Comparisons of a Constrained Least Squares Model versus Human-in-the-Loop for Spectral Unmixing to Determine Material Type of GEO Debris

NASA Technical Reports Server (NTRS)

Abercromby, Kira J.; Rapp, Jason; Bedard, Donald; Seitzer, Patrick; Cardona, Tommaso; Cowardin, Heather; Barker, Ed; Lederer, Susan

2013-01-01

Constrained Linear Least Squares model is generally more accurate than the "human-in-the-loop". However, "human-in-the-loop" can remove materials that make no sense. The speed of the model in determining a "first cut" at the material ID makes it a viable option for spectral unmixing of debris objects.

MAX UnMix: Introducing a new web application for unmixing magnetic coercivity distributions

NASA Astrophysics Data System (ADS)

Feinberg, J. M.; Maxbauer, D.; Fox, D. L.

2016-12-01

Magnetic minerals are present in a wide variety of natural systems and are often indicative of the natural or anthropogenic processes that led to their deposition, formation, or transformation. Unmixing the contribution of magnetic components to bulk field-dependent magnetization curves has become increasingly common in environmental and rock magnetic studies and has enhanced our ability to fingerprint the magnetic signatures of magnetic minerals with distinct compositions, grain sizes, and origins. A variety of programs have been developed over the past two decades to allow researchers to deconvolve field-dependent magnetization curves for these purposes, however many of these programs are either outdated or have obstacles that inhibit the programs usability. MAX UnMix is a new web application (available online at http://www.irm.umn.edu/maxunmix) built using the `shiny' package for R-studio that can be used to process coercivity distributions derived from magnetization curves (acquisition, demagnetization, or backfield data) via an online user-interface. Here, we use example datasets from lake sediments and paleosols to present details of the MAX UnMix model and the programs functionality. MAX UnMix is designed to be accessible, user friendly, and should serve as a useful resource for future research.

Unsupervised Unmixing of Hyperspectral Images Accounting for Endmember Variability.

PubMed

Halimi, Abderrahim; Dobigeon, Nicolas; Tourneret, Jean-Yves

2015-12-01

This paper presents an unsupervised Bayesian algorithm for hyperspectral image unmixing, accounting for endmember variability. The pixels are modeled by a linear combination of endmembers weighted by their corresponding abundances. However, the endmembers are assumed random to consider their variability in the image. An additive noise is also considered in the proposed model, generalizing the normal compositional model. The proposed algorithm exploits the whole image to benefit from both spectral and spatial information. It estimates both the mean and the covariance matrix of each endmember in the image. This allows the behavior of each material to be analyzed and its variability to be quantified in the scene. A spatial segmentation is also obtained based on the estimated abundances. In order to estimate the parameters associated with the proposed Bayesian model, we propose to use a Hamiltonian Monte Carlo algorithm. The performance of the resulting unmixing strategy is evaluated through simulations conducted on both synthetic and real data.

[Source apportionment of soil heavy metals in Jiapigou goldmine based on the UNMIX model].

PubMed

Ai, Jian-chao; Wang, Ning; Yang, Jing

2014-09-01

The paper determines 16 kinds of metal elements' concentration in soil samples which collected in Jipigou goldmine upper the Songhua River. The UNMIX Model which was recommended by US EPA to get the source apportionment results was applied in this study, Cd, Hg, Pb and Ag concentration contour maps were generated by using Kriging interpolation method to verify the results. The main conclusions of this study are: (1)the concentrations of Cd, Hg, Pb and Ag exceeded Jilin Province soil background values and enriched obviously in soil samples; (2)using the UNMIX Model resolved four pollution sources: source 1 represents human activities of transportation, ore mining and garbage, and the source 1's contribution is 39. 1% ; Source 2 represents the contribution of the weathering of rocks and biological effects, and the source 2's contribution is 13. 87% ; Source 3 is a comprehensive source of soil parent material and chemical fertilizer, and the source 3's contribution is 23. 93% ; Source 4 represents iron ore mining and transportation sources, and the source 4's contribution is 22. 89%. (3)the UNMIX Model results are in accordance with the survey of local land-use types, human activities and Cd, Hg and Pb content distributions.

Analysis of Forest Foliage Using a Multivariate Mixture Model

NASA Technical Reports Server (NTRS)

Hlavka, C. A.; Peterson, David L.; Johnson, L. F.; Ganapol, B.

1997-01-01

Data with wet chemical measurements and near infrared spectra of ground leaf samples were analyzed to test a multivariate regression technique for estimating component spectra which is based on a linear mixture model for absorbance. The resulting unmixed spectra for carbohydrates, lignin, and protein resemble the spectra of extracted plant starches, cellulose, lignin, and protein. The unmixed protein spectrum has prominent absorption spectra at wavelengths which have been associated with nitrogen bonds.

Unmixing Space Object’s Moderate Resolution Spectra

DTIC Science & Technology

2013-09-01

collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE SEP 2013 2. REPORT TYPE 3. DATES COVERED 00...result of spectral unmixing. In the visible, the non- resolved spectral signature is modeled as a linear mixture of spectral reflectance signatures...1 (3) In (3), the first term expresses the Euclidian distance (l2) between the observed data and the forward model . The second term (l1

Target Transformation Constrained Sparse Unmixing (ttcsu) Algorithm for Retrieving Hydrous Minerals on Mars: Application to Southwest Melas Chasma

NASA Astrophysics Data System (ADS)

Lin, H.; Zhang, X.; Wu, X.; Tarnas, J. D.; Mustard, J. F.

2018-04-01

Quantitative analysis of hydrated minerals from hyperspectral remote sensing data is fundamental for understanding Martian geologic process. Because of the difficulties for selecting endmembers from hyperspectral images, a sparse unmixing algorithm has been proposed to be applied to CRISM data on Mars. However, it's challenge when the endmember library increases dramatically. Here, we proposed a new methodology termed Target Transformation Constrained Sparse Unmixing (TTCSU) to accurately detect hydrous minerals on Mars. A new version of target transformation technique proposed in our recent work was used to obtain the potential detections from CRISM data. Sparse unmixing constrained with these detections as prior information was applied to CRISM single-scattering albedo images, which were calculated using a Hapke radiative transfer model. This methodology increases success rate of the automatic endmember selection of sparse unmixing and could get more accurate abundances. CRISM images with well analyzed in Southwest Melas Chasma was used to validate our methodology in this study. The sulfates jarosite was detected from Southwest Melas Chasma, the distribution is consistent with previous work and the abundance is comparable. More validations will be done in our future work.

Generating High-Temporal and Spatial Resolution TIR Image Data

NASA Astrophysics Data System (ADS)

Herrero-Huerta, M.; Lagüela, S.; Alfieri, S. M.; Menenti, M.

2017-09-01

Remote sensing imagery to monitor global biophysical dynamics requires the availability of thermal infrared data at high temporal and spatial resolution because of the rapid development of crops during the growing season and the fragmentation of most agricultural landscapes. Conversely, no single sensor meets these combined requirements. Data fusion approaches offer an alternative to exploit observations from multiple sensors, providing data sets with better properties. A novel spatio-temporal data fusion model based on constrained algorithms denoted as multisensor multiresolution technique (MMT) was developed and applied to generate TIR synthetic image data at both temporal and spatial high resolution. Firstly, an adaptive radiance model is applied based on spectral unmixing analysis of . TIR radiance data at TOA (top of atmosphere) collected by MODIS daily 1-km and Landsat - TIRS 16-day sampled at 30-m resolution are used to generate synthetic daily radiance images at TOA at 30-m spatial resolution. The next step consists of unmixing the 30 m (now lower resolution) images using the information about their pixel land-cover composition from co-registered images at higher spatial resolution. In our case study, TIR synthesized data were unmixed to the Sentinel 2 MSI with 10 m resolution. The constrained unmixing preserves all the available radiometric information of the 30 m images and involves the optimization of the number of land-cover classes and the size of the moving window for spatial unmixing. Results are still being evaluated, with particular attention for the quality of the data streams required to apply our approach.

Pigments identification of paintings using subspace distance unmixing algorithm

NASA Astrophysics Data System (ADS)

Li, Bin; Lyu, Shuqiang; Zhang, Dafeng; Dong, Qinghao

2018-04-01

In the digital protection of the cultural relics, the identification of the pigment mixtures on the surface of the painting has been the research spot for many years. In this paper, as a hyperspectral unmixing algorithm, sub-space distance unmixing is introduced to solve the problem of recognition of pigments mixture in paintings. Firstly, some mixtures of different pigments are designed to measure their reflectance spectra using spectrometer. Moreover, the factors affecting the unmixing accuracy of pigments' mixtures are discussed. The unmixing results of two cases with and without rice paper and its underlay as endmembers are compared. The experiment results show that the algorithm is able to unmixing the pigments effectively and the unmixing accuracy can be improved after considering the influence of spectra of the rich paper and the underlaying material.

Spectral Unmixing With Multiple Dictionaries

NASA Astrophysics Data System (ADS)

Cohen, Jeremy E.; Gillis, Nicolas

2018-02-01

Spectral unmixing aims at recovering the spectral signatures of materials, called endmembers, mixed in a hyperspectral or multispectral image, along with their abundances. A typical assumption is that the image contains one pure pixel per endmember, in which case spectral unmixing reduces to identifying these pixels. Many fully automated methods have been proposed in recent years, but little work has been done to allow users to select areas where pure pixels are present manually or using a segmentation algorithm. Additionally, in a non-blind approach, several spectral libraries may be available rather than a single one, with a fixed number (or an upper or lower bound) of endmembers to chose from each. In this paper, we propose a multiple-dictionary constrained low-rank matrix approximation model that address these two problems. We propose an algorithm to compute this model, dubbed M2PALS, and its performance is discussed on both synthetic and real hyperspectral images.

Predicting temperate forest stand types using only structural profiles from discrete return airborne lidar

NASA Astrophysics Data System (ADS)

Fedrigo, Melissa; Newnham, Glenn J.; Coops, Nicholas C.; Culvenor, Darius S.; Bolton, Douglas K.; Nitschke, Craig R.

2018-02-01

Light detection and ranging (lidar) data have been increasingly used for forest classification due to its ability to penetrate the forest canopy and provide detail about the structure of the lower strata. In this study we demonstrate forest classification approaches using airborne lidar data as inputs to random forest and linear unmixing classification algorithms. Our results demonstrated that both random forest and linear unmixing models identified a distribution of rainforest and eucalypt stands that was comparable to existing ecological vegetation class (EVC) maps based primarily on manual interpretation of high resolution aerial imagery. Rainforest stands were also identified in the region that have not previously been identified in the EVC maps. The transition between stand types was better characterised by the random forest modelling approach. In contrast, the linear unmixing model placed greater emphasis on field plots selected as endmembers which may not have captured the variability in stand structure within a single stand type. The random forest model had the highest overall accuracy (84%) and Cohen's kappa coefficient (0.62). However, the classification accuracy was only marginally better than linear unmixing. The random forest model was applied to a region in the Central Highlands of south-eastern Australia to produce maps of stand type probability, including areas of transition (the 'ecotone') between rainforest and eucalypt forest. The resulting map provided a detailed delineation of forest classes, which specifically recognised the coalescing of stand types at the landscape scale. This represents a key step towards mapping the structural and spatial complexity of these ecosystems, which is important for both their management and conservation.

Unmixing AVHRR Imagery to Assess Clearcuts and Forest Regrowth in Oregon

NASA Technical Reports Server (NTRS)

Hlavka, Christine A.; Spanner, Michael A.

1995-01-01

Advanced Very High Resolution Radiometer imagery provides frequent and low-cost coverage of the earth, but its coarse spatial resolution (approx. 1.1 km by 1.1 km) does not lend itself to standard techniques of automated categorization of land cover classes because the pixels are generally mixed; that is, the extent of the pixel includes several land use/cover classes. Unmixing procedures were developed to extract land use/cover class signatures from mixed pixels, using Landsat Thematic Mapper data as a source for the training set, and to estimate fractions of class coverage within pixels. Application of these unmixing procedures to mapping forest clearcuts and regrowth in Oregon indicated that unmixing is a promising approach for mapping major trends in land cover with AVHRR bands 1 and 2. Including thermal bands by unmixing AVHRR bands 1-4 did not lead to significant improvements in accuracy, but experiments with unmixing these four bands did indicate that use of weighted least squares techniques might lead to improvements in other applications of unmixing.

Arctic lead detection using a waveform unmixing algorithm from CryoSat-2 data

NASA Astrophysics Data System (ADS)

Lee, S.; Im, J.

2016-12-01

Arctic areas consist of ice floes, leads, and polynyas. While leads and polynyas account for small parts in the Arctic Ocean, they play a key role in exchanging heat flux, moisture, and momentum between the atmosphere and ocean in wintertime because of their huge temperature difference In this study, a linear waveform unmixing approach was proposed to detect lead fraction. CryoSat-2 waveforms for pure leads, sea ice, and ocean were used as end-members based on visual interpretation of MODIS images coincident with CryoSat-2 data. The unmixing model produced lead, sea ice, and ocean abundances and a threshold (> 0.7) was applied to make a binary classification between lead and sea ice. The unmixing model produced better results than the existing models in the literature, which are based on simple thresholding approaches. The results were also comparable with our previous research using machine learning based models (i.e., decision trees and random forest). A monthly lead fraction was calculated, dividing the number of detected leads by the total number of measurements. The lead fraction around Beaufort Sea and Fram strait was high due to the anti-cyclonic rotation of Beaufort Gyre and the outflows of sea ice to the Atlantic. The lead fraction maps produced in this study were matched well with monthly lead fraction maps in the literature. The areas with thin sea ice identified from our previous research correspond to the high lead fraction areas in the present study. Furthermore, sea ice roughness from ASCAT scatterometer was compared to a lead fraction map to see the relationship between surface roughness and lead distribution.

Component Analysis of Remanent Magnetization Curves: A Revisit with a New Model Distribution

NASA Astrophysics Data System (ADS)

Zhao, X.; Suganuma, Y.; Fujii, M.

2017-12-01

Geological samples often consist of several magnetic components that have distinct origins. As the magnetic components are often indicative of their underlying geological and environmental processes, it is therefore desirable to identify individual components to extract associated information. This component analysis can be achieved using the so-called unmixing method, which fits a mixture model of certain end-member model distribution to the measured remanent magnetization curve. In earlier studies, the lognormal, skew generalized Gaussian and skewed Gaussian distributions have been used as the end-member model distribution in previous studies, which are performed on the gradient curve of remanent magnetization curves. However, gradient curves are sensitive to measurement noise as the differentiation of the measured curve amplifies noise, which could deteriorate the component analysis. Though either smoothing or filtering can be applied to reduce the noise before differentiation, their effect on biasing component analysis is vaguely addressed. In this study, we investigated a new model function that can be directly applied to the remanent magnetization curves and therefore avoid the differentiation. The new model function can provide more flexible shape than the lognormal distribution, which is a merit for modeling the coercivity distribution of complex magnetic component. We applied the unmixing method both to model and measured data, and compared the results with those obtained using other model distributions to better understand their interchangeability, applicability and limitation. The analyses on model data suggest that unmixing methods are inherently sensitive to noise, especially when the number of component is over two. It is, therefore, recommended to verify the reliability of component analysis by running multiple analyses with synthetic noise. Marine sediments and seafloor rocks are analyzed with the new model distribution. Given the same component number, the new model distribution can provide closer fits than the lognormal distribution evidenced by reduced residuals. Moreover, the new unmixing protocol is automated so that the users are freed from the labor of providing initial guesses for the parameters, which is also helpful to improve the subjectivity of component analysis.

Spectral Unmixing Analysis of Time Series Landsat 8 Images

NASA Astrophysics Data System (ADS)

Zhuo, R.; Xu, L.; Peng, J.; Chen, Y.

2018-05-01

Temporal analysis of Landsat 8 images opens up new opportunities in the unmixing procedure. Although spectral analysis of time series Landsat imagery has its own advantage, it has rarely been studied. Nevertheless, using the temporal information can provide improved unmixing performance when compared to independent image analyses. Moreover, different land cover types may demonstrate different temporal patterns, which can aid the discrimination of different natures. Therefore, this letter presents time series K-P-Means, a new solution to the problem of unmixing time series Landsat imagery. The proposed approach is to obtain the "purified" pixels in order to achieve optimal unmixing performance. The vertex component analysis (VCA) is used to extract endmembers for endmember initialization. First, nonnegative least square (NNLS) is used to estimate abundance maps by using the endmember. Then, the estimated endmember is the mean value of "purified" pixels, which is the residual of the mixed pixel after excluding the contribution of all nondominant endmembers. Assembling two main steps (abundance estimation and endmember update) into the iterative optimization framework generates the complete algorithm. Experiments using both simulated and real Landsat 8 images show that the proposed "joint unmixing" approach provides more accurate endmember and abundance estimation results compared with "separate unmixing" approach.

EPA UNMIX 6.0 USER GUIDE

EPA Science Inventory

The underlying philosophy of Unmix is to let the data speak for itself. Unmix seeks to solve the general mixture problem where the data are assumed to be a linear combination of an unknown number of sources of unknown composition, which contribute an unknown amount to each sample...

Estimation of tissue optical parameters with hyperspectral imaging and spectral unmixing

NASA Astrophysics Data System (ADS)

Lu, Guolan; Qin, Xulei; Wang, Dongsheng; Chen, Zhuo G.; Fei, Baowei

2015-03-01

Early detection of oral cancer and its curable precursors can improve patient survival and quality of life. Hyperspectral imaging (HSI) holds the potential for noninvasive early detection of oral cancer. The quantification of tissue chromophores by spectral unmixing of hyperspectral images could provide insights for evaluating cancer progression. In this study, non-negative matrix factorization has been applied for decomposing hyperspectral images into physiologically meaningful chromophore concentration maps. The approach has been validated by computer-simulated hyperspectral images and in vivo tumor hyperspectral images from a head and neck cancer animal model.

Characterization of VOC sources in an urban area based on PTR-MS measurements and receptor modelling.

PubMed

Stojić, A; Stojić, S Stanišić; Šoštarić, A; Ilić, L; Mijić, Z; Rajšić, S

2015-09-01

In this study, the concentrations of volatile organic compounds were measured by the use of proton transfer reaction mass spectrometry, together with NO x , NO, NO2, SO2, CO and PM10 and meteorological parameters in an urban area of Belgrade during winter 2014. The multivariate receptor model US EPA Unmix was applied to the obtained dataset resolving six source profiles, which can be attributed to traffic-related emissions, gasoline evaporation/oil refineries, petrochemical industry/biogenic emissions, aged plumes, solid-fuel burning and local laboratories. Besides the vehicle exhaust, accounting for 27.6 % of the total mixing ratios, industrial emissions, which are present in three out of six resolved profiles, exert a significant impact on air quality in the urban area. The major contribution of regional and long-range transport was determined for source profiles associated with petrochemical industry/biogenic emissions (40 %) and gasoline evaporation/oil refineries (29 %) using trajectory sector analysis. The concentration-weighted trajectory model was applied with the aim of resolving the spatial distribution of potential distant sources, and the results indicated that emission sources from neighbouring countries, as well as from Slovakia, Greece, Poland and Scandinavian countries, significantly contribute to the observed concentrations.

Quadratic Blind Linear Unmixing: A Graphical User Interface for Tissue Characterization

PubMed Central

Gutierrez-Navarro, O.; Campos-Delgado, D.U.; Arce-Santana, E. R.; Jo, Javier A.

2016-01-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. PMID:26589467

Quadratic blind linear unmixing: A graphical user interface for tissue characterization.

PubMed

Gutierrez-Navarro, O; Campos-Delgado, D U; Arce-Santana, E R; Jo, Javier A

2016-02-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Distributed Unmixing of Hyperspectral Datawith Sparsity Constraint

NASA Astrophysics Data System (ADS)

Khoshsokhan, S.; Rajabi, R.; Zayyani, H.

2017-09-01

Spectral unmixing (SU) is a data processing problem in hyperspectral remote sensing. The significant challenge in the SU problem is how to identify endmembers and their weights, accurately. For estimation of signature and fractional abundance matrices in a blind problem, nonnegative matrix factorization (NMF) and its developments are used widely in the SU problem. One of the constraints which was added to NMF is sparsity constraint that was regularized by L1/2 norm. In this paper, a new algorithm based on distributed optimization has been used for spectral unmixing. In the proposed algorithm, a network including single-node clusters has been employed. Each pixel in hyperspectral images considered as a node in this network. The distributed unmixing with sparsity constraint has been optimized with diffusion LMS strategy, and then the update equations for fractional abundance and signature matrices are obtained. Simulation results based on defined performance metrics, illustrate advantage of the proposed algorithm in spectral unmixing of hyperspectral data compared with other methods. The results show that the AAD and SAD of the proposed approach are improved respectively about 6 and 27 percent toward distributed unmixing in SNR=25dB.

Automated mapping of impervious surfaces in urban and suburban areas: Linear spectral unmixing of high spatial resolution imagery

NASA Astrophysics Data System (ADS)

Yang, Jian; He, Yuhong

2017-02-01

Quantifying impervious surfaces in urban and suburban areas is a key step toward a sustainable urban planning and management strategy. With the availability of fine-scale remote sensing imagery, automated mapping of impervious surfaces has attracted growing attention. However, the vast majority of existing studies have selected pixel-based and object-based methods for impervious surface mapping, with few adopting sub-pixel analysis of high spatial resolution imagery. This research makes use of a vegetation-bright impervious-dark impervious linear spectral mixture model to characterize urban and suburban surface components. A WorldView-3 image acquired on May 9th, 2015 is analyzed for its potential in automated unmixing of meaningful surface materials for two urban subsets and one suburban subset in Toronto, ON, Canada. Given the wide distribution of shadows in urban areas, the linear spectral unmixing is implemented in non-shadowed and shadowed areas separately for the two urban subsets. The results indicate that the accuracy of impervious surface mapping in suburban areas reaches up to 86.99%, much higher than the accuracies in urban areas (80.03% and 79.67%). Despite its merits in mapping accuracy and automation, the application of our proposed vegetation-bright impervious-dark impervious model to map impervious surfaces is limited due to the absence of soil component. To further extend the operational transferability of our proposed method, especially for the areas where plenty of bare soils exist during urbanization or reclamation, it is still of great necessity to mask out bare soils by automated classification prior to the implementation of linear spectral unmixing.

Accuracy assessment of linear spectral mixture model due to terrain undulation

NASA Astrophysics Data System (ADS)

Wang, Tianxing; Chen, Songlin; Ma, Ya

2008-12-01

Mixture spectra are common in remote sensing due to the limitations of spatial resolution and the heterogeneity of land surface. During the past 30 years, a lot of subpixel model have developed to investigate the information within mixture pixels. Linear spectral mixture model (LSMM) is a simper and more general subpixel model. LSMM also known as spectral mixture analysis is a widely used procedure to determine the proportion of endmembers (constituent materials) within a pixel based on the endmembers' spectral characteristics. The unmixing accuracy of LSMM is restricted by variety of factors, but now the research about LSMM is mostly focused on appraisement of nonlinear effect relating to itself and techniques used to select endmembers, unfortunately, the environment conditions of study area which could sway the unmixing-accuracy, such as atmospheric scatting and terrain undulation, are not studied. This paper probes emphatically into the accuracy uncertainty of LSMM resulting from the terrain undulation. ASTER dataset was chosen and the C terrain correction algorithm was applied to it. Based on this, fractional abundances for different cover types were extracted from both pre- and post-C terrain illumination corrected ASTER using LSMM. Simultaneously, the regression analyses and the IKONOS image were introduced to assess the unmixing accuracy. Results showed that terrain undulation could dramatically constrain the application of LSMM in mountain area. Specifically, for vegetation abundances, a improved unmixing accuracy of 17.6% (regression against to NDVI) and 18.6% (regression against to MVI) for R2 was achieved respectively by removing terrain undulation. Anyway, this study indicated in a quantitative way that effective removal or minimization of terrain illumination effects was essential for applying LSMM. This paper could also provide a new instance for LSMM applications in mountainous areas. In addition, the methods employed in this study could be effectively used to evaluate different algorithms of terrain undulation correction for further study.

Mapping target signatures via partial unmixing of AVIRIS data

NASA Technical Reports Server (NTRS)

Boardman, Joseph W.; Kruse, Fred A.; Green, Robert O.

1995-01-01

A complete spectral unmixing of a complicated AVIRIS scene may not always be possible or even desired. High quality data of spectrally complex areas are very high dimensional and are consequently difficult to fully unravel. Partial unmixing provides a method of solving only that fraction of the data inversion problem that directly relates to the specific goals of the investigation. Many applications of imaging spectrometry can be cast in the form of the following question: 'Are my target signatures present in the scene, and if so, how much of each target material is present in each pixel?' This is a partial unmixing problem. The number of unmixing endmembers is one greater than the number of spectrally defined target materials. The one additional endmember can be thought of as the composite of all the other scene materials, or 'everything else'. Several workers have proposed partial unmixing schemes for imaging spectrometry data, but each has significant limitations for operational application. The low probability detection methods described by Farrand and Harsanyi and the foreground-background method of Smith et al are both examples of such partial unmixing strategies. The new method presented here builds on these innovative analysis concepts, combining their different positive attributes while attempting to circumvent their limitations. This new method partially unmixes AVIRIS data, mapping apparent target abundances, in the presence of an arbitrary and unknown spectrally mixed background. It permits the target materials to be present in abundances that drive significant portions of the scene covariance. Furthermore it does not require a priori knowledge of the background material spectral signatures. The challenge is to find the proper projection of the data that hides the background variance while simultaneously maximizing the variance amongst the targets.

Rotational Spectral Unmixing of Exoplanets: Degeneracies between Surface Colors and Geography

NASA Astrophysics Data System (ADS)

Fujii, Yuka; Lustig-Yaeger, Jacob; Cowan, Nicolas B.

2017-11-01

Unmixing the disk-integrated spectra of exoplanets provides hints about heterogeneous surfaces that we cannot directly resolve in the foreseeable future. It is particularly important for terrestrial planets with diverse surface compositions like Earth. Although previous work on unmixing the spectra of Earth from disk-integrated multi-band light curves appeared successful, we point out a mathematical degeneracy between the surface colors and their spatial distributions. Nevertheless, useful constraints on the spectral shape of individual surface types may be obtained from the premise that albedo is everywhere between 0 and 1. We demonstrate the degeneracy and the possible constraints using both mock data based on a toy model of Earth, as well as real observations of Earth. Despite the severe degeneracy, we are still able to recover an approximate albedo spectrum for an ocean. In general, we find that surfaces are easier to identify when they cover a large fraction of the planet and when their spectra approach zero or unity in certain bands.

Rotational Spectral Unmixing of Exoplanets: Degeneracies between Surface Colors and Geography

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

Fujii, Yuka; Lustig-Yaeger, Jacob; Cowan, Nicolas B., E-mail: yuka.fujii.ebihara@gmail.com

Unmixing the disk-integrated spectra of exoplanets provides hints about heterogeneous surfaces that we cannot directly resolve in the foreseeable future. It is particularly important for terrestrial planets with diverse surface compositions like Earth. Although previous work on unmixing the spectra of Earth from disk-integrated multi-band light curves appeared successful, we point out a mathematical degeneracy between the surface colors and their spatial distributions. Nevertheless, useful constraints on the spectral shape of individual surface types may be obtained from the premise that albedo is everywhere between 0 and 1. We demonstrate the degeneracy and the possible constraints using both mock datamore » based on a toy model of Earth, as well as real observations of Earth. Despite the severe degeneracy, we are still able to recover an approximate albedo spectrum for an ocean. In general, we find that surfaces are easier to identify when they cover a large fraction of the planet and when their spectra approach zero or unity in certain bands.« less

Rotational Spectral Unmixing of Exoplanets: Degeneracies Between Surface Colors and Geography

NASA Technical Reports Server (NTRS)

Fujii, Yuka; Lustig-Yaeger, Jacob; Cowan, Nicolas B.

2017-01-01

Unmixing the disk-integrated spectra of exoplanets provides hints about heterogeneous surfaces that we cannot directly resolve in the foreseeable future. It is particularly important for terrestrial planets with diverse surface compositions like Earth. Although previous work on unmixing the spectra of Earth from disk-integrated multi-band light curves appeared successful, we point out a mathematical degeneracy between the surface colors and their spatial distributions. Nevertheless, useful constraints on the spectral shape of individual surface types may be obtained from the premise that albedo is everywhere between 0 and 1. We demonstrate the degeneracy and the possible constraints using both mock data based on a toy model of Earth, as well as real observations of Earth. Despite the severe degeneracy, we are still able to recover an approximate albedo spectrum for an ocean. In general, we find that surfaces are easier to identify when they cover a large fraction of the planet and when their spectra approach zero or unity in certain bands.

Fingerprinting Sources of Suspended Sediment in a Canadian Agricultural Watershed Using the MixSIAR Bayesian Unmixing Model

NASA Astrophysics Data System (ADS)

Smith, J. P.; Owens, P. N.; Gaspar, L.; Lobb, D. A.; Petticrew, E. L.

2015-12-01

An understanding of sediment redistribution processes and the main sediment sources within a watershed is needed to support watershed management strategies. The fingerprinting technique is increasingly being recognized as a method for establishing the source of the sediment transported within watersheds. However, the different behaviour of the various fingerprinting properties has been recognized as a major limitation of the technique, and the uncertainty associated with tracer selection needs to be addressed. There are also questions associated with which modelling approach (frequentist or Bayesian) is the best to unmix complex environmental mixtures, such as river sediment. This study aims to compare and evaluate the differences between fingerprinting predictions provided by a Bayesian unmixing model (MixSIAR) using different groups of tracer properties for use in sediment source identification. We used fallout radionuclides (e.g. 137Cs) and geochemical elements (e.g. As) as conventional fingerprinting properties, and colour parameters as emerging properties; both alone and in combination. These fingerprinting properties are being used (i.e. Koiter et al., 2013; Barthod et al., 2015) to determine the proportional contributions of fine sediment in the South Tobacco Creek Watershed, an agricultural watershed located in Manitoba, Canada. We show that the unmixing model using a combination of fallout radionuclides and geochemical tracers gave similar results to the model based on colour parameters. Furthermore, we show that a model that combines all tracers (i.e. radionuclide/geochemical and colour) gave similar results, showing that sediment sources change from predominantly topsoil in the upper reaches of the watershed to channel bank and bedrock outcrop material in the lower reaches. Barthod LRM et al. (2015). Selecting color-based tracers and classifying sediment sources in the assessment of sediment dynamics using sediment source fingerprinting. J Environ Qual. Doi:10.2134/jeq2015.01.0043 Koiter AJ et al. (2013). Investigating the role of connectivity and scale in assessing the sources of sediment in an agricultural watershed in the Canadian prairies using sediment source fingerprinting. J Soils Sediments, 13, 1676-1691.

Sediment unmixing using detrital geochronology

USGS Publications Warehouse

Sharman, Glenn R.; Johnstone, Samuel

2017-01-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the influence of environmental forcings (e.g., tectonism, climate) on the earth’s surface. Here we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First we summarize ‘top-down’ mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions (‘parents’) that characterize a derived sample or set of samples (‘daughters’). Second we propose the use of ‘bottom-up’ methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable mixtures over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

Sediment unmixing using detrital geochronology

NASA Astrophysics Data System (ADS)

Sharman, Glenn R.; Johnstone, Samuel A.

2017-11-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the effect of environmental forcing (e.g., tectonism, climate) on the Earth's surface. Here, we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First, we summarize 'top-down' mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions ('parents') that characterize a derived sample or set of samples ('daughters'). Second, we propose the use of 'bottom-up' methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable that is well mixed over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has the potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

A clustering algorithm for sample data based on environmental pollution characteristics

NASA Astrophysics Data System (ADS)

Chen, Mei; Wang, Pengfei; Chen, Qiang; Wu, Jiadong; Chen, Xiaoyun

2015-04-01

Environmental pollution has become an issue of serious international concern in recent years. Among the receptor-oriented pollution models, CMB, PMF, UNMIX, and PCA are widely used as source apportionment models. To improve the accuracy of source apportionment and classify the sample data for these models, this study proposes an easy-to-use, high-dimensional EPC algorithm that not only organizes all of the sample data into different groups according to the similarities in pollution characteristics such as pollution sources and concentrations but also simultaneously detects outliers. The main clustering process consists of selecting the first unlabelled point as the cluster centre, then assigning each data point in the sample dataset to its most similar cluster centre according to both the user-defined threshold and the value of similarity function in each iteration, and finally modifying the clusters using a method similar to k-Means. The validity and accuracy of the algorithm are tested using both real and synthetic datasets, which makes the EPC algorithm practical and effective for appropriately classifying sample data for source apportionment models and helpful for better understanding and interpreting the sources of pollution.

Hyperspectral fluorescence imaging with multi wavelength LED excitation

NASA Astrophysics Data System (ADS)

Luthman, A. Siri; Dumitru, Sebastian; Quirós-Gonzalez, Isabel; Bohndiek, Sarah E.

2016-04-01

Hyperspectral imaging (HSI) can combine morphological and molecular information, yielding potential for real-time and high throughput multiplexed fluorescent contrast agent imaging. Multiplexed readout from targets, such as cell surface receptors overexpressed in cancer cells, could improve both sensitivity and specificity of tumor identification. There remains, however, a need for compact and cost effective implementations of the technology. We have implemented a low-cost wide-field multiplexed fluorescence imaging system, which combines LED excitation at 590, 655 and 740 nm with a compact commercial solid state HSI system operating in the range 600 - 1000 nm. A key challenge for using reflectance-based HSI is the separation of contrast agent fluorescence from the reflectance of the excitation light. Here, we illustrate how it is possible to address this challenge in software, using two offline reflectance removal methods, prior to least-squares spectral unmixing. We made a quantitative comparison of the methods using data acquired from dilutions of contrast agents prepared in well-plates. We then established the capability of our HSI system for non-invasive in vivo fluorescence imaging in small animals using the optimal reflectance removal method. The HSI presented here enables quantitative unmixing of at least four fluorescent contrast agents (Alexa Fluor 610, 647, 700 and 750) simultaneously in living mice. A successful unmixing of the four fluorescent contrast agents was possible both using the pure contrast agents and with mixtures. The system could in principle also be applied to imaging of ex vivo tissue or intraoperative imaging in a clinical setting. These data suggest a promising approach for developing clinical applications of HSI based on multiplexed fluorescence contrast agent imaging.

ℓ0 -based sparse hyperspectral unmixing using spectral information and a multi-objectives formulation

NASA Astrophysics Data System (ADS)

Xu, Xia; Shi, Zhenwei; Pan, Bin

2018-07-01

Sparse unmixing aims at recovering pure materials from hyperpspectral images and estimating their abundance fractions. Sparse unmixing is actually ℓ0 problem which is NP-h ard, and a relaxation is often used. In this paper, we attempt to deal with ℓ0 problem directly via a multi-objective based method, which is a non-convex manner. The characteristics of hyperspectral images are integrated into the proposed method, which leads to a new spectra and multi-objective based sparse unmixing method (SMoSU). In order to solve the ℓ0 norm optimization problem, the spectral library is encoded in a binary vector, and a bit-wise flipping strategy is used to generate new individuals in the evolution process. However, a multi-objective method usually produces a number of non-dominated solutions, while sparse unmixing requires a single solution. How to make the final decision for sparse unmixing is challenging. To handle this problem, we integrate the spectral characteristic of hyperspectral images into SMoSU. By considering the spectral correlation in hyperspectral data, we improve the Tchebycheff decomposition function in SMoSU via a new regularization item. This regularization item is able to enforce the individual divergence in the evolution process of SMoSU. In this way, the diversity and convergence of population is further balanced, which is beneficial to the concentration of individuals. In the experiments part, three synthetic datasets and one real-world data are used to analyse the effectiveness of SMoSU, and several state-of-art sparse unmixing algorithms are compared.

Local hyperspectral data multisharpening based on linear/linear-quadratic nonnegative matrix factorization by integrating lidar data

NASA Astrophysics Data System (ADS)

Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

2015-10-01

In this paper, a new Spectral-Unmixing-based approach, using Nonnegative Matrix Factorization (NMF), is proposed to locally multi-sharpen hyperspectral data by integrating a Digital Surface Model (DSM) obtained from LIDAR data. In this new approach, the nature of the local mixing model is detected by using the local variance of the object elevations. The hyper/multispectral images are explored using small zones. In each zone, the variance of the object elevations is calculated from the DSM data in this zone. This variance is compared to a threshold value and the adequate linear/linearquadratic spectral unmixing technique is used in the considered zone to independently unmix hyperspectral and multispectral data, using an adequate linear/linear-quadratic NMF-based approach. The obtained spectral and spatial information thus respectively extracted from the hyper/multispectral images are then recombined in the considered zone, according to the selected mixing model. Experiments based on synthetic hyper/multispectral data are carried out to evaluate the performance of the proposed multi-sharpening approach and literature linear/linear-quadratic approaches used on the whole hyper/multispectral data. In these experiments, real DSM data are used to generate synthetic data containing linear and linear-quadratic mixed pixel zones. The DSM data are also used for locally detecting the nature of the mixing model in the proposed approach. Globally, the proposed approach yields good spatial and spectral fidelities for the multi-sharpened data and significantly outperforms the used literature methods.

Terahertz spectral unmixing based method for identifying gastric cancer

NASA Astrophysics Data System (ADS)

Cao, Yuqi; Huang, Pingjie; Li, Xian; Ge, Weiting; Hou, Dibo; Zhang, Guangxin

2018-02-01

At present, many researchers are exploring biological tissue inspection using terahertz time-domain spectroscopy (THz-TDS) techniques. In this study, based on a modified hard modeling factor analysis method, terahertz spectral unmixing was applied to investigate the relationships between the absorption spectra in THz-TDS and certain biomarkers of gastric cancer in order to systematically identify gastric cancer. A probability distribution and box plot were used to extract the distinctive peaks that indicate carcinogenesis, and the corresponding weight distributions were used to discriminate the tissue types. The results of this work indicate that terahertz techniques have the potential to detect different levels of cancer, including benign tumors and polyps.

Improving the Accuracy of Mapping Urban Vegetation Carbon Density by Combining Shadow Remove, Spectral Unmixing Analysis and Spatial Modeling

NASA Astrophysics Data System (ADS)

Qie, G.; Wang, G.; Wang, M.

2016-12-01

Mixed pixels and shadows due to buildings in urban areas impede accurate estimation and mapping of city vegetation carbon density. In most of previous studies, these factors are often ignored, which thus result in underestimation of city vegetation carbon density. In this study we presented an integrated methodology to improve the accuracy of mapping city vegetation carbon density. Firstly, we applied a linear shadow remove analysis (LSRA) on remotely sensed Landsat 8 images to reduce the shadow effects on carbon estimation. Secondly, we integrated a linear spectral unmixing analysis (LSUA) with a linear stepwise regression (LSR), a logistic model-based stepwise regression (LMSR) and k-Nearest Neighbors (kNN), and utilized and compared the integrated models on shadow-removed images to map vegetation carbon density. This methodology was examined in Shenzhen City of Southeast China. A data set from a total of 175 sample plots measured in 2013 and 2014 was used to train the models. The independent variables statistically significantly contributing to improving the fit of the models to the data and reducing the sum of squared errors were selected from a total of 608 variables derived from different image band combinations and transformations. The vegetation fraction from LSUA was then added into the models as an important independent variable. The estimates obtained were evaluated using a cross-validation method. Our results showed that higher accuracies were obtained from the integrated models compared with the ones using traditional methods which ignore the effects of mixed pixels and shadows. This study indicates that the integrated method has great potential on improving the accuracy of urban vegetation carbon density estimation. Key words: Urban vegetation carbon, shadow, spectral unmixing, spatial modeling, Landsat 8 images

Spectral Unmixing Based Construction of Lunar Mineral Abundance Maps

NASA Astrophysics Data System (ADS)

Bernhardt, V.; Grumpe, A.; Wöhler, C.

2017-07-01

In this study we apply a nonlinear spectral unmixing algorithm to a nearly global lunar spectral reflectance mosaic derived from hyper-spectral image data acquired by the Moon Mineralogy Mapper (M3) instrument. Corrections for topographic effects and for thermal emission were performed. A set of 19 laboratory-based reflectance spectra of lunar samples published by the Lunar Soil Characterization Consortium (LSCC) were used as a catalog of potential endmember spectra. For a given spectrum, the multi-population population-based incremental learning (MPBIL) algorithm was used to determine the subset of endmembers actually contained in it. However, as the MPBIL algorithm is computationally expensive, it cannot be applied to all pixels of the reflectance mosaic. Hence, the reflectance mosaic was clustered into a set of 64 prototype spectra, and the MPBIL algorithm was applied to each prototype spectrum. Each pixel of the mosaic was assigned to the most similar prototype, and the set of endmembers previously determined for that prototype was used for pixel-wise nonlinear spectral unmixing using the Hapke model, implemented as linear unmixing of the single-scattering albedo spectrum. This procedure yields maps of the fractional abundances of the 19 endmembers. Based on the known modal abundances of a variety of mineral species in the LSCC samples, a conversion from endmember abundances to mineral abundances was performed. We present maps of the fractional abundances of plagioclase, pyroxene and olivine and compare our results with previously published lunar mineral abundance maps.

Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform.

PubMed

Kannan, R; Ievlev, A V; Laanait, N; Ziatdinov, M A; Vasudevan, R K; Jesse, S; Kalinin, S V

2018-01-01

Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.

Electrotransport-induced unmixing and decomposition of ternary oxides

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

Chun, Jakyu; Yoo, Han-Ill, E-mail: hiyoo@snu.ac.kr; Martin, Manfred

A general expectation is that in a uniform oxygen activity atmosphere, cation electrotransport induces a ternary or higher oxide, e.g., AB{sub 1+ξ}O{sub 3+δ}, to kinetically unmix unless the electrochemical mobilities of, say, A{sup 2+}and B{sup 4+} cations are identically equal, and eventually to decompose into the component oxides AO and BO{sub 2} once the extent of unmixing exceeds the stability range of its nonmolecularity ξ. It has, however, earlier been reported [Yoo et al., Appl. Phys. Lett. 92, 252103 (2008)] that even a massive cation electrotransport induces BaTiO{sub 3} to neither unmix nor decompose even at a voltage far exceedingmore » the so-called decomposition voltage U{sub d}, a measure of the standard formation free energy of the oxide (|ΔG{sub f}{sup o}| = nFU{sub d}). Here, we report that as expected, NiTiO{sub 3} unmixes at any voltage and even decomposes if the voltage applied exceeds seemingly a threshold value larger than U{sub d}. We demonstrate experimentally that the electrochemical mobilities of Ni{sup 2+} and Ti{sup 4+} should be necessarily unequal for unmixing. Also, we show theoretically that equal cation mobilities appear to be a sufficiency for BaTiO{sub 3} only for a thermodynamic reason.« less

Multi-objective based spectral unmixing for hyperspectral images

NASA Astrophysics Data System (ADS)

Xu, Xia; Shi, Zhenwei

2017-02-01

Sparse hyperspectral unmixing assumes that each observed pixel can be expressed by a linear combination of several pure spectra in a priori library. Sparse unmixing is challenging, since it is usually transformed to a NP-hard l0 norm based optimization problem. Existing methods usually utilize a relaxation to the original l0 norm. However, the relaxation may bring in sensitive weighted parameters and additional calculation error. In this paper, we propose a novel multi-objective based algorithm to solve the sparse unmixing problem without any relaxation. We transform sparse unmixing to a multi-objective optimization problem, which contains two correlative objectives: minimizing the reconstruction error and controlling the endmember sparsity. To improve the efficiency of multi-objective optimization, a population-based randomly flipping strategy is designed. Moreover, we theoretically prove that the proposed method is able to recover a guaranteed approximate solution from the spectral library within limited iterations. The proposed method can directly deal with l0 norm via binary coding for the spectral signatures in the library. Experiments on both synthetic and real hyperspectral datasets demonstrate the effectiveness of the proposed method.

EPA Unmix 6.0 Fundamentals & User Guide

EPA Pesticide Factsheets

Unmix seeks to solve the general mixture problem where the data are assumed to be a linear combination of an unknown number of sources of unknown composition, which contribute an unknown amount to each sample.

A novel highly parallel algorithm for linearly unmixing hyperspectral images

NASA Astrophysics Data System (ADS)

Guerra, Raúl; López, Sebastián.; Callico, Gustavo M.; López, Jose F.; Sarmiento, Roberto

2014-10-01

Endmember extraction and abundances calculation represent critical steps within the process of linearly unmixing a given hyperspectral image because of two main reasons. The first one is due to the need of computing a set of accurate endmembers in order to further obtain confident abundance maps. The second one refers to the huge amount of operations involved in these time-consuming processes. This work proposes an algorithm to estimate the endmembers of a hyperspectral image under analysis and its abundances at the same time. The main advantage of this algorithm is its high parallelization degree and the mathematical simplicity of the operations implemented. This algorithm estimates the endmembers as virtual pixels. In particular, the proposed algorithm performs the descent gradient method to iteratively refine the endmembers and the abundances, reducing the mean square error, according with the linear unmixing model. Some mathematical restrictions must be added so the method converges in a unique and realistic solution. According with the algorithm nature, these restrictions can be easily implemented. The results obtained with synthetic images demonstrate the well behavior of the algorithm proposed. Moreover, the results obtained with the well-known Cuprite dataset also corroborate the benefits of our proposal.

Robust Spectral Unmixing of Sparse Multispectral Lidar Waveforms using Gamma Markov Random Fields

DOE PAGES

Altmann, Yoann; Maccarone, Aurora; McCarthy, Aongus; ...

2017-05-10

Here, this paper presents a new Bayesian spectral un-mixing algorithm to analyse remote scenes sensed via sparse multispectral Lidar measurements. To a first approximation, in the presence of a target, each Lidar waveform consists of a main peak, whose position depends on the target distance and whose amplitude depends on the wavelength of the laser source considered (i.e, on the target reflectivity). Besides, these temporal responses are usually assumed to be corrupted by Poisson noise in the low photon count regime. When considering multiple wavelengths, it becomes possible to use spectral information in order to identify and quantify the mainmore » materials in the scene, in addition to estimation of the Lidar-based range profiles. Due to its anomaly detection capability, the proposed hierarchical Bayesian model, coupled with an efficient Markov chain Monte Carlo algorithm, allows robust estimation of depth images together with abundance and outlier maps associated with the observed 3D scene. The proposed methodology is illustrated via experiments conducted with real multispectral Lidar data acquired in a controlled environment. The results demonstrate the possibility to unmix spectral responses constructed from extremely sparse photon counts (less than 10 photons per pixel and band).« less

Sparsely-sampled hyperspectral stimulated Raman scattering microscopy: a theoretical investigation

NASA Astrophysics Data System (ADS)

Lin, Haonan; Liao, Chien-Sheng; Wang, Pu; Huang, Kai-Chih; Bouman, Charles A.; Kong, Nan; Cheng, Ji-Xin

2017-02-01

A hyperspectral image corresponds to a data cube with two spatial dimensions and one spectral dimension. Through linear un-mixing, hyperspectral images can be decomposed into spectral signatures of pure components as well as their concentration maps. Due to this distinct advantage on component identification, hyperspectral imaging becomes a rapidly emerging platform for engineering better medicine and expediting scientific discovery. Among various hyperspectral imaging techniques, hyperspectral stimulated Raman scattering (HSRS) microscopy acquires data in a pixel-by-pixel scanning manner. Nevertheless, current image acquisition speed for HSRS is insufficient to capture the dynamics of freely moving subjects. Instead of reducing the pixel dwell time to achieve speed-up, which would inevitably decrease signal-to-noise ratio (SNR), we propose to reduce the total number of sampled pixels. Location of sampled pixels are carefully engineered with triangular wave Lissajous trajectory. Followed by a model-based image in-painting algorithm, the complete data is recovered for linear unmixing. Simulation results show that by careful selection of trajectory, a fill rate as low as 10% is sufficient to generate accurate linear unmixing results. The proposed framework applies to any hyperspectral beam-scanning imaging platform which demands high acquisition speed.

Advanced receptor models for exploiting highly time-resolved data acquired in the EPA supersite preject

NASA Astrophysics Data System (ADS)

Ke, Haohao

Receptor models have been widely used in air quality studies to identify pollution sources and estimate their contributions. A common problem for most current receptor models is insufficient consideration of realistic constraints such as can be obtained from emission inventories, chemical composition profiles of the sources, and the physics of plume dispersion. In addition, poor resolving of collinear sources was often found. With the high quality time-, composition-, and size-resolved measurements during the EPA Supersite project, efforts towards resolving nearby industrial sources were made by combinative use of Positive Matrix Factorization (PMF) and the Pseudo-Deterministic Receptor Model (PDRM). The PMF modeling of Baltimore data in September 2001 revealed coal-fired and oil-fired power plants (CFPP and OFPP, respectively) with significant cross contamination, as indicated by the high Se/Ni ratio in the OFPP profile. Nevertheless, the PMF results provided a good estimate of background and the PMF-constrained emission rates well seeded the trajectory-driven PDRM modeling. Using NOx as the tracer gas for chi/Q tuning, ultimately resolved emissions from individual stacks exhibited acceptable tracer ratios and the emission rates of metals generally agreed with the TRI estimates. This approach was later applied to two metal pollution episodes in St. Louis during in November 2001 and March 2002 and met a similar success. As NOx measurements were unavailable at those metal-production facilities, highly-specific tracer metals (i.e., Cd, Zn, and Cu) for the corresponding units were used to tune chi/Qs and their contributions were well resolved with the PMF-seeded PDRM. Opportunistically a PM2.5 excursion during a windless morning in November 2002 allowed the extraction of an in-situ profile of vehicular emissions in Baltimore. The profiles obtained by direct peak observation, windless model linear regression (WMA), PMF, and UNMIX were comparable and the WMA profile showed the best predictions for non-traffic tracers. Besides, an approach to evaluate vehicular emission factors was developed by receptor measurements under windless conditions. Using SVOC tracers, seasonal variations of traffic and other sources including coal burning, heating, biomass burning, and vegetation were investigated by PMF and in particular the November traffic profile was consistent with the WMA profile obtained earlier.

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

Calder, Stuart A; Cao, Guixin; Okamoto, Satoshi

The J_eff=1/2 state is manifested in systems with large cubic crystal field splitting and spin-orbit coupling that are comparable to the on-site Coulomb interaction, U. 5d transition metal oxides host parameters in this regime and strong evidence for this state in Sr2IrO4, and additional iridates, has been presented. All the candidates, however, deviate from the cubic crystal field required to provide an unmixed canonical J_eff=1/2 state, impacting the development of a robust model of this novel insulating and magnetic state. We present experimental and theoretical results that not only show Ca4IrO6 hosts the state, but furthermore uniquely resides in themore » limit required for a canonical unmixed J_eff=1/2 state.« less

Scaling dimensions in spectroscopy of soil and vegetation

NASA Astrophysics Data System (ADS)

Malenovský, Zbyněk; Bartholomeus, Harm M.; Acerbi-Junior, Fausto W.; Schopfer, Jürg T.; Painter, Thomas H.; Epema, Gerrit F.; Bregt, Arnold K.

2007-05-01

The paper revises and clarifies definitions of the term scale and scaling conversions for imaging spectroscopy of soil and vegetation. We demonstrate a new four-dimensional scale concept that includes not only spatial but also the spectral, directional and temporal components. Three scaling remote sensing techniques are reviewed: (1) radiative transfer, (2) spectral (un)mixing, and (3) data fusion. Relevant case studies are given in the context of their up- and/or down-scaling abilities over the soil/vegetation surfaces and a multi-source approach is proposed for their integration. Radiative transfer (RT) models are described to show their capacity for spatial, spectral up-scaling, and directional down-scaling within a heterogeneous environment. Spectral information and spectral derivatives, like vegetation indices (e.g. TCARI/OSAVI), can be scaled and even tested by their means. Radiative transfer of an experimental Norway spruce ( Picea abies (L.) Karst.) research plot in the Czech Republic was simulated by the Discrete Anisotropic Radiative Transfer (DART) model to prove relevance of the correct object optical properties scaled up to image data at two different spatial resolutions. Interconnection of the successive modelling levels in vegetation is shown. A future development in measurement and simulation of the leaf directional spectral properties is discussed. We describe linear and/or non-linear spectral mixing techniques and unmixing methods that demonstrate spatial down-scaling. Relevance of proper selection or acquisition of the spectral endmembers using spectral libraries, field measurements, and pure pixels of the hyperspectral image is highlighted. An extensive list of advanced unmixing techniques, a particular example of unmixing a reflective optics system imaging spectrometer (ROSIS) image from Spain, and examples of other mixture applications give insight into the present status of scaling capabilities. Simultaneous spatial and temporal down-scaling by means of a data fusion technique is described. A demonstrative example is given for the moderate resolution imaging spectroradiometer (MODIS) and LANDSAT Thematic Mapper (TM) data from Brazil. Corresponding spectral bands of both sensors were fused via a pyramidal wavelet transform in Fourier space. New spectral and temporal information of the resultant image can be used for thematic classification or qualitative mapping. All three described scaling techniques can be integrated as the relevant methodological steps within a complex multi-source approach. We present this concept of combining numerous optical remote sensing data and methods to generate inputs for ecosystem process models.

Spectral Unmixing Modeling of the Aristarchus Pyroclastic Deposit: Assessing the Eruptive History of Glass-Rich Regional Lunar Pyroclastic Deposits

NASA Astrophysics Data System (ADS)

Jawin, E. R.; Head, J. W., III; Cannon, K.

2017-12-01

The Aristarchus pyroclastic deposit in central Oceanus Procellarum is understood to have formed in a gas-rich explosive volcanic eruption, and has been observed to contain abundant volcanic glass. However, the interpreted color (and therefore composition) of the glass has been debated. In addition, previous analyses of the pyroclastic deposit have been performed using lower resolution data than are currently available. In this work, a nonlinear spectral unmixing model was applied to Moon Mineralogy Mapper (M3) data of the Aristarchus plateau to investigate the detailed mineralogic and crystalline nature of the Aristarchus pyroclastic deposit by using spectra of laboratory endmembers including a suite of volcanic glasses returned from the Apollo 15 and 17 missions (green, orange, black beads), as well as synthetic lunar glasses (orange, green, red, yellow). Preliminary results of the M3 unmixing model suggest that spectra of the pyroclastic deposit can be modeled by a mixture composed predominantly of a featureless endmember approximating space weathering and a smaller component of glass. The modeled spectra were most accurate with a synthetic orange glass endmember, relative to the other glasses analyzed in this work. The results confirm that there is a detectable component of glass in the Aristarchus pyroclastic deposit which may be similar to the high-Ti orange glass seen in other regional pyroclastic deposits, with only minimal contributions of other crystalline minerals. The presence of volcanic glass in the pyroclastic deposit, with the low abundance of crystalline material, would support the model that the Aristarchus pyroclastic deposit formed in a long-duration, hawaiian-style fire fountain eruption. No significant detection of devitrified black beads in the spectral modeling results (as was observed at the Apollo 17 landing site in the Taurus-Littrow pyroclastic deposit), suggests the optical density of the eruptive plume remained low throughout the eruption.

Use of airborne hyperspectral data to estimate residual heavy metal contamination and acidification potential in the Guadiamar floodplain Andalusia, Spain after the Aznacollar mining accident

NASA Astrophysics Data System (ADS)

Kemper, Thomas; Sommer, Stefan

2004-10-01

Field and airborne hyperspectral data was used to map residual contamination after a mining accident, by applying spectral mixture modelling. Test case was the Aznalcollar Mine (Southern Spain) accident, where heavy metal bearing sludge from a tailings pond was distributed over large areas of the Guadiamar flood plain. Although the sludge and the contaminated topsoils have been removed mechanically in the whole affected area, still high abundance of pyritic material remained on the ground. During dedicated field campaigns in two subsequent years soil samples were collected for geochemical and spectral laboratory analysis and spectral field measurements were carried out in parallel to data acquisition with the HyMap sensor. A Variable Multiple Endmember Spectral Mixture Analysis (VMESMA) tool was used providing possibilities of multiple endmember unmixing, aiming to estimate the quantities and distribution of the remaining tailings material. A spectrally based zonal partition of the area was introduced to allow the application of different submodels to the selected areas. Based on an iterative feedback process, the unmixing performance could be improved in each stage until an optimum level was reached. The sludge abundances obtained by unmixing the hyperspectral spectral data were confirmed by the field observations and chemical measurements of samples taken in the area. The semi-quantitative sludge abundances of residual pyritic material could be transformed into quantitative information for an assessment of acidification risk and distribution of residual heavy metal contamination based on an artificial mixture experiment. The unmixing of the second year images allowed identification of secondary minerals of pyrite as indicators of pyrite oxidation and associated acidification.

Estimation of white matter fiber parameters from compressed multiresolution diffusion MRI using sparse Bayesian learning.

PubMed

Pisharady, Pramod Kumar; Sotiropoulos, Stamatios N; Duarte-Carvajalino, Julio M; Sapiro, Guillermo; Lenglet, Christophe

2018-02-15

We present a sparse Bayesian unmixing algorithm BusineX: Bayesian Unmixing for Sparse Inference-based Estimation of Fiber Crossings (X), for estimation of white matter fiber parameters from compressed (under-sampled) diffusion MRI (dMRI) data. BusineX combines compressive sensing with linear unmixing and introduces sparsity to the previously proposed multiresolution data fusion algorithm RubiX, resulting in a method for improved reconstruction, especially from data with lower number of diffusion gradients. We formulate the estimation of fiber parameters as a sparse signal recovery problem and propose a linear unmixing framework with sparse Bayesian learning for the recovery of sparse signals, the fiber orientations and volume fractions. The data is modeled using a parametric spherical deconvolution approach and represented using a dictionary created with the exponential decay components along different possible diffusion directions. Volume fractions of fibers along these directions define the dictionary weights. The proposed sparse inference, which is based on the dictionary representation, considers the sparsity of fiber populations and exploits the spatial redundancy in data representation, thereby facilitating inference from under-sampled q-space. The algorithm improves parameter estimation from dMRI through data-dependent local learning of hyperparameters, at each voxel and for each possible fiber orientation, that moderate the strength of priors governing the parameter variances. Experimental results on synthetic and in-vivo data show improved accuracy with a lower uncertainty in fiber parameter estimates. BusineX resolves a higher number of second and third fiber crossings. For under-sampled data, the algorithm is also shown to produce more reliable estimates. Copyright © 2017 Elsevier Inc. All rights reserved.

A novel edge-preserving nonnegative matrix factorization method for spectral unmixing

NASA Astrophysics Data System (ADS)

Bao, Wenxing; Ma, Ruishi

2015-12-01

Spectral unmixing technique is one of the key techniques to identify and classify the material in the hyperspectral image processing. A novel robust spectral unmixing method based on nonnegative matrix factorization(NMF) is presented in this paper. This paper used an edge-preserving function as hypersurface cost function to minimize the nonnegative matrix factorization. To minimize the hypersurface cost function, we constructed the updating functions for signature matrix of end-members and abundance fraction respectively. The two functions are updated alternatively. For evaluation purpose, synthetic data and real data have been used in this paper. Synthetic data is used based on end-members from USGS digital spectral library. AVIRIS Cuprite dataset have been used as real data. The spectral angle distance (SAD) and abundance angle distance(AAD) have been used in this research for assessment the performance of proposed method. The experimental results show that this method can obtain more ideal results and good accuracy for spectral unmixing than present methods.

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach.

PubMed

Arrieta, Jorge; Cartwright, Julyan H E; Gouillart, Emmanuelle; Piro, Nicolas; Piro, Oreste; Tuval, Idan

2015-01-01

Mixing fluid in a container at low Reynolds number--in an inertialess environment--is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the "belly phase," peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing.

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach

PubMed Central

Arrieta, Jorge; Cartwright, Julyan H. E.; Gouillart, Emmanuelle; Piro, Nicolas; Piro, Oreste; Tuval, Idan

2015-01-01

Mixing fluid in a container at low Reynolds number— in an inertialess environment—is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the “belly phase,” peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing. PMID:26154384

Linear unmixing of multidate hyperspectral imagery for crop yield estimation

USDA-ARS?s Scientific Manuscript database

In this paper, we have evaluated an unsupervised unmixing approach, vertex component analysis (VCA), for the application of crop yield estimation. The results show that abundance maps of the vegetation extracted by the approach are strongly correlated to the yield data (the correlation coefficients ...

A fast fully constrained geometric unmixing of hyperspectral images

NASA Astrophysics Data System (ADS)

Zhou, Xin; Li, Xiao-run; Cui, Jian-tao; Zhao, Liao-ying; Zheng, Jun-peng

2014-11-01

A great challenge in hyperspectral image analysis is decomposing a mixed pixel into a collection of endmembers and their corresponding abundance fractions. This paper presents an improved implementation of Barycentric Coordinate approach to unmix hyperspectral images, integrating with the Most-Negative Remove Projection method to meet the abundance sum-to-one constraint (ASC) and abundance non-negativity constraint (ANC). The original barycentric coordinate approach interprets the endmember unmixing problem as a simplex volume ratio problem, which is solved by calculate the determinants of two augmented matrix. One consists of all the members and the other consist of the to-be-unmixed pixel and all the endmembers except for the one corresponding to the specific abundance that is to be estimated. In this paper, we first modified the algorithm of Barycentric Coordinate approach by bringing in the Matrix Determinant Lemma to simplify the unmixing process, which makes the calculation only contains linear matrix and vector operations. So, the matrix determinant calculation of every pixel, as the original algorithm did, is avoided. By the end of this step, the estimated abundance meet the ASC constraint. Then, the Most-Negative Remove Projection method is used to make the abundance fractions meet the full constraints. This algorithm is demonstrated both on synthetic and real images. The resulting algorithm yields the abundance maps that are similar to those obtained by FCLS, while the runtime is outperformed as its computational simplicity.

Unmixing Magnetic Hysteresis Loops

NASA Astrophysics Data System (ADS)

Heslop, D.; Roberts, A. P.

2012-04-01

Magnetic hysteresis loops provide important information in rock and environmental magnetic studies. Natural samples often contain an assemblage of magnetic particles composed of components with different origins. Each component potentially carries important environmental information. Hysteresis loops, however, provide information concerning the bulk magnetic assemblage, which makes it difficult to isolate the specific contributions from different sources. For complex mineral assemblages an unmixing strategy with which to separate hysteresis loops into their component parts is therefore essential. Previous methods to unmix hysteresis data have aimed at separating individual loops into their constituent parts using libraries of type-curves thought to correspond to specific mineral types. We demonstrate an alternative approach, which rather than decomposing a single loop into monomineralic contributions, examines a collection of loops to determine their constituent source materials. These source materials may themselves be mineral mixtures, but they provide a genetically meaningful decomposition of a magnetic assemblage in terms of the processes that controlled its formation. We show how an empirically derived hysteresis mixing space can be created, without resorting to type-curves, based on the co-variation within a collection of measured loops. Physically realistic end-members, which respect the expected behaviour and symmetries of hysteresis loops, can then be extracted from the mixing space. These end-members allow the measured loops to be described as a combination of invariant parts that are assumed to represent the different sources in the mixing model. Particular attention is paid to model selection and estimating the complexity of the mixing model, specifically, how many end-members should be included. We demonstrate application of this approach using lake sediments from Butte Valley, northern California. Our method successfully separates the hysteresis loops into sources with a variety of terrigenous and authigenic origins.

Bulk mineralogy of the NE Syrtis and Jezero crater regions of Mars derived through thermal infrared spectral analyses

NASA Astrophysics Data System (ADS)

Salvatore, M. R.; Goudge, T. A.; Bramble, M. S.; Edwards, C. S.; Bandfield, J. L.; Amador, E. S.; Mustard, J. F.; Christensen, P. R.

2018-02-01

We investigated the area to the northwest of the Isidis impact basin (hereby referred to as "NW Isidis") using thermal infrared emission datasets to characterize and quantify bulk surface mineralogy throughout this region. This area is home to Jezero crater and the watershed associated with its two deltaic deposits in addition to NE Syrtis and the strong and diverse visible/near-infrared spectral signatures observed in well-exposed stratigraphic sections. The spectral signatures throughout this region show a diversity of primary and secondary surface mineralogies, including olivine, pyroxene, smectite clays, sulfates, and carbonates. While previous thermal infrared investigations have sought to characterize individual mineral groups within this region, none have systematically assessed bulk surface mineralogy and related these observations to visible/near-infrared studies. We utilize an iterative spectral unmixing method to statistically evaluate our linear thermal infrared spectral unmixing models to derive surface mineralogy. All relevant primary and secondary phases identified in visible/near-infrared studies are included in the unmixing models and their modeled spectral contributions are discussed in detail. While the stratigraphy and compositional diversity observed in visible/near-infrared spectra are much better exposed and more diverse than most other regions of Mars, our thermal infrared analyses suggest the dominance of basaltic compositions with less observed variability in the amount and diversity of alteration phases. These results help to constrain the mineralogical context of these previously reported visible/near-infrared spectral identifications. The results are also discussed in the context of future in situ investigations, as the NW Isidis region has long been promoted as a region of paleoenvironmental interest on Mars.

Applying spectral unmixing and support vector machine to airborne hyperspectral imagery for detecting giant reed

USDA-ARS?s Scientific Manuscript database

This study evaluated linear spectral unmixing (LSU), mixture tuned matched filtering (MTMF) and support vector machine (SVM) techniques for detecting and mapping giant reed (Arundo donax L.), an invasive weed that presents a severe threat to agroecosystems and riparian areas throughout the southern ...

Retrieving the hydrous minerals on Mars by sparse unmixing and the Hapke model using MRO/CRISM data

NASA Astrophysics Data System (ADS)

Lin, Honglei; Zhang, Xia

2017-05-01

The hydrous minerals on Mars preserve records of potential past aqueous activity. Quantitative information regarding mineralogical composition would enable a better understanding of the formation processes of these hydrous minerals, and provide unique insights into ancient habitable environments and the geological evolution of Mars. The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) has the advantage of both a high spatial and spectral resolution, which makes it suitable for the quantitative analysis of minerals on Mars. However, few studies have attempted to quantitatively retrieve the mineralogical composition of hydrous minerals on Mars using visible-infrared (VISIR) hyperspectral data due to their distribution characteristics (relatively low concentrations, located primarily in Noachian terrain, and unclear or unknown background minerals) and limitations of the spectral unmixing algorithms. In this study, we developed a modified sparse unmixing (MSU) method, combining the Hapke model with sparse unmixing. The MSU method considers the nonlinear mixed effects of minerals and avoids the difficulty of determining the spectra and number of endmembers from the image. The proposed method was tested successfully using laboratory mixture spectra and an Airborne Visible Infrared Imaging Spectrometer (AVIRIS) image of the Cuprite site (Nevada, USA). Then it was applied to CRISM hyperspectral images over Gale crater. Areas of hydrous mineral distribution were first identified by spectral features of water and hydroxyl absorption. The MSU method was performed on these areas, and the abundances were retrieved. The results indicated that the hydrous minerals consisted mostly of hydrous silicates, with abundances of up to 35%, as well as hydrous sulfates, with abundances ≤10%. Several main subclasses of hydrous minerals (e.g., Fe/Mg phyllosilicate, prehnite, and kieserite) were retrieved. Among these, Fe/Mg- phyllosilicate was the most abundant, with abundances ranging up to almost 30%, followed by prehnite and kieserite, with abundances lower than 15%. Our results are consistent with related research and in situ analyses of data from the rover Curiosity; thus, our method has the potential to be widely used for quantitative mineralogical mapping at the global scale of the surface of Mars.

Extracting Vegetation Coverage in Dry-hot Valley Regions Based on Alternating Angle Minimum Algorithm

NASA Astrophysics Data System (ADS)

Y Yang, M.; Wang, J.; Zhang, Q.

2017-07-01

Vegetation coverage is one of the most important indicators for ecological environment change, and is also an effective index for the assessment of land degradation and desertification. The dry-hot valley regions have sparse surface vegetation, and the spectral information about the vegetation in such regions usually has a weak representation in remote sensing, so there are considerable limitations for applying the commonly-used vegetation index method to calculate the vegetation coverage in the dry-hot valley regions. Therefore, in this paper, Alternating Angle Minimum (AAM) algorithm of deterministic model is adopted for selective endmember for pixel unmixing of MODIS image in order to extract the vegetation coverage, and accuracy test is carried out by the use of the Landsat TM image over the same period. As shown by the results, in the dry-hot valley regions with sparse vegetation, AAM model has a high unmixing accuracy, and the extracted vegetation coverage is close to the actual situation, so it is promising to apply the AAM model to the extraction of vegetation coverage in the dry-hot valley regions.

Encoding Strategy Changes and Spacing Effects in the Free Recall of Unmixed Lists

ERIC Educational Resources Information Center

Delaney, P.F.; Knowles, M.E.

2005-01-01

Memory for repeated items often improves when repetitions are separated by other items-a phenomenon called the spacing effect. In two experiments, we explored the complex interaction between study strategies, serial position, and spacing effects. When people studied several unmixed lists, they initially used mainly rote rehearsal, but some people…

Continental Spatio-Temporal Data Analysis with Linear Spectral Mixture Model Using FOSS

NASA Technical Reports Server (NTRS)

Kumar, Uttam; Nemani, Ramakrishna; Ganguly, Sangram; Milesi, Cristina; Raja, Kumar; Wang, Weile; Votava, Petr; Michaelis, Andrew

2015-01-01

This work demonstrates the development and implementation of a Fully Constrained Least Squares (FCLS) unmixing model developed in C++ programming language with OpenCV package and boost C++ libraries in the NASA Earth Exchange (NEX). Visualization of the results is supported by GRASS GIS and statistical analysis is carried in R in a Linux system environment. FCLS was first tested on computer simulated data with Gaussian noise of various signal-to-noise ratio, and Landsat data of an agricultural scenario and an urban environment using a set of global end members of substrate (soils, sediments, rocks, and non-photosynthetic vegetation), vegetation that includes green photosynthetic plants and dark objects which encompasses absorptive substrate materials, clear water, deep shadows, etc. For the agricultural scenario, a spectrally diverse collection of 11 scenes of Level 1 terrain corrected, cloud free Landsat-5 TM data of Fresno, California, USA were unmixed and the results were validated with the corresponding ground data. To study an urbanized landscape, a clear sky Landsat-5 TM data were unmixed and validated with coincident World View-2 abundance maps (of 2 m spatial resolution) for an area of San Francisco, California, USA. The results were evaluated using descriptive statistics, correlation coefficient, RMSE, probability of success, boxplot and bivariate distribution function. Finally, FCLS was used for sub-pixel land cover analysis of the monthly WELD (Wen-enabled Landsat data) repository from 2008 to 2011 of North America. The abundance maps in conjunction with DMSP-OLS nighttime lights data were used to extract the urban land cover features and analyze their spatial-temporal growth.

Probability of Unmixed Young Groundwater (defined using chlorofluorocarbon-11 concentrations and tritium activities) in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of unmixed young groundwater (defined using chlorofluorocarbon-11 concentrations and tritium activities) in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps were developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Continental Spatio-temporal Data Analysis with Linear Spectral Mixture Model using FOSS

NASA Astrophysics Data System (ADS)

Kumar, U.; Nemani, R. R.; Ganguly, S.; Milesi, C.; Raja, K. S.; Wang, W.; Votava, P.; Michaelis, A.

2015-12-01

This work demonstrates the development and implementation of a Fully Constrained Least Squares (FCLS) unmixing model developed in C++ programming language with OpenCV package and boost C++ libraries in the NASA Earth Exchange (NEX). Visualization of the results is supported by GRASS GIS and statistical analysis is carried in R in a Linux system environment. FCLS was first tested on computer simulated data with Gaussian noise of various signal-to-noise ratio, and Landsat data of an agricultural scenario and an urban environment using a set of global endmembers of substrate (soils, sediments, rocks, and non-photosynthetic vegetation), vegetation that includes green photosynthetic plants and dark objects which encompasses absorptive substrate materials, clear water, deep shadows, etc. For the agricultural scenario, a spectrally diverse collection of 11 scenes of Level 1 terrain corrected, cloud free Landsat-5 TM data of Fresno, California, USA were unmixed and the results were validated with the corresponding ground data. To study an urbanized landscape, a clear sky Landsat-5 TM data were unmixed and validated with coincident World View-2 abundance maps (of 2 m spatial resolution) for an area of San Francisco, California, USA. The results were evaluated using descriptive statistics, correlation coefficient, RMSE, probability of success, boxplot and bivariate distribution function. Finally, FCLS was used for sub-pixel land cover analysis of the monthly WELD (Wen-enabled Landsat data) repository from 2008 to 2011 of North America. The abundance maps in conjunction with DMSP-OLS nighttime lights data were used to extract the urban land cover features and analyze their spatial-temporal growth.

Multiphoton spectral analysis of benzo[a]pyrene uptake and metabolism in a rat liver cell line

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

Barhoumi, Rola, E-mail: rmouneimne@cvm.tamu.edu; Mouneimne, Youssef; Ramos, Ernesto

2011-05-15

Dynamic analysis of the uptake and metabolism of polycyclic aromatic hydrocarbons (PAHs) and their metabolites within live cells in real time has the potential to provide novel insights into genotoxic and non-genotoxic mechanisms of cellular injury caused by PAHs. The present work, combining the use of metabolite spectra generated from metabolite standards using multiphoton spectral analysis and an 'advanced unmixing process', identifies and quantifies the uptake, partitioning, and metabolite formation of one of the most important PAHs (benzo[a]pyrene, BaP) in viable cultured rat liver cells over a period of 24 h. The application of the advanced unmixing process resulted inmore » the simultaneous identification of 8 metabolites in live cells at any single time. The accuracy of this unmixing process was verified using specific microsomal epoxide hydrolase inhibitors, glucuronidation and sulfation inhibitors as well as several mixtures of metabolite standards. Our findings prove that the two-photon microscopy imaging surpasses the conventional fluorescence imaging techniques and the unmixing process is a mathematical technique that seems applicable to the analysis of BaP metabolites in living cells especially for analysis of changes of the ultimate carcinogen benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide. Therefore, the combination of the two-photon acquisition with the unmixing process should provide important insights into the cellular and molecular mechanisms by which BaP and other PAHs alter cellular homeostasis.« less

On the Use of FOSS4G in Land Cover Fraction Estimation with Unmixing Algorithms

NASA Astrophysics Data System (ADS)

Kumar, U.; Milesi, C.; Raja, K.; Ganguly, S.; Wang, W.; Zhang, G.; Nemani, R. R.

