Ottosen, Lisbeth M; Lepkova, Katarina; Kubal, Martin

    2006-09-01

    Electrokinetic remediation methods for removal of heavy metals from polluted soils have been subjected for quite intense research during the past years since these methods are well suitable for fine-grained soils where other remediation methods fail. Electrodialytic remediation is an electrokinetic remediation method which is based on applying an electric dc field and the use of ion exchange membranes that ensures the main transport of heavy metals to be out of the pollutes soil. An experimental investigation was made with electrodialytic removal of Cu from spiked kaolinite, spiked soil and industrially polluted soil under the same operational conditions (constant current density 0.2 mA/cm(2) and duration 28 days). The results of the present paper show that caution must be taken when generalising results obtained in spiked kaolinite to remediation of industrially polluted soils, as it was shown that the removal rate was higher in kaolinite than in both spiked soil and industrial polluted soil. The duration of spiking was found to be an important factor too, when attempting to relate remediation of spiked soil or kaolinite to remediation of industrially polluted soils. Spiking for 2 days was too short. However, spiking for 30 days resulted in a pattern that was more similar to that of industrially polluted soils with similar compositions both regarding sequential extraction and electrodialytic remediation result, though the remediation still progressed slightly faster in the spiked soil. Generalisation of remediation results to a variety of soil types must on the other hand be done with caution since the remediation results of different industrially polluted soils were very different. In one soil a total of 76% Cu was removed and in another soil no Cu was removed only redistributed within the soil. The factor with the highest influence on removal success was soil pH, which must be low in order to mobilize Cu, and thus the buffering capacity against acidification was

  4. Rating Curve Estimation from Local Levels and Upstream Discharges

    NASA Astrophysics Data System (ADS)

    Franchini, M.; Mascellani, G.

    2003-04-01

    Current technology allows for low cost and easy level measurements while the discharge measurements are still difficult and expensive. Thus, these are rarely performed and usually not in flood conditions because of lack of safety and difficulty in activating the measurement team in due time. As a consequence, long series of levels are frequently available without the corresponding discharge values. However, for the purpose of planning, management of water resources and real time flood forecasting, discharge is needed and it is therefore essential to convert local levels into discharge values by using the appropriate rating curve. Over this last decade, several methods have been proposed to relate local levels at a site of interest to data recorded at a river section located upstream where a rating curve is available. Some of these methods are based on a routing approach which uses the Muskingum model structure in different ways; others are based on the entropy concepts. Lately, fuzzy logic has been applied more and more frequently in the framework of hydraulic and hydrologic problems and this has prompted to the authors to use it for synthesising the rating curves. A comparison between all these strategies is performed, highlighting the difficulties and advantages of each of them, with reference to a long reach of the Po river in Italy, where several hydrometers and the relevant rating curves are available, thus allowing for both a parameterization and validation of the different strategies.

  5. Modeled Estimates of Soil and Dust Ingestion Rates for Children

    EPA Science Inventory

    Daily soil/dust ingestion rates typically used in exposure and risk assessments are based on tracer element studies, which have a number of limitations and do not separate contributions from soil and dust. This article presents an alternate approach of modeling soil and dust inge...

  6. Time-dependent estimates of molecular evolutionary rates: evidence and causes.

    PubMed

    Ho, Simon Y W; Duchêne, Sebastián; Molak, Martyna; Shapiro, Beth

    2015-12-01

    We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates. PMID:26769402

  7. Frame rate up conversion via Bayesian motion estimation

    NASA Astrophysics Data System (ADS)

    Wang, Yue; Ma, Siwei; Gao, Wen

    2010-07-01

    In this paper, a novel block-based motion compensated frame interpolation (MCI) algorithm is proposed to enhance the temporal resolution of video sequences. We formulated motion estimation into MAP framework, and solved it via Bayesian belief propagation. By effectively incorporating a priori knowledge of the motion field and optimizing the whole motion field synchronously, it could derive more accurate motion vectors than traditional methods. Finally, adaptive overlapped block motion compensation (OBMC) is used to reduce blocking artifacts. Experimental results show that the proposed method outperforms other methods in both objective and subjective quality.

  8. Continuous functions determined by spike trains of a neuron subject to stimulation.

    PubMed

    Awiszus, F

    1988-01-01

    Several ways of estimating a continuous function from the spike train output of a neuron subjected to repeated stimuli are compared: (i) the probability of firing function estimated by a PST-histogram (ii) the rate of discharge function estimated by a "frequencygram" (Bessou et al. 1968) and (iii) the interspike-interval function which is introduced in this paper. For a special class of neuronal responses, called deterministic, these functions may be expressed in terms of each other. It is shown that the current clamped Hodgkin-Huxley model of an action potential encoding membrane (Hodgkin and Huxley 1952) is able to generate such deterministic responses. As an experimental example, a deterministic response of a primary muscle spindle afferent is used to demonstrate the estimation of the functions. Interpretability and numerical estimatability of these spike train describing functions are discussed for deterministic neuronal responses. PMID:3382703

  9. Population trend of the Yellowstone grizzly bear as estimated from reproductive and survival rates

    USGS Publications Warehouse

    Eberhardt, L. L.; Blanchard, B. M.; Knight, R. R.

    1993-01-01

    The trend of the Yellowstone grizzly bear (Ursus arctos horribilis) population was estimated using reproductive rates calculated from 22 individual females and survival rates from 400 female bear-years. The point estimate of the rate of increase was 4.6%, with 95% confidence limits of 0 and 9%. Caution in interpreting this result is advised because of possible biases in the population parameter estimates. The main prospects for improving present knowledge of the population trend appear to be further study of possible biases in the parameter estimates, and the continued use of radiotelemetry to increase the number of samples on which the estimates are based.

  10. Occupational Injury Rate Estimates in Magnetic Fusion Experiments

    SciTech Connect

    cadwallader, lee

    2006-11-01

    In nuclear facilities, there are two primary aspects of occupational safety. The first aspect is radiological safety, which has rightly been treated in detail in nuclear facilities. Radiological exposure data have been collected from the existing tokamaks to serve as forecasts for ITER radiation safety. The second aspect of occupational safety, “traditional” industrial safety, must also be considered for a complete occupational safety program. Industrial safety data on occupational injury rates from the JET and TFTR tokamaks, three accelerators, and U.S. nuclear fission plants have been collected to set industrial safety goals for the ITER operations staff. The results of this occupational safety data collection and analysis activity are presented here. The data show that an annual lost workday case rate of 0.3 incidents per 100 workers is a conceivable goal for ITER operations.

  11. Estimation of Eddy Dissipation Rates from Mesoscale Model Simulations

    NASA Technical Reports Server (NTRS)

    Ahmad, Nashat N.; Proctor, Fred H.

    2012-01-01

    The Eddy Dissipation Rate is an important metric for representing the intensity of atmospheric turbulence and is used as an input parameter for predicting the decay of aircraft wake vortices. In this study, the forecasts of eddy dissipation rates obtained from the current state-of-the-art mesoscale model are evaluated for terminal area applications. The Weather Research and Forecast mesoscale model is used to simulate the planetary boundary layer at high horizontal and vertical mesh resolutions. The Bougeault-Lacarrer and the Mellor-Yamada-Janji schemes implemented in the Weather Research and Forecast model are evaluated against data collected during the National Aeronautics and Space Administration s Memphis Wake Vortex Field Experiment. Comparisons with other observations are included as well.

  12. Temporal Correlations and Neural Spike Train Entropy

    SciTech Connect

    Schultz, Simon R.; Panzeri, Stefano

    2001-06-18

    Sampling considerations limit the experimental conditions under which information theoretic analyses of neurophysiological data yield reliable results. We develop a procedure for computing the full temporal entropy and information of ensembles of neural spike trains, which performs reliably for limited samples of data. This approach also yields insight to the role of correlations between spikes in temporal coding mechanisms. The method, when applied to recordings from complex cells of the monkey primary visual cortex, results in lower rms error information estimates in comparison to a {open_quotes}brute force{close_quotes} approach.

  13. Estimation of the mass outflow rates around rotating black holes

    NASA Astrophysics Data System (ADS)

    Aktar, Ramiz; Das, Santabrata

    We consider steady, advective, rotating, inviscid accretion disc around the spinning black holes to compute the mass outflow rate (R_{dot{m}}) defined as the ratio of mass flux of outflowing to the inflowing matter. Due to centrifugal barrier, accreting matter suffers discontinuous shock transition and because of shock compression, the post-shock matter becomes hot and denser than the pre-shock matter. We call the post-shock disc as Post Shock Corona (PSC). During accretion, a part of the inflowing matter deflects as bipolar outflows due to the presence of excess thermal gradient force at PSC. We find that R_{dot{m}}is directly correlated with the spin of the black hole (a_{k}) for the same set of inflow parameter, namely specific energy (E) and specific angular momentum (λ). We observe that the maximum outflow rate(R_{dot{m}}^{max}) weakly depends on spin (a_{k}) that lies in the range˜ 17% - 18% of the inflow rate.

  14. Estimating division and death rates from CFSE data

    NASA Astrophysics Data System (ADS)

    de Boer, Rob J.; Perelson, Alan S.

    2005-12-01

    The division tracking dye, carboxyfluorescin diacetate succinimidyl ester (CFSE) is currently the most informative labeling technique for characterizing the division history of cells in the immune system. Gett and Hodgkin (Nat. Immunol. 1 (2000) 239-244) have proposed to normalize CFSE data by the 2-fold expansion that is associated with each division, and have argued that the mean of the normalized data increases linearly with time, t, with a slope reflecting the division rate p. We develop a number of mathematical models for the clonal expansion of quiescent cells after stimulation and show, within the context of these models, under which conditions this approach is valid. We compare three means of the distribution of cells over the CFSE profile at time t: the mean, [mu](t), the mean of the normalized distribution, [mu]2(t), and the mean of the normalized distribution excluding nondivided cells, .In the simplest models, which deal with homogeneous populations of cells with constant division and death rates, the normalized frequency distribution of the cells over the respective division numbers is a Poisson distribution with mean [mu]2(t)=pt, where p is the division rate. The fact that in the data these distributions seem Gaussian is therefore insufficient to establish that the times at which cells are recruited into the first division have a Gaussian variation because the Poisson distribution approaches the Gaussian distribution for large pt. Excluding nondivided cells complicates the data analysis because , and only approaches a slope p after an initial transient.In models where the first division of the quiescent cells takes longer than later divisions, all three means have an initial transient before they approach an asymptotic regime, which is the expected [mu](t)=2pt and . Such a transient markedly complicates the data analysis. After the same initial transients, the normalized cell numbers tend to decrease at a rate e-dt, where d is the death rate

  15. Estimate of avoidance maneuver rate for HASTOL tether boost facility

    NASA Astrophysics Data System (ADS)

    Forward, Robert L.

    2002-01-01

    The Hypersonic Airplane Space Tether Orbital Launch (HASTOL) Architecture uses a hypersonic airplane (or reusable launch vehicle) to carry a payload from the surface of the Earth to 150 km altitude and a speed of Mach 17. The hypersonic airplane makes a rendezvous with the grapple at the tip of a long, rotating, orbiting space tether boost facility, which picks up the payload from the airplane. Release of the payload at the proper point in the tether rotation boosts the payload into a higher orbit, typically into a Geosynchronous Transfer Orbit (GTO), with lower orbits and Earth escape other options. The HASTOL Tether Boost Facility will have a length of 636 km. Its center of mass will be in a 604 km by 890 km equatorial orbit. It is estimated that by the time of the start of operations of the HASTOL Tether Boost facility in the year 2020, there will be 500 operational spacecraft using the same volume of space as the HASTOL facility. These operational spacecraft would likely be made inoperative by an impact with one of the lines in the multiline HASTOL Hoytether™ and should be avoided. There will also be non-operational spacecraft and large pieces of orbital debris with effective size greater than five meters in diameter that could cut a number of lines in the HASTOL Hoytether™, and should also be avoided. It is estimated, using two different methods and combining them, that the HASTOL facility will need to make avoidance maneuvers about once every four days if the 500 operational spacecraft and large pieces of orbital debris greater than 5 m in diameter, were each protected by a 2 km diameter miss distance protection sphere. If by 2020, the ability to know the positions of operational spacecraft and large pieces of orbital debris improved to allow a 600 m diameter miss distance protection sphere around each object, then the number of HASTOL facility maneuvers needed drops to one every two weeks. .

  16. Impact of spike train autostructure on probability distribution of joint spike events.

    PubMed

    Pipa, Gordon; Grün, Sonja; van Vreeswijk, Carl

    2013-05-01

    The discussion whether temporally coordinated spiking activity really exists and whether it is relevant has been heated over the past few years. To investigate this issue, several approaches have been taken to determine whether synchronized events occur significantly above chance, that is, whether they occur more often than expected if the neurons fire independently. Most investigations ignore or destroy the autostructure of the spiking activity of individual cells or assume Poissonian spiking as a model. Such methods that ignore the autostructure can significantly bias the coincidence statistics. Here, we study the influence of the autostructure on the probability distribution of coincident spiking events between tuples of mutually independent non-Poisson renewal processes. In particular, we consider two types of renewal processes that were suggested as appropriate models of experimental spike trains: a gamma and a log-normal process. For a gamma process, we characterize the shape of the distribution analytically with the Fano factor (FFc). In addition, we perform Monte Carlo estimations to derive the full shape of the distribution and the probability for false positives if a different process type is assumed as was actually present. We also determine how manipulations of such spike trains, here dithering, used for the generation of surrogate data change the distribution of coincident events and influence the significance estimation. We find, first, that the width of the coincidence count distribution and its FFc depend critically and in a nontrivial way on the detailed properties of the structure of the spike trains as characterized by the coefficient of variation CV. Second, the dependence of the FFc on the CV is complex and mostly nonmonotonic. Third, spike dithering, even if as small as a fraction of the interspike interval, can falsify the inference on coordinated firing. PMID:23470124

  17. Uncertainty in silicate mineral weathering rate estimates: source partitioning and policy implications

    NASA Astrophysics Data System (ADS)

    Futter, M. N.; Klaminder, J.; Lucas, R. W.; Laudon, H.; Köhler, S. J.

    2012-06-01

    Precise and accurate estimates of silicate mineral weathering rates are crucial when setting policy targets for long-term forest sustainability, critical load calculations and assessing consequences of proposed geo-engineering solutions to climate change. In this paper, we scrutinize 394 individual silicate mineral weathering estimates from 82 sites on three continents. We show that within-site differences of several hundred per cent arise when different methods are used to estimate weathering rates, mainly as a result of uncertainties related to input data rather than conceptually different views of the weathering process. While different methods tend to rank sites congruently from high to low weathering rates, large within-site differences in estimated weathering rate suggest that policies relying on quantitative estimates based upon a single method may have undesirable outcomes. We recommend the use of at least three independent estimates when making management decisions related to silicate mineral weathering rates.

  18. Infrared imaging based hyperventilation monitoring through respiration rate estimation

    NASA Astrophysics Data System (ADS)

    Basu, Anushree; Routray, Aurobinda; Mukherjee, Rashmi; Shit, Suprosanna

    2016-07-01

    A change in the skin temperature is used as an indicator of physical illness which can be detected through infrared thermography. Thermograms or thermal images can be used as an effective diagnostic tool for monitoring and diagnosis of various diseases. This paper describes an infrared thermography based approach for detecting hyperventilation caused due to stress and anxiety in human beings by computing their respiration rates. The work employs computer vision techniques for tracking the region of interest from thermal video to compute the breath rate. Experiments have been performed on 30 subjects. Corner feature extraction using Minimum Eigenvalue (Shi-Tomasi) algorithm and registration using Kanade Lucas-Tomasi algorithm has been used here. Thermal signature around the extracted region is detected and subsequently filtered through a band pass filter to compute the respiration profile of an individual. If the respiration profile shows unusual pattern and exceeds the threshold we conclude that the person is stressed and tending to hyperventilate. Results obtained are compared with standard contact based methods which have shown significant correlations. It is envisaged that the thermal image based approach not only will help in detecting hyperventilation but can assist in regular stress monitoring as it is non-invasive method.

  19. Decision tree rating scales for workload estimation: Theme and variations

    NASA Technical Reports Server (NTRS)

    Wierwille, W. W.; Skipper, J. H.; Rieger, C. A.

    1984-01-01

    The Modified Cooper-Harper (MCH) scale which is a sensitive indicator of workload in several different types of aircrew tasks was examined. The study determined if variations of the scale might provide greater sensitivity and the reasons for the sensitivity of the scale. The MCH scale and five newly devised scales were examined in two different aircraft simulator experiments in which pilot loading was treated as an independent variable. It is indicated that while one of the new scales may be more sensitive in a given experiment, task dependency is a problem. The MCH scale exhibits consistent senstivity and remains the scale recommended for general use. The MCH scale results are consistent with earlier experiments. The rating scale experiments are reported and the questionnaire results which were directed to obtain a better understanding of the reasons for the relative sensitivity of the MCH scale and its variations are described.

  20. Decision Tree Rating Scales for Workload Estimation: Theme and Variations

    NASA Technical Reports Server (NTRS)

    Wietwille, W. W.; Skipper, J. H.; Rieger, C. A.

    1984-01-01

    The modified Cooper-Harper (MCH) scale has been shown to be a sensitive indicator of workload in several different types of aircrew tasks. The MCH scale was examined to determine if certain variations of the scale might provide even greater sensitivity and to determine the reasons for the sensitivity of the scale. The MCH scale and five newly devised scales were studied in two different aircraft simulator experiments in which pilot loading was treated as an independent variable. Results indicate that while one of the new scales may be more sensitive in a given experiment, task dependency is a problem. The MCH scale exhibits consistent sensitivity and remains the scale recommended for general use. The results of the rating scale experiments are presented and the questionnaire results which were directed at obtaining a better understanding of the reasons for the relative sensitivity of the MCH scale and its variations are described.

  1. Estimating taxonomic diversity, extinction rates, and speciation rates from fossil data using capture-recapture models

    USGS Publications Warehouse

    Nichols, J.D.; Pollock, K.H.

    1983-01-01

    Capture-recapture models can be used to estimate parameters of interest from paleobiological data when encouter probabilities are unknown and variable over time. These models also permit estimation of sampling variances and goodness-of-fit tests are available for assessing the fit of data to most models. The authors describe capture-recapture models which should be useful in paleobiological analyses and discuss the assumptions which underlie them. They illustrate these models with examples and discuss aspects of study design.

  2. Estimation of unemployment rates using small area estimation model by combining time series and cross-sectional data

    NASA Astrophysics Data System (ADS)

    Muchlisoh, Siti; Kurnia, Anang; Notodiputro, Khairil Anwar; Mangku, I. Wayan

    2016-02-01

    Labor force surveys conducted over time by the rotating panel design have been carried out in many countries, including Indonesia. Labor force survey in Indonesia is regularly conducted by Statistics Indonesia (Badan Pusat Statistik-BPS) and has been known as the National Labor Force Survey (Sakernas). The main purpose of Sakernas is to obtain information about unemployment rates and its changes over time. Sakernas is a quarterly survey. The quarterly survey is designed only for estimating the parameters at the provincial level. The quarterly unemployment rate published by BPS (official statistics) is calculated based on only cross-sectional methods, despite the fact that the data is collected under rotating panel design. The study purpose to estimate a quarterly unemployment rate at the district level used small area estimation (SAE) model by combining time series and cross-sectional data. The study focused on the application and comparison between the Rao-Yu model and dynamic model in context estimating the unemployment rate based on a rotating panel survey. The goodness of fit of both models was almost similar. Both models produced an almost similar estimation and better than direct estimation, but the dynamic model was more capable than the Rao-Yu model to capture a heterogeneity across area, although it was reduced over time.

  3. Spiking optical patterns and synchronization

    NASA Astrophysics Data System (ADS)

    Rosenbluh, Michael; Aviad, Yaara; Cohen, Elad; Khaykovich, Lev; Kinzel, Wolfgang; Kopelowitz, Evi; Yoskovits, Pinhas; Kanter, Ido

    2007-10-01

    We analyze the time resolved spike statistics of a solitary and two mutually interacting chaotic semiconductor lasers whose chaos is characterized by apparently random, short intensity spikes. Repulsion between two successive spikes is observed, resulting in a refractory period, which is largest at laser threshold. For time intervals between spikes greater than the refractory period, the distribution of the intervals follows a Poisson distribution. The spiking pattern is highly periodic over time windows corresponding to the optical length of the external cavity, with a slow change of the spiking pattern as time increases. When zero-lag synchronization between two lasers is established, the statistics of the nearly perfectly matched spikes are not altered. The similarity of these features to those found in complex interacting neural networks, suggests the use of laser systems as simpler physical models for neural networks.

  4. ESTIMATING THE RATE OF PLASMID TRANSFER: AN END-POINT METHOD

    EPA Science Inventory

    A method is described for determining rate parameter of conjugative plasmid transfer that is based on single estimates of donor, recipient and transconjugant densities, and the growth rate in exponential phase of the mating culture. he formula for estimating the plasmid transfer ...

  5. Spike-Timing Theory of Working Memory

    PubMed Central

    Szatmáry, Botond; Izhikevich, Eugene M.

    2010-01-01

    Working memory (WM) is the part of the brain's memory system that provides temporary storage and manipulation of information necessary for cognition. Although WM has limited capacity at any given time, it has vast memory content in the sense that it acts on the brain's nearly infinite repertoire of lifetime long-term memories. Using simulations, we show that large memory content and WM functionality emerge spontaneously if we take the spike-timing nature of neuronal processing into account. Here, memories are represented by extensively overlapping groups of neurons that exhibit stereotypical time-locked spatiotemporal spike-timing patterns, called polychronous patterns; and synapses forming such polychronous neuronal groups (PNGs) are subject to associative synaptic plasticity in the form of both long-term and short-term spike-timing dependent plasticity. While long-term potentiation is essential in PNG formation, we show how short-term plasticity can temporarily strengthen the synapses of selected PNGs and lead to an increase in the spontaneous reactivation rate of these PNGs. This increased reactivation rate, consistent with in vivo recordings during WM tasks, results in high interspike interval variability and irregular, yet systematically changing, elevated firing rate profiles within the neurons of the selected PNGs. Additionally, our theory explains the relationship between such slowly changing firing rates and precisely timed spikes, and it reveals a novel relationship between WM and the perception of time on the order of seconds. PMID:20808877

  6. Two Approaches to Estimation of Classification Accuracy Rate under Item Response Theory

    ERIC Educational Resources Information Center

    Lathrop, Quinn N.; Cheng, Ying

    2013-01-01

    Within the framework of item response theory (IRT), there are two recent lines of work on the estimation of classification accuracy (CA) rate. One approach estimates CA when decisions are made based on total sum scores, the other based on latent trait estimates. The former is referred to as the Lee approach, and the latter, the Rudner approach,…

  7. Spiking models for level-invariant encoding.

    PubMed

    Brette, Romain

    2011-01-01

    Levels of ecological sounds vary over several orders of magnitude, but the firing rate and membrane potential of a neuron are much more limited in range. In binaural neurons of the barn owl, tuning to interaural delays is independent of level differences. Yet a monaural neuron with a fixed threshold should fire earlier in response to louder sounds, which would disrupt the tuning of these neurons. How could spike timing be independent of input level? Here I derive theoretical conditions for a spiking model to be insensitive to input level. The key property is a dynamic change in spike threshold. I then show how level invariance can be physiologically implemented, with specific ionic channel properties. It appears that these ingredients are indeed present in monaural neurons of the sound localization pathway of birds and mammals. PMID:22291634

  8. Advantages of estimating rate corrections during dynamic propagation of spacecraft rates: Applications to real-time attitude determination of SAMPEX

    NASA Technical Reports Server (NTRS)

    Challa, M. S.; Natanson, G. A.; Baker, D. F.; Deutschmann, J. K.

    1994-01-01

    This paper describes real-time attitude determination results for the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX), a gyroless spacecraft, using a Kalman filter/Euler equation approach denoted the real-time sequential filter (RTSF). The RTSF is an extended Kalman filter whose state vector includes the attitude quaternion and corrections to the rates, which are modeled as Markov processes with small time constants. The rate corrections impart a significant robustness to the RTSF against errors in modeling the environmental and control torques, as well as errors in the initial attitude and rates, while maintaining a small state vector. SAMPLEX flight data from various mission phases are used to demonstrate the robustness of the RTSF against a priori attitude and rate errors of up to 90 deg and 0.5 deg/sec, respectively, as well as a sensitivity of 0.0003 deg/sec in estimating rate corrections in torque computations. In contrast, it is shown that the RTSF attitude estimates without the rate corrections can degrade rapidly. RTSF advantages over single-frame attitude determination algorithms are also demonstrated through (1) substantial improvements in attitude solutions during sun-magnetic field coalignment and (2) magnetic-field-only attitude and rate estimation during the spacecraft's sun-acquisition mode. A robust magnetometer-only attitude-and-rate determination method is also developed to provide for the contingency when both sun data as well as a priori knowledge of the spacecraft state are unavailable. This method includes a deterministic algorithm used to initialize the RTSF with coarse estimates of the spacecraft attitude and rates. The combined algorithm has been found effective, yielding accuracies of 1.5 deg in attitude and 0.01 deg/sec in the rates and convergence times as little as 400 sec.

  9. Estimating respiratory rate from FBG optical sensors by using signal quality measurement.

    PubMed

    Yongwei Zhu; Maniyeri, Jayachandran; Fook, Victor Foo Siang; Haihong Zhang

    2015-08-01

    Non-intrusiveness is one of the advantages of in-bed optical sensor device for monitoring vital signs, including heart rate and respiratory rate. Estimating respiratory rate reliably using such sensors, however, is challenging, due to body movement, signal variation according to different subjects or body positions, etc. This paper presents a method for reliable respiratory rate estimation for FBG optical sensors by introducing signal quality estimation. The method estimates the quality of the signal waveform by detecting regularly repetitive patterns using proposed spectrum and cepstrum analysis. Multiple window sizes are used to cater for a wide range of target respiratory rates. Furthermore, the readings of multiple sensors are fused to derive a final respiratory rate. Experiments with 12 subjects and 2 body positions were conducted using polysomnography belt signal as groundtruth. The results demonstrated the effectiveness of the method. PMID:26736396

  10. The Estimation and Control of the Electroslag Remelting Melt Rate by Mechanism-Based Modeling

    NASA Astrophysics Data System (ADS)

    Li, Wanzhou; Wang, Weiyu; Hu, Yuechen; Chen, Yixing

    2012-04-01

    The process control of industrial electroslag remelting production is addressed in this work. This article proposes a mechanism-based model using electrode displacement to estimate the melt rate, designs the remelting process control system, and uses practical application data to verify the validity of the model. The soft measurement of the melt rate based on mechanism modeling is proved to be an economical and reliable solution to the online melt rate estimation and control for large industrial electroslag remelting furnaces.

  11. Spiking Neurons for Analysis of Patterns

    NASA Technical Reports Server (NTRS)

    Huntsberger, Terrance

    2008-01-01

    neurons). These features enable the neurons to adapt their responses to high-rate inputs from sensors, and to adapt their firing thresholds to mitigate noise or effects of potential sensor failure. The mathematical derivation of the SVM starts from a prior model, known in the art as the point soma model, which captures all of the salient properties of neuronal response while keeping the computational cost low. The point-soma latency time is modified to be an exponentially decaying function of the strength of the applied potential. Choosing computational efficiency over biological fidelity, the dendrites surrounding a neuron are represented by simplified compartmental submodels and there are no dendritic spines. Updates to the dendritic potential, calcium-ion concentrations and conductances, and potassium-ion conductances are done by use of equations similar to those of the point soma. Diffusion processes in dendrites are modeled by averaging among nearest-neighbor compartments. Inputs to each of the dendritic compartments come from sensors. Alternatively or in addition, when an affected neuron is part of a pool, inputs can come from other spiking neurons. At present, SVM neural networks are implemented by computational simulation, using algorithms that encode the SVM and its submodels. However, it should be possible to implement these neural networks in hardware: The differential equations for the dendritic and cellular processes in the SVM model of spiking neurons map to equivalent circuits that can be implemented directly in analog very-large-scale integrated (VLSI) circuits.

  12. Solving Constraint Satisfaction Problems with Networks of Spiking Neurons.

    PubMed

    Jonke, Zeno; Habenschuss, Stefan; Maass, Wolfgang

    2016-01-01

    Network of neurons in the brain apply-unlike processors in our current generation of computer hardware-an event-based processing strategy, where short pulses (spikes) are emitted sparsely by neurons to signal the occurrence of an event at a particular point in time. Such spike-based computations promise to be substantially more power-efficient than traditional clocked processing schemes. However, it turns out to be surprisingly difficult to design networks of spiking neurons that can solve difficult computational problems on the level of single spikes, rather than rates of spikes. We present here a new method for designing networks of spiking neurons via an energy function. Furthermore, we show how the energy function of a network of stochastically firing neurons can be shaped in a transparent manner by composing the networks of simple stereotypical network motifs. We show that this design approach enables networks of spiking neurons to produce approximate solutions to difficult (NP-hard) constraint satisfaction problems from the domains of planning/optimization and verification/logical inference. The resulting networks employ noise as a computational resource. Nevertheless, the timing of spikes plays an essential role in their computations. Furthermore, networks of spiking neurons carry out for the Traveling Salesman Problem a more efficient stochastic search for good solutions compared with stochastic artificial neural networks (Boltzmann machines) and Gibbs sampling. PMID:27065785

  13. Solving Constraint Satisfaction Problems with Networks of Spiking Neurons

    PubMed Central

    Jonke, Zeno; Habenschuss, Stefan; Maass, Wolfgang

    2016-01-01

    Network of neurons in the brain apply—unlike processors in our current generation of computer hardware—an event-based processing strategy, where short pulses (spikes) are emitted sparsely by neurons to signal the occurrence of an event at a particular point in time. Such spike-based computations promise to be substantially more power-efficient than traditional clocked processing schemes. However, it turns out to be surprisingly difficult to design networks of spiking neurons that can solve difficult computational problems on the level of single spikes, rather than rates of spikes. We present here a new method for designing networks of spiking neurons via an energy function. Furthermore, we show how the energy function of a network of stochastically firing neurons can be shaped in a transparent manner by composing the networks of simple stereotypical network motifs. We show that this design approach enables networks of spiking neurons to produce approximate solutions to difficult (NP-hard) constraint satisfaction problems from the domains of planning/optimization and verification/logical inference. The resulting networks employ noise as a computational resource. Nevertheless, the timing of spikes plays an essential role in their computations. Furthermore, networks of spiking neurons carry out for the Traveling Salesman Problem a more efficient stochastic search for good solutions compared with stochastic artificial neural networks (Boltzmann machines) and Gibbs sampling. PMID:27065785

  14. Maximum likelihood estimation of population growth rates based on the coalescent.

    PubMed Central

    Kuhner, M K; Yamato, J; Felsenstein, J

    1998-01-01

    We describe a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus. PMID:9584114

  15. Child Mortality Estimation: Consistency of Under-Five Mortality Rate Estimates Using Full Birth Histories and Summary Birth Histories

    PubMed Central

    Silva, Romesh

    2012-01-01

    Background Given the lack of complete vital registration data in most developing countries, for many countries it is not possible to accurately estimate under-five mortality rates from vital registration systems. Heavy reliance is often placed on direct and indirect methods for analyzing data collected from birth histories to estimate under-five mortality rates. Yet few systematic comparisons of these methods have been undertaken. This paper investigates whether analysts should use both direct and indirect estimates from full birth histories, and under what circumstances indirect estimates derived from summary birth histories should be used. Methods and Findings Usings Demographic and Health Surveys data from West Africa, East Africa, Latin America, and South/Southeast Asia, I quantify the differences between direct and indirect estimates of under-five mortality rates, analyze data quality issues, note the relative effects of these issues, and test whether these issues explain the observed differences. I find that indirect estimates are generally consistent with direct estimates, after adjustment for fertility change and birth transference, but don't add substantial additional insight beyond direct estimates. However, choice of direct or indirect method was found to be important in terms of both the adjustment for data errors and the assumptions made about fertility. Conclusions Although adjusted indirect estimates are generally consistent with adjusted direct estimates, some notable inconsistencies were observed for countries that had experienced either a political or economic crisis or stalled health transition in their recent past. This result suggests that when a population has experienced a smooth mortality decline or only short periods of excess mortality, both adjusted methods perform equally well. However, the observed inconsistencies identified suggest that the indirect method is particularly prone to bias resulting from violations of its strong

  16. Radioxenon spiked air.

    PubMed

    Watrous, Matthew G; Delmore, James E; Hague, Robert K; Houghton, Tracy P; Jenson, Douglas D; Mann, Nick R

    2015-12-01

    Four of the radioactive xenon isotopes ((131m)Xe, (133m)Xe, (133)Xe and (135)Xe) with half-lives ranging from 9 h to 12 days are produced from nuclear fission and can be detected from days to weeks following their production and release. Being inert gases, they are readily transported through the atmosphere. Sources for release of radioactive xenon isotopes include operating nuclear reactors via leaks in fuel rods, medical isotope production facilities, and nuclear weapons' detonations. They are not normally released from fuel reprocessing due to the short half-lives. The Comprehensive Nuclear-Test-Ban Treaty has led to creation of the International Monitoring System. The International Monitoring System, when fully implemented, will consist of one component with 40 stations monitoring radioactive xenon around the globe. Monitoring these radioactive xenon isotopes is important to the Comprehensive Nuclear-Test-Ban Treaty in determining whether a seismically detected event is or is not a nuclear detonation. A variety of radioactive xenon quality control check standards, quantitatively spiked into various gas matrices, could be used to demonstrate that these stations are operating on the same basis in order to bolster defensibility of data across the International Monitoring System. This paper focuses on Idaho National Laboratory's capability to produce three of the xenon isotopes in pure form and the use of the four xenon isotopes in various combinations to produce radioactive xenon spiked air samples that could be subsequently distributed to participating facilities. PMID:26318775

  17. Radioxenon spiked air

    DOE PAGESBeta

    Watrous, Matthew G.; Delmore, James E.; Hague, Robert K.; Houghton, Tracy P.; Jenson, Douglas D.; Mann, Nick R.

    2015-08-27

    Four of the radioactive xenon isotopes (131mXe, 133mXe, 133Xe and 135Xe) with half-lives ranging from 9 h to 12 days are produced from nuclear fission and can be detected from days to weeks following their production and release. Being inert gases, they are readily transported through the atmosphere. Sources for release of radioactive xenon isotopes include operating nuclear reactors via leaks in fuel rods, medical isotope production facilities, and nuclear weapons' detonations. They are not normally released from fuel reprocessing due to the short half-lives. The Comprehensive Nuclear-Test-Ban Treaty has led to creation of the International Monitoring System. The Internationalmore » Monitoring System, when fully implemented, will consist of one component with 40 stations monitoring radioactive xenon around the globe. Monitoring these radioactive xenon isotopes is important to the Comprehensive Nuclear-Test-Ban Treaty in determining whether a seismically detected event is or is not a nuclear detonation. A variety of radioactive xenon quality control check standards, quantitatively spiked into various gas matrices, could be used to demonstrate that these stations are operating on the same basis in order to bolster defensibility of data across the International Monitoring System. This study focuses on Idaho National Laboratory's capability to produce three of the xenon isotopes in pure form and the use of the four xenon isotopes in various combinations to produce radioactive xenon spiked air samples that could be subsequently distributed to participating facilities.« less

  18. Effects of tag loss on direct estimates of population growth rate

    USGS Publications Warehouse

    Rotella, J.J.; Hines, J.E.

    2005-01-01

    The temporal symmetry approach of R. Pradel can be used with capture-recapture data to produce retrospective estimates of a population's growth rate, lambda(i), and the relative contributions to lambda(i) from different components of the population. Direct estimation of lambda(i) provides an alternative to using population projection matrices to estimate asymptotic lambda and is seeing increased use. However, the robustness of direct estimates of lambda(1) to violations of several key assumptions has not yet been investigated. Here, we consider tag loss as a possible source of bias for scenarios in which the rate of tag loss is (1) the same for all marked animals in the population and (2) a function of tag age. We computed analytic approximations of the expected values for each of the parameter estimators involved in direct estimation and used those values to calculate bias and precision for each parameter estimator. Estimates of lambda(i) were robust to homogeneous rates of tag loss. When tag loss rates varied by tag age, bias occurred for some of the sampling situations evaluated, especially those with low capture probability, a high rate of tag loss, or both. For situations with low rates of tag loss and high capture probability, bias was low and often negligible. Estimates of contributions of demographic components to lambda(i) were not robust to tag loss. Tag loss reduced the precision of all estimates because tag loss results in fewer marked animals remaining available for estimation. Clearly tag loss should be prevented if possible, and should be considered in analyses of lambda(i), but tag loss does not necessarily preclude unbiased estimation of lambda(i).

  19. Markov models and the ensemble Kalman filter for estimation of sorption rates.

    SciTech Connect

    Vugrin, Eric D.; McKenna, Sean Andrew; Vugrin, Kay White

    2007-09-01

    Non-equilibrium sorption of contaminants in ground water systems is examined from the perspective of sorption rate estimation. A previously developed Markov transition probability model for solute transport is used in conjunction with a new conditional probability-based model of the sorption and desorption rates based on breakthrough curve data. Two models for prediction of spatially varying sorption and desorption rates along a one-dimensional streamline are developed. These models are a Markov model that utilizes conditional probabilities to determine the rates and an ensemble Kalman filter (EnKF) applied to the conditional probability method. Both approaches rely on a previously developed Markov-model of mass transfer, and both models assimilate the observed concentration data into the rate estimation at each observation time. Initial values of the rates are perturbed from the true values to form ensembles of rates and the ability of both estimation approaches to recover the true rates is examined over three different sets of perturbations. The models accurately estimate the rates when the mean of the perturbations are zero, the unbiased case. For the cases containing some bias, addition of the ensemble Kalman filter is shown to improve accuracy of the rate estimation by as much as an order of magnitude.

  20. Direct Magnitude Estimation of Articulation Rate in Boys with Fragile X Syndrome

    ERIC Educational Resources Information Center

    Zajac, David J.; Harris, Adrianne A.; Roberts, Joanne E.; Martin, Gary E.

