Sample records for interactome predicts spatiotemporal

  1. Predicting Malaria Interactome Classifications from Time-Course Transcriptomic Data along the

    E-print Network

    Mishra, Bud

    Predicting Malaria Interactome Classifications from Time-Course Transcriptomic Data along Cummington Street, Boston, MA, 02215 August 4, 2009 Summary Objective: Even though a vaccine for malaria- mated method for predicting functions for the malaria parasite, which capitalizes on the importance

  2. The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses[W][OA

    PubMed Central

    Lin, Mingzhi; Zhou, Xi; Shen, Xueling; Mao, Chuanzao; Chen, Xin

    2011-01-01

    Predicted interactions are a valuable complement to experimentally reported interactions in molecular mechanism studies, particularly for higher organisms, for which reported experimental interactions represent only a small fraction of their total interactomes. With careful engineering consideration of the lessons from previous efforts, the Predicted Arabidopsis Interactome Resource (PAIR; ) presents 149,900 potential molecular interactions, which are expected to cover ~24% of the entire interactome with ~40% precision. This study demonstrates that, although PAIR still has limited coverage, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes. These inferred interactions can nicely power several network topology-based systems biology analyses, such as gene set linkage analysis, protein function prediction, and identification of regulatory genes demonstrating insignificant expression changes. The drastically expanded molecular network in PAIR has considerably improved the capability of these analyses to integrate existing knowledge and suggest novel insights into the function and coordination of genes and gene networks. PMID:21441435

  3. Revealing missing parts of the interactome via link prediction.

    PubMed

    Hulovatyy, Yuriy; Solava, Ryan W; Milenkovi?, Tijana

    2014-01-01

    Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses the existing PIN topology to predict missing and spurious links. Many of existing LP methods rely on shared immediate neighborhoods of the nodes to be linked. As such, they have limitations. Thus, in order to comprehensively study what are the topological properties of nodes in PINs that dictate whether the nodes should be linked, we introduce novel sensitive LP measures that are expected to overcome the limitations of the existing methods. We systematically evaluate the new and existing LP measures by introducing "synthetic" noise into PINs and measuring how accurate the measures are in reconstructing the original PINs. Also, we use the LP measures to de-noise the original PINs, and we measure biological correctness of the de-noised PINs with respect to functional enrichment of the predicted interactions. Our main findings are: 1) LP measures that favor nodes which are both "topologically similar" and have large shared extended neighborhoods are superior; 2) using more network topology often though not always improves LP accuracy; and 3) LP improves biological correctness of the PINs, plus we validate a significant portion of the predicted interactions in independent, external PIN data sources. Ultimately, we are less focused on identifying a superior method but more on showing that LP improves biological correctness of PINs, which is its ultimate goal in computational biology. But we note that our new methods outperform each of the existing ones with respect to at least one evaluation criterion. Alarmingly, we find that the different criteria often disagree in identifying the best method(s), which has important implications for LP communities in any domain, including social networks. PMID:24594900

  4. Revealing Missing Parts of the Interactome via Link Prediction

    PubMed Central

    Hulovatyy, Yuriy; Solava, Ryan W.; Milenkovi?, Tijana

    2014-01-01

    Protein interaction networks (PINs) are often used to “learn” new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses the existing PIN topology to predict missing and spurious links. Many of existing LP methods rely on shared immediate neighborhoods of the nodes to be linked. As such, they have limitations. Thus, in order to comprehensively study what are the topological properties of nodes in PINs that dictate whether the nodes should be linked, we introduce novel sensitive LP measures that are expected to overcome the limitations of the existing methods. We systematically evaluate the new and existing LP measures by introducing “synthetic” noise into PINs and measuring how accurate the measures are in reconstructing the original PINs. Also, we use the LP measures to de-noise the original PINs, and we measure biological correctness of the de-noised PINs with respect to functional enrichment of the predicted interactions. Our main findings are: 1) LP measures that favor nodes which are both “topologically similar” and have large shared extended neighborhoods are superior; 2) using more network topology often though not always improves LP accuracy; and 3) LP improves biological correctness of the PINs, plus we validate a significant portion of the predicted interactions in independent, external PIN data sources. Ultimately, we are less focused on identifying a superior method but more on showing that LP improves biological correctness of PINs, which is its ultimate goal in computational biology. But we note that our new methods outperform each of the existing ones with respect to at least one evaluation criterion. Alarmingly, we find that the different criteria often disagree in identifying the best method(s), which has important implications for LP communities in any domain, including social networks. PMID:24594900

  5. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize

    PubMed Central

    Musungu, Bryan; Bhatnagar, Deepak; Brown, Robert L.; Fakhoury, Ahmad M.; Geisler, Matt

    2015-01-01

    Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs) that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.

  6. Spatiotemporal patterns and predictability of cyberattacks.

    PubMed

    Chen, Yu-Zhong; Huang, Zi-Gang; Xu, Shouhuai; Lai, Ying-Cheng

    2015-01-01

    A relatively unexplored issue in cybersecurity science and engineering is whether there exist intrinsic patterns of cyberattacks. Conventional wisdom favors absence of such patterns due to the overwhelming complexity of the modern cyberspace. Surprisingly, through a detailed analysis of an extensive data set that records the time-dependent frequencies of attacks over a relatively wide range of consecutive IP addresses, we successfully uncover intrinsic spatiotemporal patterns underlying cyberattacks, where the term "spatio" refers to the IP address space. In particular, we focus on analyzing macroscopic properties of the attack traffic flows and identify two main patterns with distinct spatiotemporal characteristics: deterministic and stochastic. Strikingly, there are very few sets of major attackers committing almost all the attacks, since their attack "fingerprints" and target selection scheme can be unequivocally identified according to the very limited number of unique spatiotemporal characteristics, each of which only exists on a consecutive IP region and differs significantly from the others. We utilize a number of quantitative measures, including the flux-fluctuation law, the Markov state transition probability matrix, and predictability measures, to characterize the attack patterns in a comprehensive manner. A general finding is that the attack patterns possess high degrees of predictability, potentially paving the way to anticipating and, consequently, mitigating or even preventing large-scale cyberattacks using macroscopic approaches. PMID:25992837

  7. Rapid, optimized interactomic screening.

    PubMed

    Hakhverdyan, Zhanna; Domanski, Michal; Hough, Loren E; Oroskar, Asha A; Oroskar, Anil R; Keegan, Sarah; Dilworth, David J; Molloy, Kelly R; Sherman, Vadim; Aitchison, John D; Fenyö, David; Chait, Brian T; Jensen, Torben Heick; Rout, Michael P; LaCava, John

    2015-06-01

    We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that comprehensively explores the parameters affecting the stability of interactions in affinity-captured complexes, enabling the discovery of physiological binding partners in unparalleled detail. We have implemented this screen on several macromolecular complexes from a variety of organisms, revealing novel profiles for even well-studied proteins. Our approach is robust, economical and automatable, providing inroads to the rigorous, systematic dissection of cellular interactomes. PMID:25938370

  8. DDI-CPI, a server that predicts drug–drug interactions through implementing the chemical–protein interactome

    PubMed Central

    Luo, Heng; Zhang, Ping; Huang, Hui; Huang, Jialiang; Kao, Emily; Shi, Leming; He, Lin; Yang, Lun

    2014-01-01

    Drug–drug interactions (DDIs) may cause serious side-effects that draw great attention from both academia and industry. Since some DDIs are mediated by unexpected drug–human protein interactions, it is reasonable to analyze the chemical–protein interactome (CPI) profiles of the drugs to predict their DDIs. Here we introduce the DDI-CPI server, which can make real-time DDI predictions based only on molecular structure. When the user submits a molecule, the server will dock user's molecule across 611 human proteins, generating a CPI profile that can be used as a feature vector for the pre-constructed prediction model. It can suggest potential DDIs between the user's molecule and our library of 2515 drug molecules. In cross-validation and independent validation, the server achieved an AUC greater than 0.85. Additionally, by investigating the CPI profiles of predicted DDI, users can explore the PK/PD proteins that might be involved in a particular DDI. A 3D visualization of the drug-protein interaction will be provided as well. The DDI-CPI is freely accessible at http://cpi.bio-x.cn/ddi/. PMID:24875476

  9. DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome.

    PubMed

    Luo, Heng; Zhang, Ping; Huang, Hui; Huang, Jialiang; Kao, Emily; Shi, Leming; He, Lin; Yang, Lun

    2014-07-01

    Drug-drug interactions (DDIs) may cause serious side-effects that draw great attention from both academia and industry. Since some DDIs are mediated by unexpected drug-human protein interactions, it is reasonable to analyze the chemical-protein interactome (CPI) profiles of the drugs to predict their DDIs. Here we introduce the DDI-CPI server, which can make real-time DDI predictions based only on molecular structure. When the user submits a molecule, the server will dock user's molecule across 611 human proteins, generating a CPI profile that can be used as a feature vector for the pre-constructed prediction model. It can suggest potential DDIs between the user's molecule and our library of 2515 drug molecules. In cross-validation and independent validation, the server achieved an AUC greater than 0.85. Additionally, by investigating the CPI profiles of predicted DDI, users can explore the PK/PD proteins that might be involved in a particular DDI. A 3D visualization of the drug-protein interaction will be provided as well. The DDI-CPI is freely accessible at http://cpi.bio-x.cn/ddi/. PMID:24875476

  10. A Spatiotemporal Approach to Tornado Prediction V Lakshmanan

    E-print Network

    Lakshmanan, Valliappa

    A Spatiotemporal Approach to Tornado Prediction V Lakshmanan University of Oklahoma and National Weather Service Abstract-- Automated tornado detection or prediction tech- niques in the literature have all been based on analyzing "signa- tures" of tornadoes that appear in Doppler radar velocity data

  11. In silico prediction of physical protein interactions and characterization of interactome orphans.

    PubMed

    Kotlyar, Max; Pastrello, Chiara; Pivetta, Flavia; Lo Sardo, Alessandra; Cumbaa, Christian; Li, Han; Naranian, Taline; Niu, Yun; Ding, Zhiyong; Vafaee, Fatemeh; Broackes-Carter, Fiona; Petschnigg, Julia; Mills, Gordon B; Jurisicova, Andrea; Stagljar, Igor; Maestro, Roberta; Jurisica, Igor

    2015-01-01

    Protein-protein interactions (PPIs) are useful for understanding signaling cascades, predicting protein function, associating proteins with disease and fathoming drug mechanism of action. Currently, only ? 10% of human PPIs may be known, and about one-third of human proteins have no known interactions. We introduce FpClass, a data mining-based method for proteome-wide PPI prediction. At an estimated false discovery rate of 60%, we predicted 250,498 PPIs among 10,531 human proteins; 10,647 PPIs involved 1,089 proteins without known interactions. We experimentally tested 233 high- and medium-confidence predictions and validated 137 interactions, including seven novel putative interactors of the tumor suppressor p53. Compared to previous PPI prediction methods, FpClass achieved better agreement with experimentally detected PPIs. We provide an online database of annotated PPI predictions (http://ophid.utoronto.ca/fpclass/) and the prediction software (http://www.cs.utoronto.ca/~juris/data/fpclass/). PMID:25402006

  12. Spatiotemporal Signatures of Lexical-Semantic Prediction.

    PubMed

    Lau, Ellen F; Weber, Kirsten; Gramfort, Alexandre; Hämäläinen, Matti S; Kuperberg, Gina R

    2014-10-14

    Although there is broad agreement that top-down expectations can facilitate lexical-semantic processing, the mechanisms driving these effects are still unclear. In particular, while previous electroencephalography (EEG) research has demonstrated a reduction in the N400 response to words in a supportive context, it is often challenging to dissociate facilitation due to bottom-up spreading activation from facilitation due to top-down expectations. The goal of the current study was to specifically determine the cortical areas associated with facilitation due to top-down prediction, using magnetoencephalography (MEG) recordings supplemented by EEG and functional magnetic resonance imaging (fMRI) in a semantic priming paradigm. In order to modulate expectation processes while holding context constant, we manipulated the proportion of related pairs across 2 blocks (10 and 50% related). Event-related potential results demonstrated a larger N400 reduction when a related word was predicted, and MEG source localization of activity in this time-window (350-450 ms) localized the differential responses to left anterior temporal cortex. fMRI data from the same participants support the MEG localization, showing contextual facilitation in left anterior superior temporal gyrus for the high expectation block only. Together, these results provide strong evidence that facilitatory effects of lexical-semantic prediction on the electrophysiological response 350-450 ms postonset reflect modulation of activity in left anterior temporal cortex. PMID:25316341

  13. Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches

    PubMed Central

    2014-01-01

    Background Every year pathogenic organisms cause billions of dollars' worth damage to crops and livestock. In agriculture, study of plant-microbe interactions is demanding a special attention to develop management strategies for the destructive pathogen induced diseases that cause huge crop losses every year worldwide. Pseudomonas syringae is a major bacterial leaf pathogen that causes diseases in a wide range of plant species. Among its various strains, pathovar tomato strain DC3000 (PstDC3000) is asserted to infect the plant host Arabidopsis thaliana and thus, has been accepted as a model system for experimental characterization of the molecular dynamics of plant-pathogen interactions. Protein-protein interactions (PPIs) play a critical role in initiating pathogenesis and maintaining infection. Understanding the PPI network between a host and pathogen is a critical step for studying the molecular basis of pathogenesis. The experimental study of PPIs at a large scale is very scarce and also the high throughput experimental results show high false positive rate. Hence, there is a need for developing efficient computational models to predict the interaction between host and pathogen in a genome scale, and find novel candidate effectors and/or their targets. Results In this study, we used two computational approaches, the interolog and the domain-based to predict the interactions between Arabidopsis and PstDC3000 in genome scale. The interolog method relies on protein sequence similarity to conduct the PPI prediction. A Pseudomonas protein and an Arabidopsis protein are predicted to interact with each other if an experimentally verified interaction exists between their respective homologous proteins in another organism. The domain-based method uses domain interaction information, which is derived from known protein 3D structures, to infer the potential PPIs. If a Pseudomonas and an Arabidopsis protein contain an interacting domain pair, one can expect the two proteins to interact with each other. The interolog-based method predicts ~0.79M PPIs involving around 7700 Arabidopsis and 1068 Pseudomonas proteins in the full genome. The domain-based method predicts 85650 PPIs comprising 11432 Arabidopsis and 887 Pseudomonas proteins. Further, around 11000 PPIs have been identified as interacting from both the methods as a consensus. Conclusion The present work predicts the protein-protein interaction network between Arabidopsis thaliana and Pseudomonas syringae pv. tomato DC3000 in a genome wide scale with a high confidence. Although the predicted PPIs may contain some false positives, the computational methods provide reasonable amount of interactions which can be further validated by high throughput experiments. This can be a useful resource to the plant community to characterize the host-pathogen interaction in Arabidopsis and Pseudomonas system. Further, these prediction models can be applied to the agriculturally relevant crops. PMID:25350354

  14. Virtual Interactomics of Proteins from Biochemical Standpoint

    PubMed Central

    Kubrycht, Jaroslav; Sigler, Karel; Sou?ek, Pavel

    2012-01-01

    Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations. PMID:22928109

  15. Prediction of Spatiotemporal Patterns of Neural Activity from Pairwise Correlations

    SciTech Connect

    Marre, O.; El Boustani, S.; Fregnac, Y.; Destexhe, A. [Unite de Neurosciences Integratives et Computationnelles (UNIC), UPR CNRS 2191, Gif-sur-Yvette (France)

    2009-04-03

    We designed a model-based analysis to predict the occurrence of population patterns in distributed spiking activity. Using a maximum entropy principle with a Markovian assumption, we obtain a model that accounts for both spatial and temporal pairwise correlations among neurons. This model is tested on data generated with a Glauber spin-glass system and is shown to correctly predict the occurrence probabilities of spatiotemporal patterns significantly better than Ising models only based on spatial correlations. This increase of predictability was also observed on experimental data recorded in parietal cortex during slow-wave sleep. This approach can also be used to generate surrogates that reproduce the spatial and temporal correlations of a given data set.