2014-12-01

The popularity and usage of FOSS4G (FOSS for Geoinformatics) has increased drastically in the last two decades with increasing benefits that facilitate spatial data analysis, image processing, graphics and map production, spatial modeling and visualization. The objective of this paper is to use FOSS4G to implement and perform a quantitative analysis of three different unmixing algorithms: Constraint Least-Square (CLS), Unconstraint Least-Square, and Orthogonal Subspace Projection to estimate land cover (LC) fraction estimates from RS data. The LC fractions obtained by unmixing of mixed pixels represent mixture of more than one class per pixel rendering more accurate LC abundance estimates. The algorithms were implemented in C++ programming language with OpenCV package (http://opencv.org/) and boost C++ libraries (www.boost.org) in the NASA Earth Exchange at the NASA Advanced Supercomputing Facility. GRASS GIS was used for visualization of results and statistical analysis was carried in R in a Linux system environment. A set of global endmembers for substrate, vegetation and dark objects were used to unmix the data using the three algorithms and were compared with Singular Value decomposition unmixed outputs available in ENVI image processing software. First, computer simulated data of different signal to noise ratio were used to evaluate the algorithms. The second set of experiments was carried out in an agricultural set-up with a spectrally diverse collection of 11 Landsat-5 scenes (acquired in 2008) for an agricultural setup in Frenso, California and the ground data were collected on those specific dates when the satellite passed through the site. Finally, in the third set of experiments, a pair of coincident clear sky Landsat and World View 2 data for an urbanized area of San Francisco were used to assess the algorithm. Validation of the results using descriptive statistics, correlation coefficient (cc), RMSE, boxplot and bivariate distribution function indicated that with the computer simulated data, CLS was better than other techniques. With the real world data of an agricultural landscape, CLS was superior to other techniques with a mean absolute error for all four methods close to 7.3%. For the urban setup, CLS demonstrated highest average cc of 0.64 and lowest average RMSE of 0.19 for all the endmembers.

Quantitative detection of settled dust over green canopy

NASA Astrophysics Data System (ADS)

Brook, Anna

2016-04-01

The main task of environmental and geoscience applications are efficient and accurate quantitative classification of earth surfaces and spatial phenomena. In the past decade, there has been a significant interest in employing hyperspectral unmixing in order to retrieve accurate quantitative information latent in hyperspectral imagery data. Recently, the ground-truth and laboratory measured spectral signatures promoted by advanced algorithms are proposed as a new path toward solving the unmixing problem of hyperspectral imagery in semi-supervised fashion. This paper suggests that the sensitivity of sparse unmixing techniques provides an ideal approach to extract and identify dust settled over/upon green vegetation canopy using hyperspectral airborne data. Atmospheric dust transports a variety of chemicals, some of which pose a risk to the ecosystem and human health (Kaskaoutis, et al., 2008). Many studies deal with the impact of dust on particulate matter (PM) and atmospheric pollution. Considering the potential impact of industrial pollutants, one of the most important considerations is the fact that suspended PM can have both a physical and a chemical impact on plants, soils, and water bodies. Not only can the particles covering surfaces cause physical distortion, but particles of diverse origin and different chemistries can also serve as chemical stressors and cause irreversible damage. Sediment dust load in an indoor environment can be spectrally assessed using reflectance spectroscopy (Chudnovsky and Ben-Dor, 2009). Small amounts of particulate pollution that may carry a signature of a forthcoming environmental hazard are of key interest when considering the effects of pollution. According to the most basic distribution dynamics, dust consists of suspended particulate matter in a fine state of subdivision that are raised and carried by wind. In this context, it is increasingly important to first, understand the distribution dynamics of pollutants, and subsequently develop dedicated tools and measures to control and monitor pollutants in the free environment. The earliest effect of settled polluted dust particles is not always reflected through poor conditions of vegetation or soils, or any visible damages. In most of the cases, it has a quite long accumulation process that graduates from a polluted condition to long-term environmental hazard. Although conducted experiments with pollutant analog powders under controlled conditions have tended to confirm the findings from field studies (Brook, 2014), a major criticism of all these experiments is their short duration. The resulting conclusion is that it is difficult, if not impossible, to determine the implications of long-term exposure to realistic concentrations of pollutants from such short-term studies. Hyperspectral remote sensing (HRS) has become a common tool for environmental and geoscience applications. HRS has promoted new opportunities for exploring a wide range of materials and evaluating a variety of natural processes due to its detailed, specific, and extensive information on spectral and spatial disseminations. Hyperspectral unmixing (HU) is the technique of presuming the category type, which constitutes the mix-pixel, and its mixing ratio (Keshava and Mustard, 2002). In general, the task of unmixing is to decompose the reflectance spectrum of each pixel into a set of endmembers or principal combined spectra and their corresponding abundances (Bioucas-Dias et al., 2012). This study suggests that the sensitivity of sparse unmixing techniques provides an ideal approach to extract and identify dust settled over/upon green vegetation canopy using hyperspectral airborne data. Among the available techniques, this study present results of seven linear and non-linear unmixing algorithms: 1) Non-negative Matrix Factorization (NMF), 2) L1 sparsity-constrained NMF (L1-NMF), 3) L1/2 sparsity-constrained NMF (L1/2-NMF), 4) Graph regularized NMF (G-NMF), 5) Structured Sparse NMF (SS-NMF), 6) Alternating Least-Square (ALS), and 2) Lin's Projected Gradient (LPG). The performance is evaluated on real hyperspectral imagery data via detailed experimental assessment. The study showed that in certain compression tasks content-adapted sparse representation is provided by state-of-the-art solutions. The NMF algorithm estimates endmembers that are used to remove spurious information. If computationally feasible, it should include interaction terms to make the model more flexible. The optimal NMF algorithms, such as ALS and LPG, are assumed to be the simplest methods that achieve the minimum error on the test set. In summary, this work shows that sediment dust can be assessed using airborne HSI data, making it a potentially powerful tool for environmental studies. References Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Chudnovsky, A., & Ben-Dor, E. (2009). Reflectance spectroscopy as a tool for settled dust monitoring in office environment. International Journal of Environment and Waste Management, 4(1), 32-49. Brook, A. (2014). Quantitative Detection of Settled dust over Green Canopy using Sparse Unmixing of Airborne Hyperspectral Data. IEEE-Whispers 6th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing, 2014, Switzerland, 4-8. Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Bioucas-Dias et al. (2012). Hyperspectral unmixing overview: Geometrical, statistical, and sparse regression-based approaches, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(2), 354 -379.

An Improved STARFM with Help of an Unmixing-Based Method to Generate High Spatial and Temporal Resolution Remote Sensing Data in Complex Heterogeneous Regions.

PubMed

Xie, Dengfeng; Zhang, Jinshui; Zhu, Xiufang; Pan, Yaozhong; Liu, Hongli; Yuan, Zhoumiqi; Yun, Ya

2016-02-05

Remote sensing technology plays an important role in monitoring rapid changes of the Earth's surface. However, sensors that can simultaneously provide satellite images with both high temporal and spatial resolution haven't been designed yet. This paper proposes an improved spatial and temporal adaptive reflectance fusion model (STARFM) with the help of an Unmixing-based method (USTARFM) to generate the high spatial and temporal data needed for the study of heterogeneous areas. The results showed that the USTARFM had higher accuracy than STARFM methods in two aspects of analysis: individual bands and of heterogeneity analysis. Taking the predicted NIR band as an example, the correlation coefficients (r) for the USTARFM, STARFM and unmixing methods were 0.96, 0.95, 0.90, respectively (p-value < 0.001); Root Mean Square Error (RMSE) values were 0.0245, 0.0300, 0.0401, respectively; and ERGAS values were 0.5416, 0.6507, 0.8737, respectively. The USTARM showed consistently higher performance than STARM when the degree of heterogeneity ranged from 2 to 10, highlighting that the use of this method provides the capacity to solve the data fusion problems faced when using STARFM. Additionally, the USTARFM method could help researchers achieve better performance than STARFM at a smaller window size from its heterogeneous land surface quantitative representation.

M-estimation for robust sparse unmixing of hyperspectral images

NASA Astrophysics Data System (ADS)

Toomik, Maria; Lu, Shijian; Nelson, James D. B.

2016-10-01

Hyperspectral unmixing methods often use a conventional least squares based lasso which assumes that the data follows the Gaussian distribution. The normality assumption is an approximation which is generally invalid for real imagery data. We consider a robust (non-Gaussian) approach to sparse spectral unmixing of remotely sensed imagery which reduces the sensitivity of the estimator to outliers and relaxes the linearity assumption. The method consists of several appropriate penalties. We propose to use an lp norm with 0 < p < 1 in the sparse regression problem, which induces more sparsity in the results, but makes the problem non-convex. On the other hand, the problem, though non-convex, can be solved quite straightforwardly with an extensible algorithm based on iteratively reweighted least squares. To deal with the huge size of modern spectral libraries we introduce a library reduction step, similar to the multiple signal classification (MUSIC) array processing algorithm, which not only speeds up unmixing but also yields superior results. In the hyperspectral setting we extend the traditional least squares method to the robust heavy-tailed case and propose a generalised M-lasso solution. M-estimation replaces the Gaussian likelihood with a fixed function ρ(e) that restrains outliers. The M-estimate function reduces the effect of errors with large amplitudes or even assigns the outliers zero weights. Our experimental results on real hyperspectral data show that noise with large amplitudes (outliers) often exists in the data. This ability to mitigate the influence of such outliers can therefore offer greater robustness. Qualitative hyperspectral unmixing results on real hyperspectral image data corroborate the efficacy of the proposed method.

Scalar entrainment in the mixing layer

NASA Technical Reports Server (NTRS)

Sandham, N. D.; Mungal, M. G.; Broadwell, J. E.; Reynolds, W. C.

1988-01-01

New definitions of entrainment and mixing based on the passive scalar field in the plane mixing layer are proposed. The definitions distinguish clearly between three fluid states: (1) unmixed fluid, (2) fluid engulfed in the mixing layer, trapped between two scalar contours, and (3) mixed fluid. The difference betwen (2) and (3) is the amount of fluid which has been engulfed during the pairing process, but has not yet mixed. Trends are identified from direct numerical simulations and extensions to high Reynolds number mixing layers are made in terms of the Broadwell-Breidenthal mixing model. In the limit of high Peclet number (Pe = ReSc) it is speculated that engulfed fluid rises in steps associated with pairings, introducing unmixed fluid into the large scale structures, where it is eventually mixed at the Kolmogorov scale. From this viewpoint, pairing is a prerequisite for mixing in the turbulent plane mixing layer.

Unmixing the SNCs: Chemical, Isotopic, and Petrologic Components of the Martian Meteorites

NASA Technical Reports Server (NTRS)

2002-01-01

This volume contains abstracts that have been accepted for presentation at the conference on Unmixing the SNCs: Chemical, Isotopic, and Petrologic Components of Martian Meteorites, September 11-12, 2002, in Houston, Texas. Administration and publications support for this meeting were provided by the staff of the Publications and Program Services Department at the Lunar and Planetary Institute.

A Gaussian Mixture Model Representation of Endmember Variability in Hyperspectral Unmixing

NASA Astrophysics Data System (ADS)

Zhou, Yuan; Rangarajan, Anand; Gader, Paul D.

2018-05-01

Hyperspectral unmixing while considering endmember variability is usually performed by the normal compositional model (NCM), where the endmembers for each pixel are assumed to be sampled from unimodal Gaussian distributions. However, in real applications, the distribution of a material is often not Gaussian. In this paper, we use Gaussian mixture models (GMM) to represent the endmember variability. We show, given the GMM starting premise, that the distribution of the mixed pixel (under the linear mixing model) is also a GMM (and this is shown from two perspectives). The first perspective originates from the random variable transformation and gives a conditional density function of the pixels given the abundances and GMM parameters. With proper smoothness and sparsity prior constraints on the abundances, the conditional density function leads to a standard maximum a posteriori (MAP) problem which can be solved using generalized expectation maximization. The second perspective originates from marginalizing over the endmembers in the GMM, which provides us with a foundation to solve for the endmembers at each pixel. Hence, our model can not only estimate the abundances and distribution parameters, but also the distinct endmember set for each pixel. We tested the proposed GMM on several synthetic and real datasets, and showed its potential by comparing it to current popular methods.

Spectral unmixing of hyperspectral data to map bauxite deposits

NASA Astrophysics Data System (ADS)

Shanmugam, Sanjeevi; Abhishekh, P. V.

2006-12-01

This paper presents a study about the potential of remote sensing in bauxite exploration in the Kolli hills of Tamilnadu state, southern India. ASTER image (acquired in the VNIR and SWIR regions) has been used in conjunction with SRTM - DEM in this study. A new approach of spectral unmixing of ASTER image data delineated areas rich in alumina. Various geological and geomorphological parameters that control bauxite formation were also derived from the ASTER image. All these information, when integrated, showed that there are 16 cappings (including the existing mines) that satisfy most of the conditions favouring bauxitization in the Kolli Hills. The study concludes that spectral unmixing of hyperspectral satellite data in the VNIR and SWIR regions may be combined with the terrain parameters to get accurate information about bauxite deposits, including their quality.

Investigation on Constrained Matrix Factorization for Hyperspectral Image Analysis

DTIC Science & Technology

2005-07-25

analysis. Keywords: matrix factorization; nonnegative matrix factorization; linear mixture model ; unsupervised linear unmixing; hyperspectral imagery...spatial resolution permits different materials present in the area covered by a single pixel. The linear mixture model says that a pixel reflectance in...in r. In the linear mixture model , r is considered as the linear mixture of m1, m2, …, mP as nMαr += (1) where n is included to account for

Origins of fine aerosol mass in the Baltimore-Washington corridor: implications from observation, factor analysis, and ensemble air parcel back trajectories

NASA Astrophysics Data System (ADS)

Antony Chen, L.-W.; Doddridge, Bruce G.; Dickerson, Russell R.; Chow, Judith C.; Henry, Ronald C.

Chemically speciated fine particulate matter (PM 2.5) and trace gases (including NH 3, HNO 3, CO, SO 2, NO y) have been sampled at Fort Meade (FME: 39.10°N, 76.74°W; elevation 46 m MSL), Maryland, since July 1999. FME is suburban, located in the middle of the Baltimore-Washington corridor, and generally downwind of the highly industrialized Midwest. The PM 2.5 at FME is expected to be of both local and regional sources. Measurements over a 2-year period include eight seasonally representative months. The PM 2.5 shows an annual mean of 13 μg m -3 and primarily consists of sulfate, nitrate, ammonium, and carbonaceous material. Day-to-day and seasonal variations in the PM 2.5 chemical composition reflect changes of contribution from various sources. UNMIX, an innovative receptor model, is used to retrieve potential sources of the PM 2.5. A six-factor model, including regional sulfate, local sulfate, wood smoke, copper/iron processing industry, mobile, and secondary nitrate, is constructed and compared with reported source emission profiles. The six factors are studied further using an ensemble back trajectory method to identify possible source locations. Sources of local sulfate, mobile, and secondary nitrate are more localized around the receptor than those of other factors. Regional sulfate and wood smoke are more regional and associated with westerly and southerly transport, respectively. This study suggests that the local contribution to PM 2.5 mass can vary from <30% in summer to >60% in winter.

Application of a combined approach including contamination indexes, geographic information system and multivariate statistical models in levels, distribution and sources study of metals in soils in Northern China

PubMed Central

Huang, Kuixian; Luo, Xingzhang

2018-01-01

The purpose of this study is to recognize the contamination characteristics of trace metals in soils and apportion their potential sources in Northern China to provide a scientific basis for basic of soil environment management and pollution control. The data set of metals for 12 elements in surface soil samples was collected. The enrichment factor and geoaccumulation index were used to identify the general geochemical characteristics of trace metals in soils. The UNMIX and positive matrix factorizations (PMF) models were comparatively applied to apportion their potential sources. Furthermore, geostatistical tools were used to study the spatial distribution of pollution characteristics and to identify the affected regions of sources that were derived from apportionment models. The soils were contaminated by Cd, Hg, Pb and Zn to varying degree. Industrial activities, agricultural activities and natural sources were identified as the potential sources determining the contents of trace metals in soils with contributions of 24.8%–24.9%, 33.3%–37.2% and 38.0%–41.8%, respectively. The slightly different results obtained from UNMIX and PMF might be caused by the estimations of uncertainty and different algorithms within the models. PMID:29474412

The impact of initialization procedures on unsupervised unmixing of hyperspectral imagery using the constrained positive matrix factorization

NASA Astrophysics Data System (ADS)

Masalmah, Yahya M.; Vélez-Reyes, Miguel

2007-04-01

The authors proposed in previous papers the use of the constrained Positive Matrix Factorization (cPMF) to perform unsupervised unmixing of hyperspectral imagery. Two iterative algorithms were proposed to compute the cPMF based on the Gauss-Seidel and penalty approaches to solve optimization problems. Results presented in previous papers have shown the potential of the proposed method to perform unsupervised unmixing in HYPERION and AVIRIS imagery. The performance of iterative methods is highly dependent on the initialization scheme. Good initialization schemes can improve convergence speed, whether or not a global minimum is found, and whether or not spectra with physical relevance are retrieved as endmembers. In this paper, different initializations using random selection, longest norm pixels, and standard endmembers selection routines are studied and compared using simulated and real data.

Snow depth and snow cover retrieval from FengYun3B microwave radiation imagery based on a snow passive microwave unmixing method in Northeast China

NASA Astrophysics Data System (ADS)

Gu, Lingjia; Ren, Ruizhi; Zhao, Kai; Li, Xiaofeng

2014-01-01

The precision of snow parameter retrieval is unsatisfactory for current practical demands. The primary reason is because of the problem of mixed pixels that are caused by low spatial resolution of satellite passive microwave data. A snow passive microwave unmixing method is proposed in this paper, based on land cover type data and the antenna gain function of passive microwaves. The land cover type of Northeast China is partitioned into grass, farmland, bare soil, forest, and water body types. The component brightness temperatures (CBT), namely unmixed data, with 1 km data resolution are obtained using the proposed unmixing method. The snow depth determined by the CBT and three snow depth retrieval algorithms are validated through field measurements taken in forest and farmland areas of Northeast China in January 2012 and 2013. The results show that the overall of the retrieval precision of the snow depth is improved by 17% in farmland areas and 10% in forest areas when using the CBT in comparison with the mixed pixels. The snow cover results based on the CBT are compared with existing MODIS snow cover products. The results demonstrate that more snow cover information can be obtained with up to 86% accuracy.

Multi-tissue partial volume quantification in multi-contrast MRI using an optimised spectral unmixing approach.

PubMed

Collewet, Guylaine; Moussaoui, Saïd; Deligny, Cécile; Lucas, Tiphaine; Idier, Jérôme

2018-06-01

Multi-tissue partial volume estimation in MRI images is investigated with a viewpoint related to spectral unmixing as used in hyperspectral imaging. The main contribution of this paper is twofold. It firstly proposes a theoretical analysis of the statistical optimality conditions of the proportion estimation problem, which in the context of multi-contrast MRI data acquisition allows to appropriately set the imaging sequence parameters. Secondly, an efficient proportion quantification algorithm based on the minimisation of a penalised least-square criterion incorporating a regularity constraint on the spatial distribution of the proportions is proposed. Furthermore, the resulting developments are discussed using empirical simulations. The practical usefulness of the spectral unmixing approach for partial volume quantification in MRI is illustrated through an application to food analysis on the proving of a Danish pastry. Copyright © 2018 Elsevier Inc. All rights reserved.

Resolving fluorophores by unmixing multispectral fluorescence tomography with independent component analysis

NASA Astrophysics Data System (ADS)

Pu, Huangsheng; Zhang, Guanglei; He, Wei; Liu, Fei; Guang, Huizhi; Zhang, Yue; Bai, Jing; Luo, Jianwen

2014-09-01

It is a challenging problem to resolve and identify drug (or non-specific fluorophore) distribution throughout the whole body of small animals in vivo. In this article, an algorithm of unmixing multispectral fluorescence tomography (MFT) images based on independent component analysis (ICA) is proposed to solve this problem. ICA is used to unmix the data matrix assembled by the reconstruction results from MFT. Then the independent components (ICs) that represent spatial structures and the corresponding spectrum courses (SCs) which are associated with spectral variations can be obtained. By combining the ICs with SCs, the recovered MFT images can be generated and fluorophore concentration can be calculated. Simulation studies, phantom experiments and animal experiments with different concentration contrasts and spectrum combinations are performed to test the performance of the proposed algorithm. Results demonstrate that the proposed algorithm can not only provide the spatial information of fluorophores, but also recover the actual reconstruction of MFT images.

Quantitative detection of settled coal dust over green canopy

NASA Astrophysics Data System (ADS)

Brook, Anna; Sahar, Nir

2017-04-01

The main task of environmental and geoscience applications are efficient and accurate quantitative classification of earth surfaces and spatial phenomena. In the past decade, there has been a significant interest in employing spectral unmixing in order to retrieve accurate quantitative information latent in in situ data. Recently, the ground-truth and laboratory measured spectral signatures promoted by advanced algorithms are proposed as a new path toward solving the unmixing problem in semi-supervised fashion. This study presents a practical implementation of field spectroscopy as a quantitative tool to detect settled coal dust over green canopy in free/open environment. Coal dust is a fine powdered form of coal, which is created by the crushing, grinding, and pulverizing of coal. Since the inelastic nature of coal, coal dust can be created during transportation, or by mechanically handling coal. Coal dust, categorized at silt-clay particle size, of particular concern due to heavy metals (lead, mercury, nickel, tin, cadmium, mercury, antimony, arsenic, isotopes of thorium and strontium) which are toxic also at low concentrations. This hazard exposes risk on both environment and public health. It has been identified by medical scientist around the world as causing a range of diseases and health problems, mainly heart and respiratory diseases like asthma and lung cancer. It is due to the fact that the fine invisible coal dust particles (less than 2.5 microns) long lodge in the lungs and are not naturally expelled, so long-term exposure increases the risk of health problems. Numerus studies reported that data to conduct study of geographic distribution of the very fine coal dust (smaller than PM 2.5) and related health impacts from coal exports, is not being collected. Sediment dust load in an indoor environment can be spectrally assessed using reflectance spectroscopy (Chudnovsky and Ben-Dor, 2009). Small amounts of particulate pollution that may carry a signature of a forthcoming environmental hazard are of key interest when considering the effects of pollution. According to the most basic distribution dynamics, dust consists of suspended particulate matter in a fine state of subdivision that are raised and carried by wind. In this context, it is increasingly important to first, understand the distribution dynamics of pollutants, and subsequently develop dedicated tools and measures to control and monitor pollutants in the free environment. The earliest effect of settled polluted dust particles is not always reflected through poor conditions of vegetation or soils, or any visible damages. In most of the cases, it has a quite long accumulation process that graduates from a polluted condition to long-term environmental and health related hazard. Although conducted experiments with pollutant analog powders under controlled conditions have tended to con- firm the findings from field studies (Brook, 2014; Brook and Ben-Dor 2016; Brook, 2016), a major criticism of all these experiments is their short duration. The resulting conclusion is that it is difficult, if not impossible, to determine the implications of long-term exposure to realistic concentrations of pollutants from such short-term studies. In general, the task of unmixing is to decompose the reflectance spectrum into a set of endmembers or principal combined spectra and their corresponding abundances (Bioucas-Dias et al., 2012). This study suggests that the sensitivity of sparse unmixing techniques provides an ideal approach to extract and identify coal dust settled over/upon green vegetation canopy using in situ spectral data collected by portable spectrometer. The optimal NMF algorithms, such as ALS and LPG, are assumed to be the simplest methods that achieve the minimum error. The suggested practical approach includes the following stages: 1. In situ spectral measurements, 2. Near-real-time spectral data analysis, 3. Estimated concentration of coal dust reported as mg/sq m. The stage 2 is completed by calculating: 1. Unmixing between the green canopy and the settle dust extraction only coal dust fraction, 2. Converting spectral feature of coal dust to concentration via PLSR spectral model. The spectral model was trained and validated PLSR model developed at laboratory using spectra across MIR (FTIR reflectance spectra) and NIR regions and XRD analysis. The obtained RMSE was satisfying for both spectral regions. Thus, it was concluded that field spectroscopy can be used for this purpose, and it can provide fully quantitative measures of settle coal dust. Nowadays this approach (both spectrometer and algorithm) has been accepted as a practical operational tool for environmental monitoring near power station Orot Rabin in Hadera and will be used by the Sharon-Carmel Districts Municipal Association for Environmental Protection, Israel as a regulatory tool. In summary, this work shows that coal dust can be assessed using in situ spectroscopy, making it a potentially powerful tool for environmental studies. References Chudnovsky, A., & Ben-Dor, E. (2009). Reflectance spectroscopy as a tool for settled dust monitoring in office environment. International Journal of Environment and Waste Management, 4(1), 32-49. Brook, A. (2014). Quantitative Detection of Settled dust over Green Canopy using Sparse Unmixing of Airborne Hyperspectral Data. IEEE-Whispers 6th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing, 2014, Switzerland, 4-8. Brook, A. and Ben-Dor, E. (2016). Quantitative detection of settled dust over Green Canopy using sparse unmixing of airborne hyperspectral data. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 9(2), pp.884-897. Brook, A. (2016). Quantitative Detection and Long-Term Monitoring of Settle Dust Using Semisupervised Learning for Spectral Data. Water, Air, & Soil Pollution, 227(3), pp.1-9. Bioucas-Dias, J.M., Plaza, A., Dobigeon, N., Parente, M., Du, Q., Gader, P. and Chanussot, J. (2012). Hyperspectral unmixing overview: Geometrical, statistical, and sparse regression-based approaches. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(2), pp.354-379. Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Bioucas-Dias et al. (2012). Hyperspectral unmixing overview: Geometrical, statistical, and sparse regression-based approaches, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(2), 354 -379.

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe

PubMed Central

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R.; Niu, Gang; Chen, Xiaoyuan

2012-01-01

Purpose: The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/64Cu dual-labeled cyclic RGD peptide. Methods: The integrin αvβ3 binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. Results: The dual-labeled probe 64Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). Conclusion: The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models. PMID:22916074

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe.

PubMed

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R; Niu, Gang; Chen, Xiaoyuan

2012-01-01

The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/(64)Cu dual-labeled cyclic RGD peptide. The integrin α(v)β(3) binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. The dual-labeled probe (64)Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models.

Long-term retention as a function of word concreteness under conditions of free recall.

PubMed

Postman, L; Burns, S

1974-07-01

Acquisition and long-term retention of concrete (C) and abstract (A) words were investigated under conditions of multiple-trial free recall. Both unmixed and mixed lists were used in original learning. Retention was tested either 1 rain or 1 week after attainment of the learning criterion. Acquisition was faster and retention was higher for C than for A words. These differences were more pronounced for mixed than for unmixed lists.

Correlation between prescription of various dextropropoxyphene preparations and their involvement in fatal poisonings.

PubMed

Jonasson, U; Jonasson, B; Saldeen, T

1999-07-26

In Sweden, the frequency of fatal poisoning by dextropropoxyphene (DXP) ingestion is constantly high. There are seven preparations containing DXP on the Swedish market; in three of them DXP is the sole analgesic ingredient, while four of them are combinations of analgesics. In an attempt to assess the death rate attributable to each DXP preparation on the basis of toxicological analyses, altogether 834 cases of dextropropoxyphene-related death over a 5-year period (1992-1996) in Sweden have been reviewed. The ratio between number of fatal poisonings and prescription of defined daily dose/1000 inhabitants during a 12-month period (DDD) was determined. The highest ratio, 27, was attributed to unmixed preparations. The ratio for DXP + paracetamol-related deaths was 6.3, and for DXP + phenazone, 6.4, while the lowest ratio, 2, was found among the DXP + chlorzoxazone cases. The unmixed preparations, representing 26% of all DXP prescriptions during the study years, were implicated in 62% of the DXP fatalities, a considerable over-representation. Unmixed preparations, with their higher content of DXP, may be more attractive for many consumers because of their narcotic (euphoric) effects rather than for any analgetic superiority. Another possibility is that unmixed preparations may erroneously have been regarded as safer than when combined with paracetamol, as reports of poisoning with compounds containing DXP + paracetamol have been most frequently reported, probably due to their predominance on the market.

What Stroop tasks can tell us about selective attention from childhood to adulthood.

PubMed

Wright, Barlow C

2017-08-01

A rich body of research concerns causes of Stroop effects plus applications of Stroop. However, several questions remain. We included assessment of errors with children and adults (N = 316), who sat either a task wherein each block employed only trials of one type (unmixed task) or where every block comprised of a mix of the congruent, neutral, and incongruent trials. Children responded slower than adults and made more errors on each task. Contrary to some previous studies, interference (the difference between neutral and incongruent condition) showed no reaction time (RT) differences by group or task, although there were differences in errors. By contrast, facilitation (the difference between neutral and congruent condition) was greater in children than adults, and greater on the unmixed task than the mixed task. After considering a number of theoretical accounts, we settle on the inadvertent word-reading hypothesis, whereby facilitation stems from children and the unmixed task promoting inadvertent reading particularly in the congruent condition. Stability of interference RT is explained by fixed semantic differences between neutral and incongruent conditions, for children versus adults and for unmixed versus mixed task. We conclude that utilizing two tasks together may reveal more about how attention is affected in other groups. © 2016 The Authors. British Journal of Psychology published by John Wiley & Sons Ltd on behalf of the British Psychological Society.

Comparing Different Approaches for Mapping Urban Vegetation Cover from Landsat ETM+ Data: A Case Study on Brussels

PubMed Central

Van de Voorde, Tim; Vlaeminck, Jeroen; Canters, Frank

2008-01-01

Urban growth and its related environmental problems call for sustainable urban management policies to safeguard the quality of urban environments. Vegetation plays an important part in this as it provides ecological, social, health and economic benefits to a city's inhabitants. Remotely sensed data are of great value to monitor urban green and despite the clear advantages of contemporary high resolution images, the benefits of medium resolution data should not be discarded. The objective of this research was to estimate fractional vegetation cover from a Landsat ETM+ image with sub-pixel classification, and to compare accuracies obtained with multiple stepwise regression analysis, linear spectral unmixing and multi-layer perceptrons (MLP) at the level of meaningful urban spatial entities. Despite the small, but nevertheless statistically significant differences at pixel level between the alternative approaches, the spatial pattern of vegetation cover and estimation errors is clearly distinctive at neighbourhood level. At this spatially aggregated level, a simple regression model appears to attain sufficient accuracy. For mapping at a spatially more detailed level, the MLP seems to be the most appropriate choice. Brightness normalisation only appeared to affect the linear models, especially the linear spectral unmixing. PMID:27879914

Behavior of the main sources that contribute to ambient PM2.5 in Santiago since 1998

NASA Astrophysics Data System (ADS)

Barraza, F.; Lambert, F.; Jorquera, H.; Villalobos, A. M.; Gallardo, L.

2016-12-01

Santiago's inhabitants have been exposed to high concentrations of fine particle matter (PM2.5) for decades. To contribute to a solution for this long-standing problem it is necessary to clearly identify and quantify the agents that contribute to ambient levels of PM2.5. We present an analysis of a long historical elemental concentrations database measured in air filter particles taken in central Santiago from April 1998 to August 2012 (1243 daily samples). We identify and quantify the main sources that contribute to PM2.5 levels using the source-receptor models PMF 5.0 and UNMIX 6.0. . The 6 main sources that contribute to outdoor PM2.5 levels were: vehicles (13.26±0.42 µg/m3), industrial sulfates (6.60±0.0.47 µg/m3), copper smelters (5.12±0.29 µg/m3), residential wood burning (4.38±0.36 µg/m3), marine aerosols (3.39±0.24 µg/m3), and urban dust (1.07±0.42 µg/m3). The unexplained fraction amounts to 1.76±0.90 µg/m3). The similar results obtained with both receptor models suggest a robust estimation of the main Santiago PM2.5 source apportionment. The analysis of the time series of these sources shows that their absolute contribution to PM2.5 levels has been decreasing during the last decade (except for urban dust which is increasing), and shows the effectiveness of government emission reduction policies. However, these improvements have not been sufficient to reduce PM2.5 concentrations to daily levels below the Chilean standard of 50 µg/m3, let alone the WHO standard of 25 µg/m3.

Zoning and exsolution in cumulate alkali feldspars from the eruption (12.9 Ka) of Laacher see volcano (Western Germany) as an indicator of time-scales and dynamics of carbonate-silicate unmixing

NASA Astrophysics Data System (ADS)

Sourav Rout, Smruti; Wörner, Gerhard

2017-04-01

Time-scales extracted from the detailed analysis of chemically zoned minerals provide insights into crystal ages, magma storage and compositional evolution, including mixing and unmixing events. This allows having a better understanding of pre-eruptive history of large and potentially dangerous magma chambers. We present a comprehensive study of chemical diffusion across zoning and exsolution patterns of alkali feldspars in carbonatite-bearing cognate syenites from the 6.3 km3 (D.R.E) phonolitic Laacher See Tephra (LST) eruption 12.9 ka ago. The Laacher See volcano is located in the Quaternary East Eifel volcanic field of the Paleozoic Rhenish Massif in Western Germany and has produced a compositionally variable sequence in a single eruption from a magma chamber that was zoned from mafic phonolite at the base to highly evolved, actively degassing phonolite magma at the top. Diffusion chronometry is applied to major and trace element compositions obtained on alkali feldspars from carbonate-bearing syenitic cumulates. Methods used were laser ablation inductively coupled plasma mass spectrometry (LA ICP-MS) in combination with energy-dispersive and wavelength-dispersive electron microprobe analyses (EDS & WDS-EMPA). The grey scale values extracted from multiple accumulations of back-scattered electron images represent the K/Na ratio owing to the extremely low concentrations of Ba and Sr (<30 ppm). The numerical grey scale profiles and the quantitative compositional profiles are anatomized using three different fitting models in MATLAB®, Mathematica® and Origin® to estimate related time-scales with minimized error for a temperature range of 750 deg C to 800 deg C (on the basis of existing experimental data on phase transition and phase separation). A distinctive uphill diffusive analysis is used specifically for the phase separation in the case of exsolution features (comprising of albite- and orthoclase-rich phases) in sanidines. The error values are aggregates of propagated error through calculations and the uncertainty in temperature values. Trace element compositional data of distinct feldspar compositions that are assumed to have grown before and after silicate-carbonate unmixing are used to estimate partition coefficients between carbonate and silicate melt. The resulting values correlate well with available experimental data from the literature. We will present a genetic model based on the compositional data on feldspar zonation for the process and timing of silicate-carbonate unmixing prior to eruption of the host phonolite magma.

Sensitive Dual Color in vivo Bioluminescence Imaging Using a New Red Codon Optimized Firefly Luciferase and a Green Click Beetle Luciferase

DTIC Science & Technology

2011-04-01

Sensitive Dual Color In Vivo Bioluminescence Imaging Using a New Red Codon Optimized Firefly Luciferase and a Green Click Beetle Luciferase Laura...20 nm). Spectral unmixing algorithms were applied to the images where good separation of signals was observed. Furthermore, HEK293 cells that...spectral emissions using a suitable spectral unmixing algorithm . This new D-luciferin-dependent reporter gene couplet opens up the possibility in the future

Tetrachromacy of human vision: spectral channels and primary colors

NASA Astrophysics Data System (ADS)

Gavrik, Vitali V.

2002-06-01

Full-color imaging requires four channels as, in contrast to a colorimeter, can add no primary to matched scene colors themselves. An ideal imaging channel should have the same spectral sensitivity of scene recording as a retinal receptor and evoke the same primary color sensation. The alternating matching functions of a triad of real primaries are inconsistent with the three cones but explicable of two pairs of independent opponent receptors with their alternating blue-yellow and green-red chromatic axes in the color space. Much other controversy of trichromatic approach can also be explained with the recently proposed intra- receptor processes in the photopic rod and cone, respectively. Each of their four primary sensations, unmixed around 465, 495, 575, and 650 nm, is evoked within a different spectral region. The current trichromatic photographic systems have been found separately to approximate the blue and red receptors, as well as their spectral opponency against the respective yellow and blue- green receptors simulated with a single middle-wave imaging channel. The channel sensitivities are delimited by the neutral points of rod and cone and cannot simulate the necessary overlap of non-opponent channels for properly to render some mixed colors. The yellow and cyan positive dyes closely control the brightness of blue and red sensations, respectively. Those red and blue respectively to control the yellow and blue-green sensations on brightness scales are replaced by magenta dye, controlling them together. Accurate rendering of natural saturation metameric colors, problematic blue-green, purple-red, and low-illumination colors requires to replace the hybrid 'green' channel with the blue-green and yellow channels.

Unmixed fuel processors and methods for using the same

DOEpatents

Kulkarni, Parag Prakash; Cui, Zhe

2010-08-24

Disclosed herein are unmixed fuel processors and methods for using the same. In one embodiment, an unmixed fuel processor comprises: an oxidation reactor comprising an oxidation portion and a gasifier, a CO.sub.2 acceptor reactor, and a regeneration reactor. The oxidation portion comprises an air inlet, effluent outlet, and an oxygen transfer material. The gasifier comprises a solid hydrocarbon fuel inlet, a solids outlet, and a syngas outlet. The CO.sub.2 acceptor reactor comprises a water inlet, a hydrogen outlet, and a CO.sub.2 sorbent, and is configured to receive syngas from the gasifier. The regeneration reactor comprises a water inlet and a CO.sub.2 stream outlet. The regeneration reactor is configured to receive spent CO.sub.2 adsorption material from the gasification reactor and to return regenerated CO.sub.2 adsorption material to the gasification reactor, and configured to receive oxidized oxygen transfer material from the oxidation reactor and to return reduced oxygen transfer material to the oxidation reactor.

Spectral unmixing of multi-color tissue specific in vivo fluorescence in mice

NASA Astrophysics Data System (ADS)

Zacharakis, Giannis; Favicchio, Rosy; Garofalakis, Anikitos; Psycharakis, Stylianos; Mamalaki, Clio; Ripoll, Jorge

2007-07-01

Fluorescence Molecular Tomography (FMT) has emerged as a powerful tool for monitoring biological functions in vivo in small animals. It provides the means to determine volumetric images of fluorescent protein concentration by applying the principles of diffuse optical tomography. Using different probes tagged to different proteins or cells, different biological functions and pathways can be simultaneously imaged in the same subject. In this work we present a spectral unmixing algorithm capable of separating signal from different probes when combined with the tomographic imaging modality. We show results of two-color imaging when the algorithm is applied to separate fluorescence activity originating from phantoms containing two different fluorophores, namely CFSE and SNARF, with well separated emission spectra, as well as Dsred- and GFP-fused cells in F5-b10 transgenic mice in vivo. The same algorithm can furthermore be applied to tissue-specific spectroscopy data. Spectral analysis of a variety of organs from control, DsRed and GFP F5/B10 transgenic mice showed that fluorophore detection by optical systems is highly tissue-dependent. Spectral data collected from different organs can provide useful insight into experimental parameter optimisation (choice of filters, fluorophores, excitation wavelengths) and spectral unmixing can be applied to measure the tissue-dependency, thereby taking into account localized fluorophore efficiency. Summed up, tissue spectral unmixing can be used as criteria in choosing the most appropriate tissue targets as well as fluorescent markers for specific applications.

Time Series Remote Sensing in Monitoring the Spatio-Temporal Dynamics of Plant Invasions: A Study of Invasive Saltcedar (Tamarix Spp.)

NASA Astrophysics Data System (ADS)

Diao, Chunyuan

In today's big data era, the increasing availability of satellite and airborne platforms at various spatial and temporal scales creates unprecedented opportunities to understand the complex and dynamic systems (e.g., plant invasion). Time series remote sensing is becoming more and more important to monitor the earth system dynamics and interactions. To date, most of the time series remote sensing studies have been conducted with the images acquired at coarse spatial scale, due to their relatively high temporal resolution. The construction of time series at fine spatial scale, however, is limited to few or discrete images acquired within or across years. The objective of this research is to advance the time series remote sensing at fine spatial scale, particularly to shift from discrete time series remote sensing to continuous time series remote sensing. The objective will be achieved through the following aims: 1) Advance intra-annual time series remote sensing under the pure-pixel assumption; 2) Advance intra-annual time series remote sensing under the mixed-pixel assumption; 3) Advance inter-annual time series remote sensing in monitoring the land surface dynamics; and 4) Advance the species distribution model with time series remote sensing. Taking invasive saltcedar as an example, four methods (i.e., phenological time series remote sensing model, temporal partial unmixing method, multiyear spectral angle clustering model, and time series remote sensing-based spatially explicit species distribution model) were developed to achieve the objectives. Results indicated that the phenological time series remote sensing model could effectively map saltcedar distributions through characterizing the seasonal phenological dynamics of plant species throughout the year. The proposed temporal partial unmixing method, compared to conventional unmixing methods, could more accurately estimate saltcedar abundance within a pixel by exploiting the adequate temporal signatures of saltcedar. The multiyear spectral angle clustering model could guide the selection of the most representative remotely sensed image for repetitive saltcedar mapping over space and time. Through incorporating spatial autocorrelation, the species distribution model developed in the study could identify the suitable habitats of saltcedar at a fine spatial scale and locate appropriate areas at high risk of saltcedar infestation. Among 10 environmental variables, the distance to the river and the phenological attributes summarized by the time series remote sensing were regarded as the most important. These methods developed in the study provide new perspectives on how the continuous time series can be leveraged under various conditions to investigate the plant invasion dynamics.

a Maximum Entropy Model of the Bearded Capuchin Monkey Habitat Incorporating Topography and Spectral Unmixing Analysis

NASA Astrophysics Data System (ADS)

Howard, A. M.; Bernardes, S.; Nibbelink, N.; Biondi, L.; Presotto, A.; Fragaszy, D. M.; Madden, M.

2012-07-01

Movement patterns of bearded capuchin monkeys (Cebus (Sapajus) libidinosus) in northeastern Brazil are likely impacted by environmental features such as elevation, vegetation density, or vegetation type. Habitat preferences of these monkeys provide insights regarding the impact of environmental features on species ecology and the degree to which they incorporate these features in movement decisions. In order to evaluate environmental features influencing movement patterns and predict areas suitable for movement, we employed a maximum entropy modelling approach, using observation points along capuchin monkey daily routes as species presence points. We combined these presence points with spatial data on important environmental features from remotely sensed data on land cover and topography. A spectral mixing analysis procedure was used to generate fraction images that represent green vegetation, shade and soil of the study area. A Landsat Thematic Mapper scene of the area of study was geometrically and atmospherically corrected and used as input in a Minimum Noise Fraction (MNF) procedure and a linear spectral unmixing approach was used to generate the fraction images. These fraction images and elevation were the environmental layer inputs for our logistic MaxEnt model of capuchin movement. Our models' predictive power (test AUC) was 0.775. Areas of high elevation (>450 m) showed low probabilities of presence, and percent green vegetation was the greatest overall contributor to model AUC. This work has implications for predicting daily movement patterns of capuchins in our field site, as suitability values from our model may relate to habitat preference and facility of movement.

Estimating the formation age distribution of continental crust by unmixing zircon ages

NASA Astrophysics Data System (ADS)

Korenaga, Jun

2018-01-01

Continental crust provides first-order control on Earth's surface environment, enabling the presence of stable dry landmasses surrounded by deep oceans. The evolution of continental crust is important for atmospheric evolution, because continental crust is an essential component of deep carbon cycle and is likely to have played a critical role in the oxygenation of the atmosphere. Geochemical information stored in the mineral zircon, known for its resilience to diagenesis and metamorphism, has been central to ongoing debates on the genesis and evolution of continental crust. However, correction for crustal reworking, which is the most critical step when estimating original formation ages, has been incorrectly formulated, undermining the significance of previous estimates. Here I suggest a simple yet promising approach for reworking correction using the global compilation of zircon data. The present-day distribution of crustal formation age estimated by the new "unmixing" method serves as the lower bound to the true crustal growth, and large deviations from growth models based on mantle depletion imply the important role of crustal recycling through the Earth history.

Multispectral analysis tools can increase utility of RGB color images in histology

NASA Astrophysics Data System (ADS)

Fereidouni, Farzad; Griffin, Croix; Todd, Austin; Levenson, Richard

2018-04-01

Multispectral imaging (MSI) is increasingly finding application in the study and characterization of biological specimens. However, the methods typically used come with challenges on both the acquisition and the analysis front. MSI can be slow and photon-inefficient, leading to long imaging times and possible phototoxicity and photobleaching. The resulting datasets can be large and complex, prompting the development of a number of mathematical approaches for segmentation and signal unmixing. We show that under certain circumstances, just three spectral channels provided by standard color cameras, coupled with multispectral analysis tools, including a more recent spectral phasor approach, can efficiently provide useful insights. These findings are supported with a mathematical model relating spectral bandwidth and spectral channel number to achievable spectral accuracy. The utility of 3-band RGB and MSI analysis tools are demonstrated on images acquired using brightfield and fluorescence techniques, as well as a novel microscopy approach employing UV-surface excitation. Supervised linear unmixing, automated non-negative matrix factorization and phasor analysis tools all provide useful results, with phasors generating particularly helpful spectral display plots for sample exploration.

CHAMP: a locally adaptive unmixing-based hyperspectral anomaly detection algorithm

NASA Astrophysics Data System (ADS)

Crist, Eric P.; Thelen, Brian J.; Carrara, David A.

1998-10-01

Anomaly detection offers a means by which to identify potentially important objects in a scene without prior knowledge of their spectral signatures. As such, this approach is less sensitive to variations in target class composition, atmospheric and illumination conditions, and sensor gain settings than would be a spectral matched filter or similar algorithm. The best existing anomaly detectors generally fall into one of two categories: those based on local Gaussian statistics, and those based on linear mixing moles. Unmixing-based approaches better represent the real distribution of data in a scene, but are typically derived and applied on a global or scene-wide basis. Locally adaptive approaches allow detection of more subtle anomalies by accommodating the spatial non-homogeneity of background classes in a typical scene, but provide a poorer representation of the true underlying background distribution. The CHAMP algorithm combines the best attributes of both approaches, applying a linear-mixing model approach in a spatially adaptive manner. The algorithm itself, and teste results on simulated and actual hyperspectral image data, are presented in this paper.

Ejecta patterns of Meteor Crater, Arizona derived from the linear un-mixing of TIMS data and laboratory thermal emission spectra

NASA Technical Reports Server (NTRS)

Ramsey, Michael S.; Christensen, Philip R.

1992-01-01

Accurate interpretation of thermal infrared data depends upon the understanding and removal of complicating effects. These effects may include physical mixing of various mineralogies and particle sizes, atmospheric absorption and emission, surficial coatings, geometry effects, and differential surface temperatures. The focus is the examination of the linear spectral mixing of individual mineral or endmember spectra. Linear addition of spectra, for particles larger than the wavelength, allows for a straight-forward method of deconvolving the observed spectra, predicting a volume percent of each endmember. The 'forward analysis' of linear mixing (comparing the spectra of physical mixtures to numerical mixtures) has received much attention. The reverse approach of un-mixing thermal emission spectra was examined with remotely sensed data, but no laboratory verification exists. Understanding of the effects of spectral mixing on high resolution laboratory spectra allows for the extrapolation to lower resolution, and often more complicated, remotely gathered data. Thermal Infrared Multispectral Scanner (TIMS) data for Meteor Crater, Arizona were acquired in Sep. 1987. The spectral un-mixing of these data gives a unique test of the laboratory results. Meteor Crater (1.2 km in diameter and 180 m deep) is located in north-central Arizona, west of Canyon Diablo. The arid environment, paucity of vegetation, and low relief make the region ideal for remote data acquisition. Within the horizontal sedimentary sequence that forms the upper Colorado Plateau, the oldest unit sampled by the impact crater was the Permian Coconino Sandstone. A thin bed of the Toroweap Formation, also of Permian age, conformably overlays the Coconino. Above the Toroweap lies the Permian Kiabab Limestone which, in turn, is covered by a thin veneer of the Moenkopi Formation. The Moenkopi is Triassic in age and has two distinct sub-units in the vicinity of the crater. The lower Wupatki member is a fine-grained sandstone, while the upper Moqui member is a fissile siltstone. Ejecta from these units are preserved as inverted stratigraphy up to 2 crater radii from the rim. The mineralogical contrast between the units, relative lack of post-emplacement erosion and ejecta mixing provide a unique site to apply the un-mixing model. Selection of the aforementioned units as endmembers reveals distinct patterns in the ejecta of the crater.

Unmixing of spectral components affecting AVIRIS imagery of Tampa Bay

NASA Astrophysics Data System (ADS)

Carder, Kendall L.; Lee, Z. P.; Chen, Robert F.; Davis, Curtiss O.

1993-09-01

According to Kirk's as well as Morel and Gentili's Monte Carlo simulations, the popular simple expression, R approximately equals 0.33 bb/a, relating subsurface irradiance reflectance (R) to the ratio of the backscattering coefficient (bb) to absorption coefficient (a), is not valid for bb/a > 0.25. This means that it may no longer be valid for values of remote-sensing reflectance (above-surface ratio of water-leaving radiance to downwelling irradiance) where Rrs4/ > 0.01. Since there has been no simple Rrs expression developed for very turbid waters, we developed one based in part on Monte Carlo simulations and empirical adjustments to an Rrs model and applied it to rather turbid coastal waters near Tampa Bay to evaluate its utility for unmixing the optical components affecting the water- leaving radiance. With the high spectral (10 nm) and spatial (20 m2) resolution of Airborne Visible-InfraRed Imaging Spectrometer (AVIRIS) data, the water depth and bottom type were deduced using the model for shallow waters. This research demonstrates the necessity of further research to improve interpretations of scenes with highly variable turbid waters, and it emphasizes the utility of high spectral-resolution data as from AVIRIS for better understanding complicated coastal environments such as the west Florida shelf.

Generation, Validation, and Application of Abundance Map Reference Data for Spectral Unmixing

NASA Astrophysics Data System (ADS)

Williams, McKay D.

Reference data ("ground truth") maps traditionally have been used to assess the accuracy of imaging spectrometer classification algorithms. However, these reference data can be prohibitively expensive to produce, often do not include sub-pixel abundance estimates necessary to assess spectral unmixing algorithms, and lack published validation reports. Our research proposes methodologies to efficiently generate, validate, and apply abundance map reference data (AMRD) to airborne remote sensing scenes. We generated scene-wide AMRD for three different remote sensing scenes using our remotely sensed reference data (RSRD) technique, which spatially aggregates unmixing results from fine scale imagery (e.g., 1-m Ground Sample Distance (GSD)) to co-located coarse scale imagery (e.g., 10-m GSD or larger). We validated the accuracy of this methodology by estimating AMRD in 51 randomly-selected 10 m x 10 m plots, using seven independent methods and observers, including field surveys by two observers, imagery analysis by two observers, and RSRD using three algorithms. Results indicated statistically-significant differences between all versions of AMRD, suggesting that all forms of reference data need to be validated. Given these significant differences between the independent versions of AMRD, we proposed that the mean of all (MOA) versions of reference data for each plot and class were most likely to represent true abundances. We then compared each version of AMRD to MOA. Best case accuracy was achieved by a version of imagery analysis, which had a mean coverage area error of 2.0%, with a standard deviation of 5.6%. One of the RSRD algorithms was nearly as accurate, achieving a mean error of 3.0%, with a standard deviation of 6.3%, showing the potential of RSRD-based AMRD generation. Application of validated AMRD to specific coarse scale imagery involved three main parts: 1) spatial alignment of coarse and fine scale imagery, 2) aggregation of fine scale abundances to produce coarse scale imagery-specific AMRD, and 3) demonstration of comparisons between coarse scale unmixing abundances and AMRD. Spatial alignment was performed using our scene-wide spectral comparison (SWSC) algorithm, which aligned imagery with accuracy approaching the distance of a single fine scale pixel. We compared simple rectangular aggregation to coarse sensor point spread function (PSF) aggregation, and found that the PSF approach returned lower error, but that rectangular aggregation more accurately estimated true abundances at ground level. We demonstrated various metrics for comparing unmixing results to AMRD, including mean absolute error (MAE) and linear regression (LR). We additionally introduced reference data mean adjusted MAE (MA-MAE), and reference data confidence interval adjusted MAE (CIA-MAE), which account for known error in the reference data itself. MA-MAE analysis indicated that fully constrained linear unmixing of coarse scale imagery across all three scenes returned an error of 10.83% per class and pixel, with regression analysis yielding a slope = 0.85, intercept = 0.04, and R2 = 0.81. Our reference data research has demonstrated a viable methodology to efficiently generate, validate, and apply AMRD to specific examples of airborne remote sensing imagery, thereby enabling direct quantitative assessment of spectral unmixing performance.

Quantitative Analysis of Immunohistochemistry in Melanoma Tumors

PubMed Central

Lilyquist, Jenna; White, Kirsten Anne Meyer; Lee, Rebecca J.; Philips, Genevieve K.; Hughes, Christopher R.; Torres, Salina M.

2017-01-01

Abstract Identification of positive staining is often qualitative and subjective. This is particularly troublesome in pigmented melanoma lesions, because melanin is difficult to distinguish from the brown stain resulting from immunohistochemistry (IHC) using horse radish peroxidase developed with 3,3′-Diaminobenzidine (HRP-DAB). We sought to identify and quantify positive staining, particularly in melanoma lesions. We visualized G-protein coupled estrogen receptor (GPER) expression developed with HRP-DAB and counterstained with Azure B (stains melanin) in melanoma tissue sections (n = 3). Matched sections (n = 3), along with 22 unmatched sections, were stained only with Azure B as a control. Breast tissue (n = 1) was used as a positive HRP-DAB control. Images of the stained tissues were generated using a Nuance Spectral Imaging Camera. Analysis of the images was performed using the Nuance Spectral Imaging software and SlideBook. Data was analyzed using a Kruskal–Wallis one way analysis of variance (ANOVA). We showed that a pigmented melanoma tissue doubly stained with anti-GPER HRP-DAB and Azure B can be unmixed using spectra derived from a matched, Azure B-only section, and an anti-GPER HRP-DAB control. We unmixed each of the melanoma lesions using each of the Azure B spectra, evaluated the mean intensity of positive staining, and examined the distribution of the mean intensities (P = .73; Kruskal–Wallis). These results suggest that this method does not require a matched Azure B-only stained control tissue for every melanoma lesion, allowing precious tissues to be conserved for other studies. Importantly, this quantification method reduces the subjectivity of protein expression analysis, and provides a valuable tool for accurate evaluation, particularly for pigmented tissues. PMID:28403073

Comparing performance of standard and iterative linear unmixing methods for hyperspectral signatures

NASA Astrophysics Data System (ADS)

Gault, Travis R.; Jansen, Melissa E.; DeCoster, Mallory E.; Jansing, E. David; Rodriguez, Benjamin M.

2016-05-01

Linear unmixing is a method of decomposing a mixed signature to determine the component materials that are present in sensor's field of view, along with the abundances at which they occur. Linear unmixing assumes that energy from the materials in the field of view is mixed in a linear fashion across the spectrum of interest. Traditional unmixing methods can take advantage of adjacent pixels in the decomposition algorithm, but is not the case for point sensors. This paper explores several iterative and non-iterative methods for linear unmixing, and examines their effectiveness at identifying the individual signatures that make up simulated single pixel mixed signatures, along with their corresponding abundances. The major hurdle addressed in the proposed method is that no neighboring pixel information is available for the spectral signature of interest. Testing is performed using two collections of spectral signatures from the Johns Hopkins University Applied Physics Laboratory's Signatures Database software (SigDB): a hand-selected small dataset of 25 distinct signatures from a larger dataset of approximately 1600 pure visible/near-infrared/short-wave-infrared (VIS/NIR/SWIR) spectra. Simulated spectra are created with three and four material mixtures randomly drawn from a dataset originating from SigDB, where the abundance of one material is swept in 10% increments from 10% to 90%with the abundances of the other materials equally divided amongst the remainder. For the smaller dataset of 25 signatures, all combinations of three or four materials are used to create simulated spectra, from which the accuracy of materials returned, as well as the correctness of the abundances, is compared to the inputs. The experiment is expanded to include the signatures from the larger dataset of almost 1600 signatures evaluated using a Monte Carlo scheme with 5000 draws of three or four materials to create the simulated mixed signatures. The spectral similarity of the inputs to the output component signatures is calculated using the spectral angle mapper. Results show that iterative methods significantly outperform the traditional methods under the given test conditions.

A randomized, double-blind, placebo-controlled trial of single-dose ciprofloxacin versus erythromycin for the treatment of chancroid in Nairobi, Kenya.

PubMed

Malonza, I M; Tyndall, M W; Ndinya-Achola, J O; Maclean, I; Omar, S; MacDonald, K S; Perriens, J; Orle, K; Plummer, F A; Ronald, A R; Moses, S

1999-12-01

A randomized, double-blind, placebo-controlled clinical trial was conducted in Nairobi, Kenya, to compare single-dose ciprofloxacin with a 7-day course of erythromycin for the treatment of chancroid. In all, 208 men and 37 women presenting with genital ulcers clinically compatible with chancroid were enrolled. Ulcer etiology was determined using culture techniques for chancroid, serology for syphilis, and a multiplex polymerase chain reaction for chancroid, syphilis, and herpes simplex virus (HSV). Ulcer etiology was 31% unmixed chancroid, 23% unmixed syphilis, 16% unmixed HSV, 15% mixed etiology, and 15% unknown. For 111 participants with chancroid, cure rates were 92% with ciprofloxacin and 91% with erythromycin. For all study participants, the treatment failure rate was 15%, mostly related to ulcer etiologies of HSV infection or syphilis, and treatment failure was 3 times more frequent in human immunodeficiency virus-infected subjects than in others, mostly owing to HSV infection. Ciprofloxacin is an effective single-dose treatment for chancroid, but current recommendations for empiric therapy of genital ulcers may result in high treatment failure due to HSV infection.

Mapping tropical rainforest canopies using multi-temporal spaceborne imaging spectroscopy

NASA Astrophysics Data System (ADS)

Somers, Ben; Asner, Gregory P.

2013-10-01

The use of imaging spectroscopy for florisic mapping of forests is complicated by the spectral similarity among coexisting species. Here we evaluated an alternative spectral unmixing strategy combining a time series of EO-1 Hyperion images and an automated feature selection strategy in MESMA. Instead of using the same spectral subset to unmix each image pixel, our modified approach allowed the spectral subsets to vary on a per pixel basis such that each pixel is evaluated using a spectral subset tuned towards maximal separability of its specific endmember class combination or species mixture. The potential of the new approach for floristic mapping of tree species in Hawaiian rainforests was quantitatively demonstrated using both simulated and actual hyperspectral image time-series. With a Cohen's Kappa coefficient of 0.65, our approach provided a more accurate tree species map compared to MESMA (Kappa = 0.54). In addition, by the selection of spectral subsets our approach was about 90% faster than MESMA. The flexible or adaptive use of band sets in spectral unmixing as such provides an interesting avenue to address spectral similarities in complex vegetation canopies.

Visual enhancement of unmixed multispectral imagery using adaptive smoothing

USGS Publications Warehouse

Lemeshewsky, G.P.; Rahman, Z.-U.; Schowengerdt, R.A.; Reichenbach, S.E.

2004-01-01

Adaptive smoothing (AS) has been previously proposed as a method to smooth uniform regions of an image, retain contrast edges, and enhance edge boundaries. The method is an implementation of the anisotropic diffusion process which results in a gray scale image. This paper discusses modifications to the AS method for application to multi-band data which results in a color segmented image. The process was used to visually enhance the three most distinct abundance fraction images produced by the Lagrange constraint neural network learning-based unmixing of Landsat 7 Enhanced Thematic Mapper Plus multispectral sensor data. A mutual information-based method was applied to select the three most distinct fraction images for subsequent visualization as a red, green, and blue composite. A reported image restoration technique (partial restoration) was applied to the multispectral data to reduce unmixing error, although evaluation of the performance of this technique was beyond the scope of this paper. The modified smoothing process resulted in a color segmented image with homogeneous regions separated by sharpened, coregistered multiband edges. There was improved class separation with the segmented image, which has importance to subsequent operations involving data classification.

Ion-beam mixed ultra-thin cobalt suicide (CoSi2) films by cobalt sputtering and rapid thermal annealing

NASA Astrophysics Data System (ADS)

Kal, S.; Kasko, I.; Ryssel, H.

1995-10-01

The influence of ion-beam mixing on ultra-thin cobalt silicide (CoSi2) formation was investigated by characterizing the ion-beam mixed and unmixed CoSi2 films. A Ge+ ion-implantation through the Co film prior to silicidation causes an interface mixing of the cobalt film with the silicon substrate and results in improved silicide-to-silicon interface roughness. Rapid thermal annealing was used to form Ge+ ion mixed and unmixed thin CoSi2 layer from 10 nm sputter deposited Co film. The silicide films were characterized by secondary neutral mass spectroscopy, x-ray diffraction, tunneling electron microscopy (TEM), Rutherford backscattering, and sheet resistance measurements. The experi-mental results indicate that the final rapid thermal annealing temperature should not exceed 800°C for thin (<50 nm) CoSi2 preparation. A comparison of the plan-view and cross-section TEM micrographs of the ion-beam mixed and unmixed CoSi2 films reveals that Ge+ ion mixing (45 keV, 1 × 1015 cm-2) produces homogeneous silicide with smooth silicide-to-silicon interface.

Direct comparison of Fe-Cr unmixing characterization by atom probe tomography and small angle scattering

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

Couturier, Laurent, E-mail: laurent.couturier55@ho

The fine microstructure obtained by unmixing of a solid solution either by classical precipitation or spinodal decomposition is often characterized either by small angle scattering or atom probe tomography. This article shows that a common data analysis framework can be used to analyze data obtained from these two techniques. An example of the application of this common analysis is given for characterization of the unmixing of the Fe-Cr matrix of a 15-5 PH stainless steel during long-term ageing at 350 °C and 400 °C. A direct comparison of the Cr composition fluctuations amplitudes and characteristic lengths obtained with both techniquesmore » is made showing a quantitative agreement for the fluctuation amplitudes. The origin of the discrepancy remaining for the characteristic lengths is discussed. - Highlights: •Common analysis framework for atom probe tomography and small angle scattering •Comparison of same microstructural characteristics obtained using both techniques •Good correlation of Cr composition fluctuations amplitudes from both techniques •Good correlation of Cr composition fluctuations amplitudes with classic V parameter.« less

Evaluation of algorithm methods for fluorescence spectra of cancerous and normal human tissues

NASA Astrophysics Data System (ADS)

Pu, Yang; Wang, Wubao; Alfano, Robert R.

2016-03-01

The paper focus on the various algorithms on to unravel the fluorescence spectra by unmixing methods to identify cancerous and normal human tissues from the measured fluorescence spectroscopy. The biochemical or morphologic changes that cause fluorescence spectra variations would appear earlier than the histological approach; therefore, fluorescence spectroscopy holds a great promise as clinical tool for diagnosing early stage of carcinomas and other deceases for in vivo use. The method can further identify tissue biomarkers by decomposing the spectral contributions of different fluorescent molecules of interest. In this work, we investigate the performance of blind source un-mixing methods (backward model) and spectral fitting approaches (forward model) in decomposing the contributions of key fluorescent molecules from the tissue mixture background when certain selected excitation wavelength is applied. Pairs of adenocarcinoma as well as normal tissues confirmed by pathologist were excited by selective wavelength of 340 nm. The emission spectra of resected fresh tissue were used to evaluate the relative changes of collagen, reduced nicotinamide adenine dinucleotide (NADH), and Flavin by various spectral un-mixing methods. Two categories of algorithms: forward methods and Blind Source Separation [such as Principal Component Analysis (PCA) and Independent Component Analysis (ICA), and Nonnegative Matrix Factorization (NMF)] will be introduced and evaluated. The purpose of the spectral analysis is to discard the redundant information which conceals the difference between these two types of tissues, but keep their diagnostically significance. The facts predicted by different methods were compared to the gold standard of histopathology. The results indicate that these key fluorophores within tissue, e.g. tryptophan, collagen, and NADH, and flavin, show differences of relative contents of fluorophores among different types of human cancer and normal tissues. The sensitivity, specificity, and receiver operating characteristic (ROC) are finally employed as the criteria to evaluate the efficacy of these methods in cancer detection. The underlying physical and biological basis for these optical approaches will be discussed with examples. This ex vivo preliminary trial demonstrates that these different criteria from different methods can distinguish carcinoma from normal tissues with good sensitivity and specificity while among them, we found that ICA appears to be the superior method in predication accuracy.

Open-air multispectral fluorescence-guided surgery platform for intraoperative detection of malignant tissue under ambient lighting conditions

NASA Astrophysics Data System (ADS)

Behrooz, Ali; Vasquez, Kristine O.; Waterman, Peter; Meganck, Jeff; Peterson, Jeffrey D.; Miller, Peter; Kempner, Joshua

2017-02-01

Intraoperative resection of tumors currently relies upon the surgeon's ability to visually locate and palpate tumor nodules. Undetected residual malignant tissue often results in the need for additional treatment or surgical intervention. The Solaris platform is a multispectral open-air fluorescence imaging system designed for translational fluorescence-guided surgery. Solaris supports video-rate imaging in four fixed fluorescence channels ranging from visible to near infrared, and a multispectral channel equipped with a liquid crystal tunable filter (LCTF) for multispectral image acquisition (520-620 nm). Identification of tumor margins using reagents emitting in the visible spectrum (400-650 nm), such as fluorescein isothiocyanate (FITC), present challenges considering the presence of auto-fluorescence from tissue and food in the gastrointestinal (GI) tract. To overcome this, Solaris acquires LCTF-based multispectral images, and by applying an automated spectral unmixing algorithm to the data, separates reagent fluorescence from tissue and food auto-fluorescence. The unmixing algorithm uses vertex component analysis to automatically extract the primary pure spectra, and resolves the reagent fluorescent signal using non-negative least squares. For validation, intraoperative in vivo studies were carried out in tumor-bearing rodents injected with FITC-dextran reagent that is primarily residing in malignant tissue 24 hours post injection. In the absence of unmixing, fluorescence from tumors is not distinguishable from that of surrounding tissue. Upon spectral unmixing, the FITC-labeled malignant regions become well defined and detectable. The results of these studies substantiate the multispectral power of Solaris in resolving FITC-based agent signal in deep tumor masses, under ambient and surgical light, and enhancing the ability to surgically resect them.

Source apportionment of PM10 by positive matrix factorization in urban area of Mumbai, India.

PubMed

Gupta, Indrani; Salunkhe, Abhaysinh; Kumar, Rakesh

2012-01-01

Particulate Matter (PM(10)) has been one of the main air pollutants exceeding the ambient standards in most of the major cities in India. During last few years, receptor models such as Chemical Mass Balance, Positive Matrix Factorization (PMF), PCA-APCS and UNMIX have been used to provide solutions to the source identification and contributions which are accepted for developing effective and efficient air quality management plans. Each site poses different complexities while resolving PM(10) contributions. This paper reports the variability of four sites within Mumbai city using PMF. Industrial area of Mahul showed sources such as residual oil combustion and paved road dust (27%), traffic (20%), coal fired boiler (17%), nitrate (15%). Residential area of Khar showed sources such as residual oil combustion and construction (25%), motor vehicles (23%), marine aerosol and nitrate (19%), paved road dust (18%) compared to construction and natural dust (27%), motor vehicles and smelting work (25%), nitrate (16%) and biomass burning and paved road dust (15%) in Dharavi, a low income slum residential area. The major contributors of PM(10) at Colaba were marine aerosol, wood burning and ammonium sulphate (24%), motor vehicles and smelting work (22%), Natural soil (19%), nitrate and oil burning (18%).

Subpixel target detection and enhancement in hyperspectral images

NASA Astrophysics Data System (ADS)

Tiwari, K. C.; Arora, M.; Singh, D.

2011-06-01

Hyperspectral data due to its higher information content afforded by higher spectral resolution is increasingly being used for various remote sensing applications including information extraction at subpixel level. There is however usually a lack of matching fine spatial resolution data particularly for target detection applications. Thus, there always exists a tradeoff between the spectral and spatial resolutions due to considerations of type of application, its cost and other associated analytical and computational complexities. Typically whenever an object, either manmade, natural or any ground cover class (called target, endmembers, components or class) gets spectrally resolved but not spatially, mixed pixels in the image result. Thus, numerous manmade and/or natural disparate substances may occur inside such mixed pixels giving rise to mixed pixel classification or subpixel target detection problems. Various spectral unmixing models such as Linear Mixture Modeling (LMM) are in vogue to recover components of a mixed pixel. Spectral unmixing outputs both the endmember spectrum and their corresponding abundance fractions inside the pixel. It, however, does not provide spatial distribution of these abundance fractions within a pixel. This limits the applicability of hyperspectral data for subpixel target detection. In this paper, a new inverse Euclidean distance based super-resolution mapping method has been presented that achieves subpixel target detection in hyperspectral images by adjusting spatial distribution of abundance fraction within a pixel. Results obtained at different resolutions indicate that super-resolution mapping may effectively aid subpixel target detection.

Non-invasive monitoring of cytokine-based regenerative treatment of cartilage by hyperspectral unmixing (Conference Presentation)

NASA Astrophysics Data System (ADS)

Mahbub, Saabah B.; Succer, Peter; Gosnell, Martin E.; Anwaer, Ayad G.; Herbert, Benjamin; Vesey, Graham; Goldys, Ewa M.

2016-03-01

Extracting biochemical information from tissue autofluorescence is a promising approach to non-invasively monitor disease treatments at a cellular level, without using any external biomarkers. Our recently developed unsupervised hyperspectral unmixing by Dependent Component Analysis (DECA) provides robust and detailed metabolic information with proper account of intrinsic cellular heterogeneity. Moreover this method is compatible with established methods of fluorescent biomarker labelling. Recently adipose-derived stem cell (ADSC) - based therapies have been introduced for treating different diseases in animals and humans. ADSC have been shown promise in regenerative treatments for osteoarthritis and other bone and joint disorders. One of the mechanism of their action is their anti-inflammatory effects within osteoarthritic joints which aid the regeneration of cartilage. These therapeutic effects are known to be driven by secretions of different cytokines from the ADSCs. We have been using the hyperspectral unmixing techniques to study in-vitro the effects of ADSC-derived cytokine-rich secretions with the cartilage chip in both human and bovine samples. The study of metabolic effects of different cytokine treatment on different cartilage layers makes it possible to compare the merits of those treatments for repairing cartilage.

GPU implementation of the simplex identification via split augmented Lagrangian

NASA Astrophysics Data System (ADS)

Sevilla, Jorge; Nascimento, José M. P.

2015-10-01

Hyperspectral imaging can be used for object detection and for discriminating between different objects based on their spectral characteristics. One of the main problems of hyperspectral data analysis is the presence of mixed pixels, due to the low spatial resolution of such images. This means that several spectrally pure signatures (endmembers) are combined into the same mixed pixel. Linear spectral unmixing follows an unsupervised approach which aims at inferring pure spectral signatures and their material fractions at each pixel of the scene. The huge data volumes acquired by such sensors put stringent requirements on processing and unmixing methods. This paper proposes an efficient implementation of a unsupervised linear unmixing method on GPUs using CUDA. The method finds the smallest simplex by solving a sequence of nonsmooth convex subproblems using variable splitting to obtain a constraint formulation, and then applying an augmented Lagrangian technique. The parallel implementation of SISAL presented in this work exploits the GPU architecture at low level, using shared memory and coalesced accesses to memory. The results herein presented indicate that the GPU implementation can significantly accelerate the method's execution over big datasets while maintaining the methods accuracy.

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

Altmann, Yoann; Maccarone, Aurora; McCarthy, Aongus

Here, this paper presents a new Bayesian spectral un-mixing algorithm to analyse remote scenes sensed via sparse multispectral Lidar measurements. To a first approximation, in the presence of a target, each Lidar waveform consists of a main peak, whose position depends on the target distance and whose amplitude depends on the wavelength of the laser source considered (i.e, on the target reflectivity). Besides, these temporal responses are usually assumed to be corrupted by Poisson noise in the low photon count regime. When considering multiple wavelengths, it becomes possible to use spectral information in order to identify and quantify the mainmore » materials in the scene, in addition to estimation of the Lidar-based range profiles. Due to its anomaly detection capability, the proposed hierarchical Bayesian model, coupled with an efficient Markov chain Monte Carlo algorithm, allows robust estimation of depth images together with abundance and outlier maps associated with the observed 3D scene. The proposed methodology is illustrated via experiments conducted with real multispectral Lidar data acquired in a controlled environment. The results demonstrate the possibility to unmix spectral responses constructed from extremely sparse photon counts (less than 10 photons per pixel and band).« less

Hyperspectral and multispectral data fusion based on linear-quadratic nonnegative matrix factorization

NASA Astrophysics Data System (ADS)

Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

2017-04-01

This paper proposes three multisharpening approaches to enhance the spatial resolution of urban hyperspectral remote sensing images. These approaches, related to linear-quadratic spectral unmixing techniques, use a linear-quadratic nonnegative matrix factorization (NMF) multiplicative algorithm. These methods begin by unmixing the observable high-spectral/low-spatial resolution hyperspectral and high-spatial/low-spectral resolution multispectral images. The obtained high-spectral/high-spatial resolution features are then recombined, according to the linear-quadratic mixing model, to obtain an unobservable multisharpened high-spectral/high-spatial resolution hyperspectral image. In the first designed approach, hyperspectral and multispectral variables are independently optimized, once they have been coherently initialized. These variables are alternately updated in the second designed approach. In the third approach, the considered hyperspectral and multispectral variables are jointly updated. Experiments, using synthetic and real data, are conducted to assess the efficiency, in spatial and spectral domains, of the designed approaches and of linear NMF-based approaches from the literature. Experimental results show that the designed methods globally yield very satisfactory spectral and spatial fidelities for the multisharpened hyperspectral data. They also prove that these methods significantly outperform the used literature approaches.

The Lightning Nitrogen Oxides Model (LNOM): Status and Recent Applications

NASA Technical Reports Server (NTRS)

Koshak, William; Khan, Maudood; Peterson, Harold

2011-01-01

Improvements to the NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) are discussed. Recent results from an August 2006 run of the Community Multiscale Air Quality (CMAQ) modeling system that employs LNOM lightning NOx (= NO + NO2) estimates are provided. The LNOM analyzes Lightning Mapping Array (LMA) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning NOx. The latest LNOM estimates of (a) lightning channel length distributions, (b) lightning 1-m segment altitude distributions, and (c) the vertical profile of NOx are presented. The impact of including LNOM-estimates of lightning NOx on CMAQ output is discussed.