    2009-01-01

    Purpose: To compare the perceived articulation rate of boys with fragile X syndrome (FXS) with that of chronologically age-matched (CA) boys and to determine segmental and/or prosodic factors that account for perceived rate. Method: Ten listeners used direct magnitude estimation procedures to judge the articulation rates of 7 boys with FXS only, 5…

  1. NATURAL VOLATILE ORGANIC COMPOUND EMISSION RATE ESTIMATES FOR U.S. WOODLAND LANDSCAPES

    EPA Science Inventory

    Volatile organic compound (VOC) emission rate factors are estimated for 49 tree genera based on a review of foliar emission rate measurements. oliar VOC emissions are grouped into three categories: isoprene, monoterpenes and other VOC'S. ypical emission rates at a leaf temperatur...

  2. A computer program for estimating fish population sizes and annual production rates

    SciTech Connect

    Railsback, S.F.; Holcomb, B.D.; Ryon, M.G.

    1989-10-01

    This report documents a program that estimates fish population sizes and annual production rates in small streams from multiple-pass sampling data. A maximum weighted likelihood method is used to estimate population sizes (Carle and Strub, 1978), and a size-frequency method is used to estimate production (Garman and Waters, 1983). The program performs the following steps: (1) reads in the data and performs error checking; (2) where required, uses length-weight regression to fill in missing weights; (3) assigns length classes to the fish; (4) for each date, species, and length class, estimates the population size and its variance; (5) for each date and species, estimates the total population size and its variance; and (6) for each species, estimates the annual production rate and its variance between sampling dates selected by the user. If data from only date are used, only populations are estimated. 9 refs.

  3. Odor emission rate estimation of indoor industrial sources using a modified inverse modeling method.

    PubMed

    Li, Xiang; Wang, Tingting; Sattayatewa, Chakkrid; Venkatesan, Dhesikan; Noll, Kenneth E; Pagilla, Krishna R; Moschandreas, Demetrios J

    2011-08-01

    Odor emission rates are commonly measured in the laboratory or occasionally estimated with inverse modeling techniques. A modified inverse modeling approach is used to estimate source emission rates inside of a postdigestion centrifuge building of a water reclamation plant. Conventionally, inverse modeling methods divide an indoor environment in zones on the basis of structural design and estimate source emission rates using models that assume homogeneous distribution of agent concentrations within a zone and experimentally determined link functions to simulate airflows among zones. The modified approach segregates zones as a function of agent distribution rather than building design and identifies near and far fields. Near-field agent concentrations do not satisfy the assumption of homogeneous odor concentrations; far-field concentrations satisfy this assumption and are the only ones used to estimate emission rates. The predictive ability of the modified inverse modeling approach was validated with measured emission rate values; the difference between corresponding estimated and measured odor emission rates is not statistically significant. Similarly, the difference between measured and estimated hydrogen sulfide emission rates is also not statistically significant. The modified inverse modeling approach is easy to perform because it uses odor and odorant field measurements instead of complex chamber emission rate measurements. PMID:21874959

  4. Estimated Pregnancy Rates and Rates of Pregnancy Outcomes for the United States, 1990-2008

    MedlinePlus

    ... of decline slowed in the mid-2000s. The teenage pregnancy rate in 2008 was the lowest reported since ... 1708–12. 2000. 24. Kost K, Henshaw S. U.S. teenage pregnancies, births, and abortions, 2008: National trends by age, ...

  5. Constants in estimates for the rates of convergence in von Neumann's and Birkhoff's ergodic theorems

    SciTech Connect

    Kachurovskii, Alexander G; Sedalishchev, Vladimir V

    2011-08-31

    The paper investigates estimates which relate two equivalent phenomena: the power-type rate of convergence in von Neumann's ergodic theorem and the power-type singularity at zero (with the same exponent) exhibited by the spectral measure of the function being averaged with respect to the corresponding dynamical system. The same rate of convergence is also estimated in terms of the rate of decrease of the correlation coefficients. Also, constants are found in analogous estimates for the power-type convergence in Birkhoff's ergodic theorem. All the results have exact analogues for wide-sense stationary stochastic processes. Bibliography: 15 titles.

  6. Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays

    PubMed Central

    Muthmann, Jens-Oliver; Amin, Hayder; Sernagor, Evelyne; Maccione, Alessandro; Panas, Dagmara; Berdondini, Luca; Bhalla, Upinder S.; Hennig, Matthias H.

    2015-01-01

    An emerging generation of high-density microelectrode arrays (MEAs) is now capable of recording spiking activity simultaneously from thousands of neurons with closely spaced electrodes. Reliable spike detection and analysis in such recordings is challenging due to the large amount of raw data and the dense sampling of spikes with closely spaced electrodes. Here, we present a highly efficient, online capable spike detection algorithm, and an offline method with improved detection rates, which enables estimation of spatial event locations at a resolution higher than that provided by the array by combining information from multiple electrodes. Data acquired with a 4096 channel MEA from neuronal cultures and the neonatal retina, as well as synthetic data, was used to test and validate these methods. We demonstrate that these algorithms outperform conventional methods due to a better noise estimate and an improved signal-to-noise ratio (SNR) through combining information from multiple electrodes. Finally, we present a new approach for analyzing population activity based on the characterization of the spatio-temporal event profile, which does not require the isolation of single units. Overall, we show how the improved spatial resolution provided by high density, large scale MEAs can be reliably exploited to characterize activity from large neural populations and brain circuits. PMID:26733859

  7. Rayleigh--Taylor spike evaporation

    SciTech Connect

    Schappert, G. T.; Batha, S. H.; Klare, K. A.; Hollowell, D. E.; Mason, R. J.

    2001-09-01

    Laser-based experiments have shown that Rayleigh--Taylor (RT) growth in thin, perturbed copper foils leads to a phase dominated by narrow spikes between thin bubbles. These experiments were well modeled and diagnosed until this '' spike'' phase, but not into this spike phase. Experiments were designed, modeled, and performed on the OMEGA laser [T. R. Boehly, D. L. Brown, R. S. Craxton , Opt. Commun. 133, 495 (1997)] to study the late-time spike phase. To simulate the conditions and evolution of late time RT, a copper target was fabricated consisting of a series of thin ridges (spikes in cross section) 150 {mu}m apart on a thin flat copper backing. The target was placed on the side of a scale-1.2 hohlraum with the ridges pointing into the hohlraum, which was heated to 190 eV. Side-on radiography imaged the evolution of the ridges and flat copper backing into the typical RT bubble and spike structure including the '' mushroom-like feet'' on the tips of the spikes. RAGE computer models [R. M. Baltrusaitis, M. L. Gittings, R. P. Weaver, R. F. Benjamin, and J. M. Budzinski, Phys. Fluids 8, 2471 (1996)] show the formation of the '' mushrooms,'' as well as how the backing material converges to lengthen the spike. The computer predictions of evolving spike and bubble lengths match measurements fairly well for the thicker backing targets but not for the thinner backings.

  8. Estimation of uncertainty in tracer gas measurement of air change rates.

    PubMed

    Iizuka, Atsushi; Okuizumi, Yumiko; Yanagisawa, Yukio

    2010-12-01

    Simple and economical measurement of air change rates can be achieved with a passive-type tracer gas doser and sampler. However, this is made more complex by the fact many buildings are not a single fully mixed zone. This means many measurements are required to obtain information on ventilation conditions. In this study, we evaluated the uncertainty of tracer gas measurement of air change rate in n completely mixed zones. A single measurement with one tracer gas could be used to simply estimate the air change rate when n = 2. Accurate air change rates could not be obtained for n ≥ 2 due to a lack of information. However, the proposed method can be used to estimate an air change rate with an accuracy of <33%. Using this method, overestimation of air change rate can be avoided. The proposed estimation method will be useful in practical ventilation measurements. PMID:21318005

  9. New Method for Estimation of Aeolian Sand Transport Rate Using Ceramic Sand Flux Sensor (UD-101)

    PubMed Central

    Udo, Keiko

    2009-01-01

    In this study, a new method for the estimation of aeolian sand transport rate was developed; the method employs a ceramic sand flux sensor (UD-101). UD-101 detects wind-blown sand impacting on its surface. The method was devised by considering the results of wind tunnel experiments that were performed using a vertical sediment trap and the UD-101. Field measurements to evaluate the estimation accuracy during the prevalence of unsteady winds were performed on a flat backshore. The results showed that aeolian sand transport rates estimated using the developed method were of the same order as those estimated using the existing method for high transport rates, i.e., for transport rates greater than 0.01 kg m−1 s−1. PMID:22291553

  10. Estimating Pesticide Effects on Fecundity Rates of Wild Birds Using Current Laboratory Reproduction Tests

    EPA Science Inventory

    The manuscript reviews the issues concerning the use of results on pesticide effects from laboratory avian reproduction tests for estimating potential impacts of pesticides on fecundity rates in avian population models.

  11. Type I Error Rates and Power Estimates of Selected Parametric and Nonparametric Tests of Scale.

    ERIC Educational Resources Information Center

    Olejnik, Stephen F.; Algina, James

    1987-01-01

    Estimated Type I Error rates and power are reported for the Brown-Forsythe, O'Brien, Klotz, and Siegal-Tukey procedures. The effect of aligning the data using deviations from group means or group medians is investigated. (RB)

  12. A GIS TECHNIQUE FOR ESTIMATING NATURAL ATTENUATION RATES AND MASS BALANCES: JOURNAL ARTICLE

    EPA Science Inventory

    NRMRL-ADA-01308 Durant, ND, Srinivasan, P, Faust, CR, Burnell, DK, Klein, KL, and Burden*, D.S. A GIS Technique for Estimating Natural Attenuation Rates and Mass Balances. Battelle's Sixth International ...

  13. Radioxenon spiked air

    SciTech Connect

    Watrous, Matthew G.; Delmore, James E.; Hague, Robert K.; Houghton, Tracy P.; Jenson, Douglas D.; Mann, Nick R.

    2015-08-27

    Four of the radioactive xenon isotopes (131mXe, 133mXe, 133Xe and 135Xe) with half-lives ranging from 9 h to 12 days are produced from nuclear fission and can be detected from days to weeks following their production and release. Being inert gases, they are readily transported through the atmosphere. Sources for release of radioactive xenon isotopes include operating nuclear reactors via leaks in fuel rods, medical isotope production facilities, and nuclear weapons' detonations. They are not normally released from fuel reprocessing due to the short half-lives. The Comprehensive Nuclear-Test-Ban Treaty has led to creation of the International Monitoring System. The International Monitoring System, when fully implemented, will consist of one component with 40 stations monitoring radioactive xenon around the globe. Monitoring these radioactive xenon isotopes is important to the Comprehensive Nuclear-Test-Ban Treaty in determining whether a seismically detected event is or is not a nuclear detonation. A variety of radioactive xenon quality control check standards, quantitatively spiked into various gas matrices, could be used to demonstrate that these stations are operating on the same basis in order to bolster defensibility of data across the International Monitoring System. This study focuses on Idaho National Laboratory's capability to produce three of the xenon isotopes in pure form and the use of the four xenon isotopes in various combinations to produce radioactive xenon spiked air samples that could be subsequently distributed to participating facilities.

  14. SPIKY: a graphical user interface for monitoring spike train synchrony

    PubMed Central

    Mulansky, Mario; Bozanic, Nebojsa

    2015-01-01

    Techniques for recording large-scale neuronal spiking activity are developing very fast. This leads to an increasing demand for algorithms capable of analyzing large amounts of experimental spike train data. One of the most crucial and demanding tasks is the identification of similarity patterns with a very high temporal resolution and across different spatial scales. To address this task, in recent years three time-resolved measures of spike train synchrony have been proposed, the ISI-distance, the SPIKE-distance, and event synchronization. The Matlab source codes for calculating and visualizing these measures have been made publicly available. However, due to the many different possible representations of the results the use of these codes is rather complicated and their application requires some basic knowledge of Matlab. Thus it became desirable to provide a more user-friendly and interactive interface. Here we address this need and present SPIKY, a graphical user interface that facilitates the application of time-resolved measures of spike train synchrony to both simulated and real data. SPIKY includes implementations of the ISI-distance, the SPIKE-distance, and the SPIKE-synchronization (an improved and simplified extension of event synchronization) that have been optimized with respect to computation speed and memory demand. It also comprises a spike train generator and an event detector that makes it capable of analyzing continuous data. Finally, the SPIKY package includes additional complementary programs aimed at the analysis of large numbers of datasets and the estimation of significance levels. PMID:25744888

  15. Estimates of exposure rates and fallout arrival times near the Nevada Test Site

    SciTech Connect

    Thompson, C.B. )

    1990-11-01

    One of the tasks of the Off-Site Radiation Exposure Review Project (ORERP) was to estimate doses to individuals resulting from exposure to fallout from nuclear testing at the Nevada Test Site (NTS). Dose estimates are based on estimates of the exposure rate 12 h post-detonation (H + 12) and the time of fallout arrival from events producing discernible fallout at locations off the NTS. These estimates are derived from both published fallout patterns and survey meter readings taken by monitors in the field. Each fallout pattern is digitized, and kriging is used to interpolate estimates of exposure rate and arrival time onto a 10-km grid covering the contours of the pattern. These grid values are then used to calculate estimates at any location of interest within the pattern. Exposure rate is also estimated from the survey meter readings for a particular nuclear event by decay-correcting the measurements near a selected location to H + 12 and then aggregating them into one estimate. Estimates of discernible exposure rate and time of fallout arrival from 74 nuclear events at the NTS are contained in the Town Data Base. Estimates are given for 352 locations in Arizona, California, Nevada, and Utah. Each record in the data base contains estimates for a specified event and location. The distribution of exposure rate is represented by a geometric mean and standard deviation; the distribution of fallout arrival time is represented by an arithmetic mean and standard deviation. A more extensive description and a listing of the Town Data Base are included in a separate report.

  16. An estimating formula for ion-atom association rates in gases

    NASA Technical Reports Server (NTRS)

    Chatterjee, B. K.; Johnsen, R.

    1990-01-01

    A simple estimating formula is derived for rate coefficients of three-body ion atom association in gases and compare its predictions to experimental data on ion association and three-body radiative charge transfer reactions of singly- and doubly-charged rare-gas ions. The formula appears to reproduce most experimental data quite well. It may be useful for estimating the rates of reactions that have not been studied in the laboratory.

  17. A simple method for estimating minimum autorotative descent rate of single rotor helicopters

    NASA Technical Reports Server (NTRS)

    Talbot, P. D.; Schroers, L. G.

    1978-01-01

    Flight test results of minimum autorotative descent rate are compared with calculations based on the minimum power required for steady level flight. Empirical correction factors are derived that account for differences in energy dissipation between these two flight conditions. A method is also presented for estimating the minimum power coefficient for level flight for any helicopter for use in the empirical estimation procedure of autorotative descent rate.

  18. A 0.7 V, 40 nW Compact, Current-Mode Neural Spike Detector in 65 nm CMOS.

    PubMed

    Yao, Enyi; Chen, Yi; Basu, Arindam

    2016-04-01

    In this paper, we describe a novel low power, compact, current-mode spike detector circuit for real-time neural recording systems where neural spikes or action potentials (AP) are of interest. Such a circuit can enable massive compression of data facilitating wireless transmission. This design can generate a high signal-to-noise ratio (SNR) output by approximating the popularly used nonlinear energy operator (NEO) through standard analog blocks. We show that a low pass filter after the NEO can be used for two functions-(i) estimate and cancel low frequency interference and (ii) estimate threshold for spike detection. The circuit is implemented in a 65 nm CMOS process and occupies 200 μm × 150 μ m of chip area. Operating from a 0.7 V power supply, it consumes about 30 nW of static power and 7 nW of dynamic power for 100 Hz input spike rate making it the lowest power consuming spike detector reported so far. PMID:26168445

  19. VARIABILITY IN OBSERVED AND SENSOR BASED ESTIMATED OPTIMUM N RATES IN CORN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent research showed that active sensors such as Crop Circle can be used to estimate in-season N requirements in corn. The objective of this research was to identify the sources of variability in the observed and estimated economic optimum N rates (EONR) using Crop Circle. Field experiments were c...

  20. Variability in Observed and Sensor Based Estimated Optimum N Rates in Corn

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent research showed that active sensors such as Crop Circle can be used to estimate in-season N requirements for corn. The objective of this research was to identify sources of variability in the observed and Crop Circle-estimated optimum N rates. Field experiments were conducted at two locations...

  1. Estimating survival rates with time series of standing age-structure data

    USGS Publications Warehouse

    Udevitz, Mark S.; Gogan, Peter J.

    2014-01-01

    It has long been recognized that age-structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age-specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age-specific survival rates can be estimated using techniques such as inverse methods that combine time series of age-structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age-structure data with other demographic data to provide explicit maximum likelihood estimators of age-specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age-structure data.

  2. Estimation of eruption source parameters from umbrella cloud or downwind plume growth rate

    NASA Astrophysics Data System (ADS)

    Pouget, Solène; Bursik, Marcus; Webley, Peter; Dehn, Jon; Pavolonis, Michael

    2013-05-01

    We introduce a new method to estimate mass eruption rate (MER) and mass loading from the growth of a volcanic umbrella cloud or downwind plume using satellite images, or photographs where ground-based observations are available. This new method is compared with pre-existing models and documented mass eruption rate given in the research literature. We applied the method to five well-studied eruptions (Mount St. Helens, 1980; Redoubt, 1990; Pinatubo, 1991; Hekla, 2000 and Eyjafjallajökull, 2010) and to five less well-documented eruptions (Kliuchevsko'i, 1994; Okmok, 2008; Kasatochi, 2008; Sarychev Peak, 2009 and Bezymianny, 2012). The mass eruption rate is obtained by estimation of the radius of the umbrella cloud with time or by estimation of the width of the downwind plume with distance from the volcano. The results given by the new method show a more fully characterized MER as a function of time than do the results given by pre-existing methods, and allow a faster, remote assessment of the mass eruption rate, even for volcanoes that are difficult to study. The method thus may provide an additional important path to the estimation of source parameters and the forecasting of ash cloud propagation. In addition, in cases where numerous methods are available, use of the method yields new, independent measures of mass eruption rate, hence an ability to estimate uncertainty in mass eruption rate, which could be used in probabilistic estimations of ash cloud propagation.

  3. Estimating base rates of impairment in neuropsychological test batteries: a comparison of quantitative models.

    PubMed

    Decker, Scott L; Schneider, W Joel; Hale, James B

    2012-01-01

    Neuropsychologists frequently rely on a battery of neuropsychological tests which are normally distributed to determine impaired functioning. The statistical likelihood of Type I error in clinical decision-making is in part determined by the base rate of normative individuals obtaining atypical performance on neuropsychological tests. Base rates are most accurately obtained by co-normed measures, but this is rarely accomplished in neuropsychological testing. Several statistical methods have been proposed to estimate base rates for tests that are not co-normed. This study compared two statistical approaches (binomial and Monte Carlo models) used to estimate the base rates for flexible test batteries. The two approaches were compared against empirically derived base rates for a multitest co-normed battery of cognitive measures. Estimates were compared across a variety of conditions including age and different α levels (N =3,356). Monte Carlo R(2) estimates ranged from .980 to .997 across five different age groups, indicating a good fit. In contrast, the binomial model fit estimates ranged from 0.387 to 0.646. Results confirm that the binomial model is insufficient for estimating base rates because it does not take into account correlations among measures in a multitest battery. Although the Monte Carlo model produced more accurate results, minor biases occurred that are likely due to skewess and kurtosis of test variables. Implications for future research and applied practice are discussed. PMID:22172567

  4. An optimized method for the estimation of the respiratory rate from electrocardiographic signals: implications for estimating minute ventilation

    PubMed Central

    Weiss, Eric H.; Sayadi, Omid; Ramaswamy, Priya; Merchant, Faisal M.; Sajja, Naveen; Foley, Lori; Laferriere, Shawna

    2014-01-01

    It is well-known that respiratory activity influences electrocardiographic (ECG) morphology. In this article we present a new algorithm for the extraction of respiratory rate from either intracardiac or body surface electrograms. The algorithm optimizes selection of ECG leads for respiratory analysis, as validated in a swine model. The algorithm estimates the respiratory rate from any two ECG leads by finding the power spectral peak of the derived ratio of the estimated root-mean-squared amplitude of the QRS complexes on a beat-by-beat basis across a 32-beat window and automatically selects the lead combination with the highest power spectral signal-to-noise ratio. In 12 mechanically ventilated swine, we collected intracardiac electrograms from catheters in the right ventricle, coronary sinus, left ventricle, and epicardial surface, as well as body surface electrograms, while the ventilation rate was varied between 7 and 13 breaths/min at tidal volumes of 500 and 750 ml. We found excellent agreement between the estimated and true respiratory rate for right ventricular (R2 = 0.97), coronary sinus (R2 = 0.96), left ventricular (R2 = 0.96), and epicardial (R2 = 0.97) intracardiac leads referenced to surface lead ECGII. When applied to intracardiac right ventricular-coronary sinus bipolar leads, the algorithm exhibited an accuracy of 99.1% (R2 = 0.97). When applied to 12-lead body surface ECGs collected in 4 swine, the algorithm exhibited an accuracy of 100% (R2 = 0.93). In conclusion, the proposed algorithm provides an accurate estimation of the respiratory rate using either intracardiac or body surface signals without the need for additional hardware. PMID:24858847

  5. Influence of spiking activity on cortical local field potentials

    PubMed Central

    Waldert, Stephan; Lemon, Roger N; Kraskov, Alexander

    2013-01-01

    The intra-cortical local field potential (LFP) reflects a variety of electrophysiological processes including synaptic inputs to neurons and their spiking activity. It is still a common assumption that removing high frequencies, often above 300 Hz, is sufficient to exclude spiking activity from LFP activity prior to analysis. Conclusions based on such supposedly spike-free LFPs can result in false interpretations of neurophysiological processes and erroneous correlations between LFPs and behaviour or spiking activity. Such findings might simply arise from spike contamination rather than from genuine changes in synaptic input activity. Although the subject of recent studies, the extent of LFP contamination by spikes is unclear, and the fundamental problem remains. Using spikes recorded in the motor cortex of the awake monkey, we investigated how different factors, including spike amplitude, duration and firing rate, together with the noise statistic, can determine the extent to which spikes contaminate intra-cortical LFPs. We demonstrate that such contamination is realistic for LFPs with a frequency down to ∼10 Hz. For LFP activity below ∼10 Hz, such as movement-related potential, contamination is theoretically possible but unlikely in real situations. Importantly, LFP frequencies up to the (high-) gamma band can remain unaffected. This study shows that spike–LFP crosstalk in intra-cortical recordings should be assessed for each individual dataset to ensure that conclusions based on LFP analysis are valid. To this end, we introduce a method to detect and to visualise spike contamination, and provide a systematic guide to assess spike contamination of intra-cortical LFPs. PMID:23981719

  6. Impact of transverse and longitudinal dispersion on first-order degradation rate constant estimation

    NASA Astrophysics Data System (ADS)

    Stenback, Greg A.; Ong, Say Kee; Rogers, Shane W.; Kjartanson, Bruce H.

    2004-09-01

    A two-dimensional analytical model is employed for estimating the first-order degradation rate constant of hydrophobic organic compounds (HOCs) in contaminated groundwater under steady-state conditions. The model may utilize all aqueous concentration data collected downgradient of a source area, but does not require that any data be collected along the plume centerline. Using a least squares fit of the model to aqueous concentrations measured in monitoring wells, degradation rate constants were estimated at a former manufactured gas plant (FMGP) site in the Midwest U.S. The estimated degradation rate constants are 0.0014, 0.0034, 0.0031, 0.0019, and 0.0053 day -1 for acenaphthene, naphthalene, benzene, ethylbenzene, and toluene, respectively. These estimated rate constants were as low as one-half those estimated with the one-dimensional (centerline) approach of Buscheck and Alcantar [Buscheck, T.E., Alcantar, C.M., 1995. Regression techniques and analytical solutions to demonstrate intrinsic bioremediation. In: Hinchee, R.E., Wilson, J.T., Downey, D.C. (Eds.), Intrinsic Bioremediation, Battelle Press, Columbus, OH, pp. 109-116] which does not account for transverse dispersivity. Varying the transverse and longitudinal dispersivity values over one order of magnitude for toluene data obtained from the FMGP site resulted in nearly a threefold variation in the estimated degradation rate constant—highlighting the importance of reliable estimates of the dispersion coefficients for obtaining reasonable estimates of the degradation rate constants. These results have significant implications for decision making and site management where overestimation of a degradation rate may result in remediation times and bioconversion factors that exceed expectations. For a complex source area or non-steady-state plume, a superposition of analytical models that incorporate longitudinal and transverse dispersion and time may be used at sites where the centerline method would not be

  7. A generalized estimate of ground-water-recharge rates in the Lower Peninsula of Michigan

    USGS Publications Warehouse

    Holtschlag, David J.

    1997-01-01

    Ground-water recharge rates were estimated by analysis of streamflow, precipitation, and basin-characteristics data. Streamflow data were partitioned into ground-water-discharge and surface-water-runoff components. Regression equations relate ground-water discharge to precipitation at each basin. Basin-characteristics and long-term precipitation data were used to aid in the interpolation of recharge characteristics within gaged and ungaged areas. A multiple regression equation was developed to estimate spatial variation of recharge. The generalized estimate provides a consistent method for approximating recharge rates in the Lower Peninsula of Michigan.

  8. Estimating mortality rates of adult fish from entrainment through the propellers of river towboats

    USGS Publications Warehouse

    Gutreuter, S.; Dettmers, J.M.; Wahl, David H.

    2003-01-01

    We developed a method to estimate mortality rates of adult fish caused by entrainment through the propellers of commercial towboats operating in river channels. The method combines trawling while following towboats (to recover a fraction of the kills) and application of a hydrodynamic model of diffusion (to estimate the fraction of the total kills collected in the trawls). The sampling problem is unusual and required quantifying relatively rare events. We first examined key statistical properties of the entrainment mortality rate estimators using Monte Carlo simulation, which demonstrated that a design-based estimator and a new ad hoc estimator are both unbiased and converge to the true value as the sample size becomes large. Next, we estimated the entrainment mortality rates of adult fishes in Pool 26 of the Mississippi River and the Alton Pool of the Illinois River, where we observed kills that we attributed to entrainment. Our estimates of entrainment mortality rates were 2.52 fish/km of towboat travel (80% confidence interval, 1.00-6.09 fish/km) for gizzard shad Dorosoma cepedianum, 0.13 fish/km (0.00-0.41) for skipjack herring Alosa chrysochloris, and 0.53 fish/km (0.00-1.33) for both shovelnose sturgeon Scaphirhynchus platorynchus and smallmouth buffalo Ictiobus bubalus. Our approach applies more broadly to commercial vessels operating in confined channels, including other large rivers and intracoastal waterways.

  9. Controlling chaos in balanced neural circuits with input spike trains

    NASA Astrophysics Data System (ADS)

    Engelken, Rainer; Wolf, Fred

    The cerebral cortex can be seen as a system of neural circuits driving each other with spike trains. Here we study how the statistics of these spike trains affects chaos in balanced target circuits.Earlier studies of chaos in balanced neural circuits either used a fixed input [van Vreeswijk, Sompolinsky 1996, Monteforte, Wolf 2010] or white noise [Lajoie et al. 2014]. We study dynamical stability of balanced networks driven by input spike trains with variable statistics. The analytically obtained Jacobian enables us to calculate the complete Lyapunov spectrum. We solved the dynamics in event-based simulations and calculated Lyapunov spectra, entropy production rate and attractor dimension. We vary correlations, irregularity, coupling strength and spike rate of the input and action potential onset rapidness of recurrent neurons.We generally find a suppression of chaos by input spike trains. This is strengthened by bursty and correlated input spike trains and increased action potential onset rapidness. We find a link between response reliability and the Lyapunov spectrum. Our study extends findings in chaotic rate models [Molgedey et al. 1992] to spiking neuron models and opens a novel avenue to study the role of projections in shaping the dynamics of large neural circuits.

  10. Frequency of private electrophoretic variants and indirect estimates of mutation rate in Papua New Guinea.

    PubMed Central

    Bhatia, K K; Blake, N M; Serjeantson, S W; Kirk, R L

    1981-01-01

    Data on rare and private electrophoretic variants have been used to estimate mutation rates for populations belonging to 55 language groups in Papua New Guinea. Three different methods yield values of 1.42 x 10(-6), 1.40 x 10(-6), and 5.58 x 10(-6)/locus per generation. The estimates for three islands populations off the north coast of New Guinea--Manus, Karkar, and Siassi--are much lower. The variability in mutation rates estimated from rare electrophoretic variants as a function of population size is discussed. The mean mutation rate in Papua New Guinea is less than half the estimates obtained for Australian Aborigines and Amerindians. PMID:7468589

  11. Jackknife-corrected parametric bootstrap estimates of growth rates in bivalve mollusks using nearest living relatives.

    PubMed

    Dexter, Troy A; Kowalewski, Michał

    2013-12-01

    Quantitative estimates of growth rates can augment ecological and paleontological applications of body-size data. However, in contrast to body-size estimates, assessing growth rates is often time-consuming, expensive, or unattainable. Here we use an indirect approach, a jackknife-corrected parametric bootstrap, for efficient approximation of growth rates using nearest living relatives with known age-size relationships. The estimate is developed by (1) collecting a sample of published growth rates of closely related species, (2) calculating the average growth curve using those published age-size relationships, (3) resampling iteratively these empirically known growth curves to estimate the standard errors and confidence bands around the average growth curve, and (4) applying the resulting estimate of uncertainty to bracket age-size relationships of the species of interest. This approach was applied to three monophyletic families (Donacidae, Mactridae, and Semelidae) of mollusk bivalves, a group characterized by indeterministic shell growth, but widely used in ecological, paleontological, and geochemical research. The resulting indirect estimates were tested against two previously published geochemical studies and, in both cases, yielded highly congruent age estimates. In addition, a case study in applied fisheries was used to illustrate the potential of the proposed approach for augmenting aquaculture management practices. The resulting estimates of growth rates place body size data in a constrained temporal context and confidence intervals associated with resampling estimates allow for assessing the statistical uncertainty around derived temporal ranges. The indirect approach should allow for improved evaluation of diverse research questions, from sustainability of industrial shellfish harvesting to climatic interpretations of stable isotope proxies extracted from fossil skeletons. PMID:24071629

  12. Integer aperture bootstrapping: a new GNSS ambiguity estimator with controllable fail-rate

    NASA Astrophysics Data System (ADS)

    Teunissen, P. J. G.

    2005-08-01

    In this contribution, we introduce a new bootstrap-based method for Global Navigation Satellite System (GNSS) carrier-phase ambiguity resolution. Integer bootstrapping is known to be one of the simplest methods for integer ambiguity estimation with close-to-optimal performance. Its outcome is easy to compute due to the absence of an integer search, and its performance is close to optimal if the decorrelating Z-transformation of the LAMBDA method is used. Moreover, the bootstrapped estimator is presently the only integer estimator for which an exact and easy-to-compute expression of its fail-rate can be given. A possible disadvantage is, however, that the user has only a limited control over the fail-rate. Once the underlying mathematical model is given, the user has no freedom left in changing the value of the fail-rate. Here, we present an ambiguity estimator for which the user is given additional freedom. For this purpose, use is made of the class of integer aperture estimators as introduced in Teunissen (2003). This class is larger than the class of integer estimators. Integer aperture estimators are of a hybrid nature and can have integer outcomes as well as non-integer outcomes. The new estimator is referred to as integer aperture bootstrapping. This new estimator has all the advantages known from integer bootstrapping with the additional advantage that its fail-rate can be controlled by the user. This is made possible by giving the user the freedom over the aperture of the pull-in region. We also give an exact and easy-to-compute expression for its controllable fail-rate.

  13. Application of Statistical Methods of Rain Rate Estimation to Data From The TRMM Precipitation Radar

    NASA Technical Reports Server (NTRS)

    Meneghini, R.; Jones, J. A.; Iguchi, T.; Okamoto, K.; Liao, L.; Busalacchi, Antonio J. (Technical Monitor)

    2000-01-01

    The TRMM Precipitation Radar is well suited to statistical methods in that the measurements over any given region are sparsely sampled in time. Moreover, the instantaneous rain rate estimates are often of limited accuracy at high rain rates because of attenuation effects and at light rain rates because of receiver sensitivity. For the estimation of the time-averaged rain characteristics over an area both errors are relevant. By enlarging the space-time region over which the data are collected, the sampling error can be reduced. However. the bias and distortion of the estimated rain distribution generally will remain if estimates at the high and low rain rates are not corrected. In this paper we use the TRMM PR data to investigate the behavior of 2 statistical methods the purpose of which is to estimate the rain rate over large space-time domains. Examination of large-scale rain characteristics provides a useful starting point. The high correlation between the mean and standard deviation of rain rate implies that the conditional distribution of this quantity can be approximated by a one-parameter distribution. This property is used to explore the behavior of the area-time-integral (ATI) methods where fractional area above a threshold is related to the mean rain rate. In the usual application of the ATI method a correlation is established between these quantities. However, if a particular form of the rain rate distribution is assumed and if the ratio of the mean to standard deviation is known, then not only the mean but the full distribution can be extracted from a measurement of fractional area above a threshold. The second method is an extension of this idea where the distribution is estimated from data over a range of rain rates chosen in an intermediate range where the effects of attenuation and poor sensitivity can be neglected. The advantage of estimating the distribution itself rather than the mean value is that it yields the fraction of rain contributed by

  14. New estimates of silicate weathering rates and their uncertainties in global rivers

    NASA Astrophysics Data System (ADS)

    Moon, Seulgi; Chamberlain, C. P.; Hilley, G. E.

    2014-06-01

    This study estimated the catchment- and global-scale weathering rates of silicate rocks from global rivers using global compilation datasets from the GEMS/Water and HYBAM. These datasets include both time-series of chemical concentrations of major elements and synchronous discharge. Using these datasets, we first examined the sources of uncertainties in catchment and global silicate weathering rates. Then, we proposed future sampling strategies and geochemical analyses to estimate accurate silicate weathering rates in global rivers and to reduce uncertainties in their estimates. For catchment silicate weathering rates, we considered uncertainties due to sampling frequency and variability in river discharge, concentration, and attribution of weathering to different chemical sources. Our results showed that uncertainties in catchment-scale silicate weathering rates were due mostly to the variations in discharge and cation fractions from silicate substrates. To calculate unbiased silicate weathering rates accounting for the variations from discharge and concentrations, we suggest that at least 10 and preferably ∼40 temporal chemical data points with synchronous discharge from each river are necessary. For the global silicate weathering rate, we examined uncertainties from infrequent sampling within an individual river, the extrapolation from limited rivers to a global flux, and the inverse model selections for source differentiation. For this weathering rate, we found that the main uncertainty came from the extrapolation to the global flux and the model configurations of source differentiation methods. This suggests that to reduce the uncertainties in the global silicate weathering rates, coverage of synchronous datasets of river chemistry and discharge to rivers from tectonically active regions and volcanic provinces must be extended, and catchment-specific silicate end-members for those rivers must be characterized. With current available synchronous datasets, we

  15. ESTIMATION OF FAILURE RATES OF DIGITAL COMPONENTS USING A HIERARCHICAL BAYESIAN METHOD.

    SciTech Connect

    YUE, M.; CHU, T.L.

    2006-01-30

    One of the greatest challenges in evaluating reliability of digital I&C systems is how to obtain better failure rate estimates of digital components. A common practice of the digital component failure rate estimation is attempting to use empirical formulae to capture the impacts of various factors on the failure rates. The applicability of an empirical formula is questionable because it is not based on laws of physics and requires good data, which is scarce in general. In this study, the concept of population variability of the Hierarchical Bayesian Method (HBM) is applied to estimating the failure rate of a digital component using available data. Markov Chain Monte Carlo (MCMC) simulation is used to implement the HBM. Results are analyzed and compared by selecting different distribution types and priors distributions. Inspired by the sensitivity calculations and based on review of analytic derivations, it seems reasonable to suggest avoiding the use of gamma distribution in two-stage Bayesian analysis and HBM analysis.

  16. Evaluation and refinement of leak-rate estimation models. Revision 1

    SciTech Connect

    Paul, D.D.; Ahmad, J.; Scott, P.M.; Flanigan, L.F.; Wilkowski, G.M.

    1994-06-01

    Leak-rate estimation models are important elements in developing a leak-beforebreak methodology in piping integrity and safety analyses. Existing thermalhydraulic and crack-opening-area models used in current leak-rate estimations have been incorporated into a single computer code for leak-rate estimation. The code is called SQUIRT, which stands for Seepage Quantification of Upsets In Reactor Tubes. The SQUIRT program has been validated by comparing its thermalhydraulic predictions with the limited experimental data that have been published on two-phase flow through slits and cracks, and by comparing its crack-opening-area predictions with data from the Degraded Piping Program. In addition, leak-rate experiments were conducted to obtain validation data for a circumferential fatigue crack in a carbon steel pipe girth weld.

  17. Additional comments on the assumption of homogenous survival rates in modern bird banding estimation models

    USGS Publications Warehouse

    Nichols, J.D.; Stokes, S.L.; Hines, J.E.; Conroy, M.J.

    1982-01-01

    We examined the problem of heterogeneous survival and recovery rates in bird banding estimation models. We suggest that positively correlated subgroup survival and recovery probabilities may result from winter banding operations and that this situation will produce positively biased survival rate estimates. The magnitude of the survival estimate bias depends on the proportion of the population in each subgroup. Power of the suggested goodness-of-fit test to reject the inappropriate model for heterogeneous data sets was low for all situations examined and was poorest for positively related subgroup survival and recovery rates. Despite the magnitude of some of the biases reported and the relative inability to detect heterogeneity, we suggest that levels of heterogeneity normally encountered in real data sets will produce relatively small biases of average survival rates.

  18. Upper-limit mutation rate estimation for a plant RNA virus

    PubMed Central

    Sanjuán, Rafael; Agudelo-Romero, Patricia; Elena, Santiago F.

