Ensemble Average Method Research Articles

Assessment of CMIP5 climate models and projected temperature changes over Northern Eurasia

Assessing the performance of climate models in surface air temperature (SAT) simulation and projection have received increasing attention during the recent decades. This paper assesses the performance of the Coupled Model Intercomparison Project phase 5 (CMIP5) in simulating intra-annual, annual and decadal temperature over Northern Eurasia from 1901 to 2005. We evaluate the skill of different multi-model ensemble techniques and use the best technique to project the future SAT changes under different emission scenarios. The results show that most of the general circulation models (GCMs) overestimate the annual mean SAT in Northern Eurasia and the difference between the observation and the simulations primarily comes from the winter season. Most of the GCMs can approximately capture the decadal SAT trend; however, the accuracy of annual SAT simulation is relatively low. The correlation coefficient R between each GCM simulation and the annual observation is in the range of 0.20 to 0.56. The Taylor diagram shows that the ensemble results generated by the simple model averaging (SMA), reliability ensemble averaging (REA) and Bayesian model averaging (BMA) methods are superior to any single GCM output; and the decadal SAT change generated by SMA, REA and BMA are almost identical during 1901–2005. Heuristically, the uncertainty of BMA simulation is the smallest among the three multi-model ensemble simulations. The future SAT projection generated by the BMA shows that the SAT in Northern Eurasia will increase in the 21st century by around 1.03 °C/100 yr, 3.11 °C/100 yr and 7.14 °C/100 yr under the RCP 2.6, RCP 4.5 and RCP 8.5 scenarios, respectively; and the warming accelerates with the increasing latitude. In addition, the spring season contributes most to the decadal warming occurring under the RCP 2.6 and RCP 4.5 scenarios, while the winter season contributes most to the decadal warming occurring under the RCP 8.5 scenario. Generally, the uncertainty of the SAT projections increases with time in the 21st century.

TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers.

BackgroundSingle molecule tracking (SMT) analysis of fluorescently tagged lipid and protein probes is an attractive alternative to ensemble averaged methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) for measuring diffusion in artificial and plasma membranes. The meaningful estimation of diffusion coefficients and their errors is however not straightforward, and is heavily dependent on sample type, acquisition method, and equipment used. Many approaches require advanced computing and programming skills for their implementation.FindingsHere we present TrackArt software, an accessible graphic interface for simulation and complex analysis of multiple particle paths. Imported trajectories can be filtered to eliminate spurious or corrupted tracks, and are then analyzed using several previously described methodologies, to yield single or multiple diffusion coefficients, their population fractions, and estimated errors. We use TrackArt to analyze the single-molecule diffusion behavior of a sphingolipid analog SM-Atto647N, in mica supported DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayers. Fitting with a two-component diffusion model confirms the existence of two separate populations of diffusing particles in these bilayers on mica. As a demonstration of the TrackArt workflow, we characterize and discuss the effective activation energies required to increase the diffusion rates of these populations, obtained from Arrhenius plots of temperature-dependent diffusion. Finally, TrackArt provides a simulation module, allowing the user to generate models with multiple particle trajectories, diffusing with different characteristics. Maps of domains, acting as impermeable or permeable obstacles for particles diffusing with given rate constants and diffusion coefficients, can be simulated or imported from an image. Importantly, this allows one to use simulated data with a known diffusion behavior as a comparison for results acquired using particular algorithms on actual, “natural” samples whose diffusion behavior is to be extracted. It can also serve as a tool for demonstrating diffusion principles.ConclusionsTrackArt is an open source, platform-independent, Matlab-based graphical user interface, and is easy to use even for those unfamiliar with the Matlab programming environment. TrackArt can be used for accurate simulation and analysis of complex diffusion data, such as diffusion in lipid bilayers, providing publication-quality formatted results.