Temporal evolution of main ambient PM2. 5 sources in Santiago, Chile, from 1998 to 2012

NASA Astrophysics Data System (ADS)

Barraza, Francisco; Lambert, Fabrice; Jorquera, Héctor; María Villalobos, Ana; Gallardo, Laura

2017-08-01

The inhabitants of Santiago, Chile have been exposed to harmful levels of air pollutants for decades. The city's poor air quality is a result of steady economic growth, and stable atmospheric conditions adverse to mixing and ventilation that favor the formation of oxidants and secondary aerosols. Identifying and quantifying the sources that contribute to the ambient levels of pollutants is key for designing adequate mitigation measures. Estimating the evolution of source contributions to ambient pollution levels is also paramount to evaluating the effectiveness of pollution reduction measures that have been implemented in recent decades. Here, we quantify the main sources that have contributed to fine particulate matter (PM2. 5) between April 1998 and August 2012 in downtown Santiago by using two different source-receptor models (PMF 5.0 and UNMIX 6.0) that were applied to elemental measurements of 1243 24 h filter samples of ambient PM2.5. PMF resolved six sources that contributed to ambient PM2. 5, with UNMIX producing similar results: motor vehicles (37.3 ± 1.1 %), industrial sources (18.5 ± 1.3 %), copper smelters (14.4 ± 0.8 %), wood burning (12.3 ± 1.0 %), coastal sources (9.5 ± 0.7 %) and urban dust (3.0 ± 1.2 %). Our results show that over the 15 years analyzed here, four of the resolved sources significantly decreased [95 % confidence interval]: motor vehicles 21.3 % [2.6, 36.5], industrial sources 39.3 % [28.6, 48.4], copper smelters 81.5 % [75.5, 85.9], and coastal sources 58.9 % [38.5, 72.5], while wood burning did not significantly change and urban dust increased by 72 % [48.9, 99.9]. These changes are consistent with emission reduction measures, such as improved vehicle emission standards, cleaner smelting technology, introduction of low-sulfur diesel for vehicles and natural gas for industrial processes, public transport improvements, etc. However, it is also apparent that the mitigation expected from the above regulations has been partially offset by the increasing amount of private vehicle use in the city, with motor vehicles becoming the dominant source of ambient PM2. 5 in recent years. Consequently, Santiago still experiences ambient PM2. 5 levels above the annual and 24 h Chilean and World Health Organization standards, and further regulations are required to reach ambient air quality standards.

Enthalpy of Mixing in Al–Tb Liquid

DOE PAGES

Zhou, Shihuai; Tackes, Carl; Napolitano, Ralph

2017-06-21

The liquid-phase enthalpy of mixing for Al$-$Tb alloys is measured for 3, 5, 8, 10, and 20 at% Tb at selected temperatures in the range from 1364 to 1439 K. Methods include isothermal solution calorimetry and isoperibolic electromagnetic levitation drop calorimetry. Mixing enthalpy is determined relative to the unmixed pure (Al and Tb) components. The required formation enthalpy for the Al3Tb phase is computed from first-principles calculations. Finally, based on our measurements, three different semi-empirical solution models are offered for the excess free energy of the liquid, including regular, subregular, and associate model formulations. These models are also compared withmore » the Miedema model prediction of mixing enthalpy.« less

Report of the Workshop on Unmixing the SNCs: Chemical, Isotopic, and Petrologic Components of Martian Meteorites

NASA Technical Reports Server (NTRS)

Treiman, Allan H. (Editor); Herd, Christopher D. K. (Editor)

2002-01-01

Geochemical and petrologic studies of the Martian meteorites (nicknamed the SNCs) have proliferated in the past few years, from a wealth of new samples and the perfection of new analytical methods. An intriguing result from these studies is that the chemical and isotopic compositions of the Martian meteorites, all basalts or derived from basaltic magma, can be modeled as mixtures of a limited number of components. These mixing components were the focus of the workshop.

Molecular dynamics studies of CaAl 2Si 2O 8 liquid. Part II: Equation of state and a thermodynamic model

NASA Astrophysics Data System (ADS)

Ghiorso, Mark S.; Nevins, Dean; Cutler, Ian; Spera, Frank J.

2009-11-01

A thermodynamic model and equation of state (EOS) is developed from the molecular dynamics simulation experiments of Spera et al. (2009) for CaAl 2Si 2O 8 liquid over the temperature range 3500-6000 K and pressure interval 0-125 GPa. The model is constructed utilizing the isothermal Universal EOS of Vinet et al. (1986) combined with an expression for the temperature-dependence of the internal energy derived from density functional theory ( Rosenfeld and Tarazona, 1998). It is demonstrated that this model is more successful at reproducing the data than the temperature-dependent Universal EOS ( Vinet et al., 1987) or the volume-explicit EOS of Ghiorso (2004a). Distinct parameterizations are required to model low (<20 GPa) and high (>20 GPa) pressure regimes. This result is ascribed to the affect of liquid structure on macroscopic thermodynamic properties, specifically the interdependence of average cation-oxygen coordination number on the bulk modulus. The thermodynamic transition between the high- and low-pressure parameterizations is modeled as second order, although the nature of the transition is open to question and may well be first order or lambda-like in character. Analysis of the thermodynamic model reveals a predicted region of liquid-liquid un-mixing at low-temperatures (<1624 K) and pressures (<1.257 GPa). These pressure-temperature conditions are above the glass transition temperature but within the metastable liquid region. They represent the highest temperatures yet suggested for liquid-liquid un-mixing in a silicate bulk composition. A shock wave Hugoniot curve is calculated for comparison with the experimental data of Rigden et al. (1989) and of Asimow and Ahrens (2008). The comparison suggests that the model developed in this paper underestimates the density of the liquid by roughly 10% at pressures greater than ˜20 GPa.

Impact of JPEG2000 compression on endmember extraction and unmixing of remotely sensed hyperspectral data

NASA Astrophysics Data System (ADS)

Martin, Gabriel; Gonzalez-Ruiz, Vicente; Plaza, Antonio; Ortiz, Juan P.; Garcia, Inmaculada

2010-07-01

Lossy hyperspectral image compression has received considerable interest in recent years due to the extremely high dimensionality of the data. However, the impact of lossy compression on spectral unmixing techniques has not been widely studied. These techniques characterize mixed pixels (resulting from insufficient spatial resolution) in terms of a suitable combination of spectrally pure substances (called endmembers) weighted by their estimated fractional abundances. This paper focuses on the impact of JPEG2000-based lossy compression of hyperspectral images on the quality of the endmembers extracted by different algorithms. The three considered algorithms are the orthogonal subspace projection (OSP), which uses only spatial information, and the automatic morphological endmember extraction (AMEE) and spatial spectral endmember extraction (SSEE), which integrate both spatial and spectral information in the search for endmembers. The impact of compression on the resulting abundance estimation based on the endmembers derived by different methods is also substantiated. Experimental results are conducted using a hyperspectral data set collected by NASA Jet Propulsion Laboratory over the Cuprite mining district in Nevada. The experimental results are quantitatively analyzed using reference information available from U.S. Geological Survey, resulting in recommendations to specialists interested in applying endmember extraction and unmixing algorithms to compressed hyperspectral data.

Effects of band selection on endmember extraction for forestry applications

NASA Astrophysics Data System (ADS)

Karathanassi, Vassilia; Andreou, Charoula; Andronis, Vassilis; Kolokoussis, Polychronis

2014-10-01

In spectral unmixing theory, data reduction techniques play an important role as hyperspectral imagery contains an immense amount of data, posing many challenging problems such as data storage, computational efficiency, and the so called "curse of dimensionality". Feature extraction and feature selection are the two main approaches for dimensionality reduction. Feature extraction techniques are used for reducing the dimensionality of the hyperspectral data by applying transforms on hyperspectral data. Feature selection techniques retain the physical meaning of the data by selecting a set of bands from the input hyperspectral dataset, which mainly contain the information needed for spectral unmixing. Although feature selection techniques are well-known for their dimensionality reduction potentials they are rarely used in the unmixing process. The majority of the existing state-of-the-art dimensionality reduction methods set criteria to the spectral information, which is derived by the whole wavelength, in order to define the optimum spectral subspace. These criteria are not associated with any particular application but with the data statistics, such as correlation and entropy values. However, each application is associated with specific land c over materials, whose spectral characteristics present variations in specific wavelengths. In forestry for example, many applications focus on tree leaves, in which specific pigments such as chlorophyll, xanthophyll, etc. determine the wavelengths where tree species, diseases, etc., can be detected. For such applications, when the unmixing process is applied, the tree species, diseases, etc., are considered as the endmembers of interest. This paper focuses on investigating the effects of band selection on the endmember extraction by exploiting the information of the vegetation absorbance spectral zones. More precisely, it is explored whether endmember extraction can be optimized when specific sets of initial bands related to leaf spectral characteristics are selected. Experiments comprise application of well-known signal subspace estimation and endmember extraction methods on a hyperspectral imagery that presents a forest area. Evaluation of the extracted endmembers showed that more forest species can be extracted as endmembers using selected bands.

Assessing FRET using Spectral Techniques

PubMed Central

Leavesley, Silas J.; Britain, Andrea L.; Cichon, Lauren K.; Nikolaev, Viacheslav O.; Rich, Thomas C.

2015-01-01

Förster resonance energy transfer (FRET) techniques have proven invaluable for probing the complex nature of protein–protein interactions, protein folding, and intracellular signaling events. These techniques have traditionally been implemented with the use of one or more fluorescence band-pass filters, either as fluorescence microscopy filter cubes, or as dichroic mirrors and band-pass filters in flow cytometry. In addition, new approaches for measuring FRET, such as fluorescence lifetime and acceptor photobleaching, have been developed. Hyperspectral techniques for imaging and flow cytometry have also shown to be promising for performing FRET measurements. In this study, we have compared traditional (filter-based) FRET approaches to three spectral-based approaches: the ratio of acceptor-to-donor peak emission, linear spectral unmixing, and linear spectral unmixing with a correction for direct acceptor excitation. All methods are estimates of FRET efficiency, except for one-filter set and three-filter set FRET indices, which are included for consistency with prior literature. In the first part of this study, spectrofluorimetric data were collected from a CFP–Epac–YFP FRET probe that has been used for intracellular cAMP measurements. All comparisons were performed using the same spectrofluorimetric datasets as input data, to provide a relevant comparison. Linear spectral unmixing resulted in measurements with the lowest coefficient of variation (0.10) as well as accurate fits using the Hill equation. FRET efficiency methods produced coefficients of variation of less than 0.20, while FRET indices produced coefficients of variation greater than 8.00. These results demonstrate that spectral FRET measurements provide improved response over standard, filter-based measurements. Using spectral approaches, single-cell measurements were conducted through hyperspectral confocal microscopy, linear unmixing, and cell segmentation with quantitative image analysis. Results from these studies confirmed that spectral imaging is effective for measuring subcellular, time-dependent FRET dynamics and that additional fluorescent signals can be readily separated from FRET signals, enabling multilabel studies of molecular interactions. PMID:23929684

Assessing FRET using spectral techniques.

PubMed

Leavesley, Silas J; Britain, Andrea L; Cichon, Lauren K; Nikolaev, Viacheslav O; Rich, Thomas C

2013-10-01

Förster resonance energy transfer (FRET) techniques have proven invaluable for probing the complex nature of protein-protein interactions, protein folding, and intracellular signaling events. These techniques have traditionally been implemented with the use of one or more fluorescence band-pass filters, either as fluorescence microscopy filter cubes, or as dichroic mirrors and band-pass filters in flow cytometry. In addition, new approaches for measuring FRET, such as fluorescence lifetime and acceptor photobleaching, have been developed. Hyperspectral techniques for imaging and flow cytometry have also shown to be promising for performing FRET measurements. In this study, we have compared traditional (filter-based) FRET approaches to three spectral-based approaches: the ratio of acceptor-to-donor peak emission, linear spectral unmixing, and linear spectral unmixing with a correction for direct acceptor excitation. All methods are estimates of FRET efficiency, except for one-filter set and three-filter set FRET indices, which are included for consistency with prior literature. In the first part of this study, spectrofluorimetric data were collected from a CFP-Epac-YFP FRET probe that has been used for intracellular cAMP measurements. All comparisons were performed using the same spectrofluorimetric datasets as input data, to provide a relevant comparison. Linear spectral unmixing resulted in measurements with the lowest coefficient of variation (0.10) as well as accurate fits using the Hill equation. FRET efficiency methods produced coefficients of variation of less than 0.20, while FRET indices produced coefficients of variation greater than 8.00. These results demonstrate that spectral FRET measurements provide improved response over standard, filter-based measurements. Using spectral approaches, single-cell measurements were conducted through hyperspectral confocal microscopy, linear unmixing, and cell segmentation with quantitative image analysis. Results from these studies confirmed that spectral imaging is effective for measuring subcellular, time-dependent FRET dynamics and that additional fluorescent signals can be readily separated from FRET signals, enabling multilabel studies of molecular interactions. © 2013 International Society for Advancement of Cytometry. Copyright © 2013 International Society for Advancement of Cytometry.

Emission spectra profiling of fluorescent proteins in living plant cells

PubMed Central

2013-01-01

Background Fluorescence imaging at high spectral resolution allows the simultaneous recording of multiple fluorophores without switching optical filters, which is especially useful for time-lapse analysis of living cells. The collected emission spectra can be used to distinguish fluorophores by a computation analysis called linear unmixing. The availability of accurate reference spectra for different fluorophores is crucial for this type of analysis. The reference spectra used by plant cell biologists are in most cases derived from the analysis of fluorescent proteins in solution or produced in animal cells, although these spectra are influenced by both the cellular environment and the components of the optical system. For instance, plant cells contain various autofluorescent compounds, such as cell wall polymers and chlorophyll, that affect the spectral detection of some fluorophores. Therefore, it is important to acquire both reference and experimental spectra under the same biological conditions and through the same imaging systems. Results Entry clones (pENTR) of fluorescent proteins (FPs) were constructed in order to create C- or N-terminal protein fusions with the MultiSite Gateway recombination technology. The emission spectra for eight FPs, fused C-terminally to the A- or B-type cyclin dependent kinases (CDKA;1 and CDKB1;1) and transiently expressed in epidermal cells of tobacco (Nicotiana benthamiana), were determined by using the Olympus FluoView™ FV1000 Confocal Laser Scanning Microscope. These experimental spectra were then used in unmixing experiments in order to separate the emission of fluorophores with overlapping spectral properties in living plant cells. Conclusions Spectral imaging and linear unmixing have a great potential for efficient multicolor detection in living plant cells. The emission spectra for eight of the most commonly used FPs were obtained in epidermal cells of tobacco leaves and used in unmixing experiments. The generated set of FP Gateway entry vectors represents a valuable resource for plant cell biologists. PMID:23552272

Estimating forest species abundance through linear unmixing of CHRIS/PROBA imagery

NASA Astrophysics Data System (ADS)

Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga

2016-09-01

The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest species (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate species-specific abundance maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each species derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs abundance mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. Abundance estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each species and the actual species mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation species, under real and not optimum acquisition conditions. Its full potential remains to be investigated in further and more complex study sites in view of the upcoming satellite hyperspectral missions.

Kinetics of T-cell receptor-dependent antigen recognition determined in vivo by multi-spectral normalized epifluorescence laser scanning

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Zacharakis, Giannis; Oikonomaki, Katerina; Zacharopoulos, Athanasios; Mamalaki, Clio; Ripoll, Jorge

2012-07-01

Detection of multiple fluorophores in conditions of low signal represents a limiting factor for the application of in vivo optical imaging techniques in immunology where fluorescent labels report for different functional characteristics. A noninvasive in vivo Multi-Spectral Normalized Epifluorescence Laser scanning (M-SNELS) method was developed for the simultaneous and quantitative detection of multiple fluorophores in low signal to noise ratios and used to follow T-cell activation and clonal expansion. Colocalized DsRed- and GFP-labeled T cells were followed in tandem during the mounting of an immune response. Spectral unmixing was used to distinguish the overlapping fluorescent emissions representative of the two distinct cell populations and longitudinal data reported the discrete pattern of antigen-driven proliferation. Retrieved values were validated both in vitro and in vivo with flow cytometry and significant correlation between all methodologies was achieved. Noninvasive M-SNELS successfully quantified two colocalized fluorescent populations and provides a valid alternative imaging approach to traditional invasive methods for detecting T cell dynamics.

Characterizing Non-Resolved Debris Through Spectral and Photometric Ground-Based Telescopic Data: What Can Laboratory Ground-truth Data Do for You?

NASA Technical Reports Server (NTRS)

Lederer, Susan

2017-01-01

NASA's ODPO has recently collected data of unresolved objects at GEO with the 3.8m UKIRT infrared telescope on Mauna Kea and the 1.3m MCAT visible telescope on Ascension Island. Analyses of SWIR data of rocket bodies and HS-376 solar-panel covered buses demonstrate the uniqueness of spectral signatures. Data of 3 classes of rocket bodies show similarities amongst a given class, but distinct differences from one class to another, suggesting that infrared reflectance spectra could effectively be used toward characterizing and constraining potential parent bodies of uncorrelated targets (UCTs). The Optical Measurements Center (OMC) at NASA JSC is designed to collect photometric signatures in the laboratory that can be used for comparison with telescopic data. NASA also has a spectral database of spacecraft materials for use with spectral unmixing models. Spectral unmixing of the HS-376 bus data demonstrates how absorption features and slopes can be used to constrain material characteristics of debris. Broadband photometry likewise can be compared with MCAT data of non-resolved debris images. Similar studies have been applied to IDCSP satellites to demonstrate how color-color photometry can be compared with lab data to constrain bulk materials signatures of spacecraft and debris.

Linear Subpixel Learning Algorithm for Land Cover Classification from WELD using High Performance Computing

NASA Technical Reports Server (NTRS)

Kumar, Uttam; Nemani, Ramakrishna R.; Ganguly, Sangram; Kalia, Subodh; Michaelis, Andrew

2017-01-01

In this work, we use a Fully Constrained Least Squares Subpixel Learning Algorithm to unmix global WELD (Web Enabled Landsat Data) to obtain fractions or abundances of substrate (S), vegetation (V) and dark objects (D) classes. Because of the sheer nature of data and compute needs, we leveraged the NASA Earth Exchange (NEX) high performance computing architecture to optimize and scale our algorithm for large-scale processing. Subsequently, the S-V-D abundance maps were characterized into 4 classes namely, forest, farmland, water and urban areas (with NPP-VIIRS-national polar orbiting partnership visible infrared imaging radiometer suite nighttime lights data) over California, USA using Random Forest classifier. Validation of these land cover maps with NLCD (National Land Cover Database) 2011 products and NAFD (North American Forest Dynamics) static forest cover maps showed that an overall classification accuracy of over 91 percent was achieved, which is a 6 percent improvement in unmixing based classification relative to per-pixel-based classification. As such, abundance maps continue to offer an useful alternative to high-spatial resolution data derived classification maps for forest inventory analysis, multi-class mapping for eco-climatic models and applications, fast multi-temporal trend analysis and for societal and policy-relevant applications needed at the watershed scale.

Linear Subpixel Learning Algorithm for Land Cover Classification from WELD using High Performance Computing

NASA Astrophysics Data System (ADS)

Ganguly, S.; Kumar, U.; Nemani, R. R.; Kalia, S.; Michaelis, A.

2017-12-01

In this work, we use a Fully Constrained Least Squares Subpixel Learning Algorithm to unmix global WELD (Web Enabled Landsat Data) to obtain fractions or abundances of substrate (S), vegetation (V) and dark objects (D) classes. Because of the sheer nature of data and compute needs, we leveraged the NASA Earth Exchange (NEX) high performance computing architecture to optimize and scale our algorithm for large-scale processing. Subsequently, the S-V-D abundance maps were characterized into 4 classes namely, forest, farmland, water and urban areas (with NPP-VIIRS - national polar orbiting partnership visible infrared imaging radiometer suite nighttime lights data) over California, USA using Random Forest classifier. Validation of these land cover maps with NLCD (National Land Cover Database) 2011 products and NAFD (North American Forest Dynamics) static forest cover maps showed that an overall classification accuracy of over 91% was achieved, which is a 6% improvement in unmixing based classification relative to per-pixel based classification. As such, abundance maps continue to offer an useful alternative to high-spatial resolution data derived classification maps for forest inventory analysis, multi-class mapping for eco-climatic models and applications, fast multi-temporal trend analysis and for societal and policy-relevant applications needed at the watershed scale.

Evaluating the Effectiveness of Flood Control Strategies in Contrasting Urban Watersheds and Implications for Houston's Future Flood Vulnerability

NASA Astrophysics Data System (ADS)

Ganguly, S.; Kumar, U.; Nemani, R. R.; Kalia, S.; Michaelis, A.

2016-12-01

In this work, we use a Fully Constrained Least Squares Subpixel Learning Algorithm to unmix global WELD (Web Enabled Landsat Data) to obtain fractions or abundances of substrate (S), vegetation (V) and dark objects (D) classes. Because of the sheer nature of data and compute needs, we leveraged the NASA Earth Exchange (NEX) high performance computing architecture to optimize and scale our algorithm for large-scale processing. Subsequently, the S-V-D abundance maps were characterized into 4 classes namely, forest, farmland, water and urban areas (with NPP-VIIRS - national polar orbiting partnership visible infrared imaging radiometer suite nighttime lights data) over California, USA using Random Forest classifier. Validation of these land cover maps with NLCD (National Land Cover Database) 2011 products and NAFD (North American Forest Dynamics) static forest cover maps showed that an overall classification accuracy of over 91% was achieved, which is a 6% improvement in unmixing based classification relative to per-pixel based classification. As such, abundance maps continue to offer an useful alternative to high-spatial resolution data derived classification maps for forest inventory analysis, multi-class mapping for eco-climatic models and applications, fast multi-temporal trend analysis and for societal and policy-relevant applications needed at the watershed scale.

The ferroan-anorthositic suite and the extent of primordial lunar melting

NASA Technical Reports Server (NTRS)

Warren, Paul H.; Kallemeyn, Gregory W.

1992-01-01

The Apollo highlands rock collection includes more than 100 'pristine' fragments that survived the intense meteoritic bombardment of the ancient lunar crust with unmixed, endogenously igneous compositions. The geochemical anomaly manifested by the 'ferroan-anorthositic suite' (FAS) appears to reflect a geochemical, and probably also a genetic, bimodality among the ancient lunar cumulates. Early models that purported to account for this bimodality as a product of a single magma have been discredited. The model of the present paper implies that the Mg-suite rocks formed by a comparatively normal variety of basaltic fractional crystallization (FC) shortly after the era of magma ocean (MO) crystallization and FAS genesis.

Turbulent unmixing: how marine turbulence drives patchy distributions of motile phytoplankton

NASA Astrophysics Data System (ADS)

Durham, William; Climent, Eric; Barry, Michael; de Lillo, Filippo; Boffetta, Guido; Cencini, Massimo; Stocker, Roman

2013-11-01

Centimeter-scale patchiness in the distribution of phytoplankton increases the efficacy of many important ecological interactions in the marine food web. We show that turbulent fluid motion, usually synonymous with mixing, instead triggers intense small-scale patchiness in the distribution of motile phytoplankton. We use a suite of experiments, direct numerical simulations of turbulence, and analytical tools to show that turbulent shear and acceleration directs the motility of cells towards well-defined regions of flow, increasing local cell concentrations more than ten fold. This motility-driven `unmixing' offers an explanation for why motile cells are often more patchily distributed than non-motile cells and provides a mechanistic framework to understand how turbulence, whose strength varies profoundly in marine environments, impacts ocean productivity.

Comparisons of a Constrained Least Squares Model versus Human-in-the-Loop for Spectral Unmixing to Determine Material Type of GEO Debris

NASA Technical Reports Server (NTRS)

Abercromby, Kira J.; Rapp, Jason; Bedard, Donald; Seitzer, Patrick; Cardona, Tommaso; Cowardin, Heather; Barker, Ed; Lederer, Susan

2013-01-01

Spectral reflectance data through the visible regime was collected at Las Campanas Observatory in Chile using an imaging spectrograph on one of the twin 6.5-m Magellan telescopes. The data were obtained on 1-2 May 2012 on the 'Landon Clay' telescope with the LDSS3 (Low Dispersion Survey Spectrograph 3). Five pieces of Geosynchronous Orbit (GEO) or near-GEO debris were identified and observed with an exposure time of 30 seconds on average. In addition, laboratory spectral reflectance data was collected using an Analytical Spectral Device (ASD) field spectrometer at California Polytechnic State University (Cal Poly) in San Luis Obispo on several typical common spacecraft materials including solar cells, circuit boards, various Kapton materials used for multi-layer insulation, and various paints. The remotely collected data and the laboratory-acquired data were then incorporated in a newly developed model that uses a constrained least squares method to unmix the spectrum in specific material components. The results of this model are compared to the previous method of a human-in-the-loop (considered here the traditional method) that identifies possible material components by varying the materials and percentages until a spectral match is obtained. The traditional model was found to match the remotely collected spectral data after it had been divided by the continuum to remove the space weathering effects, or a reddening of the materials. The constrained least-squares model also used the de-reddened spectra as inputs and the results were consistent with those obtained through the traditional method. For comparison, a first-order examination of including reddening effects into the constrained least-squares model will be explored and comparisons to the remotely collected data will be examined. The identification of each object s suspected material component will be discussed herein.

Comparisons of a Constrained Least Squares Model Versus Human-in-the-Loop for Spectral Unmixing to Determine Material Type of GEO Debris

NASA Technical Reports Server (NTRS)

Rapp, Jason; Abercromby, Kira J.; Bedard, Donald; Seitzer, Patrick; Cardona, Tommaso; Cowardin, Heather; Barker, Ed; Lederer, Susan

2012-01-01

Spectral reflectance data through the visible regime was collected at Las Campanas Observatory in Chile using an imaging spectrograph on one of the twin 6.5-m Magellan telescopes. The data were obtained on 1-2 May 2012 on the 'Landon Clay' telescope with the LDSS3 (Low Dispersion Survey Spectrograph 3). Five pieces of Geosynchronous Orbit (GEO) or near-GEO debris were identified and observed with an exposure time of 30 seconds on average. In addition, laboratory spectral reflectance data was collected using an Analytical Spectral Device (ASD) field spectrometer at California Polytechnic State University in San Luis Obispo on several typical common spacecraft materials including solar cells, circuit boards, various Kapton materials used for multi-layer insulation, and various paints. The remotely collected data and the laboratory-acquired data were then incorporated in a newly developed model that uses a constrained least squares method to unmix the spectrum in specific material components. The results of this model are compared to the previous method of a human-in-the-loop (considered here the traditional method) that identifies possible material components by varying the materials and percentages until a spectral match is obtained. The traditional model was found to match the remotely collected spectral data after it had been divided by the continuum to remove the space weathering effects, or a "reddening" of the materials. The constrained least-squares model also used the de-reddened spectra as inputs and the results were consistent with those obtained through the traditional method. For comparison, a first-order examination of including reddening effects into the constrained least-squares model will be explored and comparisons to the remotely collected data will be examined. The identification of each object's suspected material component will be discussed herein.

Analysis of OMEGA/Mars Express data hyperspectral data using a Multiple-Endmember Linear Spectral Unmixing Model (MELSUM): Methodology and first results

NASA Astrophysics Data System (ADS)

OMEGA Science Team; Combe, J.-Ph.; Le Mouélic, S.; Sotin, C.; Gendrin, A.; Mustard, J. F.; Le Deit, L.; Launeau, P.; Bibring, J.-P.; Gondet, B.; Langevin, Y.; Pinet, P.; OMEGA Science Team

2008-05-01

The mineralogical composition of the Martian surface is investigated by a Multiple-Endmember Linear Spectral Unmixing Model (MELSUM) of the Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité (OMEGA) imaging spectrometer onboard Mars Express. OMEGA has fully covered the surface of the red planet at medium to low resolution (2-4 km per pixel). Several areas have been imaged at a resolution up to 300 m per pixel. One difficulty in the data processing is to extract the mineralogical composition, since rocks are mixtures of several components. MELSUM is an algorithm that selects the best linear combination of spectra among the families of minerals available in a reference library. The best fit of the observed spectrum on each pixel is calculated by the same unmixing equation used in the classical Spectral Mixture Analysis (SMA). This study shows the importance of the choice of the input library, which contains in our case 24 laboratory spectra (endmembers) of minerals that cover the diversity of the mineral families that may be found on the Martian surface. The analysis is restricted to the 1.0-2.5 μm wavelength range. Grain size variations and atmospheric scattering by aerosols induce changes in overall albedo level and continuum slopes. Synthetic flat and pure slope spectra have therefore been included in the input mineral spectral endmembers library in order to take these effects into account. The selection process for the endmembers is a systematic exploration of whole set of combinations of four components plus the straight line spectra. When negative coefficients occur, the results are discarded. This strategy is successfully tested on the terrestrial Cuprite site (Nevada, USA), for which extensive ground observations exist. It is then applied to different areas on Mars including Syrtis Major, Aram Chaos and Olympia Undae near the North Polar Cap. MELSUM on Syrtis Major reveals a region dominated by mafic minerals, with the oldest crustal regions composed of a mixing between low-calcium pyroxenes (LCPs) (orthopyroxenes (OPx)) and high-calcium pyroxenes (HCPs) (clinopyroxenes (CPx)). The Syrtis volcanic edifice appears depleted in LCP (OPx) and enriched in HCP (CPx), which is consistent with materials produced with a lower partial fusion degree at an age younger to the surrounding crust. Strong olivine signatures are found between the two calderas Nili Patera and Meroe Patera and in Nili Fossae. A strong signature of iron oxides is found within Aram Chaos, with a spatial distribution also consistent with thermal emission spectrometer (TES). Gypsum is unambiguously detected in the northern polar region, in agreement with the study of Langevin et al. [2005. Sulfates in the north polar region of Mars detected by OMEGA/Mars Express. Science 307(5715), 1584-1586]. Our results show that the linear spectral unmixing provides good first order results in a variety of mineralogical contexts, and can therefore confidently be used on a wider scale to analyze the complete archive of OMEGA data.

Improving alpine-region spectral unmixing with optimal-fit snow endmembers

NASA Technical Reports Server (NTRS)

Painter, Thomas H.; Roberts, Dar A.; Green, Robert O.; Dozier, Jeff

1995-01-01

Surface albedo and snow-covered-area (SCA) are crucial inputs to the hydrologic and climatologic modeling of alpine and seasonally snow-covered areas. Because the spectral albedo and thermal regime of pure snow depend on grain size, areal distribution of snow grain size is required. Remote sensing has been shown to be an effective (and necessary) means of deriving maps of grain size distribution and snow-covered-area. Developed here is a technique whereby maps of grain size distribution improve estimates of SCA from spectral mixture analysis with AVIRIS data.

Dictionary-Based Tensor Canonical Polyadic Decomposition

NASA Astrophysics Data System (ADS)

Cohen, Jeremy Emile; Gillis, Nicolas

2018-04-01

To ensure interpretability of extracted sources in tensor decomposition, we introduce in this paper a dictionary-based tensor canonical polyadic decomposition which enforces one factor to belong exactly to a known dictionary. A new formulation of sparse coding is proposed which enables high dimensional tensors dictionary-based canonical polyadic decomposition. The benefits of using a dictionary in tensor decomposition models are explored both in terms of parameter identifiability and estimation accuracy. Performances of the proposed algorithms are evaluated on the decomposition of simulated data and the unmixing of hyperspectral images.

Linear mixing model applied to coarse spatial resolution data from multispectral satellite sensors

NASA Technical Reports Server (NTRS)

Holben, Brent N.; Shimabukuro, Yosio E.

1993-01-01

A linear mixing model was applied to coarse spatial resolution data from the NOAA Advanced Very High Resolution Radiometer. The reflective component of the 3.55-3.95 micron channel was used with the two reflective channels 0.58-0.68 micron and 0.725-1.1 micron to run a constrained least squares model to generate fraction images for an area in the west central region of Brazil. The fraction images were compared with an unsupervised classification derived from Landsat TM data acquired on the same day. The relationship between the fraction images and normalized difference vegetation index images show the potential of the unmixing techniques when using coarse spatial resolution data for global studies.

Detailed emission profiles for on-road vehicles derived from ambient measurements during a windless traffic episode in Baltimore using a multi-model approach

NASA Astrophysics Data System (ADS)

Ke, Haohao; Ondov, John M.; Rogge, Wolfgang F.

2013-12-01

Composite chemical profiles of motor vehicle emissions were extracted from ambient measurements at a near-road site in Baltimore during a windless traffic episode in November, 2002, using four independent approaches, i.e., simple peak analysis, windless model-based linear regression, PMF, and UNMIX. Although the profiles are in general agreement, the windless-model-based profile treatment more effectively removes interference from non-traffic sources and is deemed to be more accurate for many species. In addition to abundances of routine pollutants (e.g., NOx, CO, PM2.5, EC, OC, sulfate, and nitrate), 11 particle-bound metals and 51 individual traffic-related organic compounds (including n-alkanes, PAHs, oxy-PAHs, hopanes, alkylcyclohexanes, and others) were included in the modeling.

Analyses of atmospheric pollutants in Hong Kong and the Pearl River Delta by observation-based methods

NASA Astrophysics Data System (ADS)

Yuan, Zibing

Despite continuous efforts paid on pollution control by the Hong Kong (HK) environmental authorities in the past decade, the air pollution in HK has been deteriorating in recent years. In this thesis work a variety of observation-based approaches were applied to analyze the air pollutant monitoring data in HK and the Pearl River Delta (PRD) area. The two major pollutants of interest are ozone and respirable suspended particulate (RSP, or PM10), which exceed the Air Quality Objective more frequently. Receptor models serve as powerful tools for source identification, estimation of source contributions, and source localization when incorporated with wind profiles. This thesis work presents the first-ever application of two advanced receptor-models, positive matrix factorization (PMT) and Unmix, on the PM10 and VOCs speciation data in HK. Speciated PM10 data were collected from a monitoring network in HK between July-1998 and Dec-2005. Seven and nine sources were identified by Unmix and PMF10, respectively. Overall, secondary sulfate and vehicle emissions gave the largest contribution to PM10 (27% each), followed by biomass burning/waste incineration (13%) and secondary nitrate (11%). Sources were classified as local and regional based on its seasonal and spatial variations as well as source directional analysis. Regional sources accounted for about 56% of the ambient PM10 mass on an annual basis, and even higher (67%) during winter. Regional contributions also showed an increasing trend, with their annual averaged fraction rising from 53% in 1999 to 64% in 2005. The particulate pollution in HK is therefore sensitive to the regional influence and regional air quality management strategies are crucial in reducing PM level in HK. On the other hand, many species with significant adverse health impacts were produced locally. Local control measures should be strengthened for better protection of public health. Secondary organic carbon (SOC) could be a significant portion of OC in particles. SOC was examined by using PMF-derived source apportionment results and estimated to be sum of OC present in the secondary sources. The annual average SOC in HK was estimated to be 4.1 mugC/m3 while summertime average was 1.8 RgC/m3 and wintertime average was 6.9 ggC/m 3. In comparison with the SOC estimates by the PMF method, the method that uses elemental carbon (EC) as the tracer for primary OC to derive at SOC overestimates by 78-210% for the summer samples and by 9-49% for the winter samples. The overestimation by the EC tracer method was a result of incapability of obtaining a single OC/EC ratio that represented a mixture of primary sources varying in time and space. It was found that SOC and secondary sulfate had their seasonal variation in sync, suggesting common factors that control their formation. The close tracking of SOC and sulfate appears to suggest that in-cloud pathway is also important for SOC formation. Speciated VOCs were obtained in four air quality monitoring stations (AQMSs) in HK from August-2002 to August-2003. Both Unmix and PMF identified five stable sources. Mixed solvents gave the largest contributions ranging from 34% at rural Tap Mun to 52% at urban Central/Western. The wind directional analysis indicates the main source location at the central PRD area. Regional transport accounts for about 19% of the total VOC, while the two local and vehicle-related sources are responsible for 27%. By weighing the abundance and reactivity of each VOC species, mixed solvent use is estimated to be the largest contributor of local ozone, with the contributions ranging from 42% at Tung Chung to 57% at Tap Mun. The next largest is the vehicle exhaust, accounting for about 28% in Yuen Long. Biogenic emission is responsible for nearly 20% of the ozone generation at Tap Mun but this figure is likely underestimated. Distinct secondary inorganic aerosol (SIA) responses are expected to the reduction of different precursors as a result of non-linear chemical reactions involved in its formation. The last part of this thesis work concerns developing a chemical box model to determine the sensitivity of SIA to changes to the emissions of their precursors. The model is composed of three parts. The first part is a time-dependent module to estimate the temporal variation of all species, before and after the emission has been disturbed. The second part is a gas-particle conversion module that partitions the semi-volatile species into the two phases. The last module would then calculate the aerosol forming potential for the entire simulation period. It is estimated that SIA shows the largest response to the reduction of SO2 emission in YL, followed by NH3 and NOx. Significant regional transport of SIA is discovered in YL, limiting the indication of relative effectiveness for controlling different precursors. At the end, future research directions are proposed to better refine and validate the OBM performance for SIA simulation.

THz spectral data analysis and components unmixing based on non-negative matrix factorization methods

NASA Astrophysics Data System (ADS)

Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

2017-04-01

In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification.

The nature of the fluids associated with the Monte Rosa gold district, NW Alps, Italy

NASA Astrophysics Data System (ADS)

Lattanzi, P.

1990-12-01

Recent O-isotope and fluid inclusion studies have provided evidence on the nature of the fluids associated with the late-Alpine quartz-gold deposits of the Monte Rosa district. The most abundant inclusions in quartz from these deposits contain a low salinity aqueous fluid (about 2% to 10% wt. NaCl eq.), and a CO2 phase (usually less than 20% mol), in places with minor methane. CO2 densities and total homogenization temperatures vary widely throughout the district, reflecting diverse conditions of trapping (P = 1 to 3 kb, T = 300° to 450°C). At Miniera dei Cani, unmixing between CO2-rich and H2O-rich fluids possibly occurred. A second type of inclusion contains an aqueous brine without recognizable CO2, and is especially abundant at Val Toppa. O-isotope studies suggest that fluids were largely equilibrated in a metamorphic environment. It is concluded that the gold-related fluids in the district were mainly of a metamorphic nature; at Val Toppa, both isotopic and fluid inclusion data point to contributions of unexchanged meteoric waters. Mechanisms of gold transport and precipitation are less contrained. A possible model involves transport of gold as bisulfide complexes, and precipitation due to one or more of the following processes: decrease of sulfur activity due to precipitation of sulfides, wall-rock reaction, cooling/dilution, and/or fluid unmixing.

THz spectral data analysis and components unmixing based on non-negative matrix factorization methods.

PubMed

Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

2017-04-15

In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification. Copyright © 2017 Elsevier B.V. All rights reserved.

Unmixing techniques for better segmentation of urban zones, roads, and open pit mines

NASA Astrophysics Data System (ADS)

Nikolov, Hristo; Borisova, Denitsa; Petkov, Doyno

2010-10-01

In this paper the linear unmixing method has been applied in classification of manmade objects, namely urbanized zones, roads etc. The idea is to exploit to larger extent the possibilities offered by multispectral imagers having mid spatial resolution in this case TM/ETM+ instruments. In this research unmixing is used to find consistent regression dependencies between multispectral data and those gathered in-situ and airborne-based sensors. The correct identification of the mixed pixels is key element for the subsequent segmentation forming the shape of the artificial feature is determined much more reliable. This especially holds true for objects with relatively narrow structure for example two-lane roads for which the spatial resolution is larger that the object itself. We have combined ground spectrometry of asphalt, Landsat images of RoI, and in-situ measured asphalt in order to determine the narrow roads. The reflectance of paving stones made from granite is highest compared to another ones which is true for open and stone pits. The potential for mapping is not limited to the mid-spatial Landsat data, but also may be used if the data has higher spatial resolution (as fine as 0.5 m). In this research the spectral and directional reflection properties of asphalt and concrete surfaces compared to those of paving stone made from different rocks have been measured. The in-situ measurements, which plays key role have been obtained using the Thematically Oriented Multichannel Spectrometer (TOMS) - designed in STIL-BAS.

(LMRG): Microscope Resolution, Objective Quality, Spectral Accuracy and Spectral Un-mixing

PubMed Central

Bayles, Carol J.; Cole, Richard W.; Eason, Brady; Girard, Anne-Marie; Jinadasa, Tushare; Martin, Karen; McNamara, George; Opansky, Cynthia; Schulz, Katherine; Thibault, Marc; Brown, Claire M.

2012-01-01

The second study by the LMRG focuses on measuring confocal laser scanning microscope (CLSM) resolution, objective lens quality, spectral imaging accuracy and spectral un-mixing. Affordable test samples for each aspect of the study were designed, prepared and sent to 116 labs from 23 countries across the globe. Detailed protocols were designed for the three tests and customized for most of the major confocal instruments being used by the study participants. One protocol developed for measuring resolution and objective quality was recently published in Nature Protocols (Cole, R. W., T. Jinadasa, et al. (2011). Nature Protocols 6(12): 1929–1941). The first study involved 3D imaging of sub-resolution fluorescent microspheres to determine the microscope point spread function. Results of the resolution studies as well as point spread function quality (i.e. objective lens quality) from 140 different objective lenses will be presented. The second study of spectral accuracy looked at the reflection of the laser excitation lines into the spectral detection in order to determine the accuracy of these systems to report back the accurate laser emission wavelengths. Results will be presented from 42 different spectral confocal systems. Finally, samples with double orange beads (orange core and orange coating) were imaged spectrally and the imaging software was used to un-mix fluorescence signals from the two orange dyes. Results from 26 different confocal systems will be summarized. Time will be left to discuss possibilities for the next LMRG study.

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

The NASA Lightning Nitrogen Oxides Model (LNOM): Recent Updates and Applications

NASA Technical Reports Server (NTRS)

Koshak, William; Peterson, Harold; Biazar, Arastoo; Khan, Maudood; Wang, Lihua; Park, Yee-Hun

2011-01-01

Improvements to the NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) and its application to the Community Multiscale Air Quality (CMAQ) modeling system are presented. The LNOM analyzes Lightning Mapping Array (LMA) and National Lightning Detection Network(tm) (NLDN) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning NOx (= NO + NO2). Lightning channel length distributions and lightning 10-m segment altitude distributions are also provided. In addition to NOx production from lightning return strokes, the LNOM now includes non-return stroke lightning NOx production due to: hot core stepped and dart leaders, stepped leader corona sheath, K-changes, continuing currents, and M-components. The impact of including LNOM-estimates of lightning NOx for an August 2006 run of CMAQ is discussed.

Ignition and structure of a laminar diffusion flame in the field of a vortex

NASA Technical Reports Server (NTRS)

Macaraeg, Michele G.; Jackson, T. L.; Hussaini, M. Y.

1991-01-01

The distortion of flames in flows with vortical motion is examined via asymptotic analysis and numerical simulation. The model consists of a constant density, one step, irreversible Arrhenius reaction between initially unmixed species occupying adjacent half-planes which are then allowed to mix and react in the presence of a vortex. The evolution in time of the temperature and mass fraction fields is followed. Emphasis is placed on the ignition time and location as a function of vortex Reynolds number and initial temperature differences of the reacting species. The study brings out the influence of the vortex on the chemical reaction. In all phases, good agreement is observed between asymptotic analysis and the full numerical solution of the model equations.

Radiative absorption enhancement of dust mixed with anthropogenic pollution over East Asia

NASA Astrophysics Data System (ADS)

Tian, Pengfei; Zhang, Lei; Ma, Jianmin; Tang, Kai; Xu, Lili; Wang, Yuan; Cao, Xianjie; Liang, Jiening; Ji, Yuemeng; Jiang, Jonathan H.; Yung, Yuk L.; Zhang, Renyi

2018-06-01

The particle mixing state plays a significant yet poorly quantified role in aerosol radiative forcing, especially for the mixing of dust (mineral absorbing) and anthropogenic pollution (black carbon absorbing) over East Asia. We have investigated the absorption enhancement of mixed-type aerosols over East Asia by using the Aerosol Robotic Network observations and radiative transfer model calculations. The mixed-type aerosols exhibit significantly enhanced absorbing ability than the corresponding unmixed dust and anthropogenic aerosols, as revealed in the spectral behavior of absorbing aerosol optical depth, single scattering albedo, and imaginary refractive index. The aerosol radiative efficiencies for the dust, mixed-type, and anthropogenic aerosols are -101.0, -112.9, and -98.3 Wm-2 τ-1 at the bottom of the atmosphere (BOA); -42.3, -22.5, and -39.8 Wm-2 τ-1 at the top of the atmosphere (TOA); and 58.7, 90.3, and 58.5 Wm-2 τ-1 in the atmosphere (ATM), respectively. The BOA cooling and ATM heating efficiencies of the mixed-type aerosols are significantly higher than those of the unmixed aerosol types over the East Asia region, resulting in atmospheric stabilization. In addition, the mixed-type aerosols correspond to a lower TOA cooling efficiency, indicating that the cooling effect by the corresponding individual aerosol components is partially counteracted. We conclude that the interaction between dust and anthropogenic pollution not only represents a viable aerosol formation pathway but also results in unfavorable dispersion conditions, both exacerbating the regional air pollution in East Asia. Our results highlight the necessity to accurately account for the mixing state of aerosols in atmospheric models over East Asia in order to better understand the formation mechanism for regional air pollution and to assess its impacts on human health, weather, and climate.

Quantifying the Components of Impervious Surfaces

USGS Publications Warehouse

Tilley, Janet S.; Slonecker, E. Terrence

2006-01-01

This study's objectives were to (1) determine the relative contribution of impervious surface individual components by collecting digital information from high-resolution imagery, 1-meter or better; and to (2) determine which of the more advanced techniques, such as spectral unmixing or the application of coefficients to land use or land cover data, was the most suitable method that could be used by State and local governments as well as Federal agencies to efficiently measure the imperviousness in any given watershed or area of interest. The components of impervious surfaces, combined from all the watersheds and time periods from objective one were the following: buildings 29.2-percent, roads 28.3-percent, parking lots 24.6-percent; with the remaining three totaling 14-percent - driveways, sidewalks, and other, where other were any other features that were not contained within the first five. Results from objective two were spectral unmixing techniques will ultimately be the most efficient method of determining imperviousness, but are not yet accurate enough as it is critical to achieve accuracy better than 10-percent of the truth, of which the method is not consistently accomplishing as observed in this study. Of the three techniques in coefficient application tested, land use coefficient application was not practical, while if the last two methods, coefficients applied to land cover data, were merged, their end results could be to within 5-percent or better, of the truth. Until the spectral unmixing technique has been further refined, land cover coefficients should be used, which offer quick results, but not current as they were developed for the 1992 National Land Characteristics Data.

[Orthogonal Vector Projection Algorithm for Spectral Unmixing].

PubMed

Song, Mei-ping; Xu, Xing-wei; Chang, Chein-I; An, Ju-bai; Yao, Li

2015-12-01

Spectrum unmixing is an important part of hyperspectral technologies, which is essential for material quantity analysis in hyperspectral imagery. Most linear unmixing algorithms require computations of matrix multiplication and matrix inversion or matrix determination. These are difficult for programming, especially hard for realization on hardware. At the same time, the computation costs of the algorithms increase significantly as the number of endmembers grows. Here, based on the traditional algorithm Orthogonal Subspace Projection, a new method called. Orthogonal Vector Projection is prompted using orthogonal principle. It simplifies this process by avoiding matrix multiplication and inversion. It firstly computes the final orthogonal vector via Gram-Schmidt process for each endmember spectrum. And then, these orthogonal vectors are used as projection vector for the pixel signature. The unconstrained abundance can be obtained directly by projecting the signature to the projection vectors, and computing the ratio of projected vector length and orthogonal vector length. Compared to the Orthogonal Subspace Projection and Least Squares Error algorithms, this method does not need matrix inversion, which is much computation costing and hard to implement on hardware. It just completes the orthogonalization process by repeated vector operations, easy for application on both parallel computation and hardware. The reasonability of the algorithm is proved by its relationship with Orthogonal Sub-space Projection and Least Squares Error algorithms. And its computational complexity is also compared with the other two algorithms', which is the lowest one. At last, the experimental results on synthetic image and real image are also provided, giving another evidence for effectiveness of the method.

Estimating photosynthetic vegetation, non-photosynthetic vegetation and bare soil fractions using Landsat and MODIS data: Effects of site heterogeneity, soil properties and land cover

NASA Astrophysics Data System (ADS)

Guerschman, J. P.; Scarth, P.; McVicar, T.; Malthus, T. J.; Stewart, J.; Rickards, J.; Trevithick, R.; Renzullo, L. J.

2013-12-01

Vegetation fractional cover is a key indicator for land management monitoring, both in pastoral and agricultural settings. Maintaining adequate vegetation cover protects the soil from the effects of water and wind erosion and also ensures that carbon is returned to soil through decomposition. Monitoring vegetation fractional cover across large areas and continuously in time needs good remote sensing techniques underpinned by high quality ground data to calibrate and validate algorithms. In this study we used Landsat and MODIS reflectance data together with field measurements from 1476 observations across Australia to produce estimates of vegetation fractional cover using a linear unmixing technique. Specifically, we aimed at separating fractions of photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV) and bare soil (B). We used Landsat reflectance averaged over a 3x3 pixel window representing the area actually measured on the ground and also a 'degraded' Landsat reflectance 40x40 pixel window to simulate the effect of a coarser sensor. Using these two Landsat reflectances we quantified the heterogeneity of each site. We used data from two MODIS-derived reflectance products: the Nadir BRDF-Adjusted surface Reflectance product (MCD43A4) and the MODIS 8-day surface reflectance (MOD09A1). We derived endmembers from the data and estimated fractional cover using a linear unmixing technique. Log transforms and band interaction terms were added to account for non-linearities in the spectral mixing. For each reflectance source we investigated if the residuals were correlated with site heterogeneity, soil colour, soil moisture and land cover type. As expected, the best model was obtained when Landsat data for a small region around each site was used. We obtained root mean square error (RMSE) values of 0.134, 0.175 and 0.153 for PV, NPV and B respectively. When we degraded the Landsat data to an area of ~1 km2 around each site the model performance decreased to RMSE of 0.142, 0.181 and 0.166 for PV, NPV and B. Using MODIS reflectance data (from the MCD43A4 and MOD09A1 products) we obtained similar results as when using the 'degraded' Landsat reflectance, with no significant differences between them. Model performance decreased (i.e. RMSE increased) with site heterogeneity when coarse resolution reflectance data was used. We did not find any evidence of soil colour or moisture influence on model performance. We speculate that the unmixing models may be insensitive to soil colour and/or that the soil moisture in the top few millimetres of soil, which influence reflectance in optical sensors, is decoupled from the soil moisture in the top layer (i.e. a few cm) as measured by passive microwave sensors or estimated by models. The models tended to overestimate PV in cropping areas, possibly due to a strong red/ near infrared signal in homogeneous crops which do not have a high green cover. This study sets the basis for an operational Landsat/ MODIS combined product which would benefit users with varying requirements of spatial, temporal resolution and latency and could potentially be applied to other regions in the world.

Remote sensing of particle dynamics: a two-component unmixing model in a western UK shelf sea.

NASA Astrophysics Data System (ADS)

Mitchell, Catherine; Cunningham, Alex

2014-05-01

The relationship between the backscattering and absorption coefficients, in particular the backscattering to absorption ratio, is mediated by the type of particles present in the water column. By considering the optical signals to be driven by phytoplankton and suspended minerals, with a relatively constant influence from CDOM, radiative transfer modelling is used to propose a method for retrieving the optical contribution of phytoplankton and suspended minerals to the total absorption coefficient with mean percentage errors of below 5% for both components. These contributions can be converted to constituent concentrations if the appropriate specific inherent optical properties are known or can be determined from the maximum and minimum backscattering to absorption ratios of the data. Remotely sensed absorption and backscattering coefficients from eight years of MODIS data for the Irish Sea reveal maximum backscattering to absorption coefficient ratios over the winter (with an average for the region of 0.27), which then decrease to a minimum over the summer months (with an average of 0.06) before increasing again through to winter, indicating a change in the particles present in the water column. Application of the two-component unmixing model to this data showed seasonal cycles of both phytoplankton and suspended mineral concentrations which vary in both amplitude and periodicity depending on their location. For example, in the Bristol Channel the amplitude of the suspended mineral concentration throughout one cycle is approximately 75% greater than a yearly cycle in the eastern Irish Sea. These seasonal cycles give an insight into the complex dynamics of particles in the water column, indicating the suspension of sediment throughout the winter months and the loss of sediments from the surface layer over the summer during stratification. The relationship between the timing of the phytoplankton spring bloom and changes in the availability of light in the water column can be studied to gain an understanding into the phytoplankton phenology across the region.

Using Land Surface Phenology to Detect Land Use Change in the Northern Great Plains

NASA Astrophysics Data System (ADS)

Nguyen, L. H.; Henebry, G. M.

2017-12-01

The Northern Great Plains of the US have been undergoing many types of land cover / land use change over the past two decades, including expansion of irrigation, conversion of grassland to cropland, biofuels production, urbanization, and fossil fuel mining. Much of the literature on these changes has relied on post-classification change detection based on a limited number of observations per year. Here we demonstrate an approach to characterize land dynamics through land surface phenology (LSP) by synergistic use of image time series at two scales. Our study areas include regions of interest (ROIs) across the Northern Great Plains located within Landsat path overlap zones to boost the number of valid observations (free of clouds or snow) each year. We first compute accumulated growing degree-days (AGDD) from MODIS 8-day composites of land surface temperature (MOD11A2 and MYD11A2). Using Landsat Collection 1 surface reflectance-derived vegetation indices (NDVI, EVI), we then fit at each pixel a downward convex quadratic model linking the vegetation index to each year's progression of AGDD. This quadratic equation exhibits linearity in a mathematical sense; thus, the fitted models can be linearly mixed and unmixed using a set of LSP endmembers (defined by the fitted parameter coefficients of the quadratic model) that represent "pure" land cover types with distinct seasonal patterns found within the region, such as winter wheat, spring wheat, maize, soybean, sunflower, hay/pasture/grassland, developed/built-up, among others. Information about land cover corresponding to each endmember are provided by the NLCD (National Land Cover Dataset) and CDL (Cropland Data Layer). We use linear unmixing to estimate the likely proportion of each LSP endmember within particular areas stratified by latitude. By tracking the proportions over the 2001-2011 period, we can quantify various types of land transitions in the Northern Great Plains.

Source Characterization of Heavy Gas Dispersion Models for Reactive Chemicals. Volume 1

DTIC Science & Technology

1987-12-21

Temperatura TC10263,3 K (K) f Liquid aerosol TAIRw30 0 K mass fraction in fl " 75% MO unmixed sulfur dioxide cloud 1nil 0.1 it 100 1o0 Mass Air / Mass Sulfur...Modified Sigma Theta Method for Determining Atmospheric Stability a.* Daytime Wind speed Nighttime** ( de ;6ees) stability (m s" at 10 m) stability -U>22.5 A...rate of air mass entrainment into the cloud can be represented by the equations: dE dMT d- PaUE 2 WR H and -- PaUT ’ R2 (5.2.7)dt dt where uE and u are

Oxide dispersion strengthened ferritic steels: a basic research joint program in France

NASA Astrophysics Data System (ADS)

Boutard, J.-L.; Badjeck, V.; Barguet, L.; Barouh, C.; Bhattacharya, A.; Colignon, Y.; Hatzoglou, C.; Loyer-Prost, M.; Rouffié, A. L.; Sallez, N.; Salmon-Legagneur, H.; Schuler, T.

2014-12-01

AREVA, CEA, CNRS, EDF and Mécachrome are funding a joint program of basic research on Oxide Dispersion Strengthened Steels (ODISSEE), in support to the development of oxide dispersion strengthened 9-14% Cr ferritic-martensitic steels for the fuel element cladding of future Sodium-cooled fast neutron reactors. The selected objectives and the results obtained so far will be presented concerning (i) physical-chemical characterisation of the nano-clusters as a function of ball-milling process, metallurgical conditions and irradiation, (ii) meso-scale understanding of failure mechanisms under dynamic loading and creep, and, (iii) kinetic modelling of nano-clusters nucleation and α/α‧ unmixing.

The NASA Lightning Nitrogen Oxides Model (LNOM): Application to Air Quality Modeling

NASA Technical Reports Server (NTRS)

Koshak, William; Peterson, Harold; Khan, Maudood; Biazar, Arastoo; Wang, Lihua

2011-01-01

Recent improvements to the NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) and its application to the Community Multiscale Air Quality (CMAQ) modeling system are discussed. The LNOM analyzes Lightning Mapping Array (LMA) and National Lightning Detection Network(TradeMark)(NLDN) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning NO(x) (= NO + NO2). The latest LNOM estimates of lightning channel length distributions, lightning 1-m segment altitude distributions, and the vertical profile of lightning NO(x) are presented. The primary improvement to the LNOM is the inclusion of non-return stroke lightning NOx production due to: (1) hot core stepped and dart leaders, (2) stepped leader corona sheath, K-changes, continuing currents, and M-components. The impact of including LNOM-estimates of lightning NO(x) for an August 2006 run of CMAQ is discussed.

Linear mixing model applied to AVHRR LAC data

NASA Technical Reports Server (NTRS)

Holben, Brent N.; Shimabukuro, Yosio E.

1993-01-01

A linear mixing model was applied to coarse spatial resolution data from the NOAA Advanced Very High Resolution Radiometer. The reflective component of the 3.55 - 3.93 microns channel was extracted and used with the two reflective channels 0.58 - 0.68 microns and 0.725 - 1.1 microns to run a Constraine Least Squares model to generate vegetation, soil, and shade fraction images for an area in the Western region of Brazil. The Landsat Thematic Mapper data covering the Emas National park region was used for estimating the spectral response of the mixture components and for evaluating the mixing model results. The fraction images were compared with an unsupervised classification derived from Landsat TM data acquired on the same day. The relationship between the fraction images and normalized difference vegetation index images show the potential of the unmixing techniques when using coarse resolution data for global studies.

A Novel Approach to Model the Air-Side Heat Transfer in Microchannel Condensers

NASA Astrophysics Data System (ADS)

Martínez-Ballester, S.; Corberán, José-M.; Gonzálvez-Maciá, J.

2012-11-01

The work presents a model (Fin1D×3) for microchannel condensers and gas coolers. The paper focusses on the description of the novel approach employed to model the air-side heat transfer. The model applies a segment-by-segment discretization to the heat exchanger adding, in each segment, a specific bi-dimensional grid to the air flow and fin wall. Given this discretization, the fin theory is applied by using a continuous piecewise function for the fin wall temperature. It allows taking into account implicitly the heat conduction between tubes along the fin, and the unmixed air influence on the heat capacity. The model has been validated against experimental data resulting in predicted capacity errors within ± 5%. Differences on prediction results and computational cost were studied and compared with the previous authors' model (Fin2D) and with other simplified model. Simulation time of the proposed model was reduced one order of magnitude respect the Fin2D's time retaining its same accuracy.

46 CFR 164.006-5 - Procedure for approval.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the deck covering. (2) The range of thicknesses in which it is proposed to lay the deck covering... (c). (2) Sufficient bulk material (unmixed) to lay a sample one inch thick on an area of 12″×27″. If...

Monitoring intracellular oxidative events using dynamic spectral unmixing microscopy

EPA Science Inventory

There is increasing interest in using live-cell imaging to monitor not just individual intracellular endpoints, but to investigate the interplay between multiple molecular events as they unfold in real time within the cell. A major impediment to simultaneous acquisition of multip...

Exsolution as an Example of Complex-System Behavior

NASA Astrophysics Data System (ADS)

Mogk, D. W.; Dutrow, B. L.

2010-12-01

Exsolution in minerals is an important process that occurs in a wide range of mineral groups (e.g. alkali feldspars, pyroxenes, amphiboles, carbonates, oxides, sulfides) in response to changing physical conditions. Exsolution describes a physical process in which a mineral with an initially homogeneous solid solution separates into at least two distinct derivative minerals of disparate composition and is typically interpreted as the product of unmixing in response to lattice strain during slow cooling. Such a process is typically taught in introductory mineralogy and petrology courses, in part because exsolution textures can be readily observed in hand sample or thin section. Exsolution is typically represented on equilibrium binary phase diagrams (T-X), and compositions of the unmixed products can be used in geothermobarometry to calculate temperatures and pressures of initial equilibration or compositions of the unmixed products. Although central to course content, traditional approaches to teaching exsolution are largely descriptive, and do not address the underlying principles that drive this phenomenon: that is, dissipation of energy results in segregating and self-organizing behavior of the system. This process exemplifies complex-system behavior. We use perthite formation (i.e. exsolution in the alkali feldspar system) in a series of scaffolded exercises to teach and more completely demonstrate complex-system behavior. These exercises include the use of: 1) hand samples and a series of optical and TEM photomicrographs to display the scale invariance of perthite textures; 2) a puzzle activity in which a chessboard is used as an analog model of atomic positions and nickels and pennies are used to represent individual atoms (Na and K respectively); sequential moves to optimize contacts with similar coins approximates minimization of lattice energies and reveals a power-law relationship as the system becomes increasingly segregated as a function of time to create exsolution textures; 3) the NetLogo computer modeling program to demonstrate segregating behavior; 4) visualizations based on the binary alkali feldspar phase diagram to demonstrate changes to the state of the system over a range of temperatures, and 5) a series of follow-on thought questions. An interesting apparent paradox that our students should consider concerns the flow of mass and energy in natural systems. Commonly, we simply note that mass and energy typically flow down natural gradients (thermal, chemical potential) to attain a homogeneous equilibrium state; however, exsolution produces a segregated state of the system in the lowest energy configuration. Why? Complex-system behavior can be discovered in a wide range of geological phenomena such as exsolution, and could be explicitly identified throughout the geoscience curriculum as a mechanism to teach about interacting systems.

Analyzing CRISM Data from mound B in Juventae Chasma, Mars, with the Multiple-Endmember Linear Spectral Unmixing Model MELSUM

NASA Astrophysics Data System (ADS)

Wendt, L.; Gross, C.; McGuire, P. C.; Combe, J.-P.; Neukum, G.

2009-04-01

Juventae Chasma, just north of Valles Marineris on Mars, contains several light-toned deposits (LTD), one of which is labelled mound B. Based on IR data from the imaging spectrometer OMEGA on Mars Express,[1] suggested kieserite for the lower part and gypsum for the upper part of the mound. In this study, we analyzed NIR data from the Compact Reconnaissance Imaging Spectrometer CRISM on MRO with the Multiple-Endmember Linear Spectral Unmixing Model MELSUM developed by Combe et al.[2]. We used CRISM data product FRT00009C0A from 1 to 2.6 µm. A novel, time-dependent volcano-scan technique [3] was applied to remove absorption bands related to CO2 much more effectively than the volcano-scan technique [4] that has been applied to CRISM and OMEGA data so far. In the classic SMA, a solution for the measured spectrum is calculated by a linear combination of all input spectra (which may come from a spectral library or from the image itself) at once. This can lead to negative coefficients, which have no physical meaning. MELSUM avoids this by calculating a solution for each possible combination of a subset of the reference spectra, with the maximum number of library spectra in the subset defined by the user. The solution with the lowest residual to the input spectrum is returned. We used MELSUM in a first step as similarity measure within the image by using averaged spectra from the image itself as input to MELSUM. This showed that three spectral units are enough to describe the variability in the data to first order: A lower, light-toned unit, an upper light-toned unit and a dark-toned unit. We then chose 34 laboratory spectra of sulfates, mafic minerals and iron oxides plus a spectrum for H2O ice as reference spectra for the unmixing of averaged spectra for each of these spectral regions. The best fit for the dark material was a combination of olivine, pyroxene and ice (present as cloud in the atmosphere and not on the surface). In agreement with [5], The lower unit was best modeled by a mix of the monohydrated sulfates szomolnokite and kieserite plus olivine and ice. The upper unit fits best with a combination of romerite, rozenite, (two polyhydrated iron sulfates) olivine and ice. Gypsum is not present. The excellent fit between modeled and measured spectra demonstrates the effectiveness of MELSUM as a tool to analyze hyperspectral data from CRISM. This research has been supported by the Helmholtz Association through the research alliance "Planetary Evolution and Life" and the German Space Agency under the Mars Express programme. References: [1] Gendrin, A. et al., (2005), Science, 307, 5751, 1587-1591 [2] Combe. J.-P. et al., (2008), PSS, 56, 951-975. [3] McGuire et al., (2009), in preparation), "A new volcano-scan algorithm for atmospheric correction of CRISM and OMEGA spectral data". [4] Langevin et al., (2005), Science, 307 (5715), 1584-1586. [5] Bishop, J. L. et al., (2008) LPSC XXXIX, #1391.

Using hyperspectral imagery to assist federal forest monitoring and restoration projects in the Southern Rocky Mountains, Colorado

NASA Astrophysics Data System (ADS)

Wamser, Kyle

Hyperspectral imagery and the corresponding ability to conduct analysis below the pixel level have tremendous potential to aid in landcover monitoring. During large ecosystem restoration projects, being able to monitor specific aspects of the recovery over large and often inaccessible areas under constrained finances are major challenges. The Civil Air Patrol's Airborne Real-time Cueing Hyperspectral Enhanced Reconnaissance (ARCHER) can provide hyperspectral data in most parts of the United States at relatively low cost. Although designed specifically for use in locating downed aircraft, the imagery holds the potential to identify specific aspects of landcover at far greater fidelity than traditional multispectral means. The goals of this research were to improve the use of ARCHER hyperspectral imagery to classify sub-canopy and open-area vegetation in coniferous forests located in the Southern Rockies and to determine how much fidelity might be lost from a baseline of 1 meter spatial resolution resampled to 2 and 5 meter pixel size to simulate higher altitude collection. Based on analysis comparing linear spectral unmixing with a traditional supervised classification, the linear spectral unmixing proved to be statistically superior. More importantly, however, linear spectral unmixing provided additional sub-pixel information that was unavailable using other techniques. The second goal of determining fidelity loss based on spatial resolution was more difficult to determine due to how the data are represented. Furthermore, the 2 and 5 meter imagery were obtained by resampling the 1 meter imagery and therefore may not be representative of the quality of actual 2 or 5 meter imagery. Ultimately, the information derived from this research may be useful in better utilizing hyperspectral imagery to conduct forest monitoring and assessment.

Determination of sediment provenance by unmixing the mineralogy of source-area sediments: The "SedUnMix" program

USGS Publications Warehouse

Andrews, John T.; Eberl, D.D.

2012-01-01

Along the margins of areas such as Greenland and Baffin Bay, sediment composition reflects a complex mixture of sources associated with the transport of sediment in sea ice, icebergs, melt-water and turbidite plumes. Similar situations arise in many contexts associated with sediment transport and with the mixing of sediments from different source areas. The question is: can contributions from discrete sediment (bedrock) sources be distinguished in a mixed sediment by using mineralogy, and, if so, how accurately? To solve this problem, four end-member source sediments were mixed in various proportions to form eleven artificial mixtures. Two of the end-member sediments are felsic, and the other two have more mafic compositions. End member and mixed sediment mineralogies were measured for the < 2. mm sediment fractions by quantitative X-ray diffraction (qXRD). The proportions of source sediments in the mixtures then were calculated using an Excel macro program named SedUnMix, and the results were evaluated to determine the robustness of the algorithm. The program permits the unmixing of up to six end members, each of which can be represented by up to 5 alternative compositions, so as to better simulate variability within each source region. The results indicate that we can track the relative percentages of the four end members in the mixtures. We recommend, prior to applying the technique to down-core or to other provenance problems, that a suite of known, artificial mixtures of sediments from probable source areas be prepared, scanned, analyzed for quantitative mineralogy, and then analyzed by SedUnMix to check the sensitivity of the method for each specific unmixing problem. ?? 2011 Elsevier B.V..

18 CFR 292.202 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Definitions. For purposes of this subpart: (a) Biomass means any organic material not derived from fossil.... (c) Cogeneration facility means equipment used to produce electric energy and forms of useful thermal... all forms supplied from external sources; (k) Natural gas means either natural gas unmixed, or any...

18 CFR 292.202 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Definitions. For purposes of this subpart: (a) Biomass means any organic material not derived from fossil.... (c) Cogeneration facility means equipment used to produce electric energy and forms of useful thermal... all forms supplied from external sources; (k) Natural gas means either natural gas unmixed, or any...

18 CFR 292.202 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Definitions. For purposes of this subpart: (a) Biomass means any organic material not derived from fossil.... (c) Cogeneration facility means equipment used to produce electric energy and forms of useful thermal... all forms supplied from external sources; (k) Natural gas means either natural gas unmixed, or any...

18 CFR 292.202 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Definitions. For purposes of this subpart: (a) Biomass means any organic material not derived from fossil.... (c) Cogeneration facility means equipment used to produce electric energy and forms of useful thermal... all forms supplied from external sources; (k) Natural gas means either natural gas unmixed, or any...

18 CFR 292.202 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Definitions. For purposes of this subpart: (a) Biomass means any organic material not derived from fossil.... (c) Cogeneration facility means equipment used to produce electric energy and forms of useful thermal... all forms supplied from external sources; (k) Natural gas means either natural gas unmixed, or any...

Aliasing Signal Separation of Superimposed Abrasive Debris Based on Degenerate Unmixing Estimation Technique.

PubMed

Li, Tongyang; Wang, Shaoping; Zio, Enrico; Shi, Jian; Hong, Wei

2018-03-15

Leakage is the most important failure mode in aircraft hydraulic systems caused by wear and tear between friction pairs of components. The accurate detection of abrasive debris can reveal the wear condition and predict a system's lifespan. The radial magnetic field (RMF)-based debris detection method provides an online solution for monitoring the wear condition intuitively, which potentially enables a more accurate diagnosis and prognosis on the aviation hydraulic system's ongoing failures. To address the serious mixing of pipe abrasive debris, this paper focuses on the superimposed abrasive debris separation of an RMF abrasive sensor based on the degenerate unmixing estimation technique. Through accurately separating and calculating the morphology and amount of the abrasive debris, the RMF-based abrasive sensor can provide the system with wear trend and sizes estimation of the wear particles. A well-designed experiment was conducted and the result shows that the proposed method can effectively separate the mixed debris and give an accurate count of the debris based on RMF abrasive sensor detection.

Linear mixing model applied to coarse resolution satellite data

NASA Technical Reports Server (NTRS)

Holben, Brent N.; Shimabukuro, Yosio E.

1992-01-01

A linear mixing model typically applied to high resolution data such as Airborne Visible/Infrared Imaging Spectrometer, Thematic Mapper, and Multispectral Scanner System is applied to the NOAA Advanced Very High Resolution Radiometer coarse resolution satellite data. The reflective portion extracted from the middle IR channel 3 (3.55 - 3.93 microns) is used with channels 1 (0.58 - 0.68 microns) and 2 (0.725 - 1.1 microns) to run the Constrained Least Squares model to generate fraction images for an area in the west central region of Brazil. The derived fraction images are compared with an unsupervised classification and the fraction images derived from Landsat TM data acquired in the same day. In addition, the relationship betweeen these fraction images and the well known NDVI images are presented. The results show the great potential of the unmixing techniques for applying to coarse resolution data for global studies.

Model-free data analysis for source separation based on Non-Negative Matrix Factorization and k-means clustering (NMFk)

NASA Astrophysics Data System (ADS)

Vesselinov, V. V.; Alexandrov, B.

2014-12-01

The identification of the physical sources causing spatial and temporal fluctuations of state variables such as river stage levels and aquifer hydraulic heads is challenging. The fluctuations can be caused by variations in natural and anthropogenic sources such as precipitation events, infiltration, groundwater pumping, barometric pressures, etc. The source identification and separation can be crucial for conceptualization of the hydrological conditions and characterization of system properties. If the original signals that cause the observed state-variable transients can be successfully "unmixed", decoupled physics models may then be applied to analyze the propagation of each signal independently. We propose a new model-free inverse analysis of transient data based on Non-negative Matrix Factorization (NMF) method for Blind Source Separation (BSS) coupled with k-means clustering algorithm, which we call NMFk. NMFk is capable of identifying a set of unique sources from a set of experimentally measured mixed signals, without any information about the sources, their transients, and the physical mechanisms and properties controlling the signal propagation through the system. A classical BSS conundrum is the so-called "cocktail-party" problem where several microphones are recording the sounds in a ballroom (music, conversations, noise, etc.). Each of the microphones is recording a mixture of the sounds. The goal of BSS is to "unmix'" and reconstruct the original sounds from the microphone records. Similarly to the "cocktail-party" problem, our model-freee analysis only requires information about state-variable transients at a number of observation points, m, where m > r, and r is the number of unknown unique sources causing the observed fluctuations. We apply the analysis on a dataset from the Los Alamos National Laboratory (LANL) site. We identify and estimate the impact and sources are barometric pressure and water-supply pumping effects. We also estimate the location of the water-supply pumping wells based on the available data. The possible applications of the NMFk algorithm are not limited to hydrology problems; NMFk can be applied to any problem where temporal system behavior is observed at multiple locations and an unknown number of physical sources are causing these fluctuations.

Optimizing homogenization by chaotic unmixing?

NASA Astrophysics Data System (ADS)

Weijs, Joost; Bartolo, Denis

2016-11-01

A number of industrial processes rely on the homogeneous dispersion of non-brownian particles in a viscous fluid. An ideal mixing would yield a so-called hyperuniform particle distribution. Such configurations are characterized by density fluctuations that grow slower than the standard √{ N}-fluctuations. Even though such distributions have been found in several natural structures, e.g. retina receptors in birds, they have remained out of experimental reach until very recently. Over the last 5 years independent experiments and numerical simulations have shown that periodically driven suspensions can self-assemble hyperuniformally. Simple as the recipe may be, it has one important disadvantage. The emergence of hyperuniform states co-occurs with a critical phase transition from reversible to non reversible particle dynamics. As a consequence the homogenization dynamics occurs over a time that diverges with the system size (critical slowing down). Here, we discuss how this process can be sped up by exploiting the stirring properties of chaotic advection. Among the questions that we answer are: What are the physical mechanisms in a chaotic flow that are relevant for hyperuniformity? How can we tune the flow parameters such to obtain optimal hyperuniformity in the fastest way? JW acknowledges funding by NWO (Netherlands Organisation for Scientific Research) through a Rubicon Grant.