    2009-01-01

    It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus, we calculate an upper-bound mutation rate estimation of 3×10−5 per site and per round of replication; a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals. PMID:19324646

  19. Markov Models and the Ensemble Kalman Filter for Estimation of Sorption Rates

    NASA Astrophysics Data System (ADS)

    Vugrin, E. D.; McKenna, S. A.; White Vugrin, K.

    2007-12-01

    Non-equilibrium sorption of contaminants in ground water systems is examined from the perspective of sorption rate estimation. A previously developed Markov transition probability model for solute transport is used in conjunction with a new conditional probability-based model of the sorption and desorption rates based on breakthrough curve data. Two models for prediction of spatially varying sorption and desorption rates along a one-dimensional streamline are developed. These models are a Markov model that utilizes conditional probabilities to determine the rates and an ensemble Kalman filter (EnKF) applied to the conditional probability method. Both approaches rely on a previously developed Markov-model of mass transfer, and both models assimilate the observed concentration data into the rate estimation at each observation time. Initial values of the rates are perturbed from the true values to form ensembles of rates and the ability of both estimation approaches to recover the true rates is examined over three different sets of perturbations. The models accurately estimate the rates when the mean of the perturbations are zero, the unbiased case. For the cases containing some bias, addition of the ensemble Kalman filter is shown to improve accuracy of the rate estimation by as much as an order of magnitude. Sandia is a multi program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000. This work was supported under the Sandia Laboratory Directed Research and Development program.

  20. Bayesian Procedures for the Estimation of Mutation Rates from Fluctuation Experiments

    PubMed Central

    Asteris, G.; Sarkar, S.

    1996-01-01

    Bayesian procedures are developed for estimating mutation rates from fluctuation experiments. Three Bayesian point estimators are compared with four traditional ones using the results of 10,000 simulated experiments. The Bayesian estimators were found to be at least as efficient as the best of the previously known estimators. The best Bayesian estimator is one that uses (1/m(2)) as the prior probability density function and a quadratic loss function. The advantage of using these estimators is most pronounced when the number of fluctuation test tubes is small. Bayesian estimation allows the incorporation of prior knowledge about the estimated parameter, in which case the resulting estimators are the most efficient. It enables the straightforward construction of confidence intervals for the estimated parameter. The increase of efficiency with prior information and the narrowing of the confidence intervals with additional experimental results are investigated. The results of the simulations show that any potential inaccuracy of estimation arising from lumping together all cultures with more than n mutants (the jackpots) almost disappears at n = 70 (provided that the number of mutations in a culture is low). These methods are applied to a set of experimental data to illustrate their use. PMID:8770608

  1. An online spike detection and spike classification algorithm capable of instantaneous resolution of overlapping spikes

    PubMed Central

    Natora, Michal; Boucsein, Clemens; Munk, Matthias H. J.; Obermayer, Klaus

    2009-01-01

    For the analysis of neuronal cooperativity, simultaneously recorded extracellular signals from neighboring neurons need to be sorted reliably by a spike sorting method. Many algorithms have been developed to this end, however, to date, none of them manages to fulfill a set of demanding requirements. In particular, it is desirable to have an algorithm that operates online, detects and classifies overlapping spikes in real time, and that adapts to non-stationary data. Here, we present a combined spike detection and classification algorithm, which explicitly addresses these issues. Our approach makes use of linear filters to find a new representation of the data and to optimally enhance the signal-to-noise ratio. We introduce a method called “Deconfusion” which de-correlates the filter outputs and provides source separation. Finally, a set of well-defined thresholds is applied and leads to simultaneous spike detection and spike classification. By incorporating a direct feedback, the algorithm adapts to non-stationary data and is, therefore, well suited for acute recordings. We evaluate our method on simulated and experimental data, including simultaneous intra/extra-cellular recordings made in slices of a rat cortex and recordings from the prefrontal cortex of awake behaving macaques. We compare the results to existing spike detection as well as spike sorting methods. We conclude that our algorithm meets all of the mentioned requirements and outperforms other methods under realistic signal-to-noise ratios and in the presence of overlapping spikes. PMID:19499318

  2. Graph structure modeling for multi-neuronal spike data

    NASA Astrophysics Data System (ADS)

    Akaho, Shotaro; Higuchi, Sho; Iwasaki, Taishi; Hino, Hideitsu; Tatsuno, Masami; Murata, Noboru

    2016-03-01

    We propose a method to extract connectivity between neurons for extracellularly recorded multiple spike trains. The method removes pseudo-correlation caused by propagation of information along an indirect pathway, and is also robust against the influence from unobserved neurons. The estimation algorithm consists of iterations of a simple matrix inversion, which is scalable to large data sets. The performance is examined by synthetic spike data.

  3. Mapping Spikes to Sensations

    PubMed Central

    Stüttgen, Maik C.; Schwarz, Cornelius; Jäkel, Frank

    2011-01-01

    Single-unit recordings conducted during perceptual decision-making tasks have yielded tremendous insights into the neural coding of sensory stimuli. In such experiments, detection or discrimination behavior (the psychometric data) is observed in parallel with spike trains in sensory neurons (the neurometric data). Frequently, candidate neural codes for information read-out are pitted against each other by transforming the neurometric data in some way and asking which code’s performance most closely approximates the psychometric performance. The code that matches the psychometric performance best is retained as a viable candidate and the others are rejected. In following this strategy, psychometric data is often considered to provide an unbiased measure of perceptual sensitivity. It is rarely acknowledged that psychometric data result from a complex interplay of sensory and non-sensory processes and that neglect of these processes may result in misestimating psychophysical sensitivity. This again may lead to erroneous conclusions regarding the adequacy of candidate neural codes. In this review, we first discuss requirements on the neural data for a subsequent neurometric-psychometric comparison. We then focus on different psychophysical tasks for the assessment of detection and discrimination performance and the cognitive processes that may underlie their execution. We discuss further factors that may compromise psychometric performance and how they can be detected or avoided. We believe that these considerations point to shortcomings in our understanding of the processes underlying perceptual decisions, and therefore offer potential for future research. PMID:22084627

  4. Experimental and Estimated Rate Constants for the Reactions of Hydroxyl Radicals with Several Halocarbons

    NASA Technical Reports Server (NTRS)

    DeMore, W.B.

    1996-01-01

    Relative rate experiments are used to measure rate constants and temperature dependencies of the reactions of OH with CH3F (41), CH2FCl (31), CH2BrCl (30B1), CH2Br2 (3OB2), CHBr3 (2OB3), CF2BrCHFCl (123aBl(alpha)), and CF2ClCHCl2 (122). Rate constants for additional compounds of these types are estimated using an empirical rate constant estimation method which is based on measured rate constants for a wide range of halocarbons. The experimental data are combined with the estimated and previously reported rate constants to illustrate the effects of F, Cl, and Br substitution on OH rate constants for a series of 19 halomethanes and 25 haloethanes. Application of the estimation technique is further illustrated for some higher hydrofluorocarbons (HFCs), including CHF2CF2CF2CF2H (338pcc), CF3CHFCHFCF2CF3 (43-10mee), CF3CH2CH2CF3 (356ffa), CF3CH2CF2CH2CF3 (458mfcf), CF3CH2CHF2 (245fa), and CF3CH2CF2CH3 (365mfc). The predictions are compared with literature data for these compounds.

  5. Respiratory rate estimation from the built-in cameras of smartphones and tablets.

    PubMed

    Nam, Yunyoung; Lee, Jinseok; Chon, Ki H

    2014-04-01

    This paper presents a method for respiratory rate estimation using the camera of a smartphone, an MP3 player or a tablet. The iPhone 4S, iPad 2, iPod 5, and Galaxy S3 were used to estimate respiratory rates from the pulse signal derived from a finger placed on the camera lens of these devices. Prior to estimation of respiratory rates, we systematically investigated the optimal signal quality of these 4 devices by dividing the video camera's resolution into 12 different pixel regions. We also investigated the optimal signal quality among the red, green and blue color bands for each of these 12 pixel regions for all four devices. It was found that the green color band provided the best signal quality for all 4 devices and that the left half VGA pixel region was found to be the best choice only for iPhone 4S. For the other three devices, smaller 50 × 50 pixel regions were found to provide better or equally good signal quality than the larger pixel regions. Using the green signal and the optimal pixel regions derived from the four devices, we then investigated the suitability of the smartphones, the iPod 5 and the tablet for respiratory rate estimation using three different computational methods: the autoregressive (AR) model, variable-frequency complex demodulation (VFCDM), and continuous wavelet transform (CWT) approaches. Specifically, these time-varying spectral techniques were used to identify the frequency and amplitude modulations as they contain respiratory rate information. To evaluate the performance of the three computational methods and the pixel regions for the optimal signal quality, data were collected from 10 healthy subjects. It was found that the VFCDM method provided good estimates of breathing rates that were in the normal range (12-24 breaths/min). Both CWT and VFCDM methods provided reasonably good estimates for breathing rates that were higher than 26 breaths/min but their accuracy degraded concomitantly with increased respiratory rates

  6. Collision-spike Sputtering of Au Nanoparticles.

    PubMed

    Sandoval, Luis; Urbassek, Herbert M

    2015-12-01

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For the particular case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31 % of the impact energy remains in the nanoparticles after impact; the remainder is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80 % of that of free nanoparticles due to the suppression of forward sputtering. PMID:26245857

  7. Collision-spike sputtering of Au nanoparticles

    SciTech Connect

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For this specific case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31% of the impact energy remains in the nanoparticles after impact; the remainder is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80% of that of free nanoparticles due to the suppression of forward sputtering.

  8. Collision-spike sputtering of Au nanoparticles

    DOE PAGESBeta

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For this specific case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31% of the impact energy remains in the nanoparticles after impact; the remaindermore » is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80% of that of free nanoparticles due to the suppression of forward sputtering.« less

  9. An evaluation of sediment rating curves for estimating suspended sediment concentrations for subsequent flux calculations

    USGS Publications Warehouse

    Horowitz, A.J.

    2003-01-01

    In the absence of actual suspended sediment concentration (SSC) measurements, hydrologists have used sediment rating (sediment transport) curves to estimate (predict) SSCs for subsequent flux calculations. Various evaluations of the sediment rating-curve method were made using data from long-term, daily sediment-measuring sites within large (>1 000 000 km2), medium ( 1000 km2), and small (<1000 km2) river basins in the USA and Europe relative to the estimation of suspended sediment fluxes. The evaluations address such issues as the accuracy of flux estimations for various levels of temporal resolution as well as the impact of sampling frequency on the magnitude of flux estimation errors. The sediment rating-curve method tends to underpredict high, and overpredict low SSCs. As such, the range of errors associated with concomitant flux estimates for relatively short time-frames (e.g. daily, weekly) are likely to be substantially larger than those associated with longer time-frames (e.g. quarterly, annually) because the over- and underpredictions do not have sufficient time to balance each other. Hence, when error limits must be kept under ??20%, temporal resolution probably should be limited to quarterly or greater. The evaluations indicate that over periods of 20 or more years, errors of <1% can be achieved using a single sediment rating curve based on data spanning the entire period. However, somewhat better estimates for the entire period, and markedly better annual estimates within the period, can be obtained if individual annual sediment rating curves are used instead. Relatively accurate (errors estimation

  10. Solar Flare Hard X-ray Spikes Observed by RHESSI: a Statistical Study

    NASA Astrophysics Data System (ADS)

    Cheng, Jianxia; Qiu, J.; Ding, M.; Wang, H.

    2013-07-01

    Hard X-ray (HXR) spikes refer to fine time structures on timescales of seconds to milliseconds in high-energy HXR emission profiles during solar flare eruptions. We present a preliminary statistical investigation of temporal and spectral properties of HXR spikes. Using a three-sigma spike selection rule, we detected 184 spikes in 94 out of 322 flares with significant counts at given photon energies, which were detected from demodulated HXR light curves obtained by the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). About one fifth of these spikes are also detected at photon energies higher than 100 keV. The statistical properties of the spikes are as follows. (1) HXR spikes are produced in both impulsive flares and long-duration flares with nearly the same occurrence rates. Ninety percent of the spikes occur during the rise phase of the flares, and about 70% occur around the peak times of the flares. (2) The time durations of the spikes vary from 0.2 to 2 s, with the mean being 1.0 s, which is not dependent on photon energies. The spikes exhibit symmetric time profiles with no significant difference between rise and decay times.(3) Among the most energetic spikes, nearly all of them have harder count spectra than their underlying slow-varying components. There is also a weak indication that spikes exhibiting time lags in high-energy emissions tend to have harder spectra than spikes with time lags in low-energy emissions.

  11. Accelerometry estimates field metabolic rate in giant Australian cuttlefish Sepia apama during breeding.

    PubMed

    Payne, Nicholas L; Gillanders, Bronwyn M; Seymour, Roger S; Webber, Dale M; Snelling, Edward P; Semmens, Jayson M

    2011-03-01

    1. Estimating the metabolic rate of animals in nature is central to understanding the physiological, behavioural and evolutionary ecology of animals. Doubly labelled water and heart-rate methods are the most commonly used approaches, but both have limitations that preclude their application to some systems. 2. Accelerometry has emerged as a powerful tool for estimating energy expenditure in a range of animals, but is yet to be used to estimate field metabolic rate in aquatic taxa. We combined two-dimensional accelerometry and swim-tunnel respirometry to estimate patterns of energy expenditure in giant Australian cuttlefish Sepia apama during breeding. 3. Both oxygen consumption rate (Vo2) and swimming speed showed strong positive associations with body acceleration, with coefficients of determination comparable to those using similar accelerometers on terrestrial vertebrates. Despite increased activity during the day, field metabolic rate rarely approached Vo2, and night-time Vo2 was similar to that at rest. 4. These results are consistent with the life-history strategy of this species, which has a poor capacity to exercise anaerobically, and a mating strategy that is visually based. With the logistical difficulties associated with observation in aquatic environments, accelerometry is likely to prove a valuable tool for estimating energy expenditure in aquatic animals. PMID:20880022

  12. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data

    PubMed Central

    2014-01-01

    Background Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called “uncorrelated relaxed clock” where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior. Results We develop a maximum likelihood method – Physher – that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like. Conclusions These results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at http://code.google.com/p/physher/. PMID:25055743

  13. Extinction rate estimates for plant populations in revisitation studies: Importance of detectability

    USGS Publications Warehouse

    Kery, M.

    2004-01-01

    Many researchers have obtained extinction-rate estimates for plant populations by comparing historical and current records of occurrence. A population that is no longer found is assumed to have gone extinct. Extinction can then be related to characteristics of these populations, such as habitat type, size, or species, to test ideas about what factors may affect extinction. Such studies neglect the fact that a population may be overlooked, however, which may bias estimates of extinction rates upward. In addition, if populations are unequally detectable across groups to be compared, such as habitat type or population size, comparisons become distorted to an unknown degree. To illustrate the problem, I simulated two data sets, assuming a constant extinction rate, in which populations occurred in different habitats or habitats of different size and these factors affected their detectability The conventional analysis implicitly assumed that detectability equalled 1 and used logistic regression to estimate extinction rates. It wrongly identified habitat and population size as factors affecting extinction risk. In contrast, with capture-recapture methods, unbiased estimates of extinction rates were recovered. I argue that capture-recapture methods should be considered more often in estimations of demographic parameters in plant populations and communities.

  14. A strategy for estimating the rates of recent United States land-cover changes

    USGS Publications Warehouse

    Loveland, T.R.; Sohl, T.L.; Stehman, S.V.; Gallant, A.L.; Sayler, K.L.; Napton, D.E.

    2002-01-01

    Information on the rates of land-use and land-cover change is important in addressing issues ranging from the health of aquatic resources to climate change. Unfortunately, there is a paucity of information on land-use and land-cover change except at very local levels. We describe a strategy for estimating land-cover change across the conterminous United States over the past 30 years. Change rates are estimated for 84 ecoregions using a sampling procedure and five dates of Landsat imagery. We have applied this methodology to six eastern U.S. ecoregions. Results show very high rates of change in the Plains ecoregions, high to moderate rates in the Piedmont ecoregions, and moderate to low rates in the Appalachian ecoregions. This indicates that ecoregions are appropriate strata for capturing unique patterns of land-cover change. The results of the study are being applied as we undertake the mapping of the rest of the conterminous United States.

  15. Estimation of breathing rate from respiratory sinus arrhythmia: comparison of various methods.

    PubMed

    Schäfer, Axel; Kratky, Karl W

    2008-03-01

    Although respiratory sinus arrhythmia (RSA) is a well-known and often studied phenomenon, methods to estimate (average) respiratory rate from heart rate variability via RSA have been investigated and published only sparsely. We reinvestigate three published techniques and contrast them to our own approaches. All methods were also evaluated for respiration signals to yield approximations of the true breathing rate for comparison. Our analyses are based on physiological recordings available at PhysioNet, an online database. Results show that the RSA of young supine subjects yields good approximations of mean respiratory rate in the case of time series longer than 1 min, while the estimations become noticeably less accurate for elderly persons. Our own "advanced counting method" produced the best results, and in addition principally permits even the definition of instantaneous respiratory rates. Consequently, it is recommended for further investigations. PMID:18188703

  16. Multichannel spike detector with an adaptive threshold based on a Sigma-delta control loop.

    PubMed

    Gagnon-Turcotte, G; Gosselin, B

    2015-08-01

    In this paper, we present a digital spike detector using an adaptive threshold which is suitable for real time processing of 32 electrophysiological channels in parallel. Such a new scheme is based on a Sigma-delta control loop that precisely estimates the standard deviation of the amplitude of the noise of the input signal to optimize the detection rate. Additionally, it is not dependent on the amplitude of the input signal thanks to a robust algorithm. The spike detector is implemented inside a Spartan-6 FPGA using low resources, only FPGA basic logic blocks, and is using a low clock frequency under 6 MHz for minimal power consumption. We present a comparison showing that the proposed system can compete with a dedicated off-line spike detection software. The whole system achieves up to 100% of true positive detection rate for SNRs down to 5 dB while achieving 62.3% of true positive detection rate for an SNR as low as -2 dB at a 150 AP/s firing rate. PMID:26737934

  17. Estimating the Backup Reaction Wheel Orientation Using Reaction Wheel Spin Rates Flight Telemetry from a Spacecraft

    NASA Technical Reports Server (NTRS)

    Rizvi, Farheen

    2013-01-01

    A report describes a model that estimates the orientation of the backup reaction wheel using the reaction wheel spin rates telemetry from a spacecraft. Attitude control via the reaction wheel assembly (RWA) onboard a spacecraft uses three reaction wheels (one wheel per axis) and a backup to accommodate any wheel degradation throughout the course of the mission. The spacecraft dynamics prediction depends upon the correct knowledge of the reaction wheel orientations. Thus, it is vital to determine the actual orientation of the reaction wheels such that the correct spacecraft dynamics can be predicted. The conservation of angular momentum is used to estimate the orientation of the backup reaction wheel from the prime and backup reaction wheel spin rates data. The method is applied in estimating the orientation of the backup wheel onboard the Cassini spacecraft. The flight telemetry from the March 2011 prime and backup RWA swap activity on Cassini is used to obtain the best estimate for the backup reaction wheel orientation.

  18. Improving consumption rate estimates by incorporating wild activity into a bioenergetics model.

    PubMed

    Brodie, Stephanie; Taylor, Matthew D; Smith, James A; Suthers, Iain M; Gray, Charles A; Payne, Nicholas L

    2016-04-01

    Consumption is the basis of metabolic and trophic ecology and is used to assess an animal's trophic impact. The contribution of activity to an animal's energy budget is an important parameter when estimating consumption, yet activity is usually measured in captive animals. Developments in telemetry have allowed the energetic costs of activity to be measured for wild animals; however, wild activity is seldom incorporated into estimates of consumption rates. We calculated the consumption rate of a free-ranging marine predator (yellowtail kingfish, Seriola lalandi) by integrating the energetic cost of free-ranging activity into a bioenergetics model. Accelerometry transmitters were used in conjunction with laboratory respirometry trials to estimate kingfish active metabolic rate in the wild. These field-derived consumption rate estimates were compared with those estimated by two traditional bioenergetics methods. The first method derived routine swimming speed from fish morphology as an index of activity (a "morphometric" method), and the second considered activity as a fixed proportion of standard metabolic rate (a "physiological" method). The mean consumption rate for free-ranging kingfish measured by accelerometry was 152 J·g(-1)·day(-1), which lay between the estimates from the morphometric method (μ = 134 J·g(-1)·day(-1)) and the physiological method (μ = 181 J·g(-1)·day(-1)). Incorporating field-derived activity values resulted in the smallest variance in log-normally distributed consumption rates (σ = 0.31), compared with the morphometric (σ = 0.57) and physiological (σ = 0.78) methods. Incorporating field-derived activity into bioenergetics models probably provided more realistic estimates of consumption rate compared with the traditional methods, which may further our understanding of trophic interactions that underpin ecosystem-based fisheries management. The general methods used to estimate active metabolic rates of free-ranging fish

  19. Quantitative Analysis of Calcium Spikes in Noisy Fluorescent Background

    PubMed Central

    Janicek, Radoslav; Hotka, Matej; Zahradníková, Alexandra; Zahradníková, Alexandra; Zahradník, Ivan

    2013-01-01

    Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors. PMID:23741324

  20. Post-stratification sampling in small area estimation (SAE) model for unemployment rate estimation by Bayes approach

    NASA Astrophysics Data System (ADS)

    Hanike, Yusrianti; Sadik, Kusman; Kurnia, Anang

    2016-02-01

    This research implemented unemployment rate in Indonesia that based on Poisson distribution. It would be estimated by modified the post-stratification and Small Area Estimation (SAE) model. Post-stratification was one of technique sampling that stratified after collected survey data. It's used when the survey data didn't serve for estimating the interest area. Interest area here was the education of unemployment which separated in seven category. The data was obtained by Labour Employment National survey (Sakernas) that's collected by company survey in Indonesia, BPS, Statistic Indonesia. This company served the national survey that gave too small sample for level district. Model of SAE was one of alternative to solved it. According the problem above, we combined this post-stratification sampling and SAE model. This research gave two main model of post-stratification sampling. Model I defined the category of education was the dummy variable and model II defined the category of education was the area random effect. Two model has problem wasn't complied by Poisson assumption. Using Poisson-Gamma model, model I has over dispersion problem was 1.23 solved to 0.91 chi square/df and model II has under dispersion problem was 0.35 solved to 0.94 chi square/df. Empirical Bayes was applied to estimate the proportion of every category education of unemployment. Using Bayesian Information Criteria (BIC), Model I has smaller mean square error (MSE) than model II.

  1. Estimating site occupancy rates when detection probabilities are less than one

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Lachman, G.B.; Droege, S.; Royle, J. Andrew; Langtimm, C.A.

    2002-01-01

    Nondetection of a species at a site does not imply that the species is absent unless the probability of detection is 1. We propose a model and likelihood-based method for estimating site occupancy rates when detection probabilities are 0.3). We estimated site occupancy rates for two anuran species at 32 wetland sites in Maryland, USA, from data collected during 2000 as part of an amphibian monitoring program, Frogwatch USA. Site occupancy rates were estimated as 0.49 for American toads (Bufo americanus), a 44% increase over the proportion of sites at which they were actually observed, and as 0.85 for spring peepers (Pseudacris crucifer), slightly above the observed proportion of 0.83.

  2. An Estimation of the Star Formation Rate in the Perseus Complex

    NASA Astrophysics Data System (ADS)

    Mercimek, Seyma

    2016-07-01

    The detailed study of all sources are carried on, by comparing the number of existing cores and YSOs from observations with the prediction from column density PDFs. With this investigation, we found a relation between starless cores and protostars that cores may be considered progenitors of the next generation of protostars, assuming the rate of star formation in the recent past is similar to the rate in the near future. These are also new results which have not been investigated previously. In addition, we also calculate the mean density of each starless core and its corresponding free-fall time in order to estimate star formation rate in near future. Following that, we obtained star formation efficiency from the existing stellar cores which later was used to estimate average stellar mass from standard IMF. Finally, we estimate how many starless cores will turn into stars in the predicted free fall time and how many stars will form from calculated core mass.

  3. Use of nonlinear identification in robust attitude and attitude rate estimation for SAMPEX

    NASA Astrophysics Data System (ADS)

    Mook, D. Joseph; Depena, Juan; Trost, Kelly; Wen, Jung; McPartland, Michael

    1995-05-01

    A method is described for obtaining optimal attitude estimation/identification algorithms for spacecraft lacking attitude rate measurement devices (rate gyros), and then demonstrated using actual flight data from the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX) spacecraft. SAMPEX does not have on-board rate sensing, and relies on sun sensors and a three-axis magnetometer for attitude determination. The absence of rate data normally reduces both the total amount of data available and the sampling density (in time) by a substantial fraction. In addition, attitude data is occasionally unavailable (for example, during sun occultation). As a result, the sensitivity of the estimates to model uncertainty and to measurement noise increases. In order to maintain accuracy in the attitude estimates, there is an increased need for accurate models of the rotational dynamics. The Minimum Model Error(MME)/Least Square Correlation(LSC) algorithm accurately identifies an improved model for SAMPEX to be used during periods of complete data loss or extreme noise. The model correction is determined by estimating only one orbit(the identification pass) just prior to the assumed data loss(the prediction pass). The MME estimator correctly predicted the states during the identification phase, but more importantly determines the necessary model correction trajectory, d(t). The LSC algorithm is then used to find this trajectory's functional form, H(x(t)). The results show significant improvement of the new corrected model's attitude estimates as compared to the original uncorrected model's estimates. The possible functional form of the correction term is limited at this point in the study to functions strictly of the estimated states. The results, however, strongly suggest that functions based on the relative position of the satellite may also be possible candidates for future consideration.

  4. Effects of Sample Size on Estimates of Population Growth Rates Calculated with Matrix Models

    PubMed Central

    Fiske, Ian J.; Bruna, Emilio M.; Bolker, Benjamin M.

    2008-01-01

    Background Matrix models are widely used to study the dynamics and demography of populations. An important but overlooked issue is how the number of individuals sampled influences estimates of the population growth rate (λ) calculated with matrix models. Even unbiased estimates of vital rates do not ensure unbiased estimates of λ–Jensen's Inequality implies that even when the estimates of the vital rates are accurate, small sample sizes lead to biased estimates of λ due to increased sampling variance. We investigated if sampling variability and the distribution of sampling effort among size classes lead to biases in estimates of λ. Methodology/Principal Findings Using data from a long-term field study of plant demography, we simulated the effects of sampling variance by drawing vital rates and calculating λ for increasingly larger populations drawn from a total population of 3842 plants. We then compared these estimates of λ with those based on the entire population and calculated the resulting bias. Finally, we conducted a review of the literature to determine the sample sizes typically used when parameterizing matrix models used to study plant demography. Conclusions/Significance We found significant bias at small sample sizes when survival was low (survival = 0.5), and that sampling with a more-realistic inverse J-shaped population structure exacerbated this bias. However our simulations also demonstrate that these biases rapidly become negligible with increasing sample sizes or as survival increases. For many of the sample sizes used in demographic studies, matrix models are probably robust to the biases resulting from sampling variance of vital rates. However, this conclusion may depend on the structure of populations or the distribution of sampling effort in ways that are unexplored. We suggest more intensive sampling of populations when individual survival is low and greater sampling of stages with high elasticities. PMID:18769483

  5. Order-of-Magnitude Estimate of Fast Neutron Recoil Rates in Proposed Neutrino Detector at SNS

    SciTech Connect

    Iverson, Erik B.

    2006-02-01

    Yuri Efremenko (UT-K) and Kate Scholberg (Duke) indicated, during discussions on 12 January 2006 with the SNS Neutronics Team, interest in a new type of neutrino detector to be placed within the proposed neutrino bunker at SNS, near beam-line 18, against the RTBT. The successful operation of this detector and its associated experiments would require fast-neutron recoil rates of approximately one event per day of operation or less. To this end, the author has attempted the following order-of-magnitude estimate of this recoil rate in order to judge whether or not a full calculation effort is needed or justified. For the purposes of this estimate, the author considers a one-dimensional slab geometry, in which fast and high-energy neutrons making up the general background in the target building are incident upon one side of an irbon slab. This iron slab represents the neutrino bunker walls. If we assume that a significant fraction of the dose rate throughout the target building is due to fast or high-energy neutrons, we can estimate the flux of such neutrons based upon existing shielding calculations performed for radiation protection purposes. In general, the dose rates within the target building are controlled to be less than 0.25 mrem per hour. A variety of calculations have indicated that these dose rates have significant fast and high-energy neutron components. Thus they can estimate the fast neutron flux incident on the neutrino bunker, and thereby the fast neutron flux inside that bunker. Finally, they can estimate the neutron recoil rate within a nominal detector volume. Such an estimate is outlined in Table 1.

  6. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus.

    PubMed

    Clark, Richard M; Tavaré, Simon; Doebley, John

    2005-11-01

    To estimate a rate for single nucleotide substitutions for maize (Zea mays ssp. mays), we have taken advantage of data from genetic and archaeological studies of the domestication of maize from its wild ancestor, teosinte (Z. mays ssp. parviglumis). Genetic studies have shown that the teosinte branched1 (tb1) gene was a major target of human selection during maize domestication, and sequence diversity in the intergenic region 5' to the tb1-coding sequence is extraordinarily low. We show that polymorphism in this region is consistent with new mutation following fixation for a small number of tb1 haplotypes during domestication. Archeological studies suggest that maize was domesticated approximately 6,250-10,000 years ago and subsequently the size of the maize population is thought to have expanded rapidly. Using the observed number of mutations within the region of selection at tb1, the approximate age of maize domestication, and approximations for the maize genealogy, we have derived estimates for the nucleotide substitution rate for the tb1 intergenic region. Using two approaches, one of which is a coalescent approach, we obtain rate estimates of approximately 2.9 x 10(-8) and 3.3 x 10(-8) substitutions per site per year. We also show that the pattern of polymorphism in the tb1 intergenic region appears to have been strongly affected by the mutagenic effect of DNA methylation. Excluding target sites of symmetric DNA methylation (CG and CNG sites) from analysis, the mutation rate estimates are reduced by approximately 50%-60%, while the rates for CG and CNG sites are nearly an order of magnitude higher. We use rate estimates from the tb1 region to estimate the timing of expansion of transposable elements in the maize genome and suggest that this expansion occurred primarily within the last million years. PMID:16079248

  7. Model misspecification confounds the estimation of rates and exaggerates their time dependency.

    PubMed

    Emerson, Brent C; Alvarado-Serrano, Diego F; Hickerson, Michael J

    2015-12-01

    While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using BEAST. Given the simulations, BEAST consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced. PMID:26769403

  8. Precise attitude rate estimation using star images obtained by mission telescope for satellite missions

    NASA Astrophysics Data System (ADS)

    Inamori, Takaya; Hosonuma, Takayuki; Ikari, Satoshi; Saisutjarit, Phongsatorn; Sako, Nobutada; Nakasuka, Shinichi

    2015-02-01

    Recently, small satellites have been employed in various satellite missions such as astronomical observation and remote sensing. During these missions, the attitudes of small satellites should be stabilized to a higher accuracy to obtain accurate science data and images. To achieve precise attitude stabilization, these small satellites should estimate their attitude rate under the strict constraints of mass, space, and cost. This research presents a new method for small satellites to precisely estimate angular rate using star blurred images by employing a mission telescope to achieve precise attitude stabilization. In this method, the angular velocity is estimated by assessing the quality of a star image, based on how blurred it appears to be. Because the proposed method utilizes existing mission devices, a satellite does not require additional precise rate sensors, which makes it easier to achieve precise stabilization given the strict constraints possessed by small satellites. The research studied the relationship between estimation accuracy and parameters used to achieve an attitude rate estimation, which has a precision greater than 1 × 10-6 rad/s. The method can be applied to all attitude sensors, which use optics systems such as sun sensors and star trackers (STTs). Finally, the method is applied to the nano astrometry satellite Nano-JASMINE, and we investigate the problems that are expected to arise with real small satellites by performing numerical simulations.

  9. ESTIMATING CONTACT RATES OF HAWAIIAN MONK SEALS (NEOMONACHUS SCHAUINSLANDI) USING SOCIAL NETWORK ANALYSIS.

    PubMed

    Baker, Jason D; Harting, Albert L; Barbieri, Michelle M; Johanos, Thea C; Robinson, Stacie J; Littnan, Charles L

    2016-07-01

    Understanding disease transmission dynamics, which are in part mediated by rates and patterns of social contact, is fundamental to predicting the likelihood, rate of spread, impacts, and mitigation of disease outbreaks in wildlife populations. Contact rates, which are important parameters required for epidemiologic models, are difficult to estimate. The endangered Hawaiian monk seal (Neomonachus schauinslandi) may be particularly vulnerable to morbillivirus outbreaks, due to its low abundance, lack of genetic diversity, and history of isolation from mammalian diseases. Morbillivirus epizootics have had devastating effects on other seal populations. We constructed social networks based on visual observations of individually identifiable monk seals associating onshore to estimate contact rates, assuming random mixing, and also to investigate contact patterns of different age and sex classes. Contact rates estimated from two island populations in 4 yr were remarkably similar, indicating any two individuals have about a one in 1,000 chance of making contact on any given day. Further, contact patterns within and among age and sex classes were statistically different from random. The methods we used could be broadly applied to empirically derive contact rates using association data. These rates are critical for epidemiologic modelling to simulate wildlife disease outbreaks and to inform science-based prevention and mitigation programs. PMID:27195686

  10. Geophone with depth sensitive spikes

    SciTech Connect

    Rice, J.A.; Houston, L.M.; Arevalo, R.

    1992-06-23

    This patent describes a geophone. It comprises a seismic sensitive element for sensing elastic motion and converting the motion to an electrical signal, a housing for enclosing the seismic element, and an elongated spike attachable to the housing.

  11. Wavelet analysis of epileptic spikes

    NASA Astrophysics Data System (ADS)

    Latka, Miroslaw; Was, Ziemowit; Kozik, Andrzej; West, Bruce J.

    2003-05-01

    Interictal spikes and sharp waves in human EEG are characteristic signatures of epilepsy. These potentials originate as a result of synchronous pathological discharge of many neurons. The reliable detection of such potentials has been the long standing problem in EEG analysis, especially after long-term monitoring became common in investigation of epileptic patients. The traditional definition of a spike is based on its amplitude, duration, sharpness, and emergence from its background. However, spike detection systems built solely around this definition are not reliable due to the presence of numerous transients and artifacts. We use wavelet transform to analyze the properties of EEG manifestations of epilepsy. We demonstrate that the behavior of wavelet transform of epileptic spikes across scales can constitute the foundation of a relatively simple yet effective detection algorithm.

  12. Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster

    PubMed Central

    Haag-Liautard, Cathy; Coffey, Nicole; Houle, David; Lynch, Michael; Charlesworth, Brian; Keightley, Peter D

    2008-01-01

    Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome of Drosophila melanogaster lines that had undergone approximately 200 generations of spontaneous mutation accumulation (MA). We detected a total of 28 point mutations and eight insertion-deletion (indel) mutations, yielding an estimate for the single-nucleotide mutation rate of 6.2 × 10−8 per site per fly generation. Most mutations were heteroplasmic within a line, and their frequency distribution suggests that the effective number of mitochondrial genomes transmitted per female per generation is about 30. We observed repeated occurrences of some indel mutations, suggesting that indel mutational hotspots are common. Among the point mutations, there is a large excess of G→A mutations on the major strand (the sense strand for the majority of mitochondrial genes). These mutations tend to occur at nonsynonymous sites of protein-coding genes, and they are expected to be deleterious, so do not become fixed between species. The overall mtDNA mutation rate per base pair per fly generation in Drosophila is estimated to be about 10× higher than the nuclear mutation rate, but the mitochondrial major strand G→A mutation rate is about 70× higher than the nuclear rate. Silent sites are substantially more strongly biased towards A and T than nonsynonymous sites, consistent with the extreme mutation bias towards A+T. Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of

  13. A new radial strain and strain rate estimation method using autocorrelation for carotid artery

    NASA Astrophysics Data System (ADS)

    Ye, Jihui; Kim, Hoonmin; Park, Jongho; Yeo, Sunmi; Shim, Hwan; Lim, Hyungjoon; Yoo, Yangmo

    2014-03-01

    Atherosclerosis is a leading cause of cardiovascular disease. The early diagnosis of atherosclerosis is of clinical interest since it can prevent any adverse effects of atherosclerotic vascular diseases. In this paper, a new carotid artery radial strain estimation method based on autocorrelation is presented. In the proposed method, the strain is first estimated by the autocorrelation of two complex signals from the consecutive frames. Then, the angular phase from autocorrelation is converted to strain and strain rate and they are analyzed over time. In addition, a 2D strain image over region of interest in a carotid artery can be displayed. To evaluate the feasibility of the proposed radial strain estimation method, radiofrequency (RF) data of 408 frames in the carotid artery of a volunteer were acquired by a commercial ultrasound system equipped with a research package (V10, Samsung Medison, Korea) by using a L5-13IS linear array transducer. From in vivo carotid artery data, the mean strain estimate was -0.1372 while its minimum and maximum values were -2.961 and 0.909, respectively. Moreover, the overall strain estimates are highly correlated with the reconstructed M-mode trace. Similar results were obtained from the estimation of the strain rate change over time. These results indicate that the proposed carotid artery radial strain estimation method is useful for assessing the arterial wall's stiffness noninvasively without increasing the computational complexity.

  14. Demography of forest birds in Panama: How do transients affect estimates of survival rates?

    USGS Publications Warehouse

    Brawn, J.D.; Karr, J.R.; Nichols, J.D.; Robinson, W.D.

    1998-01-01

    Estimates of annual survival rates for a multispecies sample of neotropical birds from Panama have proven controversial. Traditionally, tropical birds were thought to have high survival rates for their size, but analyses by Kart et al. (1990. Am. Nat. 136:277-91) contradicted that view, suggesting tropical birds may not have systematically high survival rates. A persistent criticism of that study has been that the estimates were biased by transient birds captured only once as they passed through the area being sampled. New models that formally adjust for transient individuals have been developed since 1990. Preliminary analyses using these models indicate that, despite some variation among species, overall estimates of survival rates for understory birds in Panama are not strongly affected by adjustments for transients. We also compare estimates of survival rates based on mark-recapture models with observations of colour-marked birds. The demographic traits of birds in the tropics (and elsewhere) vary within and among species according to combinations of historical and ongoing ecological factors. Understanding sources of this variation is the challenge for future work.