Statistical characterisation of single‐stranded DNA motion near glass surface beyond diffusion coefficient

The diffusion of single-stranded DNA (ssDNA) molecules near a glass surface by total internal reflection fluorescence microscopy has been observed. Substantially smaller diffusion coefficients compared to the bulk are caused by phenomenologically different types of surface effect that is not necessarily adsorptive. In particular, preliminary treatments of the glass substrate by low and high concentrations of KOH lead to highly and much less adsorptive effects on the ssDNA molecules, respectively. These characteristics beyond diffusion coefficients are elucidated by the difference of two ensemble-averaging methods of mean square displacement for diffusion coefficients due to the non-uniformity of the molecular motion, which is further confirmed by the distribution of displacements and tracked duration.

Experimental evidence for non-linear growth in compressible mixing layer

An experimental study of compressible mixing layers (CMLs) was conducted using planar laser Mie scattering (PLMS) visualizations from condensed ethanol droplets in the flow. Large ense mbles of digital images were collected for two flow condition s at convective Mach numbers Mc = 0.11 and 0.47. The coherent vortices, braids and eruptions in the mixing zone were observed, interpreted as evidence of multi-scale, three-dimensiona l structures at a high Reynolds number. The mixing layers with a large visualized range present two stages along the streamwise direction, corresponding to the initial mixing and the well-d eveloped stage. A new method, the gray level ensemble average method (GLEAM), by virtue of the similarity of the mixing layer, was applied to measure the growth rate of the CML thickness. New evidence for a nonlinear growth of CML is reported, providing an interpretation of previous observations of the scattering of the growth rate. compressible mixing layer, growth rate, coherent structures, flow visualization

Testing the validity of ensemble descriptions of intrinsically disordered proteins

Understanding biological function in the profusion of proteins containing significant levels of intrinsic disorder depends on how accurately we can describe their conformational behavior (1). Recently, Wang et al. used molecular dynamics (MD) techniques to study the molecular recognition element of the C-terminal domain of the measles virus nucleoprotein (MeV-NTAIL), an example of this enigmatic family of intrinsically disordered proteins (IDPs) (2). In justifying their approach, the authors state that “in general, it is not feasible to characterize IDPs by an ensemble averaged method due to the underlying structural heterogeneity.” Although the potential advantages of restraint-free MD in terms of dynamic time scales are evident, numerous developments in the field also exploit ensemble-averaged NMR data to derive molecular descriptions of IDPs.

Assessment of Surface Runoff Vulnerability to Climate Change in the Lerma-Chapala Basin, Mexico

AbstractThe Intergovernmental Panel on Climate Change (IPCC) suggests that vulnerability to climate change depends on three main factors: exposure, sensitivity, and adaptive capacity. Each factor was evaluated in a hydrologic context; for instance, exposure was interpreted as a change in surface runoff. Factors were combined using a geographic information system (GIS), and an overall methodology was proposed to map hydrologic vulnerability. The Lerma-Chapala basin was selected as a case study since the largest water body in Mexico is located at its outlet. The long-term rate of change in surface runoff was estimated considering the variation in future precipitation from 23 atmosphere–ocean general circulation models (AOGCMs) and by using the reliability ensemble averaging (REA) method. Two climate change scenarios from an IPCC special report on emissions scenarios and three time horizons (2030, 2050, and 2100) were chosen. Results showed a decrease in surface runoff of up to 29% (A1B-2100) in the northern...