Hyperspectral remote sensing of coral reefs: Deriving bathymetry, aquatic optical properties and a benthic spectral unmixing classification using AVIRIS data in the Hawaiian Islands

NASA Astrophysics Data System (ADS)

Goodman, James Ansell

My research focuses on the development and application of hyperspectral remote sensing as a valuable component in the assessment and management of coral ecosystems. Remote sensing provides an important quantitative ability to investigate the spatial dynamics of coral health and evaluate the impacts of local, regional and global change on this important natural resource. Furthermore, advances in detector capabilities and analysis methods, particularly with respect to hyperspectral remote sensing, are also increasing the accuracy and level of effectiveness of the resulting data products. Using imagery of Kaneohe Bay and French Frigate Shoals in the Hawaiian Islands, acquired in 2000 by NASA's Airborne Visible InfraRed Imaging Spectrometer (AVIRIS), I developed, applied and evaluated algorithms for analyzing coral reefs using hyperspectral remote sensing data. Research included developing methods for acquiring in situ underwater reflectance, collecting spectral measurements of the dominant bottom components in Kaneohe Bay, applying atmospheric correction and sunglint removal algorithms, employing a semianalytical optimization model to derive bathymetry and aquatic optical properties, and developing a linear unmixing approach for deriving bottom composition. Additionally, algorithm development focused on using fundamental scientific principles to facilitate the portability of methods to diverse geographic locations and across variable environmental conditions. Assessments of this methodology compared favorably with available field measurements and habitat information, and the overall analysis demonstrated the capacity to derive information on water properties, bathymetry and habitat composition. Thus, results illustrated a successful approach for extracting environmental information and habitat composition from a coral reef environment using hyperspectral remote sensing.

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

Cowan, Nicolas B.; Strait, Talia E., E-mail: n-cowan@northwestern.edu

Planned missions will spatially resolve temperate terrestrial planets from their host star. Although reflected light from such a planet encodes information about its surface, it has not been shown how to establish surface characteristics of a planet without assuming known surfaces to begin with. We present a reanalysis of disk-integrated, time-resolved, multiband photometry of Earth obtained by the Deep Impact spacecraft as part of the EPOXI Mission of Opportunity. We extract reflectance spectra of clouds, ocean, and land without a priori knowledge of the numbers or colors of these surfaces. We show that the inverse problem of extracting surface spectramore » from such data is a novel and extreme instance of spectral unmixing, a well-studied problem in remote sensing. Principal component analysis is used to determine an appropriate number of model surfaces with which to interpret the data. Shrink-wrapping a simplex to the color excursions of the planet yields a conservative estimate of the planet's endmember spectra. The resulting surface maps are unphysical, however, requiring negative or larger-than-unity surface coverage at certain locations. Our ''rotational unmixing'' supersedes the endmember analysis by simultaneously solving for the surface spectra and their geographical distributions on the planet, under the assumption of diffuse reflection and known viewing geometry. We use a Markov Chain Monte Carlo to determine best-fit parameters and their uncertainties. The resulting albedo spectra are similar to clouds, ocean, and land seen through a Rayleigh-scattering atmosphere. This study suggests that future direct-imaging efforts could identify and map unknown surfaces and clouds on exoplanets.« less

Forest Cover Mapping in Iskandar Malaysia Using Satellite Data

NASA Astrophysics Data System (ADS)

Kanniah, K. D.; Mohd Najib, N. E.; Vu, T. T.

2016-09-01

Malaysia is the third largest country in the world that had lost forest cover. Therefore, timely information on forest cover is required to help the government to ensure that the remaining forest resources are managed in a sustainable manner. This study aims to map and detect changes of forest cover (deforestation and disturbance) in Iskandar Malaysia region in the south of Peninsular Malaysia between years 1990 and 2010 using Landsat satellite images. The Carnegie Landsat Analysis System-Lite (CLASlite) programme was used to classify forest cover using Landsat images. This software is able to mask out clouds, cloud shadows, terrain shadows, and water bodies and atmospherically correct the images using 6S radiative transfer model. An Automated Monte Carlo Unmixing technique embedded in CLASlite was used to unmix each Landsat pixel into fractions of photosynthetic vegetation (PV), non photosynthetic vegetation (NPV) and soil surface (S). Forest and non-forest areas were produced from the fractional cover images using appropriate threshold values of PV, NPV and S. CLASlite software was found to be able to classify forest cover in Iskandar Malaysia with only a difference between 14% (1990) and 5% (2010) compared to the forest land use map produced by the Department of Agriculture, Malaysia. Nevertheless, the CLASlite automated software used in this study was found not to exclude other vegetation types especially rubber and oil palm that has similar reflectance to forest. Currently rubber and oil palm were discriminated from forest manually using land use maps. Therefore, CLASlite algorithm needs further adjustment to exclude these vegetation and classify only forest cover.

Determining Reflectance Spectra of Surfaces and Clouds on Exoplanets

NASA Astrophysics Data System (ADS)

Cowan, Nicolas B.; Strait, Talia E.

2013-03-01

Planned missions will spatially resolve temperate terrestrial planets from their host star. Although reflected light from such a planet encodes information about its surface, it has not been shown how to establish surface characteristics of a planet without assuming known surfaces to begin with. We present a reanalysis of disk-integrated, time-resolved, multiband photometry of Earth obtained by the Deep Impact spacecraft as part of the EPOXI Mission of Opportunity. We extract reflectance spectra of clouds, ocean, and land without a priori knowledge of the numbers or colors of these surfaces. We show that the inverse problem of extracting surface spectra from such data is a novel and extreme instance of spectral unmixing, a well-studied problem in remote sensing. Principal component analysis is used to determine an appropriate number of model surfaces with which to interpret the data. Shrink-wrapping a simplex to the color excursions of the planet yields a conservative estimate of the planet's endmember spectra. The resulting surface maps are unphysical, however, requiring negative or larger-than-unity surface coverage at certain locations. Our "rotational unmixing" supersedes the endmember analysis by simultaneously solving for the surface spectra and their geographical distributions on the planet, under the assumption of diffuse reflection and known viewing geometry. We use a Markov Chain Monte Carlo to determine best-fit parameters and their uncertainties. The resulting albedo spectra are similar to clouds, ocean, and land seen through a Rayleigh-scattering atmosphere. This study suggests that future direct-imaging efforts could identify and map unknown surfaces and clouds on exoplanets.

Overhead longwave infrared hyperspectral material identification using radiometric models

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

Zelinski, M. E.

Material detection algorithms used in hyperspectral data processing are computationally efficient but can produce relatively high numbers of false positives. Material identification performed as a secondary processing step on detected pixels can help separate true and false positives. This paper presents a material identification processing chain for longwave infrared hyperspectral data of solid materials collected from airborne platforms. The algorithms utilize unwhitened radiance data and an iterative algorithm that determines the temperature, humidity, and ozone of the atmospheric profile. Pixel unmixing is done using constrained linear regression and Bayesian Information Criteria for model selection. The resulting product includes an optimalmore » atmospheric profile and full radiance material model that includes material temperature, abundance values, and several fit statistics. A logistic regression method utilizing all model parameters to improve identification is also presented. This paper details the processing chain and provides justification for the algorithms used. Several examples are provided using modeled data at different noise levels.« less

Band selection using forward feature selection algorithm for citrus Huanglongbing disease detection

USDA-ARS?s Scientific Manuscript database

This study attempted to classify spectrally similar data – obtained from aerial images of healthy citrus plants and the citrus greening disease (Huanglongbing) infected plants - using small differences without un-mixing the endmember components and therefore without the need for endmember library. H...

Machine Learning Approach to Deconvolution of Thermal Infrared (TIR) Spectrum of Mercury Supporting MERTIS Onboard ESA/JAXA BepiColombo

NASA Astrophysics Data System (ADS)

Varatharajan, I.; D'Amore, M.; Maturilli, A.; Helbert, J.; Hiesinger, H.

2018-04-01

Machine learning approach to spectral unmixing of emissivity spectra of Mercury is carried out using endmember spectral library measured at simulated daytime surface conditions of Mercury. Study supports MERTIS payload onboard ESA/JAXA BepiColombo.

Revisiting the "Unmixing Experiment" through Argumentation

ERIC Educational Resources Information Center

Çoban, Gul Ünal; Büber, Ayse; Saglam, Merve Kocagül

2017-01-01

This paper focuses on a series of activities for students at middle school to college level, designed to instill a sound understanding of fluids and the properties of fluids. The first activities investigate diffusion and molecular size and these are followed by tasks exploring viscosity and the factors effecting viscosity. Following this, there…

Context Dependent Spectral Unmixing

DTIC Science & Technology

2014-08-01

the tar- get sizes). The targets were made of 100% cotton fabric and were emplaced so that there would be representatives of each color type completely...method for simplex-based endmember extraction algorithm,” IEEE Transactions on Geoscience and Re- mote Sensing, vol. 44, no. 10, pp. 2804–2819, 2006. [68

Assessment of spruce (Picea obovata) abundance by spectral unmixing algorithm for sustainable forest management in highland Natural Reserve (case study of Zigalga Range, South-Ural State Natural Reserve, Russia).

NASA Astrophysics Data System (ADS)

Mikheeva, Anna; Moiseev, Pavel

2017-04-01

In mountain territories climate change affects forest productivity and growth, which results in the tree line advancing and increasing of the forest density. These changes pose new challenges for forest managers whose responsibilities include forest resources inventory, monitoring and protection of ecosystems, and assessment of forest vulnerability. These activities require a range of sources of information, including exact squares of forested areas, forest densities and species abundances. Picea obovata, dominant tree species in South-Ural State Natural Reserve, Russia has regenerated, propagated and increased its relative cover during the recent 70 years. A remarkable shift of the upper limit of Picea obovata up to 60-80 m upslope was registered by repeating photography, especially on gentle slopes. The stands of Picea obovata are monitored by Reserve inspectors on the test plots to ensure that forests maintain or improve their productivity, these studies also include projective cover measurements. However, it is impossible to cover the entire territory of the Reserve by detailed field observations. Remote sensing data from Terra ASTER imagery provides valuable information for large territories (scene covers an area of 60 x 60 km) and can be used for quantitative mapping of forest and non-forest vegetation at regional scale (spatial resolution is 15-30 m for visible and infrared bands). A case study of estimating Picea obovata abundance was conducted for forest and forest-tundra sites of Zigalga Range, using 9-band ASTER multispectral imagery of 23.08.2007, field data and spectral unmixing algorithm. This type of algorithms intends to derive object and its abundance from a mixed pixel of multispectral imagery which can be further converted to object's projective cover. Atmospheric correction was applied to the imagery prior to spectral unmixing, and then pure spectra of Picea obovata were extracted from the image in 10 points and averaged. These points located in Zigalga Range and were visited in summer 2016. We used Mixture-tuned Match Filtering (MTMF) algorithm, a non-linear subpixel classification technique which allows to separate the spectral mixture containing unknown objects, and to derive only known ones. The results of spectral unmixing classification were abundance maps of Picea obovata. The values were statistically determined (there was only selected abundances with high probabilities of presence and low probabilities of absence) and then constrained to the interval [0; 1]. Verification of maps was made at the sites of Iremel Mountains on the same ASTER image, where projective cover of Picea obovata was measured in the field in 147 points. The correlation coefficient between the spectral unmixing abundances and field-measured abundances was 0.7; not a very high value is due to the low sensitivity of the algorithm to detect abundances less than 0.25. The proposed method provides a tool for defining the Picea obovata boundaries more accurately than per-pixel automatic classification and locating new spruce islands in the mixing tree line environment. The abundances can be obtained for large areas with minimum field work which makes this approach cost-effective in providing timely information to nature reserve managers for adapting forest management actions to climate change.

Large-scale compositional heterogeneity in the Earth's mantle

NASA Astrophysics Data System (ADS)

Ballmer, M.

2017-12-01

Seismic imaging of subducted Farallon and Tethys lithosphere in the lower mantle has been taken as evidence for whole-mantle convection, and efficient mantle mixing. However, cosmochemical constraints point to a lower-mantle composition that has a lower Mg/Si compared to upper-mantle pyrolite. Moreover, geochemical signatures of magmatic rocks indicate the long-term persistence of primordial reservoirs somewhere in the mantle. In this presentation, I establish geodynamic mechanisms for sustaining large-scale (primordial) heterogeneity in the Earth's mantle using numerical models. Mantle flow is controlled by rock density and viscosity. Variations in intrinsic rock density, such as due to heterogeneity in basalt or iron content, can induce layering or partial layering in the mantle. Layering can be sustained in the presence of persistent whole mantle convection due to active "unmixing" of heterogeneity in low-viscosity domains, e.g. in the transition zone or near the core-mantle boundary [1]. On the other hand, lateral variations in intrinsic rock viscosity, such as due to heterogeneity in Mg/Si, can strongly affect the mixing timescales of the mantle. In the extreme case, intrinsically strong rocks may remain unmixed through the age of the Earth, and persist as large-scale domains in the mid-mantle due to focusing of deformation along weak conveyor belts [2]. That large-scale lateral heterogeneity and/or layering can persist in the presence of whole-mantle convection can explain the stagnation of some slabs, as well as the deflection of some plumes, in the mid-mantle. These findings indeed motivate new seismic studies for rigorous testing of model predictions. [1] Ballmer, M. D., N. C. Schmerr, T. Nakagawa, and J. Ritsema (2015), Science Advances, doi:10.1126/sciadv.1500815. [2] Ballmer, M. D., C. Houser, J. W. Hernlund, R. Wentzcovitch, and K. Hirose (2017), Nature Geoscience, doi:10.1038/ngeo2898.

Mixing and unmixedness in plasma jets 1: Near-field analysis

NASA Technical Reports Server (NTRS)

Ilegbusi, Olusegun J.

1993-01-01

The flow characteristics in the near-field of a plasma jet are simulated with a two-fluid model. This model accounts for both gradient-diffusion mixing and uni-directional sifting motion resulting from pressure-gradient-body-force imbalance. This latter mechanism is believed to be responsible for the umixedness observed in plasma jets. The unmixedness is considered to be essentially a Rayleigh-Taylor kind instability. Transport equations are solved for the individual plasma and ambient gas velocities, temperatures and volume fractions. Empirical relations are employed for the interface transfers of mass, momentum and heat. The empirical coefficients are first established by comparison of predictions with available experimental data for shear flows. The model is then applied to an Argon plasma jet ejecting into stagnant air. The predicted results show the significant build-up of unmixed air within the plasma gas, even relatively far downstream of the torch. By adjusting the inlet condition, the model adequately reproduces the experimental data.

Pile mixing increases greenhouse gas emissions during composting of dairy manure

USDA-ARS?s Scientific Manuscript database

The effect of pile mixing on greenhouse gas (GHG) emissions from stored dairy manure was determined using large flux chambers designed to completely cover pilot-scale manure piles. GHG emissions from piles that were mixed four times during the 80 day trial were about 20% higher than unmixed piles. ...

Testing the Nonce Borrowing Hypothesis: Counter-Evidence from English-Origin Verbs in Welsh

ERIC Educational Resources Information Center

Stammers, Jonathan R.; Deuchar, Margaret

2012-01-01

According to the nonce borrowing hypothesis (NBH), "[n]once borrowings pattern exactly like their native counterparts in the (unmixed) recipient language" (Poplack & Meechan, 1998a, p. 137). Nonce borrowings (Sankoff, Poplack & Vanniarajan, 1990, p. 74) are "lone other-language items" which differ from established borrowings in terms of frequency…

Postfire soil burn severity mapping with hyperspectral image unmixing

Treesearch

Peter R. Robichaud; Sarah A. Lewis; Denise Y. M. Laes; Andrew T. Hudak; Raymond F. Kokaly; Joseph A. Zamudio

2007-01-01

Burn severity is mapped after wildfires to evaluate immediate and long-term fire effects on the landscape. Remotely sensed hyperspectral imagery has the potential to provide important information about fine-scale ground cover components that are indicative of burn severity after large wildland fires. Airborne hyperspectral imagery and ground data were collected after...

Method for hyperspectral imagery exploitation and pixel spectral unmixing

NASA Technical Reports Server (NTRS)

Lin, Ching-Fang (Inventor)

2003-01-01

An efficiently hybrid approach to exploit hyperspectral imagery and unmix spectral pixels. This hybrid approach uses a genetic algorithm to solve the abundance vector for the first pixel of a hyperspectral image cube. This abundance vector is used as initial state in a robust filter to derive the abundance estimate for the next pixel. By using Kalman filter, the abundance estimate for a pixel can be obtained in one iteration procedure which is much fast than genetic algorithm. The output of the robust filter is fed to genetic algorithm again to derive accurate abundance estimate for the current pixel. The using of robust filter solution as starting point of the genetic algorithm speeds up the evolution of the genetic algorithm. After obtaining the accurate abundance estimate, the procedure goes to next pixel, and uses the output of genetic algorithm as the previous state estimate to derive abundance estimate for this pixel using robust filter. And again use the genetic algorithm to derive accurate abundance estimate efficiently based on the robust filter solution. This iteration continues until pixels in a hyperspectral image cube end.

Endmember extraction from hyperspectral image based on discrete firefly algorithm (EE-DFA)

NASA Astrophysics Data System (ADS)

Zhang, Chengye; Qin, Qiming; Zhang, Tianyuan; Sun, Yuanheng; Chen, Chao

2017-04-01

This study proposed a novel method to extract endmembers from hyperspectral image based on discrete firefly algorithm (EE-DFA). Endmembers are the input of many spectral unmixing algorithms. Hence, in this paper, endmember extraction from hyperspectral image is regarded as a combinational optimization problem to get best spectral unmixing results, which can be solved by the discrete firefly algorithm. Two series of experiments were conducted on the synthetic hyperspectral datasets with different SNR and the AVIRIS Cuprite dataset, respectively. The experimental results were compared with the endmembers extracted by four popular methods: the sequential maximum angle convex cone (SMACC), N-FINDR, Vertex Component Analysis (VCA), and Minimum Volume Constrained Nonnegative Matrix Factorization (MVC-NMF). What's more, the effect of the parameters in the proposed method was tested on both synthetic hyperspectral datasets and AVIRIS Cuprite dataset, and the recommended parameters setting was proposed. The results in this study demonstrated that the proposed EE-DFA method showed better performance than the existing popular methods. Moreover, EE-DFA is robust under different SNR conditions.

Aliasing Signal Separation of Superimposed Abrasive Debris Based on Degenerate Unmixing Estimation Technique

PubMed Central

Li, Tongyang; Wang, Shaoping; Zio, Enrico; Shi, Jian; Hong, Wei

2018-01-01

Leakage is the most important failure mode in aircraft hydraulic systems caused by wear and tear between friction pairs of components. The accurate detection of abrasive debris can reveal the wear condition and predict a system’s lifespan. The radial magnetic field (RMF)-based debris detection method provides an online solution for monitoring the wear condition intuitively, which potentially enables a more accurate diagnosis and prognosis on the aviation hydraulic system’s ongoing failures. To address the serious mixing of pipe abrasive debris, this paper focuses on the superimposed abrasive debris separation of an RMF abrasive sensor based on the degenerate unmixing estimation technique. Through accurately separating and calculating the morphology and amount of the abrasive debris, the RMF-based abrasive sensor can provide the system with wear trend and sizes estimation of the wear particles. A well-designed experiment was conducted and the result shows that the proposed method can effectively separate the mixed debris and give an accurate count of the debris based on RMF abrasive sensor detection. PMID:29543733

Shallow sea-floor reflectance and water depth derived by unmixing multispectral imagery

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

Bierwirth, P.N.; Lee, T.J.; Burne, R.V.

1993-03-01

A major problem for mapping shallow water zones by the analysis of remotely sensed data is that contrast effects due to water depth obscure and distort the special nature of the substrate. This paper outlines a new method which unmixes the exponential influence of depth in each pixel by employing a mathematical constraint. This leaves a multispectral residual which represents relative substrate reflectance. Input to the process are the raw multispectral data and water attenuation coefficients derived by the co-analysis of known bathymetry and remotely sensed data. Outputs are substrate-reflectance images corresponding to the input bands and a greyscale depthmore » image. The method has been applied in the analysis of Landsat TM data at Hamelin Pool in Shark Bay, Western Australia. Algorithm derived substrate reflectance images for Landsat TM bands 1, 2, and 3 combined in color represent the optimum enhancement for mapping or classifying substrate types. As a result, this color image successfully delineated features, which were obscured in the raw data, such as the distributions of sea-grasses, microbial mats, and sandy area. 19 refs.« less

High efficiency organic photovoltaic cells employing hybridized mixed-planar heterojunctions

DOEpatents

Xue, Jiangeng; Uchida, Soichi; Rand, Barry P.; Forrest, Stephen

2015-08-18

A device is provided, having a first electrode, a second electrode, and a photoactive region disposed between the first electrode and the second electrode. The photoactive region includes a first photoactive organic layer that is a mixture of an organic acceptor material and an organic donor material, wherein the first photoactive organic layer has a thickness not greater than 0.8 characteristic charge transport lengths; a second photoactive organic layer in direct contact with the first organic layer, wherein the second photoactive organic layer is an unmixed layer of the organic acceptor material of the first photoactive organic layer, and the second photoactive organic layer has a thickness not less than about 0.1 optical absorption lengths; and a third photoactive organic layer disposed between the first electrode and the second electrode and in direct contact with the first photoactive organic layer. The third photoactive organic layer is an unmixed layer of the organic donor layer of the first photoactive organic layer and has a thickness not less than about 0.1 optical absorption lengths.

Validation of Spectral Unmixing Results from Informed Non-Negative Matrix Factorization (INMF) of Hyperspectral Imagery

NASA Astrophysics Data System (ADS)

Wright, L.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral instruments are a growing class of Earth observing sensors designed to improve remote sensing capabilities beyond discrete multi-band sensors by providing tens to hundreds of continuous spectral channels. Improved spectral resolution, range and radiometric accuracy allow the collection of large amounts of spectral data, facilitating thorough characterization of both atmospheric and surface properties. We describe the development of an Informed Non-Negative Matrix Factorization (INMF) spectral unmixing method to exploit this spectral information and separate atmospheric and surface signals based on their physical sources. INMF offers marked benefits over other commonly employed techniques including non-negativity, which avoids physically impossible results; and adaptability, which tailors the method to hyperspectral source separation. The INMF algorithm is adapted to separate contributions from physically distinct sources using constraints on spectral and spatial variability, and library spectra to improve the initial guess. Using this INMF algorithm we decompose hyperspectral imagery from the NASA Hyperspectral Imager for the Coastal Ocean (HICO), with a focus on separating surface and atmospheric signal contributions. HICO's coastal ocean focus provides a dataset with a wide range of atmospheric and surface conditions. These include atmospheres with varying aerosol optical thicknesses and cloud cover. HICO images also provide a range of surface conditions including deep ocean regions, with only minor contributions from the ocean surfaces; and more complex shallow coastal regions with contributions from the seafloor or suspended sediments. We provide extensive comparison of INMF decomposition results against independent measurements of physical properties. These include comparison against traditional model-based retrievals of water-leaving, aerosol, and molecular scattering radiances and other satellite products, such as aerosol optical thickness from the Moderate Resolution Imaging Spectroradiometer (MODIS).

Application of ensemble back trajectory and factor analysis methods to aerosol data from Fort Meade, MD: Implications for sources

NASA Astrophysics Data System (ADS)

Chen, L. A.; Doddridge, B. G.; Dickerson, R. R.

2001-12-01

As the primary field experiment for Maryland Aerosol Research and CHaracterization (MARCH-Atlantic) study, chemically speciated PM2.5 has been sampled at Fort Meade (FME, 39.10° N 76.74° W) since July 1999. FME is suburban, located in the middle of the bustling Baltimore-Washington corridor, which is generally downwind of the highly industrialized Midwest. Due to this unique sampling location, the PM2.5 observed at FME is expected to be of both local and regional sources, with relative contributions varying temporally. This variation, believed to be largely controlled by the meteorology, influences day-to-day or seasonal profiles of PM2.5 mass concentration and chemical composition. Air parcel back trajectories, which describe the path of air parcels traveling backward in time from site (receptor), reflect changes in the synoptic meteorological conditions. In this paper, an ensemble back trajectory method is employed to study the meteorology associated with each high/low PM2.5 episode in different seasons. For every sampling day, the residence time of air parcels within the eastern US at a 1° x 1° x 500 m geographic resolution can be estimated in order to resolve areas likely dominating the production of various PM2.5 components. Local sources are found to be more dominant in winter than in summer. "Factor analysis" is based on mass balance approach, providing useful insights on air pollution data. Here, a newly developed factor analysis model (UNMIX) is used to extract source profiles and contributions from the speciated PM2.5 data. Combing the model results with ensemble back trajectory method improves the understanding of the source regions and helps partition the contributions from local or more distant areas. >http://www.meto.umd.edu/~bruce/MARCH-Atl.html

Estimating urban vegetation fraction across 25 cities in pan-Pacific using Landsat time series data

NASA Astrophysics Data System (ADS)

Lu, Yuhao; Coops, Nicholas C.; Hermosilla, Txomin

2017-04-01

Urbanization globally is consistently reshaping the natural landscape to accommodate the growing human population. Urban vegetation plays a key role in moderating environmental impacts caused by urbanization and is critically important for local economic, social and cultural development. The differing patterns of human population growth, varying urban structures and development stages, results in highly varied spatial and temporal vegetation patterns particularly in the pan-Pacific region which has some of the fastest urbanization rates globally. Yet spatially-explicit temporal information on the amount and change of urban vegetation is rarely documented particularly in less developed nations. Remote sensing offers an exceptional data source and a unique perspective to map urban vegetation and change due to its consistency and ubiquitous nature. In this research, we assess the vegetation fractions of 25 cities across 12 pan-Pacific countries using annual gap-free Landsat surface reflectance products acquired from 1984 to 2012, using sub-pixel, spectral unmixing approaches. Vegetation change trends were then analyzed using Mann-Kendall statistics and Theil-Sen slope estimators. Unmixing results successfully mapped urban vegetation for pixels located in urban parks, forested mountainous regions, as well as agricultural land (correlation coefficient ranging from 0.66 to 0.77). The greatest vegetation loss from 1984 to 2012 was found in Shanghai, Tianjin, and Dalian in China. In contrast, cities including Vancouver (Canada) and Seattle (USA) showed stable vegetation trends through time. Using temporal trend analysis, our results suggest that it is possible to reduce noise and outliers caused by phenological changes particularly in cropland using dense new Landsat time series approaches. We conclude that simple yet effective approaches of unmixing Landsat time series data for assessing spatial and temporal changes of urban vegetation at regional scales can provide critical information for urban planners and anthropogenic studies globally.

Is There a Paradox of Aging: When the Negative Aging Stereotype Meets the Positivity Effect in Older Adults.

PubMed

Zhou, Liqing; Lu, Jia; Chen, Guopeng; Dong, Li; Yao, Yujia

2017-01-01

Background/Study Context: Socioemotional selectivity theory (SST) states that the positivity effect is a result of older adults' emotion regulation and that older adults derive more emotional satisfaction from prioritizing positive information processing. The authors explored whether the positivity effect appeared when the negative aging stereotype was activated in older adults and also whether the effect differed between mixed and unmixed valence conditions. Sixty younger (18-23 years of age) and 60 older (60-87 years of age) adults were randomly assigned to a control group and a priming group, in which the negative aging stereotype was activated. All the participants were asked to select 15 words that best described the elderly from a mixed-word list (positive and negative words were mixed together) and from an unmixed-word list (positive and negative words were separated). Older adults in the control group selected more positive words, whereas among younger adults, selection did not differ by valence in either the mixed- or unmixed-word list conditions. There were no differences between the positive and negative word choices of the younger and older adults in the priming group. We calculated the differences between the numbers of positive and negative words, and the differences in the older adults' word choices were larger than those among the younger adults; the differences were also larger in the control group than in the priming group. The positivity effect worked by choosing positive stimuli rather than avoiding negative stimuli. The role of emotion regulation in older adults was limited, and when the positivity effect faced the effect of the negative aging stereotype, the negative stereotype effect was dominant. Future research should explore the changes in the positivity effect in the face of a positive aging stereotype and what roles other factors (e.g., activation level of the stereotype, arousal level of affective words) might play.

Detrital illite crystals identified from crystallite thickness measurements in siliciclastic sediments

USGS Publications Warehouse

Aldega, L.; Eberl, D.D.

2005-01-01

Illite crystals in siliciclastic sediments are heterogeneous assemblages of detrital material coming from various source rocks and, at paleotemperatures >70 ??C, of superimposed diagenetic modification in the parent sediment. We distinguished the relative proportions of 2M1 detrital illite and possible diagenetic 1Md + 1M illite by a combined analysis of crystal-size distribution and illite polytype quantification. We found that the proportions of 1Md + 1M and 2M1 illite could be determined from crystallite thickness measurements (BWA method, using the MudMaster program) by unmixing measured crystallite thickness distributions using theoretical and calculated log-normal and/or asymptotic distributions. The end-member components that we used to unmix the measured distributions were three asymptotic-shaped distributions (assumed to be the diagenetic component of the mixture, the 1Md + 1M polytypes) calculated using the Galoper program (Phase A was simulated using 500 crystals per cycle of nucleation and growth, Phase B = 333/cycle, and Phase C = 250/ cycle), and one theoretical log-normal distribution (Phase D, assumed to approximate the detrital 2M1 component of the mixture). In addition, quantitative polytype analysis was carried out using the RockJock software for comparison. The two techniques gave comparable results (r2 = 0.93), which indicates that the unmixing method permits one to calculate the proportion of illite polytypes and, therefore, the proportion of 2M1 detrital illite, from crystallite thickness measurements. The overall illite crystallite thicknesses in the samples were found to be a function of the relative proportions of thick 2M1 and thin 1Md + 1M illite. The percentage of illite layers in I-S mixed layers correlates with the mean crystallite thickness of the 1Md + 1M polytypes, indicating that these polytypes, rather than the 2M1 polytype, participate in I-S mixed layering.

Physical-biopolymer characterization of polyhydroxybutyrate-co-hydroxyvalerate (PHBV) blended with natural rubber latex

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

Kuntanoo, K., E-mail: thip-kk@hotmail.com; Promkotra, S., E-mail: sarunya@kku.ac.th; Kaewkannetra, P., E-mail: paknar@kku.ac.th

A biopolymer of polyhydroxybutyrate-co-hydroxyvalerate (PHBV) is blended with bio-based materials, natural rubber latex, to improve their microstructures. The various ratios between PHBV and natural rubber latex are examined to develop their mechanical properties. In general, physical properties of PHBV are hard, brittle and low flexible while natural rubber (NR) is presented itself as high elastic materials. Concentrations of the PHBV solution are constituted at 1%, 2% and 3% (w/v). The mixtures of their PHBV solutions to natural rubber latex are produced the blended films in three different ratios of 4:6, 5:5 and 6:4, respectively. They are characterized by appearance analysesmore » which are the scanning electron microscope (SEM), universal testing machine (UTM) and differential scanning calorimetry (DSC). The SEM photomicrographs of the blended films and the controlled PHBV can provide the void distribution in the range of 12-14% and 19-21%, respectively. For mechanical properties of the blended films, the various elastic moduli of 1%, 2% and 3% (w/v) PHBV are the average of 773, 956 and 1,007 kPa, respectively. The tensile strengths of the blends increase with the increased concentrations of PHBV, similarly trend to the elastic modulus. The crystallization and melting behavior of unmixed PHBV and the blends are determined by DSC. Melting transition temperatures (T{sub m}) of the unmixed PHBV are stated two melting peak at 154°C and 173°C. Besides, the melting peaks of the blends alter in the range of 152-156°C and 168-171°C, respectively. According to morphology of the blends, the void distribution decreases twice compared to the unmixed PHBV. The results of mechanical properties and thermal analysis indicate that the blended PHBV can be developed their properties by more resilient and wide range of temperature than usual.« less

Unmixing the Mixing Cost: Contributions from Dimensional Relevance and Stimulus-Response Suppression

ERIC Educational Resources Information Center

Mari-Beffa, Paloma; Cooper, Stephen; Houghton, George

2012-01-01

When participants repeat the same task in a context in which the task may also switch (a mixed block), performance deteriorates compared to when there is only one task repeating (a pure block). Three experiments were designed to assess how perceptual and motor transitions influenced this mixing cost. Experiment 1 provided three pure block…

A cross-comparison of field, spectral, and lidar estimates of forest canopy cover

Treesearch

Alistair M. S. Smith; Michael J. Falkowski; Andrew T. Hudak; Jeffrey S. Evans; Andrew P. Robinson; Caiti M. Steele

2010-01-01

A common challenge when comparing forest canopy cover and similar metrics across different ecosystems is that there are many field- and landscape-level measurement methods. This research conducts a cross-comparison and evaluation of forest canopy cover metrics produced using unmixing of reflective spectral satellite data, light detection and ranging (lidar) data, and...

Biomass and health based forest cover delineation using spectral un-mixing

Treesearch

Mohan Tiruveedhula; Joseph Fan; Ravi R. Sadasivuni; Surya S. Durbha; David L. Evans

2009-01-01

Remote sensing is a well-suited source of information on various forest characteristics such as forest cover type, leaf area, biomass, and health. The use of appropriate layers helps to quantify the variables of interest. For example, normalized difference vegetation index (NDVI) and greenness help explain variability in biomass as well as health of forests....

7 CFR 201.60 - Purity percentages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... (2) mixtures in which the particle-weight ratio is 1:1 to 1.49:1, inclusive. Tolerances for... Component of a Purity Analysis for (1) Unmixed Seed or (2) Mixed Seed in Which the Particle Weight Ratio Is... particle-weight ratio is 1.5:1 to 20:1 and beyond: The symbols used in the formula are as follows: T...

7 CFR 201.60 - Purity percentages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (2) mixtures in which the particle-weight ratio is 1:1 to 1.49:1, inclusive. Tolerances for... Component of a Purity Analysis for (1) Unmixed Seed or (2) Mixed Seed in Which the Particle Weight Ratio Is... particle-weight ratio is 1.5:1 to 20:1 and beyond: The symbols used in the formula are as follows: T...

7 CFR 201.60 - Purity percentages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... (2) mixtures in which the particle-weight ratio is 1:1 to 1.49:1, inclusive. Tolerances for... Component of a Purity Analysis for (1) Unmixed Seed or (2) Mixed Seed in Which the Particle Weight Ratio Is... particle-weight ratio is 1.5:1 to 20:1 and beyond: The symbols used in the formula are as follows: T...

7 CFR 201.60 - Purity percentages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... (2) mixtures in which the particle-weight ratio is 1:1 to 1.49:1, inclusive. Tolerances for... Component of a Purity Analysis for (1) Unmixed Seed or (2) Mixed Seed in Which the Particle Weight Ratio Is... particle-weight ratio is 1.5:1 to 20:1 and beyond: The symbols used in the formula are as follows: T...

A Sparse Bayesian Learning Algorithm for White Matter Parameter Estimation from Compressed Multi-shell Diffusion MRI.

PubMed

Pisharady, Pramod Kumar; Sotiropoulos, Stamatios N; Sapiro, Guillermo; Lenglet, Christophe

2017-09-01

We propose a sparse Bayesian learning algorithm for improved estimation of white matter fiber parameters from compressed (under-sampled q-space) multi-shell diffusion MRI data. The multi-shell data is represented in a dictionary form using a non-monoexponential decay model of diffusion, based on continuous gamma distribution of diffusivities. The fiber volume fractions with predefined orientations, which are the unknown parameters, form the dictionary weights. These unknown parameters are estimated with a linear un-mixing framework, using a sparse Bayesian learning algorithm. A localized learning of hyperparameters at each voxel and for each possible fiber orientations improves the parameter estimation. Our experiments using synthetic data from the ISBI 2012 HARDI reconstruction challenge and in-vivo data from the Human Connectome Project demonstrate the improvements.

The Chemistry of Population III Supernova Ejecta. II. The Nucleation of Molecular Clusters as a Diagnostic for Dust in the Early Universe

NASA Astrophysics Data System (ADS)

Cherchneff, Isabelle; Dwek, Eli

2010-04-01

We study the formation of molecular precursors to dust in the ejecta of Population III supernovae (Pop. III SNe) using a chemical kinetic approach to follow the evolution of small dust cluster abundances from day 100 to day 1000 after explosion. Our work focuses on zero-metallicity 20 M sun and 170 M sun progenitors, and we consider fully macroscopically mixed and unmixed ejecta. The dust precursors comprise molecular chains, rings, and small clusters of chemical composition relevant to the initial elemental composition of the ejecta under study. The nucleation stage for small silica, metal oxides and sulfides, pure metal, and carbon clusters is described with a new chemical reaction network highly relevant to the kinetic description of dust formation in hot circumstellar environments. We consider the effect of the pressure dependence of critical nucleation rates and test the impact of microscopically mixed He+ on carbon dust formation. Two cases of metal depletion on silica clusters (full and no depletion) are considered to derive upper limits to the amounts of dust produced in SN ejecta at 1000 days, while the chemical composition of clusters gives a prescription for the type of dust formed in Pop. III SNe. We show that the cluster mass produced in the fully mixed ejecta of a 170 M sun progenitor is ~ 25 M sun whereas its 20 M sun counterpart forms ~ 0.16 M sun of clusters. The unmixed ejecta of a 170 M sun progenitor SN synthesize ~5.6 M sun of small clusters, while its 20 M sun counterpart produces ~0.103 M sun. Our results point to smaller amounts of dust formed in the ejecta of Pop. III SNe by a factor of ~ 5 compared to values derived by previous studies, and to different dust chemical compositions. Such deviations result from some erroneous assumptions made, the inappropriate use of classical nucleation theory to model dust formation, and the omission of the synthesis of molecules in SN ejecta. We also find that the unmixed ejecta of massive Pop. III SNe chiefly form silica and/or silicates, and pure silicon grains whereas their lower mass counterparts form a dust mixture dominated by silica and/or silicates, pure silicon, and iron sulfides. Amorphous carbon can only condense via the nucleation of carbon chains and rings characteristic of the synthesis of fullerenes when the ejecta carbon-rich zone is deprived of He+. The first dust enrichment to the primordial gas in the early universe from Pop. III massive SN comprises primarily pure silicon, silica, and silicates. If carbon dust is present at redshift z > 6, alternative dust sources must be considered.

Medical tourism-A New Arena.

PubMed

Puri, S; Singh, A; Yashik

2010-01-01

Globalisation has given birth to medical tourism. Health and medical tourism are the fastest growing segments in not only developed nations but in developing countries too. India has become a hot destination, as the Indian medical standards match up to the highly prescribed international standards at a very low cost. However, it is an unmixed blessing; along with advantages, it has many unintended side effects also.

The effect of high intensity mixing on the enzymatic hydrolysis of concentrated cellulose fiber suspensions

Treesearch

Joseph R. Samaniuk; C. Tim Scott; Thatcher W. Root; Daniel J. Klingenberg

2011-01-01

Enzymatic hydrolysis of lignocellulosic biomass in a high shear environment was examined. The conversion of cellulose to glucose in samples mixed in a torque rheometer producing shear flows similar to those found in twin screw extruders was greater than that of unmixed samples. In addition, there is a synergistic effect of mixing and enzymatic hydrolysis; mixing...

High spatial resolution spectral unmixing for mapping ash species across a complex urban environment

Treesearch

Jennifer Pontius; Ryan P. Hanavan; Richard A. Hallett; Bruce D. Cook; Lawrence A. Corp

2017-01-01

Ash (Fraxinus L.) species are currently threatened by the emerald ash borer (EAB; Agrilus planipennis Fairmaire) across a growing area in the eastern US. Accurate mapping of ash species is required to monitor the host resource, predict EAB spread and better understand the short- and long-term effects of EAB on the ash resource...

Anion permselective membrane

NASA Technical Reports Server (NTRS)

Hodgdon, R. B.; Waite, W. A.; Alexander, S. S.

1984-01-01

Two polymer ion exchange membranes were synthesized to fulfill the needs of both electrical resistivity and anolyte/catholyte separation for utility load leveling utilizing the DOE/NASA mixed electrolyte REDOX battery. Both membranes were shown to meet mixed electrolyte utility load leveling criteria. Several modifications of an anion exchange membrane failed to meet utility load leveling REDOX battery criteria using the unmixed electrolyte REDOX cell.

Disaggregating tree and grass phenology in tropical savannas

NASA Astrophysics Data System (ADS)

Zhou, Qiang

Savannas are mixed tree-grass systems and as one of the world's largest biomes represent an important component of the Earth system affecting water and energy balances, carbon sequestration and biodiversity as well as supporting large human populations. Savanna vegetation structure and its distribution, however, may change because of major anthropogenic disturbances from climate change, wildfire, agriculture, and livestock production. The overstory and understory may have different water use strategies, different nutrient requirements and have different responses to fire and climate variation. The accurate measurement of the spatial distribution and structure of the overstory and understory are essential for understanding the savanna ecosystem. This project developed a workflow for separating the dynamics of the overstory and understory fractional cover in savannas at the continental scale (Australia, South America, and Africa). Previous studies have successfully separated the phenology of Australian savanna vegetation into persistent and seasonal greenness using time series decomposition, and into fractions of photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV) and bare soil (BS) using linear unmixing. This study combined these methods to separate the understory and overstory signal in both the green and senescent phenological stages using remotely sensed imagery from the MODIS (MODerate resolution Imaging Spectroradiometer) sensor. The methods and parameters were adjusted based on the vegetation variation. The workflow was first tested at the Australian site. Here the PV estimates for overstory and understory showed best performance, however NPV estimates exhibited spatial variation in validation relationships. At the South American site (Cerrado), an additional method based on frequency unmixing was developed to separate green vegetation components with similar phenology. When the decomposition and frequency methods were compared, the frequency method was better for extracting the green tree phenology, but the original decomposition method was better for retrieval of understory grass phenology. Both methods, however, were less accurate than in the Cerrado than in Australia due to intermingling and intergrading of grass and small woody components. Since African savanna trees are predominantly deciduous, the frequency method was combined with the linear unmixing of fractional cover to attempt to separate the relatively similar phenology of deciduous trees and seasonal grasses. The results for Africa revealed limitations associated with both methods. There was spatial and seasonal variation in the spectral indices used to unmix fractional cover resulting in poor validation for NPV in particular. The frequency analysis revealed significant phase variation indicative of different phenology, but these could not be clearly ascribed to separate grass and tree components. Overall findings indicate that site-specific variation and vegetation structure and composition, along with MODIS pixel resolution, and the simple vegetation index approach used was not robust across the different savanna biomes. The approach showed generally better performance for estimating PV fraction, and separating green phenology, but there were major inconsistencies, errors and biases in estimation of NPV and BS outside of the Australian savanna environment.

Hydrogeology, Chemical Characteristics, and Transport Processes in the Zone of Contribution of a Public-Supply Well in York, Nebraska

USGS Publications Warehouse

Landon, Matthew K.; Clark, Brian R.; McMahon, Peter B.; McGuire, Virginia L.; Turco, Michael J.

2008-01-01

In 2001, the U.S. Geological Survey, as part of the National Water Quality Assessment (NAWQA) Program, initiated a topical study of Transport of Anthropogenic and Natural Contaminants (TANC) to PSW (public-supply wells). Local-scale and regional-scale TANC study areas were delineated within selected NAWQA study units for intensive study of processes effecting transport of contaminants to PSWs. This report describes results from a local-scale TANC study area at York, Nebraska, within the High Plains aquifer, including the hydrogeology and geochemistry of a 108-square-kilometer study area that contains the zone of contribution to a PSW selected for study (study PSW), and describes factors controlling the transport of selected anthropogenic and natural contaminants to PSWs. Within the local-scale TANC study area, the High Plains aquifer is approximately 75 m (meter) thick, and includes an unconfined aquifer, an upper confining unit, an upper confined aquifer, and a lower confining unit with lower confined sand lenses (units below the upper confining unit are referred to as confined aquifers) in unconsolidated alluvial and glacial deposits overlain by loess and underlain by Cretaceous shale. From northwest to southeast, land use in the local-scale TANC study area changes from predominantly irrigated agricultural land to residential and commercial land in the small community of York (population approximately 8,100). For the purposes of comparing water chemistry, wells were classified by degree of aquifer confinement (unconfined and confined), depth in the unconfined aquifer (shallow and deep), land use (urban and agricultural), and extent of mixing in wells in the confined aquifer with water from the unconfined aquifer (mixed and unmixed). Oxygen (delta 18O) and hydrogen (delta D) stable isotopic values indicated a clear isotopic contrast between shallow wells in the unconfined aquifer (hereinafter, unconfined shallow wells) and most monitoring wells in the confined aquifers (hereinafter, confined unmixed wells). Delta 18O and delta D values for a minority of wells in the confined aquifers were intermediate between those for the unconfined shallow wells and those for the confined unmixed wells. These intermediate values were consistent with mixing of water from unconfined and confined aquifers (hereinafter, confined mixed wells). Oxidation-reduction conditions were primarily oxic in the unconfined aquifer and variably reducing in the confined aquifers. Trace amounts of volatile organic compounds (VOC), particularly tetrachloroethylene (PCE) and trichloroethylene (TCE), were widely detected in unconfined shallow urban wells and indicated the presence of young urban recharge waters in most confined mixed wells. The presence of degradation products of agricultural pesticides (acetochlor and alachlor) in some confined mixed wells suggests that some fraction of the water in these wells also was the result of recharge in agricultural areas. In the unconfined aquifer, age-tracer data (chlorofluorocarbon and sulfur hexafluoride data, and tritium to helium-3 ratios) fit a piston-flow model, with apparent recharge ages ranging from 7 to 48 years and generally increasing with depth. Age-tracer data for the confined aquifers were consistent with mixing of 'old' water, not containing modern tracers recharged in the last 60 years, and exponentially-mixed 'young' water with modern tracers. Confined unmixed wells contained less than (=) 97% of old water. Confined mixed wells contained >30% young water and mean ages ranged from 12 to 14 years. Median concentrations of nitrate (as nitrogen, hereinafter, nitrate-N) were 17.3 and 16.0 mg/L (milligram per liter) in unconfined shallow urban and agricultural wells, respectively, indicating a range of likely nitrate sources. Septic systems are most numerous near the edge of the urban area and appear to be

Medical tourism-A New Arena

PubMed Central

Puri, S; Singh, A; Yashik

2010-01-01

Globalisation has given birth to medical tourism. Health and medical tourism are the fastest growing segments in not only developed nations but in developing countries too. India has become a hot destination, as the Indian medical standards match up to the highly prescribed international standards at a very low cost. However, it is an unmixed blessing; along with advantages, it has many unintended side effects also. PMID:23113017

Evaluation of linear spectral unmixing and deltaNBR for predicting post-fire recovery in a North American ponderosa pine forest

Treesearch

A. M. S. Smith; L. B. Lenilte; A. T. Hudak; P. Morgan

2007-01-01

The Differenced Normalized Burn Ratio (deltaNBR) is widely used to map post-fire effects in North America from multispectral satellite imagery, but has not been rigorously validated across the great diversity in vegetation types. The importance of these maps to fire rehabilitation crews highlights the need for continued assessment of alternative remote sensing...

Unmixing the Materials and Mechanics Contributions in Non-resolved Object Signatures

DTIC Science & Technology

2008-09-01

abundances from hyperspectral or multi-spectral time - resolved signatures. A Fourier analysis of temporal variation of material abundance provides...factorization technique to extract the temporal variation of material abundances from hyperspectral or multi-spectral time - resolved signatures. A Fourier...approximately one hundred wavelengths in the visible spectrum. The frame rate for the instrument was not large enough to collect time resolved data. However

Discrimination of Sedimentary Lithologies Through Unmixing of EO-1 Hyperion Data: Melville Island, Canadian High Arctic

NASA Astrophysics Data System (ADS)

Leverington, D. W.

2008-12-01

The use of remote-sensing techniques in the discrimination of rock and soil classes in northern regions can help support a diverse range of activities including environmental characterization, mineral exploration, and the study of Quaternary paleoenvironments. Images of low spectral resolution can commonly be used in the mapping of lithological classes possessing distinct spectral characteristics, but hyperspectral databases offer greater potential for discrimination of materials distinguished by more subtle reflectance properties. Orbiting sensors offer an especially flexible and cost-effective means for acquisition of data to workers unable to conduct airborne surveys. In an effort to better constrain the utility of hyperspectral datasets in northern research, this study undertook to investigate the effectiveness of EO-1 Hyperion data in the discrimination and mapping of surface classes at a study area on Melville Island, Nunavut. Bedrock units in the immediate study area consist of late-Paleozoic clastic and carbonate sequences of the Sverdrup Basin. Weathered and frost-shattered felsenmeer, predominantly taking the form of boulder- to pebble-sized clasts that have accumulated in place and that mantle parent bedrock units, is the most common surface material in the study area. Hyperion data were converted from at-sensor radiance to reflectance, and were then linearly unmixed on the basis of end-member spectra measured from field samples. Hyperion unmixing results effectively portray the general fractional cover of six end members, although the fraction images of several materials contain background values that in some areas overestimate surface exposure. The best separated end members include the snow, green vegetation, and red-weathering sandstone classes, whereas the classes most negatively affected by elevated fraction values include the mudstone, limestone, and 'other' sandstone classes. Local overestimates of fractional cover are likely related to the shared lithological and weathering characteristics of several clastic and carbonate units, and may also be related to the lower radiometric precision characteristic of Hyperion data. Despite these issues, the databases generated in this study successfully provide useful complementary information to that provided by maps of local bedrock geology.

Precombination Cloud Collapse and Baryonic Dark Matter

NASA Technical Reports Server (NTRS)

Hogan, Craig J.

1993-01-01

A simple spherical model of dense baryon clouds in the hot big bang 'strongly nonlinear primordial isocurvature baryon fluctuations' is reviewed and used to describe the dependence of cloud behavior on the model parameters, baryon mass, and initial over-density. Gravitational collapse of clouds before and during recombination is considered including radiation diffusion and trapping, remnant type and mass, and effects on linear large-scale fluctuation modes. Sufficiently dense clouds collapse early into black holes with a minimum mass of approx. 1 solar mass, which behave dynamically like collisionless cold dark matter. Clouds below a critical over-density, however, delay collapse until recombination, remaining until then dynamically coupled to the radiation like ordinary diffuse baryons, and possibly producing remnants of other kinds and lower mass. The mean density in either type of baryonic remnant is unconstrained by observed element abundances. However, mixed or unmixed spatial variations in abundance may survive in the diffuse baryon and produce observable departures from standard predictions.

A self-trained classification technique for producing 30 m percent-water maps from Landsat data

USGS Publications Warehouse

Rover, Jennifer R.; Wylie, Bruce K.; Ji, Lei

2010-01-01

Small bodies of water can be mapped with moderate-resolution satellite data using methods where water is mapped as subpixel fractions using field measurements or high-resolution images as training datasets. A new method, developed from a regression-tree technique, uses a 30 m Landsat image for training the regression tree that, in turn, is applied to the same image to map subpixel water. The self-trained method was evaluated by comparing the percent-water map with three other maps generated from established percent-water mapping methods: (1) a regression-tree model trained with a 5 m SPOT 5 image, (2) a regression-tree model based on endmembers and (3) a linear unmixing classification technique. The results suggest that subpixel water fractions can be accurately estimated when high-resolution satellite data or intensively interpreted training datasets are not available, which increases our ability to map small water bodies or small changes in lake size at a regional scale.

Ignition dynamics of a laminar diffusion flame in the field of a vortex embedded in a shear flow

NASA Technical Reports Server (NTRS)

Macaraeg, Michele G.; Jackson, T. L.; Hussaini, M. Y.

1994-01-01

The role of streamwise-spanwise vorticity interactions that occur in turbulent shear flows on flame/vortex interactions is examined by means of asymptotic analysis and numerical simulation in the limit of small Mach number. An idealized model is employed to describe the interaction process. The model consists of a one-step, irreversible Arrhenius reaction between initially unmixed species occupying adjacent half-planes which are then allowed to mix and react in the presence of a streamwise vortex embedded in a shear flow. It is found that the interaction of the streamwise vortex with shear gives rise to small-scale velocity oscillations which increase in magnitude with shear strength. These oscillations give rise to regions of strong temperature gradients via viscous heating, which can lead to multiple ignition points and substantially decrease ignition times. The evolution in time of the temperature and mass-fraction fields is followed, and emphasis is placed on the ignition time and structure as a function of vortex and shear strength.

ATMOSPHERIC AEROSOL SOURCE-RECEPTOR RELATIONSHIPS: THE ROLE OF COAL-FIRED POWER PLANTS

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

Allen L. Robinson; Spyros N. Pandis; Cliff I. Davidson

2005-04-01

This report describes the technical progress made on the Pittsburgh Air Quality Study (PAQS) during the period of September 2004 through February 2005. Significant progress was made this project period on the analysis of ambient data, source apportionment, and deterministic modeling activities. The major experimental achievement this project period was the characterization of the mercury and fine particle emissions from two modern, large, commercial pulverized coal boilers. This testing completes the field work component of the Source Characterization Activity. This report highlights results from mercury emission measurements made using a dilution sampler. The measurements clearly indicate that mercury is beingmore » transformed from an oxidized to an elemental state within the dilution. However, wall effects are significant making it difficult to determine whether or not these changes occur in the gas phase or due to some interaction with the sampler walls. This report also presents results from an analysis that uses spherical aluminum silicate (SAS) particles as a marker for primary PM{sub 2.5} emitted from coal combustion. Primary emissions from coal combustion contribute only a small fraction of the PM{sub 2.5} mass (less than 1.5% in the summer and less than 3% in the winter) at the Pittsburgh site. Ambient SAS concentrations also appear to be reasonably spatially homogeneous. Finally, SAS emission factors measured at pilot-scale are consistent with measurements made at full-scale. This report also presents results from applying the Unmix and PMF models to estimate the contribution of different sources to the PM{sub 2.5} mass concentrations in Pittsburgh using aerosol composition information. Comparison of the two models shows similar source composition and contribution for five factors: crustal material, nitrate, an Fe, Mn, and Zn factor, specialty steel production, and a cadmium factor. PMF found several additional factors. Comparison between source contributions for the similar factors shows reasonable agreement between the two models. The sulfate factor shows the highest contribution to local PM{sub 2.5} with an annual average contribution of approximately 28% (from PMF). The nitrate, crustal material, and primary OC and EC factors also show significant contributions on the order of 10-14%. The sulfate factor is affected by photochemistry and therefore shows maximum values in summer.« less

Quantitative interpretation of magnetic properties as a way to characterize biogeophysical signatures of biodegraded contaminated sites

NASA Astrophysics Data System (ADS)

Ustra, A.; Kessouri, P.; Leite, A.; Mendonça, C. A.; Bandeira, N.

2017-12-01

Magnetic minerals in soils and rocks are one way to study biogechemical and paleoenvironmental processes. The ultrafine fraction of these minerals (superparmagnetic (SP) and stable single domain (SSD)) are usually investigated in environmental magnetism studies, since changes in mineralogy, concentration, size and morphology of the magnetic grains can be related to biogeochemical processes. In this study, we use low-field frequency dependent susceptibility (FDS) and isothermal remanent magnetization (IRM) to characterize the magnetic properties of materials in environmental magnetism. Magnetic susceptibility (MS) measurements are frequently used as a proxy of magnetic minerals present in soils and rocks. MS is a complex function of magnetic mineralogy and grain size, as well as magnitude and frequency of the applied field. This work presents a method for inverting low-field FDS data. The inverted parameters can be interpreted in terms of grain size variations of magnetic particles on the SP-SSD transition. This work also presents a method for inverting IRM demagnetization curves, to obtain the saturation magnetization, the individual magnetic moment for an assemblage of ultrafine SP minerals and estimate the concentration of magnetic carriers. IRM magnetization curves can be interpreted as resulting from distinct contributions of different mineral phases, which can be described by Cummulative Log-Gaussian (CLG) distributions. Each acquisition curve provides fundamental parameters that are characteristic of the respective mineral phase. The CLG decomposition is widely used in an interpretation procedure named mineral unmixing. In this work we present an inversion method for mineral unmixing, implementing the genetic algorithm to find the parameters of distinct components. These methodologies have been tested by synthetic models and applied to data from environmental magnetism studies. In this work we apply the proposed methodologies to characterize the magnetic properties of samples from the former Brandywine MD Defense Reutilization and Marketing Office (DRMO). The results from the magnetic properties characterization will provide additional information that may assist the interpretation of the biogeophysical signatures observed at the site.

Comparative analysis of spectral unmixing and neural networks for estimating small diameter tree above-ground biomass in the State of Mississippi

Treesearch

Moham P. Tiruveedhula; Joseph Fan; Ravi R. Sadasivuni; Surya S. Durbha; David L. Evans

2010-01-01

The accumulation of small diameter trees (SDTs) is becoming a nationwide concern. Forest management practices such as fire suppression and selective cutting of high grade timber have contributed to an overabundance of SDTs in many areas. Alternative value-added utilization of SDTs (for composite wood products and biofuels) has prompted the need to estimate their...

Spectral Unmixing Applied to Desert Soils for the Detection of Sub-Pixel Disturbances

DTIC Science & Technology

2012-09-01

and Glazner, 1997). Rocks underlying Panum Crater consist of the granitic and metamorphic batholith associated with the Sierra Nevada. On top of this...of Management and Budget, Paperwork Reduction Project (0704-0188) Washington DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE September...technology can be used to detect and characterize surface disturbance both literally (visually) and non-literally (analytically). Non-literal approaches

Mineral and Lithology Mapping of Drill Core Pulps Using Visible and Infrared Spectrometry

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

Taylor, G. R., E-mail: G.Taylor@unsw.edu.au

2000-12-15

A novel approach for using field spectrometry for determining both the mineralogy and the lithology of drill core pulps (powders) is developed and evaluated. The methodology is developed using material from a single drillhole through a mineralized sequence of rocks from central New South Wales. Mineral library spectra are used in linear unmixing routines to determine the mineral abundances in drill core pulps that represent between 1 m and 3 m of core. Comparison with X-Ray Diffraction (XRD) analyses shows that for most major constituents, spectrometry provides an estimate of quantitative mineralogy that is as reliable as that provided bymore » XRD. Confusion between the absorption features of calcite and those of chlorite causes the calcite contents determined by spectrometry to be unreliable. Convex geometry is used to recognize the spectra of those samples that are extreme and are representative of unique lithologies. Linear unmixing is used to determine the abundance of these lithologies in each drillhole sample and these abundances are used to interpret the geology of the drillhole. The interpreted geology agrees well with conventional drillhole logs of the visible geology and photographs of the split core. The methods developed provide a quick and cost-effective way of determining the lithology and alteration mineralogy of drill core pulps.« less

The Yearly Variation in Fall-Winter Arctic Winter Vortex Descent

NASA Technical Reports Server (NTRS)

Schoeberl, Mark R.; Newman, Paul A.

1999-01-01

Using the change in HALOE methane profiles from early September to late March, we have estimated the minimum amount of diabatic descent within the polar which takes place during Arctic winter. The year to year variations are a result in the year to year variations in stratospheric wave activity which (1) modify the temperature of the vortex and thus the cooling rate; (2) reduce the apparent descent by mixing high amounts of methane into the vortex. The peak descent amounts from HALOE methane vary from l0km -14km near the arrival altitude of 25 km. Using a diabatic trajectory calculation, we compare forward and backward trajectories over the course of the winter using UKMO assimilated stratospheric data. The forward calculation agrees fairly well with the observed descent. The backward calculation appears to be unable to produce the observed amount of descent, but this is only an apparent effect due to the density decrease in parcels with altitude. Finally we show the results for unmixed descent experiments - where the parcels are fixed in latitude and longitude and allowed to descend based on the local cooling rate. Unmixed descent is found to always exceed mixed descent, because when normal parcel motion is included, the path average cooling is always less than the cooling at a fixed polar point.

Spectral unmixing of urban land cover using a generic library approach

NASA Astrophysics Data System (ADS)

Degerickx, Jeroen; Lordache, Marian-Daniel; Okujeni, Akpona; Hermy, Martin; van der Linden, Sebastian; Somers, Ben

2016-10-01

Remote sensing based land cover classification in urban areas generally requires the use of subpixel classification algorithms to take into account the high spatial heterogeneity. These spectral unmixing techniques often rely on spectral libraries, i.e. collections of pure material spectra (endmembers, EM), which ideally cover the large EM variability typically present in urban scenes. Despite the advent of several (semi-) automated EM detection algorithms, the collection of such image-specific libraries remains a tedious and time-consuming task. As an alternative, we suggest the use of a generic urban EM library, containing material spectra under varying conditions, acquired from different locations and sensors. This approach requires an efficient EM selection technique, capable of only selecting those spectra relevant for a specific image. In this paper, we evaluate and compare the potential of different existing library pruning algorithms (Iterative Endmember Selection and MUSIC) using simulated hyperspectral (APEX) data of the Brussels metropolitan area. In addition, we develop a new hybrid EM selection method which is shown to be highly efficient in dealing with both imagespecific and generic libraries, subsequently yielding more robust land cover classification results compared to existing methods. Future research will include further optimization of the proposed algorithm and additional tests on both simulated and real hyperspectral data.

Numerical modeling of temperature and species distributions in hydrocarbon reservoirs

NASA Astrophysics Data System (ADS)

Bolton, Edward W.; Firoozabadi, Abbas

2014-01-01

We examine bulk fluid motion and diffusion of multicomponent hydrocarbon species in porous media in the context of nonequilibrium thermodynamics, with particular focus on the phenomenology induced by horizontal thermal gradients at the upper and lower horizontal boundaries. The problem is formulated with respect to the barycentric (mass-averaged) frame of reference. Thermally induced convection, with fully time-dependent temperature distributions, can lead to nearly constant hydrocarbon composition, with minor unmixing due to thermal gradients near the horizontal boundaries. Alternately, the composition can be vertically segregated due to gravitational effects. Independent and essentially steady solutions have been found to depend on how the compositions are initialized in space and may have implications for reservoir history. We also examine injection (to represent filling) and extraction (to represent leakage) of hydrocarbons at independent points and find a large distortion of the gas-oil contact for low permeability.

S-type granitic magmas—petrogenetic issues, models and evidence

NASA Astrophysics Data System (ADS)

Clemens, J. D.

2003-04-01

Despite a perception that it represents a perverse divergence, it is perfectly possible to believe in the existence of S- and I-type granites (and the implications for the nature of their protoliths), and to disbelieve in the applicability of the restite-unmixing model for chemical variation in granitic magmas. White and Chappell erected the S-I classification with impeccable validity. The isotopic evidence demands contrasting source reservoirs for S- and I-type granitic magmas. However, the major advance was not the classification, but the recognition that highly contrasting parental materials must be involved in the genesis of granitic magmas. The restite-unmixing model is commonly seen as a companion to the S-I classification, but it is really a separate issue. This model implies that the compositions of granites 'image' those of their source rocks in a simple way. However, there are other equally valid models that can explain the data, and none of them represents a unique solution. The most cogent explanation for the high-grade metasedimentary enclaves in most S-type granites is that they represent mid-crustal xenoliths; restitic enclaves are either rare or absent. Inherited zircons in S-type rocks are certainly restitic. However, the occurrence of a substantial restitic zircon population does not imply an equally substantial restitic component in the rest of the rock. Zircon and zirconium behaviours are controlled by disequilibrium and kinetics, and Zr contents of granitic rocks can rarely be used to infer magma temperatures. Since the dominant ages among inherited zircons in Lachlan Fold Belt (LFB) S-type granites are Ordovician and Proterozoic, it seems likely that crust of this age, but geochemically different from the exposed rocks, not only underlies much of the LFB but also forms a component in the granite magma sources. The evidence is overwhelming that the dark, microgranular enclaves that occur in both S- and I-type granites are igneous in origin. They represent globules of quenched, more mafic magma mingled and modified by exchange with the host granitic magma. However, magma mixing does not appear to be a significant process affecting the chemical evolution of the host magmas. Likewise, the multicomponent mixing models erected for some granitic rock suites are mathematically nonunique and, in some cases, violate constraints from isotopic studies. S- and I-type magmas commonly retain their distinct identities. This suggests limited source mixing, limited magma mixing and limited wall-rock assimilation. Though intermediate types certainly exist, they are probably relatively minor in volume. Crystal fractionation probably plays the major role in the differentiation of very many granitic magmas, including most S-types, especially those emplaced at high crustal levels or in the volcanic environment. Minor mechanisms include magma mixing, wall-rock assimilation and restite unmixing. Isotopic variations within plutons and in granite suites could be caused by source heterogeneities, magma mixing, assimilation and even by isotopic disequilibrium. However, source heterogeneity, coupled with the inefficiency of magma mixing is probably the major cause of observed heterogeneity. Normal geothermal gradients are seldom sufficient to provide the necessary heat for partial melting of the crust, and crustal thickening likewise fails to provide sufficient heat. Generally, the mantle must be the major heat source. This might be provided through mantle upwelling and crustal thinning, and possibly through the intra- and underplating of mafic magmas. Upper crustal extension seems to have been common in regions undergoing granitic magmatism. Migmatites probably provide poor analogues of granite source regions because they are mostly formed by fluid-present reactions. Granitic magmas are mostly formed by fluid-absent processes. Where we do see rare evidence for arrested fluid-absent partial melting, the melt fraction is invariably concentrated into small shear zones, veinlets and small dykes. Thus, it seems likely that dyking is important in transporting granitic magma on a variety of scales and at many crustal levels. However, one major missing link in the chain is the mechanism by which melt fractions, in small-scale segregations occurring over a wide area, can be gathered and focused to efficiently feed much wider-spaced major magma conduits. Answers may lie in the geometry of the melting zones and in the tendency of younger propagating fractures to curve toward and merge with older ones. Self-organization almost certainly plays a role.

Concentrations and Origins of Atmospheric Lead and Other Trace Species at a Rural Site in Northern China

NASA Technical Reports Server (NTRS)

Li, Can; Wen, Tianxue; Li, Zhanqing; Dickerson, Russell R.; Yang, Yongjie; Zhao, Yanan; Wang, Yuesi; Tsay, Si-Chee

2010-01-01

In this study we analyze the ambient levels of lead and other trace species in the bulk aerosol samples from a rural site approx.70 km ESE of Beijing in spring 2005. Lead (0.28+/-0.24 micro-g/cu m, average +/- standard deviation), along with several pollution \\related trace elements, was enriched by over 100 fold relative to the Earth's crust. The ambient lead levels showing large synoptic variations were well-correlated with other anthropogenic pollutants (e.g., CO and SO2). The Unmix receptor model resolved four factors in the aerosol composition data: a biomass burning source, an industrial and coal combustion source, a secondary aerosol source, and a dust source. The first three sources were strongest in weak southerly winds ahead of cold fronts, while the dust source peaked in strong northerly winds behind cold fronts. The second source, primarily representing emissions from industrial processes and relatively small \\scale coal burning such as in home and institutional heating, was identified as the main source of ambient lead in this study. Mobile sources might also contribute to this factor, but there was no distinct evidence of emissions due to combustion of leaded gasoline, despite a correlation between lead and CO. Potential source contribution function, calculated from backward trajectories and aerosol composition, further reveals that lead observed in this study was predominantly from the populated and industrialized areas to the south and SW of Xianghe, rather than Beijing to the west. Our results and several recent studies show that the lead levels in suburban areas near big cities in China, although generally lower than those in industrial districts and urban areas, are substantial (near or above 0.15 micro-g/cu m). More extensive studies on airborne lead and its emission sources in China are called for.

Multispectral Thermal Imagery and Its Application to the Geologic Mapping of the Koobi Fora Formation, Northwestern Kenya

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

Green, Mary K.

The Koobi Fora Formation in northwestern Kenya has yielded more hominin fossils dated between 2.1 and 1.2 Ma than any other location on Earth. This research was undertaken to discover the spectral signatures of a portion of the Koobi Fora Formation using imagery from the DOE's Multispectral Thermal Imager (MTI) satellite. Creation of a digital geologic map from MTI imagery was a secondary goal of this research. MTI is unique amongst multispectral satellites in that it co-collects data from 15 spectral bands ranging from the visible to the thermal infrared with a ground sample distance of 5 meters per pixelmore » in the visible and 20 meters in the infrared. The map was created in two stages. The first was to correct the base MTI image using spatial accuracy assessment points collected in the field. The second was to mosaic various MTI images together to create the final Koobi Fora map. Absolute spatial accuracy of the final map product is 73 meters. The geologic classification of the Koobi Fora MTI map also took place in two stages. The field work stage involved location of outcrops of different lithologies within the Koobi Fora Formation. Field descriptions of these outcrops were made and their locations recorded. During the second stage, a linear spectral unmixing algorithm was applied to the MTI mosaic. In order to train the linear spectra unmixing algorithm, regions of interest representing four different classes of geologic material (tuff, alluvium, carbonate, and basalt), as well as a vegetation class were defined within the MTI mosaic. The regions of interest were based upon the aforementioned field data as well as overlays of geologic maps from the 1976 Iowa State mapping project. Pure spectra were generated for each class from the regions of interest, and then the unmixing algorithm classified each pixel according to relative percentage of classes found within the pixel based upon the pure spectra values. A total of four unique combinations of geologic classes were analyzed using the algorithm. The tuffs within the Koobi Fora Formation were defined with 100% accuracy using a combination of pure spectra from the basalt, vegetation, and tuff.« less

Hyperspectral Remote Sensing and Ecological Modeling Research and Education at Mid America Remote Sensing Center (MARC): Field and Laboratory Enhancement

NASA Technical Reports Server (NTRS)

Cetin, Haluk

1999-01-01

The purpose of this project was to establish a new hyperspectral remote sensing laboratory at the Mid-America Remote sensing Center (MARC), dedicated to in situ and laboratory measurements of environmental samples and to the manipulation, analysis, and storage of remotely sensed data for environmental monitoring and research in ecological modeling using hyperspectral remote sensing at MARC, one of three research facilities of the Center of Reservoir Research at Murray State University (MSU), a Kentucky Commonwealth Center of Excellence. The equipment purchased, a FieldSpec FR portable spectroradiometer and peripherals, and ENVI hyperspectral data processing software, allowed MARC to provide hands-on experience, education, and training for the students of the Department of Geosciences in quantitative remote sensing using hyperspectral data, Geographic Information System (GIS), digital image processing (DIP), computer, geological and geophysical mapping; to provide field support to the researchers and students collecting in situ and laboratory measurements of environmental data; to create a spectral library of the cover types and to establish a World Wide Web server to provide the spectral library to other academic, state and Federal institutions. Much of the research will soon be published in scientific journals. A World Wide Web page has been created at the web site of MARC. Results of this project are grouped in two categories, education and research accomplishments. The Principal Investigator (PI) modified remote sensing and DIP courses to introduce students to ii situ field spectra and laboratory remote sensing studies for environmental monitoring in the region by using the new equipment in the courses. The PI collected in situ measurements using the spectroradiometer for the ER-2 mission to Puerto Rico project for the Moderate Resolution Imaging Spectrometer (MODIS) Airborne Simulator (MAS). Currently MARC is mapping water quality in Kentucky Lake and vegetation in the Land-Between-the Lakes (LBL) using Landsat-TM data. A Landsat-TM scene of the same day was obtained to relate ground measurements to the satellite data. A spectral library has been created for overstory species in LBL. Some of the methods, such as NPDF and IDFD techniques for spectral unmixing and reduction of effects of shadows in classifications- comparison of hyperspectral classification techniques, and spectral nonlinear and linear unmixing techniques, are being tested using the laboratory.

Preliminary Tests of Gloss-Reduction and Coloring Agents for Camouflage of Polyvinyl Acetate Dust-Control Film

DTIC Science & Technology

1976-02-01

extenders Kaolin powder Calcium carbonate dust Paint flatteners Celite h99 Nytal 1+00 Dry pigments Chalk dust (various colors) Liquid...a dispersant or wetting agent for satisfactory mixing. Vor this purpose, one of two agents was used: (a) a commercial 10 per- cent determent...pockets of unmixed powder, and in some cases the powder settled to the bottom of the mold. The dispersants that were tried did not effectively disperse

Electrokinetic instability micromixing.

PubMed

Oddy, M H; Santiago, J G; Mikkelsen, J C

2001-12-15

We have developed an electrokinetic process to rapidly stir micro- and nanoliter volume solutions for microfluidic bioanalytical applications. We rapidly stir microflow streams by initiating a flow instability, which we have observed in sinusoidally oscillating, electroosmotic channel flows. As the effect occurs within an oscillating electroosmotic flow, we refer to it here as an electrokinetic instability (EKI). The rapid stretching and folding of material lines associated with this instability can be used to stir fluid streams with Reynolds numbers of order unity, based on channel depth and rms electroosmotic velocity. This paper presents a preliminary description of the EKI and the design and fabrication of two micromixing devices capable of rapidly stirring two fluid streams using this flow phenomenon. A high-resolution CCD camera is used to record the stirring and diffusion of fluorescein from an initially unmixed configuration. Integration of fluorescence intensity over measurement volumes (voxels) provides a measure of the degree to which two streams are mixed to within the length scales of the voxels. Ensemble-averaged probability density functions and power spectra of the instantaneous spatial intensity profiles are used to quantify the mixing processes. Two-dimensional spectral bandwidths of the mixing images are initially anisotropic for the unmixed configuration, broaden as the stirring associated with the EKI rapidly stretches and folds material lines (adding high spatial frequencies to the concentration field), and then narrow to a relatively isotropic spectrum at the well-mixed conditions.

Estimates of the Lightning NOx Profile in the Vicinity of the North Alabama Lightning Mapping Array

NASA Technical Reports Server (NTRS)

Koshak, William J.; Peterson, Harold

2010-01-01

The NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) is applied to August 2006 North Alabama Lightning Mapping Array (LMA) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning nitrogen oxides, NOx = NO + NO 2 . This is part of a larger effort aimed at building a more realistic lightning NOx emissions inventory for use by the U.S. Environmental Protection Agency (EPA) Community Multiscale Air Quality (CMAQ) modeling system. Data from the National Lightning Detection Network TM (NLDN) is also employed. Overall, special attention is given to several important lightning variables including: the frequency and geographical distribution of lightning in the vicinity of the LMA network, lightning type (ground or cloud flash), lightning channel length, channel altitude, channel peak current, and the number of strokes per flash. Laboratory spark chamber results from the literature are used to convert 1-meter channel segments (that are located at a particular known altitude; i.e., air density) to NOx concentration. The resulting raw NOx profiles are discussed.