  16. SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical–protein interactome

    PubMed Central

    Yang, Lun; Luo, Heng; Chen, Jian; Xing, Qinghe; He, Lin

    2009-01-01

    Serious adverse drug reactions (SADRs) are caused by unexpected drug–human protein interactions, and some polymorphisms within binding pockets make the population carrying these polymorphisms susceptible to SADR. Predicting which populations are likely to be susceptible to SADR will not only strengthen drug safety, but will also assist enterprises to adjust R&D and marketing strategies. Making such predictions has recently been facilitated by the introduction of a web server named SePreSA. The server has a comprehensive collection of the structural models of nearly all the well known SADR targets. Once a drug molecule is submitted, the scale of its potential interaction with multi-SADR targets is calculated using the DOCK program. The server utilizes a 2-directional Z-transformation scoring algorithm, which computes the relative drug–protein interaction strength based on the docking-score matrix of a chemical–protein interactome, thus achieve greater accuracy in prioritizing SADR targets than simply using dock scoring functions. The server also suggests the binding pattern of the lowest docking score through 3D visualization, by highlighting and visualizing amino acid residues involved in the binding on the customer's browser. Polymorphism information for different populations for each of the interactive residues will be displayed, helping users to deduce the population-specific susceptibility of their drug molecule. The server is freely available at http://SePreSA.Bio-X.cn/. PMID:19417066

  17. Decentralized Data Fusion and Active Sensing with Mobile Sensors for Modeling and Predicting Spatiotemporal Traffic Phenomena

    E-print Network

    Jaillet, Patrick

    The problem of modeling and predicting spatiotemporal traffic phenomena over an urban road network is important to many traffic applications such as detecting and forecasting congestion hotspots. This paper presents a ...

  18. Ozone Concentration Prediction via Spatiotemporal Autoregressive Model With Exogenous Variables

    NASA Astrophysics Data System (ADS)

    Kamoun, W.; Senoussi, R.

    2009-04-01

    Forecast of environmental variables are nowadays of main concern for public health or agricultural management. In this context a large literature is devoted to spatio-temporal modelling of these variables using different statistical approaches. However, most of studies ignored the potential contribution of local (e.g. meteorological and/or geographical) covariables as well as the dynamical characteristics of observations. In this study, we present a spatiotemporal short term forecasting model for ozone concentration based on regularly observed covariables in predefined geographical sites. Our driving system simply combines a multidimensional second order autoregressive structured process with a linear regression model over influent exogenous factors and reads as follows: ?2 ?q j Z (t) = A (Î&,cedil;D )Ã- [ ?iZ(t- i)]+ B (Î&,cedil;D )Ã- [ ?jX (t)]+ É?(t) i=1 j=1 Z(t)=(Z1(t),â?¦,Zn(t)) represents the vector of ozone concentration at time t of the n geographical sites, whereas Xj(t)=(X1j(t),â?¦,Xnj(t)) denotes the jth exogenous variable observed over these sites. The nxn matrix functions A and B account for the spatial relationships between sites through the inter site distance matrix D and a vector parameter Î&.cedil; Multidimensional white noise É? is assumed to be Gaussian and spatially correlated but temporally independent. A covariance structure of Z that takes account of noise spatial dependences is deduced under a stationary hypothesis and then included in the likelihood function. Statistical model and estimation procedure: Contrarily to the widely used choice of a {0,1}-valued neighbour matrix A, we put forward two more natural choices of exponential or power decay. Moreover, the model revealed enough stable to readily accommodate the crude observations without the usual tedious and somewhat arbitrarily variable transformations. Data set and preliminary analysis: In our case, ozone variable represents here the daily maximum ozone concentration recorded in n=42 stations during the year 2005 within a south region in France, covering an area of approximately 10565 km2. Meteorological covariates are the daily maxima of temperature, wind speed, daily maxima of humidity and atmospheric pressure. Actually, the meteorological factors are not recorded in ozone monitoring sites and thus preliminary interpolation techniques were used and compared subsequently (Gaussian conditional simulation, ordinary kriging or kriging with external drift). Concluding remarks: From the statistical point of view, both simulation study and data analysis showed a fairly robust behaviour of estimation procedures. In both cases, the analysis of residuals proved a significant improvement of error prediction within this framework. From the environmental point of view, the ability of accounting for pertinent local and dynamical meteorological covariates clearly provided a useful tool in prediction methods. Bib [1]: Pfeifer.P.E; Deutsh.S.J. (1980) "A Three-Stage Iterative Procedure for Space-Time Modelling." Technometrics 22: 35-47. Bib [2]: Raffaella Giacomini and Cliff W.J.Granger 2002 - 07 "Aggregation of Space-Time Process" Departement of Economics, University of California, San Diego.

  19. Interactome Networks and Human Disease

    PubMed Central

    Vidal, Marc; Cusick, Michael E.; Barabási, Albert-László

    2011-01-01

    Complex biological systems and cellular networks may underlie most genotype to phenotype relationships. Here we review basic concepts in network biology, discussing different types of interactome networks and the insights that can come from analyzing them. We elaborate on why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease. PMID:21414488

  20. Spatio-Temporal Meme Prediction: Learning What Hashtags Will Be Popular Where

    E-print Network

    Caverlee, James

    Spatio-Temporal Meme Prediction: Learning What Hashtags Will Be Popular Where Krishna Y. Kamath of predicting what online memes will be popular in what locations. Specif- ically, we develop data on the problem of predicting what online memes will be popular in what locations, which has Permission to make

  1. Panda: A Predictive Spatio-Temporal Query Processor Abdeltawab M. Hendawi Mohamed F. Mokbel

    E-print Network

    Mokbel, Mohamed F.

    Panda: A Predictive Spatio-Temporal Query Processor Abdeltawab M. Hendawi Mohamed F. Mokbel, mokbel}@cs.umn.edu ABSTRACT This paper presents the Panda system for efficient support of a wide variety, Panda targets long-term query prediction as it relies on adapting a well-designed long-term prediction

  2. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

    PubMed Central

    Cannistraci, Carlo Vittorio; Alanis-Lobato, Gregorio; Ravasi, Timothy

    2013-01-01

    Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial. PMID:23563395

  3. State-Space Reconstruction and Spatio-Temporal Prediction of Lattice Dynamical Systems

    Microsoft Academic Search

    Lingzhong Guo; Stephen A Billings

    2007-01-01

    This paper addresses the problems of state space reconstruction and spatio-temporal prediction for lattice dynamical systems. It is shown that the state space of any finite lattice dynamical system can be embedded into a reconstruction space for almost every, in the sense of prevalence, smooth measurement mapping as long as the dimension of the reconstruction space is larger than twice

  4. Retrospective prediction of intraurban spatiotemporal distribution of PM2.5 in Taipei

    NASA Astrophysics Data System (ADS)

    Hwa-Lung, Yu; Chih-Hsin, Wang

    2010-08-01

    Numerous studies have shown that fine airborne particulate matter particles (PM2.5) are more dangerous to human health than coarse particles, e.g. PM10. The assessment of the impacts to human health or ecological effects by long-term PM2.5 exposure is often limited by lack of PM2.5 measurements. In Taipei, PM2.5 was not systematically observed until August, 2005. Taipei is the largest metropolitan area in Taiwan, where a variety of industrial and traffic emissions are continuously generated and distributed across space and time. PM-related data, i.e., PM10 and Total Suspended Particles (TSP) are independently systematically collected by different central and local government institutes. In this study, the retrospective prediction of spatiotemporal distribution of monthly PM2.5 over Taipei will be performed by using Bayesian Maximum Entropy method (BME) to integrate (a) the spatiotemporal dependence among PM measurements (i.e. PM10, TSP, and PM2.5), (b) the site-specific information of PM measurements which can be certain or uncertain information, and (c) empirical evidence about the PM2.5/PM10 and PM10/TSP ratios. The performance assessment of the retrospective prediction for the spatiotemporal distribution of PM2.5 was performed over space and time during 2003-2004 by comparing the posterior pdf of PM2.5 with the observations. Results show that the incorporation of PM10 and TSP observations by BME method can effectively improve the spatiotemporal PM2.5 estimation in the sense of lower mean and standard deviation of estimation errors. Moreover, the spatiotemporal retrospective prediction with PM2.5/PM10 and PM2.5/TSP ratios can provide good estimations of the range of PM2.5 levels over space and time during 2003-2004 in Taipei.

  5. Spatiotemporal predictability alters perceived duration of visual events: Memento effect revisited.

    PubMed

    Meyerhoff, Hauke S; Vanes, Lucy D; Huff, Markus

    2015-06-01

    Does event perception alter perceived duration? Previous research has shown that the perceived duration of a short scene depicting a disk moving along a segmented path is reduced when the temporal order of the motion segments is reversed (Memento effect). This effect has been attributed to the idea that reversed segments give rise to the perception of distinct visual events, whereas continuous segments are perceived as a single event. It has been suggested that the reduction in perceived duration is a result of perceiving multiple distinct events rather than 1. Here, the authors replicate and investigate the origin of the Memento effect. In 4 experiments, they explore the role of the spatiotemporal predictability of the disk's movement as well as the influence of the number of discrete events on perceived duration. Controlling for spatiotemporal predictability eliminates the Memento effect; however, controlling for the number of distinct events does not. Thus, the authors' results suggest that violations in spatiotemporal predictability rather than a varying number of discrete events induce the Memento effect. The authors discuss the impact of these findings for the perception of more naturalistic events. (PsycINFO Database Record PMID:25775174

  6. Predictability of spatio-temporal patterns in a lattice of coupled FitzHugh–Nagumo oscillators

    PubMed Central

    Grace, Miriam; Hütt, Marc-Thorsten

    2013-01-01

    In many biological systems, variability of the components can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In pioneering work in the late 1990s, it was hypothesized that a drift of cellular parameters (along a ‘developmental path’), together with differences in cell properties (‘desynchronization’ of cells on the developmental path) can establish self-organized spatio-temporal patterns (in their example, spiral waves of cAMP in a colony of Dictyostelium discoideum cells) starting from a homogeneous state. Here, we embed a generic model of an excitable medium, a lattice of diffusively coupled FitzHugh–Nagumo oscillators, into a developmental-path framework. In this minimal model of spiral wave generation, we can now study the predictability of spatio-temporal patterns from cell properties as a function of desynchronization (or ‘spread’) of cells along the developmental path and the drift speed of cell properties on the path. As a function of drift speed and desynchronization, we observe systematically different routes towards fully established patterns, as well as strikingly different correlations between cell properties and pattern features. We show that the predictability of spatio-temporal patterns from cell properties contains important information on the pattern formation process as well as on the underlying dynamical system. PMID:23349439

  7. Learned spatiotemporal sequence recognition and prediction in primary visual cortex

    PubMed Central

    Gavornik, Jeffrey P.; Bear, Mark F.

    2014-01-01

    Learning to recognize and predict temporal sequences is fundamental to sensory perception, and is impaired in several neuropsychiatric disorders, but little is known about where and how this occurs in the brain. We discovered that repeated presentations of a visual sequence over a course of days causes evoked response potentiation in mouse V1 that is highly specific for stimulus order and timing. Remarkably, after V1 is trained to recognize a sequence, cortical activity regenerates the full sequence even when individual stimulus elements are omitted. This novel neurophysiological report of sequence learning advances the understanding of how the brain makes “intelligent guesses” based on limited information to form visual percepts and suggests that it is possible to study the mechanistic basis of this high–level cognitive ability by studying low–level sensory systems. PMID:24657967

  8. Learned spatiotemporal sequence recognition and prediction in primary visual cortex.

    PubMed

    Gavornik, Jeffrey P; Bear, Mark F

    2014-05-01

    Learning to recognize and predict temporal sequences is fundamental to sensory perception and is impaired in several neuropsychiatric disorders, but little is known about where and how this occurs in the brain. We discovered that repeated presentations of a visual sequence over a course of days resulted in evoked response potentiation in mouse V1 that was highly specific for stimulus order and timing. Notably, after V1 was trained to recognize a sequence, cortical activity regenerated the full sequence even when individual stimulus elements were omitted. Our results advance the understanding of how the brain makes 'intelligent guesses' on the basis of limited information to form visual percepts and suggest that it is possible to study the mechanistic basis of this high-level cognitive ability by studying low-level sensory systems. PMID:24657967

  9. Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis

    PubMed Central

    Kastrup, Christian J.; Runyon, Matthew K.; Shen, Feng; Ismagilov, Rustem F.

    2006-01-01

    This article demonstrates that a simple chemical model system, built by using a modular approach, may be used to predict the spatiotemporal dynamics of initiation of blood clotting in the complex network of hemostasis. Microfluidics was used to create in vitro environments that expose both the complex network and the model system to surfaces patterned with patches presenting clotting stimuli. Both systems displayed a threshold response, with clotting initiating only on isolated patches larger than a threshold size. The magnitude of the threshold patch size for both systems was described by the Damköhler number, measuring competition of reaction and diffusion. Reaction produces activators at the patch, and diffusion removes activators from the patch. The chemical model made additional predictions that were validated experimentally with human blood plasma. These experiments show that blood can be exposed to significant amounts of clot-inducing stimuli, such as tissue factor, without initiating clotting. Overall, these results demonstrate that such chemical model systems, implemented with microfluidics, may be used to predict spatiotemporal dynamics of complex biochemical networks. PMID:17043240

  10. Guest Editorial -Journal of Biogeography (2011) in press Running header: Predicting spatio-temporal patterns of species assemblages

    E-print Network

    Alvarez, Nadir

    2011-01-01

    -temporal patterns of species assemblages SESAM ­ a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages Antoine Guisan1* & Carsten@bio.ku.dk ABSTRACT Two different approaches currently prevail for predicting spatial patterns of species assemblages

  11. Predicting the rate of range expansion of an invasive alien bumblebee ( Bombus terrestris) using a stochastic spatio-temporal model

    Microsoft Academic Search

    Taku Kadoya; Izumi Washitani

    2010-01-01

    To develop effective strategies for managing biological invasions, it is important to understand and be able to predict patterns of invasion and range expansion, and particularly the rate of spread and factors controlling this rate. To predict the spatial dynamics of invasion by an alien bumblebee (Bombus terrestris) in Hokkaido, Japan, we explicitly constructed a stochastic spatio-temporal model that incorporates

  12. Spatio-temporal variation and prediction of ischemic heart disease hospitalizations in Shenzhen, China.

    PubMed

    Wang, Yanxia; Du, Qingyun; Ren, Fu; Liang, Shi; Lin, De-nan; Tian, Qin; Chen, Yan; Li, Jia-jia

    2014-05-01

    Ischemic heart disease (IHD) is a leading cause of death worldwide. Urban public health and medical management in Shenzhen, an international city in the developing country of China, is challenged by an increasing burden of IHD. This study analyzed the spatio-temporal variation of IHD hospital admissions from 2003 to 2012 utilizing spatial statistics, spatial analysis, and space-time scan statistics. The spatial statistics and spatial analysis measured the incidence rate (hospital admissions per 1,000 residents) and the standardized rate (the observed cases standardized by the expected cases) of IHD at the district level to determine the spatio-temporal distribution and identify patterns of change. The space-time scan statistics was used to identify spatio-temporal clusters of IHD hospital admissions at the district level. The other objective of this study was to forecast the IHD hospital admissions over the next three years (2013-2015) to predict the IHD incidence rates and the varying burdens of IHD-related medical services among the districts in Shenzhen. The results show that the highest hospital admissions, incidence rates, and standardized rates of IHD are in Futian. From 2003 to 2012, the IHD hospital admissions exhibited similar mean centers and directional distributions, with a slight increase in admissions toward the north in accordance with the movement of the total population. The incidence rates of IHD exhibited a gradual increase from 2003 to 2012 for all districts in Shenzhen, which may be the result of the rapid development of the economy and the increasing traffic pollution. In addition, some neighboring areas exhibited similar temporal change patterns, which were also detected by the spatio-temporal cluster analysis. Futian and Dapeng would have the highest and the lowest hospital admissions, respectively, although these districts have the highest incidence rates among all of the districts from 2013 to 2015 based on the prediction using the GM (1,1). In addition, the combined analysis of the prediction of IHD hospital admissions and the general hospital distributions shows that Pingshan and Longgang might experience the most serious burden of IHD hospital services in the near future, although Futian would still have the greatest number and the highest incidence rate of hospital admissions for IHD. PMID:24806191

  13. A climate-based spatiotemporal prediction for dengue fever epidemics: a case study in southern Taiwan

    NASA Astrophysics Data System (ADS)

    Yu, H.-L.; Yang, S.-J.; Lin, Y.-C.

    2012-04-01

    Dengue Fever (DF) has been identified by the World Health organization (WHO) as one of the most serious vector-borne infectious diseases in tropical and sub-tropical areas. DF has been one of the most important epidemics in Taiwan which occur annually especially in southern Taiwan during summer and autumn. Most DF studies have focused mainly on temporal DF patterns and its close association with climatic covariates, whereas few studies have investigated the spatial DF patterns (spatial dependence and clustering) and composite space-time effects of the DF epidemics. The present study proposes a spatio-temporal DF prediction approach based on stochastic Bayesian Maximum Entropy (BME) analysis. Core and site-specific knowledge bases are considered, including climate and health datasets under conditions of uncertainty, space-time dependence functions, and a Poisson regression model of climatic variables contributing to DF occurrences in southern Taiwan during 2007, when the highest number of DF cases was recorded in the history of Taiwan epidemics (over 2000). The obtained results show that the DF outbreaks in the study area are highly influenced by climatic conditions. Furthermore, the analysis can provide the required "one-week-ahead" outbreak warnings based on spatio-temporal predictions of DF distributions. Therefore, the proposed analysis can provide the Taiwan Disease Control Agency with a valuable tool to timely identify, control, and even efficiently prevent DF spreading across space-time.