  15. Fast entropy-based CABAC rate estimation for mode decision in HEVC.

    PubMed

    Chen, Wei-Gang; Wang, Xun

    2016-01-01

    High efficiency video coding (HEVC) seeks the best code tree configuration, the best prediction unit division and the prediction mode, by evaluating the rate-distortion functional in a recursive way and using a "try all and select the best" strategy. Further, HEVC only supports context adaptive binary arithmetic coding (CABAC), which has the disadvantage of being highly sequential and having strong data dependencies, as the entropy coder. So, the development of a fast rate estimation algorithm for CABAC-based coding has a great practical significance for mode decision in HEVC. There are three elementary steps in CABAC encoding process: binarization, context modeling, and binary arithmetic coding. Typical approaches to fast CABAC rate estimation simplify or eliminate the last two steps, but leave the binarization step unchanged. To maximize the reduction of computational complexity, we propose a fast entropy-based CABAC rate estimator in this paper. It eliminates not only the modeling and the coding steps, but also the binarization step. Experimental results demonstrate that the proposed estimator is able to reduce the computational complexity of the mode decision in HEVC by 9-23 % with negligible PSNR loss and BD-rate increment, and therefore exhibits applicability to practical HEVC encoder implementation. PMID:27386240

  16. Estimation of incidence and recovery rates of Plasmodium falciparum parasitaemia from longitudinal data

    PubMed Central

    Bekessy, A.; Molineaux, L.; Storey, J.

    1976-01-01

    A method is described of estimating the malaria incidence rate ĥ and the recovery rate r from longitudinal data. The method is based on the assumption that the phenomenon of patent parasitaemia can be represented by a reversible two-state catalytic model; it is applicable to all problems that can be represented by such a model. The method was applied to data on falciparum malaria from the West African savanna and the findings suggested that immunity increases the rate of recovery from patent parasitaemia by a factor of up to 10, and also reduces the number of episodes of patent parasitaemia resulting from one inoculation. Under the effect of propoxur, ĥ varies with the estimated man-biting rate of the vector while r̂ increases, possibly owing to reduced super-infection. PMID:800968

  17. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.

    PubMed

    Willems, Thomas; Gymrek, Melissa; Poznik, G David; Tyler-Smith, Chris; Erlich, Yaniv

    2016-05-01

    Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes. PMID:27126583

  18. A Low Cost Approach to Simultaneous Orbit, Attitude, and Rate Estimation Using an Extended Kalman Filter

    NASA Technical Reports Server (NTRS)

    Deutschmann, Julie; Harman, Rick; Bar-Itzhack, Itzhack

    1998-01-01

    An innovative approach to autonomous attitude and trajectory estimation is available using only magnetic field data and rate data. The estimation is performed simultaneously using an Extended Kalman Filter, a well known algorithm used extensively in onboard applications. The magnetic field is measured on a satellite by a magnetometer, an inexpensive and reliable sensor flown on virtually all satellites in low earth orbit. Rate data is provided by a gyro, which can be costly. This system has been developed and successfully tested in a post-processing mode using magnetometer and gyro data from 4 satellites supported by the Flight Dynamics Division at Goddard. In order for this system to be truly low cost, an alternative source for rate data must be utilized. An independent system which estimate spacecraft rate has been successfully developed and tested using only magnetometer data or a combination of magnetometer data and sun sensor data, which is less costly than a gyro. This system also uses an Extended Kalman Filter. Merging the two systems will provide an extremely low cost, autonomous approach to attitude and trajectory estimation. In this work we provide the theoretical background of the combined system. The measurement matrix is developed by combining the measurement matrix of the orbit and attitude estimation EKF with the measurement matrix of the rate estimation EKF, which is composed of a pseudo-measurement which makes the effective measurement a function of the angular velocity. Associated with this is the development of the noise covariance matrix associated with the original measurement combined with the new pseudo-measurement. In addition, the combination of the dynamics from the two systems is presented along with preliminary test results.

  19. A low cost approach to simultaneous orbit, attitude, and rate estimation using an extended Kalman filter

    NASA Technical Reports Server (NTRS)

    Deutschmann, Julie; Harman, Rick; Bar-Itzhack, Itzhack

    1998-01-01

    An innovative approach to autonomous attitude and trajectory estimation is available using only magnetic field data and rate data. The estimation is performed simultaneously using an Extended Kalman Filter (EKF), a well known algorithm used extensively in onboard applications. The magnetic field is measured on a satellite by a magnetometer, an inexpensive and reliable sensor flown on virtually all satellites in low earth orbit. Rate data is provided by a gyro, which can be costly. This system has been developed and successfully tested in a post-processing mode using magnetometer and gyro data from 4 satellites supported by the Flight Dynamics Division at Goddard. In order for this system to be truly low cost, an alternative source for rate data must be utilized. An independent system which estimates spacecraft rate has been successfully developed and tested using only magnetometer data or a combination of magnetometer data and sun sensor data, which is less costly than a gyro. This system also uses an EKF. Merging the two systems will provide an extremely low cost, autonomous approach to attitude and trajectory estimation. In this work we provide the theoretical background of the combined system. The measurement matrix is developed by combining the measurement matrix of the orbit and attitude estimation EKF with the measurement matrix of the rate estimation EKF, which is composed of a pseudo-measurement which makes the effective measurement a function of the angular velocity. Associated with this is the development of the noise covariance matrix associated with the original measurement combined with the new pseudo-measurement. In addition, the combination of the dynamics from the two systems is presented along with preliminary test results.

  20. Estimated trichloroethene transformation rates due to naturally occurring biodegradation in a fractured-rock aquifer

    USGS Publications Warehouse

    Chapelle, Francis H.; Lacombe, Pierre J.; Bradley, Paul M.

    2012-01-01

    Rates of trichloroethene (TCE) mass transformed by naturally occurring biodegradation processes in a fractured rock aquifer underlying a former Naval Air Warfare Center (NAWC) site in West Trenton, New Jersey, were estimated. The methodology included (1) dividing the site into eight elements of equal size and vertically integrating observed concentrations of two daughter products of TCE biodegradation–cis-dichloroethene (cis-DCE) and chloride–using water chemistry data from a network of 88 observation wells; (2) summing the molar mass of cis-DCE, the first biodegradation product of TCE, to provide a probable underestimate of reductive biodegradation of TCE, (3) summing the molar mass of chloride, the final product of chlorinated ethene degradation, to provide a probable overestimate of overall biodegradation. Finally, lower and higher estimates of aquifer porosities and groundwater residence times were used to estimate a range of overall transformation rates. The highest TCE transformation rates estimated using this procedure for the combined overburden and bedrock aquifers was 945 kg/yr, and the lowest was 37 kg/yr. However, hydrologic considerations suggest that approximately 100 to 500 kg/yr is the probable range for overall TCE transformation rates in this system. Estimated rates of TCE transformation were much higher in shallow overburden sediments (approximately 100 to 500 kg/yr) than in the deeper bedrock aquifer (approximately 20 to 0.15 kg/yr), which reflects the higher porosity and higher contaminant mass present in the overburden. By way of comparison, pump-and-treat operations at the NAWC site are estimated to have removed between 1,073 and 1,565 kg/yr of TCE between 1996 and 2009.

  1. Diversity Dynamics in Nymphalidae Butterflies: Effect of Phylogenetic Uncertainty on Diversification Rate Shift Estimates

    PubMed Central

    Peña, Carlos; Espeland, Marianne

    2015-01-01

    The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. PMID:25830910

  2. Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.

    PubMed

    Peña, Carlos; Espeland, Marianne

    2015-01-01

    The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. PMID:25830910

  3. Existence detection and embedding rate estimation of blended speech in covert speech communications.

    PubMed

    Li, Lijuan; Gao, Yong

    2016-01-01

    Covert speech communications may be used by terrorists to commit crimes through Internet. Steganalysis aims to detect secret information in covert communications to prevent crimes. Herein, based on the average zero crossing rate of the odd-even difference (AZCR-OED), a steganalysis algorithm for blended speech is proposed; it can detect the existence and estimate the embedding rate of blended speech. First, the odd-even difference (OED) of the speech signal is calculated and divided into frames. The average zero crossing rate (ZCR) is calculated for each OED frame, and the minimum average ZCR and AZCR-OED of the entire speech signal are extracted as features. Then, a support vector machine classifier is used to determine whether the speech signal is blended. Finally, a voice activity detection algorithm is applied to determine the hidden location of the secret speech and estimate the embedding rate. The results demonstrate that without attack, the detection accuracy can reach 80 % or more when the embedding rate is greater than 10 %, and the estimated embedding rate is similar to the real value. And when some attacks occur, it can also reach relatively high detection accuracy. The algorithm has high performance in terms of accuracy, effectiveness and robustness. PMID:27462497

  4. Demography of forest birds in Panama: How do transients affect estimates of survival rates?

    USGS Publications Warehouse

    Brawn, J.D.; Karr, J.R.; Nichols, J.D.; Robinson, W.D.

    1999-01-01

    Estimates of annual survival rates of neotropical birds have proven controversial. Traditionally, tropical birds were thought to have high survival rates for their size, but analyses of a multispecies assemblage from Panama by Karr et al. (1990) provided a counterexample to that view. One criticism of that study has been that the estimates were biased by transient birds captured only once as they passed through the area being sampled. New models that formally adjust for transient individuals have been developed since 1990. Preliminary analyses indicate that these models are indeed useful in modelling the data from Panama. Nonetheless, there is considerable interspecific variation and overall estimates of annual survival rates for understorey birds in Panama remain lower than those from other studies in the Neotropics and well below the rates long assumed for tropical birds (i.e. > 0.80). Therefore, tropical birds may not have systematically higher survival rates than temperate-zone species. Variation in survival rates among tropical species suggests that theory based on a simple tradeoff between clutch size and longevity is inadequate. The demographic traits of birds in the tropics (and elsewhere) vary within and among species according to some combination of historical and ongoing ecological factors. Understanding these processes is the challenge for future work.

  5. Spatiotemporal spike encoding of a continuous external signal.

    PubMed

    Masuda, Naoki; Aihara, Kazuyuki

    2002-07-01

    Interspike intervals of spikes emitted from an integrator neuron model of sensory neurons can encode input information represented as a continuous signal from a deterministic system. If a real brain uses spike timing as a means of information processing, other neurons receiving spatiotemporal spikes from such sensory neurons must also be capable of treating information included in deterministic interspike intervals. In this article, we examine functions of neurons modeling cortical neurons receiving spatiotemporal spikes from many sensory neurons. We show that such neuron models can encode stimulus information passed from the sensory model neurons in the form of interspike intervals. Each sensory neuron connected to the cortical neuron contributes equally to the information collection by the cortical neuron. Although the incident spike train to the cortical neuron is a superimposition of spike trains from many sensory neurons, it need not be decomposed into spike trains according to the input neurons. These results are also preserved for generalizations of sensory neurons such as a small amount of leak, noise, inhomogeneity in firing rates, or biases introduced in the phase distributions. PMID:12079548

  6. Influence of projected complication rates on estimated appropriate use rates for carotid endarterectomy. Appropriateness Project Investigators. Academic Medical Center Consortium.

    PubMed Central

    Matchar, D B; Oddone, E Z; McCrory, D C; Goldstein, L B; Landsman, P B; Samsa, G; Brook, R H; Kamberg, C; Hilborne, L; Leape, L; Horner, R

    1997-01-01

    OBJECTIVE: To examine specifically the influence of estimated perioperative mortality and stroke rate on the assessment of appropriateness of carotid endarterectomy. DATA SOURCES/STUDY SETTING: An expert panel convened to rate the appropriateness of a variety of potential indications for carotid endarterectomy based on various rates of perioperative complications. We then applied these ratings to the charts of 1,160 randomly selected patients who had carotid endarterectomy in one of the 12 participating academic medical centers. STUDY DESIGN: An expert panel evaluated indications for carotid endarterectomy using the modified Delphi approach. Charts of patients who received surgery were abstracted, and clinical indications for the procedure as well as perioperative complications were recorded. To examine the impact of surgical risk assessment on the rates of appropriateness, three different definitions of risk strata for combined perioperative death or stroke were used: Definition A, low risk < 3 percent; Definition B, low risk < 5 percent; and Definition C, low risk < 7 percent. PRINCIPAL FINDINGS: Overall hospital-specific mortality ranged from 0 percent to 4.0 percent and major complications, defined as death, stroke, intracranial hemorrhage, or myocardial infarction, varied from 2.0 percent to 11.1 percent. Most patients (72 percent) had surgery for transient ischemic attack or stroke; 24 percent of patients were asymptomatic. Most patients (82 percent) had surgery on the side of a high-grade stenosis (70-99 percent). When the thresholds for operative risk were placed at the values defined by the expert panel (Definition A), only 33.5 percent of 1,160 procedures were classified as "appropriate." When the definition of low risk was shifted upward, the proportion of cases categorized as appropriate increased to 58 percent and 81.5 percent for Definitions B and C, respectively. CONCLUSIONS: Despite the high proportion of procedures performed for symptomatic

  7. Use of the point load index in estimation of the strength rating for the RMR system

    NASA Astrophysics Data System (ADS)

    Karaman, Kadir; Kaya, Ayberk; Kesimal, Ayhan

    2015-06-01

    The Rock Mass Rating (RMR) system is a worldwide reference for design applications involving estimation of rock mass properties and tunnel support. In the RMR system, Uniaxial Compressive Strength (UCS) is an important input parameter to determine the strength rating of intact rock. In practice, there are some difficulties in determining the UCS of rocks from problematic ground conditions due to rapid data requirements. In this study, a combined strength rating chart was developed to overcome this problem based on the experience gained in the last decades from the point load test. For this purpose, a total of 490 UCS and Point Load Index (PLI) data pairs collected from the accessible world literature and obtained from the Eastern Black Sea Region (EBSR) in Turkey were evaluated together. The UCS and PLI data pairs were classified for the cases of PLI < 1 and PLI > 1 MPa, and two different strength rating charts were suggested by using the regression analyses. The Variance Account For (VAF), Root Mean Square Error (RMSE) and Mean Absolute Percentage Error (MAPE) indices were calculated to compare the performance of the prediction capacity of the suggested strength rating charts. Further, the one way analysis of variance (ANOVA) was performed to test whether the means of the calculated and predicted ratings are similar to each other. Findings of the analyses have demonstrated that the combined strength rating chart for the cases of PLI < 1 and PLI > 1 MPa can be reliably used in estimation of the strength ratings for the RMR system.

  8. Bayesian fusion of algorithms for the robust estimation of respiratory rate from the photoplethysmogram.

    PubMed

    Zhu, Tingting; Pimentel, Marco A F; Clifford, Gari D; Clifton, David A

    2015-08-01

    Respiratory rate (RR) is a key vital sign that is monitored to assess the health of patients. With the increase of the availability of wearable devices, it is important that RR is extracted in a robust and noninvasive manner from the photoplethysmogram (PPG) acquired from pulse oximeters and similar devices. However, existing methods of noninvasive RR estimation suffer from a lack of robustness, resulting in the fact that they are not used in clinical practice. We propose a Bayesian approach to fusing the outputs of many RR estimation algorithms to improve the overall robustness of the resulting estimates. Our method estimates the accuracy of each algorithm and jointly infers the fused RR estimate in an unsupervised manner, with aim of producing a fused estimate that is more accurate than any of the algorithms taken individually. This approach is novel in the literature, where the latter has so far concentrated on attempting to produce single algorithms for RR estimation, without resulting in systems that have penetrated into clinical practice. A publicly-available dataset, Capnobase, was used to validate the performance of our proposed model. Our proposed methodology was compared to the best-performing individual algorithm from the literature, as well as to the results of using common fusing methodologies such as averaging, median, and maximum likelihood (ML). Our proposed methodology resulted in a mean-absolute-error (MAE) of 1.98 breaths per minute (bpm), outperformed other fusing strategies (mean fusion: 2.95 bpm; median fusion: 2.33 bpm; ML: 2.30 bpm). It also outperformed the best single algorithm (2.39 bpm) and the benchmark algorithm proposed for use with Capnobase (2.22 bpm). We conclude that the proposed fusion methodology can be used to combine RR estimates from multiple sources derived from the PPG, to infer a reliable and robust estimation of the respiratory rate in an unsupervised manner. PMID:26737693

  9. USING STABLE CARBON ISOTOPES TO ESTIMATE THE RATE OF NATURAL BIODEGRADATION OF MTBE AT FIELD SCALE

    EPA Science Inventory

    Natural biodegradation of fuel contaminants in ground water reduces the risk of contamination of drinking water wells. It is very difficult to estimate the natural rate of biodegradation of MTBE in ground water because its primary biodegradation product, TBA, is also a component...

  10. Comparing Participants' Rating and Compendium Coding to Estimate Physical Activity Intensities

    ERIC Educational Resources Information Center

    Masse, Louise C.; Eason, Karen E.; Tortolero, Susan R.; Kelder, Steven H.

    2005-01-01

    This study assessed agreement between participants' rating (PMET) and compendium coding (CMET) of estimating physical activity intensity in a population of older minority women. As part of the Women on the Move study, 224 women completed a 7-day activity diary and wore an accelerometer for 7 days. All activities recorded were coded using PMET and…

  11. The Effect of Missing Data on Estimating a Respondent's Location Using Ratings Data.

    ERIC Educational Resources Information Center

    De Ayala, R. J.

    In social science research there are a number of instruments that use a rating scale such as a Likert response scale. For a number of reasons, a respondent's response vector may not contain responses to each item. This study investigated the effect on a respondent's location estimate when a respondent is presented an item, has ample time to answer…

  12. Estimation of the velocities and discharge rates of groundwater flows by helium and tritium distributions

    SciTech Connect

    Ivanov, V.V.; Antonenko, E.F.; Obukhova, S.N.

    1995-11-01

    Modeling is used to show that bends in the curves of groundwater flows and confluence of different-age flows demonstrate themselves in spatial variability in concentration fields of {sup 4}He, {sup 3}H, and {sup 14}C isotopes. The results are used to reveal typical flows in a section of Switzerland and to estimate their velocities and discharge rates.

  13. Estimate Of The Decay Rate Constant of Hydrogen Sulfide Generation From Landfilled Drywall

    EPA Science Inventory

    Research was conducted to investigate the impact of particle size on H2S gas emissions and estimate a decay rate constant for H2S gas generation from the anaerobic decomposition of drywall. Three different particle sizes of regular drywall and one particle size of paperless drywa...

  14. Estimation of Promotion, Repetition and Dropout Rates for Learners in South African Schools

    ERIC Educational Resources Information Center

    Uys, Daniël Wilhelm; Alant, Edward John Thomas

    2015-01-01

    A new procedure for estimating promotion, repetition and dropout rates for learners in South African schools is proposed. The procedure uses three different data sources: data from the South African General Household survey, data from the Education Management Information Systems, and data from yearly reports published by the Department of Basic…

  15. Estimating rates of local species extinction, colonization and turnover in animal communities

    USGS Publications Warehouse

    Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

    1998-01-01

    Species richness has been identified as a useful state variable for conservation and management purposes. Changes in richness over time provide a basis for predicting and evaluating community responses to management, to natural disturbance, and to changes in factors such as community composition (e.g., the removal of a keystone species). Probabilistic capture-recapture models have been used recently to estimate species richness from species count and presence-absence data. These models do not require the common assumption that all species are detected in sampling efforts. We extend this approach to the development of estimators useful for studying the vital rates responsible for changes in animal communities over time; rates of local species extinction, turnover, and colonization. Our approach to estimation is based on capture-recapture models for closed animal populations that permit heterogeneity in detection probabilities among the different species in the sampled community. We have developed a computer program, COMDYN, to compute many of these estimators and associated bootstrap variances. Analyses using data from the North American Breeding Bird Survey (BBS) suggested that the estimators performed reasonably well. We recommend estimators based on probabilistic modeling for future work on community responses to management efforts as well as on basic questions about community dynamics.

  16. Non-contact estimation of heart rate and oxygen saturation using ambient light

    PubMed Central

    Bal, Ufuk

    2014-01-01

    We propose a robust method for automated computation of heart rate (HR) from digital color video recordings of the human face. In order to extract photoplethysmographic signals, two orthogonal vectors of RGB color space are used. We used a dual tree complex wavelet transform based denoising algorithm to reduce artifacts (e.g. artificial lighting, movement, etc.). Most of the previous work on skin color based HR estimation performed experiments with healthy volunteers and focused to solve motion artifacts. In addition to healthy volunteers we performed experiments with child patients in pediatric intensive care units. In order to investigate the possible factors that affect the non-contact HR monitoring in a clinical environment, we studied the relation between hemoglobin levels and HR estimation errors. Low hemoglobin causes underestimation of HR. Nevertheless, we conclude that our method can provide acceptable accuracy to estimate mean HR of patients in a clinical environment, where the measurements can be performed remotely. In addition to mean heart rate estimation, we performed experiments to estimate oxygen saturation. We observed strong correlations between our SpO2 estimations and the commercial oximeter readings PMID:25657877

  17. Estimating the secondary attack rate and serial interval of influenza-like illnesses using social media

    PubMed Central

    Yom-Tov, Elad; Johansson-Cox, Ingemar; Lampos, Vasileios; Hayward, Andrew C

    2015-01-01

    Objectives Knowledge of the secondary attack rate (SAR) and serial interval (SI) of influenza is important for assessing the severity of seasonal epidemics of the virus. To date, such estimates have required extensive surveys of target populations. Here, we propose a method for estimating the intrafamily SAR and SI from postings on the Twitter social network. This estimate is derived from a large number of people reporting ILI symptoms in them and\\or their immediate family members. Design We analyze data from the 2012–2013 and the 2013–2014 influenza seasons in England and find that increases in the estimated SAR precede increases in ILI rates reported by physicians. Results We hypothesize that observed variations in the peak value of SAR are related to the appearance of specific strains of the virus and demonstrate this by comparing the changes in SAR values over time in relation to known virology. In addition, we estimate SI (the average time between cases) as 2·41 days for 2012 and 2·48 days for 2013. Conclusions The proposed method can assist health authorities by providing near-real-time estimation of SAR and SI, and especially in alerting to sudden increases thereof. PMID:25962320

  18. A real-time maximum-likelihood heart-rate estimator for wearable textile sensors.

    PubMed

    Cheng, Mu-Huo; Chen, Li-Chung; Hung, Ying-Che; Yang, Chang Ming

    2008-01-01

    This paper presents a real-time maximum-likelihood heart-rate estimator for ECG data measured via wearable textile sensors. The ECG signals measured from wearable dry electrodes are notorious for its susceptibility to interference from the respiration or the motion of wearing person such that the signal quality may degrade dramatically. To overcome these obstacles, in the proposed heart-rate estimator we first employ the subspace approach to remove the wandering baseline, then use a simple nonlinear absolute operation to reduce the high-frequency noise contamination, and finally apply the maximum likelihood estimation technique for estimating the interval of R-R peaks. A parameter derived from the byproduct of maximum likelihood estimation is also proposed as an indicator for signal quality. To achieve the goal of real-time, we develop a simple adaptive algorithm from the numerical power method to realize the subspace filter and apply the fast-Fourier transform (FFT) technique for realization of the correlation technique such that the whole estimator can be implemented in an FPGA system. Experiments are performed to demonstrate the viability of the proposed system. PMID:19162641

  19. Rate-constrained 3D surface estimation from noise-corrupted multiview depth videos.

    PubMed

    Sun, Wenxiu; Cheung, Gene; Chou, Philip A; Florencio, Dinei; Zhang, Cha; Au, Oscar C

    2014-07-01

    Transmitting compactly represented geometry of a dynamic 3D scene from a sender can enable a multitude of imaging functionalities at a receiver, such as synthesis of virtual images at freely chosen viewpoints via depth-image-based rendering. While depth maps—projections of 3D geometry onto 2D image planes at chosen camera viewpoints-can nowadays be readily captured by inexpensive depth sensors, they are often corrupted by non-negligible acquisition noise. Given depth maps need to be denoised and compressed at the encoder for efficient network transmission to the decoder, in this paper, we consider the denoising and compression problems jointly, arguing that doing so will result in a better overall performance than the alternative of solving the two problems separately in two stages. Specifically, we formulate a rate-constrained estimation problem, where given a set of observed noise-corrupted depth maps, the most probable (maximum a posteriori (MAP)) 3D surface is sought within a search space of surfaces with representation size no larger than a prespecified rate constraint. Our rate-constrained MAP solution reduces to the conventional unconstrained MAP 3D surface reconstruction solution if the rate constraint is loose. To solve our posed rate-constrained estimation problem, we propose an iterative algorithm, where in each iteration the structure (object boundaries) and the texture (surfaces within the object boundaries) of the depth maps are optimized alternately. Using the MVC codec for compression of multiview depth video and MPEG free viewpoint video sequences as input, experimental results show that rate-constrained estimated 3D surfaces computed by our algorithm can reduce coding rate of depth maps by up to 32% compared with unconstrained estimated surfaces for the same quality of synthesized virtual views at the decoder. PMID:24876124

  20. Estimation of the critical glass transition rate and the inorganic glass thickness

    NASA Astrophysics Data System (ADS)

    Belousov, O. K.

    2009-12-01

    Procedures are described for calculating the components of a new equation obtained to estimate critical glass transition rate R c . Reported data on R c are used to calculate critical shear frequency ν t, g( m), and a technique of its calculation using absolute entropy and elastic constants is presented. Procedures for calculating the energy of defect formation in amorphous substances H ν and for estimating glass transition temperature T g are described. It is shown that the ratio H ν / q (where q = N A k BΔ T m-g , N A is Avogadro’s number, k B is the Boltzmann constant, and Δ T m-g is the difference between the melting and glass transition temperatures) can be used to estimate critical glass transition rate R c and critical glass thickness h c .

  1. Estimating Fault Slip Rates and Deformation at Complex Strike-Slip Plate Boundaries

    NASA Astrophysics Data System (ADS)

    Thatcher, Wayne; Murray-Moraleda, Jessica

    2010-05-01

    Modeling GPS velocity fields in seismically active regions worldwide indicates deformation can be efficiently and usefully described as relative motions among elastic, fault-bounded crustal blocks. These models are providing hundreds of new decadal fault slip rate estimates that can be compared with the (much smaller) independent Holocene (<10 ka) to late Quaternary (<125 ka) rates obtained by geological methods. Updated comparisons show general agreement but a subset of apparently significant outliers. Some of these outliers have been discussed previously and attributed either to a temporal change in slip rate or systematic error in one of the estimates. Here we focus particularly on recent GPS and geologic results from southern California and discuss criteria for assessing the differing rates. In southern California (and elsewhere), subjective choices of block geometry are unavoidable and introduce significant uncertainties in model formulation and in the resultant GPS fault slip rate estimates. To facilitate comparison between GPS and geologic results in southern California we use the SCEC Community Fault Model (CFM) and geologic slip rates tabulated in the 2008 Uniform California Earthquake Rupture Forecast (UCERF2) report as starting points for identifying the most important faults and specifying the block geometry. We then apply this geometry in an inversion of the SCEC Crustal Motion Model (CMM4) GPS velocity field to estimate block motions and intra-block fault slip rates and compare our results with previous work. Here we use 4 criteria to evaluate GPS/geologic slip rate differences. First: Is there even-handed evaluation of random and systematic errors? ‘Random error' is sometimes subjectively estimated and its statistical properties are unknown or idealized. Differences between ~equally likely block models introduces a systematic error into GPS rate estimates that is difficult to assess and seldom discussed. Difficulties in constraining the true

  2. A double-observer method to estimate detection rate during aerial waterfowl surveys

    USGS Publications Warehouse

    Koneff, M.D.; Royle, J. Andrew; Otto, M.C.; Wortham, J.S.; Bidwell, J.K.

    2008-01-01

    We evaluated double-observer methods for aerial surveys as a means to adjust counts of waterfowl for incomplete detection. We conducted our study in eastern Canada and the northeast United States utilizing 3 aerial-survey crews flying 3 different types of fixed-wing aircraft. We reconciled counts of front- and rear-seat observers immediately following an observation by the rear-seat observer (i.e., on-the-fly reconciliation). We evaluated 6 a priori models containing a combination of several factors thought to influence detection probability including observer, seat position, aircraft type, and group size. We analyzed data for American black ducks (Anas rubripes) and mallards (A. platyrhynchos), which are among the most abundant duck species in this region. The best-supported model for both black ducks and mallards included observer effects. Sample sizes of black ducks were sufficient to estimate observer-specific detection rates for each crew. Estimated detection rates for black ducks were 0.62 (SE = 0.10), 0.63 (SE = 0.06), and 0.74 (SE = 0.07) for pilot-observers, 0.61 (SE = 0.08), 0.62 (SE = 0.06), and 0.81 (SE = 0.07) for other front-seat observers, and 0.43 (SE = 0.05), 0.58 (SE = 0.06), and 0.73 (SE = 0.04) for rear-seat observers. For mallards, sample sizes were adequate to generate stable maximum-likelihood estimates of observer-specific detection rates for only one aerial crew. Estimated observer-specific detection rates for that crew were 0.84 (SE = 0.04) for the pilot-observer, 0.74 (SE = 0.05) for the other front-seat observer, and 0.47 (SE = 0.03) for the rear-seat observer. Estimated observer detection rates were confounded by the position of the seat occupied by an observer, because observers did not switch seats, and by land-cover because vegetation and landform varied among crew areas. Double-observer methods with on-the-fly reconciliation, although not without challenges, offer one viable option to account for detection bias in aerial waterfowl

  3. Refinement of Eocene lapse rates, fossil-leaf altimetry, and North American Cordilleran surface elevation estimates

    NASA Astrophysics Data System (ADS)

    Feng, Ran; Poulsen, Christopher J.

    2016-02-01

    Estimates of continental paleoelevation using proxy methods are essential for understanding the geodynamic, climatic, and geomorphoric evolution of ancient orogens. Fossil-leaf paleoaltimetry, one of the few quantitative proxy approaches, uses fossil-leaf traits to quantify differences in temperature or moist enthalpy between coeval coastal and inland sites along latitudes. These environmental differences are converted to elevation differences using their rates of change with elevation (lapse rate). Here, we evaluate the uncertainty associated with this method using the Eocene North American Cordillera as a case study. To do so, we develop a series of paleoclimate simulations for the Early (∼55-49 Ma) and Middle Eocene (49-40 Ma) period using a range of elevation scenarios for the western North American Cordillera. Simulated Eocene lapse rates over western North America are ∼5 °C/km and 9.8 kJ/km, close to moist adiabatic rates but significantly different from modern rates. Further, using linear lapse rates underestimates high-altitude (>3 km) temperature variability and loss of moist enthalpy induced by non-linear circulation changes in response to increasing surface elevation. Ignoring these changes leads to kilometer-scale biases in elevation estimates. In addition to these biases, we demonstrate that previous elevation estimates of the western Cordillera are affected by local climate variability at coastal fossil-leaf sites of up to ∼8 °C in temperature and ∼20 kJ in moist enthalpy, a factor which further contributes to elevation overestimates of ∼1 km for Early Eocene floras located in the Laramide foreland basins and underestimates of ∼1 km for late Middle Eocene floras in the southern Cordillera. We suggest a new approach for estimating past elevations by comparing proxy reconstructions directly with simulated distributions of temperature and moist enthalpy under a range of elevation scenarios. Using this method, we estimate mean elevations for

  4. An Empirical Comparison between Two Recursive Filters for Attitude and Rate Estimation of Spinning Spacecraft

    NASA Technical Reports Server (NTRS)

    Harman, Richard R.

    2006-01-01

    The advantages of inducing a constant spin rate on a spacecraft are well known. A variety of science missions have used this technique as a relatively low cost method for conducting science. Starting in the late 1970s, NASA focused on building spacecraft using 3-axis control as opposed to the single-axis control mentioned above. Considerable effort was expended toward sensor and control system development, as well as the development of ground systems to independently process the data. As a result, spinning spacecraft development and their resulting ground system development stagnated. In the 1990s, shrinking budgets made spinning spacecraft an attractive option for science. The attitude requirements for recent spinning spacecraft are more stringent and the ground systems must be enhanced in order to provide the necessary attitude estimation accuracy. Since spinning spacecraft (SC) typically have no gyroscopes for measuring attitude rate, any new estimator would need to rely on the spacecraft dynamics equations. One estimation technique that utilized the SC dynamics and has been used successfully in 3-axis gyro-less spacecraft ground systems is the pseudo-linear Kalman filter algorithm. Consequently, a pseudo-linear Kalman filter has been developed which directly estimates the spacecraft attitude quaternion and rate for a spinning SC. Recently, a filter using Markley variables was developed specifically for spinning spacecraft. The pseudo-linear Kalman filter has the advantage of being easier to implement but estimates the quaternion which, due to the relatively high spinning rate, changes rapidly for a spinning spacecraft. The Markley variable filter is more complicated to implement but, being based on the SC angular momentum, estimates parameters which vary slowly. This paper presents a comparison of the performance of these two filters. Monte-Carlo simulation runs will be presented which demonstrate the advantages and disadvantages of both filters.

  5. A Bayesian Hierarchical Modeling Scheme for Estimating Erosion Rates Under Current Climate Conditions

    NASA Astrophysics Data System (ADS)

    Lowman, L.; Barros, A. P.

    2014-12-01

    Computational modeling of surface erosion processes is inherently difficult because of the four-dimensional nature of the problem and the multiple temporal and spatial scales that govern individual mechanisms. Landscapes are modified via surface and fluvial erosion and exhumation, each of which takes place over a range of time scales. Traditional field measurements of erosion/exhumation rates are scale dependent, often valid for a single point-wise location or averaging over large aerial extents and periods with intense and mild erosion. We present a method of remotely estimating erosion rates using a Bayesian hierarchical model based upon the stream power erosion law (SPEL). A Bayesian approach allows for estimating erosion rates using the deterministic relationship given by the SPEL and data on channel slopes and precipitation at the basin and sub-basin scale. The spatial scale associated with this framework is the elevation class, where each class is characterized by distinct morphologic behavior observed through different modes in the distribution of basin outlet elevations. Interestingly, the distributions of first-order outlets are similar in shape and extent to the distribution of precipitation events (i.e. individual storms) over a 14-year period between 1998-2011. We demonstrate an application of the Bayesian hierarchical modeling framework for five basins and one intermontane basin located in the central Andes between 5S and 20S. Using remotely sensed data of current annual precipitation rates from the Tropical Rainfall Measuring Mission (TRMM) and topography from a high resolution (3 arc-seconds) digital elevation map (DEM), our erosion rate estimates are consistent with decadal-scale estimates based on landslide mapping and sediment flux observations and 1-2 orders of magnitude larger than most millennial and million year timescale estimates from thermochronology and cosmogenic nuclides.

  6. Enhanced algorithm based on persistent scatterer interferometry for the estimation of high-rate land subsidence

    NASA Astrophysics Data System (ADS)

    Sadeghi, Zahra; Valadan Zoej, Mohammad Javad; Dehghani, Maryam; Chang, Ni-Bin

    2012-01-01

    Persistent scatterer interferometry (PSI) techniques using amplitude analysis and considering a temporal deformation model for PS pixel selection are unable to identify PS pixels in rural areas lacking human-made structures. In contrast, high rates of land subsidence lead to significant phase-unwrapping errors in a recently developed PSI algorithm (StaMPS) that applies phase stability and amplitude analysis to select the PS pixels in rural areas. The objective of this paper is to present an enhanced algorithm based on PSI to estimate the deformation rate in rural areas undergoing high and nearly constant rates of deformation. The proposed approach integrates the strengths of all of the existing PSI algorithms in PS pixel selection and phase unwrapping. PS pixels are first selected based on the amplitude information and phase-stability estimation as performed in StaMPS. The phase-unwrapping step, including the deformation rate and phase-ambiguity estimation, is then performed using least-squares ambiguity decorrelation adjustment (LAMBDA). The atmospheric phase screen (APS) and nonlinear deformation contribution to the phase are estimated by applying a high-pass temporal filter to the residuals derived from the LAMBDA method. The final deformation rate and the ambiguity parameter are re-estimated after subtracting the APS and the nonlinear deformation from that of the initial phase. The proposed method is applied to 22 ENVISAT ASAR images of southwestern Tehran basin captured between 2003 and 2008. A quantitative comparison with the results obtained with leveling and GPS measurements demonstrates the significant improvement of the PSI technique.

  7. Estimation of the prevalence and rate of acute transfusion reactions occurring in Windhoek, Namibia

    PubMed Central

    Meza, Benjamin P.L.; Lohrke, Britta; Wilkinson, Robert; Pitman, John P.; Shiraishi, Ray W.; Bock, Naomi; Lowrance, David W.; Kuehnert, Matthew J.; Mataranyika, Mary; Basavaraju, Sridhar V.

    2014-01-01

    Background Acute transfusion reactions are probably common in sub-Saharan Africa, but transfusion reaction surveillance systems have not been widely established. In 2008, the Blood Transfusion Service of Namibia implemented a national acute transfusion reaction surveillance system, but substantial under-reporting was suspected. We estimated the actual prevalence and rate of acute transfusion reactions occurring in Windhoek, Namibia. Methods The percentage of transfusion events resulting in a reported acute transfusion reaction was calculated. Actual percentage and rates of acute transfusion reactions per 1,000 transfused units were estimated by reviewing patients’ records from six hospitals, which transfuse >99% of all blood in Windhoek. Patients’ records for 1,162 transfusion events occurring between 1st January – 31st December 2011 were randomly selected. Clinical and demographic information were abstracted and Centers for Disease Control and Prevention National Healthcare Safety Network criteria were applied to categorize acute transfusion reactions1. Results From January 1 – December 31, 2011, there were 3,697 transfusion events (involving 10,338 blood units) in the selected hospitals. Eight (0.2%) acute transfusion reactions were reported to the surveillance system. Of the 1,162 transfusion events selected, medical records for 785 transfusion events were analysed, and 28 acute transfusion reactions were detected, of which only one had also been reported to the surveillance system. An estimated 3.4% (95% confidence interval [CI]: 2.3–4.4) of transfusion events in Windhoek resulted in an acute transfusion reaction, with an estimated rate of 11.5 (95% CI: 7.6–14.5) acute transfusion reactions per 1,000 transfused units. Conclusion The estimated actual rate of acute transfusion reactions is higher than the rate reported to the national haemovigilance system. Improved surveillance and interventions to reduce transfusion-related morbidity and mortality

  8. Estimating The Rate of Technology Adoption for Cockpit Weather Information Systems

    NASA Technical Reports Server (NTRS)

    Kauffmann, Paul; Stough, H. P.