Estimates of the Lightning NOx Profile in the Vicinity of the North Alabama Lightning Mapping Array

NASA Technical Reports Server (NTRS)

Koshak, William J.; Peterson, Harold S.; McCaul, Eugene W.; Blazar, Arastoo

2010-01-01

The NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) is applied to August 2006 North Alabama Lightning Mapping Array (NALMA) data to estimate the (unmixed and otherwise environmentally unmodified) vertical source profile of lightning nitrogen oxides, NOx = NO + NO2. Data from the National Lightning Detection Network (Trademark) (NLDN) is also employed. This is part of a larger effort aimed at building a more realistic lightning NOx emissions inventory for use by the U.S. Environmental Protection Agency (EPA) Community Multiscale Air Quality (CMAQ) modeling system. Overall, special attention is given to several important lightning variables including: the frequency and geographical distribution of lightning in the vicinity of the NALMA network, lightning type (ground or cloud flash), lightning channel length, channel altitude, channel peak current, and the number of strokes per flash. Laboratory spark chamber results from the literature are used to convert 1-meter channel segments (that are located at a particular known altitude; i.e., air density) to NOx concentration. The resulting lightning NOx source profiles are discussed.

Multispectral open-air intraoperative fluorescence imaging.

PubMed

Behrooz, Ali; Waterman, Peter; Vasquez, Kristine O; Meganck, Jeff; Peterson, Jeffrey D; Faqir, Ilias; Kempner, Joshua

2017-08-01

Intraoperative fluorescence imaging informs decisions regarding surgical margins by detecting and localizing signals from fluorescent reporters, labeling targets such as malignant tissues. This guidance reduces the likelihood of undetected malignant tissue remaining after resection, eliminating the need for additional treatment or surgery. The primary challenges in performing open-air intraoperative fluorescence imaging come from the weak intensity of the fluorescence signal in the presence of strong surgical and ambient illumination, and the auto-fluorescence of non-target components, such as tissue, especially in the visible spectral window (400-650 nm). In this work, a multispectral open-air fluorescence imaging system is presented for translational image-guided intraoperative applications, which overcomes these challenges. The system is capable of imaging weak fluorescence signals with nanomolar sensitivity in the presence of surgical illumination. This is done using synchronized fluorescence excitation and image acquisition with real-time background subtraction. Additionally, the system uses a liquid crystal tunable filter for acquisition of multispectral images that are used to spectrally unmix target fluorescence from non-target auto-fluorescence. Results are validated by preclinical studies on murine models and translational canine oncology models.

The two-state dimer receptor model: a general model for receptor dimers.

PubMed

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferrada, Carla; Ferré, Sergi; Fuxe, Kjell; Cortés, Antoni; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2006-06-01

Nonlinear Scatchard plots are often found for agonist binding to G-protein-coupled receptors. Because there is clear evidence of receptor dimerization, these nonlinear Scatchard plots can reflect cooperativity on agonist binding to the two binding sites in the dimer. According to this, the "two-state dimer receptor model" has been recently derived. In this article, the performance of the model has been analyzed in fitting data of agonist binding to A(1) adenosine receptors, which are an example of receptor displaying concave downward Scatchard plots. Analysis of agonist/antagonist competition data for dopamine D(1) receptors using the two-state dimer receptor model has also been performed. Although fitting to the two-state dimer receptor model was similar to the fitting to the "two-independent-site receptor model", the former is simpler, and a discrimination test selects the two-state dimer receptor model as the best. This model was also very robust in fitting data of estrogen binding to the estrogen receptor, for which Scatchard plots are concave upward. On the one hand, the model would predict the already demonstrated existence of estrogen receptor dimers. On the other hand, the model would predict that concave upward Scatchard plots reflect positive cooperativity, which can be neither predicted nor explained by assuming the existence of two different affinity states. In summary, the two-state dimer receptor model is good for fitting data of binding to dimeric receptors displaying either linear, concave upward, or concave downward Scatchard plots.

Quantitative methods and detection techniques in hyperspectral imaging involving medical and other applications

NASA Astrophysics Data System (ADS)

Roy, Ankita

2007-12-01

This research using Hyperspectral imaging involves recognizing targets through spatial and spectral matching and spectral un-mixing of data ranging from remote sensing to medical imaging kernels for clinical studies based on Hyperspectral data-sets generated using the VFTHSI [Visible Fourier Transform Hyperspectral Imager], whose high resolution Si detector makes the analysis achievable. The research may be broadly classified into (I) A Physically Motivated Correlation Formalism (PMCF), which places both spatial and spectral data on an equivalent mathematical footing in the context of a specific Kernel and (II) An application in RF plasma specie detection during carbon nanotube growing process. (III) Hyperspectral analysis for assessing density and distribution of retinopathies like age related macular degeneration (ARMD) and error estimation enabling the early recognition of ARMD, which is treated as an ill-conditioned inverse imaging problem. The broad statistical scopes of this research are two fold-target recognition problems and spectral unmixing problems. All processes involve experimental and computational analysis of Hyperspectral data sets is presented, which is based on the principle of a Sagnac Interferometer, calibrated to obtain high SNR levels. PMCF computes spectral/spatial/cross moments and answers the question of how optimally the entire hypercube should be sampled and finds how many spatial-spectral pixels are required precisely for a particular target recognition. Spectral analysis of RF plasma radicals, typically Methane plasma and Argon plasma using VFTHSI has enabled better process monitoring during growth of vertically aligned multi-walled carbon nanotubes by instant registration of the chemical composition or density changes temporally, which is key since a significant correlation can be found between plasma state and structural properties. A vital focus of this dissertation is towards medical Hyperspectral imaging applied to retinopathies like age related macular degeneration targets taken with a Fundus imager, which is akin to the VFTHSI. Detection of the constituent components in the diseased hyper-pigmentation area is also computed. The target or reflectance matrix is treated as a highly ill-conditioned spectral un-mixing problem, to which methodologies like inverse techniques, principal component analysis (PCA) and receiver operating curves (ROC) for precise spectral recognition of infected area. The region containing ARMD was easily distinguishable from the spectral mesh plots over the entire band-pass area. Once the location was detected the PMCF coefficients were calculated by cross correlating a target of normal oxygenated retina with the deoxygenated one. The ROCs generated using PMCF shows 30% higher detection probability with improved accuracy than ROCs based on Spectral Angle Mapper (SAM). By spectral unmixing methods, the important endmembers/carotenoids of the MD pigment were found to be Xanthophyl and lutein, while beta-carotene which showed a negative correlation in the unconstrained inverse problem is a supplement given to ARMD patients to prevent the disease and does not occur in the eye. Literature also shows degeneration of meso-zeaxanthin. Ophthalmologists may assert the presence of ARMD and commence the diagnosis process if the Xanthophyl pigment have degenerated 89.9%, while the lutein has decayed almost 80%, as found deduced computationally. This piece of current research takes it to the next level of precise investigation in the continuing process of improved clinical findings by correlating the microanatomy of the diseased fovea and shows promise of an early detection of this disease.

Hyperspectral imaging for presumptive identification of bacterial colonies on solid chromogenic culture media

NASA Astrophysics Data System (ADS)

Guillemot, Mathilde; Midahuen, Rony; Archeny, Delpine; Fulchiron, Corine; Montvernay, Regis; Perrin, Guillaume; Leroux, Denis F.

2016-04-01

BioMérieux is automating the microbiology laboratory in order to reduce cost (less manpower and consumables), to improve performance (increased sensitivity, machine algorithms) and to gain traceability through optimization of the clinical laboratory workflow. In this study, we evaluate the potential of Hyperspectral imaging (HSI) as a substitute to human visual observation when performing the task of microbiological culture interpretation. Microbial colonies from 19 strains subcategorized in 6 chromogenic classes were analyzed after a 24h-growth on a chromogenic culture medium (chromID® CPS Elite, bioMérieux, France). The HSI analysis was performed in the VNIR region (400-900 nm) using a linescan configuration. Using algorithms relying on Linear Spectral Unmixing, and using exclusively Diffuse Reflectance Spectra (DRS) as input data, we report interclass classification accuracies of 100% using a fully automatable approach and no use of morphological information. In order to eventually simplify the instrument, the performance of degraded DRS was also evaluated using only the most discriminant 14 spectral channels (a model for a multispectral approach) or 3 channels (model of a RGB image). The overall classification performance remains unchanged for our multispectral model but is degraded for the predicted RGB model, hints that a multispectral solution might bring the answer for an improved colony recognition.

Improving Automated Endmember Identification for Linear Unmixing of HyspIRI Spectral Data.

NASA Astrophysics Data System (ADS)

Gader, P.

2016-12-01

The size of data sets produced by imaging spectrometers is increasing rapidly. There is already a processing bottleneck. Part of the reason for this bottleneck is the need for expert input using interactive software tools. This process can be very time consuming and laborious but is currently crucial to ensuring the quality of the analysis. Automated algorithms can mitigate this problem. Although it is unlikely that processing systems can become completely automated, there is an urgent need to increase the level of automation. Spectral unmixing is a key component to processing HyspIRI data. Algorithms such as MESMA have been demonstrated to achieve results but require carefully, expert construction of endmember libraries. Unfortunately, many endmembers found by automated algorithms for finding endmembers are deemed unsuitable by experts because they are not physically reasonable. Unfortunately, endmembers that are not physically reasonable can achieve very low errors between the linear mixing model with those endmembers and the original data. Therefore, this error is not a reasonable way to resolve the problem on "non-physical" endmembers. There are many potential approaches for resolving these issues, including using Bayesian priors, but very little attention has been given to this problem. The study reported on here considers a modification of the Sparsity Promoting Iterated Constrained Endmember (SPICE) algorithm. SPICE finds endmembers and abundances and estimates the number of endmembers. The SPICE algorithm seeks to minimize a quadratic objective function with respect to endmembers E and fractions P. The modified SPICE algorithm, which we refer to as SPICED, is obtained by adding the term D to the objective function. The term D pressures the algorithm to minimize sum of the squared differences between each endmember and a weighted sum of the data. By appropriately modifying the, the endmembers are pushed towards a subset of the data with the potential for becoming exactly equal to the data points. The algorithm has been applied to spectral data and the differences between the endmembers resulting from ecorded. The results so far are that the endmembers found SPICED are approximately 25% closer to the data with indistinguishable reconstruction error compared to those found using SPICE.

FORCinel Version 3.0: An Integrated Environment for Processing, Analysis and Simulation of First-Order Reversal Curve Diagrams

NASA Astrophysics Data System (ADS)

Lascu, I.; Harrison, R. J.

2016-12-01

First-order reversal curve (FORC) diagrams are a powerful method to characterise the hysteresis properties of magnetic grain ensembles. Methods of processing, analysis and simulation of FORC diagrams have developed rapidly over the past few years, dramatically expanding their utility within rock magnetic research. Here we announce the latest release of FORCinel (Version 3.0), which integrates many of these developments into a unified, user-friendly package running within Igor Pro (www.wavemetrics.com). FORCinel v. 3.0 can be downloaded from https://wserv4.esc.cam.ac.uk/nanopaleomag/. The release will be accompanied by a series of video tutorials outlining each of the new features, including: i) improved work flow, with unified smoothing approach; ii) increased processing speed using multiple processors; iii) control of output resolution, enabling large datasets (> 500 FORCs) to be smoothed in a matter of seconds; iv) load, process, analyse and average multiple FORC diagrams; v) load and process non-gridded data and data acquired on non-PMC systems; vi) improved method for exploring optimal smoothing parameters; vii) interactive and un-doable data-pretreatments; viii) automated detection and removal of measurement outliers; ix) improved interactive method for the generation and optimisation of colour scales; x) full integration with FORCem1 - supervised quantitative unmixing of FORC diagrams using principle component analysis (PCA); xi) full integration with FORCulator2 - micromagnetic simulation of FORC diagrams; xiii) simulate TRM acquisition using the kinetic Monte Carlo simulation algorithm of Shcherbakov3. 1. Lascu, I., Harrison, R.J., Li, Y., Muraszko, J.R., Channell, J.E.T., Piotrowski, A.M., Hodell, D.A., 2015. Magnetic unmixing of first-order reversal curve diagrams using principal component analysis. Geochemistry, Geophys. Geosystems 16, 2900-2915. 2. Harrison, R.J., Lascu, I., 2014. FORCulator: A micromagnetic tool for simulating first-order reversal curve diagrams. Geochemistry Geophys. Geosystems 15, 4671-4691. 3. Shcherbakov, V.P., Lamash, B.E., Sycheva, N.K., 1995. Monte-Carlo modelling of thermoremanence acquisition in interacting single-domain grains. Phys. Earth Planet. Inter. 87, 197-211.

Postfire soil burn severity mapping with hyperspectral image unmixing

USGS Publications Warehouse

Robichaud, P.R.; Lewis, S.A.; Laes, D.Y.M.; Hudak, A.T.; Kokaly, R.F.; Zamudio, J.A.

2007-01-01

Burn severity is mapped after wildfires to evaluate immediate and long-term fire effects on the landscape. Remotely sensed hyperspectral imagery has the potential to provide important information about fine-scale ground cover components that are indicative of burn severity after large wildland fires. Airborne hyperspectral imagery and ground data were collected after the 2002 Hayman Fire in Colorado to assess the application of high resolution imagery for burn severity mapping and to compare it to standard burn severity mapping methods. Mixture Tuned Matched Filtering (MTMF), a partial spectral unmixing algorithm, was used to identify the spectral abundance of ash, soil, and scorched and green vegetation in the burned area. The overall performance of the MTMF for predicting the ground cover components was satisfactory (r2 = 0.21 to 0.48) based on a comparison to fractional ash, soil, and vegetation cover measured on ground validation plots. The relationship between Landsat-derived differenced Normalized Burn Ratio (dNBR) values and the ground data was also evaluated (r2 = 0.20 to 0.58) and found to be comparable to the MTMF. However, the quantitative information provided by the fine-scale hyperspectral imagery makes it possible to more accurately assess the effects of the fire on the soil surface by identifying discrete ground cover characteristics. These surface effects, especially soil and ash cover and the lack of any remaining vegetative cover, directly relate to potential postfire watershed response processes. ?? 2006 Elsevier Inc. All rights reserved.

N-Way FRET Microscopy of Multiple Protein-Protein Interactions in Live Cells

PubMed Central

Hoppe, Adam D.; Scott, Brandon L.; Welliver, Timothy P.; Straight, Samuel W.; Swanson, Joel A.

2013-01-01

Fluorescence Resonance Energy Transfer (FRET) microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET) to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells. PMID:23762252

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

PubMed Central

Monine, Michael I.; Posner, Richard G.; Savage, Paul B.; Faeder, James R.; Hlavacek, William S.

2010-01-01

Abstract We use flow cytometry to characterize equilibrium binding of a fluorophore-labeled trivalent model antigen to bivalent IgE-FcεRI complexes on RBL cells. We find that flow cytometric measurements are consistent with an equilibrium model for ligand-receptor binding in which binding sites are assumed to be equivalent and ligand-induced receptor aggregates are assumed to be acyclic. However, this model predicts extensive receptor aggregation at antigen concentrations that yield strong cellular secretory responses, which is inconsistent with the expectation that large receptor aggregates should inhibit such responses. To investigate possible explanations for this discrepancy, we evaluate four rule-based models for interaction of a trivalent ligand with a bivalent cell-surface receptor that relax simplifying assumptions of the equilibrium model. These models are simulated using a rule-based kinetic Monte Carlo approach to investigate the kinetics of ligand-induced receptor aggregation and to study how the kinetics and equilibria of ligand-receptor interaction are affected by steric constraints on receptor aggregate configurations and by the formation of cyclic receptor aggregates. The results suggest that formation of linear chains of cyclic receptor dimers may be important for generating secretory signals. Steric effects that limit receptor aggregation and transient formation of small receptor aggregates may also be important. PMID:20085718

Search at BaBar for D^0--\\overlineD^0 Mixing using Semileptonic Decays.

NASA Astrophysics Data System (ADS)

Flood, Kevin

2004-05-01

Based on a 87 fb-1 dataset acquired by the Babar experiment running on and near the Υ(4S) from 1999-2002, a new upper limit is set on the rate of D^0--\\overlineD^0 mixing using the decay modes D^*+ arrow π^+ D^0, D^0 arrow [K / K^*]eν (+c.c.). These modes offer unambiguous initial and final-state charm flavor tags, and allow the combined use of the D^0 lifetime and D^*+--D^0 mass difference (Δ M) in a global likelihood fit. The high-statistics sample of reconstructed unmixed semileptonic D^0 decays is used to model Δ M and the time-dependence of mixed events directly from the data. Neural networks are used both to select events and to fully reconstruct the D^0. The current world-best published limit on semileptonic charm mixing is 5x10-3 (90% C.L.) (E791).

Simulated altitude exposure assessment by hyperspectral imaging

NASA Astrophysics Data System (ADS)

Calin, Mihaela Antonina; Macovei, Adrian; Miclos, Sorin; Parasca, Sorin Viorel; Savastru, Roxana; Hristea, Razvan

2017-05-01

Testing the human body's reaction to hypoxia (including the one generated by high altitude) is important in aeronautic medicine. This paper presents a method of monitoring blood oxygenation during experimental hypoxia using hyperspectral imaging (HSI) and a spectral unmixing model based on a modified Beer-Lambert law. A total of 20 healthy volunteers (males) aged 25 to 60 years were included in this study. A line-scan HSI system was used to acquire images of the faces of the subjects. The method generated oxyhemoglobin and deoxyhemoglobin distribution maps from the foreheads of the subjects at 5 and 10 min of hypoxia and after recovery in a high oxygen breathing mixture. The method also generated oxygen saturation maps that were validated using pulse oximetry. An interesting pattern of desaturation on the forehead was discovered during the study, showing one of the advantages of using HSI for skin oxygenation monitoring in hypoxic conditions. This could bring new insight into the physiological response to high altitude and may become a step forward in air crew testing.

Nonlinear scalar forcing based on a reaction analogy

NASA Astrophysics Data System (ADS)

Daniel, Don; Livescu, Daniel

2017-11-01

We present a novel reaction analogy (RA) based forcing method for generating stationary passive scalar fields in incompressible turbulence. The new method can produce more general scalar PDFs (e.g. double-delta) than current methods, while ensuring that scalar fields remain bounded, unlike existent forcing methodologies that can potentially violate naturally existing bounds. Such features are useful for generating initial fields in non-premixed combustion or for studying non-Gaussian scalar turbulence. The RA method mathematically models hypothetical chemical reactions that convert reactants in a mixed state back into its pure unmixed components. Various types of chemical reactions are formulated and the corresponding mathematical expressions derived. For large values of the scalar dissipation rate, the method produces statistically steady double-delta scalar PDFs. Gaussian scalar statistics are recovered for small values of the scalar dissipation rate. In contrast, classical forcing methods consistently produce unimodal Gaussian scalar fields. The ability of the new method to produce fully developed scalar fields is discussed using 2563, 5123, and 10243 periodic box simulations.

Simulated altitude exposure assessment by hyperspectral imaging.

PubMed

Calin, Mihaela Antonina; Macovei, Adrian; Miclos, Sorin; Parasca, Sorin Viorel; Savastru, Roxana; Hristea, Razvan

2017-05-01

Testing the human body’s reaction to hypoxia (including the one generated by high altitude) is important in aeronautic medicine. This paper presents a method of monitoring blood oxygenation during experimental hypoxia using hyperspectral imaging (HSI) and a spectral unmixing model based on a modified Beer–Lambert law. A total of 20 healthy volunteers (males) aged 25 to 60 years were included in this study. A line-scan HSI system was used to acquire images of the faces of the subjects. The method generated oxyhemoglobin and deoxyhemoglobin distribution maps from the foreheads of the subjects at 5 and 10 min of hypoxia and after recovery in a high oxygen breathing mixture. The method also generated oxygen saturation maps that were validated using pulse oximetry. An interesting pattern of desaturation on the forehead was discovered during the study, showing one of the advantages of using HSI for skin oxygenation monitoring in hypoxic conditions. This could bring new insight into the physiological response to high altitude and may become a step forward in air crew testing.

Study on the Spectral Mixing Model for Mineral Pigments Based on Derivative of Ratio Spectroscopy-Take Vermilion and Stone Yellow for Example

NASA Astrophysics Data System (ADS)

Zhao, H.; Hao, Y.; Liu, X.; Hou, M.; Zhao, X.

2018-04-01

Hyperspectral remote sensing is a completely non-invasive technology for measurement of cultural relics, and has been successfully applied in identification and analysis of pigments of Chinese historical paintings. Although the phenomenon of mixing pigments is very usual in Chinese historical paintings, the quantitative analysis of the mixing pigments in the ancient paintings is still unsolved. In this research, we took two typical mineral pigments, vermilion and stone yellow as example, made precisely mixed samples using these two kinds of pigments, and measured their spectra in the laboratory. For the mixing spectra, both fully constrained least square (FCLS) method and derivative of ratio spectroscopy (DRS) were performed. Experimental results showed that the mixing spectra of vermilion and stone yellow had strong nonlinear mixing characteristics, but at some bands linear unmixing could also achieve satisfactory results. DRS using strong linear bands can reach much higher accuracy than that of FCLS using full bands.

Parametric Study of a Mixer/Ejector Nozzle with Mixing Enhancement Devices

NASA Technical Reports Server (NTRS)

DalBello, T.; Steffen, C. J., Jr.

2001-01-01

A numerical study employing a simplified model of the High Speed Civil Transport mixer/ejector nozzle has been conducted to investigate the effect of tabs (vortex generators) on the mixing process. More complete mixing of the primary and secondary flows within the confined ejector lowers peak exit velocity resulting in reduced jet noise. Tabs were modeled as vortex pairs and inserted into the computational model. The location, size, and number of tabs were varied and its effect on the mixing process is presented here both quantitatively and qualitatively. A baseline case (no tabs) along with six other cases involving two different vortex strengths at three different orientations have been computed and analyzed. The case with the highest vorticity (six vortices representing large tabs) gives the best mixing. It is shown that the influence of the vorticity acts primarily in the forward or middle portions of the duct, significantly alters the flow structure, and promotes some mixing in the lateral direction. Unmixed pockets were found at the top and bottom of the lobe, and more clever placement of tabs improved mixing in the vertical direction. The technique of replacing tabs with vortices shows promise as an efficient tool for quickly optimizing tab placement in lobed mixers.

Identification and quantification of the hydrological impacts of imperviousness in urban catchments: a review.

PubMed

Jacobson, Carol R

2011-06-01

Urbanisation produces numerous changes in the natural environments it replaces. The impacts include habitat fragmentation and changes to both the quality and quantity of the stormwater runoff, and result in changes to hydrological systems. This review integrates research in relatively diverse areas to examine how the impacts of urban imperviousness on hydrological systems can be quantified and modelled. It examines the nature of reported impacts of urbanisation on hydrological systems over four decades, including the effects of changes in imperviousness within catchments, and some inconsistencies in studies of the impacts of urbanisation. The distribution of imperviousness within urban areas is important in understanding the impacts of urbanisation and quantification requires detailed characterisation of urban areas. As a result most mapping of urban areas uses remote sensing techniques and this review examines a range of techniques using medium and high resolution imagery, including spectral unmixing. The third section examines the ways in which scientists and hydrological and environmental engineers model and quantify water flows in urban areas, the nature of hydrological models and methods for their calibration. The final section examines additional factors which influence the impact of impervious surfaces and some uncertainties that exist in current knowledge. Copyright © 2011 Elsevier Ltd. All rights reserved.

Estimation of Subpixel Snow-Covered Area by Nonparametric Regression Splines

NASA Astrophysics Data System (ADS)

Kuter, S.; Akyürek, Z.; Weber, G.-W.

2016-10-01

Measurement of the areal extent of snow cover with high accuracy plays an important role in hydrological and climate modeling. Remotely-sensed data acquired by earth-observing satellites offer great advantages for timely monitoring of snow cover. However, the main obstacle is the tradeoff between temporal and spatial resolution of satellite imageries. Soft or subpixel classification of low or moderate resolution satellite images is a preferred technique to overcome this problem. The most frequently employed snow cover fraction methods applied on Moderate Resolution Imaging Spectroradiometer (MODIS) data have evolved from spectral unmixing and empirical Normalized Difference Snow Index (NDSI) methods to latest machine learning-based artificial neural networks (ANNs). This study demonstrates the implementation of subpixel snow-covered area estimation based on the state-of-the-art nonparametric spline regression method, namely, Multivariate Adaptive Regression Splines (MARS). MARS models were trained by using MODIS top of atmospheric reflectance values of bands 1-7 as predictor variables. Reference percentage snow cover maps were generated from higher spatial resolution Landsat ETM+ binary snow cover maps. A multilayer feed-forward ANN with one hidden layer trained with backpropagation was also employed to estimate the percentage snow-covered area on the same data set. The results indicated that the developed MARS model performed better than th

Near-infrared fluorescent proteins for multicolor in vivo imaging

PubMed Central

Shcherbakova, Daria M.; Verkhusha, Vladislav V.

2013-01-01

Near-infrared fluorescent proteins are in high demand for in vivo imaging. We developed four spectrally distinct fluorescent proteins, iRFP670, iRFP682, iRFP702, and iRFP720, from bacterial phytochromes. iRFPs exhibit high brightness in mammalian cells and tissues and are suitable for long-term studies. iRFP670 and iRFP720 enable two-color imaging in living cells and mice using standard approaches. Five iRFPs including previously engineered iRFP713 allow multicolor imaging in living mice with spectral unmixing. PMID:23770755

Developing a Control Strategy for Jets in Crossflow Using Direct Numerical Simulation

DTIC Science & Technology

2010-03-29

the total volume of scalar–containing fluid ( Vsc ) for stroke ratios equal to 2 and 6. Vsc is computed as the sum of all volume elements which have...concentration allows the difference between the scalar containing fluid and unmixed ambient fluid to be represented. Vsc can be considered as a measure of the...spread of the scalar in the flow–field. Figure 2.10(a) shows that Vsc increases nearly linearly (at a rate of 1.7) until t∗ ∼ 2. In general, Vsc

Automatic building detection based on Purposive FastICA (PFICA) algorithm using monocular high resolution Google Earth images

NASA Astrophysics Data System (ADS)

Ghaffarian, Saman; Ghaffarian, Salar

2014-11-01

This paper proposes an improved FastICA model named as Purposive FastICA (PFICA) with initializing by a simple color space transformation and a novel masking approach to automatically detect buildings from high resolution Google Earth imagery. ICA and FastICA algorithms are defined as Blind Source Separation (BSS) techniques for unmixing source signals using the reference data sets. In order to overcome the limitations of the ICA and FastICA algorithms and make them purposeful, we developed a novel method involving three main steps: 1-Improving the FastICA algorithm using Moore-Penrose pseudo inverse matrix model, 2-Automated seeding of the PFICA algorithm based on LUV color space and proposed simple rules to split image into three regions; shadow + vegetation, baresoil + roads and buildings, respectively, 3-Masking out the final building detection results from PFICA outputs utilizing the K-means clustering algorithm with two number of clusters and conducting simple morphological operations to remove noises. Evaluation of the results illustrates that buildings detected from dense and suburban districts with divers characteristics and color combinations using our proposed method have 88.6% and 85.5% overall pixel-based and object-based precision performances, respectively.

More on the Possible Composition of the Meridiani Hematite-Rich Concretions

NASA Technical Reports Server (NTRS)

Jolliff, B. L.; Gellert, R.; Mittlefehldt, D. W.

2007-01-01

Elsewhere in these proceedings, Schneider et al. discuss compositional constraints on hematite-rich spherule (blueberry) formation at Meridiani Planum. Schneider et al. provide the background for work done to date to understand the composition and mineralogy of the spherules and devise a test of possible concretion growth processes. They also report the results of area analyses of spherules in targets analyzed with the Alpha Particle X-ray Spectrometer (APXS) and test several possible models for included components other than hematite. In this abstract, we use the compositional trends for spherule-rich targets to compute possible elemental compositions of the spherules. This approach differs from that of, which also used a determination of the area of spherules in APXS targets, coupled with a correction for the radial acceptance function, to try to un-mix the compositions directly, using 2 and 3-component models and mass balance. That approach contained a fair amount of uncertainty owing to problems associated with irregular and heterogeneous target geometry, unknown composition of non-spherule lithic components, and variable dust coatings on spherules. Since then, Opportunity has analyzed additional spherule-rich targets, and the compositional trends so obtained permit a more direct assessment of the data.

The effects of AVIRIS atmospheric calibration methodology on identification and quantitative mapping of surface mineralogy, Drum Mountains, Utah

NASA Technical Reports Server (NTRS)

Kruse, Fred A.; Dwyer, John L.

1993-01-01

The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) measures reflected light in 224 contiguous spectra bands in the 0.4 to 2.45 micron region of the electromagnetic spectrum. Numerous studies have used these data for mineralogic identification and mapping based on the presence of diagnostic spectral features. Quantitative mapping requires conversion of the AVIRIS data to physical units (usually reflectance) so that analysis results can be compared and validated with field and laboratory measurements. This study evaluated two different AVIRIS calibration techniques to ground reflectance: an empirically-based method and an atmospheric model based method to determine their effects on quantitative scientific analyses. Expert system analysis and linear spectral unmixing were applied to both calibrated data sets to determine the effect of the calibration on the mineral identification and quantitative mapping results. Comparison of the image-map results and image reflectance spectra indicate that the model-based calibrated data can be used with automated mapping techniques to produce accurate maps showing the spatial distribution and abundance of surface mineralogy. This has positive implications for future operational mapping using AVIRIS or similar imaging spectrometer data sets without requiring a priori knowledge.

Integrating isotopic tracer techniques with Bayesian modelling for improved assessment and management of sedimentation problems in the Gilgel-Gibe catchment, Ethiopia

NASA Astrophysics Data System (ADS)

Dume, Bayu; Amsalu, Nebiyu; Bode, Samuel; Mtei, Kelvin; Munishi, Linus; Navas, Ana; Semmens, Brice; Smith, Hugh; Stock, Brian; Blake, Will; Boeckx, Pascal

2017-04-01

Soil erosion and associated downstream siltation of dams and lakes is becoming serious threat to catchment ecosystem services supporting water, food and energy security in Ethiopia. Sediments originate on catchment hillslopes but mobilisation processes vary depending on land use and terrain. The Gilgel Gibe hydroelectric dam is one of a series of development projects launched by the Federal Government of Ethiopia. The catchment is characterised by erodible, deforested agricultural land which is also overgrazed. Siltation and nutrient enrichment are significant issues given 'hotspot' sheet erosion estimates of 2210 ton per square km. The annual contribution of sediment from the Gilgel Gibe River to the dam was estimated at 277 thousand tons per year leading to accumulations of 3.75 x 107 cubic metres per year of silt behind the dam. The primary driver for mobilisation and translocation to downstream is believed to be erosion on agricultural lands and collapse of steep banks, through landsliding into river channels in the highland headwaters. The relative importance of specific sources of siltation are unknown and sediment source apportionment has been identified as a first essential step before soil conservation measures can be implemented. Knowledge of sediment source and transfer dynamics is critical to inform management policy decisions to maintain and enhance future food, water and energy security To test the applicability of a new combination of Bayesian unmixing modelling with sediment fingerprinting in this terrain (IMIXSED approach) a demonstration sub-catchment was selected through field assessment in the upper Gilgel-Gibe water-supply catchments (Unta River) and sampling strategies designed. Accordingly, sources, i.e. soil samples from landslides (n=40), eroding channel bank (n = 5), cultivated land (n = 30), grasslands (n = 30), wooded areas (n = 10), homestead plots (n = 10) were collected alongside 10 spatially-integrated sediment deposits from the receptor cobble bed river after the 2016 rainy season. In order to extract reliable information on the sources of fine sediment delivered into rivers and dam, new isotopic techniques (e.g., Compound Specific Stable Isotopes (CSSIs)) combined with other isotopic techniques (fallout radionuclides) and geochemical tracer properties (via WD-XRF) were employed to quantify sediment sources. Results from this demonstration catchment are discussed in the context of the wider sediment pressures on the Hydro-Electric Power infrastructure of the Gilgel Gibe system.

Automatic sub-pixel coastline extraction based on spectral mixture analysis using EO-1 Hyperion data

NASA Astrophysics Data System (ADS)

Hong, Zhonghua; Li, Xuesu; Han, Yanling; Zhang, Yun; Wang, Jing; Zhou, Ruyan; Hu, Kening

2018-06-01

Many megacities (such as Shanghai) are located in coastal areas, therefore, coastline monitoring is critical for urban security and urban development sustainability. A shoreline is defined as the intersection between coastal land and a water surface and features seawater edge movements as tides rise and fall. Remote sensing techniques have increasingly been used for coastline extraction; however, traditional hard classification methods are performed only at the pixel-level and extracting subpixel accuracy using soft classification methods is both challenging and time consuming due to the complex features in coastal regions. This paper presents an automatic sub-pixel coastline extraction method (ASPCE) from high-spectral satellite imaging that performs coastline extraction based on spectral mixture analysis and, thus, achieves higher accuracy. The ASPCE method consists of three main components: 1) A Water- Vegetation-Impervious-Soil (W-V-I-S) model is first presented to detect mixed W-V-I-S pixels and determine the endmember spectra in coastal regions; 2) The linear spectral mixture unmixing technique based on Fully Constrained Least Squares (FCLS) is applied to the mixed W-V-I-S pixels to estimate seawater abundance; and 3) The spatial attraction model is used to extract the coastline. We tested this new method using EO-1 images from three coastal regions in China: the South China Sea, the East China Sea, and the Bohai Sea. The results showed that the method is accurate and robust. Root mean square error (RMSE) was utilized to evaluate the accuracy by calculating the distance differences between the extracted coastline and the digitized coastline. The classifier's performance was compared with that of the Multiple Endmember Spectral Mixture Analysis (MESMA), Mixture Tuned Matched Filtering (MTMF), Sequential Maximum Angle Convex Cone (SMACC), Constrained Energy Minimization (CEM), and one classical Normalized Difference Water Index (NDWI). The results from the three test sites indicated that the proposed ASPCE method extracted coastlines more efficiently than did the compared methods, and its coastline extraction accuracy corresponded closely to the digitized coastline, with 0.39 pixels, 0.40 pixels, and 0.35 pixels in the three test regions, showing that the ASPCE method achieves an accuracy below 12.0 m (0.40 pixels). Moreover, in the quantitative accuracy assessment for the three test sites, the ASPCE method shows the best performance in coastline extraction, achieving a 0.35 pixel-level at the Bohai Sea, China test site. Therefore, the proposed ASPCE method can extract coastline more accurately than can the hard classification methods or other spectral unmixing methods.

Molecular modeling study of the differential ligand-receptor interaction at the μ, δ and κ opioid receptors

NASA Astrophysics Data System (ADS)

Filizola, Marta; Carteni-Farina, Maria; Perez, Juan J.

1999-07-01

3D models of the opioid receptors μ, δ and κ were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.

Binding modes of dihydroquinoxalinones in a homology model of bradykinin receptor 1.

PubMed

Ha, Sookhee N; Hey, Pat J; Ransom, Rick W; Harrell, C Meacham; Murphy, Kathryn L; Chang, Ray; Chen, Tsing-Bau; Su, Dai-Shi; Markowitz, M Kristine; Bock, Mark G; Freidinger, Roger M; Hess, Fred J

2005-05-27

We report the first homology model of human bradykinin receptor B1 generated from the crystal structure of bovine rhodopsin as a template. Using an automated docking procedure, two B1 receptor antagonists of the dihydroquinoxalinone structural class were docked into the receptor model. Site-directed mutagenesis data of the amino acid residues in TM1, TM3, TM6, and TM7 were incorporated to place the compounds in the binding site of the homology model of the human B1 bradykinin receptor. The best pose in agreement with the mutation data was selected for detailed study of the receptor-antagonist interaction. To test the model, the calculated antagonist-receptor binding energy was correlated with the experimentally measured binding affinity (K(i)) for nine dihydroquinoxalinone analogs. The model was used to gain insight into the molecular mechanism for receptor function and to optimize the dihydroquinoxalinone analogs.

Spectral identification of minerals using imaging spectrometry data: Evaluating the effects of signal to noise and spectral resolution using the tricorder algorithm

NASA Technical Reports Server (NTRS)

Swayze, Gregg A.; Clark, Roger N.

1995-01-01

The rapid development of sophisticated imaging spectrometers and resulting flood of imaging spectrometry data has prompted a rapid parallel development of spectral-information extraction technology. Even though these extraction techniques have evolved along different lines (band-shape fitting, endmember unmixing, near-infrared analysis, neural-network fitting, and expert systems to name a few), all are limited by the spectrometer's signal to noise (S/N) and spectral resolution in producing useful information. This study grew from a need to quantitatively determine what effects these parameters have on our ability to differentiate between mineral absorption features using a band-shape fitting algorithm. We chose to evaluate the AVIRIS, HYDICE, MIVIS, GERIS, VIMS, NIMS, and ASTER instruments because they collect data over wide S/N and spectral-resolution ranges. The study evaluates the performance of the Tricorder algorithm, in differentiating between mineral spectra in the 0.4-2.5 micrometer spectral region. The strength of the Tricorder algorithm is in its ability to produce an easily understood comparison of band shape that can concentrate on small relevant portions of the spectra, giving it an advantage over most unmixing schemes, and in that it need not spend large amounts of time reoptimizing each time a new mineral component is added to its reference library, as is the case with neural-network schemes. We believe the flexibility of the Tricorder algorithm is unparalleled among spectral-extraction techniques and that the results from this study, although dealing with minerals, will have direct applications to spectral identification in other disciplines.

Vizualization Challenges of a Subduction Simulation Using One Billion Markers

NASA Astrophysics Data System (ADS)

Rudolph, M. L.; Gerya, T. V.; Yuen, D. A.

2004-12-01

Recent advances in supercomputing technology have permitted us to study the multiscale, multicomponent fluid dynamics of subduction zones at unprecedented resolutions down to about the length of a football field. We have performed numerical simulations using one billion tracers over a grid of about 80 thousand points in two dimensions. These runs have been performed using a thermal-chemical simulation that accounts for hydration and partial melting in the thermal, mechanical, petrological, and rheological domains. From these runs, we have observed several geophysically interesting phenomena including the development of plumes with unmixed mantle composition as well as plumes with mixed mantle/crust components. Unmixed plumes form at depths greater than 100km (5-10 km above the upper interface of subducting slab) and consist of partially molten wet peridotite. Mixed plumes form at lesser depth directly from the subducting slab and contain partially molten hydrated oceanic crust and sediments. These high resolution simulations have also spurred the development of new visualization methods. We have created a new web-based interface to data from our subduction simulation and other high-resolution 2D data that uses an hierarchical data format to achieve response times of less than one second when accessing data files on the order of 3GB. This interface, WEB-IS4, uses a Javascript and HTML frontend coupled with a C and PHP backend and allows the user to perform region of interest zooming, real-time colormap selection, and can return relevant statistics relating to the data in the region of interest.

GEMAS: Unmixing magnetic properties of European agricultural soil

NASA Astrophysics Data System (ADS)

Fabian, Karl; Reimann, Clemens; Kuzina, Dilyara; Kosareva, Lina; Fattakhova, Leysan; Nurgaliev, Danis

2016-04-01

High resolution magnetic measurements provide new methods for world-wide characterization and monitoring of agricultural soil which is essential for quantifying geologic and human impact on the critical zone environment and consequences of climatic change, for planning economic and ecological land use, and for forensic applications. Hysteresis measurements of all Ap samples from the GEMAS survey yield a comprehensive overview of mineral magnetic properties in European agricultural soil on a continental scale. Low (460 Hz), and high frequency (4600 Hz) magnetic susceptibility k were measured using a Bartington MS2B sensor. Hysteresis properties were determined by a J-coercivity spectrometer, built at the paleomagnetic laboratory of Kazan University, providing for each sample a modified hysteresis loop, backfield curve, acquisition curve of isothermal remanent magnetization, and a viscous IRM decay spectrum. Each measurement set is obtained in a single run from zero field up to 1.5 T and back to -1.5 T. The resulting data are used to create the first continental-scale maps of magnetic soil parameters. Because the GEMAS geochemical atlas contains a comprehensive set of geochemical data for the same soil samples, the new data can be used to map magnetic parameters in relation to chemical and geological parameters. The data set also provides a unique opportunity to analyze the magnetic mineral fraction of the soil samples by unmixing their IRM acquisition curves. The endmember coefficients are interpreted by linear inversion for other magnetic, physical and chemical properties which results in an unprecedented and detailed view of the mineral magnetic composition of European agricultural soils.

The effect of food bolus location on jaw movement smoothness and masticatory efficiency.

PubMed

Molenaar, W N B; Gezelle Meerburg, P J; Luraschi, J; Whittle, T; Schimmel, M; Lobbezoo, F; Peck, C C; Murray, G M; Minami, I

2012-09-01

Masticatory efficiency in individuals with extensive tooth loss has been widely discussed. However, little is known about jaw movement smoothness during chewing and the effect of differences in food bolus location on movement smoothness and masticatory efficiency. The aim of this study was to determine whether experimental differences in food bolus location (anterior versus posterior) had an effect on masticatory efficiency and jaw movement smoothness. Jaw movement smoothness was evaluated by measuring jerk-cost (calculated from acceleration) with an accelerometer that was attached to the skin of the mentum of 10 asymptomatic subjects, and acceleration was recorded during chewing on two-colour chewing gum, which was used to assessed masticatory efficiency. Chewing was performed under two conditions: posterior chewing (chewing on molars and premolars only) and anterior chewing (chewing on canine and first premolar teeth only). Jerk-cost and masticatory efficiency (calculated as the ratio of unmixed azure colour to the total area of gum, the unmixed fraction) were compared between anterior and posterior chewing with the Wilcoxon signed rank test (two-tailed). Subjects chewed significantly less efficiently during anterior chewing than during posterior chewing (P = 0·0051). There was no significant difference in jerk-cost between anterior and posterior conditions in the opening phase (P = 0·25), or closing phase (P = 0·42). This is the first characterisation of the effect of food bolus location on jaw movement smoothness at the same time as recording masticatory efficiency. The data suggest that anterior chewing decreases masticatory efficiency, but does not influence jerk-cost. © 2012 Blackwell Publishing Ltd.

Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers.

PubMed

Lichten, Catherine A; White, Rachel; Clark, Ivan B N; Swain, Peter S

2014-02-03

To connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require specialist expertise if single cells are to be followed. Fluorescence plate readers, however, a standard in many laboratories, can in principle provide similar data, albeit at a mean, population level. Nevertheless, extracting the average fluorescence per cell is challenging because autofluorescence can be substantial. Here we propose a general method for correcting plate reader measurements of fluorescent proteins that uses spectral unmixing and determines both the fluorescence per cell and the errors on that fluorescence. Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription. We illustrate the method by following the induction of the GAL genes in Saccharomyces cerevisiae for over 20 hours in different sugars and argue that the order of appearance of the Leloir enzymes may be to reduce build-up of the toxic intermediate galactose-1-phosphate. Further, we quantify protein levels of over 40 genes, again over 20 hours, after cells experience a change in carbon source (from glycerol to glucose). Our methodology is sensitive, scalable, and should be applicable to other organisms. By allowing quantitative measurements on a per cell basis over tens of hours and over hundreds of genes, it should increase our understanding of the dynamic changes that drive cellular behaviour.

Introducing causality violation for improved DPOAE component unmixing

NASA Astrophysics Data System (ADS)

Moleti, Arturo; Sisto, Renata; Shera, Christopher A.

2018-05-01

The DPOAE response consists of the linear superposition of two components, a nonlinear distortion component generated in the overlap region, and a reflection component generated by roughness in the DP resonant region. Due to approximate scaling symmetry, the DPOAE distortion component has approximately constant phase. As the reflection component may be considered as a SFOAE generated by the forward DP traveling wave, it has rapidly rotating phase, relative to that of its source, which is also equal to the phase of the DPOAE distortion component. This different phase behavior permits effective separation of the DPOAE components (unmixing), using time-domain or time-frequency domain filtering. Departures from scaling symmetry imply fluctuations around zero delay of the distortion component, which may seriously jeopardize the accuracy of these filtering techniques. The differential phase-gradient delay of the reflection component obeys causality requirements, i.e., the delay is positive only, and the fine-structure oscillations of amplitude and phase are correlated to each other, as happens for TEOAEs and SFOAEs relative to their stimulus phase. Performing the inverse Fourier (or wavelet) transform of a modified DPOAE complex spectrum, in which a constant phase function is substituted for the measured one, the time (or time-frequency) distribution shows a peak at (exactly) zero delay and long-latency specular symmetric components, with a modified (positive and negative) delay, which is that relative to that of the distortion component in the original response. Component separation, applied to this symmetrized distribution, becomes insensitive to systematic errors associated with violation of the scaling symmetry in specific frequency ranges.

Applicability of the "Emotiv EEG Neuroheadset" as a user-friendly input interface.

PubMed

Boutani, Hidenori; Ohsuga, Mieko

2013-01-01

We aimed to develop an input interface by using the P3 component of visual event-related potentials (ERPs). When using electroencephalography (EEG) in daily applications, coping with ocular-motor artifacts and ensuring that the equipment is user-friendly are both important. To address the first issue, we applied a previously proposed method that applies an unmixing matrix to acquire independent components (ICs) obtained from another dataset. For the second issue, we introduced a 14-channel EEG commercial headset called the "Emotiv EEG Neuroheadset". An advantage of the Emotiv headset is that users can put it on by themselves within 1 min without any specific skills. However, only a few studies have investigated whether EEG and ERP signals are accurately measured by Emotiv. Additionally, no electrodes of the Emotiv headset are located over the centroparietal area of the head where P3 components are reported to show large amplitudes. Therefore, we first demonstrated that the P3 components obtained by the headset and by commercial plate electrodes and a multipurpose bioelectric amplifier during an oddball task were comparable. Next, we confirmed that eye-blink and ocular movement components could be decomposed by independent component analysis (ICA) using the 14-channel signals measured by the headset. We also demonstrated that artifacts could be removed with an unmixing matrix, as long as the matrix was obtained from the same person, even if they were measured on different days. Finally, we confirmed that the fluctuation of the sampling frequency of the Emotiv headset was not a major problem.

A review of the contrasting behavior of two magmatic volatiles: Chlorine and carbon dioxide

USGS Publications Warehouse

Lowenstern, J. B.

2000-01-01

Chlorine (Cl) and carbon dioxide (CO2) are common magmatic volatiles with contrasting behaviors. CO2 solubility increases with pressure whereas Cl solubility shows relatively little pressure or temperature effect. CO2 speciation changes with silicate melt composition, dissolving as carbonate in basaltic magmas and molecular CO2 in more silicic compositions. In H2O-bearing systems, the strongly non-ideal behavior of alkali chlorides causes unmixing of the volatile phase to form a H2O-rich vapor and a hydrosaline phase with important implications for the maximum concentration of Cl in magmas. Addition of CO2 to magma hastens immiscibility at crustal pressures (<500 MPa), inducing the formation of CO2-rich vapors and Cl-rich hydrosaline melts. (C) 2000 Elsevier Science B.V. All rights reserved.Chlorine (Cl) and carbon dioxide (CO2) are common magmatic volatiles with contrasting behaviors. CO2 solubility increases with pressure whereas Cl solubility shows relatively little pressure or temperature effect. CO2 speciation changes with silicate melt composition, dissolving as carbonate in basaltic magmas and molecular CO2 in more silicic compositions. In H2O-bearing systems, the strongly non-ideal behavior of alkali chlorides causes unmixing of the volatile phase to form a H2O-rich vapor and a hydrosaline phase with important implications for the maximum concentration of Cl in magmas. Addition of CO2 to magma hastens immiscibility at crustal pressures (<500 MPa), inducing the formation of CO2-rich vapors and Cl-rich hydrosaline melts.

Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers

PubMed Central

2014-01-01

Background To connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require specialist expertise if single cells are to be followed. Fluorescence plate readers, however, a standard in many laboratories, can in principle provide similar data, albeit at a mean, population level. Nevertheless, extracting the average fluorescence per cell is challenging because autofluorescence can be substantial. Results Here we propose a general method for correcting plate reader measurements of fluorescent proteins that uses spectral unmixing and determines both the fluorescence per cell and the errors on that fluorescence. Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription. We illustrate the method by following the induction of the GAL genes in Saccharomyces cerevisiae for over 20 hours in different sugars and argue that the order of appearance of the Leloir enzymes may be to reduce build-up of the toxic intermediate galactose-1-phosphate. Further, we quantify protein levels of over 40 genes, again over 20 hours, after cells experience a change in carbon source (from glycerol to glucose). Conclusions Our methodology is sensitive, scalable, and should be applicable to other organisms. By allowing quantitative measurements on a per cell basis over tens of hours and over hundreds of genes, it should increase our understanding of the dynamic changes that drive cellular behaviour. PMID:24495318

Parallel-multiplexed excitation light-sheet microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Dongli; Zhou, Weibin; Peng, Leilei

2017-02-01

Laser scanning light-sheet imaging allows fast 3D image of live samples with minimal bleach and photo-toxicity. Existing light-sheet techniques have very limited capability in multi-label imaging. Hyper-spectral imaging is needed to unmix commonly used fluorescent proteins with large spectral overlaps. However, the challenge is how to perform hyper-spectral imaging without sacrificing the image speed, so that dynamic and complex events can be captured live. We report wavelength-encoded structured illumination light sheet imaging (λ-SIM light-sheet), a novel light-sheet technique that is capable of parallel multiplexing in multiple excitation-emission spectral channels. λ-SIM light-sheet captures images of all possible excitation-emission channels in true parallel. It does not require compromising the imaging speed and is capable of distinguish labels by both excitation and emission spectral properties, which facilitates unmixing fluorescent labels with overlapping spectral peaks and will allow more labels being used together. We build a hyper-spectral light-sheet microscope that combined λ-SIM with an extended field of view through Bessel beam illumination. The system has a 250-micron-wide field of view and confocal level resolution. The microscope, equipped with multiple laser lines and an unlimited number of spectral channels, can potentially image up to 6 commonly used fluorescent proteins from blue to red. Results from in vivo imaging of live zebrafish embryos expressing various genetic markers and sensors will be shown. Hyper-spectral images from λ-SIM light-sheet will allow multiplexed and dynamic functional imaging in live tissue and animals.

Grain size dependent magnetic discrimination of Iceland and South Greenland terrestrial sediments in the northern North Atlantic sediment record

NASA Astrophysics Data System (ADS)

Hatfield, Robert G.; Stoner, Joseph S.; Reilly, Brendan T.; Tepley, Frank J.; Wheeler, Benjamin H.; Housen, Bernard A.

2017-09-01

We use isothermal and temperature dependent in-field and magnetic remanence methods together with electron microscopy to characterize different sieved size fractions from terrestrial sediments collected in Iceland and southern Greenland. The magnetic fraction of Greenland silts (3-63 μm) and sands (>63 μm) is primarily composed of near-stoichiometric magnetite that may be oxidized in the finer clay (<3 μm) fractions. In contrast, all Icelandic fractions dominantly contain titanomagnetite of a range of compositions. Ferrimagnetic minerals preferentially reside in the silt-size fraction and exist as fine single-domain (SD) and pseudo-single-domain (PSD) size inclusions in Iceland samples, in contrast to coarser PSD and multi-domain (MD) discrete magnetites from southern Greenland. We demonstrate the potential of using magnetic properties of the silt fraction for source unmixing by creating known endmember mixtures and by using naturally mixed marine sediments from the Eirik Ridge south of Greenland. We develop a novel approach to ferrimagnetic source unmixing by using low temperature magnetic susceptibility curves that are sensitive to the different crystallinity and cation substitution characteristics of the different source regions. Covariation of these properties with hysteresis parameters suggests sediment source changes have driven the magnetic mineral variations observed in Eirik Ridge sediments since the last glacial maximum. These observations assist the development of a routine method and interpretative framework to quantitatively determine provenance in a geologically realistic and meaningful way and assess how different processes combine to drive magnetic variation in the North Atlantic sediment record.

Cubesat-Derived Detection of Seagrasses Using Planet Imagery Following Unmixing-Based Denoising: is Small the Next Big?

NASA Astrophysics Data System (ADS)

Traganos, D.; Cerra, D.; Reinartz, P.

2017-05-01

Seagrasses are one of the most productive and widespread yet threatened coastal ecosystems on Earth. Despite their importance, they are declining due to various threats, which are mainly anthropogenic. Lack of data on their distribution hinders any effort to rectify this decline through effective detection, mapping and monitoring. Remote sensing can mitigate this data gap by allowing retrospective quantitative assessment of seagrass beds over large and remote areas. In this paper, we evaluate the quantitative application of Planet high resolution imagery for the detection of seagrasses in the Thermaikos Gulf, NW Aegean Sea, Greece. The low Signal-to-noise Ratio (SNR), which characterizes spectral bands at shorter wavelengths, prompts the application of the Unmixing-based denoising (UBD) as a pre-processing step for seagrass detection. A total of 15 spectral-temporal patterns is extracted from a Planet image time series to restore the corrupted blue and green band in the processed Planet image. Subsequently, we implement Lyzenga's empirical water column correction and Support Vector Machines (SVM) to evaluate quantitative benefits of denoising. Denoising aids detection of Posidonia oceanica seagrass species by increasing its producer and user accuracy by 31.7 % and 10.4 %, correspondingly, with a respective increase in its Kappa value from 0.3 to 0.48. In the near future, our objective is to improve accuracies in seagrass detection by applying more sophisticated, analytical water column correction algorithms to Planet imagery, developing time- and cost-effective monitoring of seagrass distribution that will enable in turn the effective management and conservation of these highly valuable and productive ecosystems.

A FPGA implementation for linearly unmixing a hyperspectral image using OpenCL

NASA Astrophysics Data System (ADS)

Guerra, Raúl; López, Sebastián.; Sarmiento, Roberto

2017-10-01

Hyperspectral imaging systems provide images in which single pixels have information from across the electromagnetic spectrum of the scene under analysis. These systems divide the spectrum into many contiguos channels, which may be even out of the visible part of the spectra. The main advantage of the hyperspectral imaging technology is that certain objects leave unique fingerprints in the electromagnetic spectrum, known as spectral signatures, which allow to distinguish between different materials that may look like the same in a traditional RGB image. Accordingly, the most important hyperspectral imaging applications are related with distinguishing or identifying materials in a particular scene. In hyperspectral imaging applications under real-time constraints, the huge amount of information provided by the hyperspectral sensors has to be rapidly processed and analysed. For such purpose, parallel hardware devices, such as Field Programmable Gate Arrays (FPGAs) are typically used. However, developing hardware applications typically requires expertise in the specific targeted device, as well as in the tools and methodologies which can be used to perform the implementation of the desired algorithms in the specific device. In this scenario, the Open Computing Language (OpenCL) emerges as a very interesting solution in which a single high-level synthesis design language can be used to efficiently develop applications in multiple and different hardware devices. In this work, the Fast Algorithm for Linearly Unmixing Hyperspectral Images (FUN) has been implemented into a Bitware Stratix V Altera FPGA using OpenCL. The obtained results demonstrate the suitability of OpenCL as a viable design methodology for quickly creating efficient FPGAs designs for real-time hyperspectral imaging applications.

Dimer-based model for heptaspanning membrane receptors.

PubMed

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferré, Sergi; Fuxe, Kjell; Cortés, Antonio; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2005-07-01

The existence of intramembrane receptor-receptor interactions for heptaspanning membrane receptors is now fully accepted, but a model considering dimers as the basic unit that binds to two ligand molecules is lacking. Here, we propose a two-state-dimer model in which the ligand-induced conformational changes from one component of the dimer are communicated to the other. Our model predicts cooperativity in binding, which is relevant because the other current models fail to address this phenomenon satisfactorily. Our two-state-dimer model also predicts the variety of responses elicited by full or partial agonists, neutral antagonists and inverse agonists. This model can aid our understanding of the operation of heptaspanning receptors and receptor channels, and, potentially, be important for improving the treatment of cardiovascular, neurological and neuropsychyatric diseases.

Homology Models of Melatonin Receptors: Challenges and Recent Advances

PubMed Central

Pala, Daniele; Lodola, Alessio; Bedini, Annalida; Spadoni, Gilberto; Rivara, Silvia

2013-01-01

Melatonin exerts many of its actions through the activation of two G protein-coupled receptors (GPCRs), named MT1 and MT2. So far, a number of different MT1 and MT2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. These receptor models differ in the binding modes hypothesized for melatonin and melatonergic ligands, with distinct patterns of ligand-receptor interactions and putative bioactive conformations of ligands. The receptor models will be described, and they will be discussed in light of the available information from mutagenesis experiments and ligand-based pharmacophore models. The ability of these ligand-receptor complexes to rationalize structure-activity relationships of known series of melatonergic compounds will be commented upon. PMID:23584026

Influence of ionotropic receptor location on their dynamics at glutamatergic synapses.

PubMed

Allam, Sushmita L; Bouteiller, Jean-Marie C; Hu, Eric; Greget, Renaud; Ambert, Nicolas; Bischoff, Serge; Baudry, Michel; Berger, Theodore W

2012-01-01

In this paper we study the effects of the location of ionotropic receptors, especially AMPA and NMDA receptors, on their function at excitatory glutamatergic synapses. As few computational models only allow to evaluate the influence of receptor location on state transition and receptor dynamics, we present an elaborate computational model of a glutamatergic synapse that takes into account detailed parametric models of ionotropic receptors along with glutamate diffusion within the synaptic cleft. Our simulation results underscore the importance of the wide spread distribution of AMPA receptors which is required to avoid massive desensitization of these receptors following a single glutamate release event while NMDA receptor location is potentially optimal relative to the glutamate release site thus, emphasizing the contribution of location dependent effects of the two major ionotropic receptors to synaptic efficacy.

Structural and Molecular Modeling Features of P2X Receptors

PubMed Central

Alves, Luiz Anastacio; da Silva, João Herminio Martins; Ferreira, Dinarte Neto Moreira; Fidalgo-Neto, Antonio Augusto; Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; Caffarena, Ernesto Raúl; de Freitas, Mônica Santos

2014-01-01

Currently, adenosine 5′-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors. PMID:24637936

Modelling the interdependence between the stoichiometry of receptor oligomerization and ligand binding for a coexisting dimer/tetramer receptor system.

PubMed

Rovira, X; Vivó, M; Serra, J; Roche, D; Strange, P G; Giraldo, J

2009-01-01

Many G protein-coupled receptors have been shown to exist as oligomers, but the oligomerization state and the effects of this on receptor function are unclear. For some G protein-coupled receptors, in ligand binding assays, different radioligands provide different maximal binding capacities. Here we have developed mathematical models for co-expressed dimeric and tetrameric species of receptors. We have considered models where the dimers and tetramers are in equilibrium and where they do not interconvert and we have also considered the potential influence of the ligands on the degree of oligomerization. By analogy with agonist efficacy, we have considered ligands that promote, inhibit or have no effect on oligomerization. Cell surface receptor expression and the intrinsic capacity of receptors to oligomerize are quantitative parameters of the equations. The models can account for differences in the maximal binding capacities of radioligands in different preparations of receptors and provide a conceptual framework for simulation and data fitting in complex oligomeric receptor situations.

Pixel decomposition for tracking in low resolution videos

NASA Astrophysics Data System (ADS)

Govinda, Vivekanand; Ralph, Jason F.; Spencer, Joseph W.; Goulermas, John Y.; Yang, Lihua; Abbas, Alaa M.

2008-04-01

This paper describes a novel set of algorithms that allows indoor activity to be monitored using data from very low resolution imagers and other non-intrusive sensors. The objects are not resolved but activity may still be determined. This allows the use of such technology in sensitive environments where privacy must be maintained. Spectral un-mixing algorithms from remote sensing were adapted for this environment. These algorithms allow the fractional contributions from different colours within each pixel to be estimated and this is used to assist in the detection and monitoring of small objects or sub-pixel motion.

For geological investigations with airborne thermal infrared multispectral images: Transfer of calibration from laboratory spectrometer to TIMS as alternative for removing atmospheric effects

NASA Technical Reports Server (NTRS)

Edgett, Kenneth S.; Anderson, Donald L.

1995-01-01

This paper describes an empirical method to correct TIMS (Thermal Infrared Multispectral Scanner) data for atmospheric effects by transferring calibration from a laboratory thermal emission spectrometer to the TIMS multispectral image. The method does so by comparing the laboratory spectra of samples gathered in the field with TIMS 6-point spectra for pixels at the location of field sampling sites. The transference of calibration also makes it possible to use spectra from the laboratory as endmembers in unmixing studies of TIMS data.

Constraints on the explosion mechanism and progenitors of Type Ia supernovae

NASA Astrophysics Data System (ADS)

Dessart, Luc; Blondin, Stéphane; Hillier, D. John; Khokhlov, Alexei

2014-06-01

Observations of SN 2011fe at early times reveal an evolution analogous to a fireball model of constant colour. In contrast, our unmixed delayed detonations of Chandrasekhar-mass white dwarfs (DDC series) exhibit a faster brightening concomitant with a shift in colour to the blue. In this paper, we study the origin of these discrepancies. We find that strong chemical mixing largely resolves the photometric mismatch at early times, but it leads to an enhanced line broadening that contrasts, for example, with the markedly narrow Si II 6355 Å line of SN 2011fe. We also explore an alternative configuration with pulsational-delayed detonations (PDDEL model series). Because of the pulsation, PDDEL models retain more unburnt carbon, have little mass at high velocity, and have a much hotter outer ejecta after the explosion. The pulsation does not influence the inner ejecta, so PDDEL and DDC models exhibit similar radiative properties beyond maximum. However, at early times, PDDEL models show bluer optical colours and a higher luminosity, even for weak mixing. Their early-time radiation is derived primarily from the initial shock-deposited energy in the outer ejecta rather than radioactive-decay heating. Furthermore, PDDEL models show short-lived C II lines, reminiscent of SN 2013dy. They typically exhibit lines that are weaker, narrower, and of near-constant width, reminiscent of SN 2011fe. In addition to multidimensional effects, varying configurations for such `pulsations' offer a source of spectral diversity amongst Type Ia supernovae (SNe Ia). PDDEL and DDC models also provide one explanation for low- and high-velocity-gradient SNe Ia.

Structure-based discovery and binding site analysis of histamine receptor ligands.

PubMed

Kiss, Róbert; Keserű, György M

2016-12-01

The application of structure-based drug discovery in histamine receptor projects was previously hampered by the lack of experimental structures. The publication of the first X-ray structure of the histamine H1 receptor has been followed by several successful virtual screens and binding site analysis studies of H1-antihistamines. This structure together with several other recently solved aminergic G-protein coupled receptors (GPCRs) enabled the development of more realistic homology models for H2, H3 and H4 receptors. Areas covered: In this paper, the authors review the development of histamine receptor models and their application in drug discovery. Expert opinion: In the authors' opinion, the application of atomistic histamine receptor models has played a significant role in understanding key ligand-receptor interactions as well as in the discovery of novel chemical starting points. The recently solved H1 receptor structure is a major milestone in structure-based drug discovery; however, our analysis also demonstrates that for building H3 and H4 receptor homology models, other GPCRs may be more suitable as templates. For these receptors, the authors envisage that the development of higher quality homology models will significantly contribute to the discovery and optimization of novel H3 and H4 ligands.

Analysis of simulated advanced spaceborne thermal emission and reflection (ASTER) radiometer data of the Iron Hill, Colorado, study area for mapping lithologies

USGS Publications Warehouse

Rowan, L.C.

1998-01-01

The advanced spaceborne thermal emission and reflection (ASTER) radiometer was designed to record reflected energy in nine channels with 15 or 30 m resolution, including stereoscopic images, and emitted energy in five channels with 90 m resolution from the NASA Earth Observing System AM1 platform. A simulated ASTER data set was produced for the Iron Hill, Colorado, study area by resampling calibrated, registered airborne visible/infrared imaging spectrometer (AVIRIS) data, and thermal infrared multispectral scanner (TIMS) data to the appropriate spatial and spectral parameters. A digital elevation model was obtained to simulate ASTER-derived topographic data. The main lithologic units in the area are granitic rocks and felsite into which a carbonatite stock and associated alkalic igneous rocks were intruded; these rocks are locally covered by Jurassic sandstone, Tertiary rhyolitic tuff, and colluvial deposits. Several methods were evaluated for mapping the main lithologic units, including the unsupervised classification and spectral curve-matching techniques. In the five thermal-infrared (TIR) channels, comparison of the results of linear spectral unmixing and unsupervised classification with published geologic maps showed that the main lithologic units were mapped, but large areas with moderate to dense tree cover were not mapped in the TIR data. Compared to TIMS data, simulated ASTER data permitted slightly less discrimination in the mafic alkalic rock series, and carbonatite was not mapped in the TIMS nor in the simulated ASTER TIR data. In the nine visible and near-infrared channels, unsupervised classification did not yield useful results, but both the spectral linear unmixing and the matched filter techniques produced useful results, including mapping calcitic and dolomitic carbonatite exposures, travertine in hot spring deposits, kaolinite in argillized sandstone and tuff, and muscovite in sericitized granite and felsite, as well as commonly occurring illite/muscovite. However, the distinction made in AVIRIS data between calcite and dolomite was not consistently feasible in the simulated ASTER data. Comparison of the lithologic information produced by spectral analysis of the simulated ASTER data to a photogeologic interpretation of a simulated ASTER color image illustrates the high potential of spectral analysis of ASTER data to geologic interpretation. This paper is not subject to U.S. copyright. Published in 1998 by the American Geophysical Union.

Towards structural models of molecular recognition in olfactory receptors.

PubMed

Afshar, M; Hubbard, R E; Demaille, J

1998-02-01

The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

RECEPTOR MODEL DEVELOPMENT AND APPLICATION

EPA Science Inventory

Source apportionment (receptor) models are mathematical procedures for identifying and quantifying the sources of ambient air pollutants and their effects at a site (the receptor), primarily on the basis of species concentration measurements at the receptor, and generally without...

PM SOURCE APPORTIONMENT/RECEPTOR MODELING

EPA Science Inventory

Source apportionment (receptor) models are mathematical procedures for identifying and quantifying the sources of ambient air pollutants and their effects at a site (the receptor), primarily on the basis of species concentration measurements at the receptor, and generally without...

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

PubMed Central

Roman, Theodore; Xie, Lu

2017-01-01

With increasing appreciation for the extent and importance of intratumor heterogeneity, much attention in cancer research has focused on profiling heterogeneity on a single patient level. Although true single-cell genomic technologies are rapidly improving, they remain too noisy and costly at present for population-level studies. Bulk sequencing remains the standard for population-scale tumor genomics, creating a need for computational tools to separate contributions of multiple tumor clones and assorted stromal and infiltrating cell populations to pooled genomic data. All such methods are limited to coarse approximations of only a few cell subpopulations, however. In prior work, we demonstrated the feasibility of improving cell type deconvolution by taking advantage of substructure in genomic mixtures via a strategy called simplicial complex unmixing. We improve on past work by introducing enhancements to automate learning of substructured genomic mixtures, with specific emphasis on genome-wide copy number variation (CNV) data, as well as the ability to process quantitative RNA expression data, and heterogeneous combinations of RNA and CNV data. We introduce methods for dimensionality estimation to better decompose mixture model substructure; fuzzy clustering to better identify substructure in sparse, noisy data; and automated model inference methods for other key model parameters. We further demonstrate their effectiveness in identifying mixture substructure in true breast cancer CNV data from the Cancer Genome Atlas (TCGA). Source code is available at https://github.com/tedroman/WSCUnmix PMID:29059177

Preclinical Testing of Novel Oxytocin Receptor Activators in Models of Autism Phenotypes

DTIC Science & Technology

2014-09-01

AD_________________ Award Number: TITLE: Preclinical Testing of Novel Oxytocin Receptor Activators in Models of Autism ...AUG 2013-7 Aug 2014 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Preclinical Testing of Novel Oxytocin Receptor Activators in Models of Autism ...a genetic mouse model of autism -like phenotypes, the Grin1 knockdown mouse. The Grin1 gene encodes the NR1 subunit of the NMDA receptor . In the

Odor detection of mixtures of homologous carboxylic acids and coffee aroma compounds by humans.

PubMed

Miyazawa, Toshio; Gallagher, Michele; Preti, George; Wise, Paul M

2009-11-11

Mixture summation among homologous carboxylic acids, that is, the relationship between detection probabilities for mixtures and detection probabilities for their unmixed components, varies with similarity in carbon-chain length. The current study examined detection of acetic, butyric, hexanoic, and octanoic acids mixed with three other model odorants that differ greatly from the acids in both structure and odor character, namely, 2-hydroxy-3-methylcyclopent-2-en-1-one, furan-2-ylmethanethiol, and (3-methyl-3-sulfanylbutyl) acetate. Psychometric functions were measured for both single compounds and binary mixtures (2 of 5, forced-choice method). An air dilution olfactometer delivered stimuli, with vapor-phase calibration using gas chromatography-mass spectrometry. Across the three odorants that differed from the acids, acetic and butyric acid showed approximately additive (or perhaps even supra-additive) summation at low perithreshold concentrations, but subadditive interactions at high perithreshold concentrations. In contrast, the medium-chain acids showed subadditive interactions across a wide range of concentrations. Thus, carbon-chain length appears to influence not only summation with other carboxylic acids but also summation with at least some unrelated compounds.

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

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

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

MULTIVARIATE RECEPTOR MODELS AND MODEL UNCERTAINTY. (R825173)

EPA Science Inventory

Abstract

Estimation of the number of major pollution sources, the source composition profiles, and the source contributions are the main interests in multivariate receptor modeling. Due to lack of identifiability of the receptor model, however, the estimation cannot be...

Exact solutions to a spatially extended model of kinase-receptor interaction.

PubMed

Szopa, Piotr; Lipniacki, Tomasz; Kazmierczak, Bogdan

2011-10-01

B and Mast cells are activated by the aggregation of the immune receptors. Motivated by this phenomena we consider a simple spatially extended model of mutual interaction of kinases and membrane receptors. It is assumed that kinase activates membrane receptors and in turn the kinase molecules bound to the active receptors are activated by transphosphorylation. Such a type of interaction implies positive feedback and may lead to bistability. In this study we apply the Steklov eigenproblem theory to analyze the linearized model and find exact solutions in the case of non-uniformly distributed membrane receptors. This approach allows us to determine the critical value of receptor dephosphorylation rate at which cell activation (by arbitrary small perturbation of the inactive state) is possible. We found that cell sensitivity grows with decreasing kinase diffusion and increasing anisotropy of the receptor distribution. Moreover, these two effects are cooperating. We showed that the cell activity can be abruptly triggered by the formation of the receptor aggregate. Since the considered activation mechanism is not based on receptor crosslinking by polyvalent antigens, the proposed model can also explain B cell activation due to receptor aggregation following binding of monovalent antigens presented on the antigen presenting cell.

Fuel-Flexible Gasification-Combustion Technology for Production of H2 and Sequestration-Ready CO2

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

George Rizeq; Janice West; Raul Subia

GE Global Research is developing an innovative energy technology for coal gasification with high efficiency and near-zero pollution. This Unmixed Fuel Processor (UFP) technology simultaneously converts coal, steam and air into three separate streams of hydrogen-rich gas, sequestration-ready CO{sub 2}, and high-temperature, high-pressure vitiated air to produce electricity in gas turbines. This is the draft final report for the first stage of the DOE-funded Vision 21 program. The UFP technology development program encompassed lab-, bench- and pilot-scale studies to demonstrate the UFP concept. Modeling and economic assessments were also key parts of this program. The chemical and mechanical feasibility weremore » established via lab and bench-scale testing, and a pilot plant was designed, constructed and operated, demonstrating the major UFP features. Experimental and preliminary modeling results showed that 80% H{sub 2} purity could be achieved, and that a UFP-based energy plant is projected to meet DOE efficiency targets. Future work will include additional pilot plant testing to optimize performance and reduce environmental, operability and combined cycle integration risks. Results obtained to date have confirmed that this technology has the potential to economically meet future efficiency and environmental performance goals.« less

Fluorescent marker-based and marker-free discrimination between healthy and cancerous human tissues using hyper-spectral imaging

NASA Astrophysics Data System (ADS)

Arnold, Thomas; De Biasio, Martin; Leitner, Raimund

2015-06-01

Two problems are addressed in this paper (i) the fluorescent marker-based and the (ii) marker-free discrimination between healthy and cancerous human tissues. For both applications the performance of hyper-spectral methods are quantified. Fluorescent marker-based tissue classification uses a number of fluorescent markers to dye specific parts of a human cell. The challenge is that the emission spectra of the fluorescent dyes overlap considerably. They are, furthermore disturbed by the inherent auto-fluorescence of human tissue. This results in ambiguities and decreased image contrast causing difficulties for the treatment decision. The higher spectral resolution introduced by tunable-filter-based spectral imaging in combination with spectral unmixing techniques results in an improvement of the image contrast and therefore more reliable information for the physician to choose the treatment decision. Marker-free tissue classification is based solely on the subtle spectral features of human tissue without the use of artificial markers. The challenge in this case is that the spectral differences between healthy and cancerous tissues are subtle and embedded in intra- and inter-patient variations of these features. The contributions of this paper are (i) the evaluation of hyper-spectral imaging in combination with spectral unmixing techniques for fluorescence marker-based tissue classification, (ii) the evaluation of spectral imaging for marker-free intra surgery tissue classification. Within this paper, we consider real hyper-spectral fluorescence and endoscopy data sets to emphasize the practical capability of the proposed methods. It is shown that the combination of spectral imaging with multivariate statistical methods can improve the sensitivity and specificity of the detection and the staging of cancerous tissues compared to standard procedures.

Carbonate-silicate liquid immiscibility in the mantle propels kimberlite magma ascent

NASA Astrophysics Data System (ADS)

Kamenetsky, Vadim S.; Yaxley, Gregory M.

2015-06-01

Kimberlite is a rare volcanic rock renowned as the major host of diamonds and originated at the base of the subcontinental lithospheric mantle. Although kimberlite magmas are dense in crystals and deeply-derived rock fragments, they ascend to the surface extremely rapidly, enabling diamonds to survive. The unique physical properties of kimberlite magmas depend on the specific compositions of their parental melts that, in absence of historical eruptions and due to pervasive alteration of kimberlite rocks, remain highly debatable. We explain exceptionally rapid ascent of kimberlite magma from mantle depths by combining empirical data on the essentially carbonatite composition of the kimberlite primary melts and experimental evidence on interaction of the carbonate liquids with mantle minerals. Our experimental study shows that orthopyroxene is completely dissolved in a Na2CO3 melt at 2.0-5.0 GPa and 1000-1200 °C. The dissolution of orthopyroxene results in homogeneous silicate-carbonate melt at 5.0 GPa and 1200 °C, and is followed by unmixing of carbonate and carbonated silicate melts and formation of stable magmatic emulsion at lower pressures and temperatures. The dispersed silicate melt has a significant capacity for storing a carbonate component in the deep mantle (13 wt% CO2 at 2.0 GPa). We envisage that this component reaches saturation and is gradually released as CO2 bubbles, as the silicate melt globules are transported upwards through the lithosphere by the carbonatite magma. The globules of unmixed, CO2-rich silicate melt are continuously produced upon further reaction between the natrocarbonatite melt and mantle peridotite. On decompression the dispersed silicate melt phase ensures a continuous supply of CO2 bubbles that decrease density and increase buoyancy and promote rapid ascent of the magmatic emulsion.