  14. The Effect of Rainfall Measurement Technique and Its Spatiotemporal Resolution on Discharge Predictions in the Netherlands

    NASA Astrophysics Data System (ADS)

    Uijlenhoet, R.; Brauer, C.; Overeem, A.; Sassi, M.; Rios Gaona, M. F.

    2014-12-01

    Several rainfall measurement techniques are available for hydrological applications, each with its own spatial and temporal resolution. We investigated the effect of these spatiotemporal resolutions on discharge simulations in lowland catchments by forcing a novel rainfall-runoff model (WALRUS) with rainfall data from gauges, radars and microwave links. The hydrological model used for this analysis is the recently developed Wageningen Lowland Runoff Simulator (WALRUS). WALRUS is a rainfall-runoff model accounting for hydrological processes relevant to areas with shallow groundwater (e.g. groundwater-surface water feedback). Here, we used WALRUS for case studies in a freely draining lowland catchment and a polder with controlled water levels. We used rain gauge networks with automatic (hourly resolution but low spatial density) and manual gauges (high spatial density but daily resolution). Operational (real-time) and climatological (gauge-adjusted) C-band radar products and country-wide rainfall maps derived from microwave link data from a cellular telecommunication network were also used. Discharges simulated with these different inputs were compared to observations. We also investigated the effect of spatiotemporal resolution with a high-resolution X-band radar data set for catchments with different sizes. Uncertainty in rainfall forcing is a major source of uncertainty in discharge predictions, both with lumped and with distributed models. For lumped rainfall-runoff models, the main source of input uncertainty is associated with the way in which (effective) catchment-average rainfall is estimated. When catchments are divided into sub-catchments, rainfall spatial variability can become more important, especially during convective rainfall events, leading to spatially varying catchment wetness and spatially varying contribution of quick flow routes. Improving rainfall measurements and their spatiotemporal resolution can improve the performance of rainfall-runoff models, indicating their potential for reducing flood damage through real-time control.

  15. Predicted spatio-temporal dynamics of radiocesium deposited onto forests following the Fukushima nuclear accident

    PubMed Central

    Hashimoto, Shoji; Matsuura, Toshiya; Nanko, Kazuki; Linkov, Igor; Shaw, George; Kaneko, Shinji

    2013-01-01

    The majority of the area contaminated by the Fukushima Dai-ichi nuclear power plant accident is covered by forest. To facilitate effective countermeasure strategies to mitigate forest contamination, we simulated the spatio-temporal dynamics of radiocesium deposited into Japanese forest ecosystems in 2011 using a model that was developed after the Chernobyl accident in 1986. The simulation revealed that the radiocesium inventories in tree and soil surface organic layer components drop rapidly during the first two years after the fallout. Over a period of one to two years, the radiocesium is predicted to move from the tree and surface organic soil to the mineral soil, which eventually becomes the largest radiocesium reservoir within forest ecosystems. Although the uncertainty of our simulations should be considered, the results provide a basis for understanding and anticipating the future dynamics of radiocesium in Japanese forests following the Fukushima accident. PMID:23995073

  16. Neurobiological Mechanisms Behind the Spatiotemporal Illusions of Awareness Used for Advocating Prediction or Postdiction

    PubMed Central

    Bachmann, Talis

    2013-01-01

    The fact that it takes time for the brain to process information from the changing environment underlies many experimental phenomena of awareness of spatiotemporal events, including a number of astonishing illusions. These phenomena have been explained from the predictive and postdictive theoretical perspectives. Here I describe the most extensively studied phenomena in order to see how well the two perspectives can explain them. Next, the neurobiological perceptual retouch mechanism of producing stimulation awareness is characterized and its work in causing the listed illusions is described. A perspective on how brain mechanisms of conscious perception produce the phenomena supportive of the postdictive view is presented in this article. At the same time, some of the phenomena cannot be explained by the traditional postdictive account, but can be interpreted from the perceptual retouch theory perspective. PMID:23293625

  17. Predicted spatio-temporal dynamics of radiocesium deposited onto forests following the Fukushima nuclear accident.

    PubMed

    Hashimoto, Shoji; Matsuura, Toshiya; Nanko, Kazuki; Linkov, Igor; Shaw, George; Kaneko, Shinji

    2013-01-01

    The majority of the area contaminated by the Fukushima Dai-ichi nuclear power plant accident is covered by forest. To facilitate effective countermeasure strategies to mitigate forest contamination, we simulated the spatio-temporal dynamics of radiocesium deposited into Japanese forest ecosystems in 2011 using a model that was developed after the Chernobyl accident in 1986. The simulation revealed that the radiocesium inventories in tree and soil surface organic layer components drop rapidly during the first two years after the fallout. Over a period of one to two years, the radiocesium is predicted to move from the tree and surface organic soil to the mineral soil, which eventually becomes the largest radiocesium reservoir within forest ecosystems. Although the uncertainty of our simulations should be considered, the results provide a basis for understanding and anticipating the future dynamics of radiocesium in Japanese forests following the Fukushima accident. PMID:23995073

  18. Organization of Physical Interactomes as Uncovered by Network Schemas

    PubMed Central

    Chazelle, Bernard; Singh, Mona

    2008-01-01

    Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the S. cerevisiae interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the H. sapiens interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks. PMID:18949022

  19. A comparison of predictive soil-carbon models across multiple spatio-temporal catchment scales.

    NASA Astrophysics Data System (ADS)

    Hancock, G. R.; Kunkel, V.; Wells, T.

    2014-12-01

    Soil's potential as a carbon sink for atmospheric CO2 has been widely discussed. Studies of soil organic carbon (SOC) controls, and the subsequent models derived from their findings, have focussed mainly on North American and European regions, and more recently, in regions such as China. In Australia, agricultural practices have led to losses in SOC. This implies that Australian soils have a large potential for increases in SOC. Building on previous work, here we examine the spatial and temporal variation in soil organic carbon (SOC) and its controlling factors controls across a large catchment of approximately 600 km2 in the Upper Hunter Valley, New South Wales, Australia, using data collected from two sampling campaigns, (April 2006 and June-July 2014). Remote sensing using Landsat (30m) and MODIS (250m) NDVI was used to determine if catchment SOC could be predicted using both low and high resolution remote sensing . Relationships between SOC and elevation, aboveground biomass (as represented by NDVI), topographic wetness index (TWI), and incident solar radiation as a surrogate for soil temperature were compared. Initial results demonstrate that higher spatio-temporal resolution may not be necessary for predicting SOC at larger scales. The relationship between SOC and the environmental tracer 137-Cesium as a surrogate for the loss of SOC by erosion also suggests that sediment transport and deposition influences the distribution of SOC. A model developed for the site suggests that simple linear relationships between vegetation, climate and sediment transport could improve SOC predictions.

  20. An online spatio-temporal prediction model for dengue fever epidemic in Kaohsiung,Taiwan

    NASA Astrophysics Data System (ADS)

    Cheng, Ming-Hung; Yu, Hwa-Lung; Angulo, Jose; Christakos, George

    2013-04-01

    Dengue Fever (DF) is one of the most serious vector-borne infectious diseases in tropical and subtropical areas. DF epidemics occur in Taiwan annually especially during summer and fall seasons. Kaohsiung city has been one of the major DF hotspots in decades. The emergence and re-emergence of the DF epidemic is complex and can be influenced by various factors including space-time dynamics of human and vector populations and virus serotypes as well as the associated uncertainties. This study integrates a stochastic space-time "Susceptible-Infected-Recovered" model under Bayesian maximum entropy framework (BME-SIR) to perform real-time prediction of disease diffusion across space-time. The proposed model is applied for spatiotemporal prediction of the DF epidemic at Kaohsiung city during 2002 when the historical series of high DF cases was recorded. The online prediction by BME-SIR model updates the parameters of SIR model and infected cases across districts over time. Results show that the proposed model is rigorous to initial guess of unknown model parameters, i.e. transmission and recovery rates, which can depend upon the virus serotypes and various human interventions. This study shows that spatial diffusion can be well characterized by BME-SIR model, especially at the district surrounding the disease outbreak locations. The prediction performance at DF hotspots, i.e. Cianjhen and Sanmin, can be degraded due to the implementation of various disease control strategies during the epidemics. The proposed online disease prediction BME-SIR model can provide the governmental agency with a valuable reference to timely identify, control, and efficiently prevent DF spread across space-time.

  1. Spatiotemporal prediction applying fuzzy logic in a sequence of satellite images

    NASA Astrophysics Data System (ADS)

    Mezzadri-Centeno, Tania; Selleron, Gilles

    2002-01-01

    Spatial evolutions of anthropized ecosystems and the progressive transformation of spaces in the course of time emerge more and more as a special interest issue in researches about the environment. This evolution constitutes one of the major concerns in the domain of environmental space management. The landscape evolution of a region area and the perspectives for a future state rises an issue particularly important. What will be the state of the region in 15, 30 or 50 years? Time can produce transformations over a region area like emergence, disappearance or union of spatial entities... These transformations are called temporal phenomena. We propose to predict the forestry evolution in the forthcoming years on an experimental area, which reveals these spatial transformations. The proposed method is based on the analysis of terrain landscape given a sequence of n satellite images, which represent the state of a region area in different years. For these purposes, we have developed a specific spatio-temporal prediction approach, linking results of forestry evolution analysis and fuzzy logic. The method is supported by the analysis of the landscape dynamics of a test-site located in a tropical rain country: the oriental piedmont of Andes Mountain in Venezuela. This large area - at the scale of a spot satellite image - is typical of tropical deforestation in a pioneer front. The presented approach allows the geographer interested in environmental prospective problems to get type cartographical documents showing future conditions of a landscape. The experimental tests have showed promising results.

  2. Tumor site prediction using spatiotemporal detection of subclinical hyperemia in experimental photocarcinogenesis

    NASA Astrophysics Data System (ADS)

    Konger, Raymond L.; Xu, Zhengbin; Sahu, Ravi P.; Kim, Young L.

    2014-03-01

    We demonstrate that a spatial and temporal analysis of subclinical hyperemia reliably predicts specific areas at high risk for skin tumor development during photocarcinogenesis. To determine detailed spatiotemporal patterns of inflammatory angiogenesis foci in a relatively large area, we developed a mesoscopic (between microscopic and macroscopic) imaging approach. This method relies on our earlier finding that the combination of a spectral analysis of hemoglobin with diffuse-light-suppressed imaging can increase the image resolution, contrast and penetration depth to visualize microvasculature Hgb content in the large tissue area. In our recent study, SKH1 hairless albino mice were irradiated for 10 weeks with a carcinogen dose of UVB. Using our newly developed mesoscopic imaging methods, we imaged the mice over 20 - 30 weeks after stopping UVB, and excised hyperemic/non-hyperemic areas at several different timepoints. We show that persistent hyperemic foci can predict future tumor formation. In particular, our imaging approach allows us to assess the spatial and temporal extent of subclinical inflammatory foci, which in turn can predict sites of future overlying tumor formation. In addition, although COX-2 inhibitors are known to suppress skin cancer development in humans, it remains unclear whether the chemopreventive activity of COX-2 inhibitors are chiefly attributable to their anti-inflammatory effects. Our study provides evidence that subclinical subepithelial inflammatory foci occur prior to overt tumor formation, and that these areas are highly predictive for future tumor formation, that celecoxib's ability to suppress tumorigenesis is tightly linked to its ability to reduce the area of subclinical inflammatory foci.

  3. An empirical framework for binary interactome mapping

    Microsoft Academic Search

    Kavitha Venkatesan; Jean-François Rual; Alexei Vazquez; Ulrich Stelzl; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Martina Zenkner; Xiaofeng Xin; Kwang-Il Goh; Muhammed A Yildirim; Nicolas Simonis; Kathrin Heinzmann; Fana Gebreab; Julie M Sahalie; Sebiha Cevik; Christophe Simon; Anne-Sophie de Smet; Elizabeth Dann; Alex Smolyar; Arunachalam Vinayagam; Haiyuan Yu; David Szeto; Heather Borick; Amélie Dricot; Niels Klitgord; Ryan R Murray; Chenwei Lin; Maciej Lalowski; Jan Timm; Kirstin Rau; Charles Boone; Pascal Braun; Michael E Cusick; Frederick P Roth; David E Hill; Jan Tavernier; Erich E Wanker; Albert-László Barabási; Marc Vidal

    2008-01-01

    Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins

  4. The DAP-kinase interactome.

    PubMed

    Bialik, Shani; Kimchi, Adi

    2014-02-01

    DAP-kinase (DAPK) is a Ca(2+)/calmodulin regulated Ser/Thr kinase that activates a diverse range of cellular activities. It is subject to multiple layers of regulation involving both intramolecular signaling, and interactions with additional proteins, including other kinases and phosphatases. Its protein stability is modulated by at least three distinct ubiquitin-dependent systems. Like many kinases, DAPK participates in several signaling cascades, by phosphorylating additional kinases such as ZIP-kinase and protein kinase D (PKD), or Pin1, a phospho-directed peptidyl-prolyl isomerase that regulates the function of many phosphorylated proteins. Other substrate targets have more direct cellular effects; for example, phosphorylation of the myosin II regulatory chain and tropomyosin mediate some of DAPK's cytoskeletal functions, including membrane blebbing during cell death and cell motility. DAPK induces distinct death pathways of apoptosis, autophagy and programmed necrosis. Among the substrates implicated in these processes, phosphorylation of PKD, Beclin 1, and the NMDA receptor has been reported. Interestingly, not all cellular effects are mediated by DAPK's catalytic activity. For example, by virtue of protein-protein interactions alone, DAPK activates pyruvate kinase isoform M2, the microtubule affinity regulating kinases and inflammasome protein NLRP3, to promote glycolysis, influence microtubule dynamics, and enhance interleukin-1? production, respectively. In addition, a number of other substrates and interacting proteins have been identified, the physiological significance of which has not yet been established. All of these substrates, effectors and regulators together comprise the DAPK interactome. By presenting the components of the interactome network, this review will clarify both the mechanisms by which DAPK function is regulated, and by which it mediates its various cellular effects. PMID:24220855

  5. Spatio-temporal variability and predictability of summer monsoon onset over the Philippines

    NASA Astrophysics Data System (ADS)

    Moron, V.; Lucero, A.; Hilario, F.; Lyon, B.; Robertson, A. W.; Dewitt, D.

    2009-12-01

    The spatio-temporal variability of boreal summer monsoon onset over the Philippines is studied through the analysis of daily rainfall data across a network of 76 gauges for the period 1977 to 2004 and the pentad Merged Analysis of Precipitation from the US Climate Prediction Center from 1979 to 2006. The onset date is defined using a local agronomic definition, namely the first wet day of a 5-day period receiving at least 40 mm without any 15-day dry spell receiving <5 mm in the 30 days following the start of that period. The onset is found to occur rather abruptly across the western Philippines around mid-May on average and is associated with the set-up of a “classical” monsoonal circulation with low-level easterlies subsequently veering to southerly, and then southwesterly. The onset manifests itself merely as a seasonal increase of rainfall over the eastern Philippines, where rainfall occurs throughout most of the year. Interannual variability of the onset date is shown to consist of a spatially coherent large-scale component, rather similar over the western and eastern Philippines, with a moderate to high amount of local-scale (i.e. station scale) noise. In consequence, the large-scale signal can be easily retrieved from any sample of at least 5-6 stations across the network although the local-scale coherence and fingerprint of the large-scale signal of the onset date are found to be stronger over the central Philippines, roughly from Southern Luzon to Northern Mindanao. The seasonal predictability of local onset is analyzed through a cross-validated canonical correlation analysis using tropical Pacific and Indian Ocean sea surface temperature in March and the 850 hPa May wind field from dynamical forecast models as predictors. The regional-scale onset, defined as the average of standardized local-scale anomalies in onset date, shows good predictive skill ( r ? 0.8). Moreover, most of the stations show weak to moderate skill (median skill = 0.28-0.43 depending on the scheme) with spatial averaging across stations typically increasing skill to >0.6.

