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At least 379 records · Page 21

Implementation of Dynamic Extensible Adaptive Locally Exchangeable Measures (IDEALEM) v 0.1

Handling large streaming data is essential for various applications such as network traffic analysis, social networks, energy cost trends, and environment modeling. However, it is in general intractable to store, compute, search, and retrieve large streaming data. This software addresses a fundamental issue, which is to reduce the size of large streaming data and still obtain accurate statistical analysis. As an example, when a high-speed network such as 100 Gbps network is monitored, the collected measurement data rapidly grows so that polynomial time algorithms (e.g., Gaussian processes) become intractable. One possible solution to reduce the storage of vast amounts of measured data is to store a random sample, such as one out of 1000 network packets. However, such static sampling methods (linear sampling) have drawbacks: (1) it is not scalable for high-rate streaming data, and (2) there is no guarantee of reflecting the underlying distribution. In this software, we implemented a dynamic sampling algorithm, based on the recent technology from the relational dynamic bayesian online locally exchangeable measures, that reduces the storage of data records in a large scale, and still provides accurate analysis of large streaming data. The software can be used for both online and offline data records.

Sim, Alex↗

Network portal: a database for storage, analysis and visualization of biological networks

The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal.

59 BASIC BIOLOGICAL SCIENCES↗

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass

Abstract Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost‐effective 3′‐Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C 4 perennial grass, Panicum hallii . We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine‐scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis ‐regulatory elements and biological processes under short‐ and long‐day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod‐dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well‐known GI‐interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.

Weng, Xiaoyu↗

Neural Network Prediction of Failure of Damaged Composite Pressure Vessels from Strain Field Data Acquired by a Computer Vision Method

This effort used a new and novel method of acquiring strains called Sub-pixel Digital Video Image Correlation (SDVIC) on impact damaged Kevlar/epoxy filament wound pressure vessels during a proof test. To predict the burst pressure, the hoop strain field distribution around the impact location from three vessels was used to train a neural network. The network was then tested on additional pressure vessels. Several variations on the network were tried. The best results were obtained using a single hidden layer. SDVIC is a fill-field non-contact computer vision technique which provides in-plane deformation and strain data over a load differential. This method was used to determine hoop and axial displacements, hoop and axial linear strains, the in-plane shear strains and rotations in the regions surrounding impact sites in filament wound pressure vessels (FWPV) during proof loading by internal pressurization. The relationship between these deformation measurement values and the remaining life of the pressure vessels, however, requires a complex theoretical model or numerical simulation. Both of these techniques are time consuming and complicated. Previous results using neural network methods had been successful in predicting the burst pressure for graphite/epoxy pressure vessels based upon acoustic emission (AE) measurements in similar tests. The neural network associates the character of the AE amplitude distribution, which depends upon the extent of impact damage, with the burst pressure. Similarly, higher amounts of impact damage are theorized to cause a higher amount of strain concentration in the damage effected zone at a given pressure and result in lower burst pressures. This relationship suggests that a neural network might be able to find an empirical relationship between the SDVIC strain field data and the burst pressure, analogous to the AE method, with greater speed and simplicity than theoretical or finite element modeling. The process of testing SDVIC neural network analysis and some encouraging preliminary results are presented in this paper. Details are given concerning the processing of SDVIC output data such that it may be used as back propagation neural network (BPNN) input data. The software written to perform this processing and the BPNN algorithm are also discussed. It will be shown that, with limited training, test results indicate an average error in burst pressure prediction of approximately six percent,

Russell, Samuel S.↗

Illinois crop-acreage estimation experiment

The University of Illinois and the U.S. Department of Agriculture have collaborated to examine the feasibility of Landsat imagery analysis for USDA crop-acreage estimation purposes. The region chosen for the experiment was ten western counties of Illinois. Preliminary crop-acreage estimates derived from the ILLIAC IV-ARPA Network analysis of Landsat data are presented for these ten counties. Assuming the practicality of similar analyses covering the entire state, a procedure is discussed for evaluating statistically the information to be gained by estimating state crop-acreage totals from Landsat imagery classification results where SRS sample survey data are used as ground truth information for classification training as opposed to estimating state crop-acreage totals directly from SRS survey data alone.

Ray, R. M., III↗

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2 , N 2 and N 2 O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal river stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

54 ENVIRONMENTAL SCIENCES↗

Application of artificial neural networks in nonlinear analysis of trusses

A method is developed to incorporate neural network model based upon the Backpropagation algorithm for material response into nonlinear elastic truss analysis using the initial stiffness method. Different network configurations are developed to assess the accuracy of neural network modeling of nonlinear material response. In addition to this, a scheme based upon linear interpolation for material data, is also implemented for comparison purposes. It is found that neural network approach can yield very accurate results if used with care. For the type of problems under consideration, it offers a viable alternative to other material modeling methods.