Modulation of EGFR Dimer Stability by Manipulation of Phosphorilation in Situ

Deregulation of the epidermal growth factor receptor (EGFR) signalling has been correlated with the development of a variety of human carcinomas. Receptor dimerization and phosphorylation are amongst the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change which unfolds an ectodomain loop required for dimerization. It may also induce important allosteric changes in the cytoplasmic domain. Despite these findings, ensemble-averaging methods could not resolve the details of receptor activation in situ. Here, we used two-color single-molecule imaging to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKI) and phosphatase-based manipulation of EGFR phosphorylation on live cells. Ligand bound receptors were tracked on the plasma membrane with a sophisticated Bayesian segmentation tracking algorithm and the distribution of dimer lifetimes was fitted to a single-exponential to extract dimer off-rates (koff). Our data show that, pre-treatment with type I TKI, gefitinib (active conformation binder) stabilizes the EGFR homodimer. Over-expression of EGFR specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. When a nonactivating anti-EGFR antibody, Snap-425 single-chain variable fragment that competes for EGF binding was used as a ligand, no significant difference in the koff of the dimer could be detected. Conformational changes of the cytoplasmic part of the receptor upon gefitinib pre-treatment were also confirmed by changes in Fluorescence Resonance Energy Transfer (FRET) efficiency detected by ensemble FRET/FLIM (Fluorescence Lifetime Intensity Microscopy). These results provide direct evidence that receptor phosphorylation is linked to dimer stability. The phosphorylated and non-phosphorylated receptors exhibit different kinetics and cytoplasmic conformations which may account for the heterogeneity in ligand-binding affinity observed through a concave-up Scatchard plot.

Rotating angled plate diffusing wave spectroscopy

Solid-like non-ergodic samples can be difficult to study using standard single speckle diffusing wave spectroscopy as the measurement may lack requisite ensemble averaging. We demonstrate here that this required ensemble averaging can be induced by translating the speckle over the collection optics so that multiple speckles are observed over the duration of the experiment. Translation is achieved by refraction through a transparent rotating plate with a surface normal angled slightly with respect to the axis of rotation. As with other ensemble averaging methods based on rotation, the measured time averaged correlation is that of the ensemble average correlation modulated by a periodic Gaussian-like function. By rotating the plate slowly, the short time behaviour of the ensemble averaged intensity correlation can be measured with good fidelity using a standard multi-tau correlator. Because the method combines easily with camera-based multispeckle approaches, the long-time behaviour can be recovered using concurrent multispeckle measurements if necessary. No additional scattering is required beyond that produced by the sample and the technique also works in the single scattering regime which is not possible with the other commonly used alternatives for ensemble averaging: two cell or rotating diffusor approaches.

A globally Eulerian locally Lagrangian particle concentration scheme

For gas flows, a Lagrangian Concentration Differential Equation (LCDE) was solved along a particle path using Eulerian derivatives for the particle velocity divergence field. This equation is solved by a Globally Eulerian Locally Lagrangian (GELL) discretization technique which avoids the computationally intensive Jacobian calculations of the Full Lagrangian method, the steady-state assumption of the area method, and the computational inefficiency of the box-counting methods. The LCDE–GELL method was compared to such methods using a high-order temporal integration technique and evaluated for two fundamental flowfields: flow past a corner and past a cylinder. In the dilute limit, the particle concentration fields were predicted for various particle inertias (characterized by a range of Stokes numbers) including the zero-mass (tracer) limit for which an exact particle concentration solution exists. Both the weighted-average and ensemble-average methods required far more parcels to achieve the same accuracy demonstrated by the LCDE–GELL method. It is recommended that future work investigates the LCDE approach for three-dimensional, complex flows with particle–particle interaction to investigate its robustness.

Efficient Dithering Technique With Periodic Waveforms for RF Test and Characterization

A dithering technique based on ensemble averaging of waveforms is proposed. In the proposed method, we perform a single measurement of multiple periods of a sine-dithered periodic waveform, whereas in the existing ensemble averaging methods several different measurements with dithering additive noise are performed. The measured waveform is then segmented and the segments are averaged to obtain a noise-reduced post-processed waveform. This technique provides improved efficiency in test and characterization applications where accuracy higher than that of the built-in data converters of the measurement equipment is required. Moreover, we show that by using large dithering signals in the proposed technique, we can reduce the nonideal effects found in real applications. As an example, we show in a simulated example that by using the approach with an ensemble size of five in an ideal quantizer, we are able to reduce the mean-square error and adjacent channel distortion by 11 dB. A reduction of 6 dB is achieved when we use the same ensemble size in a nonideal quantizer. An experiment is then conducted to evaluate the reduction in the adjacent channel power of a modulated signal emanating from an arbitrary waveform, by using the proposed technique. The experimental results show that even for a modulated signal with 160-MHz bandwidth at 4.5 GHz, by using an ensemble size of four, we are able to reduce the adjacent channel distortion by 5 dB.