Unmixing-Based Denoising as a Pre-Processing Step for Coral Reef Analysis

NASA Astrophysics Data System (ADS)

Cerra, D.; Traganos, D.; Gege, P.; Reinartz, P.

2017-05-01

Coral reefs, among the world's most biodiverse and productive submerged habitats, have faced several mass bleaching events due to climate change during the past 35 years. In the course of this century, global warming and ocean acidification are expected to cause corals to become increasingly rare on reef systems. This will result in a sharp decrease in the biodiversity of reef communities and carbonate reef structures. Coral reefs may be mapped, characterized and monitored through remote sensing. Hyperspectral images in particular excel in being used in coral monitoring, being characterized by very rich spectral information, which results in a strong discrimination power to characterize a target of interest, and separate healthy corals from bleached ones. Being submerged habitats, coral reef systems are difficult to analyse in airborne or satellite images, as relevant information is conveyed in bands in the blue range which exhibit lower signal-to-noise ratio (SNR) with respect to other spectral ranges; furthermore, water is absorbing most of the incident solar radiation, further decreasing the SNR. Derivative features, which are important in coral analysis, result greatly affected by the resulting noise present in relevant spectral bands, justifying the need of new denoising techniques able to keep local spatial and spectral features. In this paper, Unmixing-based Denoising (UBD) is used to enable analysis of a hyperspectral image acquired over a coral reef system in the Red Sea based on derivative features. UBD reconstructs pixelwise a dataset with reduced noise effects, by forcing each spectrum to a linear combination of other reference spectra, exploiting the high dimensionality of hyperspectral datasets. Results show clear enhancements with respect to traditional denoising methods based on spatial and spectral smoothing, facilitating the coral detection task.

Spectral imaging perspective on cytomics.

PubMed

Levenson, Richard M

2006-07-01

Cytomics involves the analysis of cellular morphology and molecular phenotypes, with reference to tissue architecture and to additional metadata. To this end, a variety of imaging and nonimaging technologies need to be integrated. Spectral imaging is proposed as a tool that can simplify and enrich the extraction of morphological and molecular information. Simple-to-use instrumentation is available that mounts on standard microscopes and can generate spectral image datasets with excellent spatial and spectral resolution; these can be exploited by sophisticated analysis tools. This report focuses on brightfield microscopy-based approaches. Cytological and histological samples were stained using nonspecific standard stains (Giemsa; hematoxylin and eosin (H&E)) or immunohistochemical (IHC) techniques employing three chromogens plus a hematoxylin counterstain. The samples were imaged using the Nuance system, a commercially available, liquid-crystal tunable-filter-based multispectral imaging platform. The resulting data sets were analyzed using spectral unmixing algorithms and/or learn-by-example classification tools. Spectral unmixing of Giemsa-stained guinea-pig blood films readily classified the major blood elements. Machine-learning classifiers were also successful at the same task, as well in distinguishing normal from malignant regions in a colon-cancer example, and in delineating regions of inflammation in an H&E-stained kidney sample. In an example of a multiplexed ICH sample, brown, red, and blue chromogens were isolated into separate images without crosstalk or interference from the (also blue) hematoxylin counterstain. Cytomics requires both accurate architectural segmentation as well as multiplexed molecular imaging to associate molecular phenotypes with relevant cellular and tissue compartments. Multispectral imaging can assist in both these tasks, and conveys new utility to brightfield-based microscopy approaches. Copyright 2006 International Society for Analytical Cytology.

Geology and geochemistry of the Clear Creek intrusion-related gold occurrences, Tintina Gold Province, Yukon, Canada

USGS Publications Warehouse

Marsh, E.E.; Goldfarb, R.J.; Hart, C.J.R.; Johnson, C.A.

2003-01-01

The Clear Creek gold occurrences lie within deformed lower greenschist-facies rocks of the western Selwyn basin. They consist of auriferous, sheeted quartz veins that cut six Cretaceous stocks and their hornfels. The veins contain 1-2% combined pyrite and arsenopyrite, with lesser pyrrhotite, bismuthinite, and scheelite, as well as 2-5 g/t Au. New 40Ar/39Ar geochronology of hydrothermal micas indicates that the veins formed within 1-2 million years of granitoid emplacement. Fluid inclusion microthermometry defines a parent ore fluid of -81 mol.% H2O, 14 mol.% CO2, 4 mol.% NaCl ?? KCl, and 1 mol.% CH4, which unmixed into a low- and high-salinity immiscible pair. This suggests a more saline parent fluid and a greater degree of fluid unmixing relative to the other occurrences in the eastern Tintina Gold Province. Inclusions trapped in As- and Bi-rich, high-gold grade veins have homogenization temperatures of 300-350??C, whereas inclusions found in more Ag- and Pb-rich veins are characterized by temperatures of 250-300??C. Fluid inclusion geobarometry suggests hydro-fracturing and gold deposition at 5-7 km depth. The ??18O values of quartz samples range from 13-16??? (per mil) and ??34S for sulfides are also consistent between -3.0???, 0???, with the exception of some outliers from the Contact Zone of the Pukelman stock that indicate a lower temperature second phase of mineralization. It remains uncertain as to whether the Clear Creek ore fluids were exsolved from magmas at depth or from devolatilization reactions within the contact metamorphic aureoles of the intrusions.

Variation in photosynthetic and nonphotosynthetic vegetation along edaphic and compositional gradients in northwestern Amazonia

NASA Astrophysics Data System (ADS)

Higgins, M. A.; Asner, G. P.; Perez, E.; Elespuru, N.; Alonso, A.

2014-03-01

Tropical forests vary substantially in aboveground properties such as canopy height, canopy structure, and plant species composition, corresponding to underlying variations in soils and geology. Forest properties are often difficult to detect and map in the field, however, due to the remoteness and inaccessibility of these forests. Spectral mixture analysis of Landsat imagery allows mapping of photosynthetic and nonphotosynthetic vegetation quantities (PV and NPV), corresponding to biophysical properties such as canopy openness, forest productivity, and disturbance. Spectral unmixing has been used for applications ranging from deforestation monitoring to identifying burn scars from past fires, but little is known about variations in PV and NPV in intact rainforest. Here we use spectral unmixing of Landsat imagery to map PV and NPV in northern Amazonia, and to test their relationship to soils and plant species composition. To do this we sampled 117 sites crossing a geological boundary in northwestern Amazonia for soil cation concentrations and plant species composition. We then used the Carnegie Landsat Analysis System to map PV and NPV for these sites from multiple dates of Landsat imagery. We found that soil cation concentrations and plant species composition consistently explain a majority of the variation in remotely sensed PV and NPV values. After combining PV and NPV into a single variable (PV-NPV), we determined that the influence of soil properties on canopy properties was inseparable from the influence of plant species composition. In all cases, patterns in PV and NPV corresponded to underlying geological patterns. Our findings suggest that geology and soils regulate canopy PV and NPV values in intact tropical forest, possibly through changes in plant species composition.

Variation in photosynthetic and nonphotosynthetic vegetation along edaphic and compositional gradients in northwestern Amazonia

NASA Astrophysics Data System (ADS)

Higgins, M. A.; Asner, G. P.; Perez, E.; Elespuru, N.; Alonso, A.

2014-07-01

Tropical forests vary substantially in aboveground properties such as canopy height, canopy structure, and plant species composition, corresponding to underlying variations in soils and geology. Forest properties are often difficult to detect and map in the field, however, due to the remoteness and inaccessibility of these forests. Spectral mixture analysis of Landsat imagery allows mapping of photosynthetic and nonphotosynthetic vegetation quantities (PV and NPV), corresponding to biophysical properties such as canopy openness, forest productivity, and disturbance. Spectral unmixing has been used for applications ranging from deforestation monitoring to identifying burn scars from past fires, but little is known about variations in PV and NPV in intact rainforests. Here we use spectral unmixing of Landsat imagery to map PV and NPV in northern Amazonia, and to test their relationship to soils and plant species composition. To do this we sampled 117 sites crossing a geological boundary in northwestern Amazonia for soil cation concentrations and plant species composition. We then used the Carnegie Landsat Analysis System to map PV and NPV for these sites from multiple dates of Landsat imagery. We found that soil cation concentrations and plant species composition consistently explain a majority of the variation in remotely sensed PV and NPV values. After combining PV and NPV into a single variable (PV-NPV), we determined that the influence of soil properties on canopy properties was inseparable from the influence of plant species composition. In all cases, patterns in PV and NPV corresponded to underlying geological patterns. Our findings suggest that geology and soils regulate canopy PV and NPV values in intact tropical forests, possibly through changes in plant species composition.

Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

PubMed

Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan

2011-07-01

We present a comparative account on 3D-structures of human type-1 receptor (AT1) for angiotensin II (AngII), modeled using three different methodologies. AngII activates a wide spectrum of signaling responses via the AT1 receptor that mediates physiological control of blood pressure and diverse pathological actions in cardiovascular, renal, and other cell types. Availability of 3D-model of AT1 receptor would significantly enhance the development of new drugs for cardiovascular diseases. However, templates of AT1 receptor with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies in order to use the models for sensitive applications such as rational drug design. Three models were generated for AT1 receptor by, (1) homology modeling with bovine rhodopsin as template, (2) homology modeling with multiple templates and (3) threading using I-TASSER web server. Molecular dynamics (MD) simulation (15 ns) of models in explicit membrane-water system, Ramachandran plot analysis and molecular docking with antagonists led to the conclusion that multiple template-based homology modeling outweighs other methodologies for AT1 modeling.

Is receptor oligomerization causally linked to activation of the EGF receptor kinase?

NASA Technical Reports Server (NTRS)

Rintoul, D. A.; Spooner, B. S. (Principal Investigator)

1992-01-01

Transduction of a signal from an extracellular peptide hormone to produce an intracellular response is often mediated by a cell surface receptor, which is usually a glycoprotein. The secondary intracellular signal(s) generated after hormone binding to the receptor have been intensively studied. The nature of the primary signal generated by ligand binding to the receptor is understood less well in most cases. The particular case of the epidermal growth factor (EGF) receptor is analyzed, and evidence for or against two dissimilar models of primary signal transduction is reviewed. Evidence for the most widely accepted current model is found to be unconvincing. Evidence for the other model is substantial but indirect; a direct test of this model remains to be done.

The cubic ternary complex receptor-occupancy model. III. resurrecting efficacy.

PubMed

Weiss, J M; Morgan, P H; Lutz, M W; Kenakin, T P

1996-08-21

Early work in pharmacology characterized the interaction of receptors and ligands in terms of two parameters, affinity and efficacy, an approach we term the bipartite view. A precise formulation of efficacy only exists for very simple pharmacological models. Here we extend the notion of efficacy to models that incorporate receptor activation and G-protein coupling. Using the cubic ternary complex model, we show that efficacy is not purely a property of the ligand-receptor interaction; it also depends upon the distributional details of the receptor species in the native receptor ensemble. This suggests a distinction between what we call potential efficacy (a vector) and realized efficacy (a scalar). To each receptor species in the native receptor ensemble we assign a part-worth utility; taken together these utilities comprise the potential efficacy vector. Realized efficacy is the expectation of these part-worth utilities with respect to the frequency distribution of receptor species in the native receptor ensemble. In the parlance of statistical decision theory, the binding of a ligand to a receptor ensemble is a random prospect and realized efficacy is the utility of this prospect. We explore the implications that our definition of efficacy has for understanding agonism and in assessing the legitimacy of the bipartite view in pharmacology.

Structure-activity relationships of seco-prezizaane and picrotoxane/picrodendrane terpenoids by Quasar receptor-surface modeling.

PubMed

Schmidt, Thomas J; Gurrath, Marion; Ozoe, Yoshihisa

2004-08-01

The seco-prezizaane-type sesquiterpenes pseudoanisatin and parviflorolide from Illicium are noncompetitive antagonists at housefly (Musca domestica) gamma-aminobutyric acid (GABA) receptors. They show selectivity toward the insect receptor and thus represent new leads toward selective insecticides. Based on the binding data for 13 seco-prezizaane terpenoids and 17 picrotoxane and picrodendrane-type terpenoids to housefly and rat GABA receptors, a QSAR study was conducted by quasi-atomistic receptor-surface modeling (Quasar). The resulting models provide insight into the structural basis of selectivity and properties of the binding sites at GABA receptor-coupled chloride channels of insects and mammals.

Customizing G Protein-coupled receptor models for structure-based virtual screening.

PubMed

de Graaf, Chris; Rognan, Didier

2009-01-01

This review will focus on the construction, refinement, and validation of G Protein-coupled receptor models for the purpose of structure-based virtual screening. Practical tips and tricks derived from concrete modeling and virtual screening exercises to overcome the problems and pitfalls associated with the different steps of the receptor modeling workflow will be presented. These examples will not only include rhodopsin-like (class A), but also secretine-like (class B), and glutamate-like (class C) receptors. In addition, the review will present a careful comparative analysis of current crystal structures and their implication on homology modeling. The following themes will be discussed: i) the use of experimental anchors in guiding the modeling procedure; ii) amino acid sequence alignments; iii) ligand binding mode accommodation and binding cavity expansion; iv) proline-induced kinks in transmembrane helices; v) binding mode prediction and virtual screening by receptor-ligand interaction fingerprint scoring; vi) extracellular loop modeling; vii) virtual filtering schemes. Finally, an overview of several successful structure-based screening shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands.

Exploration of N-arylpiperazine Binding Sites of D2 Dopaminergic Receptor.

PubMed

Soskic, Vukic; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana

2015-01-01

The crystal structures of the D3 dopamine receptor and several other G-protein coupled receptors (GPCRs) were published in recent times. Those 3D structures are used by us and other scientists as a template for the homology modeling and ligand docking analysis of related GPCRs. Our main scientific interest lies in the field of pharmacologically active N-arylpiperazines that exhibit antipsychotic and/or antidepressant properties, and as such are dopaminergic and serotonergic receptor ligands. In this short review article we are presenting synthesis and biological data on the new N-arylpipereazine as well our results on molecular modeling of the interactions of those N-arylpiperazines with the model of D2 dopamine receptors. To obtain that model the crystal structure of the D3 dopamine receptor was used. Our results show that the N-arylpiperazines binding site consists of two pockets: one is the orthosteric binding site where the N-arylpiperazine part of the ligand is docked and the second is a non-canonical accessory binding site for N-arylpipereazine that is formed by a second extracellular loop (ecl2) of the receptor. Until now, the structure of this receptor region was unresolved in crystal structure analyses of the D3 dopamine receptor. To get a more complete picture of the ligand - receptor interaction, DFT quantum mechanical calculations on N-arylpiperazine were performed and the obtained models were used to examine those interactions.

Dimensionality of Motion and Binding Valency Govern Receptor-Ligand Kinetics As Revealed by Agent-Based Modeling.

PubMed

Lehnert, Teresa; Figge, Marc Thilo

2017-01-01

Mathematical modeling and computer simulations have become an integral part of modern biological research. The strength of theoretical approaches is in the simplification of complex biological systems. We here consider the general problem of receptor-ligand binding in the context of antibody-antigen binding. On the one hand, we establish a quantitative mapping between macroscopic binding rates of a deterministic differential equation model and their microscopic equivalents as obtained from simulating the spatiotemporal binding kinetics by stochastic agent-based models. On the other hand, we investigate the impact of various properties of B cell-derived receptors-such as their dimensionality of motion, morphology, and binding valency-on the receptor-ligand binding kinetics. To this end, we implemented an algorithm that simulates antigen binding by B cell-derived receptors with a Y-shaped morphology that can move in different dimensionalities, i.e., either as membrane-anchored receptors or as soluble receptors. The mapping of the macroscopic and microscopic binding rates allowed us to quantitatively compare different agent-based model variants for the different types of B cell-derived receptors. Our results indicate that the dimensionality of motion governs the binding kinetics and that this predominant impact is quantitatively compensated by the bivalency of these receptors.

Old and new physics interpretations of the NuTeV anomaly

NASA Astrophysics Data System (ADS)

Davidson, Sacha; Forte, Stefano; Gambino, Paolo; Rius, Nuria; Strumia, Alessandro

2002-02-01

We discuss whether the NuTeV anomaly can be explained, compatibly with all other data, by QCD effects (maybe, if the strange sea is asymmetric, or there is a tiny violation of isospin), new physics in propagators or couplings of the vector bosons (not really), loops of supersymmetric particles (no), dimension six operators (yes, for one specific SU(2)L-invariant operator), leptoquarks (not in a minimal way), extra U(1) gauge bosons (maybe: an unmixed Z' coupled to B-3Lμ also increases the muon g-2 by about 10-9 and gives a `burst' to cosmic rays above the GZK cutoff).

Depth profiles of Mn-53 in lunar rocks and soils

NASA Technical Reports Server (NTRS)

Imamura, M.; Nishiizumi, K.; Honda, M.; Finkel, R. C.; Arnold, J. R.; Kohl, C. P.

1974-01-01

Results of measurements of cosmic-ray-produced Mn-53 taken down the length of the Apollo 16 deep drill core are presented. They indicate that the lunar regolith has been unmixed, on a meter scale, for the past 5 million years at the location of this core. The data are in agreement with earlier Mn-53 measurements on the Apollo 15 drill core. Mn-53 activity profiles in 14310, 12002, and 14321 are compared to each other; all three rocks have probably been on the lunar surface long enough to saturate their solar cosmic-ray-produced Mn-53 (half-life = 3.7 m.y.) activity.

Fractal reaction kinetics.

PubMed

Kopelman, R

1988-09-23

Classical reaction kinetics has been found to be unsatisfactory when the reactants are spatially constrained on the microscopic level by either walls, phase boundaries, or force fields. Recently discovered theories of heterogeneous reaction kinetics have dramatic consequences, such as fractal orders for elementary reactions, self-ordering and self-unmixing of reactants, and rate coefficients with temporal "memories." The new theories were needed to explain the results of experiments and supercomputer simulations of reactions that were confined to low dimensions or fractal dimensions or both. Among the practical examples of "fractal-like kinetics" are chemical reactions in pores of membranes, excitation trapping in molecular aggregates, exciton fusion in composite materials, and charge recombination in colloids and clouds.

Lattice Independent Component Analysis for Mobile Robot Localization

NASA Astrophysics Data System (ADS)

Villaverde, Ivan; Fernandez-Gauna, Borja; Zulueta, Ekaitz

This paper introduces an approach to appearance based mobile robot localization using Lattice Independent Component Analysis (LICA). The Endmember Induction Heuristic Algorithm (EIHA) is used to select a set of Strong Lattice Independent (SLI) vectors, which can be assumed to be Affine Independent, and therefore candidates to be the endmembers of the data. Selected endmembers are used to compute the linear unmixing of the robot's acquired images. The resulting mixing coefficients are used as feature vectors for view recognition through classification. We show on a sample path experiment that our approach can recognise the localization of the robot and we compare the results with the Independent Component Analysis (ICA).

Acoustic response of a rectangular levitator with orifices

NASA Technical Reports Server (NTRS)

El-Raheb, Michael; Wagner, Paul

1990-01-01

The acoustic response of a rectangular cavity to speaker-generated excitation through waveguides terminating at orifices in the cavity walls is analyzed. To find the effects of orifices, acoustic pressure is expressed by eigenfunctions satisfying Neumann boundary conditions as well as by those satisfying Dirichlet ones. Some of the excess unknowns can be eliminated by point constraints set over the boundary, by appeal to Lagrange undetermined multipliers. The resulting transfer matrix must be further reduced by partial condensation to the order of a matrix describing unmixed boundary conditions. If the cavity is subjected to an axial temperature dependence, the transfer matrix is determined numerically.

Evaluation of a metering, mixing, and dispensing system for mixing polysulfide adhesive

NASA Technical Reports Server (NTRS)

Evans, Kurt B.

1989-01-01

Tests were performed to evaluate whether a metered mixing system can mix PR-1221 polysulfide adhesive as well as or better than batch-mixed adhesive; also, to evaluate the quality of meter-mixed PR-1860 and PS-875 polysulfide adhesives. These adhesives are candidate replacements for PR-1221 which will not be manufactured in the future. The following material properties were evaluated: peel strength, specific gravity and adhesive components of mixed adhesives, Shore A hardness, tensile adhesion strength, and flow rate. Finally, a visual test called the butterfly test was performed to observe for bubbles and unmixed adhesive. The results of these tests are reported and discussed.

Development of a phase-sensitive Fourier domain optical coherence tomography system to measure mouse organ of Corti vibrations in two cochlear turns

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

Ramamoorthy, Sripriya; Zhang, Yuan; Jacques, Steven

In this study, we have developed a phase-sensitive Fourier-domain optical coherence tomography system to simultaneously measure the in vivo inner ear vibrations in the hook area and second turn of the mouse cochlea. This technical development will enable measurement of intra-cochlear distortion products at ideal locations such as the distortion product generation site and reflection site. This information is necessary to un-mix the complex mixture of intra-cochlear waves comprising the DPOAE and thus leads to the non-invasive identification of the local region of cochlear damage.

Screening prostate cancer using a portable near infrared scanning imaging unit with an optical fiber-based rectal probe

NASA Astrophysics Data System (ADS)

Pu, Yang; Wang, Wubao; Tang, Guichen; Budansky, Yury; Sharonov, Mikhail; Xu, Min; Achilefu, Samuel; Eastham, James A.; Alfano, Robert R.

2012-01-01

A portable near infrared scanning polarization imaging unit with an optical fiber-based rectal probe, namely Photonic Finger, was designed and developed o locate the 3D position of abnormal prostate site inside normal prostate tissue. An inverse algorithm, Optical Tomography using Independent Component Analysis (OPTICA) was improved particularly to unmix the signal from targets (cancerous tissue) embedded in a turbid medium (normal tissue) in the backscattering imaging geometry. Photonic Finger combined with OPTICA was tested to characterize different target(s) inside different tissue medium, including cancerous prostate tissue embedded by large piece of normal tissue.

Mu-Opioid (MOP) receptor mediated G-protein signaling is impaired in specific brain regions in a rat model of schizophrenia.

PubMed

Szűcs, Edina; Büki, Alexandra; Kékesi, Gabriella; Horváth, Gyöngyi; Benyhe, Sándor

2016-04-21

Schizophrenia is a complex mental health disorder. Clinical reports suggest that many patients with schizophrenia are less sensitive to pain than other individuals. Animal models do not interpret schizophrenia completely, but they can model a number of symptoms of the disease, including decreased pain sensitivities and increased pain thresholds of various modalities. Opioid receptors and endogenous opioid peptides have a substantial role in analgesia. In this biochemical study we investigated changes in the signaling properties of the mu-opioid (MOP) receptor in different brain regions, which are involved in the pain transmission, i.e., thalamus, olfactory bulb, prefrontal cortex and hippocampus. Our goal was to compare the transmembrane signaling mediated by MOP receptors in control rats and in a recently developed rat model of schizophrenia. Regulatory G-protein activation via MOP receptors were measured in [(35)S]GTPγS binding assays in the presence of a highly selective MOP receptor peptide agonist, DAMGO. It was found that the MOP receptor mediated activation of G-proteins was substantially lower in membranes prepared from the 'schizophrenic' model rats than in control animals. The potency of DAMGO to activate MOP receptor was also decreased in all brain regions studied. Taken together in our rat model of schizophrenia, MOP receptor mediated G-proteins have a reduced stimulatory activity compared to membrane preparations taken from control animals. The observed distinct changes of opioid receptor functions in different areas of the brain do not explain the augmented nociceptive threshold described in these animals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Multiscale Modeling of Virus Entry via Receptor-Mediated Endocytosis

NASA Astrophysics Data System (ADS)

Liu, Jin

2012-11-01

Virus infections are ubiquitous and remain major threats to human health worldwide. Viruses are intracellular parasites and must enter host cells to initiate infection. Receptor-mediated endocytosis is the most common entry pathway taken by viruses, the whole process is highly complex and dictated by various events, such as virus motions, membrane deformations, receptor diffusion and ligand-receptor reactions, occurring at multiple length and time scales. We develop a multiscale model for virus entry through receptor-mediated endocytosis. The binding of virus to cell surface is based on a mesoscale three dimensional stochastic adhesion model, the internalization (endocytosis) of virus and cellular membrane deformation is based on the discretization of Helfrich Hamiltonian in a curvilinear space using Monte Carlo method. The multiscale model is based on the combination of these two models. We will implement this model to study the herpes simplex virus entry into B78 cells and compare the model predictions with experimental measurements.

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Association between p75 neurotrophin receptor gene expression and cell apoptosis in tissues surrounding hematomas in rat models of intracerebral hemorrhage.

PubMed

He, Baixiang; Bao, Gang; Guo, Shiwen; Xu, Gaofeng; Li, Qi; Wang, Ning

2012-03-15

Animal models of intracerebral hemorrhage were established by injection of autologous blood into the caudate nucleus in rats. Cell apoptosis was measured by flow cytometry and immunohistochemical staining of the p75 neurotrophin receptor. p75 neurotrophin receptor protein was detected by immunohistochemistry. p75 neurotrophin receptor mRNA was examined by quantitative real-time polymerase chain reactions. At 24 hours after modeling, cellular apoptosis occured around hematoma with upregulation of p75 neurotrophin receptor protein and mRNA was observed, which directly correlated to apoptosis. This observation indicated that p75 neurotrophin receptor upregulation was associated with cell apoptosis around hematomas after intracerebral hemorrhage.

Further evidence of no linkage between schizophrenia and the dopamine D{sub 3} receptor gene locus

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

Nanko, S.; Fukuda, R.; Hattori, M.

The dopamine hypothesis of schizophrenia proposed that dopaminergic pathways are involved in the etiology of the disease. In particular, interest among psychiatrists has focused on the D{sub 2} receptor because of its affinity to antipsychotic drugs. Recently a new dopamine receptor gene has been cloned and named the dopamine D{sub 3} receptor. The D{sub 3} receptor is a potential site for antipsychotic drug action and may be involved in the pathophysiology of schizophrenia. We have carried out a linkage study between the susceptibility gene for schizophrenia and polymorphism of the dopamine D{sub 3} receptor gene in two Japanese pedigrees. Themore » LOD scores were negative for all genetic models and for all affective status at a recombination fraction {theta} = 0. Linkage of DRD{sub 3} has been excluded for the model 1 (dominant model) and the model 3 (recessive model). The LOD score was -3.43 at {theta} = 0 for model 1 (dominant model) and broad definition of affected status. These results were consistent with previous studies. 19 refs., 2 figs., 3 tabs.« less

Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models

NASA Astrophysics Data System (ADS)

Deshpande, Sneha A.; Pawar, Aiswarya B.; Dighe, Anish; Athale, Chaitanya A.; Sengupta, Durba

2017-06-01

G protein-coupled receptor (GPCR) association is an emerging paradigm with far reaching implications in the regulation of signalling pathways and therapeutic interventions. Recent super resolution microscopy studies have revealed that receptor dimer steady state exhibits sub-second dynamics. In particular the GPCRs, muscarinic acetylcholine receptor M1 (M1MR) and formyl peptide receptor (FPR), have been demonstrated to exhibit a fast association/dissociation kinetics, independent of ligand binding. In this work, we have developed a spatial kinetic Monte Carlo model to investigate receptor homo-dimerisation at a single receptor resolution. Experimentally measured association/dissociation kinetic parameters and diffusion coefficients were used as inputs to the model. To test the effect of membrane spatial heterogeneity on the simulated steady state, simulations were compared to experimental statistics of dimerisation. In the simplest case the receptors are assumed to be diffusing in a spatially homogeneous environment, while spatial heterogeneity is modelled to result from crowding, membrane micro-domains and cytoskeletal compartmentalisation or ‘corrals’. We show that a simple association-diffusion model is sufficient to reproduce M1MR association statistics, but fails to reproduce FPR statistics despite comparable kinetic constants. A parameter sensitivity analysis is required to reproduce the association statistics of FPR. The model reveals the complex interplay between cytoskeletal components and their influence on receptor association kinetics within the features of the membrane landscape. These results constitute an important step towards understanding the factors modulating GPCR organisation.

Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics

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

Shankaran, Harish; Zhang, Yi; Chrisler, William B.

2012-10-02

The epidermal growth factor receptor (EGFR) belongs to the ErbB family of receptor tyrosine kinases, and controls a diverse set of cellular responses relevant to development and tumorigenesis. ErbB activation is a complex process involving receptor-ligand binding, receptor dimerization, phosphorylation, and trafficking (internalization, recycling and degradation), which together dictate the spatio-temporal distribution of active receptors within the cell. The ability to predict this distribution, and elucidation of the factors regulating it, would help to establish a mechanistic link between ErbB expression levels and the cellular response. Towards this end, we constructed mathematical models for deconvolving the contributions of receptor dimerizationmore » and phosphorylation to EGFR activation, and to examine the dependence of these processes on sub-cellular location. We collected experimental datasets for EGFR activation dynamics in human mammary epithelial cells, with the specific goal of model parameterization, and used the data to estimate parameters for several alternate models. Model-based analysis indicated that: 1) signal termination via receptor dephosphorylation in late endosomes, prior to degradation, is an important component of the response, 2) less than 40% of the receptors in the cell are phosphorylated at any given time, even at saturating ligand doses, and 3) receptor dephosphorylation rates at the cell surface and early endosomes are comparable. We validated the last finding by measuring EGFR dephosphorylation rates at various times following ligand addition both in whole cells, and in endosomes using ELISAs and fluorescent imaging. Overall, our results provide important information on how EGFR phosphorylation levels are regulated within cells. Further, the mathematical model described here can be extended to determine receptor dimer abundances in cells co-expressing various levels of ErbB receptors. This study demonstrates that an iterative cycle of experiments and modeling can be used to gain mechanistic insight regarding complex cell signaling networks.« less

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.

PubMed

Malo, Marcus; Persson, Ronnie; Svensson, Peder; Luthman, Kristina; Brive, Lars

2013-03-01

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β1 adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D2 receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D2 receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.

Homology Modeling of Class A G Protein-Coupled Receptors

PubMed Central

Costanzi, Stefano

2012-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that hold great pharmaceutical interest. Since experimentally elucidated structures are available only for a very limited number of receptors, homology modeling has become a widespread technique for the construction of GPCR models intended to study the structure-function relationships of the receptors and aid the discovery and development of ligands capable of modulating their activity. Through this chapter, various aspects involved in the constructions of homology models of the serpentine domain of the largest class of GPCRs, known as class A or rhodopsin family, are illustrated. In particular, the chapter provides suggestions, guidelines and critical thoughts on some of the most crucial aspect of GPCR modeling, including: collection of candidate templates and a structure-based alignment of their sequences; identification and alignment of the transmembrane helices of the query receptor to the corresponding domains of the candidate templates; selection of one or more templates receptor; election of homology or de novo modeling for the construction of specific extracellular and intracellular domains; construction of the three-dimensional models, with special consideration to extracellular regions, disulfide bridges, and interhelical cavity; validation of the models through controlled virtual screening experiments. PMID:22323225

Exploring the Interaction between TSC2, PTEN, and the NMDA Receptor in Animal Models of Tuberous Sclerosis

DTIC Science & Technology

2014-09-01

Sunnen CN, Crowell B, Lee GH, Anderson AE, and D’Arcangelo G. Examination of the Role of Pten in Ionotropic Glutamate Receptor Expression. National...PTEN, and the NMDA Receptor in Animal Models of Tuberous Sclerosis PRINCIPAL INVESTIGATOR: D’Arcangelo, Gabriella CONTRACTING...June 2014 4. TITLE AND SUBTITLE Exploring the Interaction between TSC2, PTEN, and the NMDA Receptor in Animal Models of Tuberous Sclerosis 5a

Odor Preference Learning and Memory Modify GluA1 Phosphorylation and GluA1 Distribution in the Neonate Rat Olfactory Bulb: Testing the AMPA Receptor Hypothesis in an Appetitive Learning Model

ERIC Educational Resources Information Center

Cui, Wen; Darby-King, Andrea; Grimes, Matthew T.; Howland, John G.; Wang, Yu Tian; McLean, John H.; Harley, Carolyn W.

2011-01-01

An increase in synaptic AMPA receptors is hypothesized to mediate learning and memory. AMPA receptor increases have been reported in aversive learning models, although it is not clear if they are seen with memory maintenance. Here we examine AMPA receptor changes in a cAMP/PKA/CREB-dependent appetitive learning model: odor preference learning in…

Operational models of pharmacological agonism.

PubMed

Black, J W; Leff, P

1983-12-22

The traditional receptor-stimulus model of agonism began with a description of drug action based on the law of mass action and has developed by a series of modifications, each accounting for new experimental evidence. By contrast, in this paper an approach to modelling agonism is taken that begins with the observation that experimental agonist-concentration effect, E/[A], curves are commonly hyperbolic and develops using the deduction that the relation between occupancy and effect must be hyperbolic if the law of mass action applies at the agonist-receptor level. The result is a general model that explicitly describes agonism by three parameters: an agonist-receptor dissociation constant, KA; the total receptor concentration, [R0]; and a parameter, KE, defining the transduction of agonist-receptor complex, AR, into pharmacological effect. The ratio, [R0]/KE, described here as the 'transducer ratio', tau, is a logical definition for the efficacy of an agonist in a system. The model may be extended to account for non-hyperbolic E/[A] curves with no loss of meaning. Analysis shows that an explicit formulation of the traditional receptor-stimulus model is one particular form of the general model but that it is not the simplest. An alternative model is proposed, representing the cognitive and transducer functions of a receptor, that describes agonist action with one fewer parameter than the traditional model. In addition, this model provides a chemical definition of intrinsic efficacy making this parameter experimentally accessible in principle. The alternative models are compared and contrasted with regard to their practical and conceptual utilities in experimental pharmacology.

Soil erosion modelled with USLE and PESERA using QuickBird derived vegetation parameters in an alpine catchment

NASA Astrophysics Data System (ADS)

Meusburger, K.; Konz, N.; Schaub, M.; Alewell, C.

2010-06-01

The focus of soil erosion research in the Alps has been in two categories: (i) on-site measurements, which are rather small scale point measurements on selected plots often constrained to irrigation experiments or (ii) off-site quantification of sediment delivery at the outlet of the catchment. Results of both categories pointed towards the importance of an intact vegetation cover to prevent soil loss. With the recent availability of high-resolution satellites such as IKONOS and QuickBird options for detecting and monitoring vegetation parameters in heterogeneous terrain have increased. The aim of this study is to evaluate the usefulness of QuickBird derived vegetation parameters in soil erosion models for alpine sites by comparison to Cesium-137 (Cs-137) derived soil erosion estimates. The study site (67 km 2) is located in the Central Swiss Alps (Urseren Valley) and is characterised by scarce forest cover and strong anthropogenic influences due to grassland farming for centuries. A fractional vegetation cover (FVC) map for grassland and detailed land-cover maps are available from linear spectral unmixing and supervised classification of QuickBird imagery. The maps were introduced to the Pan-European Soil Erosion Risk Assessment (PESERA) model as well as to the Universal Soil Loss Equation (USLE). Regarding the latter model, the FVC was indirectly incorporated by adapting the C factor. Both models show an increase in absolute soil erosion values when FVC is considered. In contrast to USLE and the Cs-137 soil erosion rates, PESERA estimates are low. For the USLE model also the spatial patterns improved and showed "hotspots" of high erosion of up to 16 t ha -1 a -1. In conclusion field measurements of Cs-137 confirmed the improvement of soil erosion estimates using the satellite-derived vegetation data.

Influence of fracture anisotropy on ground water ages and chemistry, Valley and Ridge province, Pennsylvania

USGS Publications Warehouse

Burton, W.C.; Plummer, Niel; Busenberg, E.; Lindsey, B.D.; Gburek, W.J.

2002-01-01

Model ground water ages based on chlorofluorocarbons (CFCs) and tritium/helium-3 (3H/3He) data were obtained from two arrays of nested piezometers located on the north limb of an anticline in fractured sedimentary rocks in the Valley and Ridge geologic province of Pennsylvania. The fracture geometry of the gently east plunging fold is very regular and consists predominately of south dipping to subhorizontal to north dipping bedding-plane parting and east striking, steeply dipping axial-plane spaced cleavage. In the area of the piezometer arrays, which trend north-south on the north limb of the fold, north dipping bedding-plane parting is a more dominant fracture set than is steeply south dipping axial-plane cleavage. The dating of ground water from the piezometer arrays reveals that ground water traveling along paths parallel to the dip direction of bedding-plane parting has younger 3H/3He and CFC model ages, or a greater component of young water, than does ground water traveling along paths opposite to the dip direction. In predominantly unmixed samples there is a strong positive correlation between age of the young fraction of water and dissolved sodium concentration. The travel times inferred from the model ages are significantly longer than those previously calculated by a ground water flow model, which assumed isotropically fractured layers parallel to topography. A revised model factors in the directional anisotropy to produce longer travel times. Ground water travel times in the watershed therefore appear to be more influenced by anisotropic fracture geometry than previously realized. This could have significant implications for ground water models in other areas underlain by similarly tilted or folded sedimentary rock, such as elsewhere in the Valley and Ridge or the early Mesozoic basins.

Using dark current data to estimate AVIRIS noise covariance and improve spectral analyses

NASA Technical Reports Server (NTRS)

Boardman, Joseph W.

1995-01-01

Starting in 1994, all AVIRIS data distributions include a new product useful for quantification and modeling of the noise in the reported radiance data. The 'postcal' file contains approximately 100 lines of dark current data collected at the end of each data acquisition run. In essence this is a regular spectral-image cube, with 614 samples, 100 lines and 224 channels, collected with a closed shutter. Since there is no incident radiance signal, the recorded DN measure only the DC signal level and the noise in the system. Similar dark current measurements, made at the end of each line are used, with a 100 line moving average, to remove the DC signal offset. Therefore, the pixel-by-pixel fluctuations about the mean of this dark current image provide an excellent model for the additive noise that is present in AVIRIS reported radiance data. The 61,400 dark current spectra can be used to calculate the noise levels in each channel and the noise covariance matrix. Both of these noise parameters should be used to improve spectral processing techniques. Some processing techniques, such as spectral curve fitting, will benefit from a robust estimate of the channel-dependent noise levels. Other techniques, such as automated unmixing and classification, will be improved by the stable and scene-independence noise covariance estimate. Future imaging spectrometry systems should have a similar ability to record dark current data, permitting this noise characterization and modeling.

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Homology modeling, binding site identification and docking study of human angiotensin II type I (Ang II-AT1) receptor.

PubMed

Vyas, Vivek K; Ghate, Manjunath; Patel, Kinjal; Qureshi, Gulamnizami; Shah, Surmil

2015-08-01

Ang II-AT1 receptors play an important role in mediating virtually all of the physiological actions of Ang II. Several drugs (SARTANs) are available, which can block the AT1 receptor effectively and lower the blood pressure in the patients with hypertension. Currently, there is no experimental Ang II-AT1 structure available; therefore, in this study we modeled Ang II-AT1 receptor structure using homology modeling followed by identification and characterization of binding sites and thereby assessing druggability of the receptor. Homology models were constructed using MODELLER and I-TASSER server, refined and validated using PROCHECK in which 96.9% of 318 residues were present in the favoured regions of the Ramachandran plots. Various Ang II-AT1 receptor antagonist drugs are available in the market as antihypertensive drug, so we have performed docking study with the binding site prediction algorithms to predict different binding pockets on the modeled proteins. The identification of 3D structures and binding sites for various known drugs will guide us for the structure-based drug design of novel compounds as Ang II-AT1 receptor antagonists for the treatment of hypertension. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Spring-Loaded Model Revisited: Paramyxovirus Fusion Requires Engagement of a Receptor Binding Protein beyond Initial Triggering of the Fusion Protein▿

PubMed Central

Porotto, Matteo; DeVito, Ilaria; Palmer, Samantha G.; Jurgens, Eric M.; Yee, Jia L.; Yokoyama, Christine C.; Pessi, Antonello; Moscona, Anne

2011-01-01

During paramyxovirus entry into a host cell, receptor engagement by a specialized binding protein triggers conformational changes in the adjacent fusion protein (F), leading to fusion between the viral and cell membranes. According to the existing paradigm of paramyxovirus membrane fusion, the initial activation of F by the receptor binding protein sets off a spring-loaded mechanism whereby the F protein progresses independently through the subsequent steps in the fusion process, ending in membrane merger. For human parainfluenza virus type 3 (HPIV3), the receptor binding protein (hemagglutinin-neuraminidase [HN]) has three functions: receptor binding, receptor cleaving, and activating F. We report that continuous receptor engagement by HN activates F to advance through the series of structural rearrangements required for fusion. In contrast to the prevailing model, the role of HN-receptor engagement in the fusion process is required beyond an initiating step, i.e., it is still required even after the insertion of the fusion peptide into the target cell membrane, enabling F to mediate membrane merger. We also report that for Nipah virus, whose receptor binding protein has no receptor-cleaving activity, the continuous stimulation of the F protein by a receptor-engaged binding protein is key for fusion. We suggest a general model for paramyxovirus fusion activation in which receptor engagement plays an active role in F activation, and the continued engagement of the receptor binding protein is essential to F protein function until the onset of membrane merger. This model has broad implications for the mechanism of paramyxovirus fusion and for strategies to prevent viral entry. PMID:21976650

Spring-loaded model revisited: paramyxovirus fusion requires engagement of a receptor binding protein beyond initial triggering of the fusion protein.

PubMed

Porotto, Matteo; Devito, Ilaria; Palmer, Samantha G; Jurgens, Eric M; Yee, Jia L; Yokoyama, Christine C; Pessi, Antonello; Moscona, Anne

2011-12-01

During paramyxovirus entry into a host cell, receptor engagement by a specialized binding protein triggers conformational changes in the adjacent fusion protein (F), leading to fusion between the viral and cell membranes. According to the existing paradigm of paramyxovirus membrane fusion, the initial activation of F by the receptor binding protein sets off a spring-loaded mechanism whereby the F protein progresses independently through the subsequent steps in the fusion process, ending in membrane merger. For human parainfluenza virus type 3 (HPIV3), the receptor binding protein (hemagglutinin-neuraminidase [HN]) has three functions: receptor binding, receptor cleaving, and activating F. We report that continuous receptor engagement by HN activates F to advance through the series of structural rearrangements required for fusion. In contrast to the prevailing model, the role of HN-receptor engagement in the fusion process is required beyond an initiating step, i.e., it is still required even after the insertion of the fusion peptide into the target cell membrane, enabling F to mediate membrane merger. We also report that for Nipah virus, whose receptor binding protein has no receptor-cleaving activity, the continuous stimulation of the F protein by a receptor-engaged binding protein is key for fusion. We suggest a general model for paramyxovirus fusion activation in which receptor engagement plays an active role in F activation, and the continued engagement of the receptor binding protein is essential to F protein function until the onset of membrane merger. This model has broad implications for the mechanism of paramyxovirus fusion and for strategies to prevent viral entry.

A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist

NASA Astrophysics Data System (ADS)

Singh, Nidhi; Chevé, Gwénaël; Ferguson, David M.; McCurdy, Christopher R.

2006-08-01

Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based "agonist-bound" hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental p K i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.

Molecular modelling studies on the ORL1-receptor and ORL1-agonists

NASA Astrophysics Data System (ADS)

Bröer, Britta M.; Gurrath, Marion; Höltje, Hans-Dieter

2003-11-01

The ORL1 ( opioid receptor like 1)- receptor is a member of the family of rhodopsin-like G protein-coupled receptors (GPCR) and represents an interesting new therapeutical target since it is involved in a variety of biomedical important processes, such as anxiety, nociception, feeding, and memory. In order to shed light on the molecular basis of the interactions of the GPCR with its ligands, the receptor protein and a dataset of specific agonists were examined using molecular modelling methods. For that purpose, the conformational space of a very potent non-peptide ORL1-receptor agonist (Ro 64-6198) with a small number of rotatable bonds was analysed in order to derive a pharmacophoric arrangement. The conformational analyses yielded a conformation that served as template for the superposition of a set of related analogues. Structural superposition was achieved by employing the program FlexS. Using the experimental binding data and the superposition of the ligands, a 3D-QSAR analysis applying the GRID/GOLPE method was carried out. After the ligand-based modelling approach, a 3D model of the ORL1-receptor has been constructed using homology modelling methods based on the crystal structure of bovine rhodopsin. A representative structure of the model taken from molecular dynamics simulations was used for a manual docking procedure. Asp-130 and Thr-305 within the ORL1-receptor model served as important hydrophilic interaction partners. Furthermore, a hydrophobic cavity was identified stabilizing the agonists within their binding site. The manual docking results were supported using FlexX, which identified the same protein-ligand interaction points.

CoMFA analyses of C-2 position salvinorin A analogs at the kappa-opioid receptor provides insights into epimer selectivity.

PubMed

McGovern, Donna L; Mosier, Philip D; Roth, Bryan L; Westkaemper, Richard B

2010-04-01

The highly potent and kappa-opioid (KOP) receptor-selective hallucinogen Salvinorin A and selected analogs have been analyzed using the 3D quantitative structure-affinity relationship technique Comparative Molecular Field Analysis (CoMFA) in an effort to derive a statistically significant and predictive model of salvinorin affinity at the KOP receptor and to provide additional statistical support for the validity of previously proposed structure-based interaction models. Two CoMFA models of Salvinorin A analogs substituted at the C-2 position are presented. Separate models were developed based on the radioligand used in the kappa-opioid binding assay, [(3)H]diprenorphine or [(125)I]6 beta-iodo-3,14-dihydroxy-17-cyclopropylmethyl-4,5 alpha-epoxymorphinan ([(125)I]IOXY). For each dataset, three methods of alignment were employed: a receptor-docked alignment derived from the structure-based docking algorithm GOLD, another from the ligand-based alignment algorithm FlexS, and a rigid realignment of the poses from the receptor-docked alignment. The receptor-docked alignment produced statistically superior results compared to either the FlexS alignment or the realignment in both datasets. The [(125)I]IOXY set (Model 1) and [(3)H]diprenorphine set (Model 2) gave q(2) values of 0.592 and 0.620, respectively, using the receptor-docked alignment, and both models produced similar CoMFA contour maps that reflected the stereoelectronic features of the receptor model from which they were derived. Each model gave significantly predictive CoMFA statistics (Model 1 PSET r(2)=0.833; Model 2 PSET r(2)=0.813). Based on the CoMFA contour maps, a binding mode was proposed for amine-containing Salvinorin A analogs that provides a rationale for the observation that the beta-epimers (R-configuration) of protonated amines at the C-2 position have a higher affinity than the corresponding alpha-epimers (S-configuration). (c) 2010. Published by Elsevier Inc.

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

A combined computational and structural model of the full-length human prolactin receptor

PubMed Central

Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

2016-01-01

The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg. PMID:27174498

All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

PubMed Central

Mohammadiarani, Hossein; Vashisth, Harish

2016-01-01

The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID:27379020

Long-term responses of rainforest erosional systems at different spatial scales to selective logging and climatic change.

PubMed

Walsh, R P D; Bidin, K; Blake, W H; Chappell, N A; Clarke, M A; Douglas, I; Ghazali, R; Sayer, A M; Suhaimi, J; Tych, W; Annammala, K V

2011-11-27

Long-term (21-30 years) erosional responses of rainforest terrain in the Upper Segama catchment, Sabah, to selective logging are assessed at slope, small and large catchment scales. In the 0.44 km(2) Baru catchment, slope erosion measurements over 1990-2010 and sediment fingerprinting indicate that sediment sources 21 years after logging in 1989 are mainly road-linked, including fresh landslips and gullying of scars and toe deposits of 1994-1996 landslides. Analysis and modelling of 5-15 min stream-suspended sediment and discharge data demonstrate a reduction in storm-sediment response between 1996 and 2009, but not yet to pre-logging levels. An unmixing model using bed-sediment geochemical data indicates that 49 per cent of the 216 t km(-2) a(-1) 2009 sediment yield comes from 10 per cent of its area affected by road-linked landslides. Fallout (210)Pb and (137)Cs values from a lateral bench core indicate that sedimentation rates in the 721 km(2) Upper Segama catchment less than doubled with initially highly selective, low-slope logging in the 1980s, but rose 7-13 times when steep terrain was logged in 1992-1993 and 1999-2000. The need to keep steeplands under forest is emphasized if landsliding associated with current and predicted rises in extreme rainstorm magnitude-frequency is to be reduced in scale.

Mapping invasive species and spectral mixture relationships with neotropical woody formations in southeastern Brazil

NASA Astrophysics Data System (ADS)

Amaral, Cibele H.; Roberts, Dar A.; Almeida, Teodoro I. R.; Souza Filho, Carlos R.

2015-10-01

Biological invasion substantially contributes to the increasing extinction rates of native vegetative species. The remote detection and mapping of invasive species is critical for environmental monitoring. This study aims to assess the performance of a Multiple Endmember Spectral Mixture Analysis (MESMA) applied to imaging spectroscopy data for mapping Dendrocalamus sp. (bamboo) and Pinus elliottii L. (slash pine), which are invasive plant species, in a Brazilian neotropical landscape within the tropical Brazilian savanna biome. The work also investigates the spectral mixture between these exotic species and the native woody formations, including woodland savanna, submontane and alluvial seasonal semideciduous forests (SSF). Visible to Shortwave Infrared (VSWIR) imaging spectroscopy data at one-meter spatial resolution were atmospherically corrected and subset into the different spectral ranges (VIS-NIR1: 530-919 nm; and NIR2-SWIR: 1141-2352 nm). The data were further normalized via continuum removal (CR). Multiple endmember selection methods, including Interactive Endmember Selection (IES), Endmember average root mean square error (EAR), Minimum average spectral angle (MASA) and Count-based (CoB) (collectively called EMC), were employed to create endmember libraries for the targeted vegetation classes. The performance of the MESMA was assessed at the pixel and crown scales. Statistically significant differences (α = 0.05) were observed between overall accuracies that were obtained at various spectral ranges. The infrared region (IR) was critical for detecting the vegetation classes using spectral data. The invasive species endmembers exhibited spectral patterns in the IR that were not observed in the native formations. Bamboo was characterized as having a high green vegetation (GV) fraction, lower non-photosynthetic vegetation (NPV) and a low shade fraction, while pine exhibited higher NPV and shade fractions. The invasive species showed a statistically significant larger number of spectra erroneously assigned to the woodland savanna class versus the alluvial and submontane SSF classes. Consequently, the invasive species tended to be overestimated, especially in the woodland savanna. Bamboo was best classified using the VSWIR(CR) data with the EMC endmember selection method (User's accuracy and Producer's accuracy = 98.11% and 72.22%, respectively). Pine was best classified using NIR2-SWIR(CR) data with the IES selected endmembers (97.06% and 62.26%, respectively). The results obtained during the two-endmember modeling were fully translated into the three-endmember unmixed images. The sub-pixel invasive species abundance analysis showed that MESMA performs well when unmixing at the pixel scale and for mapping invasive species fractions in a complex neotropical environment, at pixel and crown scales with 1-m spatial resolution data.

Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics

PubMed Central

Shankaran, Harish; Zhang, Yi; Chrisler, William B.; Ewald, Jonathan A.; Wiley, H. Steven; Resat, Haluk

2012-01-01

The epidermal growth factor receptor (EGFR) belongs to the ErbB family of receptor tyrosine kinases, and controls a diverse set of cellular responses relevant to development and tumorigenesis. ErbB activation is a complex process involving receptor-ligand binding, receptor dimerization, phosphorylation, and trafficking (internalization, recycling and degradation), which together dictate the spatio-temporal distribution of active receptors within the cell. The ability to predict this distribution, and elucidation of the factors regulating it, would help to establish a mechanistic link between ErbB expression levels and the cellular response. Towards this end, we constructed mathematical models to determine the contributions of receptor dimerization and phosphorylation to EGFR activation, and to examine the dependence of these processes on sub-cellular location. We collected experimental datasets for EGFR activation dynamics in human mammary epithelial cells, with the specific goal of model parameterization, and used the data to estimate parameters for several alternate models. Model-based analysis indicated that: 1) signal termination via receptor dephosphorylation in late endosomes, prior to degradation, is an important component of the response, 2) less than 40% of the receptors in the cell are phosphorylated at any given time, even at saturating ligand doses, and 3) receptor phosphorylation kinetics at the cell surface and early endosomes are comparable. We validated the last finding by measuring the EGFR dephosphorylation rates at various times following ligand addition both in whole cells and in endosomes using ELISAs and fluorescent imaging. Overall, our results provide important information on how EGFR phosphorylation levels are regulated within cells. This study demonstrates that an iterative cycle of experiments and modeling can be used to gain mechanistic insight regarding complex cell signaling networks. PMID:22952062

Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

NASA Astrophysics Data System (ADS)

Sippl, Wolfgang

2000-08-01

One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient ( r 2 = 0.617, q 2 LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained ( r 2 = 0.991, q 2 LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

The innovative concept of three-dimensional hybrid receptor modeling

NASA Astrophysics Data System (ADS)

Stojić, A.; Stanišić Stojić, S.

2017-09-01

The aim of this study was to improve the current understanding of air pollution transport processes at regional and long-range scale. For this purpose, three-dimensional (3D) potential source contribution function and concentration weighted trajectory models, as well as new hybrid receptor model, concentration weighted boundary layer (CWBL), which uses a two-dimensional grid and a planetary boundary layer height as a frame of reference, are presented. The refined approach to hybrid receptor modeling has two advantages. At first, it considers whether each trajectory endpoint meets the inclusion criteria based on planetary boundary layer height, which is expected to provide a more realistic representation of the spatial distribution of emission sources and pollutant transport pathways. Secondly, it includes pollutant time series preprocessing to make hybrid receptor models more applicable for suburban and urban locations. The 3D hybrid receptor models presented herein are designed to identify altitude distribution of potential sources, whereas CWBL can be used for analyzing the vertical distribution of pollutant concentrations along the transport pathway.

Quantitative comparison between full-spectrum and filter-based imaging in hyperspectral fluorescence microscopy

PubMed Central

GAO, L.; HAGEN, N.; TKACZYK, T.S.

2012-01-01

Summary We implement a filterless illumination scheme on a hyperspectral fluorescence microscope to achieve full-range spectral imaging. The microscope employs polarisation filtering, spatial filtering and spectral unmixing filtering to replace the role of traditional filters. Quantitative comparisons between full-spectrum and filter-based microscopy are provided in the context of signal dynamic range and accuracy of measured fluorophores’ emission spectra. To show potential applications, a five-colour cell immunofluorescence imaging experiment is theoretically simulated. Simulation results indicate that the use of proposed full-spectrum imaging technique may result in three times improvement in signal dynamic range compared to that can be achieved in the filter-based imaging. PMID:22356127

Edge Diffusion Flame Propagation and Stabilization Studied

NASA Technical Reports Server (NTRS)

Takahashi, Fumiaki; Katta, Viswanath R.

2004-01-01

In most practical combustion systems or fires, fuel and air are initially unmixed, thus forming diffusion flames. As a result of flame-surface interactions, the diffusion flame often forms an edge, which may attach to burner walls, spread over condensed fuel surfaces, jump to another location through the fuel-air mixture formed, or extinguish by destabilization (blowoff). Flame holding in combustors is necessary to achieve design performance and safe operation of the system. Fires aboard spacecraft behave differently from those on Earth because of the absence of buoyancy in microgravity. This ongoing in-house flame-stability research at the NASA Glenn Research Center is important in spacecraft fire safety and Earth-bound combustion systems.

Hyperspectral light sheet microscopy

NASA Astrophysics Data System (ADS)

Jahr, Wiebke; Schmid, Benjamin; Schmied, Christopher; Fahrbach, Florian O.; Huisken, Jan

2015-09-01

To study the development and interactions of cells and tissues, multiple fluorescent markers need to be imaged efficiently in a single living organism. Instead of acquiring individual colours sequentially with filters, we created a platform based on line-scanning light sheet microscopy to record the entire spectrum for each pixel in a three-dimensional volume. We evaluated data sets with varying spectral sampling and determined the optimal channel width to be around 5 nm. With the help of these data sets, we show that our setup outperforms filter-based approaches with regard to image quality and discrimination of fluorophores. By spectral unmixing we resolved overlapping fluorophores with up to nanometre resolution and removed autofluorescence in zebrafish and fruit fly embryos.

Hyperspectral light sheet microscopy.

PubMed

Jahr, Wiebke; Schmid, Benjamin; Schmied, Christopher; Fahrbach, Florian O; Huisken, Jan

2015-09-02

To study the development and interactions of cells and tissues, multiple fluorescent markers need to be imaged efficiently in a single living organism. Instead of acquiring individual colours sequentially with filters, we created a platform based on line-scanning light sheet microscopy to record the entire spectrum for each pixel in a three-dimensional volume. We evaluated data sets with varying spectral sampling and determined the optimal channel width to be around 5 nm. With the help of these data sets, we show that our setup outperforms filter-based approaches with regard to image quality and discrimination of fluorophores. By spectral unmixing we resolved overlapping fluorophores with up to nanometre resolution and removed autofluorescence in zebrafish and fruit fly embryos.

Local coexistence of VO 2 phases revealed by deep data analysis

DOE PAGES

Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; ...

2016-07-07

We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO 2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffermore » from information misinterpretation due to low resolving power.« less

Generalized paired-agent kinetic model for in vivo quantification of cancer cell-surface receptors under receptor saturation conditions

NASA Astrophysics Data System (ADS)

Sadeghipour, N.; Davis, S. C.; Tichauer, K. M.

2017-01-01

New precision medicine drugs oftentimes act through binding to specific cell-surface cancer receptors, and thus their efficacy is highly dependent on the availability of those receptors and the receptor concentration per cell. Paired-agent molecular imaging can provide quantitative information on receptor status in vivo, especially in tumor tissue; however, to date, published approaches to paired-agent quantitative imaging require that only ‘trace’ levels of imaging agent exist compared to receptor concentration. This strict requirement may limit applicability, particularly in drug binding studies, which seek to report on a biological effect in response to saturating receptors with a drug moiety. To extend the regime over which paired-agent imaging may be used, this work presents a generalized simplified reference tissue model (GSRTM) for paired-agent imaging developed to approximate receptor concentration in both non-receptor-saturated and receptor-saturated conditions. Extensive simulation studies show that tumor receptor concentration estimates recovered using the GSRTM are more accurate in receptor-saturation conditions than the standard simple reference tissue model (SRTM) (% error (mean  ±  sd): GSRTM 0  ±  1 and SRTM 50  ±  1) and match the SRTM accuracy in non-saturated conditions (% error (mean  ±  sd): GSRTM 5  ±  5 and SRTM 0  ±  5). To further test the approach, GSRTM-estimated receptor concentration was compared to SRTM-estimated values extracted from tumor xenograft in vivo mouse model data. The GSRTM estimates were observed to deviate from the SRTM in tumors with low receptor saturation (which are likely in a saturated regime). Finally, a general ‘rule-of-thumb’ algorithm is presented to estimate the expected level of receptor saturation that would be achieved in a given tissue provided dose and pharmacokinetic information about the drug or imaging agent being used, and physiological information about the tissue. These studies suggest that the GSRTM is necessary when receptor saturation exceeds 20% and highlight the potential for GSRTM to accurately measure receptor concentrations under saturation conditions, such as might be required during high dose drug studies, or for imaging applications where high concentrations of imaging agent are required to optimize signal-to-noise conditions. This model can also be applied to PET and SPECT imaging studies that tend to suffer from noisier data, but require one less parameter to fit if images are converted to imaging agent concentration (quantitative PET/SPECT).

An assessment of the effects of serotonin 6 (5-HT6) receptor antagonists in rodent models of learning.

PubMed

Lindner, Mark D; Hodges, Donald B; Hogan, John B; Orie, Anitra F; Corsa, Jason A; Barten, Donna M; Polson, Craig; Robertson, Barbara J; Guss, Valerie L; Gillman, Kevin W; Starrett, John E; Gribkoff, Valentin K

2003-11-01

Antagonists of serotonin 6 (5-HT6) receptors have been reported to enhance cognition in animal models of learning, although this finding has not been universal. We have assessed the therapeutic potential of the specific 5-HT6 receptor antagonists 4-amino-N-(2,6-bis-methylamino-pyrimidin-4-yl)-benzenesulfonamide (Ro 04-6790) and 5-chloro-N-(4-methoxy-3-piperazin-1-yl-phenyl)-3-methyl-2-benzothiophenesulfonamide (SB-271046) in rodent models of cognitive function. Although mice express the 5-HT6 receptor and the function of this receptor has been investigated in mice, all reports of activity with 5-HT6 receptor antagonists have used rat models. In the present study, receptor binding revealed that the pharmacological properties of the mouse receptor are different from the rat and human receptor: Ro 04-6790 does not bind to the mouse 5-HT6 receptor, so all in vivo testing included in the present report was conducted in rats. We replicated previous reports that 5-HT6 receptor antagonists produce a stretching syndrome previously shown to be mediated through cholinergic mechanisms, but Ro 04-6790 and SB-271046 failed to attenuate scopolamine-induced deficits in a test of contextual fear conditioning. We also failed to replicate the significant effects reported previously in both an autoshaping task and in a version of the Morris water maze. The results of our experiments are not consistent with previous reports that suggested that 5-HT6 antagonists might have therapeutic potential for cognitive disorders.

Melanocortin MC1 receptor in human genetics and model systems

PubMed Central

Beaumont, Kimberley A.; Wong, Shu S.; Ainger, Stephen A.; Liu, Yan Yan; Patel, Mira P.; Millhauser, Glenn L.; Smith, Jennifer J.; Alewood, Paul F.; Leonard, J. Helen; Sturm, Richard A.

2011-01-01

The melanocortin MC1 receptor is a G -protein coupled receptor expressed in melanocytes of the skin and hair and is known for its key role in regulation of human pigmentation. Melanocortin MC1 receptor activation after ultraviolet radiation exposure results in a switch from the red/yellow pheomelanin to the brown/black eumelanin pigment synthesis within cutaneous melanocytes; this pigment is then transferred to the surrounding keratinocytes of the skin. The increase in melanin maturation and uptake results in tanning of the skin, providing a physical protection of skin cells from ultraviolet radiation induced DNA damage. Melanocortin MC 1 receptor polymorphism is widespread within the Caucasian population and some variant alleles are associated with red hair colour, fair skin, poor tanning and increased risk of skin cancer. Here we will discuss the use of mouse coat colour models, human genetic association studies, and in vitro cell culture studies to determine the complex functions of the melanocortin MC1 receptor and the molecular mechanisms underlying the association between melanocortin MC1 receptor variant alleles and the red hair colour phenotype. Recent research indicates that melanocortin MC1 receptor has many non-pigmentary functions, and that the increased risk of skin cancer conferred by melanocortin MC1 receptor variant alleles is to some extent independent of pigmentation phenotypes. The use of new transgenic mouse models, the study of novel melanocortin MC1 receptor response genes and the use of more advanced human skin models such as 3D skin reconstruction may provide key elements in understanding the pharmacogenetics of human melanocortin MC1 receptor polymorphism . PMID:21199646

They Came from the Deep in the Supernova: The Origin of TiC and Metal Subgrains in Presolar Graphite Grains

NASA Astrophysics Data System (ADS)

Lodders, Katharina

2006-08-01

A new formation scenario for TiC and Fe-Ni metal inclusions in presolar graphite grains of supernova origin is described. The mineralogy and chemistry require condensation of Fe-Ni titanides from Fe-, Ni-, and Ti-rich gaseous ejecta, subsequent carburization to make TiC and metal, and encapsulation into graphite. Titanides only condense if Si is depleted relative to heavier elements, which requires α-rich freeze-out and a deep mass cut for the supernova ejecta. This Si-poor core material must remain unmixed with other supernova zones until the titanides condense. This can be accomplished by transport of core ejecta in bipolar jets through the major expanding supernova zone ejecta. If the jets stall in regions dominated by C-rich ejecta such as the C-He zone, where graphite condenses, thermochemically favored in situ carburization of the titanides-either before or during encapsulation into condensing graphite-leads to a TiC-and-metal composite. This scenario agrees with theoretical models and observations of asymmetric core collapse in supernovae that are associated with bipolar jets loaded with iron-peak elements.

In situ measurement of magnesium carbonate formation from CO2 using static high-pressure and -temperature 13C NMR.

PubMed

Surface, J Andrew; Skemer, Philip; Hayes, Sophia E; Conradi, Mark S

2013-01-02

We explore a new in situ NMR spectroscopy method that possesses the ability to monitor the chemical evolution of supercritical CO(2) in relevant conditions for geological CO(2) sequestration. As a model, we use the fast reaction of the mineral brucite, Mg(OH)(2), with supercritical CO(2) (88 bar) in aqueous conditions at 80 °C. The in situ conversion of CO(2) into metastable and stable carbonates is observed throughout the reaction. After more than 58 h of reaction, the sample was depressurized and analyzed using in situ Raman spectroscopy, where the laser was focused on the undisturbed products through the glass reaction tube. Postreaction, ex situ analysis was performed on the extracted and dried products using Raman spectroscopy, powder X-ray diffraction, and magic-angle spinning (1)H-decoupled (13)C NMR. These separate methods of analysis confirmed a spatial dependence of products, possibly caused by a gradient of reactant availability, pH, and/or a reaction mechanism that involves first forming hydroxy-hydrated (basic, hydrated) carbonates that convert to the end-product, anhydrous magnesite. This carbonation reaction illustrates the importance of static (unmixed) reaction systems at sequestration-like conditions.

Unmixing the Galactic halo with RR Lyrae tagging

NASA Astrophysics Data System (ADS)

Belokurov, V.; Deason, A. J.; Koposov, S. E.; Catelan, M.; Erkal, D.; Drake, A. J.; Evans, N. W.

2018-06-01

We show that tagging RR Lyrae stars according to their location in the period-amplitude diagram can be used to shed light on the genesis of the Galactic stellar halo. The mixture of RR Lyrae of ab type, separated into classes along the lines suggested by Oosterhoff, displays a strong and coherent evolution with Galactocentric radius. The change in the RR Lyrae composition appears to coincide with the break in the halo's radial density profile at ˜25 kpc. Using simple models of the stellar halo, we establish that at least three different types of accretion events are necessary to explain the observed RRab behaviour. Given that there exists a correlation between the RRab class fraction and the total stellar content of a dwarf satellite, we hypothesize that the field halo RRab composition is controlled by the mass of the progenitor contributing the bulk of the stellar debris at the given radius. This idea is tested against a suite of cosmological zoom-in simulations of Milky Way-like stellar halo formation. Finally, we study some of the most prominent stellar streams in the Milky Way halo and demonstrate that their RRab class fractions follow the trends established previously.

A competitive binding model predicts the response of mammalian olfactory receptors to mixtures

NASA Astrophysics Data System (ADS)

Singh, Vijay; Murphy, Nicolle; Mainland, Joel; Balasubramanian, Vijay

Most natural odors are complex mixtures of many odorants, but due to the large number of possible mixtures only a small fraction can be studied experimentally. To get a realistic understanding of the olfactory system we need methods to predict responses to complex mixtures from single odorant responses. Focusing on mammalian olfactory receptors (ORs in mouse and human), we propose a simple biophysical model for odor-receptor interactions where only one odor molecule can bind to a receptor at a time. The resulting competition for occupancy of the receptor accounts for the experimentally observed nonlinear mixture responses. We first fit a dose-response relationship to individual odor responses and then use those parameters in a competitive binding model to predict mixture responses. With no additional parameters, the model predicts responses of 15 (of 18 tested) receptors to within 10 - 30 % of the observed values, for mixtures with 2, 3 and 12 odorants chosen from a panel of 30. Extensions of our basic model with odorant interactions lead to additional nonlinearities observed in mixture response like suppression, cooperativity, and overshadowing. Our model provides a systematic framework for characterizing and parameterizing such mixing nonlinearities from mixture response data.

Modelling and simulation of biased agonism dynamics at a G protein-coupled receptor.

PubMed

Bridge, L J; Mead, J; Frattini, E; Winfield, I; Ladds, G

2018-04-07

Theoretical models of G protein-coupled receptor (GPCR) concentration-response relationships often assume an agonist producing a single functional response via a single active state of the receptor. These models have largely been analysed assuming steady-state conditions. There is now much experimental evidence to suggest that many GPCRs can exist in multiple receptor conformations and elicit numerous functional responses, with ligands having the potential to activate different signalling pathways to varying extents-a concept referred to as biased agonism, functional selectivity or pluri-dimensional efficacy. Moreover, recent experimental results indicate a clear possibility for time-dependent bias, whereby an agonist's bias with respect to different pathways may vary dynamically. Efforts towards understanding the implications of temporal bias by characterising and quantifying ligand effects on multiple pathways will clearly be aided by extending current equilibrium binding and biased activation models to include G protein activation dynamics. Here, we present a new model of time-dependent biased agonism, based on ordinary differential equations for multiple cubic ternary complex activation models with G protein cycle dynamics. This model allows simulation and analysis of multi-pathway activation bias dynamics at a single receptor for the first time, at the level of active G protein (α GTP ), towards the analysis of dynamic functional responses. The model is generally applicable to systems with N G G proteins and N* active receptor states. Numerical simulations for N G =N * =2 reveal new insights into the effects of system parameters (including cooperativities, and ligand and receptor concentrations) on bias dynamics, highlighting new phenomena including the dynamic inter-conversion of bias direction. Further, we fit this model to 'wet' experimental data for two competing G proteins (G i and G s ) that become activated upon stimulation of the adenosine A 1 receptor with adenosine derivative compounds. Finally, we show that our model can qualitatively describe the temporal dynamics of this competing G protein activation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

An Allosteric Coagonist Model for Propofol Effects on α1β2γ2L γ-Aminobutyric Acid Type A Receptors

PubMed Central

Ruesch, Dirk; Neumann, Elena; Wulf, Hinnerk; Forman, Stuart A.

2011-01-01

Background Propofol produces its major actions via γ-aminobutyric acid type A (GABAA) receptors. At low concentrations, propofol enhances agonist-stimulated GABAA receptor activity, and high propofol concentrations directly activate receptors. Etomidate produces similar effects, and there is convincing evidence that a single class of etomidate sites mediate both agonist modulation and direct GABAA receptor activation. It is unknown if the propofol binding site(s) on GABAA receptors that modulate agonist-induced activity also mediate direct activation. Methods GABAA α1β2γ2L receptors were heterologously expressed in Xenopus oocytes and activity was quantified using voltage clamp electrophysiology. We tested whether propofol and etomidate display the same linkage between agonist modulation and direct activation of GABAA receptors by identifying equi-efficacious drug solutions for direct activation. We then determined whether these drug solutions produce equal modulation of GABA-induced receptor activity. We also measured propofol-dependent direct activation and modulation of low GABA responses. Allosteric coagonist models similar to that established for etomidate, but with variable numbers of propofol sites, were fitted to combined data. Results Solutions of 19 μM propofol and 10 μM etomidate were found to equally activate GABAA receptors. These two drug solutions also produced indistinguishable modulation of GABA-induced receptor activity. Combined electrophysiological data behaved in a manner consistent with allosteric co-agonist models with more than one propofol site. The best fit was observed when the model assumed three equivalent propofol sites. Conclusions Our results support the hypothesis that propofol, like etomidate, acts at GABAA receptor sites mediating both GABA modulation and direct activation. PMID:22104494

Aeolian sand as a tool for understanding Mars: Thermal infrared remote sensing of volcaniclastic Mars-analog sand dunes in Christmas Lake Valley, Oregon, U.S.A.

NASA Astrophysics Data System (ADS)

Edgett, Kenneth S.