    2000-01-01

    In February 1997, President Clinton announced a national goal to reduce the weather related fatal accident rate for aviation by 80% in ten years. To support that goal, NASA established an Aviation Weather Information Distribution and Presentation Project to develop technologies that will provide timely and intuitive information to pilots, dispatchers, and air traffic controllers. This information should enable the detection and avoidance of atmospheric hazards and support an improvement in the fatal accident rate related to weather. A critical issue in the success of NASA's weather information program is the rate at which the market place will adopt this new weather information technology. This paper examines that question by developing estimated adoption curves for weather information systems in five critical aviation segments: commercial, commuter, business, general aviation, and rotorcraft. The paper begins with development of general product descriptions. Using this data, key adopters are surveyed and estimates of adoption rates are obtained. These estimates are regressed to develop adoption curves and equations for weather related information systems. The paper demonstrates the use of adoption rate curves in product development and research planning to improve managerial decision processes and resource allocation.

  9. GPS-based Real-Time and High-Rate Estimation of Earth Orientation Parameters

    NASA Astrophysics Data System (ADS)

    Bertiger, W. I.; Bar-Sever, Y. E.; Gross, R. S.

    2014-12-01

    Accurate real-time values of Earth orientation parameters (EOP) (X and Y polar motion and rates, UT1-UTC rates) are desirable for a number of real-time applications, including GNSS orbit determination, positioning and timing, and deep space navigation. We will demonstrate a new capability to estimate EOPs, namely, X and Y polar motion and rates, UT1-UTC rates from GPS data alone in real time, and at high rate. Using RTGx, a new GNSS modeling and data analysis software developed at JPL to replace GIPSY and Real Time GIPSY (RTG), we explore estimation of EOPs within a real-time GPS orbit determination operation. We first characterize the errors in the conventional 1-2 days EOP predictions available through the IERS Bulletin A, and assess the impact of these errors on GPS orbit determination accuracy and on other key performance metrics. We then evaluate a variety of EOP stochastic estimation schemes, and demonstrate the ability to recover, in real-time, accurate EOP values with very high temporal granularity.

  10. Estimating resting metabolic rate by biologging core and subcutaneous temperature in a mammal.

    PubMed

    Rey, Benjamin; Halsey, Lewis G; Hetem, Robyn S; Fuller, Andrea; Mitchell, Duncan; Rouanet, Jean-Louis

    2015-05-01

    Tri-axial accelerometry has been used to continuously and remotely assess field metabolic rates in free-living endotherms. However, in cold environments, the use of accelerometry may underestimate resting metabolic rate because cold-induced stimulation of metabolic rate causes no measurable acceleration. To overcome this problem, we investigated if logging the difference between core and subcutaneous temperatures (ΔTc-s) could reveal the metabolic costs associated with cold exposure. Using implanted temperature data loggers, we recorded core and subcutaneous temperatures continuously in eight captive rabbits (Oryctolagus cuniculus) and concurrently measured their resting metabolic rate by indirect calorimetry, at ambient temperatures ranging from -7 to +25°C. ΔTc-s showed no circadian fluctuations in warm (+23°C) or cold (+5°C) environments implying that the ΔTc-s was not affected by an endogenous circadian rhythm in our laboratory conditions. ΔTc-s correlated well with resting metabolic rate (R(2)=0.77) across all ambient temperatures except above the upper limit of the thermoneutral zone (+25°C). Determining ΔTc-s could therefore provide a complementary approach for better estimating resting metabolic rate of animals within and below their thermoneutral zone. Combining data from accelerometers with such measures of body temperature could improve estimates of the overall field metabolic rate of free-living endotherms. PMID:25636902

  11. Relationships between recapture rates from different gears for estimating walleye abundance in northern Wisconsin lakes

    USGS Publications Warehouse

    Rogers, M.W.; Hansen, M.J.; Beard, T.D., Jr.

    2005-01-01

    Maximizing sampling efficiency and reducing sampling costs are desirable goals for fisheries management agencies. Expensive and labor-intensive methods (such as mark-recapture) are commonly used to estimate the population abundance of walleye Sander vitreus, but more efficient methods may be available. We compared recapture rates from surveys and harvests to evaluate the efficiency of currently used recapture gears and the potential for using gears that require less effort. To evaluate the usefulness of walleye harvest as mark-recapture samples, we used errors-in-variables models to determine whether recapture rates differed between fyke-netting and spearing, electrofishing and spearing, and electrofishing and angling. We found no significant differences between fyke-netting and adult walleye electrofishing recapture rates or between spearing and adult walleye electrofishing recapture rates. In contrast, we found that recapture rates from angling and electrofishing differed significantly in lakes with and without minimum length limits. We concluded that the lack of significant differences between the slopes of some harvest and survey recapture rates may allow the use of harvest recapture rates to estimate walleye abundance, but the biases associated with each gear should be considered. We also concluded that more attention should be given to understanding the biases of recapture gears. ?? Copyright by the American Fisheries Society 2005.

  12. Accuracy of pulse oximeters in estimating heart rate at rest and during exercise.

    PubMed Central

    Iyriboz, Y; Powers, S; Morrow, J; Ayers, D; Landry, G

    1991-01-01

    Pulse oximeters are being widely used for non-invasive, simultaneous assessment of haemoglobin oxygen saturation. They are reliable, accurate, relatively inexpensive and portable. Pulse oximeters are often used for estimating heart rate at rest and during exercise. However, at present the data available to validate their use as heart rate monitors are not sufficient. We evaluated the accuracy of two oximeters (Radiometer, ear and finger probe; Ohmeda 3700, ear probe) in monitoring heart rate during incremental exercise by comparing the pulse oximeters with simultaneous ECG readings. Data were collected on eight men (713 heart rate readings) during graded cycle ergometer and treadmill exercise to volitional fatigue. Analysis by linear regression revealed that general oximeter readings significantly correlated with those of ECG (r = 0.91, P less than 0.0001). However, comparison of heart rate at each level of work showed that oximeter readings significantly (P less than 0.05) under-estimated rates above 155 beats/min. These results indicate that the use of pulse oximeters as heart rate monitors during strenuous exercise is questionable. This inaccuracy may well originate from the instability of the probes, sweating, other artefacts during exercise, and measurement of different components in the cardiovascular cycle. PMID:1777787

  13. Computing Complex Visual Features with Retinal Spike Times

    PubMed Central

    Sompolinsky, Haim; Meister, Markus

    2013-01-01

    Neurons in sensory systems can represent information not only by their firing rate, but also by the precise timing of individual spikes. For example, certain retinal ganglion cells, first identified in the salamander, encode the spatial structure of a new image by their first-spike latencies. Here we explore how this temporal code can be used by downstream neural circuits for computing complex features of the image that are not available from the signals of individual ganglion cells. To this end, we feed the experimentally observed spike trains from a population of retinal ganglion cells to an integrate-and-fire model of post-synaptic integration. The synaptic weights of this integration are tuned according to the recently introduced tempotron learning rule. We find that this model neuron can perform complex visual detection tasks in a single synaptic stage that would require multiple stages for neurons operating instead on neural spike counts. Furthermore, the model computes rapidly, using only a single spike per afferent, and can signal its decision in turn by just a single spike. Extending these analyses to large ensembles of simulated retinal signals, we show that the model can detect the orientation of a visual pattern independent of its phase, an operation thought to be one of the primitives in early visual processing. We analyze how these computations work and compare the performance of this model to other schemes for reading out spike-timing information. These results demonstrate that the retina formats spatial information into temporal spike sequences in a way that favors computation in the time domain. Moreover, complex image analysis can be achieved already by a simple integrate-and-fire model neuron, emphasizing the power and plausibility of rapid neural computing with spike times. PMID:23301021

  14. Cuff-Free Blood Pressure Estimation Using Pulse Transit Time and Heart Rate

    PubMed Central

    Wang, Ruiping; Jia, Wenyan; Mao, Zhi-Hong; Sclabassi, Robert J.

    2015-01-01

    It has been reported that the pulse transit time (PTT), the interval between the peak of the R-wave in electrocardiogram (ECG) and the fingertip photoplethysmogram (PPG), is related to arterial stiffness, and can be used to estimate the systolic blood pressure (SBP) and diastolic blood pressure (DBP). This phenomenon has been used as the basis to design portable systems for continuously cuff-less blood pressure measurement, benefiting numerous people with heart conditions. However, the PTT-based blood pressure estimation may not be sufficiently accurate because the regulation of blood pressure within the human body is a complex, multivariate physiological process. Considering the negative feedback mechanism in the blood pressure control, we introduce the heart rate (HR) and the blood pressure estimate in the previous step to obtain the current estimate. We validate this method using a clinical database. Our results show that the PTT, HR and previous estimate reduce the estimated error significantly when compared to the conventional PTT estimation approach (p<0.05). PMID:26213717

  15. Simultaneous use of mark-recapture and radiotelemetry to estimate survival, movement, and capture rates

    USGS Publications Warehouse

    Powell, L.A.; Conroy, M.J.; Hines, J.E.; Nichols, J.D.; Krementz, D.G.

    2000-01-01

    Biologists often estimate separate survival and movement rates from radio-telemetry and mark-recapture data from the same study population. We describe a method for combining these data types in a single model to obtain joint, potentially less biased estimates of survival and movement that use all available data. We furnish an example using wood thrushes (Hylocichla mustelina) captured at the Piedmont National Wildlife Refuge in central Georgia in 1996. The model structure allows estimation of survival and capture probabilities, as well as estimation of movements away from and into the study area. In addition, the model structure provides many possibilities for hypothesis testing. Using the combined model structure, we estimated that wood thrush weekly survival was 0.989 ? 0.007 ( ?SE). Survival rates of banded and radio-marked individuals were not different (alpha hat [S_radioed, ~ S_banded]=log [S hat _radioed/ S hat _banded]=0.0239 ? 0.0435). Fidelity rates (weekly probability of remaining in a stratum) did not differ between geographic strata (psi hat=0.911 ? 0.020; alpha hat [psi11, psi22]=0.0161 ? 0.047), and recapture rates ( = 0.097 ? 0.016) banded and radio-marked individuals were not different (alpha hat [p_radioed, p_banded]=0.145 ? 0.655). Combining these data types in a common model resulted in more precise estimates of movement and recapture rates than separate estimation, but ability to detect stratum or mark-specific differences in parameters was week. We conducted simulation trials to investigate the effects of varying study designs on parameter accuracy and statistical power to detect important differences. Parameter accuracy was high (relative bias [RBIAS] <2 %) and confidence interval coverage close to nominal, except for survival estimates of banded birds for the 'off study area' stratum, which were negatively biased (RBIAS -7 to -15%) when sample sizes were small (5-10 banded or radioed animals 'released' per time interval). To provide

  16. Empirical Bayes estimation of proportions with application to cowbird parasitism rates

    USGS Publications Warehouse

    Link, W.A.; Hahn, D.C.

    1996-01-01

    Bayesian models provide a structure for studying collections of parameters such as are considered in the investigation of communities, ecosystems, and landscapes. This structure allows for improved estimation of individual parameters, by considering them in the context of a group of related parameters. Individual estimates are differentially adjusted toward an overall mean, with the magnitude of their adjustment based on their precision. Consequently, Bayesian estimation allows for a more credible identification of extreme values in a collection of estimates. Bayesian models regard individual parameters as values sampled from a specified probability distribution, called a prior. The requirement that the prior be known is often regarded as an unattractive feature of Bayesian analysis and may be the reason why Bayesian analyses are not frequently applied in ecological studies. Empirical Bayes methods provide an alternative approach that incorporates the structural advantages of Bayesian models while requiring a less stringent specification of prior knowledge. Rather than requiring that the prior distribution be known, empirical Bayes methods require only that it be in a certain family of distributions, indexed by hyperparameters that can be estimated from the available data. This structure is of interest per se, in addition to its value in allowing for improved estimation of individual parameters; for example, hypotheses regarding the existence of distinct subgroups in a collection of parameters can be considered under the empirical Bayes framework by allowing the hyperparameters to vary among subgroups. Though empirical Bayes methods have been applied in a variety of contexts, they have received little attention in the ecological literature. We describe the empirical Bayes approach in application to estimation of proportions, using data obtained in a community-wide study of cowbird parasitism rates for illustration. Since observed proportions based on small sample

  17. Estimating streambed travel times and respiration rates based on temperature and oxygen consumption

    NASA Astrophysics Data System (ADS)

    Vieweg, M.; Fleckenstein, J. H.; Schmidt, C.

    2015-12-01

    Oxygen consumption is a common proxy for aerobic respiration and novel in situ measurement techniques with high spatial resolution enable an accurate determination of the oxygen distribution in the streambed. The oxygen concentration at a certain location in the streambed depends on the input concentration, the respiration rate, temperature, and the travel time of the infiltrating flowpath. While oxygen concentrations and temperature can directly be measured, respiration rate and travel time must be estimated from the data. We investigated the interplay of these factors using a 6 month long, 5-min resolution dataset collected in a 3rdorder gravel-bed stream. Our objective was twofold, to determine transient rates of hyporheic respiration and to estimate travel times in the streambed based solely on oxygen and temperature measurements. Our results show that temperature and travel time explains ~70% of the variation in oxygen concentration in the streambed. Independent travel times were obtained using natural variations in the electrical conductivity (EC) of the stream water as tracer (µ=4.1 h; σ=2.3 h). By combining these travel times with the oxygen consumption, we calculated a first order respiration rate (µ=9.7 d-1; σ=6.1 d-1). Variations in the calculated respiration rate are largely explained by variations in streambed temperature. An empirical relationship between our respiration rate and temperature agrees with the theoretical Boltzmann-Arrhenius equation. With this relationship, a temperature-based respiration rate can be estimated and used to re-estimate subsurface travel times. The resulting travel times distinctively resemble the EC-derived travel times (R20.47; Nash-Sutcliffe coefficient 0.32). Both calculations of travel time are correlated to stream water levels and increase during discharge events, enhancing the oxygen consumption for these periods. No other physical factors besides temperature were significantly correlated with the respiration

  18. A reward band study of mallards to estimate band reporting rates

    USGS Publications Warehouse

    Henny, C.J.; Burnham, K.P.

    1976-01-01

    Reward bands ($10) were placed on 2,122 hatching-year mallards (Anas platyrhynchos), and an additional 11,490 received conventional bands (controls) to estimate band reporting rates. An analysis of band recoveries indicated that the reporting rate was dependent primarily upon three factors: (1) the distance banded birds were recovered from the banding site, (2) band collecting activities of conservation agencies (usually near banding sites), and ( 3) the intensity of banding effort in the region (frequency of banded birds in the population of the region). Reporting rates were uniformly depressed near the banding sites, but they showed an east-west cline at distances greater than 80 km from the banding sites. The reporting rate was highest in the west. Limited data on historical band reporting rates were compiled. Recommendations are given for adjusting band recoveries to account for the nonreporting of bands for 1957-73.

  19. Testing the accuracy of a 1-D volcanic plume model in estimating mass eruption rate

    USGS Publications Warehouse

    Mastin, Larry G.

    2014-01-01

    During volcanic eruptions, empirical relationships are used to estimate mass eruption rate from plume height. Although simple, such relationships can be inaccurate and can underestimate rates in windy conditions. One-dimensional plume models can incorporate atmospheric conditions and give potentially more accurate estimates. Here I present a 1-D model for plumes in crosswind and simulate 25 historical eruptions where plume height Hobs was well observed and mass eruption rate Mobs could be calculated from mapped deposit mass and observed duration. The simulations considered wind, temperature, and phase changes of water. Atmospheric conditions were obtained from the National Center for Atmospheric Research Reanalysis 2.5° model. Simulations calculate the minimum, maximum, and average values (Mmin, Mmax, and Mavg) that fit the plume height. Eruption rates were also estimated from the empirical formula Mempir = 140Hobs4.14 (Mempir is in kilogram per second, Hobs is in kilometer). For these eruptions, the standard error of the residual in log space is about 0.53 for Mavg and 0.50 for Mempir. Thus, for this data set, the model is slightly less accurate at predicting Mobs than the empirical curve. The inability of this model to improve eruption rate estimates may lie in the limited accuracy of even well-observed plume heights, inaccurate model formulation, or the fact that most eruptions examined were not highly influenced by wind. For the low, wind-blown plume of 14–18 April 2010 at Eyjafjallajökull, where an accurate plume height time series is available, modeled rates do agree better with Mobs than Mempir.

  20. A stimulus-dependent spike threshold is an optimal neural coder

    PubMed Central

    Jones, Douglas L.; Johnson, Erik C.; Ratnam, Rama

    2015-01-01

    A neural code based on sequences of spikes can consume a significant portion of the brain's energy budget. Thus, energy considerations would dictate that spiking activity be kept as low as possible. However, a high spike-rate improves the coding and representation of signals in spike trains, particularly in sensory systems. These are competing demands, and selective pressure has presumably worked to optimize coding by apportioning a minimum number of spikes so as to maximize coding fidelity. The mechanisms by which a neuron generates spikes while maintaining a fidelity criterion are not known. Here, we show that a signal-dependent neural threshold, similar to a dynamic or adapting threshold, optimizes the trade-off between spike generation (encoding) and fidelity (decoding). The threshold mimics a post-synaptic membrane (a low-pass filter) and serves as an internal decoder. Further, it sets the average firing rate (the energy constraint). The decoding process provides an internal copy of the coding error to the spike-generator which emits a spike when the error equals or exceeds a spike threshold. When optimized, the trade-off leads to a deterministic spike firing-rule that generates optimally timed spikes so as to maximize fidelity. The optimal coder is derived in closed-form in the limit of high spike-rates, when the signal can be approximated as a piece-wise constant signal. The predicted spike-times are close to those obtained experimentally in the primary electrosensory afferent neurons of weakly electric fish (Apteronotus leptorhynchus) and pyramidal neurons from the somatosensory cortex of the rat. We suggest that KCNQ/Kv7 channels (underlying the M-current) are good candidates for the decoder. They are widely coupled to metabolic processes and do not inactivate. We conclude that the neural threshold is optimized to generate an energy-efficient and high-fidelity neural code. PMID:26082710

  1. Measured rates of sedimentation: What exactly are we estimating, and why?

    NASA Astrophysics Data System (ADS)

    Tipper, John C.

    2016-06-01

    radionuclide concentrations. These two strategies are reviewed in this paper. Sets of measurements made in systems that are active today can certainly be used to estimate the rate of sedimentation for the system as a whole. This estimation is best carried out using geostatistical estimation techniques. The alternative is simply to average the measured rate values. This latter approach should not be used, however, because the mean sedimentation rate in a system gives information only about the net sediment movement at the system boundaries. It says nothing at all about how the system is operating or about its spatial and temporal variability. Measurements of rates of sedimentation made for source-to-sink studies are necessarily made in stratigraphic successions. The measurements are used to estimate quantities in the sediment mass budget equation. The amount of decumulation is inherently incapable of being measured in stratigraphic successions, therefore there are always unknowns in the mass budget equation whenever the lithic surface at the start of the time interval considered cannot be recognised everywhere. This means that the mass budget equation is applicable in practice only when all the systems involved in the study are entirely non-erosional for that entire time interval - a highly unrealistic situation. The consistently inverse relationship documented between accumulation rates and measurement timespan is taken usually to indicate that this relationship is substantially scale-invariant. This in turn is often taken as indicating that the stratigraphic record is fractal in nature. There are nevertheless grounds for doubt, all of which relate to the ways that the data are collected and used for estimation. The relationship is in fact the natural mathematical result of last-in-first-out (LIFO) operation and is produced in any type of system in which addition and removal processes both operate. It says nothing particular about sedimentation processes. The future analysis

  2. The Effect of Sensor Failure on the Attitude and Rate Estimation of MAP Spacecraft

    NASA Technical Reports Server (NTRS)

    Bar-Itzhack, Itzhack Y.; Harman, Richard R.

    2003-01-01

    This work describes two algorithms for computing the angular rate and attitude in case of a gyro and a Star Tracker failure in the Microwave Anisotropy Probe (MAP) satellite, which was placed in the L2 parking point from where it collects data to determine the origin of the universe. The nature of the problem is described, two algorithms are suggested, an observability study is carried out and real MAP data are used to determine the merit of the algorithms. It is shown that one of the algorithms yields a good estimate of the rates but not of the attitude whereas the other algorithm yields a good estimate of the rate as well as two of the three attitude angles. The estimation of the third angle depends on the initial state estimate. There is a contradiction between this result and the outcome of the observability analysis. An explanation of this contradiction is given in the paper. Although this work treats a particular spacecraft, its conclusions are more general.

  3. Sleep Quality Estimation based on Chaos Analysis for Heart Rate Variability

    NASA Astrophysics Data System (ADS)

    Fukuda, Toshio; Wakuda, Yuki; Hasegawa, Yasuhisa; Arai, Fumihito; Kawaguchi, Mitsuo; Noda, Akiko

    In this paper, we propose an algorithm to estimate sleep quality based on a heart rate variability using chaos analysis. Polysomnography(PSG) is a conventional and reliable system to diagnose sleep disorder and to evaluate its severity and therapeatic effect, by estimating sleep quality based on multiple channels. However, a recording process requires a lot of time and a controlled environment for measurement and then an analyzing process of PSG data is hard work because the huge sensed data should be manually evaluated. On the other hand, it is focused that some people make a mistake or cause an accident due to lost of regular sleep and of homeostasis these days. Therefore a simple home system for checking own sleep is required and then the estimation algorithm for the system should be developed. Therefore we propose an algorithm to estimate sleep quality based only on a heart rate variability which can be measured by a simple sensor such as a pressure sensor and an infrared sensor in an uncontrolled environment, by experimentally finding the relationship between chaos indices and sleep quality. The system including the estimation algorithm can inform patterns and quality of own daily sleep to a user, and then the user can previously arranges his life schedule, pays more attention based on sleep results and consult with a doctor.

  4. Fetal QRS detection and heart rate estimation: a wavelet-based approach.

    PubMed

    Almeida, Rute; Gonçalves, Hernâni; Bernardes, João; Rocha, Ana Paula

    2014-08-01

    Fetal heart rate monitoring is used for pregnancy surveillance in obstetric units all over the world but in spite of recent advances in analysis methods, there are still inherent technical limitations that bound its contribution to the improvement of perinatal indicators. In this work, a previously published wavelet transform based QRS detector, validated over standard electrocardiogram (ECG) databases, is adapted to fetal QRS detection over abdominal fetal ECG. Maternal ECG waves were first located using the original detector and afterwards a version with parameters adapted for fetal physiology was applied to detect fetal QRS, excluding signal singularities associated with maternal heartbeats. Single lead (SL) based marks were combined in a single annotator with post processing rules (SLR) from which fetal RR and fetal heart rate (FHR) measures can be computed. Data from PhysioNet with reference fetal QRS locations was considered for validation, with SLR outperforming SL including ICA based detections. The error in estimated FHR using SLR was lower than 20 bpm for more than 80% of the processed files. The median error in 1 min based FHR estimation was 0.13 bpm, with a correlation between reference and estimated FHR of 0.48, which increased to 0.73 when considering only records for which estimated FHR > 110 bpm. This allows us to conclude that the proposed methodology is able to provide a clinically useful estimation of the FHR. PMID:25070210

  5. Estimation of suspended-sediment rating curves and mean suspended-sediment loads

    USGS Publications Warehouse

    Crawford, Charles G.

    1991-01-01

    A simulation study was done to evaluate: (1) the accuracy and precision of parameter estimates for the bias-corrected, transformed-linear and non-linear models obtained by the method of least squares; (2) the accuracy of mean suspended-sediment loads calculated by the flow-duration, rating-curve method using model parameters obtained by the alternative methods. Parameter estimates obtained by least squares for the bias-corrected, transformed-linear model were considerably more precise than those obtained for the non-linear or weighted non-linear model. The accuracy of parameter estimates obtained for the biascorrected, transformed-linear and weighted non-linear model was similar and was much greater than the accuracy obtained by non-linear least squares. The improved parameter estimates obtained by the biascorrected, transformed-linear or weighted non-linear model yield estimates of mean suspended-sediment load calculated by the flow-duration, rating-curve method that are more accurate and precise than those obtained for the non-linear model.

  6. Recombination in the Ge-spiked monoemitter of the SiGe:C HBTs

    NASA Astrophysics Data System (ADS)

    You, Shuzhen; Decoutere, Stefaan; Sibaja-Hernandez, Arturo; Venegas, Rafael; Huylenbroeck, Stefaan Van; Meyer, Kristin De

    2011-07-01

    A SiGe spike in the monoemitter of a SiGe:C HBT locally increases the recombination rate. The narrower energy bandgap of SiGe compared to Si increases the minority charge storage, resulting in higher recombination rate. The SiGe spike acts as a virtual contact and increases the base current. This results in lower current gain, and hence higher BV CEO. This paper studies the physical mechanism for this higher recombination rate in the SiGe spike, and it calculates the minority carrier lifetime in the SiGe spike.

  7. Estimating sustainable bycatch rates for California sea lion populations in the Gulf of California.

    PubMed

    Underwood, Jared G; Hernandez Camacho, Claudia J; Aurioles-Gamboa, David; Gerber, Leah R

    2008-06-01

    Commercial and subsistence fisheries pressure is increasing in the Gulf of California, Mexico. One consequence often associated with high levels of fishing pressure is an increase in bycatch of marine mammals and birds. Fisheries bycatch has contributed to declines in several pinniped species and may be affecting the California sea lion (Zalophus californianus) population in the Gulf of California. We used data on fisheries and sea lion entanglement in gill nets to estimate current fishing pressure and fishing rates under which viable sea lion populations could be sustained at 11 breeding sites in the Gulf of California. We used 3 models to estimate sustainable bycatch rates: a simple population-growth model, a demographic model, and an estimate of the potential biological removal. All models were based on life history and census data collected for sea lions in the Gulf of California. We estimated the current level of fishing pressure and the acceptable level of fishing required to maintain viable sea lion populations as the number of fishing days (1 fisher/boat setting and retrieving 1 day's worth of nets) per year. Estimates of current fishing pressure ranged from 101 (0-405) fishing days around the Los Machos breeding site to 1887 (842-3140) around the Los Islotes rookery. To maintain viable sea lion populations at each site, the current level of fishing permissible could be augmented at some sites and should be reduced at other sites. For example, the area around San Esteban could support up to 1428 (935-2337) additional fishing days, whereas fishing around Lobos should be reduced by at least 165 days (107-268). Our results provide conservation practitioners with site-specific guidelines for maintaining sustainable sea lion populations and provide a method to estimate fishing pressure and sustainable bycatch rates that could be used for other marine mammals and birds. PMID:18410402

  8. Efficient High-Rate Satellite Clock Estimation for PPP Ambiguity Resolution Using Carrier-Ranges

    PubMed Central

    Chen, Hua; Jiang, Weiping; Ge, Maorong; Wickert, Jens; Schuh, Harald

    2014-01-01

    In order to catch up the short-term clock variation of GNSS satellites, clock corrections must be estimated and updated at a high-rate for Precise Point Positioning (PPP). This estimation is already very time-consuming for the GPS constellation only as a great number of ambiguities need to be simultaneously estimated. However, on the one hand better estimates are expected by including more stations, and on the other hand satellites from different GNSS systems must be processed integratively for a reliable multi-GNSS positioning service. To alleviate the heavy computational burden, epoch-differenced observations are always employed where ambiguities are eliminated. As the epoch-differenced method can only derive temporal clock changes which have to be aligned to the absolute clocks but always in a rather complicated way, in this paper, an efficient method for high-rate clock estimation is proposed using the concept of “carrier-range” realized by means of PPP with integer ambiguity resolution. Processing procedures for both post- and real-time processing are developed, respectively. The experimental validation shows that the computation time could be reduced to about one sixth of that of the existing methods for post-processing and less than 1 s for processing a single epoch of a network with about 200 stations in real-time mode after all ambiguities are fixed. This confirms that the proposed processing strategy will enable the high-rate clock estimation for future multi-GNSS networks in post-processing and possibly also in real-time mode. PMID:25429413

  9. Efficient high-rate satellite clock estimation for PPP ambiguity resolution using carrier-ranges.

    PubMed

    Chen, Hua; Jiang, Weiping; Ge, Maorong; Wickert, Jens; Schuh, Harald

    2014-01-01

    In order to catch up the short-term clock variation of GNSS satellites, clock corrections must be estimated and updated at a high-rate for Precise Point Positioning (PPP). This estimation is already very time-consuming for the GPS constellation only as a great number of ambiguities need to be simultaneously estimated. However, on the one hand better estimates are expected by including more stations, and on the other hand satellites from different GNSS systems must be processed integratively for a reliable multi-GNSS positioning service. To alleviate the heavy computational burden, epoch-differenced observations are always employed where ambiguities are eliminated. As the epoch-differenced method can only derive temporal clock changes which have to be aligned to the absolute clocks but always in a rather complicated way, in this paper, an efficient method for high-rate clock estimation is proposed using the concept of "carrier-range" realized by means of PPP with integer ambiguity resolution. Processing procedures for both post- and real-time processing are developed, respectively. The experimental validation shows that the computation time could be reduced to about one sixth of that of the existing methods for post-processing and less than 1 s for processing a single epoch of a network with about 200 stations in real-time mode after all ambiguities are fixed. This confirms that the proposed processing strategy will enable the high-rate clock estimation for future multi-GNSS networks in post-processing and possibly also in real-time mode. PMID:25429413

  10. Data-driven Casualty Estimation and Disease Nonbattle Injury/Battle Injury Rates in Recent Campaigns.

    PubMed

    Wojcik, Barbara E; Humphrey, Rebecca J; Hosek, Barbara J; Stein, Catherine R

    2016-01-01

    To ensure Soldiers are properly equipped and mission capable to perform full spectrum operations, Army medical planners use disease nonbattle injury (DNBI) and battle injury (BI) admission rates in the Total Army Analysis process to support medical deployment and force structure planning for deployed settings. For more than a decade, as the proponent for the DNBI/BI methodology and admission rates, the Statistical Analysis Cell (previously Statistical Analysis Branch, Center for Army Medical Department Strategic Studies) has provided Army medical planners with DNBI/BI rates based upon actual data from recent operations. This article presents the data-driven methodology and casualty estimation rates developed by the Statistical Analysis Cell and accredited for use by 2 Army Surgeon Generals, displays the top 5 principal International Classification of Disease, 9th Revision, Clinical Modification (ICD-9-CM) diagnoses for DNBI/BI in Operation Iraqi Freedom/Operation New Dawn (OIF/OND), and discusses trends in DNBI rates in OIF/OND during the stabilization period. Our methodology uses 95th percentile daily admission rates as a planning factor to ensure that 95% of days in theater are supported by adequate staff and medical equipment. We also present our DNBI/BI estimation methodology for non-Army populations treated at Role 3 US Army medical treatment facilities. PMID:27215860

  11. A Bayesian hierarchical model with novel prior specifications for estimating HIV testing rates.

    PubMed

    An, Qian; Kang, Jian; Song, Ruiguang; Hall, H Irene

    2016-04-30

    Human immunodeficiency virus (HIV) infection is a severe infectious disease actively spreading globally, and acquired immunodeficiency syndrome (AIDS) is an advanced stage of HIV infection. The HIV testing rate, that is, the probability that an AIDS-free HIV infected person seeks a test for HIV during a particular time interval, given no previous positive test has been obtained prior to the start of the time, is an important parameter for public health. In this paper, we propose a Bayesian hierarchical model with two levels of hierarchy to estimate the HIV testing rate using annual AIDS and AIDS-free HIV diagnoses data. At level one, we model the latent number of HIV infections for each year using a Poisson distribution with the intensity parameter representing the HIV incidence rate. At level two, the annual numbers of AIDS and AIDS-free HIV diagnosed cases and all undiagnosed cases stratified by the HIV infections at different years are modeled using a multinomial distribution with parameters including the HIV testing rate. We propose a new class of priors for the HIV incidence rate and HIV testing rate taking into account the temporal dependence of these parameters to improve the estimation accuracy. We develop an efficient posterior computation algorithm based on the adaptive rejection metropolis sampling technique. We demonstrate our model using simulation studies and the analysis of the national HIV surveillance data in the USA. PMID:26567891

  12. A Bayesian hierarchical model with novel prior specifications for estimating HIV testing rates

    PubMed Central

    An, Qian; Kang, Jian; Song, Ruiguang; Hall, H. Irene

    2016-01-01

    Human immunodeficiency virus (HIV) infection is a severe infectious disease actively spreading globally, and acquired immunodeficiency syndrome (AIDS) is an advanced stage of HIV infection. The HIV testing rate, that is, the probability that an AIDS-free HIV infected person seeks a test for HIV during a particular time interval, given no previous positive test has been obtained prior to the start of the time, is an important parameter for public health. In this paper, we propose a Bayesian hierarchical model with two levels of hierarchy to estimate the HIV testing rate using annual AIDS and AIDS-free HIV diagnoses data. At level one, we model the latent number of HIV infections for each year using a Poisson distribution with the intensity parameter representing the HIV incidence rate. At level two, the annual numbers of AIDS and AIDS-free HIV diagnosed cases and all undiagnosed cases stratified by the HIV infections at different years are modeled using a multinomial distribution with parameters including the HIV testing rate. We propose a new class of priors for the HIV incidence rate and HIV testing rate taking into account the temporal dependence of these parameters to improve the estimation accuracy. We develop an efficient posterior computation algorithm based on the adaptive rejection metropolis sampling technique. We demonstrate our model using simulation studies and the analysis of the national HIV surveillance data in the USA. PMID:26567891

  13. Estimation of heart rate variability using a compact radiofrequency motion sensor.

    PubMed

    Sugita, Norihiro; Matsuoka, Narumi; Yoshizawa, Makoto; Abe, Makoto; Homma, Noriyasu; Otake, Hideharu; Kim, Junghyun; Ohtaki, Yukio

    2015-12-01

    Physiological indices that reflect autonomic nervous activity are considered useful for monitoring peoples' health on a daily basis. A number of such indices are derived from heart rate variability, which is obtained by a radiofrequency (RF) motion sensor without making physical contact with the user's body. However, the bulkiness of RF motion sensors used in previous studies makes them unsuitable for home use. In this study, a new method to measure heart rate variability using a compact RF motion sensor that is sufficiently small to fit in a user's shirt pocket is proposed. To extract a heart rate related component from the sensor signal, an algorithm that optimizes a digital filter based on the power spectral density of the signal is proposed. The signals of the RF motion sensor were measured for 29 subjects during the resting state and their heart rate variability was estimated from the measured signals using the proposed method and a conventional method. A correlation coefficient between true heart rate and heart rate estimated from the proposed method was 0.69. Further, the experimental results showed the viability of the RF sensor for monitoring autonomic nervous activity. However, some improvements such as controlling the direction of sensing were necessary for stable measurement. PMID:26603507

  14. One-day rate measurements for estimating net nitrification potential in humid forest soils

    USGS Publications Warehouse

    Ross, D.S.; Fredriksen, G.; Jamison, A.E.; Wemple, B.C.; Bailey, S.W.; Shanley, J.B.; Lawrence, G.B.

    2006-01-01

    Measurements of net nitrification rates in forest soils have usually been performed by extended sample incubation (2-8 weeks), either in the field or in the lab. Because of disturbance effects, these measurements are only estimates of nitrification potential and shorter incubations may suffice. In three separate studies of northeastern USA forest soil surface horizons, we found that laboratory nitrification rates measured over 1 day related well to those measured over 4 weeks. Soil samples of Oa or A horizons were mixed by hand and the initial extraction of subsamples, using 2 mol L-1 KCl, occurred in the field as soon as feasible after sampling. Soils were kept near field temperature and subsampled again the following day in the laboratory. Rates measured by this method were about three times higher than the 4-week rates. Variability in measured rates was similar over either incubation period. Because NO3- concentrations were usually quite low in the field, average rates from 10 research watersheds could be estimated with only a single, 1-day extraction. Methodological studies showed that the concentration of NH4+ increased slowly during contact time with the KCl extractant and, thus, this contact time should be kept similar during the procedure. This method allows a large number of samples to be rapidly assessed. ?? 2006 Elsevier B.V. All rights reserved.

  15. Vector Observation-Aided/Attitude-Rate Estimation Using Global Positioning System Signals

    NASA Technical Reports Server (NTRS)

    Oshman, Yaakov; Markley, F. Landis

    1997-01-01

    A sequential filtering algorithm is presented for attitude and attitude-rate estimation from Global Positioning System (GPS) differential carrier phase measurements. A third-order, minimal-parameter method for solving the attitude matrix kinematic equation is used to parameterize the filter's state, which renders the resulting estimator computationally efficient. Borrowing from tracking theory concepts, the angular acceleration is modeled as an exponentially autocorrelated stochastic process, thus avoiding the use of the uncertain spacecraft dynamic model. The new formulation facilitates the use of aiding vector observations in a unified filtering algorithm, which can enhance the method's robustness and accuracy. Numerical examples are used to demonstrate the performance of the method.

  16. Estimate of the genomic mutation rate deleterious to overall fitness in E. coll

    NASA Astrophysics Data System (ADS)

    Kibota, Travis T.; Lynch, Michael

    1996-06-01

    MUTATIONS are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful1. Deleterious mutations of small effect can escape natural selection, and should accumulate in small populations2-4. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex5-7, mate choice8,9, and diploid life-cycles10, and in the extinction of small populations11,12. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in Drosophila melanogaster are surprisingly high1,13,14, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation5,6. Here we use Escherichia coli to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.