  6. Learning Sets of Sub-Models for Spatio-Temporal Prediction

    E-print Network

    Fernandez, Thomas

    a network of CCTV cameras. 1 Introduction Events over time may be described using a spatio-temporal data of CCTV cameras. Both of these approaches benefit from breaking the solution down into its component parts-model for each of the outcomes in the game. In the CCTV scenario this means learning the actions of single

  7. Using Genetic Programming to Learn Predictive Models from Spatio-Temporal Data

    E-print Network

    Fernandez, Thomas

    . D. Bennett and D. R. Magee, "Using Genetic Programming to Learn Models Containing Temporal Relations, Greece, 2008. A. D. Bennett and D. R. Magee, "Learning Sets of Sub-Models for Spatio-Temporal Predic Bennett Submitted in accordance with the requirements for the degree of Doctor of Philosophy

  8. Inferring modules from human protein interactome classes

    PubMed Central

    2010-01-01

    Background The integration of protein-protein interaction networks derived from high-throughput screening approaches and complementary sources is a key topic in systems biology. Although integration of protein interaction data is conventionally performed, the effects of this procedure on the result of network analyses has not been examined yet. In particular, in order to optimize the fusion of heterogeneous interaction datasets, it is crucial to consider not only their degree of coverage and accuracy, but also their mutual dependencies and additional salient features. Results We examined this issue based on the analysis of modules detected by network clustering methods applied to both integrated and individual (disaggregated) data sources, which we call interactome classes. Due to class diversity, we deal with variable dependencies of data features arising from structural specificities and biases, but also from possible overlaps. Since highly connected regions of the human interactome may point to potential protein complexes, we have focused on the concept of modularity, and elucidated the detection power of module extraction algorithms by independent validations based on GO, MIPS and KEGG. From the combination of protein interactions with gene expressions, a confidence scoring scheme has been proposed before proceeding via GO with further classification in permanent and transient modules. Conclusions Disaggregated interactomes are shown to be informative for inferring modularity, thus contributing to perform an effective integrative analysis. Validation of the extracted modules by multiple annotation allows for the assessment of confidence measures assigned to the modules in a protein pathway context. Notably, the proposed multilayer confidence scheme can be used for network calibration by enabling a transition from unweighted to weighted interactomes based on biological evidence. PMID:20653930

  9. A Viral-Human Interactome Based on Structural Motif-Domain Interactions Captures the Human Infectome

    PubMed Central

    Guo, Xianwu; Rodríguez-Pérez, Mario A.

    2013-01-01

    Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB). The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome) and non-infectious diseases (human diseasome). The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets. PMID:23951184

  10. Air temperature suitability for Plasmodium falciparum malaria transmission in Africa 2000-2012: a high-resolution spatiotemporal prediction

    PubMed Central

    2014-01-01

    Background Temperature suitability for malaria transmission is a useful predictor variable for spatial models of malaria infection prevalence. Existing continental or global models, however, are synoptic in nature and so do not characterize inter-annual variability in seasonal patterns of temperature suitability, reducing their utility for predicting malaria risk. Methods A malaria Temperature Suitability Index (TSI) was created by first modeling minimum and maximum air temperature with an eight-day temporal resolution from gap-filled MODerate Resolution Imaging Spectroradiometer (MODIS) daytime and night-time Land Surface Temperature (LST) datasets. An improved version of an existing biological model for malaria temperature suitability was then applied to the resulting temperature information for a 13-year data series. The mechanism underlying this biological model is simulation of emergent mosquito cohorts on a two-hour time-step and tracking of each cohort throughout its life to quantify the impact air temperature has on both mosquito survival and sporozoite development. Results The results of this research consist of 154 monthly raster surfaces that characterize spatiotemporal patterns in TSI across Africa from April 2000 through December 2012 at a 1 km spatial resolution. Generalized TSI patterns were as expected, with consistently high values in equatorial rain forests, seasonally variable values in tropical savannas (wet and dry) and montane areas, and low values in arid, subtropical regions. Comparisons with synoptic approaches demonstrated the additional information available within the dynamic TSI dataset that is lost in equivalent synoptic products derived from long-term monthly averages. Conclusions The dynamic TSI dataset presented here provides a new product with far richer spatial and temporal information than any other presently available for Africa. As spatiotemporal malaria modeling endeavors evolve, dynamic predictor variables such as the malaria temperature suitability data developed here will be essential for the rational assessment of changing patterns of malaria risk. PMID:24886586

  11. AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

    PubMed

    Wang, Yi; Thilmony, Roger; Zhao, Yunjun; Chen, Guoping; Gu, Yong Q

    2014-01-01

    Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM PMID:25480687

  12. Interactome analysis of myeloid-derived suppressor cells in murine models of colon and breast cancer

    PubMed Central

    Aliper, Alexander M.; Frieden-Korovkina, Victoria P.; Buzdin, Anton; Roumiantsev, Sergey A.; Zhavoronkov, Alex

    2014-01-01

    In solid cancers, myeloid derived suppressor cells (MDSC) infiltrate (peri)tumoral tissues to induce immune tolerance and hence to establish a microenvironment permissive to tumor growth. Importantly, the mechanisms that facilitate such infiltration or a subsequent immune suppression are not fully understood. Hence, in this study, we aimed to delineate disparate molecular pathways which MDSC utilize in murine models of colon or breast cancer. Using pathways enrichment analysis, we completed interactome maps of multiple signaling pathways in CD11b+/Gr1(high/low) MDSC from spleens and tumor infiltrates of mice with c26GM colon cancer and tumor infiltrates of MDSC in 4T1 breast cancer. In both cancer models, infiltrating MDSC, but not CD11b+ splenic cells, have been found to be enriched in multiple signaling molecules suggestive of their enhanced proliferative and invasive phenotypes. The interactome data has been subsequently used to reconstruct a previously unexplored regulation of MDSC cell cycle by the c-myc transcription factor which was predicted by the analysis. Thus, this study represents a first interactome mapping of distinct multiple molecular pathways whereby MDSC sustain cancer progression. PMID:25294811

  13. Computational analysis of the LRRK2 interactome.

    PubMed

    Manzoni, Claudia; Denny, Paul; Lovering, Ruth C; Lewis, Patrick A

    2015-01-01

    LRRK2 was identified in 2004 as the causative protein product of the Parkinson's disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson's disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson's. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around the LRRK2 locus to be associated with risk of developing sporadic Parkinson's disease and inflammatory bowel disorder. The functional research that has followed these genetic breakthroughs has generated an extensive literature regarding LRRK2 pathophysiology; however, there is still no consensus as to the biological function of LRRK2. To provide insight into the aspects of cell biology that are consistently related to LRRK2 activity, we analysed the plethora of candidate LRRK2 interactors available through the BioGRID and IntAct data repositories. We then performed GO terms enrichment for the LRRK2 interactome. We found that, in two different enrichment portals, the LRRK2 interactome was associated with terms referring to transport, cellular organization, vesicles and the cytoskeleton. We also verified that 21 of the LRRK2 interactors are genetically linked to risk for Parkinson's disease or inflammatory bowel disorder. The implications of these findings are discussed, with particular regard to potential novel areas of investigation. PMID:25737818

  14. Spatiotemporal characteristics of the vertical structure of predictability and information transport in Northern Hemisphere

    E-print Network

    Feng, A X; Wang, Q G; Feng, G L

    2011-01-01

    Based on nonlinear prediction and information theory, vertical heterogeneity of predictability and information loss rate was obtained over the Northern Hemisphere. In seasonal to interannual time scales, the predictability is low in lower troposphere and high in mid-upper troposphere. But within mid-upper subtropics troposphere over some ocean area there is a relatively poor prediction. The conclusions fit the seasonal time scale too. When it goes to the interannual time scale, the predictability is high in lower troposphere and low in mid-upper troposphere contrary to the formers. And on the whole the interannual trend is more predictable than the seasonal trend. The average information loss rate is low over mid-east Pacific, west of North America, Atlantic and Eurasia, and the atmosphere over other places have a relatively high information loss rate in all time scales. Two channels were found steadily over the Pacific Ocean and Atlantic Ocean in subtropics. There exist unstable channels as well. The four-se...

  15. Characterizing the skill of CFSv2-based seasonal drought prediction at multiple spatiotemporal scales over China

    NASA Astrophysics Data System (ADS)

    Luo, L.; Lang, Y.; Casey, M.; Duan, Q.

    2014-12-01

    A climate model's predictive skill for seasonal temperature and precipitation generally varies with multiple factors, such as location, lead-time, season, and temporal and spatial scales. To fully understand the potential and limitation of the NCEP Climate Forecast System version 2 (CFSv2) in predicting seasonal drought in China, this study investigated how the seasonal drought predictive skill varies with such multiple factors in China. Six-month standardized precipitation index (SPI6) is used as the primary drought indicator to measure the medium-term meteorological drought. The predictive skill was then assessed by the correlation coefficient between observation-based SPI6 and CFSv2 forecast-based SPI6 at multiple spatial scales as well as multiple lead times during the period 1982-2008. Through this analysis, we will better characterize the capability of CFSv2 in seasonal climate forecast, which can help us to better utilize forecast information from such a system in drought prediction and water resource management.

  16. An online spatiotemporal prediction model for dengue fever epidemic in Kaohsiung (Taiwan).

    PubMed

    Yu, Hwa-Lung; Angulo, José M; Cheng, Ming-Hung; Wu, Jiaping; Christakos, George

    2014-05-01

    The emergence and re-emergence of disease epidemics is a complex question that may be influenced by diverse factors, including the space-time dynamics of human populations, environmental conditions, and associated uncertainties. This study proposes a stochastic framework to integrate space-time dynamics in the form of a Susceptible-Infected-Recovered (SIR) model, together with uncertain disease observations, into a Bayesian maximum entropy (BME) framework. The resulting model (BME-SIR) can be used to predict space-time disease spread. Specifically, it was applied to obtain a space-time prediction of the dengue fever (DF) epidemic that took place in Kaohsiung City (Taiwan) during 2002. In implementing the model, the SIR parameters were continually updated and information on new cases of infection was incorporated. The results obtained show that the proposed model is rigorous to user-specified initial values of unknown model parameters, that is, transmission and recovery rates. In general, this model provides a good characterization of the spatial diffusion of the DF epidemic, especially in the city districts proximal to the location of the outbreak. Prediction performance may be affected by various factors, such as virus serotypes and human intervention, which can change the space-time dynamics of disease diffusion. The proposed BME-SIR disease prediction model can provide government agencies with a valuable reference for the timely identification, control, and prevention of DF spread in space and time. PMID:24615833

  17. Predicting the spatio-temporal distribution of Culicoides imicola in Sardinia using a discrete-time population model

    PubMed Central

    2012-01-01

    Background Culicoides imicola KIEFFER, 1913 (Diptera: Ceratopogonidae) is the principal vector of Bluetongue disease in the Mediterranean basin, Africa and Asia. Previous studies have identified a range of eco-climatic variables associated with the distribution of C. imicola, and these relationships have been used to predict the large-scale distribution of the vector. However, these studies are not temporally-explicit and can not be used to predict the seasonality in C. imicola abundances. Between 2001 and 2006, longitudinal entomological surveillance was carried out throughout Italy, and provided a comprehensive spatio-temporal dataset of C. imicola catches in Onderstepoort-type black-light traps, in particular in Sardinia where the species is considered endemic. Methods We built a dynamic model that allows describing the effect of eco-climatic indicators on the monthly abundances of C. imicola in Sardinia. Model precision and accuracy were evaluated according to the influence of process and observation errors. Results A first-order autoregressive cofactor, a digital elevation model and MODIS Land Surface Temperature (LST)/or temperatures acquired from weather stations explained ~77% of the variability encountered in the samplings carried out in 9 sites during 6?years. Incorporating Normalized Difference Vegetation Index (NDVI) or rainfall did not increase the model's predictive capacity. On average, dynamics simulations showed good accuracy (predicted vs. observed r corr?=?0.9). Although the model did not always reproduce the absolute levels of monthly abundances peaks, it succeeded in reproducing the seasonality in population level and allowed identifying the periods of low abundances and with no apparent activity. On that basis, we mapped C. imicola monthly distribution over the entire Sardinian region. Conclusions This study demonstrated prospects for modelling data arising from Culicoides longitudinal entomological surveillance. The framework explicitly incorporates the influence of eco-climatic factors on population growth rates and accounts for observation and process errors. Upon validation, such a model could be used to predict monthly population abundances on the basis of environmental conditions, and hence can potentially reduce the amount of entomological surveillance. PMID:23174043

  18. Remote flow sensing of complex systems: steps towards spatio-temporal prediction of flow patterns

    NASA Astrophysics Data System (ADS)

    Monnier, Bruno; Mokhasi, Paritosh; Rempfer, Dietmar; Wark, Candace

    2009-11-01

    Prediction of the spatial and temporal phenomena of wind flow patterns through urban areas is investigated. Typically sparse measurements are used in wind forecasting models for updating and prediction via a method called variational data assimilation. To improve upon this method, an experimental investigation combining various measurement tools (Hot Wire Anemometry, Stereoscopic Particle Image Velocimetry SPIV), static pressure measurements and Laser Doppler Velocimetry(LDV)) is carried out to study the airflow around wall mounted obstacles in a turbulent boundary layer. The method of Proper Orthogonal Decomposition (POD) is used to decompose the flow field into a finite set of POD coefficients which vary only in time associated with a corresponding set of POD basis functions which vary only in space. Direct measurement models utilizing the measurements from SPIV and LDV, along with indirect measurement models using sparse measurements from microphones are investigated and may ultimately be combined with state-space models to obtain more robust dynamical models.

  19. Spatio-temporal Whitening of Imaging Sensor Data Streams Using Three-Dimensional Linear Prediction

    Microsoft Academic Search

    Hugh L. Kennedy

    2008-01-01

    A three-dimensional whitening filter based on linear prediction is described. It is designed to remove textured backgrounds, with spatial and temporal correlation, in data streams acquired from imaging electro-optic sensors operating in visible, Ultra-Violet (UV) or Infra-Red (IR) bands. The background is modeled as an Auto-Regressive (AR) process. The operation of the filter is examined using real images of ocean

  20. Predicting breeding habitat for amphibians: a spatiotemporal analysis across Yellowstone National Park

    USGS Publications Warehouse

    Bartelt, Paul E.; Gallant, Alisa L.; Klaver, Robert W.; Wright, Christopher K.; Patla, Debra A.; Peterson, Charles R.

    2011-01-01

    The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probabililty, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from 1) field survey site data only, 2) field data combined with data from geospatial models, and 3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 - 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative for areas that could be protected for each species, including 6828-10 764 ha for tiger salamanders; 971-3017 ha for western toads; 4732-16 696 ha for boreal chorus frogs; 4940-19 690 hectares for Columbia spotted frogs.

  1. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    Microsoft Academic Search

    Ian W Taylor; Rune Linding; David Warde-Farley; Yongmei Liu; Catia Pesquita; Daniel Faria; Shelley Bull; Tony Pawson; Quaid Morris; Jeffrey L Wrana

    2009-01-01

    Changes in the biochemical wiring of oncogenic cells drives phenotypic transformations that directly affect disease outcome. Here we examine the dynamic structure of the human protein interaction network (interactome) to determine whether changes in the organization of the interactome can be used to predict patient outcome. An analysis of hub proteins identified inter- modular hub proteins that are co-expressed with

  2. Evidence for Network Evolution in an Arabidopsis Interactome Map

    PubMed Central

    2011-01-01

    Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops. PMID:21798944

  3. Geomapping generalized eigenvalue frequency distributions for predicting prolific Aedes albopictus and Culex quinquefasciatus habitats based on spatiotemporal field-sampled count data.