Alam, J.↗

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

mycorrhizal fungi↗

A communications model for an ISAS to NASA span link

The authors propose that an initial computer-to-computer communication link use the public packet switched networks (PPSN) Venus-P in Japan and TELENET in the U.S. When the traffic warrants it, this link would then be upgraded to a dedicated leased line that directly connects into the Space Physics Analysis Network (SPAN). The proposed system of hardware and software will easily support migration to such a dedicated link. It therefore provides a cost effective approach to the network problem. Once a dedicated line becomes operation it is suggested that the public networks link and continue to coexist, providing a backup capability.

Green, James L.↗

Considerations for AMI-Based Operations for Distribution Feeders

More than $5 billion in investments in advanced metering infrastructure (AMI) technologies, AMI deployments, as pervasive secondary network voltage monitoring systems, provide opportunities for utility operations and controls. This paper focuses on the considerations for AMI-based tools and techniques as the industry moves toward operationalizing such large data sets. Phase identification is a first such tool. Numerous distribution network analysis, monitoring, and control applications - including volt/volt-ampere reactive control, state estimation, and distribution automation - require accurate phase connectivity information in the system models. The phase connectivity database maintained by utilities is inaccurate because of a significant amount of missing data, restoration activities, and network reconfiguration. Existing phase identification techniques that estimate phase connectivity work well in distribution feeders that have low or no photovoltaic (PV) generation; however, they fail to identify the phases accurately when considerable PV generation is present. This work addresses the phase identification problem in the presence of high PV generation using statistical analysis methods. Further, insights into the AMI data requirements for this application in terms of data window length and resolution are provided using sensitivity analysis performed on an actual distribution feeder model of San Diego Gas & Electric Company. The results of this study show that the phase connectivity, even in the presence of high PV generation, can be accurately identified using statistical analysis of AMI data of 1 day.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Considerations for AMI-Based Operations for Distribution Feeders: Preprint

More than $5 billion in investments in advanced metering infrastructure (AMI) technologies, AMI deployments, as pervasive secondary network voltage monitoring systems, provide opportunities for utility operations and controls. This paper focuses on the considerations for AMI-based tools and techniques as the industry moves toward operationalizing such large data sets. Phase identification is a first such tool. Numerous distribution network analysis, monitoring, and control applications - including volt/volt-ampere reactive control, state estimation, and distribution automation - require accurate phase connectivity information in the system models. The phase connectivity database maintained by utilities is inaccurate because of a significant amount of missing data, restoration activities, and network reconfiguration. Existing phase identification techniques that estimate phase connectivity work well in distribution feeders that have low or no photovoltaic (PV) generation; however, they fail to identify the phases accurately when considerable PV generation is present. This work addresses the phase identification problem in the presence of high PV generation using statistical analysis methods. Further, insights into the AMI data requirements for this application in terms of data window length and resolution are provided using sensitivity analysis performed on an actual distribution feeder model of San Diego Gas & Electric Company. The results of this study show that the phase connectivity, even in the presence of high PV generation, can be accurately identified using statistical analysis of AMI data of 1 day.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A review and analysis of neural networks for classification of remotely sensed multispectral imagery

A literature survey and analysis of the use of neural networks for the classification of remotely sensed multispectral imagery is presented. As part of a brief mathematical review, the backpropagation algorithm, which is the most common method of training multi-layer networks, is discussed with an emphasis on its application to pattern recognition. The analysis is divided into five aspects of neural network classification: (1) input data preprocessing, structure, and encoding; (2) output encoding and extraction of classes; (3) network architecture, (4) training algorithms; and (5) comparisons to conventional classifiers. The advantages of the neural network method over traditional classifiers are its non-parametric nature, arbitrary decision boundary capabilities, easy adaptation to different types of data and input structures, fuzzy output values that can enhance classification, and good generalization for use with multiple images. The disadvantages of the method are slow training time, inconsistent results due to random initial weights, and the requirement of obscure initialization values (e.g., learning rate and hidden layer size). Possible techniques for ameliorating these problems are discussed. It is concluded that, although the neural network method has several unique capabilities, it will become a useful tool in remote sensing only if it is made faster, more predictable, and easier to use.