  17. Fusarium graminearum infection and deoxynivalenol concentrations during development of wheat spikes.

    PubMed

    Cowger, Christina; Arellano, Consuelo

    2013-05-01

    Fusarium head blight (FHB) affects whole spikes of small grain plants, yet little is known about how FHB develops following infection, or about the concentration or progression of the mycotoxin deoxynivalenol (DON) in non-grain spike tissues. Fusarium mycotoxin levels in whole small-grain spikes are of concern to producers of whole-crop silage, as well as users of straw containing chaff for animal bedding or winter livestock rations. A 2-year field experiment was performed in Kinston, NC to reveal the time course of FHB development. Eight winter wheat cultivars with varying levels of FHB resistance were used in the 2006 experiment, and four of them were used in 2007. Plots were spray-inoculated with Fusarium graminearum macroconidia at mid-anthesis. Four durations of post-anthesis mist were applied: 0, 10, 20, or 30 days. Spike samples were collected and bulked by plot at 15, 25, 35, 45, 55, and 65 days after anthesis (daa); samples were separated into grain, glume, and rachis fractions. Increasing durations of post-anthesis moisture elevated grain DON and reduced the effect of cultivar on DON, presumably by affecting the expression of resistance, in all spike tissues. Fusarium-damaged kernels increased from early kernel-hard to harvest-ripe in both years. Percent infected kernels increased from medium-milk to harvest-ripe. During grainfill, DON concentrations declined in grain but increased in rachises and glumes, peaking at early kernel-hard, before declining. Higher mean and maximum DON levels were observed in rachises and glumes than in grain. Estimated whole-spike DON peaked at early kernel-hard. In a high-FHB year, whole-plant harvest for forage should be conducted as early as possible. Straw that may be consumed by livestock could contain significant amounts of DON in chaff, and DON can be minimized if straw is sourced from low-symptom crops. Cultivar FHB resistance ratings and disease data should be useful in predicting whole-spike DON levels. Overall

  18. Joint analysis of spikes and local field potentials using copula.

    PubMed

    Hu, Meng; Li, Mingyao; Li, Wu; Liang, Hualou

    2016-06-01

    Recent technological advances, which allow for simultaneous recording of spikes and local field potentials (LFPs) at multiple sites in a given cortical area or across different areas, have greatly increased our understanding of signal processing in brain circuits. Joint analysis of simultaneously collected spike and LFP signals is an important step to explicate how the brain orchestrates information processing. In this contribution, we present a novel statistical framework based on Gaussian copula to jointly model spikes and LFP. In our approach, we use copula to link separate, marginal regression models to construct a joint regression model, in which the binary-valued spike train data are modeled using generalized linear model (GLM) and the continuous-valued LFP data are modeled using linear regression. Model parameters can be efficiently estimated via maximum-likelihood. In particular, we show that our model offers a means to statistically detect directional influence between spikes and LFP, akin to Granger causality measure, and that we are able to assess its statistical significance by conducting a Wald test. Through extensive simulations, we also show that our method is able to reliably recover the true model used to generate the data. To demonstrate the effectiveness of our approach in real setting, we further apply the method to a mixed neural dataset, consisting of spikes and LFP simultaneously recorded from the visual cortex of a monkey performing a contour detection task. PMID:27012500

  19. Comparison of Erosion Rates Estimated by Sediment Budget Techniques and Suspended Sediment Monitoring and Regulatory Implications

    NASA Astrophysics Data System (ADS)

    O'Connor, M.; Eads, R.

    2007-12-01

    Watersheds in the northern California Coast Range have been designated as "impaired" with respect to water quality because of excessive sediment loads and/or high water temperature. Sediment budget techniques have typically been used by regulatory authorities to estimate current erosion rates and to develop targets for future desired erosion rates. This study examines erosion rates estimated by various methods for portions of the Gualala River watershed, designated as having water quality impaired by sediment under provisions of the Clean Water Act Section 303(d), located in northwest Sonoma County (~90 miles north of San Francisco). The watershed is underlain by Jurassic age sedimentary and meta-sedimentary rocks of the Franciscan formation. The San Andreas Fault passes through the western edge of watershed, and other active faults are present. A substantial portion of the watershed is mantled by rock slides and earth flows, many of which are considered dormant. The Coast Range is geologically young, and rapid rates of uplift are believed to have contributed to high erosion rates. This study compares quantitative erosion rate estimates developed at different spatial and temporal scales. It is motivated by a proposed vineyard development project in the watershed, and the need to document conditions in the project area, assess project environmental impacts and meet regulatory requirements pertaining to water quality. Erosion rate estimates were previously developed using sediment budget techniques for relatively large drainage areas (~100 to 1,000 km2) by the North Coast Regional Water Quality Control Board and US EPA and by the California Geological Survey. In this study, similar sediment budget techniques were used for smaller watersheds (~3 to 8 km2), and were supplemented by a suspended sediment monitoring program utilizing Turbidity Threshold Sampling techniques (as described in a companion study in this session). The duration of the monitoring program to date

  20. Measured rates of sedimentation: What exactly are we estimating, and why?

    NASA Astrophysics Data System (ADS)

    Tipper, John C.

    2016-06-01

    radionuclide concentrations. These two strategies are reviewed in this paper. Sets of measurements made in systems that are active today can certainly be used to estimate the rate of sedimentation for the system as a whole. This estimation is best carried out using geostatistical estimation techniques. The alternative is simply to average the measured rate values. This latter approach should not be used, however, because the mean sedimentation rate in a system gives information only about the net sediment movement at the system boundaries. It says nothing at all about how the system is operating or about its spatial and temporal variability. Measurements of rates of sedimentation made for source-to-sink studies are necessarily made in stratigraphic successions. The measurements are used to estimate quantities in the sediment mass budget equation. The amount of decumulation is inherently incapable of being measured in stratigraphic successions, therefore there are always unknowns in the mass budget equation whenever the lithic surface at the start of the time interval considered cannot be recognised everywhere. This means that the mass budget equation is applicable in practice only when all the systems involved in the study are entirely non-erosional for that entire time interval - a highly unrealistic situation. The consistently inverse relationship documented between accumulation rates and measurement timespan is taken usually to indicate that this relationship is substantially scale-invariant. This in turn is often taken as indicating that the stratigraphic record is fractal in nature. There are nevertheless grounds for doubt, all of which relate to the ways that the data are collected and used for estimation. The relationship is in fact the natural mathematical result of last-in-first-out (LIFO) operation and is produced in any type of system in which addition and removal processes both operate. It says nothing particular about sedimentation processes. The future analysis

  1. Dendrogeomorphic estimate of changes in sedimentation rate along the Kankakee River near Momence, Illinois

    USGS Publications Warehouse

    Phipps, R.L.; Johnson, G.P.; Terrio, P.J.

    1995-01-01

    Changes in sedimentation rates wee estimated using root-burial depth and tree-age data at six selected data-collection sites along the Kankakee River near Momence in Kankakee County, Illinois. Five sites were in backwater areas away from the river channel, and one site was on a natural levee near the channel. A summary of the dendrogeomorphic data at the six sites indicates that sedimentation rates were greater after 1950 than before 1950. Greater sedimentation rates after 1950 were observed at four of the five backwater sites, whereas no change in sedimentation rate after 1950 was observed at the fifth backwater site. The observed rates could have been affected by any combination of soil erosion, soil compaction, or increased streamflow. A greater sedimentation rate after 1950 was observed at the levee site, which appeared to have been affected by erosion from a flood in 1950. Effects of erosion were not observed at any of th other sites. No erosional effects and soil not susceptible to compaction at the five backwater sites indicate that neither erosion nor compaction affected observed sedimentation rates. The effect of increased stream- flow in the Kankakee River Basin since the early 1900's on the observed sedimentation rates is not known.

  2. Recording system and data fusion algorithm for enhancing the estimation of the respiratory rate from photoplethysmogram.

    PubMed

    Cernat, Roxana A; Ciorecan, Silvia I; Ungureanu, Constantin; Arends, Johan; Strungaru, Rodica; Ungureanu, G Mihaela

    2015-08-01

    The respiratory rate is a vital parameter that can provide valuable information about the health condition of a patient. The extraction of respiratory information from photoplethysmographic signal (PPG) was actually encouraged by the reported results, our main goal being to obtain accurate respiratory rate estimation from the PPG signal. We developed a fusion algorithm that identifies the best derived respiratory signals, from which is possible to extract the respiratory rate; based on these, a global respiratory rate is computed using the proposed fusion algorithm. The algorithm is qualitatively tested on real PPG signals recorded by an acquisition system we implemented, using a reflection pulse oximeter sensor. Its performance is also statistically evaluated using benchmark dataset publically available from CapnoBase.Org. PMID:26737653

  3. Magnitude estimation and categorical rating scaling in social sciences: a theoretical and psychometric controversy.

    PubMed

    Beltyukova, Svetlana A; Stone, Gregory E; Fox, Christine M

    2008-01-01

    This paper revisits a half-century long theoretical controversy associated with the use of magnitude estimation scaling (MES) and category rating scaling (CRS) procedures in measurement. The MES procedure in this study involved instructing participants to write a number that matched their impression of difficulty of a test item. Participants were not restricted in the range of numbers they could choose for their scale. They also had the choice of disclosing their individual scale. After the MES task was completed, participants were given a blank copy of the test to rate the perceived difficulty of each item using a researcher-imposed categorical rating scale from 1 (very easy) to 6 (very difficult). The MES and CRS data were both analyzed using Rasch Rating scale model. Additionally, the MES data were examined with Rasch Partial Credit model. Results indicate that knowing each person's scale is associated with smaller errors of measurement. PMID:18480511

  4. Estimates of Biogenic Methane Production Rates in Deep Marine Sediments at Hydrate Ridge, Cascadia Margin

    SciTech Connect

    F. S. Colwell; S. Boyd; M. E. Delwiche; D. W. Reed; T. J. Phelps; D. T. Newby

    2008-06-01

    Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor Methanoculleus submarinus produced ca. 0.017 fmol methane/cell/day. Quantitative polymerase chain reaction (QPCR) directed at the methyl coenzyme M reductase subunit A (mcrA) gene indicated that 75% of the HR sediments analyzed contained <1000 methanogens/g. The highest methanogen numbers were mostly from sediments <10 meters below seafloor. By combining methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported from such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.

  5. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin.

    PubMed

    Colwell, F S; Boyd, S; Delwiche, M E; Reed, D W; Phelps, T J; Newby, D T

    2008-06-01

    Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor, Methanoculleus submarinus produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (mcrA) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle. PMID:18344348

  6. Can the cerebral metabolic rate of oxygen be estimated with near-infrared spectroscopy?

    NASA Astrophysics Data System (ADS)

    Boas, D. A.; Strangman, G.; Culver, J. P.; Hoge, R. D.; Jasdzewski, G.; Poldrack, R. A.; Rosen, B. R.; Mandeville, J. B.

    2003-08-01

    We have measured the changes in oxy-haemoglobin and deoxy-haemoglobin in the adult human brain during a brief finger tapping exercise using near-infrared spectroscopy (NIRS). The cerebral metabolic rate of oxygen (CMRO2) can be estimated from these NIRS data provided certain model assumptions. The change in CMRO2 is related to changes in the total haemoglobin concentration, deoxy-haemoglobin concentration and blood flow. As NIRS does not provide a measure of dynamic changes in blood flow during brain activation, we relied on a Windkessel model that relates dynamic blood volume and flow changes, which has been used previously for estimating CMRO2 from functional magnetic resonance imaging (fMRI) data. Because of the partial volume effect we are unable to quantify the absolute changes in the local brain haemoglobin concentrations with NIRS and thus are unable to obtain an estimate of the absolute CMRO2 change. An absolute estimate is also confounded by uncertainty in the flow-volume relationship. However, the ratio of the flow change to the CMRO2 change is relatively insensitive to these uncertainties. For the finger tapping task, we estimate a most probable flow-consumption ratio ranging from 1.5 to 3 in agreement with previous findings presented in the literature, although we cannot exclude the possibility that there is no CMRO2 change. The large range in the ratio arises from the large number of model parameters that must be estimated from the data. A more precise estimate of the flow-consumption ratio will require better estimates of the model parameters or flow information, as can be provided by combining NIRS with fMRI.

  7. Automated rain rate estimates using the Ka-band ARM zenith radar (KAZR)

    NASA Astrophysics Data System (ADS)

    Chandra, A.; Zhang, C.; Kollias, P.; Matrosov, S.; Szyrmer, W.

    2015-09-01

    The use of millimeter wavelength radars for probing precipitation has recently gained interest. However, estimation of precipitation variables is not straightforward due to strong signal attenuation, radar receiver saturation, antenna wet radome effects and natural microphysical variability. Here, an automated algorithm is developed for routinely retrieving rain rates from the profiling Ka-band (35-GHz) ARM (Atmospheric Radiation Measurement) zenith radars (KAZR). A 1-dimensional, simple, steady state microphysical model is used to estimate impacts of microphysical processes and attenuation on the profiles of radar observables at 35-GHz and thus provide criteria for identifying situations when attenuation or microphysical processes dominate KAZR observations. KAZR observations are also screened for signal saturation and wet radome effects. The algorithm is implemented in two steps: high rain rates are retrieved by using the amount of attenuation in rain layers, while low rain rates are retrieved from the reflectivity-rain rate (Ze-R) relation. Observations collected by the KAZR, rain gauge, disdrometer and scanning precipitating radars during the DYNAMO/AMIE field campaign at the Gan Island of the tropical Indian Ocean are used to validate the proposed approach. The differences in the rain accumulation from the proposed algorithm are quantified. The results indicate that the proposed algorithm has a potential for deriving continuous rain rate statistics in the tropics.

  8. Automated rain rate estimates using the Ka-band ARM Zenith Radar (KAZR)

    NASA Astrophysics Data System (ADS)

    Chandra, A.; Zhang, C.; Kollias, P.; Matrosov, S.; Szyrmer, W.

    2014-02-01

    The use of millimeter wavelength radars for probing precipitation has recently gained interest. However, estimation of precipitation variables is not straightforward due to strong attenuation, radar receiver saturation, antenna wet radome effects and natural microphysical variability. Here, an automated algorithm is developed for routinely retrieving rain rates from profiling Ka-band (35-GHz) ARM zenith radars (KAZR). A 1-D simple, steady state microphysical model is used to estimate the impact of microphysical processes and attenuation on the profiles of the radar observables at 35-GHz and thus provide criteria for identifying when attenuation or microphysical processes dominate KAZR observations. KAZR observations are also screened for saturation and wet radome effects. The proposed algorithm is implemented in two steps: high rain rates are retrieved by using the amount of attenuation in rain layers, while lower rain rates by the Ze-R (reflectivity-rain rate) relation is implemented. Observations collected by the KAZR, disdrometer and scanning weather radars during the DYNAMO/AMIE field campaign at Gan Island of the tropical Indian Ocean are used to validate the proposed approach. The results indicate that the proposed algorithm can be used to derive robust statistics of rain rates in the tropics from KAZR observations.

  9. Estimation of rates of aerobic hydrocarbon biodegradation by simulation of gas transport in the unsaturated zone

    USGS Publications Warehouse

    Lahvis, M.A.; Baehr, A.L.

    1996-01-01

    The distribution of oxygen and carbon dioxide gases in the unsaturated zone provides a geochemical signature of aerobic hydrocarbon degradation at petroleum product spill sites. The fluxes of these gases are proportional to the rate of aerobic biodegradation and are quantified by calibrating a mathematical transport model to the oxygen and carbon dioxide gas concentration data. Reaction stoichiometry is assumed to convert the gas fluxes to a corresponding rate of hydrocarbon degradation. The method is applied at a gasoline spill site in Galloway Township, New Jersey, to determine the rate of aerobic degradation of hydrocarbons associated with passive and bioventing remediation field experiments. At the site, microbial degradation of hydrocarbons near the water table limits the migration of hydrocarbon solutes in groundwater and prevents hydrocarbon volatilization into the unsaturated zone. In the passive remediation experiment a site-wide degradation rate estimate of 34,400 g yr-1 (11.7 gal. yr-1) of hydrocarbon was obtained by model calibration to carbon dioxide gas concentration data collected in December 1989. In the bioventing experiment, degradation rate estimates of 46.0 and 47.9 g m-2 yr-1 (1.45 x 10-3 and 1.51 x 10-3 gal. ft.-2 yr-1) of hydrocarbon were obtained by model calibration to oxygen and carbon dioxide gas concentration data, respectively. Method application was successful in quantifying the significance of a naturally occurring process that can effectively contribute to plume stabilization.

  10. Comparison of estimated and background subsidence rates in Texas-Louisiana geopressured geothermal areas

    SciTech Connect

    Lee, L.M.; Clayton, M.; Everingham, J.; Harding, R.C.; Massa, A.

    1982-06-01

    A comparison of background and potential geopressured geothermal development-related subsidence rates is given. Estimated potential geopressured-related rates at six prospects are presented. The effect of subsidence on the Texas-Louisiana Gulf Coast is examined including the various associated ground movements and the possible effects of these ground movements on surficial processes. The relationships between ecosystems and subsidence, including the capability of geologic and biologic systems to adapt to subsidence, are analyzed. The actual potential for environmental impact caused by potential geopressured-related subsidence at each of four prospects is addressed. (MHR)

  11. 210Pb method for estimating the rate of carbonate sand sedimentation

    USGS Publications Warehouse

    Holmes, Charles W.

    1981-01-01

    The plot of 210Pb activity against depth in carbonate sands on the Virgin Island Bank is a negative asymmetric hyperbolic curve. As depth increases, an initial rapid decrease in 210Pb activity caused by the decay of unsupported 210Pb and 226Ra is followed by increasing activity as a result of 210Pb achieving equilibrium with in growing 230Th. As this curve is time dependent, an estimate of the relative ages in carbonate sequences and the rates of net carbonate accumulation can be made. The ease of 210Pb activity determinations makes this procedure an attractive method in obtaining carbonate sand accumulation rates.

  12. Flow rate estimation by optical coherence tomography using contrast dilution approach

    NASA Astrophysics Data System (ADS)

    Štohanzlová, Petra; Kolář, Radim

    2015-07-01

    This paper describes experiments and methodology for flow rate estimation using optical coherence tomography and dilution method in single fiber setup. The single fiber is created from custom made glass capillary and polypropylene hollow fiber. As a data source, measurements on single fiber phantom with continuous flow of carrier medium and bolus of Intralipid solution as a contrast agent were used using Thorlabs OCT OCS1300SS. The measured data were processed by methods of image processing, in order to precisely align the individual images in the sequence and extract dilution curves from the area inside the fiber. An experiment proved that optical coherence tomography can be used for flow rate estimation by the dilution method with precision around 7%.

  13. A nonlinear estimator for reconstructing the angular velocity of a spacecraft without rate gyros

    NASA Technical Reports Server (NTRS)

    Polites, M. E.; Lightsey, W. D.

    1991-01-01

    A scheme for estimating the angular velocity of a spacecraft without rate gyros is presented. It is based upon a nonlinear estimator whose inputs are measured inertial vectors and their calculated time derivatives relative to vehicle axes. It works for all spacecraft attitudes and requires no knowledge of attitude. It can use measurements from a variety of onboard sensors like Sun sensors, star trackers, or magnetometers, and in concert. It can also use look angle measurements from onboard tracking antennas for tracking and data relay satellites or global positioning system satellites. In this paper, it is applied to a Sun point scheme on the Hubble Space Telescope assuming all or most of its onboard rate gyros have failed. Simulation results are presented for verification.

  14. Swimmer detection and pose estimation for continuous stroke-rate determination

    NASA Astrophysics Data System (ADS)

    Zecha, Dan; Greif, Thomas; Lienhart, Rainer

    2012-02-01

    In this work we propose a novel approach to automatically detect a swimmer and estimate his/her pose continuously in order to derive an estimate of his/her stroke rate given that we observe the swimmer from the side. We divide a swimming cycle of each stroke into several intervals. Each interval represents a pose of the stroke. We use specifically trained object detectors to detect each pose of a stroke within a video and count the number of occurrences per time unit of the most distinctive poses (so-called key poses) of a stroke to continuously infer the stroke rate. We extensively evaluate the overall performance and the influence of the selected poses for all swimming styles on a data set consisting of a variety of swimmers.

  15. Heart rate variability estimation in photoplethysmography signals using Bayesian learning approach

    PubMed Central

    Alwosheel, Ahmad; Alasaad, Amr

    2016-01-01

    Heart rate variability (HRV) has become a marker for various health and disease conditions. Photoplethysmography (PPG) sensors integrated in wearable devices such as smart watches and phones are widely used to measure heart activities. HRV requires accurate estimation of time interval between consecutive peaks in the PPG signal. However, PPG signal is very sensitive to motion artefact which may lead to poor HRV estimation if false peaks are detected. In this Letter, the authors propose a probabilistic approach based on Bayesian learning to better estimate HRV from PPG signal recorded by wearable devices and enhance the performance of the automatic multi scale-based peak detection (AMPD) algorithm used for peak detection. The authors’ experiments show that their approach enhances the performance of the AMPD algorithm in terms of number of HRV related metrics such as sensitivity, positive predictive value, and average temporal resolution. PMID:27382483

  16. False discovery rate estimation for large-scale homogeneous discrete p-values.

    PubMed

    Liang, Kun

    2016-06-01

    Large-scale homogeneous discrete p-values are encountered frequently in high-throughput genomics studies, and the related multiple testing problems become challenging because most existing methods for the false discovery rate (FDR) assume continuous p-values. In this article, we study the estimation of the null proportion and FDR for discrete p-values with common support. In the finite sample setting, we propose a novel class of conservative FDR estimators. Furthermore, we show that a broad class of FDR estimators is simultaneously conservative over all support points under some weak dependence condition in the asymptotic setting. We further demonstrate the significant improvement of a newly proposed method over existing methods through simulation studies and a case study. PMID:26492596

  17. Heart rate variability estimation in photoplethysmography signals using Bayesian learning approach.

    PubMed

    Alqaraawi, Ahmed; Alwosheel, Ahmad; Alasaad, Amr

    2016-06-01

    Heart rate variability (HRV) has become a marker for various health and disease conditions. Photoplethysmography (PPG) sensors integrated in wearable devices such as smart watches and phones are widely used to measure heart activities. HRV requires accurate estimation of time interval between consecutive peaks in the PPG signal. However, PPG signal is very sensitive to motion artefact which may lead to poor HRV estimation if false peaks are detected. In this Letter, the authors propose a probabilistic approach based on Bayesian learning to better estimate HRV from PPG signal recorded by wearable devices and enhance the performance of the automatic multi scale-based peak detection (AMPD) algorithm used for peak detection. The authors' experiments show that their approach enhances the performance of the AMPD algorithm in terms of number of HRV related metrics such as sensitivity, positive predictive value, and average temporal resolution. PMID:27382483

  18. The use of a new indirect method to estimate ethnic-group fertility rates for subnational projections for England.

    PubMed

    Norman, Paul; Rees, Philip; Wohland, Pia

    2014-03-01

    To project the ethnic-group populations of local authorities in England to 2051, estimates of ethnic-specific fertility rates were needed. In the absence of ethnic information on birth records, we developed indirect estimation methods that use a combination of vital statistics, the census (both microdata and aggregate tables), and survey data (Labour Force Survey). We estimated age-specific and total fertility rates successively for five broad ethnic groups encompassed by all data-sets, and for eight ethnic groups encompassed by the 1991 and 2001 Censuses for England. We then used census data to disaggregate the estimates to the 16 ethnic groups required for the subnational projections and the Hadwiger function to estimate single-year-of-age estimates. We estimated the uncertainty around the fertility estimates and used a logistic model to project rates to 2021, after which we assumed rates would remain constant. PMID:23879768

  19. An approach for estimating time-variable rates from geodetic time series

    NASA Astrophysics Data System (ADS)

    Didova, Olga; Gunter, Brian; Riva, Riccardo; Klees, Roland; Roese-Koerner, Lutz

    2016-06-01

    There has been considerable research in the literature focused on computing and forecasting sea-level changes in terms of constant trends or rates. The Antarctic ice sheet is one of the main contributors to sea-level change with highly uncertain rates of glacial thinning and accumulation. Geodetic observing systems such as the Gravity Recovery and Climate Experiment (GRACE) and the Global Positioning System (GPS) are routinely used to estimate these trends. In an effort to improve the accuracy and reliability of these trends, this study investigates a technique that allows the estimated rates, along with co-estimated seasonal components, to vary in time. For this, state space models are defined and then solved by a Kalman filter (KF). The reliable estimation of noise parameters is one of the main problems encountered when using a KF approach, which is solved by numerically optimizing likelihood. Since the optimization problem is non-convex, it is challenging to find an optimal solution. To address this issue, we limited the parameter search space using classical least-squares adjustment (LSA). In this context, we also tested the usage of inequality constraints by directly verifying whether they are supported by the data. The suggested technique for time-series analysis is expanded to classify and handle time-correlated observational noise within the state space framework. The performance of the method is demonstrated using GRACE and GPS data at the CAS1 station located in East Antarctica and compared to commonly used LSA. The results suggest that the outlined technique allows for more reliable trend estimates, as well as for more physically valuable interpretations, while validating independent observing systems.

  20. Estimating gully erosion contribution to large catchment sediment yield rate in Tanzania

    NASA Astrophysics Data System (ADS)

    Ndomba, Preksedis Marco; Mtalo, Felix; Killingtveit, Aanund

    The objective of this paper is to report on the issues and proposed approaches in estimating the contribution of gully erosion to sediment yield at large catchment. The case study is the upstream of Pangani River Basin (PRB) located in the North Eastern part of Tanzania. Little has been done by other researchers to study and/or extrapolate gully erosion results from plot or field scale to large catchment. In this study multi-temporal aerial photos at selected sampling sites were used to estimate gully size and morphology changes over time. The laboratory aerial photo interpretation results were groundtruthed. A data mining tool, Cubist, was used to develop predictive gully density stepwise regression models using aerial photos and environment variables. The delivery ratio was applied to estimate the sediment yield rate. The spatial variations of gully density were mapped under Arc View GIS Environment. Gully erosion sediment yield contribution was estimated as a ratio between gully erosion sediment yield and total sediment yield at the catchment outlet. The general observation is that gullies are localized features and not continuous spatially and mostly located on some mountains’ foot slopes. The estimated sediment yield rate from gullies erosion is 6800 t/year, which is about 1.6% of the long-term total catchment sediment yield rate. The result is comparable to other study findings in the same catchment. In order to improve the result larger scale aerial photos and high resolution spatial data on soil-textural class and saturated hydraulic conductivity - are recommended.

  1. Estimation of Leak Rate from the Emergency Pump Well in L-Area Complex Basin

    SciTech Connect

    Duncan, A

    2005-12-19

    This report provides an estimate of the leak rate from the emergency pump well in L-basin that is to be expected during an off-normal event. This estimate is based on expected shrinkage of the engineered grout (i.e., controlled low strength material) used to fill the emergency pump well and the header pipes that provide the dominant leak path from the basin to the lower levels of the L-Area Complex. The estimate will be used to provide input into the operating safety basis to ensure that the water level in the basin will remain above a certain minimum level. The minimum basin water level is specified to ensure adequate shielding for personnel and maintain the ''as low as reasonably achievable'' concept of radiological exposure. The need for the leak rate estimation is the existence of a gap between the fill material and the header pipes, which penetrate the basin wall and would be the primary leak path in the event of a breach in those pipes. The gap between the pipe and fill material was estimated based on a full scale demonstration pour that was performed and examined. Leak tests were performed on full scale pipes as a part of this examination. Leak rates were measured to be on the order of 0.01 gallons/minute for completely filled pipe (vertically positioned) and 0.25 gallons/minute for partially filled pipe (horizontally positioned). This measurement was for water at 16 feet head pressure and with minimal corrosion or biofilm present. The effect of the grout fill on the inside surface biofilm of the pipes is the subject of a previous memorandum.

  2. General decay rate estimates for viscoelastic wave equation with Balakrishnan-Taylor damping

    NASA Astrophysics Data System (ADS)

    Ha, Tae Gab

    2016-04-01

    In this paper, we consider the viscoelastic wave equation with Balakrishnan-Taylor damping. This work is devoted to prove uniform decay rates of the energy without imposing any restrictive growth assumption on the damping term and weakening the usual assumptions on the relaxation function. Our estimate depends both on the behavior of the damping term near zero and on behavior of the relaxation function at infinity.

  3. A comparison of analytic models for estimating dose equivalent rates in shielding with beam spill measurements

    SciTech Connect

    Frankle, S.C.; Fitzgerald, D.H.; Hutson, R.L.; Macek, R.J.; Wilkinson, C.A.

    1992-12-31

    A comparison of 800-MeV proton beam spill measurements at the Los Alamos Meson Physics Facility (LAMPF) with analytical model calculations of neutron dose equivalent rates (DER) show agreement within factors of 2-3 for simple shielding geometries. The DER estimates were based on a modified Moyer model for transverse angles and a Monte Carlo based forward angle model described in the proceeding paper.

  4. Statistics of rain-rate estimates for a single attenuating radar

    NASA Technical Reports Server (NTRS)

    Meneghini, R.

    1976-01-01

    The effects of fluctuations in return power and the rain-rate/reflectivity relationship, are included in the estimates, as well as errors introduced in the attempt to recover the unattenuated return power. In addition to the Hitschfeld-Bordan correction, two alternative techniques are considered. The performance of the radar is shown to be dependent on the method by which attenuation correction is made.

  5. Geodetic estimates of fault slip rates in the San Francisco Bay area

    USGS Publications Warehouse

    Savage, J.C.; Svarc, J.L.; Prescott, W.H.

    1999-01-01

    Bourne et al. [1998] have suggested that the interseismic velocity profile at the surface across a transform plate boundary is a replica of the secular velocity profile at depth in the plastosphere. On the other hand, in the viscoelastic coupling model the shape of the interseismic surface velocity profile is a consequence of plastosphere relaxation following the previous rupture of the faults that make up the plate boundary and is not directly related to the secular flow in the plastosphere. The two models appear to be incompatible. If the plate boundary is composed of several subparallel faults and the interseismic surface velocity profile across the boundary known, each model predicts the secular slip rates on the faults which make up the boundary. As suggested by Bourne et al., the models can then be tested by comparing the predicted secular slip rates to those estimated from long-term offsets inferred from geology. Here we apply that test to the secular slip rates predicted for the principal faults (San Andreas, San Gregorio, Hayward, Calaveras, Rodgers Creek, Green Valley and Greenville faults) in the San Andreas fault system in the San Francisco Bay area. The estimates from the two models generally agree with one another and to a lesser extent with the geologic estimate. Because the viscoelastic coupling model has been equally successful in estimating secular slip rates on the various fault strands at a diffuse plate boundary, the success of the model of Bourne et al. [1998] in doing the same thing should not be taken as proof that the interseismic velocity profile across the plate boundary at the surface is a replica of the velocity profile at depth in the plastosphere.

  6. Estimating the rate of retinal ganglion cell loss to detect glaucoma progression: An observational cohort study.

    PubMed

    Hirooka, Kazuyuki; Izumibata, Saeko; Ukegawa, Kaori; Nitta, Eri; Tsujikawa, Akitaka

    2016-07-01

    This study aimed to evaluate the relationship between glaucoma progression and estimates of the retinal ganglion cells (RGCs) obtained by combining structural and functional measurements in patients with glaucoma.In the present observational cohort study, we examined 116 eyes of 62 glaucoma patients. Using Cirrus optical coherence tomography (OCT), a minimum of 5 serial retinal nerve fiber layer (RNFL) measurements were performed in all eyes. There was a 3-year separation between the first and last measurements. Visual field (VF) testing was performed on the same day as the RNFL imaging using the Swedish Interactive Threshold Algorithm Standard 30-2 program of the Humphrey Field Analyzer. Estimates of the RGC counts were obtained from standard automated perimetry (SAP) and OCT, with a weighted average then used to determine a final estimate of the number of RGCs for each eye. Linear regression was used to calculate the rate of the RGC loss, and trend analysis was used to evaluate both serial RNFL thicknesses and VF progression.Use of the average RNFL thickness parameter of OCT led to detection of progression in 14 of 116 eyes examined, whereas the mean deviation slope detected progression in 31 eyes. When the rates of RGC loss were used, progression was detected in 41 of the 116 eyes, with a mean rate of RGC loss of -28,260 ± 8110 cells/year.Estimation of the rate of RGC loss by combining structural and functional measurements resulted in better detection of glaucoma progression compared to either OCT or SAP. PMID:27472691

  7. Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

    PubMed Central

    Raquin, Anne-Laure; Depaulis, Frantz; Lambert, Amaury; Galic, Nathalie; Brabant, Philippe; Goldringer, Isabelle

    2008-01-01

    Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 × 10−3 per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues. PMID:18689900

  8. Estimating the Esophagus Cancer Incidence Rate in Ardabil, Iran: A Capture-Recapture Method

    PubMed Central

    Khodadost, Mahmoud; Yavari, Parvin; Khodadost, Behnam; Babaei, Masoud; Sarvi, Fatemeh; Khatibi, Seyed Reza; Barzegari, Saeed

    2016-01-01

    Background: Accurate cancer registry and awareness of cancer incidence rate is essential in order to define strategies for cancer prevention and control programs. Capture-recapture methods have been recommended for reducing bias and increase the accuracy of cancer incidence estimation. Objectives: This study aimed to estimate the esophagus cancer incidence by capture-recapture method based on Ardabil population-based cancer registry data. Patients and Methods: Total new cases of esophagus cancer reported by three sources of pathology reports, medical records, and death certificates to Ardabil province cancer registry center in 2006 and 2008 were enrolled in the study. All duplicated cases between three sources were identified and removed using Excel software. Some characteristics such as name, surname, father’s name, date of birth and ICD codes related to their cancer type were used for data linkage and finding the common cases among three sources. The incidence rate per 100,000 was estimated based on capture-recapture method using the log-linear models. We used BIC, G2 and AIC statistics to select the best-fit model. Results: After removing duplicates, total 471 new cases of esophagus cancer were reported from three sources. The model with linkage between pathology reports, medical record sources and independence with the death certificates source was the best fitted model. The reported incidence rate for the years 2006 and 2008 was 18.77 and 18.51 per 100,000, respectively. In log-linear analysis, the estimated incidence rate for the years 2006 and 2008 was 49.71 and 53.87 per 100,000 populations, respectively. Conclusions: Based on the obtained results, it can be concluded that none of the sources of pathology reports, death certificates and medical records individually or collectively were fully covered the incidence cases of esophagus cancer and need to apply some changes in data abstracting and case finding.

  9. Estimation of the occurrence rate of strong earthquakes based on hidden semi-Markov models

    NASA Astrophysics Data System (ADS)

    Votsi, I.; Limnios, N.; Tsaklidis, G.; Papadimitriou, E.

    2012-04-01

    The present paper aims at the application of hidden semi-Markov models (HSMMs) in an attempt to reveal key features for the earthquake generation, associated with the actual stress field, which is not accessible to direct observation. The models generalize the hidden Markov models by considering the hidden process to form actually a semi-Markov chain. Considering that the states of the models correspond to levels of actual stress fields, the stress field level at the occurrence time of each strong event is revealed. The dataset concerns a well catalogued seismically active region incorporating a variety of tectonic styles. More specifically, the models are applied in Greece and its surrounding lands, concerning a complete data sample with strong (M≥ 6.5) earthquakes that occurred in the study area since 1845 up to present. The earthquakes that occurred are grouped according to their magnitudes and the cases of two and three magnitude ranges for a corresponding number of states are examined. The parameters of the HSMMs are estimated and their confidence intervals are calculated based on their asymptotic behavior. The rate of the earthquake occurrence is introduced through the proposed HSMMs and its maximum likelihood estimator is calculated. The asymptotic properties of the estimator are studied, including the uniformly strongly consistency and the asymptotical normality. The confidence interval for the proposed estimator is given. We assume the state space of both the observable and the hidden process to be finite, the hidden Markov chain to be homogeneous and stationary and the observations to be conditionally independent. The hidden states at the occurrence time of each strong event are revealed and the rate of occurrence of an anticipated earthquake is estimated on the basis of the proposed HSMMs. Moreover, the mean time for the first occurrence of a strong anticipated earthquake is estimated and its confidence interval is calculated.

  10. A Hierarchical Distance Sampling Approach to Estimating Mortality Rates from Opportunistic Carcass Surveillance Data

    PubMed Central

    Bellan, Steve E.; Gimenez, Olivier; Choquet, Rémi; Getz, Wayne M.

    2012-01-01

    Summary Distance sampling is widely used to estimate the abundance or density of wildlife populations. Methods to estimate wildlife mortality rates have developed largely independently from distance sampling, despite the conceptual similarities between estimation of cumulative mortality and the population density of living animals. Conventional distance sampling analyses rely on the assumption that animals are distributed uniformly with respect to transects and thus require randomized placement of transects during survey design. Because mortality events are rare, however, it is often not possible to obtain precise estimates in this way without infeasible levels of effort. A great deal of wildlife data, including mortality data, is available via road-based surveys. Interpreting these data in a distance sampling framework requires accounting for the non-uniformity sampling. Additionally, analyses of opportunistic mortality data must account for the decline in carcass detectability through time. We develop several extensions to distance sampling theory to address these problems.We build mortality estimators in a hierarchical framework that integrates animal movement data, surveillance effort data, and motion-sensor camera trap data, respectively, to relax the uniformity assumption, account for spatiotemporal variation in surveillance effort, and explicitly model carcass detection and disappearance as competing ongoing processes.Analysis of simulated data showed that our estimators were unbiased and that their confidence intervals had good coverage.We also illustrate our approach on opportunistic carcass surveillance data acquired in 2010 during an anthrax outbreak in the plains zebra of Etosha National Park, Namibia.The methods developed here will allow researchers and managers to infer mortality rates from opportunistic surveillance data. PMID:24224079

  11. Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes.