    PubMed

    Jacob, Benjamin G; Morris, Joel A; Caamano, Erick X; Griffith, Daniel A; Novak, Robert J

    2011-02-01

    Marked spatiotemporal variabilities in mosquito infection of arboviruses require adaptive strategies for determining optimal field-sampling timeframes, pool screening, and data analyses. In particular, the error distribution and aggregation patterns of adult arboviral mosquitoes can vary significantly by species, which can statistically bias analyses of spatiotemporal-sampled predictor variables generating misinterpretation of prolific habitat surveillance locations. Currently, there is a lack of reliable and consistent measures of risk exposure based on field-sampled georeferenced explanatory covariates which can compromise quantitative predictions generated from arboviral mosquito surveillance models for implementing larval control strategies targeting productive habitats. In this research we used spatial statistics and QuickBird visible and near-infra-red data for determining trapping sites that were related to Culex quinquefasciatus and Aedes albopictus species abundance and distribution in Birmingham, Alabama. Initially, a Land Use Land Cover (LULC) model was constructed from multiple spatiotemporal-sampled georeferenced predictors and the QuickBird data. A Poisson regression model with a non-homogenous, gamma-distributed mean then decomposed the data into positive and negative spatial filter eigenvectors. An autoregressive process in the error term then was used to derive the sample distribution of the Moran's I statistic for determining latent autocorrelation components in the model. Spatial filter algorithms established means, variances, distributional functions, and pairwise correlations for the predictor variables. In doing so, the eigenfunction spatial filter quantified the residual autocorrelation error in the mean response term of the model as a linear combination of various distinct Cx. quinquefasciatus and Ae. albopictus habitat map patterns. The analyses revealed 18-27% redundant information in the data. Prolific habitats of Cx. quinquefasciatus and Ae. albopictus can be accurately spatially targeted based on georeferenced field-sampled count data using QuickBird data, LULC explanatory covariates, robust negative binomial regression estimates and space-time eigenfunctions. PMID:20969828

  4. Intrinsic Disorder in the BK Channel and Its Interactome

    PubMed Central

    Peng, Zhenling; Sakai, Yoshihisa; Kurgan, Lukasz; Sokolowski, Bernd; Uversky, Vladimir

    2014-01-01

    The large-conductance Ca2+-activated K+ (BK) channel is broadly expressed in various mammalian cells and tissues such as neurons, skeletal and smooth muscles, exocrine cells, and sensory cells of the inner ear. Previous studies suggest that BK channels are promiscuous binders involved in a multitude of protein-protein interactions. To gain a better understanding of the potential mechanisms underlying BK interactions, we analyzed the abundance, distribution, and potential mechanisms of intrinsic disorder in 27 BK channel variants from mouse cochlea, 104 previously reported BK-associated proteins (BKAPS) from cytoplasmic and membrane/cytoskeletal regions, plus BK ?- and ?-subunits. Disorder was evaluated using the MFDp algorithm, which is a consensus-based predictor that provides a strong and competitive predictive quality and PONDR, which can determine long intrinsically disordered regions (IDRs). Disorder-based binding sites or molecular recognition features (MoRFs) were found using MoRFpred and ANCHOR. BKAP functions were categorized based on Gene Ontology (GO) terms. The analyses revealed that the BK variants contain a number of IDRs. Intrinsic disorder is also common in BKAPs, of which ?5% are completely disordered. However, intrinsic disorder is very differently distributed within BK and its partners. Approximately 65% of the disordered segments in BK channels are long (IDRs) (>50 residues), whereas >60% of the disordered segments in BKAPs are short IDRs that range in length from 4 to 30 residues. Both ? and ? subunits showed various amounts of disorder as did hub proteins of the BK interactome. Our analyses suggest that intrinsic disorder is important for the function of BK and its BKAPs. Long IDRs in BK are engaged in protein-protein and protein-ligand interactions, contain multiple post-translational modification sites, and are subjected to alternative splicing. The disordered structure of BK and its BKAPs suggests one of the underlying mechanisms of their interaction. PMID:24727949

  5. Improved Microarray-Based Decision Support with Graph Encoded Interactome Data

    PubMed Central

    Daemen, Anneleen; Signoretto, Marco; Gevaert, Olivier; Suykens, Johan A. K.; De Moor, Bart

    2010-01-01

    In the past, microarray studies have been criticized due to noise and the limited overlap between gene signatures. Prior biological knowledge should therefore be incorporated as side information in models based on gene expression data to improve the accuracy of diagnosis and prognosis in cancer. As prior knowledge, we investigated interaction and pathway information from the human interactome on different aspects of biological systems. By exploiting the properties of kernel methods, relations between genes with similar functions but active in alternative pathways could be incorporated in a support vector machine classifier based on spectral graph theory. Using 10 microarray data sets, we first reduced the number of data sources relevant for multiple cancer types and outcomes. Three sources on metabolic pathway information (KEGG), protein-protein interactions (OPHID) and miRNA-gene targeting (microRNA.org) outperformed the other sources with regard to the considered class of models. Both fixed and adaptive approaches were subsequently considered to combine the three corresponding classifiers. Averaging the predictions of these classifiers performed best and was significantly better than the model based on microarray data only. These results were confirmed on 6 validation microarray sets, with a significantly improved performance in 4 of them. Integrating interactome data thus improves classification of cancer outcome for the investigated microarray technologies and cancer types. Moreover, this strategy can be incorporated in any kernel method or non-linear version of a non-kernel method. PMID:20419106

  6. A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome

    PubMed Central

    2013-01-01

    Background The complexity of the skeletal muscle and the identification of numerous human disease-causing mutations in its constitutive proteins make it an interesting tissue for proteomic studies aimed at understanding functional relationships of interacting proteins in both health and diseases. Method We undertook a large-scale study using two-hybrid screens and a human skeletal-muscle cDNA library to establish a proteome-scale map of protein-protein interactions centered on proteins involved in limb-girdle muscular dystrophies (LGMD). LGMD is a group of more than 20 different neuromuscular disorders that principally affect the proximal pelvic and shoulder girdle muscles. Results and conclusion The interaction network we unraveled incorporates 1018 proteins connected by 1492 direct binary interactions and includes 1420 novel protein-protein interactions. Computational, experimental and literature-based analyses were performed to assess the overall quality of this network. Interestingly, LGMD proteins were shown to be highly interconnected, in particular indirectly through sarcomeric proteins. In-depth mining of the LGMD-centered interactome identified new candidate genes for orphan LGMDs and other neuromuscular disorders. The data also suggest the existence of functional links between LGMD2B/dysferlin and gene regulation, between LGMD2C/?-sarcoglycan and energy control and between LGMD2G/telethonin and maintenance of genome integrity. This dataset represents a valuable resource for future functional investigations. PMID:23414517

  7. Interactome: gateway into systems biology Michael E. Cusick1,*, Niels Klitgord1

    E-print Network

    Bulyk, Martha L.

    of the structure, function and dynamics of the networks in which macromolecules function. We consider the full as complex networks or `interactome' maps. Protein­protein interaction mapping projects that follow stringent as elucidating individual protein function and interactome network topology. Although far from complete

  8. A comparative study of disease genes and drug targets in the human protein interactome

    PubMed Central

    2015-01-01

    Background Disease genes cause or contribute genetically to the development of the most complex diseases. Drugs are the major approaches to treat the complex disease through interacting with their targets. Thus, drug targets are critical for treatment efficacy. However, the interrelationship between the disease genes and drug targets is not clear. Results In this study, we comprehensively compared the network properties of disease genes and drug targets for five major disease categories (cancer, cardiovascular disease, immune system disease, metabolic disease, and nervous system disease). We first collected disease genes from genome-wide association studies (GWAS) for five disease categories and collected their corresponding drugs based on drugs' Anatomical Therapeutic Chemical (ATC) classification. Then, we obtained the drug targets for these five different disease categories. We found that, though the intersections between disease genes and drug targets were small, disease genes were significantly enriched in targets compared to their enrichment in human protein-coding genes. We further compared network properties of the proteins encoded by disease genes and drug targets in human protein-protein interaction networks (interactome). The results showed that the drug targets tended to have higher degree, higher betweenness, and lower clustering coefficient in cancer Furthermore, we observed a clear fraction increase of disease proteins or drug targets in the near neighborhood compared with the randomized genes. Conclusions The study presents the first comprehensive comparison of the disease genes and drug targets in the context of interactome. The results provide some foundational network characteristics for further designing computational strategies to predict novel drug targets and drug repurposing. PMID:25861037

  9. A human XPC protein interactome--a resource.

    PubMed

    Lubin, Abigail; Zhang, Ling; Chen, Hua; White, Victoria M; Gong, Feng

    2014-01-01

    Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP), a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions. PMID:24366067

  10. Dissecting noncoding and pathogen RNA–protein interactomes

    PubMed Central

    Flynn, Ryan A.; Martin, Lance; Spitale, Robert C.; Do, Brian T.; Sagan, Selena M.; Zarnegar, Brian; Qu, Kun; Khavari, Paul A.; Quake, Stephen R.; Sarnow, Peter

    2015-01-01

    RNA–protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA–protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and nonhuman transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA–protein recognition across the diversity of human and pathogen RNAs. PMID:25411354

  11. Predicted spatio-temporal dynamics of radiocesium deposited on forests following the Fukushima Dai-ichi nuclear power plant accident

    NASA Astrophysics Data System (ADS)

    Hashimoto, Shoji; Matsuura, Toshiya; Nanko, Kazuki; Linkov, Igor; Shaw, George; Kaneko, Shinji

    2013-04-01

    Radiocesium (134Cs and 137Cs) released from the Fukushima Dai-ichi nuclear power plant to the atmosphere contaminated a large area of Japan's land surface, the majority of which is covered by forest. Here we simulated the dynamics of radiocesium deposited on Japanese forest ecosystems in 2011 using a model that was developed for tracking radionuclides in forest ecosystems after the Chernobyl accident in 1986. The fate of the radiocesium was simulated using the initial conditions observed following the Fukushima accident. In addition, the simulation results were incorporated with a spatial distribution map of deposited radionuclides that was based on an air-borne survey. The simulation demonstrated that in the first two years after initial deposition radiocesium is retained primarily in the soil surface organic layer. Over a period of five to ten years radiocesium is predicted to move from the surface organic soil to the deeper mineral soil, which will eventually become the largest reservoir of radiocesium within forest ecosystems. Spatial analysis clearly shows the reduction in the extent of contaminated areas which will occur as a result of natural decay of radiocesium, as well as the spatial distribution of radiocesium in each forest component. Considering the heavier rainfall and warmer conditions in Japan than in the countries contaminated by the Chernobyl accident, migration of radiocesium from organic to mineral soil may be faster than predicted. Although the uncertainty of our simulations should be taken into account, they provide a basis for understanding and anticipating the future dynamics of radiocesium in Japanese forests following the Fukushima accident.

  12. ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome.

    PubMed

    Tinti, Michele; Madeira, Fábio; Murugesan, Gavuthami; Hoxhaj, Gerta; Toth, Rachel; Mackintosh, Carol

    2014-01-01

    The dimeric 14-3-3 proteins dock onto pairs of phosphorylated Ser and Thr residues on hundreds of proteins, and thereby regulate many events in mammalian cells. To facilitate global analyses of these interactions, we developed a web resource named ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome, which integrates multiple data sets on 14-3-3-binding phosphoproteins. ANIA also pinpoints candidate 14-3-3-binding phosphosites using predictor algorithms, assisted by our recent discovery that the human 14-3-3-interactome is highly enriched in 2R-ohnologues. 2R-ohnologues are proteins in families of two to four, generated by two rounds of whole genome duplication at the origin of the vertebrate animals. ANIA identifies candidate 'lynchpins', which are 14-3-3-binding phosphosites that are conserved across members of a given 2R-ohnologue protein family. Other features of ANIA include a link to the catalogue of somatic mutations in cancer database to find cancer polymorphisms that map to 14-3-3-binding phosphosites, which would be expected to interfere with 14-3-3 interactions. We used ANIA to map known and candidate 14-3-3-binding enzymes within the 2R-ohnologue complement of the human kinome. Our projections indicate that 14-3-3s dock onto many more human kinases than has been realized. Guided by ANIA, PAK4, 6 and 7 (p21-activated kinases 4, 6 and 7) were experimentally validated as a 2R-ohnologue family of 14-3-3-binding phosphoproteins. PAK4 binding to 14-3-3 is stimulated by phorbol ester, and involves the 'lynchpin' site phosphoSer99 and a major contribution from Ser181. In contrast, PAK6 and PAK7 display strong phorbol ester-independent binding to 14-3-3, with Ser113 critical for the interaction with PAK6. These data point to differential 14-3-3 regulation of PAKs in control of cell morphology. Database URL: https://ania-1433.lifesci.dundee.ac.uk/prediction/webserver/index.py. PMID:24501395

  13. Uncover disease genes by maximizing information flow in the phenome–interactome network

    PubMed Central

    Chen, Yong; Jiang, Tao; Jiang, Rui

    2011-01-01

    Motivation: Pinpointing genes that underlie human inherited diseases among candidate genes in susceptibility genetic regions is the primary step towards the understanding of pathogenesis of diseases. Although several probabilistic models have been proposed to prioritize candidate genes using phenotype similarities and protein–protein interactions, no combinatorial approaches have been proposed in the literature. Results: We propose the first combinatorial approach for prioritizing candidate genes. We first construct a phenome–interactome network by integrating the given phenotype similarity profile, protein–protein interaction network and associations between diseases and genes. Then, we introduce a computational method called MAXIF to maximize the information flow in this network for uncovering genes that underlie diseases. We demonstrate the effectiveness of this method in prioritizing candidate genes through a series of cross-validation experiments, and we show the possibility of using this method to identify diseases with which a query gene may be associated. We demonstrate the competitive performance of our method through a comparison with two existing state-of-the-art methods, and we analyze the robustness of our method with respect to the parameters involved. As an example application, we apply our method to predict driver genes in 50 copy number aberration regions of melanoma. Our method is not only able to identify several driver genes that have been reported in the literature, it also shed some new biological insights on the understanding of the modular property and transcriptional regulation scheme of these driver genes. Contact: ruijiang@tsinghua.edu.cn PMID:21685067

  14. Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment

    PubMed Central

    Jorda, Julien; Liu, Yu; Bobik, Thomas A.; Yeates, Todd O.

    2015-01-01

    Bacterial microcompartments (MCPs) are protein-bound organelles that carry out diverse metabolic pathways in a wide range of bacteria. These supramolecular assemblies consist of a thin outer protein shell, reminiscent of a viral capsid, which encapsulates sequentially acting enzymes. The most complex MCP elucidated so far is the propanediol utilizing (Pdu) microcompartment. It contains the reactions for degrading 1,2-propanediol. While several experimental studies on the Pdu system have provided hints about its organization, a clear picture of how all the individual components interact has not emerged yet. Here we use co-evolution-based methods, involving pairwise comparisons of protein phylogenetic trees, to predict the protein-protein interaction (PPI) network governing the assembly of the Pdu MCP. We propose a model of the Pdu interactome, from which selected PPIs are further inspected via computational docking simulations. We find that shell protein PduA is able to serve as a “universal hub” for targeting an array of enzymes presenting special N-terminal extensions, namely PduC, D, E, L and P. The varied N-terminal peptides are predicted to bind in the same cleft on the presumptive luminal face of the PduA hexamer. We also propose that PduV, a protein of unknown function with remote homology to the Ras-like GTPase superfamily, is likely to localize outside the MCP, interacting with the protruding ?-barrel of the hexameric PduU shell protein. Preliminary experiments involving a bacterial two-hybrid assay are presented that corroborate the existence of a PduU-PduV interaction. This first systematic computational study aimed at characterizing the interactome of a bacterial microcompartment provides fresh insight into the organization of the Pdu MCP. PMID:25646976

  15. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

    PubMed Central

    Luo, Heng; Chen, Jian; Shi, Leming; Mikailov, Mike; Zhu, Huang; Wang, Kejian; He, Lin; Yang, Lun

    2011-01-01

    Identifying new indications for existing drugs (drug repositioning) is an efficient way of maximizing their potential. Adverse drug reaction (ADR) is one of the leading causes of death among hospitalized patients. As both new indications and ADRs are caused by unexpected chemical–protein interactions on off-targets, it is reasonable to predict these interactions by mining the chemical–protein interactome (CPI). Making such predictions has recently been facilitated by a web server named DRAR-CPI. This server has a representative collection of drug molecules and targetable human proteins built up from our work in drug repositioning and ADR. When a user submits a molecule, the server will give the positive or negative association scores between the user’s molecule and our library drugs based on their interaction profiles towards the targets. Users can thus predict the indications or ADRs of their molecule based on the association scores towards our library drugs. We have matched our predictions of drug–drug associations with those predicted via gene-expression profiles, achieving a matching rate as high as 74%. We have also successfully predicted the connections between anti-psychotics and anti-infectives, indicating the underlying relevance of anti-psychotics in the potential treatment of infections, vice versa. This server is freely available at http://cpi.bio-x.cn/drar/. PMID:21558322

  16. Interactome Analysis Reveals Ezrin Can Adopt Multiple Conformational States*

    PubMed Central

    Viswanatha, Raghuvir; Wayt, Jessica; Ohouo, Patrice Y.; Smolka, Marcus B.; Bretscher, Anthony

    2013-01-01

    Ezrin, a member of the ezrin-radixin-moesin family (ERM), is an essential regulator of the structure of microvilli on the apical aspect of epithelial cells. Ezrin provides a linkage between membrane-associated proteins and F-actin, oscillating between active/open and inactive/closed states, and is regulated in part by phosphorylation of a C-terminal threonine. In the open state, ezrin can bind a number of ligands, but in the closed state the ligand-binding sites are inaccessible. In vitro analysis has proposed that there may be a third hyperactivated form of ezrin. To gain a better understanding of ezrin, we conducted an unbiased proteomic analysis of ezrin-binding proteins in an epithelial cell line, Jeg-3. We refined our list of interactors by comparing the interactomes using quantitative mass spectrometry between wild-type ezrin, closed ezrin, open ezrin, and hyperactivated ezrin. The analysis reveals several novel interactors confirmed by their localization to microvilli, as well as a significant class of proteins that bind closed ezrin. Taken together, the data indicate that ezrin can exist in three different conformational states, and different ligands “perceive” ezrin conformational states differently. PMID:24151071

  17. SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

    PubMed Central

    Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

    2015-01-01

    We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

  18. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

    PubMed

    Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

    2014-07-01

    Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. PMID:24803680

  19. Examining the Interactome of Huperzine A by Magnetic Biopanning

    PubMed Central

    Guo, Wei; Liu, Shupeng; Peng, Jinliang; Wei, Xiaohui; Sun, Ye; Qiu, Yangsheng; Gao, Guangwei; Wang, Peng; Xu, Yuhong