1996-10-01

INTRODUCTION: On Earth, aeolian sand dunes are used as tools of scientific inquiry. Holocene and Pleistocene dunes preserve clues about Quaternary climate variations and human activities ranging from Ice Age hunting practices to Twentieth Century warfare. Modern dunes contain the sedimentary textures and structures necessary for interpreting ancient sandstones, and they provide natural laboratories for investigation of aeolian physics and desertification processes. The dunes of Mars can likewise be used as scientific tools. Dunes provide relatively dust-free surfaces. From a remote sensing perspective, martian dunes have much potential for providing clues about surface mineralogy and the interaction between the surface and atmosphere. Such information can in turn provide insights regarding crust composition, volcanic evolution, present and past climate events, and perhaps weathering rates. The Mars Global Surveyor Thermal Emission Spectrometer (TES) is expected to reach the planet in September 1997. TES will provide 6 to 50 micrometer spectra of the martian surface at ground resolutions of 3 to 9 km. Sandy aeolian environments on Mars might provide key information about bedrock composition. To prepare for the TES investigation, I have been examining a thermal infrared image of a Mars-composition analog dune field in Christmas Lake Valley, Oregon. COMPOSITION AND GEOLOGIC SETTING: The "Shifting Sand Dunes" dune field is located at the eastern end of Christmas Lake Valley, in what was once the Pleistocene Fort Rock Lake [1]. Much of the sand that makes up the Shifting Sand Dunes dune field is reworked Mt. Mazama airfall from its terminal eruption 6,800 years ago, plus material deflated from the lake bed [1, 2]. The main constituents of the dunes are volcanic glass and devitrified glass fragments, plagioclase crystals, basalt lithic fragments, aggregates of silt and clay-size volcanic ash, pyroxenes, opaque oxide minerals (mostly magnetite), and trace occurrences of fossil fragments and other minerals [3]. THERMAL INFRARED IMAGE: The thermal infrared images used in this study was obtained by the NASA Ames Research Center C-130 Earth Resources airborne Thermal Infrared Multispectral Scanner (TIMS) on 21 September 1991. The image has 6 spectral bands between 8 and 12 micrometers and a ground resolution of 9 m/pixel. The raw image was converted to calibrated radiance, from which normalized emittance was computed for each of the six bands, following the method of Realmutto [4]. Atmospheric effects were corrected using an empirical method described by Edgett and Anderson [5]. The resulting 6-band image provides quantitative determination of the surface emissivity. Dune spectra in the image match spectra obtained in our laboratory using samples collected from the field area [3, 5]. ACTIVE DUNES, INACTIVE DUNES, AND INTERDUNE AREAS FROM EMISSIVITY VARIATION: This study shows that in a modern dune field, the location of active dunes, interdune surfaces, and inactive dunes can be mapped using emissivity in the thermal infrared band that shows the most spectral variation [6]. In this case, TIMS band 3 (9.2 micrometers) had the most variation, although the entire emissivity range was only from 0.89 to 1.0. Active dunes had the lowest emissivities (0.89 to 0.91), inactive dunes were distinguished by higher emissivities (.094 to 1.0), and interdune surfaces had intermediate values (0.90 to 0.95). These emissivity variations result from differences in particle size, as inactive dunes tend to have finer-grained silt and dust on them. LINEAR UNMIXING USING IMAGE ENDMEMBERS: Quantitative estimates of thermal infrared spectral emissivity are ideally suited to unmixing analysis. For grains larger than the wavelength (e.g., dune sand), a linear unmixing approach provides geologically useful results [7]. In the present study, image endmembers were selected for a preliminary unmixing study: (1) "regular sand," which contains nearly 50% plagioclase and nearly 20% volcanic glass; (2) "dark sand, which consists mainly of basalt clasts (> 25%) and glass (> 30%); (3) "mud chips," which are volcanic ash aggregates broken into sand-sized pieces, (4) sagebrush and grass; and (5) thick vegetation, such as an alfalfa farm near the dunes. The most important result of this preliminary unmixing work is an image that shows the distribution of ash aggregates and "dark sand," both of which vary throughout the dune field as a function of proximity to the source. The volcanic ash aggregates, in particular, are locally eroded from a layer that caps the Pleistocene lake beds that underlie the dunes [3]. SUMMARY: This study highlights the use of thermal infrared spectra to map local contributions of sand to a dune field, and to distinguish active versus inactive dune fields. Mapping of local contributions to active dune fields on Mars using TES or other multispectral images has potential to provide indications of local bedrock composition. REFERENCES: [1] Allison, I. S. (1979) Oregon Dept. Geol. Minl. Res. Spec. Pap. 7. [2] Dole, H. M. (1942) M.S. Thesis, Oregon State, Corvallis, Or. [3] Edgett, K. S. (1994) in Ph.D. Diss., pp. 145-201, Arizona State, Tempe, AZ. [4] Realmutto, V. J. (1990) in JPL Publ. 90-55, pp. 31-35. [5] Edgett, K. S., and D. L. Anderson (1995) in JPL Publ. 95-1, v. 2, pp. 9-12. [6] Edgett, K. S. et al. (1995) in JPL Publ. 95-1, v. 2, pp. 13-16. [7] Ramsey, M. S. (1996) Ph.D. Diss, Arizona State, Tempe, AZ.

Molecular modeling of ligand-receptor interactions in the OR5 olfactory receptor.

PubMed

Singer, M S; Shepherd, G M

1994-06-02

Olfactory receptors belong to the superfamily of seven transmembrane domain, G protein-coupled receptors. In order to begin analysis of mechanisms of receptor activation, a computer model of the OR5 olfactory receptor has been constructed and compared with other members of this superfamily. We have tested docking of the odor molecule lyral, which is known to activate the OR5 receptor. The results point to specific ligand-binding residues on helices III through VII that form a binding pocket in the receptor. Some of these residues occupy sequence positions identical to ligand-binding residues conserved among other superfamily members. The results provide new insights into possible molecular mechanisms of odor recognition and suggest hypotheses to guide future experimental studies using site-directed mutagenesis.

The heterodimeric sweet taste receptor has multiple potential ligand binding sites.

PubMed

Cui, Meng; Jiang, Peihua; Maillet, Emeline; Max, Marianna; Margolskee, Robert F; Osman, Roman

2006-01-01

The sweet taste receptor is a heterodimer of two G protein coupled receptors, T1R2 and T1R3. This discovery has increased our understanding at the molecular level of the mechanisms underlying sweet taste. Previous experimental studies using sweet receptor chimeras and mutants show that there are at least three potential binding sites in this heterodimeric receptor. Receptor activity toward the artificial sweeteners aspartame and neotame depends on residues in the amino terminal domain of human T1R2. In contrast, receptor activity toward the sweetener cyclamate and the sweet taste inhibitor lactisole depends on residues within the transmembrane domain of human T1R3. Furthermore, receptor activity toward the sweet protein brazzein depends on the cysteine rich domain of human T1R3. Although crystal structures are not available for the sweet taste receptor, useful homology models can be developed based on appropriate templates. The amino terminal domain, cysteine rich domain and transmembrane helix domain of T1R2 and T1R3 have been modeled based on the crystal structures of metabotropic glutamate receptor type 1, tumor necrosis factor receptor, and bovine rhodopsin, respectively. We have used homology models of the sweet taste receptors, molecular docking of sweet ligands to the receptors, and site-directed mutagenesis of the receptors to identify potential ligand binding sites of the sweet taste receptor. These studies have led to a better understanding of the structure and function of this heterodimeric receptor, and can act as a guide for rational structure-based design of novel non-caloric sweeteners, which can be used in the fighting against obesity and diabetes.

Quantitative in vivo receptor binding. III. Tracer kinetic modeling of muscarinic cholinergic receptor binding

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

Frey, K.A.; Hichwa, R.D.; Ehrenkaufer, R.L.

1985-10-01

A tracer kinetic method is developed for the in vivo estimation of high-affinity radioligand binding to central nervous system receptors. Ligand is considered to exist in three brain pools corresponding to free, nonspecifically bound, and specifically bound tracer. These environments, in addition to that of intravascular tracer, are interrelated by a compartmental model of in vivo ligand distribution. A mathematical description of the model is derived, which allows determination of regional blood-brain barrier permeability, nonspecific binding, the rate of receptor-ligand association, and the rate of dissociation of bound ligand, from the time courses of arterial blood and tissue tracer concentrations.more » The term ''free receptor density'' is introduced to describe the receptor population measured by this method. The technique is applied to the in vivo determination of regional muscarinic acetylcholine receptors in the rat, with the use of (TH)scopolamine. Kinetic estimates of free muscarinic receptor density are in general agreement with binding capacities obtained from previous in vivo and in vitro equilibrium binding studies. In the striatum, however, kinetic estimates of free receptor density are less than those in the neocortex--a reversal of the rank ordering of these regions derived from equilibrium determinations. A simplified model is presented that is applicable to tracers that do not readily dissociate from specific binding sites during the experimental period.« less

The neuropsychopharmacology of phencyclidine: from NMDA receptor hypofunction to the dopamine hypothesis of schizophrenia.

PubMed

Jentsch, J D; Roth, R H

1999-03-01

Administration of noncompetitive NMDA/glutamate receptor antagonists, such as phencyclidine (PCP) and ketamine, to humans induces a broad range of schizophrenic-like symptomatology, findings that have contributed to a hypoglutamatergic hypothesis of schizophrenia. Moreover, a history of experimental investigations of the effects of these drugs in animals suggests that NMDA receptor antagonists may model some behavioral symptoms of schizophrenia in nonhuman subjects. In this review, the usefulness of PCP administration as a potential animal model of schizophrenia is considered. To support the contention that NMDA receptor antagonist administration represents a viable model of schizophrenia, the behavioral and neurobiological effects of these drugs are discussed, especially with regard to differing profiles following single-dose and long-term exposure. The neurochemical effects of NMDA receptor antagonist administration are argued to support a neurobiological hypothesis of schizophrenia, which includes pathophysiology within several neurotransmitter systems, manifested in behavioral pathology. Future directions for the application of NMDA receptor antagonist models of schizophrenia to preclinical and pathophysiological research are offered.

Constrained positive matrix factorization: Elemental ratios, spatial distinction, and chemical transport model source contributions

NASA Astrophysics Data System (ADS)

Sturtz, Timothy M.

Source apportionment models attempt to untangle the relationship between pollution sources and the impacts at downwind receptors. Two frameworks of source apportionment models exist: source-oriented and receptor-oriented. Source based apportionment models use presumed emissions and atmospheric processes to estimate the downwind source contributions. Conversely, receptor based models leverage speciated concentration data from downwind receptors and apply statistical methods to predict source contributions. Integration of both source-oriented and receptor-oriented models could lead to a better understanding of the implications sources have on the environment and society. The research presented here investigated three different types of constraints applied to the Positive Matrix Factorization (PMF) receptor model within the framework of the Multilinear Engine (ME-2): element ratio constraints, spatial separation constraints, and chemical transport model (CTM) source attribution constraints. PM10-2.5 mass and trace element concentrations were measured in Winston-Salem, Chicago, and St. Paul at up to 60 sites per city during two different seasons in 2010. PMF was used to explore the underlying sources of variability. Information on previously reported PM10-2.5 tire and brake wear profiles were used to constrain these features in PMF by prior specification of selected species ratios. We also modified PMF to allow for combining the measurements from all three cities into a single model while preserving city-specific soil features. Relatively minor differences were observed between model predictions with and without the prior ratio constraints, increasing confidence in our ability to identify separate brake wear and tire wear features. Using separate data, source contributions to total fine particle carbon predicted by a CTM were incorporated into the PMF receptor model to form a receptor-oriented hybrid model. The level of influence of the CTM versus traditional PMF was varied using a weighting parameter applied to an object function as implemented in ME-2. The resulting hybrid model was used to quantify the contributions of total carbon from both wildfires and biogenic sources at two Interagency Monitoring of Protected Visual Environment monitoring sites, Monture and Sula Peak, Montana, from 2006 through 2008.

Nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates of typical desert vegetation in western China.

PubMed

Ji, Cuicui; Jia, Yonghong; Gao, Zhihai; Wei, Huaidong; Li, Xiaosong

2017-01-01

Desert vegetation plays significant roles in securing the ecological integrity of oasis ecosystems in western China. Timely monitoring of photosynthetic/non-photosynthetic desert vegetation cover is necessary to guide management practices on land desertification and research into the mechanisms driving vegetation recession. In this study, nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates are investigated through comparing the performance of linear and nonlinear spectral mixture models with different endmembers applied to field spectral measurements of two types of typical desert vegetation, namely, Nitraria shrubs and Haloxylon. The main results were as follows. (1) The correct selection of endmembers is important for improving the accuracy of vegetation cover estimates, and in particular, shadow endmembers cannot be neglected. (2) For both the Nitraria shrubs and Haloxylon, the Kernel-based Nonlinear Spectral Mixture Model (KNSMM) with nonlinear parameters was the best unmixing model. In consideration of the computational complexity and accuracy requirements, the Linear Spectral Mixture Model (LSMM) could be adopted for Nitraria shrubs plots, but this will result in significant errors for the Haloxylon plots since the nonlinear spectral mixture effects were more obvious for this vegetation type. (3) The vegetation canopy structure (planophile or erectophile) determines the strength of the nonlinear spectral mixture effects. Therefore, no matter for Nitraria shrubs or Haloxylon, the non-linear spectral mixing effects between the photosynthetic / non-photosynthetic vegetation and the bare soil do exist, and its strength is dependent on the three-dimensional structure of the vegetation canopy. The choice of linear or nonlinear spectral mixture models is up to the consideration of computational complexity and the accuracy requirement.

Nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates of typical desert vegetation in western China

PubMed Central

Jia, Yonghong; Gao, Zhihai; Wei, Huaidong

2017-01-01

Desert vegetation plays significant roles in securing the ecological integrity of oasis ecosystems in western China. Timely monitoring of photosynthetic/non-photosynthetic desert vegetation cover is necessary to guide management practices on land desertification and research into the mechanisms driving vegetation recession. In this study, nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates are investigated through comparing the performance of linear and nonlinear spectral mixture models with different endmembers applied to field spectral measurements of two types of typical desert vegetation, namely, Nitraria shrubs and Haloxylon. The main results were as follows. (1) The correct selection of endmembers is important for improving the accuracy of vegetation cover estimates, and in particular, shadow endmembers cannot be neglected. (2) For both the Nitraria shrubs and Haloxylon, the Kernel-based Nonlinear Spectral Mixture Model (KNSMM) with nonlinear parameters was the best unmixing model. In consideration of the computational complexity and accuracy requirements, the Linear Spectral Mixture Model (LSMM) could be adopted for Nitraria shrubs plots, but this will result in significant errors for the Haloxylon plots since the nonlinear spectral mixture effects were more obvious for this vegetation type. (3) The vegetation canopy structure (planophile or erectophile) determines the strength of the nonlinear spectral mixture effects. Therefore, no matter for Nitraria shrubs or Haloxylon, the non-linear spectral mixing effects between the photosynthetic / non-photosynthetic vegetation and the bare soil do exist, and its strength is dependent on the three-dimensional structure of the vegetation canopy. The choice of linear or nonlinear spectral mixture models is up to the consideration of computational complexity and the accuracy requirement. PMID:29240777

Measurement and modeling of diffusion time dependence of apparent diffusion coefficient and fractional anisotropy in prostate tissue ex vivo.

PubMed

Bourne, Roger; Liang, Sisi; Panagiotaki, Eleftheria; Bongers, Andre; Sved, Paul; Watson, Geoffrey

2017-10-01

The purpose of this study was to measure and model the diffusion time dependence of apparent diffusion coefficient (ADC) and fractional anisotropy (FA) derived from conventional prostate diffusion-weighted imaging methods as used in recommended multiparametric MRI protocols. Diffusion tensor imaging (DTI) was performed at 9.4 T with three radical prostatectomy specimens, with diffusion times in the range 10-120 ms and b-values 0-3000 s/mm 2 . ADC and FA were calculated from DTI measurements at b-values of 800 and 1600 s/mm 2 . Independently, a two-component model (restricted isotropic plus Gaussian anisotropic) was used to synthesize DTI data, from which ADC and FA were predicted and compared with the measured values. Measured ADC and FA exhibited a diffusion time dependence, which was closely predicted by the two-component model. ADC decreased by about 0.10-0.15 μm 2 /ms as diffusion time increased from 10 to 120 ms. FA increased with diffusion time at b-values of 800 and 1600 s/mm 2 but was predicted to be independent of diffusion time at b = 3000 s/mm 2 . Both ADC and FA exhibited diffusion time dependence that could be modeled as two unmixed water pools - one having isotropic restricted dynamics, and the other unrestricted anisotropic dynamics. These results highlight the importance of considering and reporting diffusion times in conventional ADC and FA calculations and protocol recommendations, and inform the development of improved diffusion methods for prostate cancer imaging. Copyright © 2017 John Wiley & Sons, Ltd.

Mechanistic analysis of the function of agonists and allosteric modulators: reconciling two-state and operational models

PubMed Central

Roche, David; Gil, Debora; Giraldo, Jesús

2013-01-01

Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism. Linked Articles Another recent review on allosteric modulation can be found at: Kenakin, T (2013). New concepts in pharmacological efficacy at 7TM receptors: IUPHAR Review 2. British Journal of Pharmacology 168: 554–575. doi: 10.1111/j.1476-5381.2012.02223.x And in this issue of BJP there is an article on a new allosteric modulator: Newman AS, Batis N, Grafton G, Caputo F, Brady CA, Lambert J, Peters JA, Gordon J, Brain KL, Powell AD and Barnes NM (2013). 5-Chloroindole: a potent allosteric modulator of the 5-HT3 receptor. British Journal of Pharmacology 169: 1228–1238. doi: 10.1111/bph.12213 PMID:23647200

(−) Arctigenin and (+) Pinoresinol Are Antagonists of the Human Thyroid Hormone Receptor β

PubMed Central

2015-01-01

Lignans are important biologically active dietary polyphenolic compounds. Consumption of foods that are rich in lignans is associated with positive health effects. Using modeling tools to probe the ligand-binding pockets of molecular receptors, we found that lignans have high docking affinity for the human thyroid hormone receptor β. Follow-up experimental results show that lignans (−) arctigenin and (+) pinoresinol are antagonists of the human thyroid hormone receptor β. The modeled complexes show key plausible interactions between the two ligands and important amino acid residues of the receptor. PMID:25383984

The CCK(-like) receptor in the animal kingdom: functions, evolution and structures.

PubMed

Staljanssens, Dorien; Azari, Elnaz Karimian; Christiaens, Olivier; Beaufays, Jérôme; Lins, Laurence; Van Camp, John; Smagghe, Guy

2011-03-01

In this review, the cholecystokinin (CCK)(-like) receptors throughout the animal kingdom are compared on the level of physiological functions, evolutionary basis and molecular structure. In vertebrates, the CCK receptor is an important member of the G-protein coupled receptors as it is involved in the regulation of many physiological functions like satiety, gastrointestinal motility, gastric acid secretion, gall bladder contraction, pancreatic secretion, panic, anxiety and memory and learning processes. A homolog for this receptor is also found in nematodes and arthropods, called CK receptor and sulfakinin (SK) receptor, respectively. These receptors seem to have evolved from a common ancestor which is probably still closely related to the nematode CK receptor. The SK receptor is more closely related to the CCK receptor and seems to have similar functions. A molecular 3D-model for the CCK receptor type 1 has been built together with the docking of the natural ligands for the CCK and SK receptors in the CCK receptor type 1. These molecular models can help to study ligand-receptor interactions, that can in turn be useful in the development of new CCK(-like) receptor agonists and antagonists with beneficial health effects in humans or potential for pest control. Copyright © 2010 Elsevier Inc. All rights reserved.

Fluctuation correlation models for receptor immobilization

NASA Astrophysics Data System (ADS)

Fourcade, B.

2017-12-01

Nanoscale dynamics with cycles of receptor diffusion and immobilization by cell-external-or-internal factors is a key process in living cell adhesion phenomena at the origin of a plethora of signal transduction pathways. Motivated by modern correlation microscopy approaches, the receptor correlation functions in physical models based on diffusion-influenced reaction is studied. Using analytical and stochastic modeling, this paper focuses on the hybrid regime where diffusion and reaction are not truly separable. The time receptor autocorrelation functions are shown to be indexed by different time scales and their asymptotic expansions are given. Stochastic simulations show that this analysis can be extended to situations with a small number of molecules. It is also demonstrated that this analysis applies when receptor immobilization is coupled to environmental noise.

Shifting physician prescribing to a preferred histamine-2-receptor antagonist. Effects of a multifactorial intervention in a mixed-model health maintenance organization.

PubMed

Brufsky, J W; Ross-Degnan, D; Calabrese, D; Gao, X; Soumerai, S B

1998-03-01

This study was undertaken to determine whether a program of education, therapeutic reevaluation of eligible patients, and performance feedback could shift prescribing to cimetidine from other histamine-2 receptor antagonists, which commonly are used in the management of ulcers and reflux, and reduce costs without increasing rates of ulcer-related hospital admissions. This study used an interrupted monthly time series with comparison series in a large mixed-model health maintenance organization. Physicians employed in health centers (staff model) and physicians in independent medical groups contracting to provide health maintenance organization services (group model) participated. The comparative percentage prescribed of specific histamine-2 receptor antagonists (market share), total histamine-2 receptor antagonist prescribing, cost per histamine-2 receptor antagonist prescription, and the rate of hospitalization for gastrointestinal illness were assessed. In the staff model, therapeutic reevaluation resulted in a sudden increase in market share of the preferred histamine-2 receptor antagonist cimetidine (+53.8%) and a sudden decrease in ranitidine (-44.7%) and famotidine (-4.8%); subsequently, cimetidine market share grew by 1.1% per month. In the group model, therapeutic reevaluation resulted in increased cimetidine market share (+9.7%) and decreased prescribing of other histamine-2 receptor antagonists (ranitidine -11.6%; famotidine -1.2%). Performance feedback did not result in further changes in prescribing in either setting. Use of omeprazole, an expensive alternative, essentially was unchanged by the interventions, as were overall histamine-2 receptor antagonist prescribing and hospital admissions for gastrointestinal illnesses. This intervention, which cost approximately $60,000 to implement, resulted in estimated annual savings in histamine-2 receptor antagonist expenditures of $1.06 million. Annual savings in histamine-2 receptor antagonist expenditures after this multifaceted intervention were more than implementation costs, with no discernible effects on numbers of hospitalizations. The magnitude of effect and cost savings were much greater in the staff model; organizational factors and economic incentives may have contributed to these differences. More research is needed to determine the generalizability of this approach to other technologies and managed care settings.

Stimulation of postsynapse adrenergic α2A receptor improves attention/cognition performance in an animal model of attention deficit hyperactivity disorder.

PubMed

Kawaura, Kazuaki; Karasawa, Jun-ichi; Chaki, Shigeyuki; Hikichi, Hirohiko

2014-08-15

A 5-trial inhibitory avoidance test using spontaneously hypertensive rat (SHR) pups has been used as an animal model of attention deficit hyperactivity disorder (ADHD). However, the roles of noradrenergic systems, which are involved in the pathophysiology of ADHD, have not been investigated in this model. In the present study, the effects of adrenergic α2 receptor stimulation, which has been an effective treatment for ADHD, on attention/cognition performance were investigated in this model. Moreover, neuronal mechanisms mediated through adrenergic α2 receptors were investigated. We evaluated the effects of both clonidine, a non-selective adrenergic α2 receptor agonist, and guanfacine, a selective adrenergic α2A receptor agonist, using a 5-trial inhibitory avoidance test with SHR pups. Juvenile SHR exhibited a shorter transfer latency, compared with juvenile Wistar Kyoto (WKY) rats. Both clonidine and guanfacine significantly prolonged the transfer latency of juvenile SHR. The effects of clonidine and guanfacine were significantly blocked by pretreatment with an adrenergic α2A receptor antagonist. In contrast, the effect of clonidine was not attenuated by pretreatment with an adrenergic α2B receptor antagonist, or an adrenergic α2C receptor antagonist, while it was attenuated by a non-selective adrenergic α2 receptor antagonist. Furthermore, the effects of neither clonidine nor guanfacine were blocked by pretreatment with a selective noradrenergic neurotoxin. These results suggest that the stimulation of the adrenergic α2A receptor improves the attention/cognition performance of juvenile SHR in the 5-trial inhibitory avoidance test and that postsynaptic, rather than presynaptic, adrenergic α2A receptor is involved in this effect. Copyright © 2014 Elsevier B.V. All rights reserved.

Receptors as a master key for synchronization of rhythms

NASA Astrophysics Data System (ADS)

Nagano, Seido

2004-03-01

A simple, but general scheme to achieve synchronization of rhythms was derived. The scheme has been inductively generalized from the modelling study of cellular slime mold. It was clarified that biological receptors work as apparatuses that can convert external stimulus to the form of nonlinear interaction within individual oscillators. Namely, the mathematical model receptor works as a nonlinear coupling apparatus between nonlinear oscillators. Thus, synchronization is achieved as a result of competition between two kinds of non-linearities, and to achieve synchronization, even a small external stimulation via model receptors can change the characteristics of individual oscillators significantly. The derived scheme is very simple mathematically, but it is a very powerful scheme as numerically demonstrated. The biological receptor scheme should significantly help understanding of synchronization phenomena in biology since groups of limit cycle oscillators and receptors are ubiquitous in biological systems. Reference: S. Nagano, Phys Rev. E67, 056215(2003)

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196

NASA Technical Reports Server (NTRS)

Garduno-Juarez, R.; Shibata, M.; Zielinski, T. J.; Rein, R.

1987-01-01

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

Application of agonist-receptor modeling to the sweetness synergy between high fructose corn syrup and sucralose, and between high-potency sweeteners.

PubMed

Wolf, P A; Bridges, J R; Wicklund, R

2010-03-01

The agonist-receptor-transducer model of D. Ennis is applied to beverage formulations sweetened with high fructose corn syrup, sucralose, and other high-potency sweeteners, confirming the utility of the model, and supports the growing volume of evidence for multiple binding sites on the sweetness receptor. The model is further simplified to require less parameters for other sweetener blend systems whenever potency information is available for the single sweeteners.

A hyperspectral image projector for hyperspectral imagers

NASA Astrophysics Data System (ADS)

Rice, Joseph P.; Brown, Steven W.; Neira, Jorge E.; Bousquet, Robert R.

2007-04-01

We have developed and demonstrated a Hyperspectral Image Projector (HIP) intended for system-level validation testing of hyperspectral imagers, including the instrument and any associated spectral unmixing algorithms. HIP, based on the same digital micromirror arrays used in commercial digital light processing (DLP*) displays, is capable of projecting any combination of many different arbitrarily programmable basis spectra into each image pixel at up to video frame rates. We use a scheme whereby one micromirror array is used to produce light having the spectra of endmembers (i.e. vegetation, water, minerals, etc.), and a second micromirror array, optically in series with the first, projects any combination of these arbitrarily-programmable spectra into the pixels of a 1024 x 768 element spatial image, thereby producing temporally-integrated images having spectrally mixed pixels. HIP goes beyond conventional DLP projectors in that each spatial pixel can have an arbitrary spectrum, not just arbitrary color. As such, the resulting spectral and spatial content of the projected image can simulate realistic scenes that a hyperspectral imager will measure during its use. Also, the spectral radiance of the projected scenes can be measured with a calibrated spectroradiometer, such that the spectral radiance projected into each pixel of the hyperspectral imager can be accurately known. Use of such projected scenes in a controlled laboratory setting would alleviate expensive field testing of instruments, allow better separation of environmental effects from instrument effects, and enable system-level performance testing and validation of hyperspectral imagers as used with analysis algorithms. For example, known mixtures of relevant endmember spectra could be projected into arbitrary spatial pixels in a hyperspectral imager, enabling tests of how well a full system, consisting of the instrument + calibration + analysis algorithm, performs in unmixing (i.e. de-convolving) the spectra in all pixels. We discuss here the performance of a visible prototype HIP. The technology is readily extendable to the ultraviolet and infrared spectral ranges, and the scenes can be static or dynamic.

Sensitive dual color in vivo bioluminescence imaging using a new red codon optimized firefly luciferase and a green click beetle luciferase.

PubMed

Mezzanotte, Laura; Que, Ivo; Kaijzel, Eric; Branchini, Bruce; Roda, Aldo; Löwik, Clemens

2011-04-22

Despite a plethora of bioluminescent reporter genes being cloned and used for cell assays and molecular imaging purposes, the simultaneous monitoring of multiple events in small animals is still challenging. This is partly attributable to the lack of optimization of cell reporter gene expression as well as too much spectral overlap of the color-coupled reporter genes. A new red emitting codon-optimized luciferase reporter gene mutant of Photinus pyralis, Ppy RE8, has been developed and used in combination with the green click beetle luciferase, CBG99. Human embryonic kidney cells (HEK293) were transfected with vectors that expressed red Ppy RE8 and green CBG99 luciferases. Populations of red and green emitting cells were mixed in different ratios. After addition of the shared single substrate, D-luciferin, bioluminescent (BL) signals were imaged with an ultrasensitive cooled CCD camera using a series of band pass filters (20 nm). Spectral unmixing algorithms were applied to the images where good separation of signals was observed. Furthermore, HEK293 cells that expressed the two luciferases were injected at different depth in the animals. Spectrally-separate images and quantification of the dual BL signals in a mixed population of cells was achieved when cells were either injected subcutaneously or directly into the prostate. We report here the re-engineering of different luciferase genes for in vitro and in vivo dual color imaging applications to address the technical issues of using dual luciferases for imaging. In respect to previously used dual assays, our study demonstrated enhanced sensitivity combined with spatially separate BL spectral emissions using a suitable spectral unmixing algorithm. This new D-luciferin-dependent reporter gene couplet opens up the possibility in the future for more accurate quantitative gene expression studies in vivo by simultaneously monitoring two events in real time.

Nutrient Losses during Winter and Summer Storage of Separated and Unseparated Digested Cattle Slurry.

PubMed

Perazzolo, Francesca; Mattachini, Gabriele; Riva, Elisabetta; Provolo, Giorgio

2017-07-01

Management factors affect nutrient loss during animal manure slurry storage in different ways. We conducted a pilot-scale study to evaluate carbon (C) and nitrogen (N) losses from unseparated and digested dairy slurry during winter and summer storage. In addition to season, treatments included mechanical separation of digestate into liquid and solid fractions and bimonthly mixing. Chemical analyses were performed every 2 wk for the mixed materials and at the start and end of storage for unmixed materials. The parameters examined allowed us to estimate C and N losses and examine the factors that determine these losses as well as emission patterns. Gas measurements were done every 2 wk to determine the main forms in which gaseous losses occurred. To evaluate the effect of separation, measured losses and emissions of separated liquid and solid fractions were mathematically combined using the mass separation efficiency of the mechanical separator. Nutrient losses were mainly affected by climatic conditions. Losses of C (up to 23%) from unseparated, unmixed digestate and of N (38% from combined separated fractions and from unseparated digestate) were much greater in summer than in winter, when C and N losses were <7%. Mixing tended to significantly increase N losses ( < 0.1) only in winter. Mechanical separation resulted in lower GHG emissions from combined separated fractions than from unseparated digestate. Results indicate that to maximize the fertilizer value of digested slurry, dairy farmers must carefully choose management practices, especially in summer. For separated digestates, practices should focus on storage of the liquid fraction, the major contributor of C and N losses (up to 64 and 90% of total losses, respectively) in summer. Moreover, management practices should limit NH, the main form of N losses (up to 99.5%). Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Sensitive Dual Color In Vivo Bioluminescence Imaging Using a New Red Codon Optimized Firefly Luciferase and a Green Click Beetle Luciferase

PubMed Central

Mezzanotte, Laura; Que, Ivo; Kaijzel, Eric; Branchini, Bruce; Roda, Aldo; Löwik, Clemens

2011-01-01

Background Despite a plethora of bioluminescent reporter genes being cloned and used for cell assays and molecular imaging purposes, the simultaneous monitoring of multiple events in small animals is still challenging. This is partly attributable to the lack of optimization of cell reporter gene expression as well as too much spectral overlap of the color-coupled reporter genes. A new red emitting codon-optimized luciferase reporter gene mutant of Photinus pyralis, Ppy RE8, has been developed and used in combination with the green click beetle luciferase, CBG99. Principal Findings Human embryonic kidney cells (HEK293) were transfected with vectors that expressed red Ppy RE8 and green CBG99 luciferases. Populations of red and green emitting cells were mixed in different ratios. After addition of the shared single substrate, D-luciferin, bioluminescent (BL) signals were imaged with an ultrasensitive cooled CCD camera using a series of band pass filters (20 nm). Spectral unmixing algorithms were applied to the images where good separation of signals was observed. Furthermore, HEK293 cells that expressed the two luciferases were injected at different depth in the animals. Spectrally-separate images and quantification of the dual BL signals in a mixed population of cells was achieved when cells were either injected subcutaneously or directly into the prostate. Significance We report here the re-engineering of different luciferase genes for in vitro and in vivo dual color imaging applications to address the technical issues of using dual luciferases for imaging. In respect to previously used dual assays, our study demonstrated enhanced sensitivity combined with spatially separate BL spectral emissions using a suitable spectral unmixing algorithm. This new D-luciferin-dependent reporter gene couplet opens up the possibility in the future for more accurate quantitative gene expression studies in vivo by simultaneously monitoring two events in real time. PMID:21544210

Ferrobasalt-rhyolite immiscibility in tholeiitic volcanic and plutonic series (Invited)

NASA Astrophysics Data System (ADS)

Charlier, B.; Namur, O.; Kamenetsky, V. S.; Grove, T. L.

2013-12-01

One atmosphere experiments show that silicate liquid immiscibility develops between Fe-rich and Si-rich melts below 1000-1020°C in compositionally diverse lavas that represent classical tholeiitic trends, such as Mull, Iceland, Snake River Plain and Sept Iles. Extreme iron enrichment along the evolution trend is not necessary; immiscibility also develops during iron depletion and silica enrichment after Fe-Ti oxide saturation. Natural liquid lines of descent for major tholeiitic series also approach or intersect the experimentally-defined compositional space of immiscibility. The importance of ferrobasalt-rhyolite unmixing in both volcanic and plutonic environments is supported by worldwide occurrence of immiscible globules in the mesostasis of erupted basalts, and by unmixed melt inclusions in cumulus phases of major layered intrusions such as Sept Iles, Skaergaard and Sudbury. A clear case of liquid immiscibility is also recorded in intrusive tholeiitic gabbros from the Siberian Large Igneous Province and is evidenced by textures and compositions of millimeter-sized silicate melt pools trapped in native iron. An important implication of immiscibility in natural ferrobasaltic provinces is the development of a compositional gap characterized by the absence of intermediate compositions, a major feature observed in many tholeiitic provinces and referred to as the Daly gap. The compositions of experimental silica-rich immiscible melts coincide with those of natural rhyolites with high FeOtot and low Al2O3, which suggests a potential role for large-scale immiscibility in the petrogenesis of late-stage ferroan silicic melts. No evidence for the paired ferrobasaltic melt is observed in volcanic provinces, probably because of its uneruptable characteristics. Instead, Fe-Ti×P-rich gabbros crystallized at depth and are the cumulate products of immiscible Fe-rich melts in plutonic settings, a feature clearly evidenced in the Sept Iles intrusion. The production of immiscible Fe-Ti-Ca-P liquids has also important implications for the formation of some iron deposits associated with alkaline lavas.

Comparison of Kinetic Models for Dual-Tracer Receptor Concentration Imaging in Tumors

PubMed Central

Hamzei, Nazanin; Samkoe, Kimberley S; Elliott, Jonathan T; Holt, Robert W; Gunn, Jason R; Hasan, Tayyaba; Pogue, Brian W; Tichauer, Kenneth M

2014-01-01

Molecular differences between cancerous and healthy tissue have become key targets for novel therapeutics specific to tumor receptors. However, cancer cell receptor expression can vary within and amongst different tumors, making strategies that can quantify receptor concentration in vivo critical for the progression of targeted therapies. Recently a dual-tracer imaging approach capable of providing quantitative measures of receptor concentration in vivo was developed. It relies on the simultaneous injection and imaging of receptor-targeted tracer and an untargeted tracer (to account for non-specific uptake of the targeted tracer). Early implementations of this approach have been structured on existing “reference tissue” imaging methods that have not been optimized for or validated in dual-tracer imaging. Using simulations and mouse tumor model experimental data, the salient findings in this study were that all widely used reference tissue kinetic models can be used for dual-tracer imaging, with the linearized simplified reference tissue model offering a good balance of accuracy and computational efficiency. Moreover, an alternate version of the full two-compartment reference tissue model can be employed accurately by assuming that the K1s of the targeted and untargeted tracers are similar to avoid assuming an instantaneous equilibrium between bound and free states (made by all other models). PMID:25414912

Is the Acute NMDA Receptor Hypofunction a Valid Model of Schizophrenia?

PubMed Central

Adell, Albert; Jiménez-Sánchez, Laura; López-Gil, Xavier; Romón, Tamara

2012-01-01

Several genetic, neurodevelopmental, and pharmacological animal models of schizophrenia have been established. This short review examines the validity of one of the most used pharmacological model of the illness, ie, the acute administration of N-methyl-D-aspartate (NMDA) receptor antagonists in rodents. In some cases, data on chronic or prenatal NMDA receptor antagonist exposure have been introduced for comparison. The face validity of acute NMDA receptor blockade is granted inasmuch as hyperlocomotion and stereotypies induced by phencyclidine, ketamine, and MK-801 are regarded as a surrogate for the positive symptoms of schizophrenia. In addition, the loss of parvalbumin-containing cells (which is one of the most compelling finding in postmortem schizophrenia brain) following NMDA receptor blockade adds construct validity to this model. However, the lack of changes in glutamic acid decarboxylase (GAD67) is at variance with human studies. It is possible that changes in GAD67 are more reflective of the neurodevelopmental condition of schizophrenia. Finally, the model also has predictive validity, in that its behavioral and transmitter activation in rodents are responsive to antipsychotic treatment. Overall, although not devoid of drawbacks, the acute administration of NMDA receptor antagonists can be considered as a good model of schizophrenia bearing a satisfactory degree of validity. PMID:21965469

Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction.

PubMed

Costa, Michelle N; Radhakrishnan, Krishnan; Wilson, Bridget S; Vlachos, Dionisios G; Edwards, Jeremy S

2009-07-23

The ErbB family of receptors activates intracellular signaling pathways that control cellular proliferation, growth, differentiation and apoptosis. Given these central roles, it is not surprising that overexpression of the ErbB receptors is often associated with carcinogenesis. Therefore, extensive laboratory studies have been devoted to understanding the signaling events associated with ErbB activation. Systems biology has contributed significantly to our current understanding of ErbB signaling networks. However, although computational models have grown in complexity over the years, little work has been done to consider the spatial-temporal dynamics of receptor interactions and to evaluate how spatial organization of membrane receptors influences signaling transduction. Herein, we explore the impact of spatial organization of the epidermal growth factor receptor (ErbB1/EGFR) on the initiation of downstream signaling. We describe the development of an algorithm that couples a spatial stochastic model of membrane receptors with a nonspatial stochastic model of the reactions and interactions in the cytosol. This novel algorithm provides a computationally efficient method to evaluate the effects of spatial heterogeneity on the coupling of receptors to cytosolic signaling partners. Mathematical models of signal transduction rarely consider the contributions of spatial organization due to high computational costs. A hybrid stochastic approach simplifies analyses of the spatio-temporal aspects of cell signaling and, as an example, demonstrates that receptor clustering contributes significantly to the efficiency of signal propagation from ligand-engaged growth factor receptors.

Kinetic modeling of benzodiazepine receptor binding with PET and high specific activity [(11)C]Iomazenil in healthy human subjects.

PubMed

Bremner, J D; Horti, A; Staib, L H; Zea-Ponce, Y; Soufer, R; Charney, D S; Baldwin, R

2000-01-01

Quantitation of the PET benzodiazepine receptor antagonist, [(11)C]Iomazenil, using low specific activity radioligand was recently described. The purpose of this study was to quantitate benzodiazepine receptor binding in human subjects using PET and high specific activity [(11)C]Iomazenil. Six healthy human subjects underwent PET imaging following a bolus injection of high specific activity (>100 Ci/mmol) [(11)C]iomazenil. Arterial samples were collected at multiple time points after injection for measurement of unmetabolized total and nonprotein-bound parent compound in plasma. Time activity curves of radioligand concentration in brain and plasma were analyzed using two and three compartment model. Kinetic rate constants of transfer of radioligand between plasma, nonspecifically bound brain tissue, and specifically bound brain tissue compartments were fitted to the model. Values for fitted kinetic rate constants were used in the calculation of measures of benzodiazepine receptor binding, including binding potential (the ratio of receptor density to affinity), and product of BP and the fraction of free nonprotein-bound parent compound (V(3)'). Use of the three compartment model improved the goodness of fit in comparison to the two compartment model. Values for kinetic rate constants and measures of benzodiazepine receptor binding, including BP and V(3)', were similar to results obtained with the SPECT radioligand [(123)I]iomazenil, and a prior report with low specific activity [(11)C]Iomazenil. Kinetic modeling using the three compartment model with PET and high specific activity [(11)C]Iomazenil provides a reliable measure of benzodiazepine receptor binding. Synapse 35:68-77, 2000. Published 2000 Wiley-Liss, Inc.

Ethylene Regulates Levels of Ethylene Receptor/CTR1 Signaling Complexes in Arabidopsis thaliana

DOE PAGES

Shakeel, Samina N.; Gao, Zhiyong; Amir, Madiha; ...

2015-03-26

The plant hormone ethylene is perceived by a five-member family of receptors in Arabidopsis thaliana. The receptors function in conjunction with the Raf-like kinase CTR1 to negatively regulate ethylene signal transduction. CTR1 interacts with multiple members of the receptor family based on co-purification analysis, interacting more strongly with receptors containing a receiver domain. Levels of membrane-associated CTR1 vary in response to ethylene, doing so in a post-transcriptional manner that correlates with ethylene-mediated changes in levels of the ethylene receptors ERS1, ERS2, EIN4, and ETR2. Interactions between CTR1 and the receptor ETR1 protect ETR1 from ethylene-induced turnover. Kinetic and dose-response analysesmore » support a model in which two opposing factors control levels of the ethylene receptor/CTR1 complexes. Ethylene stimulates the production of new complexes largely through transcriptional induction of the receptors. However, ethylene also induces turnover of receptors, such that levels of ethylene receptor/CTR1 complexes decrease at higher ethylene concentrations. Lastly, we discuss implications of this model for ethylene signaling.« less

Ethylene Regulates Levels of Ethylene Receptor/CTR1 Signaling Complexes in Arabidopsis thaliana*

PubMed Central

Shakeel, Samina N.; Gao, Zhiyong; Amir, Madiha; Chen, Yi-Feng; Rai, Muneeza Iqbal; Haq, Noor Ul; Schaller, G. Eric

2015-01-01

The plant hormone ethylene is perceived by a five-member family of receptors in Arabidopsis thaliana. The receptors function in conjunction with the Raf-like kinase CTR1 to negatively regulate ethylene signal transduction. CTR1 interacts with multiple members of the receptor family based on co-purification analysis, interacting more strongly with receptors containing a receiver domain. Levels of membrane-associated CTR1 vary in response to ethylene, doing so in a post-transcriptional manner that correlates with ethylene-mediated changes in levels of the ethylene receptors ERS1, ERS2, EIN4, and ETR2. Interactions between CTR1 and the receptor ETR1 protect ETR1 from ethylene-induced turnover. Kinetic and dose-response analyses support a model in which two opposing factors control levels of the ethylene receptor/CTR1 complexes. Ethylene stimulates the production of new complexes largely through transcriptional induction of the receptors. However, ethylene also induces turnover of receptors, such that levels of ethylene receptor/CTR1 complexes decrease at higher ethylene concentrations. Implications of this model for ethylene signaling are discussed. PMID:25814663

Pain-relieving prospects for adenosine receptors and ectonucleotidases

PubMed Central

Zylka, Mark J.

2010-01-01

Adenosine receptor agonists have potent antinociceptive effects in diverse preclinical models of chronic pain. In contrast, the efficacy of adenosine or adenosine receptor agonists at treating pain in humans is unclear. Two ectonucleotidases that generate adenosine in nociceptive neurons were recently identified. When injected spinally, these enzymes have long-lasting adenosine A1 receptor (A1R)-dependent antinociceptive effects in inflammatory and neuropathic pain models. Furthermore, recent findings indicate that spinal adenosine A2A receptor activation can enduringly inhibit neuropathic pain symptoms. Collectively, these studies suggest the possibility of treating chronic pain in humans by targeting specific adenosine receptor subtypes in anatomically defined regions with agonists or with ectonucleotidases that generate adenosine. PMID:21236731

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.

PubMed

Busato, Mirko; Giorgetti, Alejandro

2016-08-01

Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection and Identification of potentially toxic elements in urban soil using in situ spectroscopy

NASA Astrophysics Data System (ADS)

Brook, Anna; Kopel, Daniella; Wittenberg, Lea

2017-04-01

Anthropogenic urban soils are the foundation of the urban green infrastructure, the green net quality is as good as each of its patches. In early days of pedology urban soil has been recognized with respect to contamination and the risks for human health but in study performed since the 70s, the importance of urban soil for the urban ecology became increasingly significant. Urban soils are highly disturbed land that was created by the process of urbanization. The dominant agent in the creation of urban soils is human activity which modifies the natural soil through mixing, filling or by contamination of land surfaces so as to create a layer of urban soil which can be more than 50 cm thick. The objective of this study is to determine the extent to which field spectroscopy methods can be used to extend the knowledge of toxic elements in urban soils. The majority of the studies on urban soils concentrate on identifying and mapping of known pollution mostly certain heavy metals, we are focusing on almost non disturbed soils where no direct disturbance occurred but the urban matrix inflicted on it. The elements in those soils where an-knowns features. In this study a top-down analysis is applied for detecting the presence of minerals, organic matter and pollutants in mixed soil samples. Results of the proposed top-down unmixing method suggest that the analysis is made very fast due to the simplified hierarchy which avoids the high-learning curve associated with unmixing algorithms showed that the most abundant components were coarse organic matter 12% followed by concrete dust, plastic crumbs, other man made materials, clay and other minerals. The results of the soils pH, measured electrometrically and the particle size distribution, measured by Laser diffraction, indicate there is no big different between the samples particle size distribution and the pH values of the samples but they are not significantly different from the expected, except for the OM percentage which is significantly higher in most samples. The suggested method was very effective for tracing the man-made substances, we could find concrete and asphalt, plastic and synthetic polymers after they were assimilated, broken down and decomposed into soil particles. By the top-down un-mixing method we did not limit the substances we characterize and so we could detect unexpected materials and contaminants. In five location we have traces of cyanide cadmium Cd(CN)2 probably residues of old television scenes, traces of schwertmannite Fe8O8(OH)6(SO4)·nH2O or Fe3+16O16(OH,SO4)12-13·10-12H2O acid drainage were found in four sites and the most alarmingly the detecting of actinolite Ca2(Mg4.5-2.5Fe2+0.5-2.5)Si8O22(OH)2 and tremolite Ca2(Mg5.0-4.5Fe2+0.0-0.5)Si8O22(OH), asbestos minerals, originate from the construction debris in almost all of the sites.

Delta-opioid receptors as targets for migraine therapy.

PubMed

Charles, Andrew; Pradhan, Amynah A

2016-06-01

The purpose of this review is to contrast the properties of the δ-opioid receptor with those of the μ-opioid receptor, which is the primary target of most currently available opioid analgesics. We also discuss preclinical evidence that indicates the potential efficacy of δ-opioid receptor agonists as migraine therapy. The use of currently available opioid analgesics is highly problematic for patients with migraine. Delta-opioid receptors have key differences from μ receptors; these differences make the δ receptor an attractive therapeutic target for migraine. Delta-opioid receptors are expressed in both the peripheral and central nervous system in anatomical regions and cell types that are believed to play a role in migraine. Delta-receptor agonists have also shown promising effects in multiple migraine models, including nitroglycerin evoked hyperalgesia and conditioned place aversion, and cortical spreading depression. Evidence from animal models indicates that activation of δ receptors is less likely to cause tolerance and dependence, and less likely to cause hyperalgesia. In addition, δ receptors may have antidepressant and anxiolytic properties that are distinct from those of μ receptors. In human studies investigating other conditions, δ-receptor agonists have been generally safe and well tolerated. Delta-opioid receptor agonists have promising potential as acute and/or preventive migraine therapies, without the problems associated with currently used opioid analgesics.

[The potential of group II metabotropic glutamate receptor antagonists as a novel antidepressant].

PubMed

Chaki, Shigeyuki

2012-08-01

Recently, abnormalities of glutamatergic transmission have been implicated in the pathophysiology of depression. Moreover, both ketamine, an NMDA receptor antagonist, and riluzole, a modulator of glutamatergic, transmission have been reported to be effective for the treatment of patients with treatment-refractory depression. Based on these findings, extensive studies to develop agents acting on glutamatergic transmission have been conducted. Glutamate receptors are divided into two main subtypes, ionotropic glutamate receptors and metabotropic glutamate (mGlu) receptors, both of which have subtypes. Of these, much attention has been paid to mGlu2/3 receptors. mGlu2/3 receptor antagonists such as MGS0039 and LY341495 have been reported to exert antidepressant effects in animal models of depression including the forced swim test, tail suspension test, learned helplessness paradigm, olfactory bulmectomy model and isolation rearing model, and to enhance serotonin release in the prefrontal cortex and dopamine release in the nucleus accumbens. Moreover, activation of AMPA receptor and mTOR signaling have been suggested to be involved in the antidepressant effects of mGlu2/3 receptor antagonists, as demonstrated in the actions of ketamine. Thus, mGlu2/3 receptor antagonists may share some neural networks with ketamine in exerting their antidepressant effects. In addition, the potential of other agents targeting glutamatergic transmission for novel antidepressants is being investigated.

Designing peptide inhibitor of insulin receptor to induce diabetes mellitus type 2 in animal model Mus musculus.

PubMed

Permatasari, Galuh W; Utomo, Didik H; Widodo

2016-10-01

A designing peptide as agent for inducing diabetes mellitus type 2 (T2DM) in an animal model is challenging. The computational approach provides a sophisticated tool to design a functional peptide that may block the insulin receptor activity. The peptide that able to inhibit the binding between insulin and insulin receptor is a warrant for inducing T2DM. Therefore, we designed a potential peptide inhibitor of insulin receptor as an agent to generate T2DM animal model by bioinformatics approach. The peptide has been developed based on the structure of insulin receptor binding site of insulin and then modified it to obtain the best properties of half life, hydrophobicity, antigenicity, and stability binding into insulin receptor. The results showed that the modified peptide has characteristics 100h half-life, high-affinity -95.1±20, and high stability 28.17 in complex with the insulin receptor. Moreover, the modified peptide has molecular weight 4420.8g/Mol and has no antigenic regions. Based on the molecular dynamic simulation, the complex of modified peptide-insulin receptor is more stable than the commercial insulin receptor blocker. This study suggested that the modified peptide has the promising performance to block the insulin receptor activity that potentially induce diabetes mellitus type 2 in mice. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular characterization of the receptor binding structure-activity relationships of influenza B virus hemagglutinin.

PubMed

Carbone, V; Kim, H; Huang, J X; Baker, M A; Ong, C; Cooper, M A; Li, J; Rockman, S; Velkov, T

2013-01-01

Selectivity of α2,6-linked human-like receptors by B hemagglutinin (HA) is yet to be fully understood. This study integrates binding data with structure-recognition models to examine the impact of regional-specific sequence variations within the receptor-binding pocket on selectivity and structure activity relationships (SAR). The receptor-binding selectivity of influenza B HAs corresponding to either B/Victoria/2/1987 or the B/Yamagata/16/88 lineages was examined using surface plasmon resonance, solid-phase ELISA and gel-capture assays. Our SAR data showed that the presence of asialyl sugar units is the main determinant of receptor preference of α2,6 versus α2,3 receptor binding. Changes to the type of sialyl-glycan linkage present on receptors exhibit only a minor effect upon binding affinity. Homology-based structural models revealed that structural properties within the HA pocket, such as a glyco-conjugate at Asn194 on the 190-helix, sterically interfere with binding to avian receptor analogs by blocking the exit path of the asialyl sugars. Similarly, naturally occurring substitutions in the C-terminal region of the 190-helix and near the N-terminal end of the 140-loop narrows the horizontal borders of the binding pocket, which restricts access of the avian receptor analog LSTa. This study helps bridge the gap between ligand structure and receptor recognition for influenza B HA; and provides a consensus SAR model for the binding of human and avian receptor analogs to influenza B HA.

Crosslinking Constraints and Computational Models as Complementary Tools in Modeling the Extracellular Domain of the Glycine Receptor

PubMed Central

Liu, Zhenyu; Szarecka, Agnieszka; Yonkunas, Michael; Speranskiy, Kirill; Kurnikova, Maria; Cascio, Michael

2014-01-01

The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel superfamily, is the major inhibitory neurotransmitter-gated receptor in the spinal cord and brainstem. In these receptors, the extracellular domain binds agonists, antagonists and various other modulatory ligands that act allosterically to modulate receptor function. The structures of homologous receptors and binding proteins provide templates for modeling of the ligand-binding domain of GlyR, but limitations in sequence homology and structure resolution impact on modeling studies. The determination of distance constraints via chemical crosslinking studies coupled with mass spectrometry can provide additional structural information to aid in model refinement, however it is critical to be able to distinguish between intra- and inter-subunit constraints. In this report we model the structure of GlyBP, a structural and functional homolog of the extracellular domain of human homomeric α1 GlyR. We then show that intra- and intersubunit Lys-Lys crosslinks in trypsinized samples of purified monomeric and oligomeric protein bands from SDS-polyacrylamide gels may be identified and differentiated by MALDI-TOF MS studies of limited resolution. Thus, broadly available MS platforms are capable of providing distance constraints that may be utilized in characterizing large complexes that may be less amenable to NMR and crystallographic studies. Systematic studies of state-dependent chemical crosslinking and mass spectrometric identification of crosslinked sites has the potential to complement computational modeling efforts by providing constraints that can validate and refine allosteric models. PMID:25025226

Homology modeling, active site prediction, and targeting the anti hypertension activity through molecular docking on endothelin – B receptor domain

PubMed Central

Rayalu, Daddam Jayasimha; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Ganeshan, Ramakrishan; Kumar, Nagapatla Udaya; Seshapani, Panthangi

2012-01-01

In cardiovascular system, activation of Endothelin receptors causes vasoconstriction which leads to Pulmonary Arterial Hypertension (PAH). Endothelin receptor antagonism has emerged as an important therapeutic strategy in pulmonary arterial hypertension. Bosentan is intended to affect vasoconstriction, hypertrophic and fibrotic effects by blocking the actions of receptors ETA and ETB. In this study we identified the action of Bosentan on endothelin B receptor using docking studies with homology modeled endothelin B receptor. Through the modeled protein, the flexible Docking study was performed with Bosentan and its derivatives with theoretically predicted active sites. The results indicated that amino acid ARG82, ARG84 and HIS197 present in endothelin B receptor are core important for binding activities and these residues are having strong hydrogen bond interactions with Bosentan. We have investigated the Bosentan and its derivatives interactions and scoring parameters using gold docking package. Among the docked compounds, one of the Bosentan derivatives BD6 shows better interaction than Bosentan with endothelin B receptor. Our results may be helpful for further investigations in both in vivo and in vitro conditions. PMID:22359440

Refinement of the conformation of a critical region of charge-charge interaction between cholecystokinin and its receptor.

PubMed

Ding, Xi-Qin; Pinon, Delia I; Furse, Kristina E; Lybrand, Terry P; Miller, Laurence J

2002-05-01

Insight into the molecular basis of cholecystokinin (CCK) binding to its receptor has come from receptor mutagenesis and photoaffinity labeling studies, with both contributing to the current hypothesis that the acidic Tyr-sulfate-27 residue within the peptide is situated adjacent to basic Arg(197) in the second loop of the receptor. Here, we refine our understanding of this region of interaction by examining a structure-activity series of these positions within both ligand and receptor and by performing three-dimensional molecular modeling of key pairs of modified ligand and receptor constructs. The important roles of Arg(197) and Tyr-sulfate-27 were supported by the marked negative impact on binding and biological response with their natural partner molecule when the receptor residue was replaced by acidic Asp or Glu and when the peptide residue was replaced by basic Arg, Lys, p-amino-Phe, p-guanidino-Phe, or p-methylamino-Phe. Complementary ligand-receptor charge-exchange experiments were unable to regain the lost function. This was supported by the molecular modeling, which demonstrated that the charge-reversed double mutants could not form a good interaction without extensive rearrangement of receptor conformation. The models further predicted that R197D and R197E mutations would lead to conformational changes in the extracellular domain, and this was experimentally supported by data showing that these mutations decreased peptide agonist and antagonist binding and increased nonpeptidyl antagonist binding. These receptor constructs also had increased susceptibility to trypsin degradation relative to the wild-type receptor. In contrast, the relatively conservative R197K mutation had modest negative impact on peptide agonist binding, again consistent with the modeling demonstration of loss of a series of stabilizing inter- and intramolecular bonds. The strong correlation between predicted and experimental results support the reported refinement in the three-dimensional structure of the CCK-occupied receptor.

Elimination of a ligand gating site generates a supersensitive olfactory receptor.

PubMed

Sharma, Kanika; Ahuja, Gaurav; Hussain, Ashiq; Balfanz, Sabine; Baumann, Arnd; Korsching, Sigrun I

2016-06-21

Olfaction poses one of the most complex ligand-receptor matching problems in biology due to the unparalleled multitude of odor molecules facing a large number of cognate olfactory receptors. We have recently deorphanized an olfactory receptor, TAAR13c, as a specific receptor for the death-associated odor cadaverine. Here we have modeled the cadaverine/TAAR13c interaction, exchanged predicted binding residues by site-directed mutagenesis, and measured the activity of the mutant receptors. Unexpectedly we observed a binding site for cadaverine at the external surface of the receptor, in addition to an internal binding site, whose mutation resulted in complete loss of activity. In stark contrast, elimination of the external binding site generated supersensitive receptors. Modeling suggests this site to act as a gate, limiting access of the ligand to the internal binding site and thereby downregulating the affinity of the native receptor. This constitutes a novel mechanism to fine-tune physiological sensitivity to socially relevant odors.

Elimination of a ligand gating site generates a supersensitive olfactory receptor

PubMed Central

Sharma, Kanika; Ahuja, Gaurav; Hussain, Ashiq; Balfanz, Sabine; Baumann, Arnd; Korsching, Sigrun I.

2016-01-01

Olfaction poses one of the most complex ligand-receptor matching problems in biology due to the unparalleled multitude of odor molecules facing a large number of cognate olfactory receptors. We have recently deorphanized an olfactory receptor, TAAR13c, as a specific receptor for the death-associated odor cadaverine. Here we have modeled the cadaverine/TAAR13c interaction, exchanged predicted binding residues by site-directed mutagenesis, and measured the activity of the mutant receptors. Unexpectedly we observed a binding site for cadaverine at the external surface of the receptor, in addition to an internal binding site, whose mutation resulted in complete loss of activity. In stark contrast, elimination of the external binding site generated supersensitive receptors. Modeling suggests this site to act as a gate, limiting access of the ligand to the internal binding site and thereby downregulating the affinity of the native receptor. This constitutes a novel mechanism to fine-tune physiological sensitivity to socially relevant odors. PMID:27323929

Formation of the long range Dpp morphogen gradient.

PubMed

Schwank, Gerald; Dalessi, Sascha; Yang, Schu-Fee; Yagi, Ryohei; de Lachapelle, Aitana Morton; Affolter, Markus; Bergmann, Sven; Basler, Konrad

2011-07-01

The TGF-β homolog Decapentaplegic (Dpp) acts as a secreted morphogen in the Drosophila wing disc, and spreads through the target tissue in order to form a long range concentration gradient. Despite extensive studies, the mechanism by which the Dpp gradient is formed remains controversial. Two opposing mechanisms have been proposed: receptor-mediated transcytosis (RMT) and restricted extracellular diffusion (RED). In these scenarios the receptor for Dpp plays different roles. In the RMT model it is essential for endocytosis, re-secretion, and thus transport of Dpp, whereas in the RED model it merely modulates Dpp distribution by binding it at the cell surface for internalization and subsequent degradation. Here we analyzed the effect of receptor mutant clones on the Dpp profile in quantitative mathematical models representing transport by either RMT or RED. We then, using novel genetic tools, experimentally monitored the actual Dpp gradient in wing discs containing receptor gain-of-function and loss-of-function clones. Gain-of-function clones reveal that Dpp binds in vivo strongly to the type I receptor Thick veins, but not to the type II receptor Punt. Importantly, results with the loss-of-function clones then refute the RMT model for Dpp gradient formation, while supporting the RED model in which the majority of Dpp is not bound to Thick veins. Together our results show that receptor-mediated transcytosis cannot account for Dpp gradient formation, and support restricted extracellular diffusion as the main mechanism for Dpp dispersal. The properties of this mechanism, in which only a minority of Dpp is receptor-bound, may facilitate long-range distribution.

An intrinsic agonist mechanism for activation of glucagon-like peptide-1 receptor by its extracellular domain

PubMed Central

Yin, Yanting; Zhou, X Edward; Hou, Li; Zhao, Li-Hua; Liu, Bo; Wang, Gaihong; Jiang, Yi; Melcher, Karsten; Xu, H Eric

2016-01-01

The glucagon-like peptide-1 receptor is a class B G protein coupled receptor (GPCR) that plays key roles in glucose metabolism and is a major therapeutic target for diabetes. The classic two-domain model for class B GPCR activation proposes that the apo-state receptor is auto-inhibited by its extracellular domain, which physically interacts with the transmembrane domain. The binding of the C-terminus of the peptide hormone to the extracellular domain allows the N-terminus of the hormone to insert into the transmembrane domain to induce receptor activation. In contrast to this model, here we demonstrate that glucagon-like peptide-1 receptor can be activated by N-terminally truncated glucagon-like peptide-1 or exendin-4 when fused to the receptor, raising the question regarding the role of N-terminal residues of peptide hormone in glucagon-like peptide-1 receptor activation. Mutations of cysteine 347 to lysine or arginine in intracellular loop 3 transform the receptor into a G protein-biased receptor and allow it to be activated by a nonspecific five-residue linker that is completely devoid of exendin-4 or glucagon-like peptide-1 sequence but still requires the presence of an intact extracellular domain. Moreover, the extracellular domain can activate the receptor in trans in the presence of an intact peptide hormone, and specific mutations in three extracellular loops abolished this extracellular domain trans-activation. Together, our data reveal a dominant role of the extracellular domain in glucagon-like peptide-1 receptor activation and support an intrinsic agonist model of the extracellular domain, in which peptide binding switches the receptor from the auto-inhibited state to the auto-activated state by releasing the intrinsic agonist activity of the extracellular domain. PMID:27917297

Preliminary Results of the first European Source Apportionment intercomparison for Receptor and Chemical Transport Models

NASA Astrophysics Data System (ADS)

Belis, Claudio A.; Pernigotti, Denise; Pirovano, Guido

2017-04-01

Source Apportionment (SA) is the identification of ambient air pollution sources and the quantification of their contribution to pollution levels. This task can be accomplished using different approaches: chemical transport models and receptor models. Receptor models are derived from measurements and therefore are considered as a reference for primary sources urban background levels. Chemical transport model have better estimation of the secondary pollutants (inorganic) and are capable to provide gridded results with high time resolution. Assessing the performance of SA model results is essential to guarantee reliable information on source contributions to be used for the reporting to the Commission and in the development of pollution abatement strategies. This is the first intercomparison ever designed to test both receptor oriented models (or receptor models) and chemical transport models (or source oriented models) using a comprehensive method based on model quality indicators and pre-established criteria. The target pollutant of this exercise, organised in the frame of FAIRMODE WG 3, is PM10. Both receptor models and chemical transport models present good performances when evaluated against their respective references. Both types of models demonstrate quite satisfactory capabilities to estimate the yearly source contributions while the estimation of the source contributions at the daily level (time series) is more critical. Chemical transport models showed a tendency to underestimate the contribution of some single sources when compared to receptor models. For receptor models the most critical source category is industry. This is probably due to the variety of single sources with different characteristics that belong to this category. Dust is the most problematic source for Chemical Transport Models, likely due to the poor information about this kind of source in the emission inventories, particularly concerning road dust re-suspension, and consequently the little detail about the chemical components of this source used in the models. The sensitivity tests show that chemical transport models show better performances when displaying a detailed set of sources (14) than when using a simplified one (only 8). It was also observed that an enhanced vertical profiling can improve the estimation of specific sources, such as industry, under complex meteorological conditions and that an insufficient spatial resolution in urban areas can impact on the capabilities of models to estimate the contribution of diffuse primary sources (e.g. traffic). Both families of models identify traffic and biomass burning as the first and second most contributing categories, respectively, to elemental carbon. The results of this study demonstrate that the source apportionment assessment methodology developed by the JRC is applicable to any kind of SA model. The same methodology is implemented in the on-line DeltaSA tool to support source apportionment model evaluation (http://source-apportionment.jrc.ec.europa.eu/).

Mechanisms of signal transduction by ethylene: overlapping and non-overlapping signalling roles in a receptor family

PubMed Central

Shakeel, Samina N.; Wang, Xiaomin; Binder, Brad M.; Schaller, G. Eric

2013-01-01

The plant hormone ethylene regulates growth and development as well as responses to biotic and abiotic stresses. Over the last few decades, key elements involved in ethylene signal transduction have been identified through genetic approaches, these elements defining a pathway that extends from initial ethylene perception at the endoplasmic reticulum to changes in transcriptional regulation within the nucleus. Here, we present our current understanding of ethylene signal transduction, focusing on recent developments that support a model with overlapping and non-overlapping roles for members of the ethylene receptor family. We consider the evidence supporting this model for sub-functionalization within the receptor family, and then discuss mechanisms by which such a sub-functionalization may occur. To this end, we consider the importance of receptor interactions in modulating their signal output and how such interactions vary in the receptor family. In addition, we consider evidence indicating that ethylene signal output by the receptors involves both phosphorylation-dependent and phosphorylation-independent mechanisms. We conclude with a current model for signalling by the ethylene receptors placed within the overall context of ethylene signal transduction. PMID:23543258

The modulatory role of spinally located histamine receptors in the regulation of the blood glucose level in d-glucose-fed mice.

PubMed

Sim, Yun-Beom; Park, Soo-Hyun; Kim, Sung-Su; Kim, Chea-Ha; Kim, Su-Jin; Lim, Su-Min; Jung, Jun-Sub; Ryu, Ohk-Hyun; Choi, Moon-Gi; Suh, Hong-Won

2014-02-01

The possible roles of spinal histamine receptors in the regulation of the blood glucose level were studied in ICR mice. Mice were intrathecally (i.t.) treated with histamine 1 (H1) receptor agonist (2-pyridylethylamine) or antagonist (cetirizine), histamine 2 (H2) receptor agonist (dimaprit) or antagonist (ranitidine), histamine 3 (H3) receptor agonist (α-methylhistamine) or antagonist (carcinine) and histamine 4 (H4) receptor agonist (VUF 8430) or antagonist (JNJ 7777120), and the blood glucose level was measured at 30, 60 and 120 min after i.t. administration. The i.t. injection with α-methylhistamine, but not carcinine slightly caused an elevation of the blood glucose level. In addition, histamine H1, H2, and H4 receptor agonists and antagonists did not affect the blood glucose level. In D-glucose-fed model, i.t. pretreatment with cetirizine enhanced the blood glucose level, whereas 2-pyridylethylamine did not affect. The i.t. pretreatment with dimaprit, but not ranitidine, enhanced the blood glucose level in D-glucose-fed model. In addition, α-methylhistamine, but not carcinine, slightly but significantly enhanced the blood glucose level D-glucose-fed model. Finally, i.t. pretreatment with JNJ 7777120, but not VUF 8430, slightly but significantly increased the blood glucose level. Although histamine receptors themselves located at the spinal cord do not exert any effect on the regulation of the blood glucose level, our results suggest that the activation of spinal histamine H2 receptors and the blockade of spinal histamine H1 or H3 receptors may play modulatory roles for up-regulation and down-regulation, respectively, of the blood glucose level in D-glucose fed model.

Role of dopamine D2 receptors in human reinforcement learning.

PubMed

Eisenegger, Christoph; Naef, Michael; Linssen, Anke; Clark, Luke; Gandamaneni, Praveen K; Müller, Ulrich; Robbins, Trevor W

2014-09-01

Influential neurocomputational models emphasize dopamine (DA) as an electrophysiological and neurochemical correlate of reinforcement learning. However, evidence of a specific causal role of DA receptors in learning has been less forthcoming, especially in humans. Here we combine, in a between-subjects design, administration of a high dose of the selective DA D2/3-receptor antagonist sulpiride with genetic analysis of the DA D2 receptor in a behavioral study of reinforcement learning in a sample of 78 healthy male volunteers. In contrast to predictions of prevailing models emphasizing DA's pivotal role in learning via prediction errors, we found that sulpiride did not disrupt learning, but rather induced profound impairments in choice performance. The disruption was selective for stimuli indicating reward, whereas loss avoidance performance was unaffected. Effects were driven by volunteers with higher serum levels of the drug, and in those with genetically determined lower density of striatal DA D2 receptors. This is the clearest demonstration to date for a causal modulatory role of the DA D2 receptor in choice performance that might be distinct from learning. Our findings challenge current reward prediction error models of reinforcement learning, and suggest that classical animal models emphasizing a role of postsynaptic DA D2 receptors in motivational aspects of reinforcement learning may apply to humans as well.

Role of Dopamine D2 Receptors in Human Reinforcement Learning

PubMed Central

Eisenegger, Christoph; Naef, Michael; Linssen, Anke; Clark, Luke; Gandamaneni, Praveen K; Müller, Ulrich; Robbins, Trevor W

2014-01-01

Influential neurocomputational models emphasize dopamine (DA) as an electrophysiological and neurochemical correlate of reinforcement learning. However, evidence of a specific causal role of DA receptors in learning has been less forthcoming, especially in humans. Here we combine, in a between-subjects design, administration of a high dose of the selective DA D2/3-receptor antagonist sulpiride with genetic analysis of the DA D2 receptor in a behavioral study of reinforcement learning in a sample of 78 healthy male volunteers. In contrast to predictions of prevailing models emphasizing DA's pivotal role in learning via prediction errors, we found that sulpiride did not disrupt learning, but rather induced profound impairments in choice performance. The disruption was selective for stimuli indicating reward, whereas loss avoidance performance was unaffected. Effects were driven by volunteers with higher serum levels of the drug, and in those with genetically determined lower density of striatal DA D2 receptors. This is the clearest demonstration to date for a causal modulatory role of the DA D2 receptor in choice performance that might be distinct from learning. Our findings challenge current reward prediction error models of reinforcement learning, and suggest that classical animal models emphasizing a role of postsynaptic DA D2 receptors in motivational aspects of reinforcement learning may apply to humans as well. PMID:24713613

Mechanism-based pharmacokinetic-pharmacodynamic modeling of the antinociceptive effect of buprenorphine in healthy volunteers.

PubMed

Yassen, Ashraf; Olofsen, Erik; Romberg, Raymonda; Sarton, Elise; Danhof, Meindert; Dahan, Albert

2006-06-01

The objective of this investigation was to characterize the pharmacokinetic-pharmacodynamic relation of buprenorphine's antinociceptive effect in healthy volunteers. Data on the time course of the antinociceptive effect after intravenous administration of 0.05-0.6 mg/70 kg buprenorphine in healthy volunteers was analyzed in conjunction with plasma concentrations by nonlinear mixed-effects analysis. A three-compartment pharmacokinetic model best described the concentration time course. Four structurally different pharmacokinetic-pharmacodynamic models were evaluated for their appropriateness to describe the time course of buprenorphine's antinociceptive effect: (1) E(max) model with an effect compartment model, (2) "power" model with an effect compartment model, (3) receptor association-dissociation model with a linear transduction function, and (4) combined biophase equilibration/receptor association-dissociation model with a linear transduction function. The latter pharmacokinetic-pharmacodynamic model described the time course of effect best and was used to explain time dependencies in buprenorphine's pharmacodynamics. The model converged, yielding precise estimation of the parameters characterizing hysteresis and the relation between relative receptor occupancy and antinociceptive effect. The rate constant describing biophase equilibration (k(eo)) was 0.00447 min(-1) (95% confidence interval, 0.00299-0.00595 min(-1)). The receptor dissociation rate constant (k(off)) was 0.0785 min(-1) (95% confidence interval, 0.0352-0.122 min(-1)), and k(on) was 0.0631 ml . ng(-1) . min(-1) (95% confidence interval, 0.0390-0.0872 ml . ng(-1) . min(-1)). This is consistent with observations in rats, suggesting that the rate-limiting step in the onset and offset of the antinociceptive effect is biophase distribution rather than slow receptor association-dissociation. In the dose range studied, no saturation of receptor occupancy occurred explaining the lack of a ceiling effect for antinociception.

A probabilistic approach to remote compositional analysis of planetary surfaces

USGS Publications Warehouse

Lapotre, Mathieu G.A.; Ehlmann, Bethany L.; Minson, Sarah E.

2017-01-01

Reflected light from planetary surfaces provides information, including mineral/ice compositions and grain sizes, by study of albedo and absorption features as a function of wavelength. However, deconvolving the compositional signal in spectra is complicated by the nonuniqueness of the inverse problem. Trade-offs between mineral abundances and grain sizes in setting reflectance, instrument noise, and systematic errors in the forward model are potential sources of uncertainty, which are often unquantified. Here we adopt a Bayesian implementation of the Hapke model to determine sets of acceptable-fit mineral assemblages, as opposed to single best fit solutions. We quantify errors and uncertainties in mineral abundances and grain sizes that arise from instrument noise, compositional end members, optical constants, and systematic forward model errors for two suites of ternary mixtures (olivine-enstatite-anorthite and olivine-nontronite-basaltic glass) in a series of six experiments in the visible-shortwave infrared (VSWIR) wavelength range. We show that grain sizes are generally poorly constrained from VSWIR spectroscopy. Abundance and grain size trade-offs lead to typical abundance errors of ≤1 wt % (occasionally up to ~5 wt %), while ~3% noise in the data increases errors by up to ~2 wt %. Systematic errors further increase inaccuracies by a factor of 4. Finally, phases with low spectral contrast or inaccurate optical constants can further increase errors. Overall, typical errors in abundance are <10%, but sometimes significantly increase for specific mixtures, prone to abundance/grain-size trade-offs that lead to high unmixing uncertainties. These results highlight the need for probabilistic approaches to remote determination of planetary surface composition.

Use of sediment source fingerprinting to assess the role of subsurface erosion in the supply of fine sediment in a degraded catchment in the Eastern Cape, South Africa.

PubMed

Manjoro, Munyaradzi; Rowntree, Kate; Kakembo, Vincent; Foster, Ian; Collins, Adrian L

2017-06-01

Sediment source fingerprinting has been successfully deployed to provide information on the surface and subsurface sources of sediment in many catchments around the world. However, there is still scope to re-examine some of the major assumptions of the technique with reference to the number of fingerprint properties used in the model, the number of model iterations and the potential uncertainties of using more than one sediment core collected from the same floodplain sink. We investigated the role of subsurface erosion in the supply of fine sediment to two sediment cores collected from a floodplain in a small degraded catchment in the Eastern Cape, South Africa. The results showed that increasing the number of individual fingerprint properties in the composite signature did not improve the model goodness-of-fit. This is still a much debated issue in sediment source fingerprinting. To test the goodness-of-fit further, the number of model repeat iterations was increased from 5000 to 30,000. However, this did not reduce uncertainty ranges in modelled source proportions nor improve the model goodness-of-fit. The estimated sediment source contributions were not consistent with the available published data on erosion processes in the study catchment. The temporal pattern of sediment source contributions predicted for the two sediment cores was very different despite the cores being collected in close proximity from the same floodplain. This highlights some of the potential limitations associated with using floodplain cores to reconstruct catchment erosion processes and associated sediment source contributions. For the source tracing approach in general, the findings here suggest the need for further investigations into uncertainties related to the number of fingerprint properties included in un-mixing models. The findings support the current widespread use of ≤5000 model repeat iterations for estimating the key sources of sediment samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Kufareva, Irina; Gustavsson, Martin; Zheng, Yi

Chemokines and their cell surface G protein–coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novelmore » epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.« less

Gβ promotes pheromone receptor polarization and yeast chemotropism by inhibiting receptor phosphorylation.