    PubMed

    Rummer, Jodie L; Binning, Sandra A; Roche, Dominique G; Johansen, Jacob L

    2016-01-01

    Respirometry is frequently used to estimate metabolic rates and examine organismal responses to environmental change. Although a range of methodologies exists, it remains unclear whether differences in chamber design and exercise (type and duration) produce comparable results within individuals and whether the most appropriate method differs across taxa. We used a repeated-measures design to compare estimates of maximal and standard metabolic rates (MMR and SMR) in four coral reef fish species using the following three methods: (i) prolonged swimming in a traditional swimming respirometer; (ii) short-duration exhaustive chase with air exposure followed by resting respirometry; and (iii) short-duration exhaustive swimming in a circular chamber. We chose species that are steady/prolonged swimmers, using either a body-caudal fin or a median-paired fin swimming mode during routine swimming. Individual MMR estimates differed significantly depending on the method used. Swimming respirometry consistently provided the best (i.e. highest) estimate of MMR in all four species irrespective of swimming mode. Both short-duration protocols (exhaustive chase and swimming in a circular chamber) produced similar MMR estimates, which were up to 38% lower than those obtained during prolonged swimming. Furthermore, underestimates were not consistent across swimming modes or species, indicating that a general correction factor cannot be used. However, SMR estimates (upon recovery from both of the exhausting swimming methods) were consistent across both short-duration methods. Given the increasing use of metabolic data to assess organismal responses to environmental stressors, we recommend carefully considering respirometry protocols before experimentation. Specifically, results should not readily be compared across methods; discrepancies could result in misinterpretation of MMR and aerobic scope. PMID:27382471

  12. A Hierarchical Distance Sampling Approach to Estimating Mortality Rates from Opportunistic Carcass Surveillance Data.

    PubMed

    Bellan, Steve E; Gimenez, Olivier; Choquet, Rémi; Getz, Wayne M

    2013-04-01

    Distance sampling is widely used to estimate the abundance or density of wildlife populations. Methods to estimate wildlife mortality rates have developed largely independently from distance sampling, despite the conceptual similarities between estimation of cumulative mortality and the population density of living animals. Conventional distance sampling analyses rely on the assumption that animals are distributed uniformly with respect to transects and thus require randomized placement of transects during survey design. Because mortality events are rare, however, it is often not possible to obtain precise estimates in this way without infeasible levels of effort. A great deal of wildlife data, including mortality data, is available via road-based surveys. Interpreting these data in a distance sampling framework requires accounting for the non-uniformity sampling. Additionally, analyses of opportunistic mortality data must account for the decline in carcass detectability through time. We develop several extensions to distance sampling theory to address these problems.We build mortality estimators in a hierarchical framework that integrates animal movement data, surveillance effort data, and motion-sensor camera trap data, respectively, to relax the uniformity assumption, account for spatiotemporal variation in surveillance effort, and explicitly model carcass detection and disappearance as competing ongoing processes.Analysis of simulated data showed that our estimators were unbiased and that their confidence intervals had good coverage.We also illustrate our approach on opportunistic carcass surveillance data acquired in 2010 during an anthrax outbreak in the plains zebra of Etosha National Park, Namibia.The methods developed here will allow researchers and managers to infer mortality rates from opportunistic surveillance data. PMID:24224079

  13. Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes

    PubMed Central

    Rummer, Jodie L.; Binning, Sandra A.; Roche, Dominique G.; Johansen, Jacob L.

    2016-01-01

    Respirometry is frequently used to estimate metabolic rates and examine organismal responses to environmental change. Although a range of methodologies exists, it remains unclear whether differences in chamber design and exercise (type and duration) produce comparable results within individuals and whether the most appropriate method differs across taxa. We used a repeated-measures design to compare estimates of maximal and standard metabolic rates (MMR and SMR) in four coral reef fish species using the following three methods: (i) prolonged swimming in a traditional swimming respirometer; (ii) short-duration exhaustive chase with air exposure followed by resting respirometry; and (iii) short-duration exhaustive swimming in a circular chamber. We chose species that are steady/prolonged swimmers, using either a body–caudal fin or a median–paired fin swimming mode during routine swimming. Individual MMR estimates differed significantly depending on the method used. Swimming respirometry consistently provided the best (i.e. highest) estimate of MMR in all four species irrespective of swimming mode. Both short-duration protocols (exhaustive chase and swimming in a circular chamber) produced similar MMR estimates, which were up to 38% lower than those obtained during prolonged swimming. Furthermore, underestimates were not consistent across swimming modes or species, indicating that a general correction factor cannot be used. However, SMR estimates (upon recovery from both of the exhausting swimming methods) were consistent across both short-duration methods. Given the increasing use of metabolic data to assess organismal responses to environmental stressors, we recommend carefully considering respirometry protocols before experimentation. Specifically, results should not readily be compared across methods; discrepancies could result in misinterpretation of MMR and aerobic scope. PMID:27382471

  14. Developing a methodology to estimate historical sheet erosion rates using exposed roots and terrestrial laser scanner

    NASA Astrophysics Data System (ADS)

    Gómez, Á.; Schnabel, S.; Lavado, F.; Rubio, J.

    2012-04-01

    In the present paper a new technique for estimating medium-term sheet erosion rates is presented. The methodology is based on analyzing the morphology of tree stems, exposed roots and surface micro-topography using data obtained with a Laser Terrestrial Scanner. A Leica Scan Station C10 was used to capture a surface of 70 000 square meters in a rangeland in southwest Spain. The resulting point cloud presented 20 000 000 points with spatial (x, y and z coordinates) and radiometric (RGB) information with a file size of 1.5 Gb. The point cloud was processed with Cyclone, Realworks and Pointools Edit software to obtain a 3D model of the study area. Afterwards, a Digital Terrain Model with high resolution was elaborated using ArcGIS 10 software. Using the base of tree stems and exposed roots, the initial level of the surface was estimated (initial or antecedent surface). On the other hand, existing tree growth models were applied to the trees in the study area in order to estimate their age. Finally, with the antecedent surface, the current surface and the estimated age of every tree soil erosion rates were calculated and compared with available information on land use and management in the study area.

  15. Uncertainties in Instantaneous Rainfall Rate Estimates: Satellite vs. Ground-Based Observations

    NASA Astrophysics Data System (ADS)

    Amitai, E.; Huffman, G. J.; Goodrich, D. C.

    2012-12-01

    High-resolution precipitation intensities are significant in many fields. For example, hydrological applications such as flood forecasting, runoff accommodation, erosion prediction, and urban hydrological studies depend on an accurate representation of the rainfall that does not infiltrate the soil, which is controlled by the rain intensities. Changes in the rain rate pdf over long periods are important for climate studies. Are our estimates accurate enough to detect such changes? While most evaluation studies are focusing on the accuracy of rainfall accumulation estimates, evaluation of instantaneous rainfall intensity estimates is relatively rare. Can a speceborne radar help in assessing ground-based radar estimates of precipitation intensities or is it the other way around? In this presentation we will provide some insight on the relative accuracy of instantaneous precipitation intensity fields from satellite and ground-based observations. We will examine satellite products such as those from the TRMM Precipitation Radar and those from several passive microwave imagers and sounders by comparing them with advanced high-resolution ground-based products taken at overpass time (snapshot comparisons). The ground based instantaneous rain rate fields are based on in situ measurements (i.e., the USDA/ARS Walnut Gulch dense rain gauge network), remote sensing observations (i.e., the NOAA/NSSL NMQ/Q2 radar-only national mosaic), and multi-sensor products (i.e., high-resolution gauge adjusted radar national mosaics, which we have developed by applying a gauge correction on the Q2 products).

  16. Estimating effective population size and migration rates from genetic samples over space and time.

    PubMed Central

    Wang, Jinliang; Whitlock, Michael C

    2003-01-01

    In the past, moment and likelihood methods have been developed to estimate the effective population size (N(e)) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of N(e) if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N(e) and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N(e), respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N(e) and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers. PMID:12586728

  17. COMPACT OBJECT COALESCENCE RATE ESTIMATION FROM SHORT GAMMA-RAY BURST OBSERVATIONS

    SciTech Connect

    Petrillo, Carlo Enrico; Dietz, Alexander; Cavaglia, Marco

    2013-04-20

    Recent observational and theoretical results suggest that short-duration gamma-ray bursts (SGRBs) originate from the merger of compact binary systems of two neutron stars or a neutron star and a black hole. The observation of SGRBs with known redshifts allows astronomers to infer the merger rate of these systems in the local universe. We use data from the SWIFT satellite to estimate this rate to be in the range {approx}500-1500 Gpc{sup -3} yr{sup -1}. This result is consistent with earlier published results which were obtained through alternative approaches. We estimate the number of coincident observations of gravitational-wave signals with SGRBs in the advanced gravitational-wave detector era. By assuming that all SGRBs are created by neutron star-neutron star (neutron star-black hole) mergers, we estimate the expected rate of coincident observations to be in the range {approx_equal} 0.2-1 ({approx_equal} 1-3) yr{sup -1}.

  18. Mixture models for estimating the size of a closed population when capture rates vary among individuals

    USGS Publications Warehouse

    Dorazio, R.M.; Royle, J. Andrew

    2003-01-01

    We develop a parameterization of the beta-binomial mixture that provides sensible inferences about the size of a closed population when probabilities of capture or detection vary among individuals. Three classes of mixture models (beta-binomial, logistic-normal, and latent-class) are fitted to recaptures of snowshoe hares for estimating abundance and to counts of bird species for estimating species richness. In both sets of data, rates of detection appear to vary more among individuals (animals or species) than among sampling occasions or locations. The estimates of population size and species richness are sensitive to model-specific assumptions about the latent distribution of individual rates of detection. We demonstrate using simulation experiments that conventional diagnostics for assessing model adequacy, such as deviance, cannot be relied on for selecting classes of mixture models that produce valid inferences about population size. Prior knowledge about sources of individual heterogeneity in detection rates, if available, should be used to help select among classes of mixture models that are to be used for inference.

  19. Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae.

    PubMed Central

    Zeyl, C; DeVisser, J A

    2001-01-01

    The per-genome, per-generation rate of spontaneous mutation affecting fitness (U) and the mean fitness cost per mutation (s) are important parameters in evolutionary genetics, but have been estimated for few species. We estimated U and sh (the heterozygous effect of mutations) for two diploid yeast strains differing only in the DNA mismatch-repair deficiency used to elevate the mutation rate in one (mutator) strain. Mutations were allowed to accumulate in 50 replicate lines of each strain, during 36 transfers of randomly chosen single colonies (approximately 600 generations). Among wild-type lines, fitnesses were bimodal, with one mode showing no change in mean fitness. The other mode showed a mean 29.6% fitness decline and the petite phenotype, usually caused by partial deletion of the mitochondrial genome. Excluding petites, maximum-likelihood estimates adjusted for the effect of selection were U = 9.5 x 10(-5) and sh = 0.217 for the wild type. Among the mutator lines, the best fit was obtained with 0.005 < or = U < or = 0.94 and 0.049 > or = sh > or = 0.0003. Like other recently tested model organisms, wild-type yeast have low mutation rates, with high mean fitness costs per mutation. Inactivation of mismatch repair increases the frequency of slightly deleterious mutations by approximately two orders of magnitude. PMID:11139491

  20. Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.

    PubMed

    Kamm, John A; Spence, Jeffrey P; Chan, Jeffrey; Song, Yun S

    2016-07-01

    Two-locus sampling probabilities have played a central role in devising an efficient composite-likelihood method for estimating fine-scale recombination rates. Due to mathematical and computational challenges, these sampling probabilities are typically computed under the unrealistic assumption of a constant population size, and simulation studies have shown that resulting recombination rate estimates can be severely biased in certain cases of historical population size changes. To alleviate this problem, we develop here new methods to compute the sampling probability for variable population size functions that are piecewise constant. Our main theoretical result, implemented in a new software package called LDpop, is a novel formula for the sampling probability that can be evaluated by numerically exponentiating a large but sparse matrix. This formula can handle moderate sample sizes ([Formula: see text]) and demographic size histories with a large number of epochs ([Formula: see text]). In addition, LDpop implements an approximate formula for the sampling probability that is reasonably accurate and scales to hundreds in sample size ([Formula: see text]). Finally, LDpop includes an importance sampler for the posterior distribution of two-locus genealogies, based on a new result for the optimal proposal distribution in the variable-size setting. Using our methods, we study how a sharp population bottleneck followed by rapid growth affects the correlation between partially linked sites. Then, through an extensive simulation study, we show that accounting for population size changes under such a demographic model leads to substantial improvements in fine-scale recombination rate estimation. PMID:27182948

  1. Spacecraft Angular Rates Estimation with Gyrowheel Based on Extended High Gain Observer

    PubMed Central

    Liu, Xiaokun; Yao, Yu; Ma, Kemao; Zhao, Hui; He, Fenghua

    2016-01-01

    A gyrowheel (GW) is a kind of electronic electric-mechanical servo system, which can be applied to a spacecraft attitude control system (ACS) as both an actuator and a sensor simultaneously. In order to solve the problem of two-dimensional spacecraft angular rate sensing as a GW outputting three-dimensional control torque, this paper proposed a method of an extended high gain observer (EHGO) with the derived GW mathematical model to implement the spacecraft angular rate estimation when the GW rotor is working at large angles. For this purpose, the GW dynamic equation is firstly derived with the second kind Lagrange method, and the relationship between the measurable and unmeasurable variables is built. Then, the EHGO is designed to estimate and calculate spacecraft angular rates with the GW, and the stability of the designed EHGO is proven by the Lyapunov function. Moreover, considering the engineering application, the effect of measurement noise in the tilt angle sensors on the estimation accuracy of the EHGO is analyzed. Finally, the numerical simulation is performed to illustrate the validity of the method proposed in this paper. PMID:27089347

  2. Problems in estimating age-specific survival rates from recovery data of birds ringed as young

    USGS Publications Warehouse

    Anderson, D.R.; Burnham, Kenneth P.; White, Gary C.

    1985-01-01

    (1) The life table model is frequently employed in the analysis of ringer samples of young in bird populations. The basic model is biologically unrealistic and of little use in making inferences concerning age-specific survival probabilities. (2) This model rests on a number of restrictive assumptions, the failure of which causes serious biases. Several important assumptions are not met with real data and the estimators of age-specific survival are not robust enough to these failures. (3) Five major problems in the use of the life table method are reviewed. Examples are provided to illustrate several of the problems involved in using this method in making inferences about survival rates and its age-specific nature. (4) We conclude that this is an invalid procedure and it should not be used. Furthermore, ringing studies involving only young birds are pointless as regards survival estimation because no valid method exists for estimating age-specific or time-specific survival rates from such data. (5) In our view, inferences about age-specific survival rates are possible only if both young and adult (or young, subadult and adult) age classes are ringed each year for k years (k ≥ 2).

  3. Spacecraft Angular Rates Estimation with Gyrowheel Based on Extended High Gain Observer.

    PubMed

    Liu, Xiaokun; Yao, Yu; Ma, Kemao; Zhao, Hui; He, Fenghua

    2016-01-01

    A gyrowheel (GW) is a kind of electronic electric-mechanical servo system, which can be applied to a spacecraft attitude control system (ACS) as both an actuator and a sensor simultaneously. In order to solve the problem of two-dimensional spacecraft angular rate sensing as a GW outputting three-dimensional control torque, this paper proposed a method of an extended high gain observer (EHGO) with the derived GW mathematical model to implement the spacecraft angular rate estimation when the GW rotor is working at large angles. For this purpose, the GW dynamic equation is firstly derived with the second kind Lagrange method, and the relationship between the measurable and unmeasurable variables is built. Then, the EHGO is designed to estimate and calculate spacecraft angular rates with the GW, and the stability of the designed EHGO is proven by the Lyapunov function. Moreover, considering the engineering application, the effect of measurement noise in the tilt angle sensors on the estimation accuracy of the EHGO is analyzed. Finally, the numerical simulation is performed to illustrate the validity of the method proposed in this paper. PMID:27089347

  4. Dose rate estimates from irradiated light-water-reactor fuel assemblies in air

    SciTech Connect

    Lloyd, W.R.; Sheaffer, M.K.; Sutcliffe, W.G.

    1994-01-31

    It is generally considered that irradiated spent fuel is so radioactive (self-protecting) that it can only be moved and processed with specialized equipment and facilities. However, a small, possibly subnational, group acting in secret with no concern for the environment (other than the reduction of signatures) and willing to incur substantial but not lethal radiation doses, could obtain plutonium by stealing and processing irradiated spent fuel that has cooled for several years. In this paper, we estimate the dose rate at various distances and directions from typical pressurized-water reactor (PWR) and boiling-water reactor (BWR) spent-fuel assemblies as a function of cooling time. Our results show that the dose rate is reduced rapidly for the first ten years after exposure in the reactor, and that it is reduced by a factor of {approx}10 (from the one year dose rate) after 15 years. Even for fuel that has cooled for 15 years, a lethal dose (LD50) of 450 rem would be received at 1 m from the center of the fuel assembly after several minutes. However, moving from 1 to 5 m reduces the dose rate by over a factor of 10, and moving from 1 to 10 m reduces the dose rate by about a factor of 50. The dose rates 1 m from the top or bottom of the assembly are considerably less (about 10 and 22%, respectively) than 1 m from the center of the assembly, which is the direction of the maximum dose rate.

  5. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.

    PubMed

    Yang, Z

    1994-09-01

    Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called "fixed-rates model", classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368-376) model, which assumes a single rate for all the sites. PMID:7932792

  6. Simultaneous estimates of synechococcus spp. Growth and grazing mortality rates in the English Channel

    NASA Astrophysics Data System (ADS)

    Ning, Xiu-Ren; Vaulot, Daniel

    1996-03-01

    The marine chroococooid phycoerythrin-containing Synechococcus spp. cyanobacterium has been implicated as a substantial component of the photosynthetic picoplankton in the ocean. Although its importance as food source for heterotrophic nanoplankton is now recognized, information about the cycling of Synechococcus biomass and its diel pattern is limited and study methodology varies among authors. The selective metabolic inhibitor method was used to simultaneously estimate growth and grazing disappearance rates of Synechococcus in the English Channel where growth rates ranged from 0.25 to 0.72/d (mean ±SD=0.51±0.17/d) and grazing mortality rates ranged from 0.19 to 0.64/d (mean ±SD=0.48±0.17/d). Size-fractionated experiments demonstrated that up to 70% of Synechococcus disappearance could be attributed to grazers going through a 2 μm Nuclepore filter. Synechococcus grazing mortality rates (mean=0.74 ±0.25/d) during the day were always higher than that (mean=0.2±0.20/d) during the night, while growth rates showed no clear diel pattern. A positive correlation was observed between growth rates and in situ temperature ranging from 9 to 17°C, while in contrast grazing was independent of temperature. The close similatiry between average growth and grazing rates suggests a rapid recycling of Synechococcus biomass in English Channel coastal waters.

  7. Estimation of microbial respiration rates in groundwater by geochemical modeling constrained with stable isotopes

    SciTech Connect

    Murphy, E.M.; Schramke, J.A.

    1998-11-01

    Changes in geochemistry and stable isotopes along a well-established groundwater flow path were used to estimate in situ microbial respiration rates in the Middendorf aquifer in the southeastern United States. Respiration rates were determined for individual terminal electron acceptors including O{sub 2}, MnO{sub 2}, Fe{sup 3+}, and SO{sub 4}{sup 2{minus}}. The extent of biotic reactions were constrained by the fractionation of stable isotopes of carbon and sulfur. Sulfur isotopes and the presence of sulfur-oxidizing microorganisms indicated that sulfate is produced through the oxidation of reduced sulfur species in the aquifer and not by the dissolution of gypsum, as previously reported. The respiration rates varied along the flow path as the groundwater transitioned between primarily oxic to anoxic conditions. Iron-reducing microorganisms were the largest contributors to the oxidation of organic matter along the portion of the groundwater flow path investigated in this study. The transition zone between oxic and anoxic groundwater contained a wide range of terminal electron acceptors and showed the greatest diversity and numbers of culturable microorganisms and the highest respiration rates. A comparison of respiration rates measured from core samples and pumped groundwater suggests that variability in respiration rates may often reflect the measurement scales, both in the sample volume and the time-frame over which the respiration measurement is averaged. Chemical heterogeneity may create a wide range of respiration rates when the scale of the observation is below the scale of the heterogeneity.

  8. Three-Axis Attitude Estimation With a High-Bandwidth Angular Rate Sensor

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Green, Joseph J.

    2013-01-01

    A continuing challenge for modern instrument pointing control systems is to meet the increasingly stringent pointing performance requirements imposed by emerging advanced scientific, defense, and civilian payloads. Instruments such as adaptive optics telescopes, space interferometers, and optical communications make unprecedented demands on precision pointing capabilities. A cost-effective method was developed for increasing the pointing performance for this class of NASA applications. The solution was to develop an attitude estimator that fuses star tracker and gyro measurements with a high-bandwidth angular rotation sensor (ARS). An ARS is a rate sensor whose bandwidth extends well beyond that of the gyro, typically up to 1,000 Hz or higher. The most promising ARS sensor technology is based on a magnetohydrodynamic concept, and has recently become available commercially. The key idea is that the sensor fusion of the star tracker, gyro, and ARS provides a high-bandwidth attitude estimate suitable for supporting pointing control with a fast-steering mirror or other type of tip/tilt correction for increased performance. The ARS is relatively inexpensive and can be bolted directly next to the gyro and star tracker on the spacecraft bus. The high-bandwidth attitude estimator fuses an ARS sensor with a standard three-axis suite comprised of a gyro and star tracker. The estimation architecture is based on a dual-complementary filter (DCF) structure. The DCF takes a frequency- weighted combination of the sensors such that each sensor is most heavily weighted in a frequency region where it has the lowest noise. An important property of the DCF is that it avoids the need to model disturbance torques in the filter mechanization. This is important because the disturbance torques are generally not known in applications. This property represents an advantage over the prior art because it overcomes a weakness of the Kalman filter that arises when fusing more than one rate

  9. Spike Pattern Structure Influences Synaptic Efficacy Variability under STDP and Synaptic Homeostasis. I: Spike Generating Models on Converging Motifs

    PubMed Central

    Bi, Zedong; Zhou, Changsong

    2016-01-01

    In neural systems, synaptic plasticity is usually driven by spike trains. Due to the inherent noises of neurons and synapses as well as the randomness of connection details, spike trains typically exhibit variability such as spatial randomness and temporal stochasticity, resulting in variability of synaptic changes under plasticity, which we call efficacy variability. How the variability of spike trains influences the efficacy variability of synapses remains unclear. In this paper, we try to understand this influence under pair-wise additive spike-timing dependent plasticity (STDP) when the mean strength of plastic synapses into a neuron is bounded (synaptic homeostasis). Specifically, we systematically study, analytically and numerically, how four aspects of statistical features, i.e., synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations, as well as their interactions influence the efficacy variability in converging motifs (simple networks in which one neuron receives from many other neurons). Neurons (including the post-synaptic neuron) in a converging motif generate spikes according to statistical models with tunable parameters. In this way, we can explicitly control the statistics of the spike patterns, and investigate their influence onto the efficacy variability, without worrying about the feedback from synaptic changes onto the dynamics of the post-synaptic neuron. We separate efficacy variability into two parts: the drift part (DriftV) induced by the heterogeneity of change rates of different synapses, and the diffusion part (DiffV) induced by weight diffusion caused by stochasticity of spike trains. Our main findings are: (1) synchronous firing and burstiness tend to increase DiffV, (2) heterogeneity of rates induces DriftV when potentiation and depression in STDP are not balanced, and (3) heterogeneity of cross-correlations induces DriftV together with heterogeneity of rates. We anticipate our work

  10. Incorporation of radiometric tracers in peat and implications for estimating accumulation rates.

    PubMed

    Hansson, Sophia V; Kaste, James M; Olid, Carolina; Bindler, Richard

    2014-09-15

    Accurate dating of peat accumulation is essential for quantitatively reconstructing past changes in atmospheric metal deposition and carbon burial. By analyzing fallout radionuclides (210)Pb, (137)Cs, (241)Am, and (7)Be, and total Pb and Hg in 5 cores from two Swedish peatlands we addressed the consequence of estimating accumulation rates due to downwashing of atmospherically supplied elements within peat. The detection of (7)Be down to 18-20 cm for some cores, and the broad vertical distribution of (241)Am without a well-defined peak, suggest some downward transport by percolating rainwater and smearing of atmospherically deposited elements in the uppermost peat layers. Application of the CRS age-depth model leads to unrealistic peat mass accumulation rates (400-600 g m(-2) yr(-1)), and inaccurate estimates of past Pb and Hg deposition rates and trends, based on comparisons to deposition monitoring data (forest moss biomonitoring and wet deposition). After applying a newly proposed IP-CRS model that assumes a potential downward transport of (210)Pb through the uppermost peat layers, recent peat accumulation rates (200-300 g m(-2) yr(-1)) comparable to published values were obtained. Furthermore, the rates and temporal trends in Pb and Hg accumulation correspond more closely to monitoring data, although some off-set is still evident. We suggest that downwashing can be successfully traced using (7)Be, and if this information is incorporated into age-depth models, better calibration of peat records with monitoring data and better quantitative estimates of peat accumulation and past deposition are possible, although more work is needed to characterize how downwashing may vary between seasons or years. PMID:24946030

  11. Optimal Estimation of Rain-Rate Profiles from Single-Frequency Radar Echoes

    NASA Technical Reports Server (NTRS)

    Haddad, Ziad S.; Im, Eastwood; Durden, Stephen L.

    1996-01-01

    The significant ambiguities inherent in the determination of a particular vertical rain intensity profile from a given time profile of radar echo powers measured by a downward-looking (spaceborne or airborne) radar at a single attenuating frequency are well documented. Indeed, one already knows that by appropriately varying the parameters of the reflectivity-rain rate (Z-R) and/or attenuation-rain rate (k- R) relationships one can produce several substantially different rain-rate profiles that would produce the same radar power profile. Imposing the additional constraint that the path-averaged rain rate be a given fixed number does reduce the ambiguities but falls far short of eliminating them. While formulas to generate all mutually ambiguous rain-rate profiles from a given profile of received radar reflectivities have already been derived, there remains to be produced a quantitative measure to assess how likely each of these profiles is, what the appropriate "average" profile should be, and what the "variance" of these multiple solutions is. To do this, one needs to spell out the stochastic constraints that can allow us to make sense of the words "average" and "variance" in a mathematically rigorous way. Such a quantitative approach would be particularly well suited for such systems as the planned precipitation radar of the Tropical Rainfall Measuring Mission (TRMM). Indeed, one would then be able to use the radar reflectivities measured by the TRMM radar to estimate the rain-rate profile that would most likely have produced the measurements, as well as the uncertainty in the estimated rain rates as a function of range. Such an optimal approach is described in this paper.

  12. Optimal Estimation of Rain Rate Profiles from Single-Frequency Radar Echoes

    NASA Technical Reports Server (NTRS)

    Haddad, Ziad S.; Im, Eastwood

    1992-01-01

    The significant ambiguities inherent in the determination of a particular vertical rain intensity profile from a given time profile of radar echo powers measured by a downward-looking (spaceborne or airborne) radar at a single attenuating frequency are well-documented. Indeed, one already knows that by appropriately varying the parameters of the reflectivity-rain-rate (Z - R) and/or attenuation-rain-rate (k - R) relationships, one can produce several substantially different hypothetical rain rate profiles which would have the same radar power profile. Imposing the additional constraint that the path-averaged rain-rate be a given fixed number does reduce the ambiguities but falls far short of eliminating them. While we now know how to generate as many mutually ambiguous rain-rate profiles from a given profile of received radar reflectivities as we like, there remains to produce a quantitative measure to assess how likely each of these profiles is, what the appropriate 'average' profile should be, and what the 'variance' of these multiple solutions is. Of course, in order to do this, one needs to spell out the stochastic constraints that can allow us to make sense of the words 'average' and 'variance' in a mathematically rigorous way. Such a quantitative approach would be particularly well-suited for such systems as the proposed Precipitation Radar of the Tropical Rainfall Measuring Mission (TRMM). Indeed, one would then be able to use the radar reflectivities measured by the TRMM radar from one particular look in order to estimate the most likely rain-rate profile that would have produced the measurements, as well as the uncertainty in the estimated rain-rates as a function of range. Such an optimal approach is described in this paper.

  13. GEO-to-GEO Optical Sensors: Estimating the Detection Rate of Uncataloged Debris Objects

    NASA Astrophysics Data System (ADS)

    Shell, J.

    2013-09-01

    The GEO debris environment remains ill-characterized, in particular the population of small (< 1m) debris objects. While the space object catalog only contains debris attributed to two GEO fragmentation events, many estimate that ten or more GEO fragmentation events have occurred. Further complicating the small debris estimates are wide-ranging assumptions on fragmentation event kinematics, and the extent to which the NASA breakup model applies. However, candidate efforts may enable GEO-hosted optical sensors, thus providing an opportunity for empirical examination of the small debris population. These potential missions beg the question of exactly what will be seen from such payloads. Will the exponentially increasing small debris population flood such sensors with many detection events from small objects at relatively short ranges? Or, will the angular rates of such objects at required ranges for adequate signal result in minimal small objects detected? A physics-based model is employed to estimate detection events given an optical payload with a parameterized estimate of the GEO small debris environment. It is found that only for the most aggressive small debris population estimates that small objects dominate detections. Object sizes on the order of 10 cm and larger are found to comprise the majority of detection events.

  14. A hand speed-duty cycle equation for estimating the ACGIH hand activity level rating.

    PubMed

    Akkas, Oguz; Azari, David P; Chen, Chia-Hsiung Eric; Hu, Yu Hen; Ulin, Sheryl S; Armstrong, Thomas J; Rempel, David; Radwin, Robert G

    2015-01-01

    An equation was developed for estimating hand activity level (HAL) directly from tracked root mean square (RMS) hand speed (S) and duty cycle (D). Table lookup, equation or marker-less video tracking can estimate HAL from motion/exertion frequency (F) and D. Since automatically estimating F is sometimes complex, HAL may be more readily assessed using S. Hands from 33 videos originally used for the HAL rating were tracked to estimate S, scaled relative to hand breadth (HB), and single-frame analysis was used to measure D. Since HBs were unknown, a Monte Carlo method was employed for iteratively estimating the regression coefficients from US Army anthropometry survey data. The equation: HAL = 10[e(-15:87+0:02D+2:25 ln S)/(1+e(-15:87+0:02D+2:25 ln S)], R(2) = 0.97, had a residual range ± 0.5 HAL. The S equation superiorly fits the Latko et al. ( 1997 ) data and predicted independently observed HAL values (Harris 2011) better (MSE = 0.16) than the F equation (MSE = 1.28). PMID:25343278

  15. Estimation and Simulation of Slow Crack Growth Parameters from Constant Stress Rate Data

    NASA Technical Reports Server (NTRS)

    Salem, Jonathan A.; Weaver, Aaron S.

    2003-01-01

    Closed form, approximate functions for estimating the variances and degrees-of-freedom associated with the slow crack growth parameters n, D, B, and A(sup *) as measured using constant stress rate ('dynamic fatigue') testing were derived by using propagation of errors. Estimates made with the resulting functions and slow crack growth data for a sapphire window were compared to the results of Monte Carlo simulations. The functions for estimation of the variances of the parameters were derived both with and without logarithmic transformation of the initial slow crack growth equations. The transformation was performed to make the functions both more linear and more normal. Comparison of the Monte Carlo results and the closed form expressions derived with propagation of errors indicated that linearization is not required for good estimates of the variances of parameters n and D by the propagation of errors method. However, good estimates variances of the parameters B and A(sup *) could only be made when the starting slow crack growth equation was transformed and the coefficients of variation of the input parameters were not too large. This was partially a result of the skewered distributions of B and A(sup *). Parametric variation of the input parameters was used to determine an acceptable range for using closed form approximate equations derived from propagation of errors.

  16. Estimates of vital rates for a declining loggerhead turtle (Caretta caretta) subpopulation: implications for management

    USGS Publications Warehouse

    Lamont, Margaret M.; Fujisaki, Ikuko; Carthy, Raymond R.

    2014-01-01

    Because subpopulations can differ geographically, genetically and/or phenotypically, using data from one subpopulation to derive vital rates for another, while often unavoidable, is not optimal. We used a two-state open robust design model to analyze a 14-year dataset (1998–2011) from the St. Joseph Peninsula, Florida (USA; 29.748°, −85.400°) which is the densest loggerhead (Caretta caretta) nesting beach in the Northern Gulf of Mexico subpopulation. For these analyses, 433 individuals were marked of which only 7.2 % were observed re-nesting in the study area in subsequent years during the study period. Survival was estimated at 0.86 and is among the highest estimates for all subpopulations in the Northwest Atlantic population. The robust model estimated a nesting assemblage size that ranged from 32 to 230 individuals each year with an annual average of 110. The model estimates indicated an overall population decline of 17 %. The results presented here for this nesting group represent the first estimates for this subpopulation. These data provide managers with information specific to this subpopulation that can be used to develop recovery plans and conduct subpopulation-specific modeling exercises explicit to the challenges faced by turtles nesting in this region.

  17. Path-integral virial estimator for reaction rate calculation basedon the quantum instanton aproximation

    SciTech Connect

    Yang, Sandy; Yamamoto, Takeshi; Miller, William H.

    2005-11-28

    The quantum instanton approximation is a type of quantum transition state theory that calculates the chemical reaction rate using the reactive flux correlation function and its low order derivatives at time zero. Here we present several path-integral estimators for the latter quantities, which characterize the initial decay profile of the flux correlation function. As with the internal energy or heat capacity calculation, different estimators yield different variances (and therefore different convergence properties) in a Monte Carlo calculation. Here we obtain a virial(-type) estimator by using a coordinate scaling procedure rather than integration by parts, which allows more computational benefits. We also consider two different methods for treating the flux operator, i.e., local-path and global-path approaches, in which the latter achieves a smaller variance at the cost of using second-order potential derivatives. Numerical tests are performed for a one-dimensional Eckart barrier and a model proton transfer reaction in a polar solvent, which illustrates the reduced variance of the virial estimator over the corresponding thermodynamic estimator.

  18. Combined methodology for estimating dose rates and health effects from exposure to radioactive pollutants

    SciTech Connect

    Dunning, D.E. Jr.; Leggett, R.W.; Yalcintas, M.G.

    1980-12-01

    The work described in the report is basically a synthesis of two previously existing computer codes: INREM II, developed at the Oak Ridge National Laboratory (ORNL); and CAIRD, developed by the Environmental Protection Agency (EPA). The INREM II code uses contemporary dosimetric methods to estimate doses to specified reference organs due to inhalation or ingestion of a radionuclide. The CAIRD code employs actuarial life tables to account for competing risks in estimating numbers of health effects resulting from exposure of a cohort to some incremental risk. The combined computer code, referred to as RADRISK, estimates numbers of health effects in a hypothetical cohort of 100,000 persons due to continuous lifetime inhalation or ingestion of a radionuclide. Also briefly discussed in this report is a method of estimating numbers of health effects in a hypothetical cohort due to continuous lifetime exposure to external radiation. This method employs the CAIRD methodology together with dose conversion factors generated by the computer code DOSFACTER, developed at ORNL; these dose conversion factors are used to estimate dose rates to persons due to radionuclides in the air or on the ground surface. The combination of the life table and dosimetric guidelines for the release of radioactive pollutants to the atmosphere, as required by the Clean Air Act Amendments of 1977.

  19. Satellite Rainfall Uncertainty Estimation by Mathematical Models Using Geophysical Features and Rainfall Rate

    NASA Astrophysics Data System (ADS)

    Gebregiorgis, A. S.; Hossain, F.

    2012-12-01

    This study addresses the estimation of error variance of three satellite rainfall products: i) Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) product of 3B42RT; ii) Climate Prediction Center (CPC) Morph (CMORPH); and iii) Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks - Cloud Classification System (PERSIANN-CCS). Nonlinear regression model is used to fit the response variable (satellite rainfall error variance) with explanatory variable (satellite rainfall rate) by grouping them as function of three key geophysical features: topography, climate, and season. The results of the study suggest that the error variance of a rainfall product is strongly correlated with rainfall rate and can be expressed as a power-law function. The geophysical feature based error classification analysis helps in achieving superior functional accuracy for prognostic error variance quantification in the absence of ground truth data. The multiple correlation coefficients between the estimated and observed error variance over an independent validation region (Upper Mississippi River basin) and time period (2007 - 2010) are found to be 0.75, 0.86, and 0.87 for 3B42RT, CMORPH, and PERSIANN-CCS products, respectively. In another validation region (Arkansas-Red River basin), the correlation coefficients are 0.59, 0.89, and 0.92 for the same products, respectively. Results of the assessment of error variance models reveal that the type of error component present in a satellite rainfall product directly impacts on the accuracy of estimated error variance. The model estimates the error variance more accurately when the precipitation error components are mostly hit bias or false precipitation, while for a product with extensive missed precipitation, the accuracy of estimated error variance is significantly compromised. The study clearly demonstrates the feasibility of quantifying the error variance of satellite

  20. Learning Universal Computations with Spikes

    PubMed Central

    Thalmeier, Dominik; Uhlmann, Marvin; Kappen, Hilbert J.; Memmesheimer, Raoul-Martin

    2016-01-01

    Providing the neurobiological basis of information processing in higher animals, spiking neural networks must be able to learn a variety of complicated computations, including the generation of appropriate, possibly delayed reactions to inputs and the self-sustained generation of complex activity patterns, e.g. for locomotion. Many such computations require previous building of intrinsic world models. Here we show how spiking neural networks may solve these different tasks. Firstly, we derive constraints under which classes of spiking neural networks lend themselves to substrates of powerful general purpose computing. The networks contain dendritic or synaptic nonlinearities and have a constrained connectivity. We then combine such networks with learning rules for outputs or recurrent connections. We show that this allows to learn even difficult benchmark tasks such as the self-sustained generation of desired low-dimensional chaotic dynamics or memory-dependent computations. Furthermore, we show how spiking networks can build models of external world systems and use the acquired knowledge to control them. PMID:27309381

  1. Estimating the Attack Rate of Pregnancy-Associated Listeriosis during a Large Outbreak

    PubMed Central

    Imanishi, Maho; Routh, Janell A.; Klaber, Marigny; Gu, Weidong; Vanselow, Michelle S.; Jackson, Kelly A.; Sullivan-Chang, Loretta; Heinrichs, Gretchen; Jain, Neena; Albanese, Bernadette; Callaghan, William M.; Mahon, Barbara E.; Silk, Benjamin J.