    2012-01-01

    Huperzine A is a bioactive compound derived from traditional Chinese medicine plant Qian Ceng Ta (Huperzia serrata), and was found to have multiple neuroprotective effects. In addition to being a potent acetylcholinesterase inhibitor, it was thought to act through other mechanisms such as antioxidation, antiapoptosis, etc. However, the molecular targets involved with these mechanisms were not identified. In this study, we attempted to exam the interactome of Huperzine A using a cDNA phage display library and also mammalian brain tissue extracts. The drugs were chemically linked on the surface of magnetic particles and the interactive phages or proteins were collected and analyzed. Among the various cDNA expressing phages selected, one was identified to encode the mitochondria NADH dehydrogenase subunit 1. Specific bindings between the drug and the target phages and target proteins were confirmed. Another enriched phage clone was identified as mitochondria ATP synthase, which was also panned out from the proteome of mouse brain tissue lysate. These data indicated the possible involvement of mitochondrial respiratory chain matrix enzymes in Huperzine A's pharmacological effects. Such involvement had been suggested by previous studies based on enzyme activity changes. Our data supported the new mechanism. Overall we demonstrated the feasibility of using magnetic biopanning as a simple and viable method for investigating the complex molecular mechanisms of bioactive molecules. PMID:22615909

  20. Computational polypharmacology analysis of the heat shock protein 90 interactome.

    PubMed

    Anighoro, Andrew; Stumpfe, Dagmar; Heikamp, Kathrin; Beebe, Kristin; Neckers, Leonard M; Bajorath, Jürgen; Rastelli, Giulio

    2015-03-23

    The design of a single drug molecule that is able to simultaneously and specifically interact with multiple biological targets is gaining major consideration in drug discovery. However, the rational design of drugs with a desired polypharmacology profile is still a challenging task, especially when these targets are distantly related or unrelated. In this work, we present a computational approach aimed at the identification of suitable target combinations for multitarget drug design within an ensemble of biologically relevant proteins. The target selection relies on the analysis of activity annotations present in molecular databases and on ligand-based virtual screening. A few target combinations were also inspected with structure-based methods to demonstrate that the identified dual-activity compounds are able to bind target combinations characterized by remote binding site similarities. Our approach was applied to the heat shock protein 90 (Hsp90) interactome, which contains several targets of key importance in cancer. Promising target combinations were identified, providing a basis for the computational design of compounds with dual activity. The approach may be used on any ensemble of proteins of interest for which known inhibitors are available. PMID:25686391

  1. A Tumorigenic Factor Interactome Connected Through Tumor Suppressor MicroRNA-198 in Human Pancreatic Cancer

    PubMed Central

    Marin-Muller, Christian; Li, Dali; Bharadwaj, Uddalak; Li, Min; Chen, Changyi; Hodges, Sally E.; Fisher, William E.; Mo, Qianxing; Hung, Mien-Chie; Yao, Qizhi

    2013-01-01

    Purpose The majority of pancreatic cancers (PCs) overexpress mesothelin (MSLN), which contributes to enhanced proliferation, invasion and migration. However, the MSLN regulatory network is still unclear. Here, we investigated the regulation of a panel of tumorigenic factors, and explored the potential of MSLN regulated miR-198 treatment in vivo. Experimental Design The expression and functional regulation of the tumorigenic factors MSLN, NF-?B, and the homeobox transcription factors (TFs) POU2F2 (OCT-2), Pre-B-cell leukemia homeobox factor 1 (PBX-1), valosin-containing protein (VCP), and miR-198 were studied in PC cell lines, patient tumor samples and in xenograft PC mouse models. Results We found that miR-198 is downregulated in PC and is involved in an intricate reciprocal regulatory loop with MSLN, which represses miR-198 through NF-?B-mediated OCT-2 induction. Furthermore, miR-198 repression leads to overexpression of PBX-1 and VCP. The dysregulated PBX-1/VCP axis leads to increased tumorigenicity. Reconstitution of miR-198 in PC cells results in reduced tumor growth, metastasis, and increased survival through direct targeting MSLN, PBX-1, and VCP. Most interestingly, reduced levels of miR-198 in human tissue samples are associated with upregulation of these tumorigenic factors (MSLN, OCT-2, PBX-1, VCP) and predict poor survival. Reduced miR-198 expression links this tumor network signature and prognosticates poor patient outcome. High miR-198 disrupts the network and predicts better prognosis and increased survival. Conclusions MiR-198 acts as a central tumor suppressor and modulates the molecular makeup of a critical interactome in PC, indicating a potential prognostic marker signature and the therapeutic potential of attacking this tumorigenic network through a central vantage point. PMID:23989979

  2. Neurodevelopmental disorders: mechanisms and boundary definitions from genomes, interactomes and proteomes

    PubMed Central

    Mullin, A P; Gokhale, A; Moreno-De-Luca, A; Sanyal, S; Waddington, J L; Faundez, V

    2013-01-01

    Neurodevelopmental disorders such as intellectual disability, autism spectrum disorder and schizophrenia lack precise boundaries in their clinical definitions, epidemiology, genetics and protein–protein interactomes. This calls into question the appropriateness of current categorical disease concepts. Recently, there has been a rising tide to reformulate neurodevelopmental nosological entities from biology upward. To facilitate this developing trend, we propose that identification of unique proteomic signatures that can be strongly associated with patient's risk alleles and proteome-interactome-guided exploration of patient genomes could define biological mechanisms necessary to reformulate disorder definitions. PMID:24301647

  3. Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

    PubMed Central

    Mosca, Roberto; Pons, Carles; Fernández-Recio, Juan; Aloy, Patrick

    2009-01-01

    The last several years have seen the consolidation of high-throughput proteomics initiatives to identify and characterize protein interactions and macromolecular complexes in model organisms. In particular, more that 10,000 high-confidence protein-protein interactions have been described between the roughly 6,000 proteins encoded in the budding yeast genome (Saccharomyces cerevisiae). However, unfortunately, high-resolution three-dimensional structures are only available for less than one hundred of these interacting pairs. Here, we expand this structural information on yeast protein interactions by running the first-ever high-throughput docking experiment with some of the best state-of-the-art methodologies, according to our benchmarks. To increase the coverage of the interaction space, we also explore the possibility of using homology models of varying quality in the docking experiments, instead of experimental structures, and assess how it would affect the global performance of the methods. In total, we have applied the docking procedure to 217 experimental structures and 1,023 homology models, providing putative structural models for over 3,000 protein-protein interactions in the yeast interactome. Finally, we analyze in detail the structural models obtained for the interaction between SAM1-anthranilate synthase complex and the MET30-RNA polymerase III to illustrate how our predictions can be straightforwardly used by the scientific community. The results of our experiment will be integrated into the general 3D-Repertoire pipeline, a European initiative to solve the structures of as many as possible protein complexes in yeast at the best possible resolution. All docking results are available at http://gatealoy.pcb.ub.es/HT_docking/. PMID:19714207

  4. Construction and application of a protein and genetic interaction network (yeast interactome)

    PubMed Central

    Stuart, Gregory R.; Copeland, William C.; Strand, Micheline K.

    2009-01-01

    Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome. PMID:19273534

  5. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis

    E-print Network

    Jones, Alan M.

    REPORT Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates Carbohydrate Research Center, University of Georgia, Athens, GA, USA, 8 School of Biological Sciences in planta. Co-expression analysis in combination with phenotyping of loss-of-function mutations in a set

  6. Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation

    Microsoft Academic Search

    Om V. Singh; Nagathihalli S. Nagaraj

    2006-01-01

    Microbial mediated bioremediation has a great potential to effectively restore contaminated environment, but the lack of information about factors regulating the growth and metabolism of various microbial communities in polluted environment often limits its implementation. Newly seeded techniques such as transcriptomics, proteomics and interactomics offer remarkable promise as tools to address longstanding questions regarding the molecular mechanisms involved in the

  7. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets

    Microsoft Academic Search

    T K B Gandhi; Jun Zhong; Suresh Mathivanan; L Karthick; K N Chandrika; S Sujatha Mohan; Salil Sharma; Stefan Pinkert; Shilpa Nagaraju; Balamurugan Periaswamy; Goparani Mishra; Kannabiran Nandakumar; Beiyi Shen; Nandan Deshpande; Rashmi Nayak; Malabika Sarker; Jef D Boeke; Giovanni Parmigiani; Jörg Schultz; Joel S Bader; Akhilesh Pandey

    2006-01-01

    We present the first analysis of the human proteome with regard to interactions between proteins. We also compare the human interactome with the available interaction datasets from yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans) and fly (Drosophila melanogaster). Of >70,000 binary interactions, only 42 were common to human, worm and fly, and only 16 were common to all four datasets. An

  8. RESEARCH Open Access Host-pathogen interactome mapping for HTLV-1

    E-print Network

    Paris-Sud XI, Université de

    for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two and presents new insights on biological pathways involved in retroviral infection. Keywords: HTLV, Interactome and proliferation path- ways [6]. Modulations of viral and cellular function upon infection rely on crosstalk

  9. A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

    PubMed Central

    Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

    2015-01-01

    The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly. PMID:25572661

  10. Align human interactome with phenome to identify causative genes and networks underlying disease families

    Microsoft Academic Search

    Xuebing Wu; Qifang Liu; Rui Jiang

    2009-01-01

    Motivation: Understanding the complexity in gene-phenotype relationship is vital for revealing the genetic basis of common diseases. Recent studies on the basis of human interactome and phenome not only uncovers prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human diseases, providing new opportunities to reduce the complexity in dissecting

  11. Parabolic Resonance: A Route to Hamiltonian Spatiotemporal Chaos

    SciTech Connect

    Shlizerman, Eli; Rom-Kedar, Vered [Faculty of Mathematics and Computer Science, Weizmann Institute of Science, Post Office Box 26, Rehovot 76100 (Israel)

    2009-01-23

    We show that initial data near an unperturbed stable plane wave can evolve into a regime of spatiotemporal chaos in the slightly forced conservative periodic one-dimensional nonlinear Schroedinger equation. Statistical measures are employed to demonstrate that this spatiotemporal chaos is intermittent: there are windows in time for which the solution gains spatial coherence. The parameters and initial profiles that lead to such intermittency are predicted by utilizing a novel geometrical description of the integrable unforced equation.

  12. Efficient Mining of Spatiotemporal Patterns

    Microsoft Academic Search

    Ilias Tsoukatos; Dimitrios Gunopulos

    2001-01-01

    Abstract. The problem of mining spatiotemporal ,patterns is finding sequences,of events ,that occur frequently in spatiotemporal datasets. Spatiotemporal datasets store the evolution of objects over time. Examples include sequences of sensor images of a geographical region, data that describes the location and movement of individual objects over time, or data that describes the evolution of natural phenomena, such as forest

  13. Proteomics, metabolomics, and protein interactomics in the characterization of the molecular features of major depressive disorder.

    PubMed

    Martins-de-Souza, Daniel

    2014-03-01

    Omics technologies emerged as complementary strategies to genomics in the attempt to understand human illnesses. In general, proteomics technologies emerged earlier than those of metabolomics for major depressive disorder (MDD) research, but both are driven by the identification of proteins and/or metabolites that can delineate a comprehensive characterization of MDD's molecular mechanisms, as well as lead to the identification of biomarker candidates of all types-prognosis, diagnosis, treatment, and patient stratification. Also, one can explore protein and metabolite interactomes in order to pinpoint additional molecules associated with the disease that had not been picked up initially. Here, results and methodological aspects of MDD research using proteomics, metabolomics, and protein interactomics are reviewed, focusing on human samples. PMID:24733971

  14. Towards Personalized Medicine Mediated by in Vitro Virus-Based Interactome Approaches

    PubMed Central

    Ohashi, Hiroyuki; Miyamoto-Sato, Etsuko

    2014-01-01

    We have developed a simple in vitro virus (IVV) selection system based on cell-free co-translation, using a highly stable and efficient mRNA display method. The IVV system is applicable to the high-throughput and comprehensive analysis of proteins and protein–ligand interactions. Huge amounts of genomic sequence data have been generated over the last decade. The accumulated genetic alterations and the interactome networks identified within cells represent a universal feature of a disease, and knowledge of these aspects can help to determine the optimal therapy for the disease. The concept of the “integrome” has been developed as a means of integrating large amounts of data. We have developed an interactome analysis method aimed at providing individually-targeted health care. We also consider future prospects for this system. PMID:24756093

  15. Expression of DISC1-Interactome Members Correlates with Cognitive Phenotypes Related to Schizophrenia

    PubMed Central

    Rampino, Antonio; Walker, Rosie May; Torrance, Helen Scott; Anderson, Susan Maguire; Fazio, Leonardo; Di Giorgio, Annabella; Taurisano, Paolo; Gelao, Barbara; Romano, Raffaella; Masellis, Rita; Ursini, Gianluca; Caforio, Grazia; Blasi, Giuseppe; Millar, J. Kirsty; Porteous, David John; Thomson, Pippa Ann; Bertolino, Alessandro; Evans, Kathryn Louise

    2014-01-01

    Cognitive dysfunction is central to the schizophrenia phenotype. Genetic and functional studies have implicated Disrupted-in-Schizophrenia 1 (DISC1), a leading candidate gene for schizophrenia and related psychiatric conditions, in cognitive function. Altered expression of DISC1 and DISC1-interactors has been identified in schizophrenia. Dysregulated expression of DISC1-interactome genes might, therefore, contribute to schizophrenia susceptibility via disruption of molecular systems required for normal cognitive function. Here, the blood RNA expression levels of DISC1 and DISC1-interacting proteins were measured in 63 control subjects. Cognitive function was assessed using neuropsychiatric tests and functional magnetic resonance imaging was used to assess the activity of prefrontal cortical regions during the N-back working memory task, which is abnormal in schizophrenia. Pairwise correlations between gene expression levels and the relationship between gene expression levels and cognitive function and N-back-elicited brain activity were assessed. Finally, the expression levels of DISC1, AKAP9, FEZ1, NDEL1 and PCM1 were compared between 63 controls and 69 schizophrenic subjects. We found that DISC1-interactome genes showed correlated expression in the blood of healthy individuals. The expression levels of several interactome members were correlated with cognitive performance and N-back-elicited activity in the prefrontal cortex. In addition, DISC1 and NDEL1 showed decreased expression in schizophrenic subjects compared to healthy controls. Our findings highlight the importance of the coordinated expression of DISC1-interactome genes for normal cognitive function and suggest that dysregulated DISC1 and NDEL1 expression might, in part, contribute to susceptibility for schizophrenia via disruption of prefrontal cortex-dependent cognitive functions. PMID:24940743

  16. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

    Microsoft Academic Search

    Nicolas Simonis; Jean-François Rual; Anne-Ruxandra Carvunis; Murat Tasan; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Julie M Sahalie; Kavitha Venkatesan; Fana Gebreab; Sebiha Cevik; Niels Klitgord; Changyu Fan; Pascal Braun; Ning Li; Nono Ayivi-Guedehoussou; Elizabeth Dann; Nicolas Bertin; David Szeto; Amélie Dricot; Muhammed A Yildirim; Chenwei Lin; Anne-Sophie de Smet; Huey-Ling Kao; Christophe Simon; Alex Smolyar; Jin Sook Ahn; Muneesh Tewari; Mike Boxem; Stuart Milstein; Haiyuan Yu; Matija Dreze; Jean Vandenhaute; Kristin C Gunsalus; Michael E Cusick; David E Hill; Jan Tavernier; Frederick P Roth; Marc Vidal

    2008-01-01

    To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards. We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of ?10,000 × ?10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we

  17. Interactome Mapping of the Phosphatidylinositol 3-Kinase-Mammalian Target of Rapamycin

    E-print Network

    §§¶¶ The phosphatidylinositol 3-kinase-mammalian target of rapamycin (PI3K-mTOR) pathway plays pivotal roles in cell survival and regulation of this pathway, we initiated a large scale yeast two-hybrid screen for 33 components of the PI3K-mTOR annotated interactome of 802 interactions for the PI3K-mTOR pathway. Our screen revealed a predominant place

  18. Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

    Microsoft Academic Search

    Nina C. Hubner; Matthias Mann

    2011-01-01

    Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein–protein interaction studies are of great interest. In recent years many protein–protein interactions have been determined by affinity purification followed by mass spectrometry (AP–MS). Among many different AP–MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive

  19. A human phenome-interactome network of protein complexes implicated in genetic disorders

    Microsoft Academic Search

    Kasper Lage; E Olof Karlberg; Zenia M Størling; Páll Í Ólason; Anders G Pedersen; Olga Rigina; Anders M Hinsby; Zeynep Tümer; Flemming Pociot; Niels Tommerup; Yves Moreau; Søren Brunak