PubMed

Ismael, Amber; Tian, Wei; Waszczak, Nicholas; Wang, Xin; Cao, Youfang; Suchkov, Dmitry; Bar, Eli; Metodiev, Metodi V; Liang, Jie; Arkowitz, Robert A; Stone, David E

2016-04-12

Gradient-directed cell migration (chemotaxis) and growth (chemotropism) are processes that are essential to the development and life cycles of all species. Cells use surface receptors to sense the shallow chemical gradients that elicit chemotaxis and chemotropism. Slight asymmetries in receptor activation are amplified by downstream signaling systems, which ultimately induce dynamic reorganization of the cytoskeleton. During the mating response of budding yeast, a model chemotropic system, the pheromone receptors on the plasma membrane polarize to the side of the cell closest to the stimulus. Although receptor polarization occurs before and independently of actin cable-dependent delivery of vesicles to the plasma membrane (directed secretion), it requires receptor internalization. Phosphorylation of pheromone receptors by yeast casein kinase 1 or 2 (Yck1/2) stimulates their internalization. We showed that the pheromone-responsive Gβγ dimer promotes the polarization of the pheromone receptor by interacting with Yck1/2 and locally inhibiting receptor phosphorylation. We also found that receptor phosphorylation is essential for chemotropism, independently of its role in inducing receptor internalization. A mathematical model supports the idea that the interaction between Gβγ and Yck1/2 results in differential phosphorylation and internalization of the pheromone receptor and accounts for its polarization before the initiation of directed secretion. Copyright © 2016, American Association for the Advancement of Science.

Purinergic P2X receptors: structural models and analysis of ligand-target interaction.

PubMed

Dal Ben, Diego; Buccioni, Michela; Lambertucci, Catia; Marucci, Gabriella; Thomas, Ajiroghene; Volpini, Rosaria

2015-01-07

The purinergic P2X receptors are ligand-gated cation channels activated by the endogenous ligand ATP. They assemble as homo- or heterotrimers from seven cloned subtypes (P2X1-7) and all trimer subunits present a common topology consisting in intracellular N- and C- termini, two transmembrane domains and a large extracellular domain. These membrane proteins are present in virtually all mammalian tissues and regulate a large variety of responses in physio- and pathological conditions. The development of ligands that selectively activate or block specific P2X receptor subtypes hence represents a promising strategy to obtain novel pharmacological tools for the treatment of pain, cancer, inflammation, and neurological, cardiovascular, and endocrine diseases. The publication of the crystal structures of zebrafish P2X4 receptor in inactive and ATP-bound active forms provided structural data for the analysis of the receptor structure, the interpretation of mutagenesis data, and the depiction of ligand binding and receptor activation mechanism. In addition, the availability of ATP-competitive ligands presenting selectivity for P2X receptor subtypes supports the design of new potent and selective ligands with possibly improved pharmacokinetic profiles, with the final aim to obtain new drugs. This study describes molecular modelling studies performed to develop structural models of the human and rat P2X receptors in inactive and active states. These models allowed to analyse the role of some non-conserved residues at ATP binding site and to study the receptor interaction with some non-specific or subtype selective agonists and antagonists. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Development of a Sigma-2 Receptor affinity filter through a Monte Carlo based QSAR analysis.

PubMed

Rescifina, Antonio; Floresta, Giuseppe; Marrazzo, Agostino; Parenti, Carmela; Prezzavento, Orazio; Nastasi, Giovanni; Dichiara, Maria; Amata, Emanuele

2017-08-30

For the first time in sigma-2 (σ 2 ) receptor field, a quantitative structure-activity relationship (QSAR) model has been built using pK i values of the whole set of known selective σ 2 receptor ligands (548 compounds), taken from the Sigma-2 Receptor Selective Ligands Database (S2RSLDB) (http://www.researchdsf.unict.it/S2RSLDB/), through the Monte Carlo technique and employing the software CORAL. The model has been developed by using a large and structurally diverse set of compounds, allowing for a prediction of different populations of chemical compounds endpoint (σ 2 receptor pK i ). The statistical quality reached, suggested that model for pK i determination is robust and possesses a satisfactory predictive potential. The statistical quality is high for both visible and invisible sets. The screening of the FDA approved drugs, external to our dataset, suggested that sixteen compounds might be repositioned as σ 2 receptor ligands (predicted pK i ≥8). A literature check showed that six of these compounds have already been tested for affinity at σ 2 receptor and, of these, two (Flunarizine and Terbinafine) have shown an experimental σ 2 receptor pK i >7. This suggests that this QSAR model may be used as focusing screening filter in order to prospectively find or repurpose new drugs with high affinity for the σ 2 receptor, and overall allowing for an enhanced hit rate respect to a random screening. Copyright © 2017 Elsevier B.V. All rights reserved.

Improving Mode of Action Analysis Using Transcript Profiling in Nullizygous Mouse Models

EPA Science Inventory

A number of nuclear receptors (NR) mediate transcriptional, hepatocyte growth and carcinogenic effects in the rodent liver after chemical exposure. These receptors include the constitutive activated/androstane receptor (CAR), pregnane X receptor (PXR), and peroxisome proliferator...

Exsolution in clinoamphiboles

USGS Publications Warehouse

Ross, M.; Papike, J.J.; Weiblen, P.W.

1968-01-01

Ten amphibole specimens from a variety of metamorphic rocks such as talc schists, eclogites, and metamorphosed iron formations contain lamellae of a second amphibole oriented parallel to (101) or (100), or both, of the host. Tremolites, actinolites, and hornblendes commonly have lamellae of a calcium-poor clinoamphibole with P21/m space-group symmetry, or lamellae of citmmingtonite with C2/m space-group symmetry. Likewise ciimmingtonites and P21/m clinoamphiboles commonly contain lamellae of calcium-rich C2/m amphiboles such as tremolite. Results of x-ray diffraction, electron-probe, and microscope studies indicate that most lamellae result from unmixing of a homogeneous amphibole. The P21/m clinoampliibole is analogous to the clinopyroxene pigeonite in agreement with the results of M. G. Bown.

Leptin- and Leptin Receptor-Deficient Rodent Models: Relevance for Human Type 2 Diabetes

PubMed Central

Wang, Bingxuan; P., Charukeshi Chandrasekera; Pippin, John J.

2014-01-01

Among the most widely used animal models in obesity-induced type 2 diabetes mellitus (T2DM) research are the congenital leptin- and leptin receptor-deficient rodent models. These include the leptin-deficient ob/ob mice and the leptin receptor-deficient db/db mice, Zucker fatty rats, Zucker diabetic fatty rats, SHR/N-cp rats, and JCR:LA-cp rats. After decades of mechanistic and therapeutic research schemes with these animal models, many species differences have been uncovered, but researchers continue to overlook these differences, leading to untranslatable research. The purpose of this review is to analyze and comprehensively recapitulate the most common leptin/leptin receptor-based animal models with respect to their relevance and translatability to human T2DM. Our analysis revealed that, although these rodents develop obesity due to hyperphagia caused by abnormal leptin/leptin receptor signaling with the subsequent appearance of T2DM-like manifestations, these are in fact secondary to genetic mutations that do not reflect disease etiology in humans, for whom leptin or leptin receptor deficiency is not an important contributor to T2DM. A detailed comparison of the roles of genetic susceptibility, obesity, hyperglycemia, hyperinsulinemia, insulin resistance, and diabetic complications as well as leptin expression, signaling, and other factors that confound translation are presented here. There are substantial differences between these animal models and human T2DM that limit reliable, reproducible, and translatable insight into human T2DM. Therefore, it is imperative that researchers recognize and acknowledge the limitations of the leptin/leptin receptor-based rodent models and invest in research methods that would be directly and reliably applicable to humans in order to advance T2DM management. PMID:24809394

Leptin- and leptin receptor-deficient rodent models: relevance for human type 2 diabetes.

PubMed

Wang, Bingxuan; Chandrasekera, P Charukeshi; Pippin, John J

2014-03-01

Among the most widely used animal models in obesity-induced type 2 diabetes mellitus (T2DM) research are the congenital leptin- and leptin receptor-deficient rodent models. These include the leptin-deficient ob/ob mice and the leptin receptor-deficient db/db mice, Zucker fatty rats, Zucker diabetic fatty rats, SHR/N-cp rats, and JCR:LA-cp rats. After decades of mechanistic and therapeutic research schemes with these animal models, many species differences have been uncovered, but researchers continue to overlook these differences, leading to untranslatable research. The purpose of this review is to analyze and comprehensively recapitulate the most common leptin/leptin receptor-based animal models with respect to their relevance and translatability to human T2DM. Our analysis revealed that, although these rodents develop obesity due to hyperphagia caused by abnormal leptin/leptin receptor signaling with the subsequent appearance of T2DM-like manifestations, these are in fact secondary to genetic mutations that do not reflect disease etiology in humans, for whom leptin or leptin receptor deficiency is not an important contributor to T2DM. A detailed comparison of the roles of genetic susceptibility, obesity, hyperglycemia, hyperinsulinemia, insulin resistance, and diabetic complications as well as leptin expression, signaling, and other factors that confound translation are presented here. There are substantial differences between these animal models and human T2DM that limit reliable, reproducible, and translatable insight into human T2DM. Therefore, it is imperative that researchers recognize and acknowledge the limitations of the leptin/leptin receptor- based rodent models and invest in research methods that would be directly and reliably applicable to humans in order to advance T2DM management.

5D-QSAR for spirocyclic sigma1 receptor ligands by Quasar receptor surface modeling.

PubMed

Oberdorf, Christoph; Schmidt, Thomas J; Wünsch, Bernhard

2010-07-01

Based on a contiguous and structurally as well as biologically diverse set of 87 sigma(1) ligands, a 5D-QSAR study was conducted in which a quasi-atomistic receptor surface modeling approach (program package Quasar) was applied. The superposition of the ligands was performed with the tool Pharmacophore Elucidation (MOE-package), which takes all conformations of the ligands into account. This procedure led to four pharmacophoric structural elements with aromatic, hydrophobic, cationic and H-bond acceptor properties. Using the aligned structures a 3D-model of the ligand binding site of the sigma(1) receptor was obtained, whose general features are in good agreement with previous assumptions on the receptor structure, but revealed some novel insights since it represents the receptor surface in more detail. Thus, e.g., our model indicates the presence of an H-bond acceptor moiety in the binding site as counterpart to the ligands' cationic ammonium center, rather than a negatively charged carboxylate group. The presented QSAR model is statistically valid and represents the biological data of all tested compounds, including a test set of 21 ligands not used in the modeling process, with very good to excellent accuracy [q(2) (training set, n=66; leave 1/3 out) = 0.84, p(2) (test set, n=21)=0.64]. Moreover, the binding affinities of 13 further spirocyclic sigma(1) ligands were predicted with reasonable accuracy (mean deviation in pK(i) approximately 0.8). Thus, in addition to novel insights into the requirements for binding of spirocyclic piperidines to the sigma(1) receptor, the presented model can be used successfully in the rational design of new sigma(1) ligands. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Translational PK-PD modelling of molecular target modulation for the AMPA receptor positive allosteric modulator Org 26576.

PubMed

Bursi, Roberta; Erdemli, Gul; Campbell, Robert; Hutmacher, Matthew M; Kerbusch, Thomas; Spanswick, David; Jeggo, Ross; Nations, Kari R; Dogterom, Peter; Schipper, Jacques; Shahid, Mohammed

2011-12-01

The α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor potentiator Org 26576 represents an interesting pharmacological tool to evaluate the utility of glutamatergic enhancement towards the treatment of psychiatric disorders. In this study, a rat-human translational pharmacokinetic-pharmacodynamic (PK-PD) model of AMPA receptor modulation was used to predict human target engagement and inform dose selection in efficacy clinical trials. Modelling and simulation was applied to rat plasma and cerebrospinal fluid (CSF) pharmacokinetic and pharmacodynamic measurements to identify a target concentration (EC(80)) for AMPA receptor modulation. Human plasma pharmacokinetics was determined from 33 healthy volunteers and eight major depressive disorder patients. From four out of these eight patients, CSF PK was also determined. Simulations of human CSF levels were performed for several doses of Org 26576. Org 26576 (0.1-10 mg/kg, i.v.) potentiated rat hippocampal AMPA receptor responses in an exposure-dependant manner. The rat plasma and CSF PK data were fitted by one-compartment model each. The rat CSF PK-PD model yielded an EC(80) value of 593 ng/ml (90% confidence interval 406.8, 1,264.1). The human plasma and CSF PK data were simultaneously well described by a two-compartment model. Simulations showed that in humans at 100 mg QD, CSF levels of Org 26576 would exceed the EC(80) target concentration for about 2 h and that 400 mg BID would engage AMPA receptors for 24 h. The modelling approach provided useful insight on the likely human dose-molecular target engagement relationship for Org 26576. Based on the current analysis, 100 and 400 mg BID would be suitable to provide 'phasic' and 'continuous' AMPA receptor engagement, respectively.

Validating SWE reconstruction using Airborne Snow Observatory measurements in the Sierra Nevada

NASA Astrophysics Data System (ADS)

Bair, N.; Rittger, K.; Davis, R. E.; Dozier, J.

2015-12-01

The Airborne Snow Observatory (ASO) program offers high resolution estimates of snow water equivalent (SWE) in several small basins across California during the melt season. Primarily, water managers use this information to model snowmelt runoff into reservoirs. Another, and potentially more impactful, use of ASO SWE measurements is in validating and improving satellite-based SWE estimates which can be used in austere regions with no ground-based snow or water measurements, such as Afghanistan's Hindu Kush. Using the entire ASO dataset to date (2013-2015) which is mostly from the Upper Tuolumne basin, but also includes measurements from 2015 in the Kings, Rush Creek, Merced, and Mammoth Lakes basins, we compare ASO measurements to those from a SWE reconstruction method. Briefly, SWE reconstruction involves downscaling energy balance forcings to compute potential melt energy, then using satellite-derived estimates of fractional snow covered area (fSCA) to estimate snow melt from potential melt. The snowpack can then be built in reverse, given a remotely-sensed date of snow disappearance (fSCA=0). Our model has improvements over previous iterations in that it: uses the full energy balance (compared to a modified degree-day) approach, models bulk and surface snow temperatures, accounts for ephemeral snow, and uses a remotely-sensed snow albedo adjusted for impurities. To check that ASO provides accurate snow measurements, we compare fSCA derived from ASO snow depth at 3 m resolution with fSCA from a spectral unmixing algorithm for LandSAT at 30 m, and from binary SCA estimates from Geoeye at 0.5 m from supervised classification. To conclude, we document how our reconstruction model has evolved over the years and provide specific examples where improvements have been made using ASO and other verification sources.

3D-QSAR comparative molecular field analysis on opioid receptor antagonists: pooling data from different studies.

PubMed

Peng, Youyi; Keenan, Susan M; Zhang, Qiang; Kholodovych, Vladyslav; Welsh, William J

2005-03-10

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) on a series of opioid receptor antagonists. To obtain statistically significant and robust CoMFA models, a sizable data set of naltrindole and naltrexone analogues was assembled by pooling biological and structural data from independent studies. A process of "leave one data set out", similar to the traditional "leave one out" cross-validation procedure employed in partial least squares (PLS) analysis, was utilized to study the feasibility of pooling data in the present case. These studies indicate that our approach yields statistically significant and highly predictive CoMFA models from the pooled data set of delta, mu, and kappa opioid receptor antagonists. All models showed excellent internal predictability and self-consistency: q(2) = 0.69/r(2) = 0.91 (delta), q(2) = 0.67/r(2) = 0.92 (mu), and q(2) = 0.60/r(2) = 0.96 (kappa). The CoMFA models were further validated using two separate test sets: one test set was selected randomly from the pooled data set, while the other test set was retrieved from other published sources. The overall excellent agreement between CoMFA-predicted and experimental binding affinities for a structurally diverse array of ligands across all three opioid receptor subtypes gives testimony to the superb predictive power of these models. CoMFA field analysis demonstrated that the variations in binding affinity of opioid antagonists are dominated by steric rather than electrostatic interactions with the three opioid receptor binding sites. The CoMFA steric-electrostatic contour maps corresponding to the delta, mu, and kappa opioid receptor subtypes reflected the characteristic similarities and differences in the familiar "message-address" concept of opioid receptor ligands. Structural modifications to increase selectivity for the delta over mu and kappa opioid receptors have been predicted on the basis of the CoMFA contour maps. The structure-activity relationships (SARs) together with the CoMFA models should find utility for the rational design of subtype-selective opioid receptor antagonists.

Correlated receptor transport processes buffer single-cell heterogeneity

PubMed Central

Kallenberger, Stefan M.; Unger, Anne L.; Legewie, Stefan; Lymperopoulos, Konstantinos; Eils, Roland

2017-01-01

Cells typically vary in their response to extracellular ligands. Receptor transport processes modulate ligand-receptor induced signal transduction and impact the variability in cellular responses. Here, we quantitatively characterized cellular variability in erythropoietin receptor (EpoR) trafficking at the single-cell level based on live-cell imaging and mathematical modeling. Using ensembles of single-cell mathematical models reduced parameter uncertainties and showed that rapid EpoR turnover, transport of internalized EpoR back to the plasma membrane, and degradation of Epo-EpoR complexes were essential for receptor trafficking. EpoR trafficking dynamics in adherent H838 lung cancer cells closely resembled the dynamics previously characterized by mathematical modeling in suspension cells, indicating that dynamic properties of the EpoR system are widely conserved. Receptor transport processes differed by one order of magnitude between individual cells. However, the concentration of activated Epo-EpoR complexes was less variable due to the correlated kinetics of opposing transport processes acting as a buffering system. PMID:28945754

A Monte Carlo model reveals independent signaling at central glutamatergic synapses.

PubMed Central

Franks, Kevin M; Bartol, Thomas M; Sejnowski, Terrence J

2002-01-01

We have developed a biophysically realistic model of receptor activation at an idealized central glutamatergic synapse that uses Monte Carlo techniques to simulate the stochastic nature of transmission following release of a single synaptic vesicle. For the a synapse with 80 AMPA and 20 NMDA receptors, a single quantum, with 3000 glutamate molecules, opened approximately 3 NMDARs and 20 AMPARs. The number of open receptors varied directly with the total number of receptors, and the fraction of open receptors did not depend on the ratio of co-localized AMPARs and NMDARs. Variability decreased with increases in either total receptor number or quantal size, and differences between the variability of AMPAR and NMDAR responses were due solely to unequal numbers of receptors at the synapse. Despite NMDARs having a much higher affinity for glutamate than AMPARs, quantal release resulted in similar occupancy levels in both receptor types. Receptor activation increased with number of transmitter molecules released or total receptor number, whereas occupancy levels were only dependent on quantal size. Tortuous diffusion spaces reduced the extent of spillover and the activation of extrasynaptic receptors. These results support the conclusion that signaling is spatially independent within and between central glutamatergic synapses. PMID:12414671

Increased Accuracy of Ligand Sensing by Receptor Internalization and Lateral Receptor Diffusion

NASA Astrophysics Data System (ADS)

Aquino, Gerardo; Endres, Robert

2010-03-01

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as overcounting of the same ligand molecules is reduced. A similar role may be played by receptor diffusion om the cell membrane. Fast, lateral receptor diffusion is known to be relevant in neurotransmission initiated by release of neurotransmitter glutamate in the synaptic cleft between neurons. By binding ligand and removal by diffusion from the region of release of the neurotransmitter, diffusing receptors can be reasonably expected to reduce the local overcounting of the same ligand molecules in the region of signaling. By extending simple ligand-receptor models to out-of-equilibrium thermodynamics, we show that both receptor internalization and lateral diffusion increase the accuracy with which cells can measure ligand concentrations in the external environment. We confirm this with our model and give quantitative predictions for experimental parameters values. We give quantitative predictions, which compare favorably to experimental data of real receptors.

Hypoxia facilitates neurogenic dural plasma protein extravasation in mice: a novel animal model for migraine pathophysiology

PubMed Central

Hunfeld, Anika; Segelcke, Daniel; Bäcker, Ingo; Mecheri, Badreddine; Hemmer, Kathrin; Dlugosch, Elisabeth; Andriske, Michael; Paris, Frank; Zhu, Xinran; Lübbert, Hermann

2015-01-01

Migraine animal models generally mimic the onset of attacks and acute treatment processes. A guinea pig model used the application of meta-chlorophenylpiperazine (mCPP) to trigger immediate dural plasma protein extravasation (PPE) mediated by 5-HT2B receptors. This model has predictive value for antimigraine drugs but cannot explain the delayed onset of efficacy of 5-HT2B receptor antagonists when clinically used for migraine prophylaxis. We found that mCPP failed to induce dural PPE in mice. Considering the role 5-HT2B receptors play in hypoxia-induced pulmonary vessel muscularization, we were encouraged to keep mice under hypoxic conditions and tested whether this treatment will render them susceptible to mCPP-induced dural PPE. Following four-week of hypoxia, PPE, associated with increased transendothelial transport, was induced by mCPP. The effect was blocked by sumatriptan. Chronic application of 5-HT2B receptor or nitric oxide synthase blockers during hypoxia prevented the development of susceptibility. Here we present a migraine model that distinguishes between a migraine-like state (hypoxic mice) and normal, normoxic mice and mimics processes that are related to chronic activation of 5-HT2B receptors under hypoxia. It seems striking, that chronic endogenous activation of 5-HT2B receptors is crucial for the sensitization since 5-HT2B receptor antagonists have strong, albeit delayed migraine prophylactic efficacy. PMID:26644235

Buprenorphine-elicited alteration of adenylate cyclase activity in human embryonic kidney 293 cells coexpressing κ-, μ-opioid and nociceptin receptors

PubMed Central

Wang, Pei-Chen; Ho, Ing-Kang; Lee, Cynthia Wei-Sheng

2015-01-01

Buprenorphine, a maintenance drug for heroin addicts, exerts its pharmacological function via κ- (KOP), μ-opioid (MOP) and nociceptin/opioid receptor-like 1 (NOP) receptors. Previously, we investigated its effects in an in vitro model expressing human MOP and NOP receptors individually or simultaneously (MOP, NOP, and MOP+NOP) in human embryonic kidney 293 cells. Here, we expanded this cell model by expressing human KOP, MOP and NOP receptors individually or simultaneously (KOP, KOP+MOP, KOP+NOP and KOP+MOP+NOP). Radioligand binding with tritium-labelled diprenorphine confirmed the expression of KOP receptors. Immunoblotting and immunocytochemistry indicated that the expressed KOP, MOP and NOP receptors are N-linked glycoproteins and colocalized in cytoplasmic compartments. Acute application of the opioid receptor agonists— U-69593, DAMGO and nociceptin— inhibited adenylate cyclase (AC) activity in cells expressing KOP, MOP and NOP receptors respectively. Buprenorphine, when applied acutely, inhibited AC activity to ~90% in cells expressing KOP+MOP+NOP receptors. Chronic exposure to buprenorphine induced concentration-dependent AC superactivation in cells expressing KOP+NOP receptors, and the level of this superactivation was even higher in KOP+MOP+NOP-expressing cells. Our study demonstrated that MOP receptor could enhance AC regulation in the presence of coexpressed KOP and NOP receptors, and NOP receptor is essential for concentration-dependent AC superactivation elicited by chronic buprenorphine exposure. PMID:26153065

Metformin sensitizes triple-negative breast cancer to proapoptotic TRAIL receptor agonists by suppressing XIAP expression.

PubMed

Strekalova, Elena; Malin, Dmitry; Rajanala, Harisha; Cryns, Vincent L

2017-06-01

Despite robust antitumor activity in diverse preclinical models, TNF-related apoptosis-inducing ligand (TRAIL) receptor agonists have not demonstrated efficacy in clinical trials, underscoring the need to identify agents that enhance their activity. We postulated that the metabolic stress induced by the diabetes drug metformin would sensitize breast cancer cells to TRAIL receptor agonists. Human triple (estrogen receptor, progesterone receptor, and HER2)-negative breast cancer (TNBC) cell lines were treated with TRAIL receptor agonists (monoclonal antibodies or TRAIL peptide), metformin, or the combination. The effects on cell survival, caspase activation, and expression of TRAIL receptors and the antiapoptotic protein XIAP were determined. In addition, XIAP was silenced by RNAi in TNBC cells and the effects on sensitivity to TRAIL were determined. The antitumor effects of metformin, TRAIL, or the combination were evaluated in an orthotopic model of metastatic TNBC. Metformin sensitized diverse TNBC cells to TRAIL receptor agonists. Metformin selectively enhanced the sensitivity of transformed breast epithelial cells to TRAIL receptor agonist-induced caspase activation and apoptosis with little effect on untransformed breast epithelial cells. These effects of metformin were accompanied by robust reductions in the protein levels of XIAP, a negative regulator of TRAIL-induced apoptosis. Silencing XIAP in TNBC cells mimicked the TRAIL-sensitizing effects of metformin. Metformin also enhanced the antitumor effects of TRAIL in a metastatic murine TNBC model. Our findings indicate that metformin enhances the activity of TRAIL receptor agonists, thereby supporting the rationale for additional translational studies combining these agents.

Enhanced effects of amphetamine but reduced effects of the hallucinogen, 5-MeO-DMT, on locomotor activity in 5-HT(1A) receptor knockout mice: implications for schizophrenia.

PubMed

van den Buuse, Maarten; Ruimschotel, Emma; Martin, Sally; Risbrough, Victoria B; Halberstadt, Adam L

2011-01-01

Serotonin-1A (5-HT(1A)) receptors may play a role in schizophrenia and the effects of certain antipsychotic drugs. However, the mechanism of interaction of 5-HT(1A) receptors with brain systems involved in schizophrenia, remains unclear. Here we show that 5-HT(1A) receptor knockout mice display enhanced locomotor hyperactivity to acute treatment with amphetamine, a widely used animal model of hyperdopaminergic mechanisms in psychosis. In contrast, the effect of MK-801 on locomotor activity, modeling NMDA receptor hypoactivity, was unchanged in the knockouts. The effect of the hallucinogen 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) was markedly reduced in 5-HT(1A) receptor knockout mice. There were no changes in apomorphine-induced disruption of PPI, a model of sensory gating deficits seen in schizophrenia. Similarly, there were no major changes in density of dopamine transporters (DAT) or dopamine D(1) or D(2) receptors which could explain the behavioural changes observed in 5-HT(1A) receptor knockout mice. These results extend our insight into the possible role of these receptors in aspects of schizophrenia. As also suggested by previous studies using agonist and antagonist drugs, 5-HT(1A) receptors may play an important role in hallucinations and to modulate dopaminergic activity in the brain. Copyright © 2011 Elsevier Ltd. All rights reserved.

Residues within the Transmembrane Domain of the Glucagon-Like Peptide-1 Receptor Involved in Ligand Binding and Receptor Activation: Modelling the Ligand-Bound Receptor

PubMed Central

Coopman, K.; Wallis, R.; Robb, G.; Brown, A. J. H.; Wilkinson, G. F.; Timms, D.

2011-01-01

The C-terminal regions of glucagon-like peptide-1 (GLP-1) bind to the N terminus of the GLP-1 receptor (GLP-1R), facilitating interaction of the ligand N terminus with the receptor transmembrane domain. In contrast, the agonist exendin-4 relies less on the transmembrane domain, and truncated antagonist analogs (e.g. exendin 9–39) may interact solely with the receptor N terminus. Here we used mutagenesis to explore the role of residues highly conserved in the predicted transmembrane helices of mammalian GLP-1Rs and conserved in family B G protein coupled receptors in ligand binding and GLP-1R activation. By iteration using information from the mutagenesis, along with the available crystal structure of the receptor N terminus and a model of the active opsin transmembrane domain, we developed a structural receptor model with GLP-1 bound and used this to better understand consequences of mutations. Mutation at Y152 [transmembrane helix (TM) 1], R190 (TM2), Y235 (TM3), H363 (TM6), and E364 (TM6) produced similar reductions in affinity for GLP-1 and exendin 9–39. In contrast, other mutations either preferentially [K197 (TM2), Q234 (TM3), and W284 (extracellular loop 2)] or solely [D198 (TM2) and R310 (TM5)] reduced GLP-1 affinity. Reduced agonist affinity was always associated with reduced potency. However, reductions in potency exceeded reductions in agonist affinity for K197A, W284A, and R310A, while H363A was uncoupled from cAMP generation, highlighting critical roles of these residues in translating binding to activation. Data show important roles in ligand binding and receptor activation of conserved residues within the transmembrane domain of the GLP-1R. The receptor structural model provides insight into the roles of these residues. PMID:21868452

Mode of Action and Human Relevance Analysis for Nuclear Receptor-Mediated Liver Toxicity: A Case Study with Phenobarbital as a Model Constitutive Androstane Receptor (CAR) Activator

EPA Science Inventory

The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are key nuclear receptors involved in the regulation of cellular responses. to exposure to many xenobiotics and various physiological processes. Phenobarbital (PB) is a non­ genotoxic i...

Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

PubMed Central

Fierro, Fabrizio; Suku, Eda; Alfonso-Prieto, Mercedes; Giorgetti, Alejandro; Cichon, Sven; Carloni, Paolo

2017-01-01

Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation. PMID:28932739

Bayesian multivariate Poisson abundance models for T-cell receptor data.

PubMed

Greene, Joshua; Birtwistle, Marc R; Ignatowicz, Leszek; Rempala, Grzegorz A

2013-06-07

A major feature of an adaptive immune system is its ability to generate B- and T-cell clones capable of recognizing and neutralizing specific antigens. These clones recognize antigens with the help of the surface molecules, called antigen receptors, acquired individually during the clonal development process. In order to ensure a response to a broad range of antigens, the number of different receptor molecules is extremely large, resulting in a huge clonal diversity of both B- and T-cell receptor populations and making their experimental comparisons statistically challenging. To facilitate such comparisons, we propose a flexible parametric model of multivariate count data and illustrate its use in a simultaneous analysis of multiple antigen receptor populations derived from mammalian T-cells. The model relies on a representation of the observed receptor counts as a multivariate Poisson abundance mixture (m PAM). A Bayesian parameter fitting procedure is proposed, based on the complete posterior likelihood, rather than the conditional one used typically in similar settings. The new procedure is shown to be considerably more efficient than its conditional counterpart (as measured by the Fisher information) in the regions of m PAM parameter space relevant to model T-cell data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nuclear Receptors in Neurodegenerative Diseases

PubMed Central

Skerrett, Rebecca; Malm, Tarja; Landreth, Gary

2014-01-01

Nuclear receptors have generated substantial interest in the past decade as potential therapeutic targets for the treatment of neurodegenerative disorders. Despite years of effort, effective treatments for progressive neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and ALS remain elusive, making non-classical drug targets such as nuclear receptors an attractive alternative. A substantial literature in mouse models of disease and several clinical trials have investigated the role of nuclear receptors in various neurodegenerative disorders, most prominently AD. These studies have met with mixed results, yet the majority of studies in mouse models report positive outcomes. The mechanisms by which nuclear receptor agonists affect disease pathology remain unclear. Deciphering the complex signaling underlying nuclear receptor action in neurodegenerative diseases is essential for understanding this variability in preclinical studies, and for the successful translation of nuclear receptor agonists into clinical therapies. PMID:24874548

Quantitative structure-activity relationships of selective antagonists of glucagon receptor using QuaSAR descriptors.

PubMed

Manoj Kumar, Palanivelu; Karthikeyan, Chandrabose; Hari Narayana Moorthy, Narayana Subbiah; Trivedi, Piyush

2006-11-01

In the present paper, quantitative structure activity relationship (QSAR) approach was applied to understand the affinity and selectivity of a novel series of triaryl imidazole derivatives towards glucagon receptor. Statistically significant and highly predictive QSARs were derived for glucagon receptor inhibition by triaryl imidazoles using QuaSAR descriptors of molecular operating environment (MOE) employing computer-assisted multiple regression procedure. The generated QSAR models revealed that factors related to hydrophobicity, molecular shape and geometry predominantly influences glucagon receptor binding affinity of the triaryl imidazoles indicating the relevance of shape specific steric interactions between the molecule and the receptor. Further, QSAR models formulated for selective inhibition of glucagon receptor over p38 mitogen activated protein (MAP) kinase of the compounds in the series highlights that the same structural features, which influence the glucagon receptor affinity, also contribute to their selective inhibition.

Computational Design of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Subrahmanyam, Sreenath; Piletsky, Sergey A.

Artificial receptors have been in use for several decades as sensor elements, in affinity separation, and as models for investigation of molecular recognition. Although there have been numerous publications on the use of molecular modeling in characterization of their affinity and selectivity, very few attempts have been made on the application of molecular modeling in computational design of synthetic receptors. This chapter discusses recent successes in the use of computational design for the development of one particular branch of synthetic receptors - molecularly imprinted polymers.

Structural basis of ligand interaction with atypical chemokine receptor 3

NASA Astrophysics Data System (ADS)

Gustavsson, Martin; Wang, Liwen; van Gils, Noortje; Stephens, Bryan S.; Zhang, Penglie; Schall, Thomas J.; Yang, Sichun; Abagyan, Ruben; Chance, Mark R.; Kufareva, Irina; Handel, Tracy M.

2017-01-01

Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally driven models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.

Structural basis of ligand interaction with atypical chemokine receptor 3

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

Gustavsson, Martin; Wang, Liwen; van Gils, Noortje

2017-01-18

Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally drivenmore » models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.« less

Long-term responses of rainforest erosional systems at different spatial scales to selective logging and climatic change

PubMed Central

Walsh, R. P. D.; Bidin, K.; Blake, W. H.; Chappell, N. A.; Clarke, M. A.; Douglas, I.; Ghazali, R.; Sayer, A. M.; Suhaimi, J.; Tych, W.; Annammala, K. V.

2011-01-01

Long-term (21–30 years) erosional responses of rainforest terrain in the Upper Segama catchment, Sabah, to selective logging are assessed at slope, small and large catchment scales. In the 0.44 km2 Baru catchment, slope erosion measurements over 1990–2010 and sediment fingerprinting indicate that sediment sources 21 years after logging in 1989 are mainly road-linked, including fresh landslips and gullying of scars and toe deposits of 1994–1996 landslides. Analysis and modelling of 5–15 min stream-suspended sediment and discharge data demonstrate a reduction in storm-sediment response between 1996 and 2009, but not yet to pre-logging levels. An unmixing model using bed-sediment geochemical data indicates that 49 per cent of the 216 t km−2 a−1 2009 sediment yield comes from 10 per cent of its area affected by road-linked landslides. Fallout 210Pb and 137Cs values from a lateral bench core indicate that sedimentation rates in the 721 km2 Upper Segama catchment less than doubled with initially highly selective, low-slope logging in the 1980s, but rose 7–13 times when steep terrain was logged in 1992–1993 and 1999–2000. The need to keep steeplands under forest is emphasized if landsliding associated with current and predicted rises in extreme rainstorm magnitude-frequency is to be reduced in scale. PMID:22006973

A spectroscopic analysis of Martian crater central peaks: Formation of the ancient crust

NASA Astrophysics Data System (ADS)

Skok, J. R.; Mustard, J. F.; Tornabene, L. L.; Pan, C.; Rogers, D.; Murchie, S. L.

2012-11-01

The earliest formed crust on a single plate planet such as Mars should be preserved, deeply buried under subsequent surface materials. Mars' extensive cratering history would have fractured and disrupted the upper layers of this ancient crust. Large impacts occurring late in Martian geologic history would have excavated and exposed this deeply buried material. We report the compositional analysis of unaltered mafic Martian crater central peaks with high-resolution spectral data that was used to characterize the presence, distribution and composition of mafic mineralogy. Reflectance spectra of mafic outcrops are modeled with the Modified Gaussian Model (MGM) to determine cation composition of olivine and pyroxene mineral deposits. Observations show that central peaks with unaltered mafic units are only observed in four general regions of Mars. Each mafic unit exhibits spectrally unmixed outcrops of olivine or pyroxene, indicating dunite and pyroxenite dominated compositions instead of basaltic composition common throughout much of the planet. Compositional analysis shows a wide range of olivine Fo# ranging from Fo60 to Fo5. This variation is best explained by a high degree of fractionation in a slowly cooling, differentiating magma body. Pyroxene analysis shows that all the sites in the Southern Highlands are consistent with moderately Fe-rich, low-Ca pyroxene. Mineral segregation in the ancient crust could be caused by cumulate crystallization and settling in a large, potentially global, lava lake or near surface plutons driven by a hypothesized early Martian mantle overturn.

Conditions for super-adiabatic droplet growth after entrainment mixing

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

Yang, Fan; Shaw, Raymond; Xue, Huiwen

Cloud droplet response to entrainment and mixing between a cloud and its environment is considered, accounting for subsequent droplet growth during adiabatic ascent following a mixing event. The vertical profile for liquid water mixing ratio after a mixing event is derived analytically, allowing the reduction to be predicted from the mixing fraction and from the temperature and humidity for both the cloud and environment. It is derived for the limit of homogeneous mixing. The expression leads to a critical height above the mixing level: at the critical height the cloud droplet radius is the same for both mixed and unmixedmore » parcels, and the critical height is independent of the updraft velocity and mixing fraction. Cloud droplets in a mixed parcel are larger than in an unmixed parcel above the critical height, which we refer to as the “super-adiabatic” growth region. Analytical results are confirmed with a bin microphysics cloud model. Using the model, we explore the effects of updraft velocity, aerosol source in the environmental air, and polydisperse cloud droplets. Results show that the mixed parcel is more likely to reach the super-adiabatic growth region when the environmental air is humid and clean. It is also confirmed that the analytical predictions are matched by the volume-mean cloud droplet radius for polydisperse size distributions. Lastly, these findings have implications for the origin of large cloud droplets that may contribute to onset of collision–coalescence in warm clouds.« less

Probability of Elevated Volatile Organic Compound (VOC) Concentrations in Groundwater in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of elevated volatile organic compound (VOC) concentrations in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps was developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Probability of Elevated Nitrate Concentrations in Groundwater in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of elevated nitrate concentrations in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps was developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Conditions for super-adiabatic droplet growth after entrainment mixing

DOE PAGES

Yang, Fan; Shaw, Raymond; Xue, Huiwen

2016-07-29

Cloud droplet response to entrainment and mixing between a cloud and its environment is considered, accounting for subsequent droplet growth during adiabatic ascent following a mixing event. The vertical profile for liquid water mixing ratio after a mixing event is derived analytically, allowing the reduction to be predicted from the mixing fraction and from the temperature and humidity for both the cloud and environment. It is derived for the limit of homogeneous mixing. The expression leads to a critical height above the mixing level: at the critical height the cloud droplet radius is the same for both mixed and unmixedmore » parcels, and the critical height is independent of the updraft velocity and mixing fraction. Cloud droplets in a mixed parcel are larger than in an unmixed parcel above the critical height, which we refer to as the “super-adiabatic” growth region. Analytical results are confirmed with a bin microphysics cloud model. Using the model, we explore the effects of updraft velocity, aerosol source in the environmental air, and polydisperse cloud droplets. Results show that the mixed parcel is more likely to reach the super-adiabatic growth region when the environmental air is humid and clean. It is also confirmed that the analytical predictions are matched by the volume-mean cloud droplet radius for polydisperse size distributions. Lastly, these findings have implications for the origin of large cloud droplets that may contribute to onset of collision–coalescence in warm clouds.« less

A restricted population of CB1 cannabinoid receptors with neuroprotective activity.

PubMed

Chiarlone, Anna; Bellocchio, Luigi; Blázquez, Cristina; Resel, Eva; Soria-Gómez, Edgar; Cannich, Astrid; Ferrero, José J; Sagredo, Onintza; Benito, Cristina; Romero, Julián; Sánchez-Prieto, José; Lutz, Beat; Fernández-Ruiz, Javier; Galve-Roperh, Ismael; Guzmán, Manuel

2014-06-03

The CB1 cannabinoid receptor, the main molecular target of endocannabinoids and cannabis active components, is the most abundant G protein-coupled receptor in the mammalian brain. Of note, CB1 receptors are expressed at the synapses of two opposing (i.e., GABAergic/inhibitory and glutamatergic/excitatory) neuronal populations, so the activation of one and/or another receptor population may conceivably evoke different effects. Despite the widely reported neuroprotective activity of the CB1 receptor in animal models, the precise pathophysiological relevance of those two CB1 receptor pools in neurodegenerative processes is unknown. Here, we first induced excitotoxic damage in the mouse brain by (i) administering quinolinic acid to conditional mutant animals lacking CB1 receptors selectively in GABAergic or glutamatergic neurons, and (ii) manipulating corticostriatal glutamatergic projections remotely with a designer receptor exclusively activated by designer drug pharmacogenetic approach. We next examined the alterations that occur in the R6/2 mouse, a well-established model of Huntington disease, upon (i) fully knocking out CB1 receptors, and (ii) deleting CB1 receptors selectively in corticostriatal glutamatergic or striatal GABAergic neurons. The data unequivocally identify the restricted population of CB1 receptors located on glutamatergic terminals as an indispensable player in the neuroprotective activity of (endo)cannabinoids, therefore suggesting that this precise receptor pool constitutes a promising target for neuroprotective therapeutic strategies.

Modeling the Effects of HER/ErbB1-3 Coexpression on Receptor Dimerization and Biological Response

PubMed Central

Shankaran, Harish; Wiley, H. Steven; Resat, Haluk

2006-01-01

The human epidermal growth factor receptor (HER/ErbB) system comprises the epidermal growth factor receptor (EGFR/HER1) and three other homologs, namely HERs 2–4. This receptor system plays a critical role in cell proliferation and differentiation and receptor overexpression has been associated with poor prognosis in cancers of the epithelium. Here, we examine the effect of coexpressing varying levels of HERs 1–3 on the receptor dimerization patterns using a detailed kinetic model for HER/ErbB dimerization and trafficking. Our results indicate that coexpression of EGFR with HER2 or HER3 biases signaling to the cell surface and retards signal downregulation. In addition, simultaneous coexpression of HERs 1–3 leads to an abundance of HER2-HER3 heterodimers, which are known to be potent inducers of cell growth and transformation. Our new approach to use parameter dependence analysis in experimental design reveals that measurements of HER3 phosphorylation and HER2 internalization ratio may prove to be especially useful for the estimation of critical model parameters. Further, we examine the effect of receptor dimerization patterns on biological response using a simple phenomenological model. Results indicate that coexpression of EGFR with HER2 and HER3 at low to moderate levels may enable cells to match the response of a high HER2 expresser. PMID:16533841

Influence of ER leak on resting cytoplasmic Ca2+ and receptor-mediated Ca2+ signalling in human macrophage.

PubMed

Layhadi, Janice A; Fountain, Samuel J

2017-06-03

Mechanisms controlling endoplasmic reticulum (ER) Ca 2+ homeostasis are important regulators of resting cytoplasmic Ca 2+ concentration ([Ca 2+ ] cyto ) and receptor-mediated Ca 2+ signalling. Here we investigate channels responsible for ER Ca 2+ leak in THP-1 macrophage and human primary macrophage. In the absence of extracellular Ca 2+ we employ ionomycin action at the plasma membrane to stimulate ER Ca 2+ leak. Under these conditions ionomycin elevates [Ca 2+ ] cyto revealing a Ca 2+ leak response which is abolished by thapsigargin. IP 3 receptors (Xestospongin C, 2-APB), ryanodine receptors (dantrolene), and translocon (anisomycin) inhibition facilitated ER Ca 2+ leak in model macrophage, with translocon inhibition also reducing resting [Ca 2+ ] cyto . In primary macrophage, translocon inhibition blocks Ca 2+ leak but does not influence resting [Ca 2+ ] cyto . We identify a role for translocon-mediated ER Ca 2+ leak in receptor-mediated Ca 2+ signalling in both model and primary human macrophage, whereby the Ca 2+ response to ADP (P2Y receptor agonist) is augmented following anisomycin treatment. In conclusion, we demonstrate a role of ER Ca 2+ leak via the translocon in controlling resting cytoplasmic Ca 2+ in model macrophage and receptor-mediated Ca 2+ signalling in model macrophage and primary macrophage. Copyright © 2017 Elsevier Inc. All rights reserved.

Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions

NASA Astrophysics Data System (ADS)

Chaudhari, Rajan; Heim, Andrew J.; Li, Zhijun

2015-05-01

Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy of "modeling first, refinement next". In the present work, we developed an alternative modeling approach through the novel application of available multiple templates. First, conserved inter-residue interactions are derived from each additional template through conservation analysis of each template-target pairwise alignment. Then, these interactions are converted into distance restraints and incorporated in the homology modeling process. This approach was applied to modeling of the human β2 adrenergic receptor using the bovin rhodopsin and the human protease-activated receptor 1 as templates and improved model quality was demonstrated compared to the homology model generated by standard single-template and multiple-template methods. This method of "refined restraints first, modeling next", provides a fast and complementary way to the current modeling approaches. It allows rational identification and implementation of additional conserved distance restraints extracted from multiple templates and/or experimental data, and has the potential to be applicable to modeling of all helical transmembrane proteins.

Novel agonists for serotonin 5-HT7 receptors reverse metabotropic glutamate receptor-mediated long-term depression in the hippocampus of wild-type and Fmr1 KO mice, a model of Fragile X Syndrome

PubMed Central

Costa, Lara; Sardone, Lara M.; Lacivita, Enza; Leopoldo, Marcello; Ciranna, Lucia

2015-01-01

Serotonin 5-HT7 receptors are expressed in the hippocampus and modulate the excitability of hippocampal neurons. We have previously shown that 5-HT7 receptors modulate glutamate-mediated hippocampal synaptic transmission and long-term synaptic plasticity. In particular, we have shown that activation of 5-HT7 receptors reversed metabotropic glutamate receptor-mediated long-term depression (mGluR-LTD) in wild-type (wt) and in Fmr1 KO mice, a mouse model of Fragile X Syndrome in which mGluR-LTD is abnormally enhanced, suggesting that 5-HT7 receptor agonists might be envisaged as a novel therapeutic strategy for Fragile X Syndrome. In this perspective, we have characterized the basic in vitro pharmacokinetic properties of novel molecules with high binding affinity and selectivity for 5-HT7 receptors and we have tested their effects on synaptic plasticity using patch clamp on acute hippocampal slices. Here we show that LP-211, a high affinity selective agonist of 5-HT7 receptors, reverses mGluR-LTD in wt and Fmr1 KO mice, correcting a synaptic malfunction in the mouse model of Fragile X Syndrome. Among novel putative agonists of 5-HT7 receptors, the compound BA-10 displayed improved affinity and selectivity for 5-HT7 receptors and improved in vitro pharmacokinetic properties with respect to LP-211. BA-10 significantly reversed mGluR-LTD in the CA3-CA1 synapse in wt and Fmr1KO mice, indicating that BA-10 behaved as a highly effective agonist of 5-HT7 receptors and reduced exaggerated mGluR-LTD in a mouse model of Fragile X Syndrome. On the other side, the compounds RA-7 and PM-20, respectively arising from in vivo metabolism of LP-211 and BA-10, had no effect on mGluR-LTD thus did not behave as agonists of 5-HT7 receptors in our conditions. The present results provide information about the structure-activity relationship of novel 5-HT7 receptor agonists and indicate that LP-211 and BA-10 might be used as novel pharmacological tools for the therapy of Fragile X Syndrome. PMID:25814945

Identification of key residues for the binding of glucagon to the N-terminal domain of its receptor: an alanine scan and modeling study.

PubMed

Prévost, M; Vertongen, P; Waelbroeck, M

2012-10-01

Glucagon plays an essential role in the glycemia maintenance during fasting, but also aggravates hyperglycemia in diabetic patients. A series of analogues of glucagon were synthesized replacing each amino acid of the C-terminal region (residues 15-29) with alanine. The residues affecting the binding to the glucagon receptor are found to be located on one face of the glucagon helix. Several 3-dimensional models of the N-terminal domain of the glucagon receptor in complex with its ligand peptide were built and used to analyze the peptide-receptor interface in terms of the nature of the peptide residues and the interactions they form with the receptor. The models suggest that glucagon keeps its native helical structure upon binding, and that a large part of the interface formed with the receptor is hydrophobic. We find that in the C-terminal region, F22, V23, M27, and D15 are the most important residues for peptide binding. They bury a large portion of their solvent accessible surface area and make numerous interactions with the receptor mainly of the hydrophobic type. © Georg Thieme Verlag KG Stuttgart · New York.

Improper activation of D1 and D2 receptors leads to excess noise in prefrontal cortex

PubMed Central

Avery, Michael C.; Krichmar, Jeffrey L.

2015-01-01

The dopaminergic system has been shown to control the amount of noise in the prefrontal cortex (PFC) and likely plays an important role in working memory and the pathophysiology of schizophrenia. We developed a model that takes into account the known receptor distributions of D1 and D2 receptors, the changes these receptors have on neuron response properties, as well as identified circuitry involved in working memory. Our model suggests that D1 receptor under-stimulation in supragranular layers gates internal noise into the PFC leading to cognitive symptoms as has been proposed in attention disorders, while D2 over-stimulation gates noise into the PFC by over-activation of cortico-striatal projecting neurons in infragranular layers. We apply this model in the context of a memory-guided saccade paradigm and show deficits similar to those observed in schizophrenic patients. We also show set-shifting impairments similar to those observed in rodents with D1 and D2 receptor manipulations. We discuss how the introduction of noise through changes in D1 and D2 receptor activation may account for many of the symptoms of schizophrenia depending on where this dysfunction occurs in the PFC. PMID:25814948

Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

PubMed Central

Frimurer, Thomas M.; Meiler, Jens

2013-01-01

The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs) creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD) of 2.2 Å for the transmembrane region and 5 Å for the second extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves, however, it remains difficult to unambiguously identify correct binding modes by score alone. On average, sampling performance was improved by 103 fold over random using knowledge-based and energy-based filters. In assessing the applicability of experimental constraints, we found that sampling performance is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining receptor-ligand complexes. PMID:23844000

wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model

PubMed Central

De Paris, Renata; Frantz, Fábio A.; Norberto de Souza, Osmar; Ruiz, Duncan D. A.

2013-01-01

Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docking Workflow (wFReDoW), which reduces the CPU time in the molecular docking simulations of FFR models to small molecules. It is based on the new workflow data pattern called self-adaptive multiple instances (P-SaMIs) and on a middleware built on Amazon EC2 instances. P-SaMI reduces the number of molecular docking simulations while the middleware speeds up the docking experiments using a High Performance Computing (HPC) environment on the cloud. The experimental results show a reduction in the total elapsed time of docking experiments and the quality of the new reduced receptor models produced by discarding the nonpromising conformations from an FFR model ruled by the P-SaMI data pattern. PMID:23691504

Decreased CB receptor binding and cannabinoid signaling in three brain regions of a rat model of schizophrenia.

PubMed

Szűcs, Edina; Dvorácskó, Szabolcs; Tömböly, Csaba; Büki, Alexandra; Kékesi, Gabriella; Horváth, Gyöngyi; Benyhe, Sándor

2016-10-28

Schizophrenia is a serious mental health disorder characterized by several behavioral and biochemicel abnormalities. In a previous study we have shown that mu-opioid (MOP) receptor signaling is impaired in specific brain regions of our three-hit animal model of schizophrenia. Since the cannabinoid system is significantly influenced in schizophrenic patients, in the present work we investigated cannabinoid (CB) receptor binding and G-protein activation in cortical, subcortical and cerebellar regions of control and 'schizophrenic' rats. Cannabinoid agonist (WIN-55,212-2 mesylate) mediated G-protein activation was consistently decreased in all areas tested, and the difference was extremely significant in membranes prepared from the cerebellum. Interestingly, the cerebellar activity of WIN-55,212-2 stimulated G-proteins was substantially higher than those of cerebral cortex and subcortical region in control animals, indicating a primordial role of the cannabinoid system in the cerebellum. At the level of radioligand binding, the affinities of the CB receptors were also markedly decreased in the model animals. Capacity of the [ 3 H]WIN-55,212-2 binding was only higher in the cerebellum of 'schizophrenic' model rats. Taken together, in all three brain areas of model rats both cannabinoid receptor binding and cannabinoid agonist-mediated G-protein activation were regularly decreased. Our results revealed that besides the opioids, the endocannabinoid - cannabis receptor system also shows impairment in our rat model, increasing its face validity and translational utility. Copyright © 2016. Published by Elsevier Ireland Ltd.

A Novel Method for Analyzing Extremely Biased Agonism at G Protein–Coupled Receptors

PubMed Central

Zhou, Lei; Ehlert, Frederick J.; Bohn, Laura M.

2015-01-01

Seven transmembrane receptors were originally named and characterized based on their ability to couple to heterotrimeric G proteins. The assortment of coupling partners for G protein–coupled receptors has subsequently expanded to include other effectors (most notably the βarrestins). This diversity of partners available to the receptor has prompted the pursuit of ligands that selectively activate only a subset of the available partners. A biased or functionally selective ligand may be able to distinguish between different active states of the receptor, and this would result in the preferential activation of one signaling cascade more than another. Although application of the “standard” operational model for analyzing ligand bias is useful and suitable in most cases, there are limitations that arise when the biased agonist fails to induce a significant response in one of the assays being compared. In this article, we describe a quantitative method for measuring ligand bias that is particularly useful for such cases of extreme bias. Using simulations and experimental evidence from several κ opioid receptor agonists, we illustrate a “competitive” model for quantitating the degree and direction of bias. By comparing the results obtained from the competitive model with the standard model, we demonstrate that the competitive model expands the potential for evaluating the bias of very partial agonists. We conclude the competitive model provides a useful mechanism for analyzing the bias of partial agonists that exhibit extreme bias. PMID:25680753

Simvastatin Prevents Dopaminergic Neurodegeneration in Experimental Parkinsonian Models: The Association with Anti-Inflammatory Responses

PubMed Central

Zhang, Limin; Wu, Aimin; Yang, Yu; Xiong, Zhaojun; Deng, Chao; Huang, Xu-Feng; Yenari, Midori A.; Yang, Yuan-Guo; Ying, Weihai; Wang, Qing

2011-01-01

Background In addition to their original applications to lowering cholesterol, statins display multiple neuroprotective effects. N-methyl-D-aspartate (NMDA) receptors interact closely with the dopaminergic system and are strongly implicated in therapeutic paradigms of Parkinson's disease (PD). This study aims to investigate how simvastatin impacts on experimental parkinsonian models via regulating NMDA receptors. Methodology/Principal Findings Regional changes in NMDA receptors in the rat brain and anxiolytic-like activity were examined after unilateral medial forebrain bundle lesion by 6-hydroxydopamine via a 3-week administration of simvastatin. NMDA receptor alterations in the post-mortem rat brain were detected by [3H]MK-801(Dizocilpine) binding autoradiography. 6-hydroxydopamine treated PC12 was applied to investigate the neuroprotection of simvastatin, the association with NMDA receptors, and the anti-inflammation. 6-hydroxydopamine induced anxiety and the downregulation of NMDA receptors in the hippocampus, CA1(Cornu Ammonis 1 Area), amygdala and caudate putamen was observed in 6-OHDA(6-hydroxydopamine) lesioned rats whereas simvastatin significantly ameliorated the anxiety-like activity and restored the expression of NMDA receptors in examined brain regions. Significant positive correlations were identified between anxiolytic-like activity and the restoration of expression of NMDA receptors in the hippocampus, amygdala and CA1 following simvastatin administration. Simvastatin exerted neuroprotection in 6-hydroxydopamine-lesioned rat brain and 6-hydroxydopamine treated PC12, partially by regulating NMDA receptors, MMP9 (matrix metalloproteinase-9), and TNF-a (tumour necrosis factor-alpha). Conclusions/Significance Our results provide strong evidence that NMDA receptor modulation after simvastatin treatment could partially explain its anxiolytic-like activity and anti-inflammatory mechanisms in experimental parkinsonian models. These findings contribute to a better understanding of the critical roles of simvastatin in treating PD via NMDA receptors. PMID:21731633

Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques.

PubMed

Durdagi, Serdar; Salmas, Ramin Ekhteiari; Stein, Matthias; Yurtsever, Mine; Seeman, Philip

2016-02-17

We have recently reported G-protein coupled receptor (GPCR) model structures for the active and inactive states of the human dopamine D2 receptor (D2R) using adrenergic crystal structures as templates. Since the therapeutic concentrations of dopamine agonists that suppress the release of prolactin are the same as those that act at the high-affinity state of the D2 receptor (D2High), D2High in the anterior pituitary gland is considered to be the functional state of the receptor. In addition, the therapeutic concentrations of anti-Parkinson drugs are also related to the dissociation constants in the D2High form of the receptor. The discrimination between the high- and low-affinity (D2Low) components of the D2R is not obvious and requires advanced computer-assisted structural biology investigations. Therefore, in this work, the derived D2High and D2Low receptor models (GPCR monomer and dimer three-dimensional structures) are used as drug-binding targets to investigate binding interactions of dopamine and apomorphine. The study reveals a match between the experimental dissociation constants of dopamine and apomorphine at their high- and low-affinity sites of the D2 receptor in monomer and dimer and their calculated dissociation constants. The allosteric receptor-receptor interaction for dopamine D2R dimer is associated with the accessibility of adjacent residues of transmembrane region 4. The measured negative cooperativity between agonist ligand at dopamine D2 receptor is also correctly predicted using the D2R homodimerization model.

Yeast as a model system for mammalian seven-transmembrane segment receptors

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

Jeansonne, N.E.

1994-05-01

Investigators have used the budding yeast Saccharomyces cerevisiae as a model system in which to study the {beta}-adrenergic receptor, the T-cell receptor pathway, initiation of mammalian DNA replication, initiation of mammalian transcription, secretion, the CDC2 kinase system, cell cycle control, and aging, as well as the function of oncogenes. This list continues to growth with the discovery of an immunoglobulin heavy-chain binding homologue in yeast, an Rb binding protein homologue, and a possible yeast arrestin. Yeast is relatively easy to maintain, to grow, and to genetically manipulate. A single gene can be overexpressed, selectively mutated or deleted from its chromosomalmore » location. In this way, the in vivo function of a gene can be studied. It has become reasonable to consider yeast as a model system for studying the seven transmembrane segments (7-TMS) receptor family. Currently, subtypes of the {beta}-adrenergic receptor are being studied in yeast. The receptor and its G{sub {alpha}}-G-protein, trigger the mating pheromone receptor pathway. This provides a powerful assay for determining receptor function. Studies expressing the muscarinic cholinergic receptor in yeast are underway. The yeast pheromone receptor belongs to this receptor family, sharing sequences and secondary structure homology. An effective strategy has been to identify a yeast pathway or process which is homologous to a mammalian system. The pathway is delineated in yeast, identifying other genetic components. Then yeast genes are used to screen for human homologues of these components. The putative human homologues are then expressed in yeast and in mammalian cells to determine function. When this type of {open_quotes}mixing and matching{close_quotes} works, yeast genetics can be a powerful tool. 115 refs.« less

Activation of spinal and supraspinal cannabinoid-1 receptors lead to antinociception in a rat model of neuropathic spinal cord injury pain

PubMed Central

Hama, Aldric; Sagen, Jacqueline

2011-01-01

Activation of CNS cannabinoid subtype-1 (CB1) receptors has been shown to mediate the antinociceptive and other effects of systemically administered CB receptor agonists. The endogenous peptide CB receptor ligand hemopressin (HE) has previously demonstrated an antinociceptive effect in rats with a hind paw inflammation, without exhibiting characteristic CB1 receptor-mediated side-effects. The current study evaluated the effect of intrathecal (i.t.) and intracerebroventricular (i.c.v.) injection of HE in a rat model of neuropathic spinal cord injury (SCI) pain. The non-subtype selective CB receptor agonist WIN 55,212-2 was also centrally administered in SCI rats as a comparator. Four weeks following an acute compression of the mid-thoracic spinal cord, rats displayed markedly decreased hind paw withdrawal thresholds, indicative of below-level neuropathic pain. Central administration of WIN 55,212-2 significantly increased withdrawal thresholds, whereas HE did not. Hemopressin has been reported to block CB1 receptors in vitro, similar to the CB1 receptor antagonist rimonabant. Pretreatment with rimonabant completely blocked the antinociceptive effect of centrally administered WIN 55,212-2, but pretreatment with HE did not. While the data confirm that activation of either supraspinal or spinal CB1 receptors leads to significant antinociception in SCI rats, the current data do not support an antinociceptive effect from an acute blockade of central CB1 receptors, HE’s putative antinociceptive mechanism, in neuropathic SCI rats. Although such a mechanism could be useful in other models of pain with a significant inflammatory component, the current data indicate that activation of CB1 receptors is needed to ameliorate neuropathic SCI pain. PMID:21813113

Simvastatin prevents dopaminergic neurodegeneration in experimental parkinsonian models: the association with anti-inflammatory responses.

PubMed

Yan, Junqiang; Xu, Yunqi; Zhu, Cansheng; Zhang, Limin; Wu, Aimin; Yang, Yu; Xiong, Zhaojun; Deng, Chao; Huang, Xu-Feng; Yenari, Midori A; Yang, Yuan-Guo; Ying, Weihai; Wang, Qing

2011-01-01

In addition to their original applications to lowering cholesterol, statins display multiple neuroprotective effects. N-methyl-D-aspartate (NMDA) receptors interact closely with the dopaminergic system and are strongly implicated in therapeutic paradigms of Parkinson's disease (PD). This study aims to investigate how simvastatin impacts on experimental parkinsonian models via regulating NMDA receptors. Regional changes in NMDA receptors in the rat brain and anxiolytic-like activity were examined after unilateral medial forebrain bundle lesion by 6-hydroxydopamine via a 3-week administration of simvastatin. NMDA receptor alterations in the post-mortem rat brain were detected by [³H]MK-801(Dizocilpine) binding autoradiography. 6-hydroxydopamine treated PC12 was applied to investigate the neuroprotection of simvastatin, the association with NMDA receptors, and the anti-inflammation. 6-hydroxydopamine induced anxiety and the downregulation of NMDA receptors in the hippocampus, CA1(Cornu Ammonis 1 Area), amygdala and caudate putamen was observed in 6-OHDA(6-hydroxydopamine) lesioned rats whereas simvastatin significantly ameliorated the anxiety-like activity and restored the expression of NMDA receptors in examined brain regions. Significant positive correlations were identified between anxiolytic-like activity and the restoration of expression of NMDA receptors in the hippocampus, amygdala and CA1 following simvastatin administration. Simvastatin exerted neuroprotection in 6-hydroxydopamine-lesioned rat brain and 6-hydroxydopamine treated PC12, partially by regulating NMDA receptors, MMP9 (matrix metalloproteinase-9), and TNF-a (tumour necrosis factor-alpha). Our results provide strong evidence that NMDA receptor modulation after simvastatin treatment could partially explain its anxiolytic-like activity and anti-inflammatory mechanisms in experimental parkinsonian models. These findings contribute to a better understanding of the critical roles of simvastatin in treating PD via NMDA receptors.

Use of polyclonal and monoclonal antibodies to study hCG-receptor interactions

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

Milius, R.P.

1985-01-01

Although the glycoprotein hormones lutropin (LH), follitropin (FSH), and thyrotropin (TSH) bind to different receptors, each contains an identical alpha subunit. Specificity is somehow endowed by theta subunits which are distinct for each hormone. Human choriogonadotropin (hCG) is a natural LH analog that contains a beta subunit nearly identical to that of LH. The roles of these subunits in the recognition and high affinity binding of hCG to receptor was examined. Polyclonal and monoclonal antibodies specific for the individual subunits of hCG were used to probe the hormone-receptor interaction. Conformation-specific and sequence-specific antibodies were examined for their abilities to bindmore » Triton X-100-solubilized /sup 125/I-hCG-receptor complex and to inhibit hormone binding to crude rat ovarian membranes containing receptor. Even though the immunoreactive sites are not located on the receptor binding surface of the beta subunit, most, but not all, of these polyclonal and monoclonal antibodies were able to inhibit /sup 125/I-hCG binding to receptor. Although the inhibition of binding may be due to steric interference due to the size of the antibody molecules, a two-step model for hCG binding to receptor is presented that also explains these results. In this model, the beta subunit initially binds with the receptor with a highly specific but low affinity interaction. This activates a site for the high affinity binding of the alpha subunit and stabilization of the complex. This is an attractive model as it may be applied to other glycoprotein hormones sharing an alpha subunit.« less

Losartan suppresses the kainate-induced changes of angiotensin AT1 receptor expression in a model of comorbid hypertension and epilepsy.

PubMed

Atanasova, Dimitrinka; Tchekalarova, Jana; Ivanova, Natasha; Nenchovska, Zlatina; Pavlova, Ekaterina; Atanassova, Nina; Lazarov, Nikolai

2018-01-15

Experimental and clinical studies have demonstrated that components of renin-angiotensin system are elevated in the hippocampus in epileptogenic conditions. In the present work, we explored the changes in the expression of angiotensin II receptor, type 1 (AT 1 receptor) in limbic structures, as well as the effect of the AT1 receptor antagonist losartan in a model of comorbid hypertension and epilepsy. The expression of AT 1 receptors was compared between spontaneously hypertensive rats (SHRs) and Wistar rats by using immunohistochemistry in the kainate (KA) model of temporal lobe epilepsy (TLE). The effect of losartan was studied on AT 1 receptor expression in epileptic rats that were treated for a period of 4weeks after status epilepticus. The naive and epileptic SHRs were characterized by stronger protein expression of AT 1 receptor than normotensive Wistar rats in the CA1, CA3a, CA3b, CA3c field and the hilus of the dentate gyrus of the dorsal hippocampus but fewer cells were immunostained in the piriform cortex. Increased AT 1 immunostaining was observed in the basolateral amygdala of epileptic SHRs but not of epileptic Wistar rats. Losartan exerted stronger and structure-dependent suppression of AT 1 receptor expression in SHRs compared to Wistar rats. Our results confirm the important role of AT 1 receptor in epilepsy and suggest that the AT 1 receptor antagonists could be used as a therapeutic strategy for treatment of comorbid hypertension and epilepsy. Copyright © 2017 Elsevier Inc. All rights reserved.

Treatment of Fragile X Syndrome with a Neuroactive Steroid

DTIC Science & Technology

2015-08-01

in the fragile X mouse model and the Drosophila (fruit fly) models of FXS that the GABAA system, including multiple receptors, is dramatically down... Drosophila (fruit fly) models of FXS that the GABAA system, including multiple receptors, is dramatically down-regulated. Ganaxolone is a drug that

MULTIVARIATE RECEPTOR MODELS-CURRENT PRACTICE AND FUTURE TRENDS. (R826238)

EPA Science Inventory

Multivariate receptor models have been applied to the analysis of air quality data for sometime. However, solving the general mixture problem is important in several other fields. This paper looks at the panoply of these models with a view of identifying common challenges and ...

Fingerprinting of bed sediment in the Tay Estuary, Scotland: an environmental magnetism approach

NASA Astrophysics Data System (ADS)

Jenkins, Pierre A.; Duck, Rob W.; Rowan, John S.; Walden, John

Sediment fingerprinting is commonly used for sediment provenance studies in lakes, rivers and reservoirs and on hillslopes and floodplains. This investigation explores the mixing of terrestrial and marine-derived sediment in the Tay Estuary, Scotland, using mineral magnetic attributes for fingerprinting. Samples representative of the estuary sediments and of four sources (end-members) were subjected to a suite of magnetic susceptibility and remanence measurements. Sediment samples from the beds of the Rivers Tay and Earn represented fluvial inputs while samples from the Angus and Fife coasts represented marine input. Multivariate discriminant and factor analysis showed that the sources could be separated on the basis of six magnetic parameters in a simple multivariate unmixing model to identify source contributions to estuarine bed sediments. Multi-domain magnetite signatures, characteristic of unweathered bedrock, dominate the magnetic measurements. Overall contributions of 3% from the River Earn, 17% from the River Tay, 29% from the Angus coast and 51% from the Fife coast source end-members, demonstrated the present-day regime of marine sediment derivation in the Tay Estuary. However, this conceals considerable spatial variability both along-estuary and in terms of sub-environments, with small-scale variations in sediment provenance reflecting local morphology, particularly areas of channel convergence.

Isograde mapping and mineral identification on the island of Naxos, Greece, using DAIS 7915 hyperspectral data

NASA Astrophysics Data System (ADS)

Echtler, Helmut; Segl, Karl; Dickerhof, Corinna; Chabrillat, Sabine; Kaufmann, Hermann J.

2003-03-01

The ESF-LSF 1997 flight campaign conducted by the German Aerospace Center (DLR) recorded several transects across the island of Naxos using the airborne hyperspectral scanner DAIS. The geological targets cover all major litho-tectonic units of a metamorphic dome with the transition of metamorphic zonations from the outer meta-sedimentary greenschist envelope to the gneissic amphibolite facies and migmatitic core. Mineral identification of alternating marble-dolomite sequences and interlayered schists bearing muscovite and biotite has been accomplished using the airborne hyperspectral DAIS 7915 sensor. Data have been noise filtered based on maximum noise fraction (MNF) and fast Fourier transform (FFT) and converted from radiance to reflectance. For mineral identification, constrained linear spectral unmixing and spectral angle mapper (SAM) algorithms were tested. Due to their unsatisfying results a new approach was developed which consists of a linear mixture modeling and spectral feature fitting. This approach provides more detailed and accurate information. Results are discussed in comparison with detailed geological mapping and additional information. Calcites are clearly separated from dolomites as well as the mica-schist sequences by a good resolution of the mineral muscovite. Thereon an outstanding result represents the very good resolution of the chlorite/mica (muscovite, biotite)-transition defining a metamorphic isograde.

Mapping Environmental Contaminants at Ray Mine, AZ

NASA Technical Reports Server (NTRS)

McCubbin, Ian; Lang, Harold

2000-01-01

Airborne Visible and InfraRed Imaging Spectrometer (AVIRIS) data was collected over Ray Mine as part of a demonstration project for the Environmental Protection Agency (EPA) through the Advanced Measurement Initiative (AMI). The overall goal of AMI is to accelerate adoption and application of advanced measurement technologies for cost effective environmental monitoring. The site was selected to demonstrate the benefit to EPA in using advanced remote sensing technologies for the detection of environmental contaminants due to the mineral extraction industry. The role of the Jet Propulsion Laboratory in this pilot study is to provide data as well as performing calibration, data analysis, and validation of the AVIRIS results. EPA is also interested in developing protocols that use commercial software to perform such work on other high priority EPA sites. Reflectance retrieval was performed using outputs generated by the MODTRAN radiative transfer model and field spectra collected for the purpose of calibration. We are presenting advanced applications of the ENVI software package using n-Dimensional Partial Unmixing to identify image-derived endmembers that best match target materials reference spectra from multiple spectral libraries. Upon identification of the image endmembers the Mixture Tuned Match Filter algorithm was applied to map the endmembers within each scene. Using this technique it was possible to map four different mineral classes that are associated with mine generated acid waste.

Spectroscopic identification of individual fluorophores using photoluminescence excitation spectra.

PubMed

Czerski, J; Colomb, W; Cannataro, F; Sarkar, S K

2018-01-25

The identity of a fluorophore can be ambiguous if other fluorophores or nonspecific fluorescent impurities have overlapping emission spectra. The presence of overlapping spectra makes it difficult to differentiate fluorescent species using discrete detection channels and unmixing of spectra. The unique absorption and emission signatures of fluorophores provide an opportunity for spectroscopic identification. However, absorption spectroscopy may be affected by scattering, whereas fluorescence emission spectroscopy suffers from signal loss by gratings or other dispersive optics. Photoluminescence excitation spectra, where excitation is varied and emission is detected at a fixed wavelength, allows hyperspectral imaging with a single emission filter for high signal-to-background ratio without any moving optics on the emission side. We report a high throughput method for measuring the photoluminescence excitation spectra of individual fluorophores using a tunable supercontinuum laser and prism-type total internal reflection fluorescence microscope. We used the system to measure and sort the photoluminescence excitation spectra of individual Alexa dyes, fluorescent nanodiamonds (FNDs), and fluorescent polystyrene beads. We used a Gaussian mixture model with maximum likelihood estimation to objectively separate the spectra. Finally, we spectroscopically identified different species of fluorescent nanodiamonds with overlapping spectra and characterized the heterogeneity of fluorescent nanodiamonds of varying size. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Numerical Study on Crossflow Printed Circuit Heat Exchanger for Advanced Small Modular Reactors

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

Yoon, Su-Jong; Sabharwall, Piyush; Kim, Eung-Soo

2014-03-01

Various fluids such as water, gases (helium), molten salts (FLiNaK, FLiBe) and liquid metal (sodium) are used as a coolant of advanced small modular reactors (SMRs). The printed circuit heat exchanger (PCHE) has been adopted as the intermediate and/or secondary heat exchanger of SMR systems because this heat exchanger is compact and effective. The size and cost of PCHE can be changed by the coolant type of each SMR. In this study, the crossflow PCHE analysis code for advanced small modular reactor has been developed for the thermal design and cost estimation of the heat exchanger. The analytical solution ofmore » single pass, both unmixed fluids crossflow heat exchanger model was employed to calculate a two dimensional temperature profile of a crossflow PCHE. The analytical solution of crossflow heat exchanger was simply implemented by using built in function of the MATLAB program. The effect of fluid property uncertainty on the calculation results was evaluated. In addition, the effect of heat transfer correlations on the calculated temperature profile was analyzed by taking into account possible combinations of primary and secondary coolants in the SMR systems. Size and cost of heat exchanger were evaluated for the given temperature requirement of each SMR.« less

A comparison of spectral mixture analysis an NDVI for ascertaining ecological variables

NASA Technical Reports Server (NTRS)

Wessman, Carol A.; Bateson, C. Ann; Curtiss, Brian; Benning, Tracy L.

1993-01-01

In this study, we compare the performance of spectral mixture analysis to the Normalized Difference Vegetation Index (NDVI) in detecting change in a grassland across topographically-induced nutrient gradients and different management schemes. The Konza Prairie Research Natural Area, Kansas, is a relatively homogeneous tallgrass prairie in which change in vegetation productivity occurs with respect to topographic positions in each watershed. The area is the site of long-term studies of the influence of fire and grazing on tallgrass production and was the site of the First ISLSCP (International Satellite Land Surface Climatology Project) Field Experiment (FIFE) from 1987 to 1989. Vegetation indices such as NDVI are commonly used with imagery collected in few (less than 10) spectral bands. However, the use of only two bands (e.g. NDVI) does not adequately account for the complex of signals making up most surface reflectance. Influences from background spectral variation and spatial heterogeneity may confound the direct relationship with biological or biophysical variables. High dimensional multispectral data allows for the application position of techniques such as derivative analysis and spectral curve fitting, thereby increasing the probability of successfully modeling the reflectance from mixed surfaces. The higher number of bands permits unmixing of a greater number of surface components, separating the vegetation signal for further analyses relevant to biological variables.