    2015-01-01

    Background. In 2011, a multistate outbreak of listeriosis linked to contaminated cantaloupes raised concerns that many pregnant women might have been exposed to Listeria monocytogenes. Listeriosis during pregnancy can cause fetal death, premature delivery, and neonatal sepsis and meningitis. Little information is available to guide healthcare providers who care for asymptomatic pregnant women with suspected L. monocytogenes exposure. Methods. We tracked pregnancy-associated listeriosis cases using reportable diseases surveillance and enhanced surveillance for fetal death using vital records and inpatient fetal deaths data in Colorado. We surveyed 1,060 pregnant women about symptoms and exposures. We developed three methods to estimate how many pregnant women in Colorado ate the implicated cantaloupes, and we calculated attack rates. Results. One laboratory-confirmed case of listeriosis was associated with pregnancy. The fetal death rate did not increase significantly compared to preoutbreak periods. Approximately 6,500–12,000 pregnant women in Colorado might have eaten the contaminated cantaloupes, an attack rate of ~1 per 10,000 exposed pregnant women. Conclusions. Despite many exposures, the risk of pregnancy-associated listeriosis was low. Our methods for estimating attack rates may help during future outbreaks and product recalls. Our findings offer relevant considerations for management of asymptomatic pregnant women with possible L. monocytogenes exposure. PMID:25784782

  2. The use of intraallelic variability for testing neutrality and estimating population growth rate.

    PubMed Central

    Slatkin, M; Bertorelle, G

    2001-01-01

    To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely linked marker loci (the intraallelic variability). We model three types of intraallelic variability: (a) the number of nonrecombinants at a linked biallelic marker locus, (b) the length of a conserved haplotype, and (c) the number of mutations at a linked marker locus. If the population growth rate is known, the joint distribution provides the basis for a test of neutrality by testing whether the observed level of intraallelic variability is consistent with the observed allele frequency. If the population growth rate is unknown but neutrality can be assumed, the joint distribution provides the likelihood of the growth rate and leads to a maximum-likelihood estimate. We apply the method to data from published data sets for four loci in humans. We conclude that the Delta32 allele at CCR5 and a disease-associated allele at MLH1 arose recently and have been subject to strong selection. Alleles at PAH appear to be neutral and we estimate the recent growth rate of the European population to be approximately 0.027 per generation with a support interval of (0.017-0.037). Four of the relatively common alleles at CFTR also appear to be neutral but DeltaF508 appears to be significantly advantageous to heterozygous carriers. PMID:11404347

  3. The repeatability of genome-wide mutation rate and spectrum estimates.

    PubMed

    Behringer, Megan G; Hall, David W

    2016-08-01

    Over the last decade, mutation studies have grown in popularity due to the affordability and accessibility of whole genome sequencing. As the number of species in which spontaneous mutation has been directly estimated approaches 20 across two domains of life, questions arise over the repeatability of results in such experiments. Five species were identified in which duplicate mutation studies have been performed. Across these studies the difference in estimated spontaneous mutation rate is at most, weakly significant (p < 0.01). However, a highly significant (p < 10(-5)), threefold difference in the rate of insertions/deletions (indels) exists between two recent studies in Schizosaccharomyces pombe. Upon investigation of the ancestral genome sequence for both studies, a possible anti-mutator allele was identified. The observed variation in indel rate may imply that the use of indel markers, such as microsatellites, for the investigation of genetic diversity within and among populations may be inappropriate because of the assumption of uniform mutation rate within a species. PMID:26919990

  4. Thunderstorm cloud height-rainfall rate relations for use with satellite rainfall estimation techniques

    NASA Technical Reports Server (NTRS)

    Adler, R. F.; Mack, R. A.

    1984-01-01

    Observational studies of thunderstorm cloud height-rainfall rate and cloud height-volume rainfall rate relations are reviewed with significant variations being noted among climatological regimes. Analysis of the Florida (summer) and Oklahoma (spring) relations are made using a one-dimensional cloud model to ascertain the important factors in determining the individual cloud-rain relations and the differences between the two regimes. In general, the observed relations are well simulated by the model-based calculations. The generally lower predicted rain rates in Oklahoma (as compared to Florida) result from lower precipitation efficiencies which are due to a combination of larger entrainment (related to larger vertical wind shear) and drier environment. The generally steeper slope of the Oklahoma rain rate height curves is shown to be due to a stronger variation in maximum vertical velocity with cloud top height, which, in turn, is related to the greater static stability in the range of cloud tops. The impact of the regime-to-regime variations on empirical rain estimation schemes based on satellite-observed cloud height or cloud temperature information is discussed and a rain estimation approach based on model-generated cloud-rain relations is outlined.

  5. TMI Rain Rate Estimation Over Land and Ocean Utilizing Convective and Stratiform Discrimination

    NASA Technical Reports Server (NTRS)

    Prabhakara, C.; Iacovazzi, R., Jr.; Weinman, J. A.; Dalu, G.

    1999-01-01

    Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) radiometer brightness temperature data in the 85 GHz channel (T85) reveal distinct local minima in a regional map containing a Mesoscale Convective System (MCS). This is because of relatively small footprint size (approximately 5.5 km) and strong extinction properties in this channel of the TMI. A map of rain rate for that region, deduced from simultaneous measurements made by the Precipitation Radar (PR) on board the TRMM satellite, reveals that these T85 minima, produced by scattering, correspond to local PR rain maxima. Utilizing the PR rain rate map as a guide, we infer from TMI data the presence of three different kinds of thunderstorms or Cbs. They are young, mature, and decaying Cbs that have a scale of about 20 km on the average. Two parameters enable us to infer these three kinds of Cbs objectively: a) the magnitude of scattering depression deduced from local T85 minima and b) the mean horizontal gradient of T85 around such minima. Knowing the category of a given Cb, we can estimate the rain rate associated with it. Such estimation is done with the help of relationships linking T85 minimum to rain rate in each Cb type. Similarly, a weak background rain rate in all the areas where T85 is less than 260 K is deduced with another relationship linking T85 to rain rate. In our rain retrieval model, this background rain constitutes the stratiform rain where the Cbs are absent. Initially, these relationships are optimized or tuned utilizing the PR and TMI data of a few MCS events. After such tuning, the model is applied to independent MCS cases. The areal distribution of light (1-10 mm/hr), moderate (10-20 mm/hr), and intense (> 20 mm/hr) rain rates are retrieved satisfactorally. Accuracy in the estimates of the light, moderate and intense rain areas and the mean rain rates associated with such areas in these independent MCS cases is on the average about 15%. Taking advantage of this ability of our

  6. A TRMM Microwave Radiometer Rain Rate Estimation Method with Convective and Stratiform Discrimination

    NASA Technical Reports Server (NTRS)

    Prabhakara, C.; Iacovazzi, R., Jr.; Weinman, J. A.; Dalu, G.

    1999-01-01

    Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) radiometer brightness temperature data in the 85 GHz channel (T85) reveal distinct local minima (T85min) in a regional map containing a Mesoscale Convective System (MCS). This is because of relatively small footprint size (approximately 5.5 km) and strong extinction properties in this channel of the TMI. A map of surface rain rate for that region, deduced from simultaneous measurements made by the Precipitation Radar (PR) on board the TRMM satellite, reveals that these T85(sub min), produced by scattering, correspond to local PR rain maxima. Utilizing the PR rain rate map as a guide, we infer empirically from TMI data the presence of three different kinds of thunderstorms or Cbs. These Cbs are classified as young, mature, and decaying types, and are assumed to have a scale of about 20 km on the average. Two parameters are used to classify these three kinds of Cbs based on the T85 data: a) the magnitude of scattering depression deduced from local T85(sub min) and b) the mean horizontal gradient of T85 around such minima. Knowing the category of a given Cb, we can estimate the rain rate associated with it. Such estimation is done with the help of relationships linking T85min to rain rate in each Cb type. Similarly, a weak background rain rate in all the areas where T85 is less than 260 K is deduced with another relationship linking T85 to rain rate. In our rain retrieval model, this background rain constitutes stratiform rain where the Cbs are absent. Initially, these relationships are optimized or tuned utilizing the PR and TMI data of a few MCS events. After such tuning, the model is applied to independent MCS cases. The areal distribution of light (1-10 mm/hr), moderate (10-20 mm/hr), and intense (>= 20 mm/hr) rain rates are retrieved satisfactorily. Accuracy in the estimates of the light, moderate, and intense rain areas and the mean rain rates associated with such areas in these independent MCS

  7. Dose rate estimation of the Tohoku hynobiid salamander, Hynobius lichenatus, in Fukushima.

    PubMed

    Fuma, Shoichi; Ihara, Sadao; Kawaguchi, Isao; Ishikawa, Takahiro; Watanabe, Yoshito; Kubota, Yoshihisa; Sato, Youji; Takahashi, Hiroyuki; Aono, Tatsuo; Ishii, Nobuyoshi; Soeda, Haruhi; Matsui, Kumi; Une, Yumi; Minamiya, Yukio; Yoshida, Satoshi

    2015-05-01

    The radiological risks to the Tohoku hynobiid salamanders (class Amphibia), Hynobius lichenatus due to the Fukushima Dai-ichi Nuclear Power Plant accident were assessed in Fukushima Prefecture, including evacuation areas. Aquatic egg clutches (n = 1 for each sampling date and site; n = 4 in total), overwintering larvae (n = 1-5 for each sampling date and site; n = 17 in total), and terrestrial juveniles or adults (n = 1 or 3 for each sampling date and site; n = 12 in total) of H. lichenatus were collected from the end of April 2011 to April 2013. Environmental media such as litter (n = 1-5 for each sampling date and site; n = 30 in total), soil (n = 1-8 for each sampling date and site; n = 31 in total), water (n = 1 for each sampling date and site; n = 17 in total), and sediment (n = 1 for each sampling date and site; n = 17 in total) were also collected. Activity concentrations of (134)Cs + (137)Cs were 1.9-2800, 0.13-320, and 0.51-220 kBq (dry kg) (-1) in the litter, soil, and sediment samples, respectively, and were 0.31-220 and <0.29-40 kBq (wet kg)(-1) in the adult and larval salamanders, respectively. External and internal absorbed dose rates to H. lichenatus were calculated from these activity concentration data, using the ERICA Assessment Tool methodology. External dose rates were also measured in situ with glass dosimeters. There was agreement within a factor of 2 between the calculated and measured external dose rates. In the most severely contaminated habitat of this salamander, a northern part of Abukuma Mountains, the highest total dose rates were estimated to be 50 and 15 μGy h(-1) for the adults and overwintering larvae, respectively. Growth and survival of H. lichenatus was not affected at a dose rate of up to 490 μGy h(-1) in the previous laboratory chronic gamma-irradiation experiment, and thus growth and survival of this salamander would not be affected, even in the most severely contaminated habitat in Fukushima Prefecture. However, further

  8. Plutonium Discharge Rates and Spent Nuclear Fuel Inventory Estimates for Nuclear Reactors Worldwide

    SciTech Connect

    Brian K. Castle; Shauna A. Hoiland; Richard A. Rankin; James W. Sterbentz

    2012-09-01

    This report presents a preliminary survey and analysis of the five primary types of commercial nuclear power reactors currently in use around the world. Plutonium mass discharge rates from the reactors’ spent fuel at reload are estimated based on a simple methodology that is able to use limited reactor burnup and operational characteristics collected from a variety of public domain sources. Selected commercial reactor operating and nuclear core characteristics are also given for each reactor type. In addition to the worldwide commercial reactors survey, a materials test reactor survey was conducted to identify reactors of this type with a significant core power rating. Over 100 material or research reactors with a core power rating >1 MW fall into this category. Fuel characteristics and spent fuel inventories for these material test reactors are also provided herein.

  9. Simple and robust symbol rate estimation method for digital coherent optical receivers

    NASA Astrophysics Data System (ADS)

    Cui, Sheng; Xia, Wenjuan; Shang, Jin; Ke, Changjian; Fu, Songnian; Liu, Deming

    2016-05-01

    A novel symbol rate estimation (SRE) technique utilizing the clock tone (CT) obtained by Godard timing recovery algorithm is proposed. By this technique, the known sampling rate of the analog-to-digital converter (ADC) in digital coherent optical receivers can used as a reference to directly determine the unknown signal symbol rate. The impact of polarization mode dispersion (PMD) on the CT magnitude can be mitigated by using the hybrid correlation function (HCF) consisting of both auto-correlation function (ACF) and cross-correlation function (XCF) of the received signal spectrum, while the chromatic dispersion (CD) impact can be mitigated by adaptive CD compensation techniques. This technique is simple, accurate, applicable to advanced modulation formats commonly used, and robust to various link impairments. Numerical simulations and experimental results are presented to validate this technique.

  10. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate.

    PubMed

    Hardy, Olivier J

    2016-01-01

    Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids. PMID:25981126

  11. Estimators of the local false discovery rate designed for small numbers of tests.

    PubMed

    Padilla, Marta; Bickel, David R

    2012-01-01

    Histogram-based empirical Bayes methods developed for analyzing data for large numbers of genes, SNPs, or other biological features tend to have large biases when applied to data with a smaller number of features such as genes with expression measured conventionally, proteins, and metabolites. To analyze such small-scale and medium-scale data in an empirical Bayes framework, we introduce corrections of maximum likelihood estimators (MLEs) of the local false discovery rate (LFDR). In this context, the MLE estimates the LFDR, which is a posterior probability of null hypothesis truth, by estimating the prior distribution. The corrections lie in excluding each feature when estimating one or more parameters on which the prior depends. In addition, we propose the expected LFDR (ELFDR) in order to propagate the uncertainty involved in estimating the prior. We also introduce an optimally weighted combination of the best of the corrected MLEs with a previous estimator that, being based on a binomial distribution, does not require a parametric model of the data distribution across features. An application of the new estimators and previous estimators to protein abundance data illustrates the extent to which different estimators lead to different conclusions about which proteins are affected by cancer. A simulation study was conducted to approximate the bias of the new estimators relative to previous LFDR estimators. Data were simulated for two different numbers of features (N), two different noncentrality parameter values or detectability levels (dalt), and several proportions of unaffected features (p0). One of these previous estimators is a histogram-based estimator (HBE) designed for a large number of features. The simulations show that some of the corrected MLEs and the ELFDR that corrects the HBE reduce the negative bias relative to the MLE and the HBE, respectively. For every method, we defined the worst-case performance as the maximum of the absolute value of the bias

  12. Estimation of the reaction rate constant of HOCl by SMILES observation

    NASA Astrophysics Data System (ADS)

    Kuribayashi, Kouta; Kasai, Yasuko; Sato, Tomohiro; Sagawa, Hideo

    2012-07-01

    Hypochlorous acid, HOCl plays an important role to link the odd ClOx and the odd HOx in the atmospheric chemistry with the reaction: {ClO} + {HO_{2}} \\longrightarrow {HOCl} + {O_{2}} Quantitative understanding of the rate constant of the reaction (1.1) is essential for understanding the ozone loss in the mid-latitude region because of a view point of its rate controlling role in the ozone depletion chemistry. Reassessment of the reaction rate constant was pointed out from MIPAS/Envisat observations (von Clarmann et al., 2011) and balloon-borne observations (Kovalenko et al., 2007). Several laboratory studies had been reported, although the reaction rate constants have large uncertainties, as k{_{HOCl}} = (1.75 ± 0.52) × 10^{-12} exp[(368 ± 78)/T] (Hickson et al., 2007), and large discrepancies (Hickson et al., 2007;Stimpfle et al., 1979). Moreover, theoretical ab initio studies pointed out the pressure dependence of the reaction (1.1) (Xu et al., 2003). A new high-sensitive remote sensing technology named Superconducting SubMillimeter-wave Limb-Emission Sounder (SMILES) on the International Space Station (ISS) had observed diurnal variations of HOCl in the upper stratosphere/lower mesosphere (US/LM) region for the first time. ClO and HO_{2} were slso observed simultaneously with HOCl. SMILES performed the observations between 12^{{th}} October 2009 and 21^{{th}} April 2010. The latitude coverage of SMILES observation is normally 38°S-65°N. The altitude region of HOCl observation is about 28-70 km. We estimated the time period in which the reaction (1.1) becomes dominant in the ClO_{y} diurnal chemistry in US/LM. The reaction rate constant was directly estimated by decay of [ClO] and [HO_{2}] amounts in that period. The derived reaction rate constant represented well the increase of [HOCl] amount.

  13. RATE COEFFICIENTS FOR THE COLLISIONAL EXCITATION OF MOLECULES: ESTIMATES FROM AN ARTIFICIAL NEURAL NETWORK

    SciTech Connect

    Neufeld, David A.

    2010-01-01

    An artificial neural network (ANN) is investigated as a tool for estimating rate coefficients for the collisional excitation of molecules. The performance of such a tool can be evaluated by testing it on a data set of collisionally induced transitions for which rate coefficients are already known: the network is trained on a subset of that data set and tested on the remainder. Results obtained by this method are typically accurate to within a factor of approx2.1 (median value) for transitions with low excitation rates and approx1.7 for those with medium or high excitation rates, although 4% of the ANN outputs are discrepant by a factor of 10 or more. The results suggest that ANNs will be valuable in extrapolating a data set of collisional rate coefficients to include high-lying transitions that have not yet been calculated. For the asymmetric top molecules considered in this paper, the favored architecture is a cascade-correlation network that creates 16 hidden neurons during the course of training, with three input neurons to characterize the nature of the transition and one output neuron to provide the logarithm of the rate coefficient.

  14. Influence of Initial Leaf Pack Size on Estimates of Breakdown Rates in Streams

    NASA Astrophysics Data System (ADS)

    Stone, M. L.; Whiles, M. R.; McTammany, M. E.; Gallo, T. M.

    2005-05-01

    Experiments to determine the influence of leaf pack size on estimates of breakdown rates were conducted in Stony Run, a moderately hardwater stream in central Pennsylvania draining mature second-growth forest. We deployed 5-mm mesh bags containing different initial amounts (2, 5, 10, 20, and 50 g) of white oak leaves at 3 sites in Stony Run during October 2004. Bags have been retrieved monthly and were processed to determine ash-free dry mass remaining and abundance of shredder-detritivores in the bags. Breakdown rates varied from 0.018 d-1 in 50 g bags to 0.015 d-1 in 2 g bags and were strongly correlated with initial weight of leaf litter (log10 initial leaf mass vs. breakdown rate r = 0.99). Total invertebrate abundance was initially higher in heavier leaf bags, and proportion of shredders increased as leaf mass declined throughout the study. Shredder abundance was positively correlated with leaf pack size (r = 0.76) and breakdown rate (r = 0.82), which indicates that shredders were more important in determining breakdown rates than mechanical fragmentation or microbial activity. These results suggest that models of stream organic matter dynamics should incorporate distribution of natural leaf packs and higher breakdown rates associated with densely packed leaves.

  15. On the Spike Train Variability Characterized by Variance-to-Mean Power Relationship.

    PubMed

    Koyama, Shinsuke

    2015-07-01

    We propose a statistical method for modeling the non-Poisson variability of spike trains observed in a wide range of brain regions. Central to our approach is the assumption that the variance and the mean of interspike intervals are related by a power function characterized by two parameters: the scale factor and exponent. It is shown that this single assumption allows the variability of spike trains to have an arbitrary scale and various dependencies on the firing rate in the spike count statistics, as well as in the interval statistics, depending on the two parameters of the power function. We also propose a statistical model for spike trains that exhibits the variance-to-mean power relationship. Based on this, a maximum likelihood method is developed for inferring the parameters from rate-modulated spike trains. The proposed method is illustrated on simulated and experimental spike trains. PMID:25973546

  16. Spike Pattern Structure Influences Synaptic Efficacy Variability under STDP and Synaptic Homeostasis. II: Spike Shuffling Methods on LIF Networks.

    PubMed

    Bi, Zedong; Zhou, Changsong

    2016-01-01

    Synapses may undergo variable changes during plasticity because of the variability of spike patterns such as temporal stochasticity and spatial randomness. Here, we call the variability of synaptic weight changes during plasticity to be efficacy variability. In this paper, we investigate how four aspects of spike pattern statistics (i.e., synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations) influence the efficacy variability under pair-wise additive spike-timing dependent plasticity (STDP) and synaptic homeostasis (the mean strength of plastic synapses into a neuron is bounded), by implementing spike shuffling methods onto spike patterns self-organized by a network of excitatory and inhibitory leaky integrate-and-fire (LIF) neurons. With the increase of the decay time scale of the inhibitory synaptic currents, the LIF network undergoes a transition from asynchronous state to weak synchronous state and then to synchronous bursting state. We first shuffle these spike patterns using a variety of methods, each designed to evidently change a specific pattern statistics; and then investigate the change of efficacy variability of the synapses under STDP and synaptic homeostasis, when the neurons in the network fire according to the spike patterns before and after being treated by a shuffling method. In this way, we can understand how the change of pattern statistics may cause the change of efficacy variability. Our results are consistent with those of our previous study which implements spike-generating models on converging motifs. We also find that burstiness/regularity is important to determine the efficacy variability under asynchronous states, while heterogeneity of cross-correlations is the main factor to cause efficacy variability when the network moves into synchronous bursting states (the states observed in epilepsy). PMID:27555816

  17. Spike Pattern Structure Influences Synaptic Efficacy Variability under STDP and Synaptic Homeostasis. II: Spike Shuffling Methods on LIF Networks

    PubMed Central

    Bi, Zedong; Zhou, Changsong

    2016-01-01

    Synapses may undergo variable changes during plasticity because of the variability of spike patterns such as temporal stochasticity and spatial randomness. Here, we call the variability of synaptic weight changes during plasticity to be efficacy variability. In this paper, we investigate how four aspects of spike pattern statistics (i.e., synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations) influence the efficacy variability under pair-wise additive spike-timing dependent plasticity (STDP) and synaptic homeostasis (the mean strength of plastic synapses into a neuron is bounded), by implementing spike shuffling methods onto spike patterns self-organized by a network of excitatory and inhibitory leaky integrate-and-fire (LIF) neurons. With the increase of the decay time scale of the inhibitory synaptic currents, the LIF network undergoes a transition from asynchronous state to weak synchronous state and then to synchronous bursting state. We first shuffle these spike patterns using a variety of methods, each designed to evidently change a specific pattern statistics; and then investigate the change of efficacy variability of the synapses under STDP and synaptic homeostasis, when the neurons in the network fire according to the spike patterns before and after being treated by a shuffling method. In this way, we can understand how the change of pattern statistics may cause the change of efficacy variability. Our results are consistent with those of our previous study which implements spike-generating models on converging motifs. We also find that burstiness/regularity is important to determine the efficacy variability under asynchronous states, while heterogeneity of cross-correlations is the main factor to cause efficacy variability when the network moves into synchronous bursting states (the states observed in epilepsy). PMID:27555816

  18. Quasi-real time estimation of intense rainfall rates from weather radar

    NASA Astrophysics Data System (ADS)

    Libertino, Andrea; Allamano, Paola; Claps, Pierluigi; Cremonini, Roberto; Laio, Francesco

    2015-04-01

    Rainfall intensity estimation from radar is known to be prone to different sources of uncertainty, both in the detection and in the processing phase. These sources of uncertainty are especially relevant when severe rainfall rates are considered, thus calling for the adoption of advanced methods for the estimation of the rainfall rate from radar observations. We introduce a quasi-real time procedure for the adaptive estimation of the coefficients of the Z-R relation that links radar reflectivity to rainfall rate. The proposed quasi-real time calibration can grant Z-R relationships consistent with the evolution of the event while the use of a spatially adaptive approach makes the technique amenable to be applied in large areas with complex orography. The aim is to define a simple and operative methodology suitable for a systematic and possibly unsupervised application, capable to reconstruct the whole spectrum of intensities occurred during an intense rainfall event. We propose to readjust the power-law equation commonly used to transform reflectivity to rainfall intensity at each time step, calibrating its parameters by means of Z-R pairs collected in the time proximity of the considered instant. Z-R data are filtered with a reflectivity threshold, which varies in time, in order to discriminate between the presence and absence of rainfall. For every location, the spatial calibration domain is limited to the rain gauges belonging to a neighbourhood. Z-R coefficients are estimated for each location and each time step by minimizing the standard deviation between observed and estimated rainfall, through a non-linear procedure. The case study includes a set of 16 severe rainfall events occurred in the north-west of Italy. The technique outperforms the classical estimation methods for most of the analysed events and shows significant potential for operational uses. The determination coefficient undergoes up to 30% improvements and the BIAS values are reduced, for

  19. Estimation of snag carbon transfer rates by ecozone and lead species for forests in Canada.

    PubMed

    Hilger, A B; Shaw, C H; Metsaranta, J M; Kurz, W A

    2012-12-01

    Standing dead trees (snags) and downed woody debris contribute substantially to the carbon (C) budget of Canada's forest. Accurate parameterization of the C transfer rates (CTRs) from snags to downed woody debris is important for forest C dynamics models such as the Carbon Budget Model of the Canadian Forest Sector (CBM-CFS3), but CTRs are rarely measured or reported in the literature. Therefore, forest C models generally use snag fall rates (FRs) available in the literature, as a proxy for CTRs. However, FRs are based on stem counts while CTRs refer to mass transfers. Stem mass and stem number are not linearly related, with small diameter trees representing disproportionately lower C mass transfers. Therefore this proxy, while convenient, may bias C transfer from standing dead to downed woody material. Here, we combined tree data from 10802 sample plots and previously published species-specific individual-tree relationships between tree diameter (diameter at breast height, dbh) and fall rate to derive stand-level estimates of CTRs for the CBM-CFS3. We estimated CTRs and FRs and used the FR values to validate this approach by comparing them with standardized FR values compiled from the literature. FRs generally differed from CTRs. The overall CTR (4.78% +/- 0.02% per year, mean +/- SE) was significantly smaller than the overall FR (5.40% +/- 0.02% per year; mean +/- SE). Both the difference between FR and CTR (FR - CTR) and the CTR itself varied by ecozone, with ecozone means for CTR ranging from 3.94% per year to 10.02% per year. This variation was explained, in part, by heterogeneity in species composition, size (dbh distribution), structure, and age of the stands. The overall mean CTR estimated for the Snag_Stemwood (4.78% per year) and the Snag_Branches (11.95% per year) pools of the CBM-CFS3 were approximately 50% and 20% higher than the current default rates used in the CBM-CFS3 of 3.2% and 10.0%, respectively. Our results demonstrate that using CTRs to

  20. State-Dependent Pseudo-Linear Filter for Spacecraft Attitude and Rate Estimation

    NASA Technical Reports Server (NTRS)

    Bar-Itzhack, Itzhack Y.; Harman, Richard R.

    2001-01-01

    This paper presents the development and performance of a special algorithm for estimating the attitude and angular rate of a spacecraft. The algorithm is a pseudo-linear Kalman filter, which is an ordinary linear Kalman filter that operates on a linear model whose matrices are current state estimate dependent. The nonlinear rotational dynamics equation of the spacecraft is presented in the state space as a state-dependent linear system. Two types of measurements are considered. One type is a measurement of the quaternion of rotation, which is obtained from a newly introduced star tracker based apparatus. The other type of measurement is that of vectors, which permits the use of a variety of vector measuring sensors like sun sensors and magnetometers. While quaternion measurements are related linearly to the state vector, vector measurements constitute a nonlinear function of the state vector. Therefore, in this paper, a state-dependent linear measurement equation is developed for the vector measurement case. The state-dependent pseudo linear filter is applied to simulated spacecraft rotations and adequate estimates of the spacecraft attitude and rate are obtained for the case of quaternion measurements as well as of vector measurements.

  1. An alternative approach to estimating rainfall rate by radar using propagation differential phase shift

    NASA Technical Reports Server (NTRS)

    Jameson, A. R.

    1994-01-01

    In this work it is shown that for frequencies from 3 to 13 GHz, the ratio of the specific propagation differential phase shift phi(sub DP) to the rainfall rate can be specified essentially independently of the form of the drop size distribution by a function only of the mass-weighted mean drop size D(sub m). This significantly reduces one source of substantial bias errors common to most other techniques for measuring rain by radar. For frequencies 9 GHz and greater, the coefficient can be well estimated from the ratio of the specific differential attenuation to phi(sub DP), while at nonattenuating frequencies such as 3 GHz, the coefficient can be well estimated using the differential reflectivity. In practice it appears that this approach yields better estimates of the rainfall rate than any other current technique. The best results are most likely at 13.80 GHz, followed by those at 2.80 GHz. An optimum radar system for measuring rain should probably include components at a both frequencies so that when signals at 13.8 GHz are lost because of attenuation, good measurements are still possible at the lower frequency.

  2. Estimating oxygen consumption from heart rate using adaptive neuro-fuzzy inference system and analytical approaches.

    PubMed

    Kolus, Ahmet; Dubé, Philippe-Antoine; Imbeau, Daniel; Labib, Richard; Dubeau, Denise

    2014-11-01

    In new approaches based on adaptive neuro-fuzzy systems (ANFIS) and analytical method, heart rate (HR) measurements were used to estimate oxygen consumption (VO2). Thirty-five participants performed Meyer and Flenghi's step-test (eight of which performed regeneration release work), during which heart rate and oxygen consumption were measured. Two individualized models and a General ANFIS model that does not require individual calibration were developed. Results indicated the superior precision achieved with individualized ANFIS modelling (RMSE = 1.0 and 2.8 ml/kg min in laboratory and field, respectively). The analytical model outperformed the traditional linear calibration and Flex-HR methods with field data. The General ANFIS model's estimates of VO2 were not significantly different from actual field VO2 measurements (RMSE = 3.5 ml/kg min). With its ease of use and low implementation cost, the General ANFIS model shows potential to replace any of the traditional individualized methods for VO2 estimation from HR data collected in the field. PMID:24793823

  3. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    PubMed

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-01

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort. PMID:27609008

  4. Comparisons of Instantaneous TRMM Ground Validation and Satellite Rain Rate Estimates at Different Spatial Scales

    NASA Technical Reports Server (NTRS)

    Wolff, David B.; Fisher, Brad L.

    2007-01-01

    This study provides a comprehensive inter-comparison of instantaneous rain estimates from the two rain sensors aboard the TRMM satellite with ground data from thee designated Ground Validation Sites: Kwajalein Atoll, Melbourne, Florida and Houston, Texas. The satellite rain retrievals utilize rain observations collected by the TRMM microwave imager (TMI) and the Precipitation Radar (PR) aboard the TRMM satellite. Three standard instantaneous rain products are the generated from the rain information retrieved from the satellite using the TMI, PR and Combined (COM) rain algorithms. The validation data set used in this study was obtained from instantaneous rain rates inferred from ground radars at each GV site. The first comparison used 0.5(sup 0) x 0.5(sup 0) gridded data obtained from the TRMM 3668 product, and similarly gridded GV data obtained from ground-based radars. The comparisons were made at the same spatial and temporal scales in order to eliminate sampling biases in our comparisons. An additional comparison was made by averaging rain rates for the PR, COM and GV estimates within each TMI footprint (approx. 150 square kilometers). For this analysis, unconditional mean rain rates from PR, COM and GV estimates were calculated within each TMI footprint that was observed within 100 km from the respective GV site (and also observed by the PR). This analysis used all the available matching data from the period 1999-2004, representing a sample size of over 50,000 footprints for each site. In the first analysis our results showed that all of the respective rain rate estimates agree well, with some exceptions. The more salient differences were associated with heavy rain events in which one or more of the algorithms failed to properly retrieve these extreme events. Also, it appears that there is a preferred mode of precipitation for TMI rain rates at or near 2 mm per hour over the ocean. This mode was noted over ocean areas of Melbourne, Florida and Kwajalein

  5. Modeling data from double-tagging experiments to estimate heterogeneous rates of tag shedding in lake trout (Salvelinus namaycush)

    USGS Publications Warehouse

    Fabrizio, Mary C.; Nichols, James D.; Hines, James E.; Swanson, Bruce L.; Schram, Stephen T.

    1999-01-01

    Data from mark-recapture studies are used to estimate population rates such as exploitation, survival, and growth. Many of these applications assume negligible tag loss, so tag shedding can be a significant problem. Various tag shedding models have been developed for use with data from double-tagging experiments, including models to estimate constant instantaneous rates, time-dependent rates, and type I and II shedding rates. In this study, we used conditional (on recaptures) multinomial models implemented using the program SURVIV (G.C. White. 1983. J. Wildl. Manage. 47: 716-728) to estimate tag shedding rates of lake trout (Salvelinus namaycush) and explore various potential sources of variation in these rates. We applied the models to data from several long-term double-tagging experiments with Lake Superior lake trout and estimated shedding rates for anchor tags in hatchery-reared and wild fish and for various tag types applied in these experiments. Estimates of annual tag retention rates for lake trout were fairly high (80-90%), but we found evidence (among wild fish only) that retention rates may be significantly lower in the first year due to type I losses. Annual retention rates for some tag types varied between male and female fish, but there was no consistent pattern across years. Our estimates of annual tag retention rates will be used in future studies of survival rates for these fish.

  6. Estimating Energy Expenditure from Heart Rate in Older Adults: A Case for Calibration

    PubMed Central

    Schrack, Jennifer A.; Zipunnikov, Vadim; Goldsmith, Jeff; Bandeen-Roche, Karen; Crainiceanu, Ciprian M.; Ferrucci, Luigi

    2014-01-01

    Background Accurate measurement of free-living energy expenditure is vital to understanding changes in energy metabolism with aging. The efficacy of heart rate as a surrogate for energy expenditure is rooted in the assumption of a linear function between heart rate and energy expenditure, but its validity and reliability in older adults remains unclear. Objective To assess the validity and reliability of the linear function between heart rate and energy expenditure in older adults using different levels of calibration. Design Heart rate and energy expenditure were assessed across five levels of exertion in 290 adults participating in the Baltimore Longitudinal Study of Aging. Correlation and random effects regression analyses assessed the linearity of the relationship between heart rate and energy expenditure and cross-validation models assessed predictive performance. Results Heart rate and energy expenditure were highly correlated (r = 0.98) and linear regardless of age or sex. Intra-person variability was low but inter-person variability was high, with substantial heterogeneity of the random intercept (s.d. = 0.372) despite similar slopes. Cross-validation models indicated individual calibration data substantially improves accuracy predictions of energy expenditure from heart rate, reducing the potential for considerable measurement bias. Although using five calibration measures provided the greatest reduction in the standard deviation of prediction errors (1.08 kcals/min), substantial improvement was also noted with two (0.75 kcals/min). Conclusion These findings indicate standard regression equations may be used to make population-level inferences when estimating energy expenditure from heart rate in older adults but caution should be exercised when making inferences at the individual level without proper calibration. PMID:24787146

  7. Methodology for estimating radiation dose rates to freshwater biota exposed to radionuclides in the environment

    SciTech Connect

    Blaylock, B.G.; Frank, M.L.; O`Neal, B.R.

    1993-08-01

    The purpose of this report is to present a methodology for evaluating the potential for aquatic biota to incur effects from exposure to chronic low-level radiation in the environment. Aquatic organisms inhabiting an environment contaminated with radioactivity receive external radiation from radionuclides in water, sediment, and from other biota such as vegetation. Aquatic organisms receive internal radiation from radionuclides ingested via food and water and, in some cases, from radionuclides absorbed through the skin and respiratory organs. Dose rate equations, which have been developed previously, are presented for estimating the radiation dose rate to representative aquatic organisms from alpha, beta, and gamma irradiation from external and internal sources. Tables containing parameter values for calculating radiation doses from selected alpha, beta, and gamma emitters are presented in the appendix to facilitate dose rate calculations. The risk of detrimental effects to aquatic biota from radiation exposure is evaluated by comparing the calculated radiation dose rate to biota to the U.S. Department of Energy`s (DOE`s) recommended dose rate limit of 0.4 mGy h{sup {minus}1} (1 rad d{sup {minus}1}). A dose rate no greater than 0.4 mGy h{sup {minus}1} to the most sensitive organisms should ensure the protection of populations of aquatic organisms. DOE`s recommended dose rate is based on a number of published reviews on the effects of radiation on aquatic organisms that are summarized in the National Council on Radiation Protection and Measurements Report No. 109 (NCRP 1991). DOE recommends that if the results of radiological models or dosimetric measurements indicate that a radiation dose rate of 0. 1 mGy h{sup {minus}1} will be exceeded, then a more detailed evaluation of the potential ecological consequences of radiation exposure to endemic populations should be conducted.

  8. Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications

    SciTech Connect

    Du, Xiuxia; Yang, Feng; Manes, Nathan P.; Stenoien, David L.; Monroe, Matthew E.; Adkins, Joshua N.; States, David J.; Purvine, Samuel O.; Camp, David G.; Smith, Richard D.

    2008-07-03

    This paper describes a method to estimate the False Discovery Rate (FDR) of phosphopeptide identifications. The method starts with a re-assignment of the phosphorylation site/sites to those phosphopeptides for which there exists an ambiguity in the original assignment of the phosphorylation site/sites. It then performs an online data training using Expectation Maximization to estimate the joint distribution underlying the observed search results of multiple parameters from search engines. A Linear Discriminant Analysis (LDA) is subsequently carried out to optimally combine the search results into a discriminant score that possesses the most discriminating power. Based on the discriminant score, the p-value and q-value (explain a little bit more) for each identified phosphopeptide are calculated and the FDR for the set of phosphopeptides which are claimed correct identifications can then be rigorously estimated based on its definition. The approach can be easily extended to estimate the FDR of unmodified peptides. The proposed approach has been applied to datasets from a study of the effect of high-dose radiation on human skin fibroblast cells. The data analysis procedure has been coded into a software package which is freely available.

  9. Removing the thermal component from heart rate provides an accurate VO2 estimation in forest work.

    PubMed

    Dubé, Philippe-Antoine; Imbeau, Daniel; Dubeau, Denise; Lebel, Luc; Kolus, Ahmet

    2016-05-01

    Heart rate (HR) was monitored continuously in 41 forest workers performing brushcutting or tree planting work. 10-min seated rest periods were imposed during the workday to estimate the HR thermal component (ΔHRT) per Vogt et al. (1970, 1973). VO2 was measured using a portable gas analyzer during a morning submaximal step-test conducted at th