    2007-01-01

    We performed a systematic, large-scale analysis of human protein complexes comprising gene products implicated in many different categories of human disease to create a phenome-interactome network. This was done by integrating quality-controlled interactions of human proteins with a validated, computationally derived phenotype similarity score, permitting identification of previously unknown complexes likely to be associated with disease. Using a phenomic ranking

  20. Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs

    PubMed Central

    Cao, Jianhua; Huang, Tinghua; Li, Xinyun; Zhao, Shuhong

    2014-01-01

    The regulatory relationship and connectivity among genes involved in myogenesis and hypertrophy of skeletal muscle in pigs still remain large challenges. Presentation of gene interactions is a potential way to understand the mechanisms of developmental events in skeletal muscle. In this study, genome-wide transcripts and miRNA profiling was determined for Landrace pigs at four time points using microarray chips. A comprehensive method integrating gene ontology annotation and interactome network mapping was conducted to analyze the biological patterns and interaction modules of muscle development events based on differentially expressed genes and miRNAs. Our results showed that in total 484 genes and 34 miRNAs were detected for the duration from embryonic stage to adult in pigs, which composed two linear expression patterns with consensus changes. Moreover, the gene ontology analysis also disclosed that there were three typical biological events i.e., microstructure assembly of sarcomere at early embryonic stage, myofibril formation at later embryonic stage and function establishments of myoblast cells at postnatal stage. The interactome mappings of different time points also found the down-regulated trend of gene expression existed across the whole duration, which brought a possibility to introduce the myogenesis related miRNAs into the interactome regulatory networks of skeletal muscle in pigs. PMID:25431924

  1. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    E-print Network

    Morris, Quaid

    the dynamic structure of the human protein interaction network (interactome) to determine whether changesDynamic modularity in protein interaction networks predicts breast cancer outcome Ian W Taylor1 identified proteins that have many interacting partners (so called `hubs') in a network of protein-protein

  2. Wong L, Liu G. Protein interactome analysis for countering pathogen drug resistance. JOURNAL OF COMPUTER SCI-ENCE AND TECHNOLOGY 25(1): 1 Jan. 2010

    E-print Network

    Wong, Limsoon

    Wong L, Liu G. Protein interactome analysis for countering pathogen drug resistance. JOURNAL OF COMPUTER SCI- ENCE AND TECHNOLOGY 25(1): 1­ Jan. 2010 Protein Interactome Analysis for Countering Pathogen, 2009; revised November 16, 2009. Abstract Drug-resistant varieties of pathogens are now a recognized

  3. Spatiotemporal multipartite entanglement

    SciTech Connect

    Kolobov, Mikhail I.; Patera, Giuseppe [Laboratoire de Physique des Lasers, Atomes et Molecules, Universite Lille 1, F-59655 Villeneuve d'Ascq Cedex (France)

    2011-05-15

    In this Rapid Communication, we propose, following the spirit of quantum imaging, to generalize the theory of multipartite entanglement for the continuous-variable Gaussian states by considering, instead of the global covariance matrix, the local correlation matrix at two different spatiotemporal points ({rho}-vector,t) and ({rho}-vector{sup '},t{sup '}), with {rho}-vector being the transverse coordinate. Our approach makes it possible to introduce the characteristic spatial length and the characteristic time of the multipartite entanglement, which in general depend on the number of 'parties' in the system. As an example, we consider tripartite entanglement in spontaneous parametric down-conversion with a spatially structured pump. We investigate spatiotemporal properties of such entanglement and calculate its characteristic spatial length and time.

  4. Impaired autophagy and APP processing in Alzheimer's disease: The potential role of Beclin 1 interactome.

    PubMed

    Salminen, Antero; Kaarniranta, Kai; Kauppinen, Anu; Ojala, Johanna; Haapasalo, Annakaisa; Soininen, Hilkka; Hiltunen, Mikko

    2013-01-01

    The accumulation of amyloid-?-containing neuritic plaques and intracellular tau protein tangles are key histopathological hallmarks of Alzheimer's disease (AD). This type of pathology clearly indicates that the mechanisms of neuronal housekeeping and protein quality control are compromised in AD. There is mounting evidence that the autophagosome-lysosomal degradation is impaired, which could disturb the processing of APP and provoke AD pathology. Beclin 1 is a molecular platform assembling an interactome with stimulating and suppressive components which regulate the initiation of the autophagosome formation. Recent studies have indicated that the expression Beclin 1 is reduced in AD brain. Moreover, the deficiency of Beclin 1 in cultured neurons and transgenic mice provokes the deposition of amyloid-? peptides whereas its overexpression reduces the accumulation of amyloid-?. There are several potential mechanisms, which could inhibit the function of Beclin 1 interactome and thus impair autophagy and promote AD pathology. The mechanisms include (i) reduction of Beclin 1 expression or its increased proteolytic cleavage by caspases, (ii) sequestration of Beclin 1 to non-functional locations, such as tau tangles, (iii) formation of inhibitory complexes between Beclin 1 and antiapoptotic Bcl-2 proteins or inflammasomes, (iv) interaction of Beclin 1 with inhibitory neurovirulent proteins, e.g. herpex simplex ICP34.5, or (v) inhibition of the Beclin 1/Vps34 complex through the activation of CDK1 and CDK5. We will shortly introduce the function of Beclin 1 interactome in autophagy and phagocytosis, review the recent evidence indicating that Beclin 1 regulates autophagy and APP processing in AD, and finally examine the potential mechanisms through which Beclin 1 dysfunction could be involved in the pathogenesis of AD. PMID:23827971

  5. MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria.

    PubMed

    Wang, Jiabin; Yang, Jian; Mao, Song; Chai, Xiaoqiang; Hu, Yuling; Hou, Xugang; Tang, Yiheng; Bi, Cheng; Li, Xiao

    2014-01-01

    Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of complicated biological mechanisms underlying mitochondrial functions and human mitochondrial diseases. MitProNet is freely accessible at http://bio.scu.edu.cn:8085/MitProNet. PMID:25347823

  6. Time-space Kriging to address the spatiotemporal misalignment in the large datasets

    PubMed Central

    Liang, Dong; Kumar, Naresh

    2013-01-01

    This paper presents a Bayesian hierarchical spatiotemporal method of interpolation, termed as Markov Cube Kriging (MCK). The classical Kriging methods become computationally prohibitive, especially for large datasets due to the O(n3) matrix decomposition. MCK offers novel and computationally efficient solutions to address spatiotemporal misalignment, mismatch in the spatiotemporal scales and missing values across space and time in large spatiotemporal datasets. MCK is flexible in that it allows for non-separable spatiotemporal structure and nonstationary covariance at the hierarchical spatiotemporal scales. Employing MCK we developed estimates of daily concentration of fine particulates matter ?2.5 ?m in aerodynamic diameter (PM2.5) at 2.5 km spatial grid for the Cleveland Metropolitan Statistical Area, 2000 to 2009. Our validation and cross-validation suggest that MCK achieved robust prediction of spatiotemporal random effects and underlying hierarchical and nonstationary spatiotemporal structure in air pollution data. MCK has important implications for environmental epidemiology and environmental sciences for exposure quantification and collocation of data from different sources, available at different spatiotemporal scales. PMID:24039539

  7. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    PubMed Central

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  8. Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.

    PubMed

    Cheng, Feixiong; Jia, Peilin; Wang, Quan; Lin, Chen-Ching; Li, Wen-Hsiung; Zhao, Zhongming

    2014-08-01

    Cells govern biological functions through complex biological networks. Perturbations to networks may drive cells to new phenotypic states, for example, tumorigenesis. Identifying how genetic lesions perturb molecular networks is a fundamental challenge. This study used large-scale human interactome data to systematically explore the relationship among network topology, somatic mutation, evolutionary rate, and evolutionary origin of cancer genes. We found the unique network centrality of cancer proteins, which is largely independent of gene essentiality. Cancer genes likely have experienced a lower evolutionary rate and stronger purifying selection than those of noncancer, Mendelian disease, and orphan disease genes. Cancer proteins tend to have ancient histories, likely originated in early metazoan, although they are younger than proteins encoded by Mendelian disease genes, orphan disease genes, and essential genes. We found that the protein evolutionary origin (age) positively correlates with protein connectivity in the human interactome. Furthermore, we investigated the network-attacking perturbations due to somatic mutations identified from 3,268 tumors across 12 cancer types in The Cancer Genome Atlas. We observed a positive correlation between protein connectivity and the number of nonsynonymous somatic mutations, whereas a weaker or insignificant correlation between protein connectivity and the number of synonymous somatic mutations. These observations suggest that somatic mutational network-attacking perturbations to hub genes play an important role in tumor emergence and evolution. Collectively, this work has broad biomedical implications for both basic cancer biology and the development of personalized cancer therapy. PMID:24881052

  9. Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC).

    PubMed

    Hubner, Nina C; Mann, Matthias

    2011-04-01

    Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein-protein interaction studies are of great interest. In recent years many protein-protein interactions have been determined by affinity purification followed by mass spectrometry (AP-MS). Among many different AP-MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive as it uses tagged, full-length baits that are expressed under endogenous control. For QUBIC large cell line collections expressing tagged proteins from BAC transgenes or gene trap loci have been developed and are freely available. Here we describe detailed workflows on how to obtain specific protein binding partners with high confidence under physiological conditions. The methods are based on fast, streamlined and generic purification procedures followed by single run liquid chromatography-mass spectrometric analysis. Quantification is achieved either by the stable isotope labeling of amino acids in cell culture (SILAC) method or by a 'label-free' procedure. In either case data analysis is performed by using the freely available MaxQuant environment. The QUBIC approach enables biologists with access to high resolution mass spectrometry to perform small and large-scale protein interactome mappings. PMID:21184827

  10. Oxidative status interactome map: towards novel approaches in experiment planning, data analysis, diagnostics and therapy.

    PubMed

    Zolotukhin, Peter; Kozlova, Yulia; Dovzhik, Anastasiya; Kovalenko, Konstantin; Kutsyn, Kseniya; Aleksandrova, Anzhela; Shkurat, Tatyana

    2013-08-01

    Experimental evidence suggests an immense variety of processes associated with and aimed at producing reactive oxygen and/or nitrogen species. Clinical studies implicate an enormous range of pathologies associated with reactive oxygen/nitrogen species metabolism deregulation, particularly oxidative stress. Recent advances in biochemistry, proteomics and molecular biology/biophysics of cells suggest oxidative stress to be an endpoint of complex dysregulation events of conjugated pathways consolidated under the term, proposed here, "oxidative status". The oxidative status concept, in order to allow for novel diagnostic and therapeutic approaches, requires elaboration of a new logic system comprehending all the features, versatility and complexity of cellular pro- and antioxidative components of different nature. We have developed a curated and regularly updated interactive interactome map of human cellular-level oxidative status allowing for systematization of the related most up-to-date experimental data. A total of more than 600 papers were selected for the initial creation of the map. The map comprises more than 300 individual factors with respective interactions, all subdivided hierarchically for logical analysis purposes. The pilot application of the interactome map suggested several points for further development of oxidative status-based technologies. PMID:23698602

  11. Intro Temporal Poisson Spatiotemporal exchangeability Discussion Are Declustered Earthquake Catalogs Poisson?

    E-print Network

    Stark, Philip B.

    Phenomenology · Earthquakes destroy and kill. Studied since ancient times. Prediction is an old goal: save livesIntro Temporal Poisson Spatiotemporal exchangeability Discussion Are Declustered Earthquake fit Poisson process models have used tests that ignore earthquake locations. They divide time

  12. Contrast Adaptation Implies Two Spatiotemporal Channels but Three Adapting Processes

    ERIC Educational Resources Information Center

    Langley, Keith; Bex, Peter J.

    2007-01-01

    The contrast gain control model of adaptation predicts that the effects of contrast adaptation correlate with contrast sensitivity. This article reports that the effects of high contrast spatiotemporal adaptors are maximum when adapting around 19 Hz, which is a factor of two or more greater than the peak in contrast sensitivity. To explain the…

  13. Support Vector Machines for Spatiotemporal Tornado INDRA ADRIANTO1

    E-print Network

    Lakshmanan, Valliappa

    1 Support Vector Machines for Spatiotemporal Tornado Prediction INDRA ADRIANTO1 , THEODORE B and time of tornadoes is presented. In this paper, we extend the work by Lakshmanan et al. (2005a) to use the probability of a tornado event at a particular spatial location within a given time window. We utilize a least

  14. Grouping Annotations on the Subcellular Layered Interactome Demonstrates Enhanced Autophagy Activity in a Recurrent Experimental Autoimmune Uveitis T Cell Line

    PubMed Central

    Zhao, Yu; Dong, Yucui; Ju, Huanyu; Yang, Jinfeng; Sun, Jianhua; Li, Xia; Ren, Huan

    2014-01-01

    Human uveitis is a type of T cell-mediated autoimmune disease that often shows relapse–remitting courses affecting multiple biological processes. As a cytoplasmic process, autophagy has been seen as an adaptive response to cell death and survival, yet the link between autophagy and T cell-mediated autoimmunity is not certain. In this study, based on the differentially expressed genes (GSE19652) between the recurrent versus monophasic T cell lines, whose adoptive transfer to susceptible animals may result in respective recurrent or monophasic uveitis, we proposed grouping annotations on a subcellular layered interactome framework to analyze the specific bioprocesses that are linked to the recurrence of T cell autoimmunity. That is, the subcellular layered interactome was established by the Cytoscape and Cerebral plugin based on differential expression, global interactome, and subcellular localization information. Then, the layered interactomes were grouping annotated by the ClueGO plugin based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. The analysis showed that significant bioprocesses with autophagy were orchestrated in the cytoplasmic layered interactome and that mTOR may have a regulatory role in it. Furthermore, by setting up recurrent and monophasic uveitis in Lewis rats, we confirmed by transmission electron microscopy that, in comparison to the monophasic disease, recurrent uveitis in vivo showed significantly increased autophagy activity and extended lymphocyte infiltration to the affected retina. In summary, our framework methodology is a useful tool to disclose specific bioprocesses and molecular targets that can be attributed to a certain disease. Our results indicated that targeted inhibition of autophagy pathways may perturb the recurrence of uveitis. PMID:25116327

  15. Indeterminacy of spatiotemporal cardiac alternans

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaopeng

    2008-07-01

    Cardiac alternans, a beat-to-beat alternation in action potential duration (at the cellular level) or in electrocardiogram morphology (at the whole heart level), is a marker of ventricular fibrillation, a fatal heart rhythm that kills hundreds of thousands of people in the United States each year. Investigating cardiac alternans may lead to a better understanding of the mechanisms of cardiac arrhythmias and eventually better algorithms for the prediction and prevention of such dreadful diseases. In paced cardiac tissue, alternans develops under increasingly shorter pacing period. Existing experimental and theoretical studies adopt the assumption that alternans in homogeneous cardiac tissue is exclusively determined by the pacing period. In contrast, we find that, when calcium-driven alternans develops in cardiac fibers, it may take different spatiotemporal patterns depending on the pacing history. Because there coexist multiple alternans solutions for a given pacing period, the alternans pattern on a fiber becomes unpredictable. Using numerical simulation and theoretical analysis, we show that the coexistence of multiple alternans patterns is induced by the interaction between electrotonic coupling and an instability in calcium cycling.