Single Lipid Vesicle Assay for Characterizing Single-Enzyme Kinetics of Phospholipid Hydrolysis in a Complex Biological Fluid

Imaging of individual lipid vesicles is used to track single-enzyme kinetics of phospholipid hydrolysis. The method is employed to quantify the catalytic activity of phospholipase A2 (PLA2) in both pure and complex biological fluids. The measurements are demonstrated to offer a subpicomolar limit of detection (LOD) of human secretory PLA2 (sPLA2) in up to 1000-fold-diluted cerebrospinal fluid (CSF). An additional new feature provided by the single-enzyme sensitivity is that information about both relative concentration variations of active sPLA2 in CSF and the specific enzymatic activity can be simultaneously obtained. When CSF samples from healthy controls and individuals diagnosed with Alzheimer's disease (AD) are analyzed, the specific enzymatic activity is found to be preserved within 7% in the different CSF samples whereas the enzyme concentration differs by up to 56%. This suggests that the previously reported difference in PLA2 activity in CSF samples from healthy and AD individuals originates from differences in the PLA2 expression level rather than from the enzyme activity. Conventional ensemble averaging methods used to probe sPLA2 activity do not allow one to obtain such information. Together with an improvement in the LOD of at least 1 order of magnitude compared to that of conventional assays, this suggests that the method will become useful in furthering our understanding of the role of PLA2 in health and disease and in detecting the pharmacodynamic effects of PLA2-targeting drug candidates.

Downscaling technique to estimate hydrologic vulnerability to climate change: an application to the Conchos River Basin, Mexico

The Intergovernmental Panel on Climate Change (IPCC) suggests that vulnerability to climate change depends on three main factors: exposure, sensitivity and adaptive capacity. Each factor was evaluated in a hydrologic context, for instance exposure was interpreted as a change in surface runoff. Factors were combined using a Geographic Information System (GIS) and an overall methodology to map hydrologic vulnerability was proposed. The Conchos River Basin, which is the main tributary of the Rio Grande, was used as a case study. The long-term rate of change in surface runoff was estimated considering the variation in future precipitation from 23 Atmosphere-Ocean General Circulation Models (AOGCM) by using the Reliability Ensemble Averaging (REA) method. Two climate change scenarios (A1B and A2) and three time horizons (2030, 2050 and 2100) were chosen. Results showed a decrease in surface runoff up to 28% (A1B-2100) north of the Basin. Hence, it is likely to have more frequent droughts. However, it would be challenging to compensate the lack of surface runoff since groundwater resources are already depleted. Finally, overall hydrologic vulnerability maps were obtained to locate the most vulnerable regions, where precisely adaption efforts would be more necessary to sustain environmental conditions.

English

This paper presents the application of an in situ measurement technique of sound absorption characteristics, namely the “Ensemble Averaged Method”. Previously, a measurement technique of material surface normal impedance by using a twomicrophone (p-p) technique and ambient noise was proposed by some of the authors. This includes the concept of “ensemble averaged” surface normal impedance to extend the usage of the obtained values to various applications, such as architectural acoustics and computational simulations. With the development of a particle velocity (p-u) sensor, the practicality of techniques for the direct measurement of impedance becomes feasible. A concept of the ensemble averaged surface normal impedance is addressed, including a basic technique to measure it by using p-p and p-u sensors. Then, the agreements between p-p and p-u sensors are discussed and the discrepancies of absorption coefficients are shown to be small. The paper reveals the reliability, applicability and feasibility of the method throughout the investigation as an in situ measurement technique.