Paola, Justin D.↗

Report on activities and findings under DOE grant “Collaborative research. An Interactive Multi-Model for Consensus on Climate Change”

The project takes a hierarchical approach. The supermodeling scheme was first studied exhaustively with simple systems of ordinary differential equations. Results were described in detail in the previous report. The principal findings were that 1) for highly non-linear systems, such as Lorenz-63, including systems which describe phenomena on very different (atmosphere/ocean) times scales, supermodeling is far superior to any form of output-averaging; 2) negative coefficients can be used to advantage in situations where all models err in the same way, but to different degrees; 3) an interesting variant of supermodeling, “weighted supermodeling”, is the limiting case where inter-model nudging coefficients in the originally conceived “connected supermodel” become infinite, but with fixed ratios, corresponding to a direct combination of the tendencies that appear in corresponding equations for the alternative models; 4) noise is useful for avoiding local optima in training the inter-model coefficients in the supermodel. The supermodeling scheme was then investigated with simple quasigeostrophic (QG) models. As described in the previous report, it was found that QG models on a sphere can be coupled most efficaciously by working in a basis which captures the most variance, rather than the most instability, a somewhat unexpected result that still deserves scrutiny in a broader context. Further studies (since the last report) with QG channel models addressed the central question of when supermodeling is superior to output averaging in situations where nonlinearites are less extreme than with the ODEs initially studied. It was found that for realistic variations in a parameter in the QG model, output averaging is sufficient to capture all but the most subtle quantitative and qualitative behavior. Supermodeling helps when qualitative differences between the models result from unrealistically large parameter differences, or when very detailed spatial structure of the modes of variability are of interest. Therefore, the scheme may still be useful in the case of full climate models with qualitatively different parametrization schemes. A supermodel was constructed from the intermediate-complexity SPEEDO model, a primitive equation model with ocean and land. Versions defined by different parameter choices, in a realistic range, were connected and the coefficients trained. Some improvement was found as compared to output averaging. The learning algorithm used thus far gives sub-optimal, but still useful results when the CO 2 level and other parameters are varied. Spatial structure remains to be studied. The first use of supermodeling with full climate models has been with variants of the ECHAM model that use different convection schemes. As yet the models are only connected at the ocean-atmosphere interface, where weighted combinations of fluxes from the two atmospheres are passed to a common ocean, and the weights adapted during a training period. The supermodel was surprisingly successful at avoiding unrealistic features such as the double-ITCZ (Intertropical Convergence Zone), a problem that arises in both of the two models run separately. The supermodels constructed thus far have not identified dynamical regime shifts in future climate. Thus the planned connection with the work of Tsonis on the relationship between regime shifts and synchronization/de-synchronization among the major climate modes (see U. Wisconsin report) has not yet been made. However the network analysis of the climate system, in observations and models, that was done in conjunction with that study, shows that models differ strongly from one another and from observations in regard to the dynamical structure described by correlation networks [Steinhaeuser and Tsonis 2013], providing a further justification for supermodeling. Toward a general software framework for supermodeling, three versions of CAM (the Community Atmosphere Model) at NCAR were configured for inter-model nudging using the DART (Data Assimilation Research Testbed) capability to stop and re-start models in synchrony. It was clearly established that the inter-model nudging adds almost no computational burden to the runs, but there appears to be a problem with the re-initialization software that is still being debugged. Publications: Several papers were published on the basic idea of the interactive multi-model (supermodel) including demonstrations with low-order ODEs. The last of these, a semi-philosophical review paper on the relevance of synchronization generally, encountered considerable resistance but was finally published in Entropy [Duane 2015]. A paper on the ECHAM/COSMOS supermodel, containing the most promising results so far [Shen et al. 2015] is presently under review.

58 GEOSCIENCES↗

Using Digital Trace Data to Identify Regions and Cities

A greater understanding of human dynamics as they play out in both physical space and through inter-personal communication is vital for the design and development of intelligent and resilient cities. Physical context provides insight in to the space-time distribution of population and their activity patterns, while inter-personal communication can, for the first time, be measured at scale through virtual interactions. The confluence of these two enables spatial social network analysis in the built environment for edge computing, knowledge discovery, and artificial intelligence activities. In this work, we propose a novel method to discover such dynamics. We use a dataset of 72 million tweets to develop a spatially embedded network of communication, and then use community detection algorithms to explore regional and urban delineation in the United States. We find that the broad spatial delineation of communities and community sub-structure is consistent with major United States socio-cultural regions, states, and major metropolitan areas. We describe how these methods could be extended to generate a measure of socially cohesive regions that can be consistently applied anywhere there is a sufficiently rich data source. We hope the proposed methods will generate new perspectives on smart and resilient cities.

Brelsford, Christa↗

Networking ground-based images of Comet Halley during the Giotto encounter

During the period immediately before and after the European, Russian, and Japanese spacecraft encounters with Comet Halley in early March 1986, sequences of ground-based electronic images of the comet, obtained at Table Mountain Observatory (TMO), CA, were transmitted via the Space Physics Analysis Network (SPAN) to the European Space Operations Centre (ESOC), and to University College London (UCL). During the 48-h period when the European Space Agency spacecraft Giotto was within the extended coma of Comet Halley, the ground-based images revealed that the comet displayed several spectacular near-nuclear and large-scale features. The TMO images provided a format for the interpretation of the unique in situ results obtained during the closest of the five spacecraft encounters with Comet Halley.

Rees, David↗

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying

Abstract Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis , a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

59 BASIC BIOLOGICAL SCIENCES↗