Numerical Simulations for Hydrodynamics of Air-Water External Loop Airlift Reactor Flows With Bubble Break-Up and Coalescence Effects

The external loop airlift reactor (ELALR) is a modified bubble column reactor that is composed of two vertical columns interconnected with two horizontal tubes and is often preferred over traditional bubble column reactors because it can operate over a wider range of conditions. In the present work, the gas-liquid flow dynamics in an ELALR were simulated using an Eulerian–Eulerian ensemble-averaging method with bubble breakup and coalescence effects in a three-dimensional system. The population balance models (PBM) of Luo and Svendsen (1996, “Theoretical Model for Drop and Bubble Breakup in Turbulent Dispersions,” AIChE J., 42, pp. 1225–1233) and Prince and Blanch (1990, “Bubble Coalescence and Breakup in Air-Sparged Bubble Columns,” AIChE J., 36, pp. 1485–1499) were used to simulate the bubble breakup and coalescence effects, respectively. The bubble breakup and coalescence closure models were implemented into CFDLib, a multiphase flow source code developed by Los Alamos National Laboratory, and validated with experiments. The computational fluid dynamics (CFD) simulations were then compared to experimental measurements from a 10.2 cm diameter ELALR for superficial gas velocities ranging from 1 to 20 cm/s. From this work, the 3D PBM simulations of an external loop airlift reactor were generally comparable with the 3D single bubble size simulations. However, the 3D PBM simulations have closer agreement with experimental findings than the single bubble size simulations especially regarding the length of gas bubbles in the downcomer.

A New Assay for Ion Channel Function using Stopped Flow Spectrofluorometry

Functional studies of purified ion channels reconstituted in a defined membrane environment usually are conducted using single-channel electrophysiology. Ensemble-averaged methods are used infrequently, compared to single-channel electrophysiology because of the technical challenges involved in giant unilamellar liposome preparation and patching−though these methods yield important information that may be difficult to obtain from single-channel studies, e.g. (Chakrapani et al., 2007). To overcome some of the limitations encountered, we developed a sequential-push fluorescence-based stopped-flow assay to characterize channel function, using KcsA as the prototype. The method is based on earlier studies (Moore and Raftery 1980; Wu et al., 1981; Ingólfsson and Andersen), where channel activity was determined using the KcsA-permeable ANTS quencher, thallium (Tl+). We evaluate KcsA function from the rate of ANTS quenching in sequential-push stopped-flow measurements on the millisecond timescale. Detergent was removed using BioBeads, which minimizes ANTS consumption. To illustrate the method, we determined the KcsA activation by extravesicular H+ for WT KcsA and the non-inactivating E71A mutant channels. Our results demonstrate efficient and reproducible reconstitution. Fitting the activation curve using the Hill equation yields a pH for half-activation (pH0.5) similar to that obtained from single-channel electrophysiology for the E71A mutant (Thompson et al., 2008) and higher than that reported for WT KcsA (Chakrapani et al.). The Hill coefficients, n, were lower than those obtained with single-channel recording for E71A mutant but higher for WT KcsA. Our results suggest that both pH0.5 and n vary with changes in lipid bilayer thickness and bulk properties such as elasticity. The ease of vesicle preparation, cost effectiveness, reproducibility and time resolution makes this a powerful assay to explore KcsA activation and inactivation, and how they vary with changes in the channels' lipid bilayer environment.

音圧−粒子速度センサの安定性への湿度の影響

To examine humidity influence on stability of pu-sensors, we applied calibration and the ensemble averaged surface normal impedance method (EA-Method) under controlled relative humidity (φ =35-60%) in a reverberation room. Experiments revealed that calibration results (i.e. correction values) changed as humidity levels varied. A comparison of standard deviations on absorption coefficients generated increasing value as the humidity difference between calibration and measurement increased (Δφ =0-25%). Repeatability was demonstrated by using two identical pu-sensors in four set measurements. Furthermore, a partial correlation test demonstrated the dominance of humidity over other environmental factors influencing sensor sensitivity.

Nanoscale Inhomogeneities in Thermoresponsive Polymers

This article highlights the occurrence and nature of nanoscale inhomogeneities in thermoresponsive polymers and focuses on different experimental techniques for their observation and characterization. Such inhomogeneities can be regarded as nanoscopic domains of collapsed polymer segments (or of a small number of unimers), which provide a nonpolar, hydrophobic interior. Continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy on amphiphilic reporter molecules (spin probes) as an intrinsically local technique is particularly emphasized. In combination with different ensemble-averaging methods, it provides a holistic understanding of the often inhomogeneous nanoscale processes during the temperature-induced collapse of a thermoresponsive polymer.

Ensemble and single particle fluorimetric techniques in concerted action to study the diffusion and aggregation of the glycine receptor α3 isoforms in the cell plasma membrane

The spatio-temporal membrane behavior of glycine receptors (GlyRs) is known to be of influence on receptor homeostasis and functionality. In this work, an elaborate fluorimetric strategy was applied to study the GlyR α3K and L isoforms. Previously established differential clustering, desensitization and synaptic localization of these isoforms imply that membrane behavior is crucial in determining GlyR α3 physiology. Therefore diffusion and aggregation of homomeric α3 isoform-containing GlyRs were studied in HEK 293 cells. A unique combination of multiple diffraction-limited ensemble average methods and subdiffraction single particle techniques was used in order to achieve an integrated view of receptor properties. Static measurements of aggregation were performed with image correlation spectroscopy (ICS) and, single particle based, direct stochastic optical reconstruction microscopy (dSTORM). Receptor diffusion was measured by means of raster image correlation spectroscopy (RICS), temporal image correlation spectroscopy (TICS), fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT). The results show a significant difference in diffusion coefficient and cluster size between the isoforms. This reveals a positive correlation between desensitization and diffusion and disproves the notion that receptor aggregation is a universal mechanism for accelerated desensitization. The difference in diffusion coefficient between the clustering GlyR α3L and the non-clustering GlyR α3K cannot be explained by normal diffusion. SPT measurements indicate that the α3L receptors undergo transient trapping and directed motion, while the GlyR α3K displays mild hindered diffusion. These findings are suggestive of differential molecular interaction of the isoforms after incorporation in the membrane.

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

The "soft" (i.e., noncovalent) interactions between molecules and surfaces are complex and highly varied (e.g., hydrophobic, hydrogen bonding, and ionic), often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from the spatial variation of the surface/interface itself or from molecular configurations (i.e., conformation, orientation, aggregation state, etc.). By observing the adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to track the molecular configuration and simultaneously directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius-activated interfacial transport, spatially dependent interactions, and many more.

Spectral Profiles of Complex Fractionated Atrial Electrograms Are Different in Longstanding and Acute Onset Atrial Fibrillation Atrial Electrogram Spectra

Spectral Profiles of CFAE. Spectral analysis of complex fractionated atrial electrograms (CFAE) may be useful for gaining insight into mechanisms underlying paroxysmal and longstanding atrial fibrillation (AF). The commonly used dominant frequency (DF) measurement has limitations. CFAE recordings were acquired from outside the 4 pulmonary vein ostia and at 2 left atrial free wall sites in 10 paroxysmal and 10 persistent AF patients. Two consecutive 8s-series were analyzed from recordings >16s in duration. Power spectra were computed for each 8s-series in the range 3-12 Hz and normalized. The mean and standard deviation of normalized power spectra (MPS and SPS, respectively) were compared for paroxysmal versus persistent CFAE. Also, the DF and its peak amplitude (ADF) were compared for pulmonary vein sites only. Power spectra were computed using ensemble average and Fourier methods. No significant changes occurred in any parameter from the first to second recording sequence. For both sequences, MPS and SPS were significantly greater, and DF and ADF were significantly less, in paroxysmals versus persistents. The MPS and ADF measurements from ensemble spectra produced the most significant differences in paroxysmals versus persistents (P < 0.0001). DF differences were less significant, which can be attributed to the relatively high variability of DF in paroxysmals. The MPS was correlated to the duration of uninterrupted persistent AF prior to electrophysiologic study (P = 0.01), and to left atrial volume for all AF (P < 0.05). The MPS and ADF measurements introduced in this study are probably superior to DF for discerning power spectral differences in paroxysmal versus longstanding CFAE. (J Cardiovasc Electrophysiol, Vol. 23, pp. 971-979, September 2012).