  16. Spatiotemporal characteristics of pandemic influenza

    PubMed Central

    2014-01-01

    Background Prediction of timing for the onset and peak of an influenza pandemic is of vital importance for preventive measures. In order to identify common spatiotemporal patterns and climate influences for pandemics in Sweden we have studied the propagation in space and time of A(H1N1)pdm09 (10,000 laboratory verified cases), the Asian Influenza 1957–1958 (275,000 cases of influenza-like illness (ILI), reported by local physicians) and the Russian Influenza 1889–1890 (32,600 ILI cases reported by physicians shortly after the end of the outbreak). Methods All cases were geocoded and analysed in space and time. Animated video sequences, showing weekly incidence per municipality and its geographically weighted mean (GWM), were created to depict and compare the spread of the pandemics. Daily data from 1957–1958 on temperature and precipitation from 39 weather stations were collected and analysed with the case data to examine possible climatological effects on the influenza dissemination. Results The epidemic period lasted 11 weeks for the Russian Influenza, 10 weeks for the Asian Influenza and 9 weeks for the A(H1N1)pdm09. The Russian Influenza arrived in Sweden during the winter and was immediately disseminated, while both the Asian Influenza and the A(H1N1)pdm09 arrived during the spring. They were seeded over the country during the summer, but did not peak until October-November. The weekly GWM of the incidence moved along a line from southwest to northeast for the Russian and Asian Influenza but northeast to southwest for the A(H1N1)pdm09. The local epidemic periods of the Asian Influenza were preceded by falling temperature in all but one of the locations analysed. Conclusions The power of spatiotemporal analysis and modeling for pandemic spread was clearly demonstrated. The epidemic period lasted approximately 10 weeks for all pandemics. None of the pandemics had its epidemic period before late autumn. The epidemic period of the Asian Influenza was preceded by falling temperatures. Climate influences on pandemic spread seem important and should be further investigated. PMID:25011543

  17. Spatiotemporal relational random forest (SRRF)

    E-print Network

    McGovern, Amy

    · Object-oriented · Rain, convection, hail, lightning, clouds, aircraft · In-situ aircraft data ØWRF with the thunderstorm · Problem for aircraft · Delays · Structural Damage · Injuries to passengers · Airline- Method · Spatiotemporal Relational Random Forests · Aircraft centric · Temporally and spatially varying

  18. Ocean plankton. Determinants of community structure in the global plankton interactome.

    PubMed

    Lima-Mendez, Gipsi; Faust, Karoline; Henry, Nicolas; Decelle, Johan; Colin, Sébastien; Carcillo, Fabrizio; Chaffron, Samuel; Ignacio-Espinosa, J Cesar; Roux, Simon; Vincent, Flora; Bittner, Lucie; Darzi, Youssef; Wang, Jun; Audic, Stéphane; Berline, Léo; Bontempi, Gianluca; Cabello, Ana M; Coppola, Laurent; Cornejo-Castillo, Francisco M; d'Ovidio, Francesco; De Meester, Luc; Ferrera, Isabel; Garet-Delmas, Marie-José; Guidi, Lionel; Lara, Elena; Pesant, Stéphane; Royo-Llonch, Marta; Salazar, Guillem; Sánchez, Pablo; Sebastian, Marta; Souffreau, Caroline; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Gorsky, Gabriel; Not, Fabrice; Ogata, Hiroyuki; Speich, Sabrina; Stemmann, Lars; Weissenbach, Jean; Wincker, Patrick; Acinas, Silvia G; Sunagawa, Shinichi; Bork, Peer; Sullivan, Matthew B; Karsenti, Eric; Bowler, Chris; de Vargas, Colomban; Raes, Jeroen

    2015-05-22

    Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models. PMID:25999517

  19. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation.

    PubMed

    Minajigi, Anand; Froberg, John E; Wei, Chunyao; Sunwoo, Hongjae; Kesner, Barry; Colognori, David; Lessing, Derek; Payer, Bernhard; Boukhali, Myriam; Haas, Wilhelm; Lee, Jeannie T

    2015-07-17

    The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform "identification of direct RNA interacting proteins" (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors-including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers, and modifiers-that synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. Although Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes. PMID:26089354

  20. Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth.

    PubMed

    Mertz, Joseph; Tan, Haiyan; Pagala, Vishwajeeth; Bai, Bing; Chen, Ping-Chung; Li, Yuxin; Cho, Ji-Hoon; Shaw, Timothy; Wang, Xusheng; Peng, Junmin

    2015-07-01

    The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It is also expressed in postmitotic neurons and regulates neuronal morphogenesis and synaptic activity by mechanisms that are largely unknown. We sought to comprehensively characterize the Mib1 interactome and study its potential function in neuron development utilizing a novel sequential elution strategy for affinity purification, in which Mib1 binding proteins were eluted under different stringency and then quantified by the isobaric labeling method. The strategy identified the Mib1 interactome with both deep coverage and the ability to distinguish high-affinity partners from low-affinity partners. A total of 817 proteins were identified during the Mib1 affinity purification, including 56 high-affinity partners and 335 low-affinity partners, whereas the remaining 426 proteins are likely copurified contaminants or extremely weak binding proteins. The analysis detected all previously known Mib1-interacting proteins and revealed a large number of novel components involved in Notch and Wnt pathways, endocytosis and vesicle transport, the ubiquitin-proteasome system, cellular morphogenesis, and synaptic activities. Immunofluorescence studies further showed colocalization of Mib1 with five selected proteins: the Usp9x (FAM) deubiquitinating enzyme, alpha-, beta-, and delta-catenins, and CDKL5. Mutations of CDKL5 are associated with early infantile epileptic encephalopathy-2 (EIEE2), a severe form of mental retardation. We found that the expression of Mib1 down-regulated the protein level of CDKL5 by ubiquitination, and antagonized CDKL5 function during the formation of dendritic spines. Thus, the sequential elution strategy enables biochemical characterization of protein interactomes; and Mib1 analysis provides a comprehensive interactome for investigating its role in signaling networks and neuronal development. PMID:25931508

  1. Comparative analysis of virus-host interactomes with a mammalian high- throughput protein complementation assay based on Gaussia princeps luciferase

    PubMed Central

    Neveu, Grégory; Cassonnet, Patricia; Vidalain, Pierre-Olivier; Rolloy, Caroline; Mendoza, José; Jones, Louis; Tangy, Frédéric; Muller, Mandy; Demeret, Caroline; Tafforeau, Lionel; Lotteau, Vincent; Rabourdin-Combe, Chantal; Travé, Gilles; Dricot, Amélie; Hill, David E.; Vidal, Marc; Favre, Michel; Jacob, Yves

    2012-01-01

    Comparative interactomics is a strategy for inferring potential interactions among orthologous proteins or “iginterologs”. Herein we focus, in contrast to standard homology-based inference, on the divergence of protein interaction profiles among closely related organisms, showing that the approach can correlate specific traits to phenotypic differences. As a model, this new comparative interactomic approach was applied at a large scale to human papillomaviruses (HPVs) proteins. The oncogenic potential of HPVs is mainly determined by the E6 and E7 early proteins. We have mapped and overlapped the virus-host protein interaction networks of E6 and E7 proteins from 11 distinct HPV genotypes, selected for their different tropisms and pathologies. We generated robust and comprehensive datasets by combining two orthogonal protein interation assays: yeast two-hybrid (Y2H), and our recently described “High-Throughput Gaussia princeps Protein Complementation Assay” (HT-GPCA). HT-GPCA detects protein interaction by measuring the interaction-mediated reconstitution of activity of a split Gaussia princeps luciferase. Hierarchical clustering of interaction profiles recapitulated HPV phylogeny and was used to correlate specific virus-host interaction profiles with pathological traits, reflecting the distinct carcinogenic potentials of different HPVs. This comparative interactomics constitutes a reliable and powerful strategy to decipher molecular relationships in virtually any combination of microorganism-host interactions. PMID:22898364

  2. Targets of drugs are generally, and targets of drugs having side effects are specifically good spreaders of human interactome perturbations

    E-print Network

    Perez-Lopez, Aron R; Turei, Denes; Modos, Dezso; Lenti, Katalin; Korcsmaros, Tamas; Csermely, Peter

    2015-01-01

    Network-based methods are playing an increasingly important role in drug design. Our main question in this paper was whether the efficiency of drug target proteins to spread perturbations in the human interactome is larger if the binding drugs have side effects, as compared to those which have no reported side effects. Our results showed that in general, drug targets were better spreaders of perturbations than non-target proteins, and in particular, targets of drugs with side effects were also better spreaders of perturbations than targets of drugs having no reported side effects in human protein-protein interaction networks. Colorectal cancer-related proteins were good spreaders and had a high centrality, while type 2 diabetes-related proteins showed an average spreading efficiency and had an average centrality in the human interactome. Moreover, the interactome-distance between drug targets and disease-related proteins was higher in diabetes than in colorectal cancer. Our results may help a better understan...

  3. Discovery of Periodic Patterns in Spatiotemporal Sequences

    E-print Network

    Cheung, David Wai-lok

    Discovery of Periodic Patterns in Spatiotemporal Sequences Huiping Cao, Nikos Mamoulis, Member and analyze spatiotemporal data, movements obey periodic patterns; the objects follow the same routes the same route to their work everyday. The discovery of hidden periodic patterns in spatiotemporal data

  4. Toward mining of spatiotemporal maximal frequent patterns

    E-print Network

    Malerba, Donato

    spatiotemporal data including envi- ronmental and medical data, keystroke dynamics data or text. We intro- duceToward mining of spatiotemporal maximal frequent patterns Lubos Popel´insk´y and Jan Blat´ak KD Lab show that propositional spatiotemporal logic PSTL is a powerful tool for mining in various

  5. Spatiotemporal correlations of aftershock sequences

    E-print Network

    Tiago P. Peixoto; Katharina Doblhoff-Dier; Jörn Davidsen

    2010-04-12

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  6. Implicit learning of spatiotemporal contingencies in spatial cueing.

    PubMed

    Rieth, Cory A; Huber, David E

    2013-08-01

    We investigated the role of implicit spatiotemporal learning in the Posner spatial cueing of attention task. During initial training, the proportion of different trial types was altered to produce a complex pattern of spatiotemporal contingencies between cues and targets. For example, in the short invalid and long valid condition, targets reliably appeared either at an uncued location after a short stimulus onset asynchrony (SOA; 100 ms) or at a cued location after a long SOA (350 ms). As revealed by postexperiment questioning, most participants were unaware of these manipulations. Whereas prior studies have examined reaction times during training, the current study examined the long-term effect of training on subsequent testing that removed these contingencies. An initial experiment found training effects only for the long SOAs that typically produce inhibition of return (IOR) effects. For instance, after short invalid and long valid training, there was a benefit at long SOAs rather than an IOR effect. A 2nd experiment ruled out target-cue overlap as an explanation of the difference between learning for long versus short SOAs. Rather than a mix of perfectly predictable spatiotemporal contingencies, Experiment 3 used only short SOA trials during training with a probabilistic spatial contingency. There was a smaller but reliable training effect in subsequent testing. These results demonstrate that implicit learning for specific combinations of location and SOA can affect behavior in spatial cueing paradigms, which is a necessary result if more generally spatial cueing reflects learned spatiotemporal regularities. PMID:23181686

  7. Finding Spatio-Temporal Patterns in Earth Science Data

    Microsoft Academic Search

    Pang-Ning Tan; Michael Steinbach; Vipin Kumar; Christopher Potter; Steven Klooster; Alicia Torregrosa

    2001-01-01

    This paper presents preliminary work in using data mining techniques to find interesting spatio-temporal patterns from Earth Science data. The data consists of time series measurements for various Earth science and climate variables (e.g. soil moisture, temperature, and precipitation), along with additional data from existing ecosystem models (e.g. Net Primary Production). The ecological patterns of interest include associations, clusters, predictive

  8. Optical flow using spatiotemporal filters

    Microsoft Academic Search

    David J. Heeger

    1988-01-01

    A model is presented, consonant with current views regarding the neurophysiology and psychophysics of motion perception, that combines the outputs of a set of spatiotemporal motion-energy filters to estimate image velocity. A parallel implementation computes a distributed representation of image velocity. A measure of image-flow uncertainty is formulated; preliminary results indicate that this uncertainty measure may be used to recognize

  9. “Stop Ne(c)king around”: How interactomics contributes to functionally characterize Nek family kinases

    PubMed Central

    Meirelles, Gabriela Vaz; Perez, Arina Marina; de Souza, Edmárcia Elisa; Basei, Fernanda Luisa; Papa, Priscila Ferreira; Melo Hanchuk, Talita Diniz; Cardoso, Vanessa Bomfim; Kobarg, Jörg

    2014-01-01

    Aside from Polo and Aurora, a third but less studied kinase family involved in mitosis regulation is the never in mitosis-gene A (NIMA)-related kinases (Neks). The founding member of this family is the sole member NIMA of Aspergillus nidulans, which is crucial for the initiation of mitosis in that organism. All 11 human Neks have been functionally assigned to one of the three core functions established for this family in mammals: (1) centrioles/mitosis; (2) primary ciliary function/ciliopathies; and (3) DNA damage response (DDR). Recent findings, especially on Nek 1 and 8, showed however, that several Neks participate in parallel in at least two of these contexts: primary ciliary function and DDR. In the core section of this in-depth review, we report the current detailed functional knowledge on each of the 11 Neks. In the discussion, we return to the cross-connections among Neks and point out how our and other groups’ functional and interactomics studies revealed that most Neks interact with protein partners associated with two if not all three of the functional contexts. We then raise the hypothesis that Neks may be the connecting regulatory elements that allow the cell to fine tune and synchronize the cellular events associated with these three core functions. The new and exciting findings on the Nek family open new perspectives and should allow the Neks to finally claim the attention they deserve in the field of kinases and cell cycle biology. PMID:24921005

  10. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

    PubMed Central

    Kwon, Kyong-Rim Kieffer; Tang, Zhonghui; Mathe, Ewy; Qian, Jason; Sung, Myong-Hee; Li, Guoliang; Resch, Wolfgang; Baek, Songjoon; Pruett, Nathanael; Grøntved, Lars; Vian, Laura; Nelson, Steevenson; Zare, Hossein; Hakim, Ofir; Reyon, Deepak; Yamane, Arito; Nakahashi, Hirotaka; Kovalchuk, Alexander L.; Zou, Jizhong; Joung, J. Keith; Sartorelli, Vittorio; Wei, Chia-Lin; Ruan, Xiaoan; Hager, Gordon L.; Ruan, Yijun; Casellas, Rafael

    2014-01-01

    A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-Seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly-transcribed genes, including Myc and Pim1 cell cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner. PMID:24360274

  11. Intrinsic Disorder in PTEN and its Interactome Confers Structural Plasticity and Functional Versatility

    PubMed Central

    Malaney, Prerna; Pathak, Ravi Ramesh; Xue, Bin; Uversky, Vladimir N.; Davé, Vrushank

    2013-01-01

    IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which its intrinsically disordered region (IDR) at the carboxyl-terminus (C-tail) executes its functions. Post-translational modifications, conserved eukaryotic linear motifs and molecular recognition features present in the C-tail IDR enhance PTEN's protein-protein interactions that are required for its myriad cellular functions. PTEN primary and secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN functions emanate from and are nucleated by the C-tail IDR, which form pliable network-hubs. Together, PTEN higher order functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR. Targeting PTEN IDR and its interaction hubs emerges as a new paradigm for treatment of PTEN related pathologies. PMID:23783762

  12. Interactome of the negative regulator of nuclear import BRCA1-binding protein 2.

    PubMed

    Fatima, Shadma; Wagstaff, Kylie M; Loveland, Kate L; Jans, David A

    2015-01-01

    Although the negative regulator of nuclear import (NRNI) BRCA1 binding protein 2 (BRAP2) is highly expressed in testis, its role is largely unknown. Here we address this question by documenting the BRAP2 interactome from human testis, using the yeast 2-hybrid system to identify BRAP2-interacting proteins with roles in diverse cellular processes, including regulation of the actin cytoskeleton, ubiquitinylation, cell cycle/apoptosis and transcription. Interaction with BRAP2 in adult mouse testis with three of these, PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1), A-Kinase anchor protein (AKAP3) and DNA methyl transferase 1 (DNMT1), was confirmed by coimmunoprecipitation assays. BRAP2's ability to inhibit PHLPP1 and DNMT1 nuclear localisation was also confirmed by quantitative confocal microscopy. Importantly, the physiological relevance thereof was implied by the cytoplasmic localisation of PHLPP1, AKAP3 and DNMT1 in pachytene spermatocytes/round spermatids where BRAP2 is present at high levels, and nuclear localisation of PHLPP1 and DNMT1 in spermatogonia concomitant with lower levels of BRAP2. Interestingly, BRAP2 was also present in murine spermatozoa, in part colocalised with AKAP3. Together the results indicate for the first time that BRAP2 may play an important NRNI role in germ cells of the testis, with an additional, scaffold/structural role in mature spermatozoa. PMID:25820252

  13. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

    Microsoft Academic Search

    Denis Dupuy; Nicolas Bertin; César A Hidalgo; Kavitha Venkatesan; Domena Tu; David Lee; Jennifer Rosenberg; Nenad Svrzikapa; Aurélie Blanc; Alain Carnec; Anne-Ruxandra Carvunis; Rock Pulak; Jane Shingles; John Reece-Hoyes; Rebecca Hunt-Newbury; Ryan Viveiros; William A Mohler; Murat Tasan; Frederick P Roth; Christian Le Peuch; Ian A Hope; Robert Johnsen; Donald G Moerman; Albert-László Barabási; David Baillie; Marc Vidal

    2007-01-01

    Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for ?900 predicted C. elegans promoters (?5% of the predicted protein-coding genes), each driving the expression of

  14. Anticancer activity of galactoxyloglucan polysaccharide-conjugated doxorubicin nanoparticles: Mechanistic insights and interactome analysis.

    PubMed

    Joseph, Manu M; Aravind, S R; George, Suraj K; Raveendran Pillai, K; Mini, S; Sreelekha, T T

    2015-06-01

    Toxicity associated with chemotherapeutic drugs such as doxorubicin (Dox), is one of the major obstacles that is currently affecting patients. PST-Dox (Galactoxyloglucan, PST001-conjugated Dox) nanoparticles were synthesized by encapsulating Dox with polysaccharide PST001, isolated from Tamarindus indica (Ti) by ionic gelation with tripolyphosphate (TPP). Herein, we demonstrate a detailed mechanistic and interactome network analysis that is specific to PST-Dox action in cancer cells and normal lymphocytes. Our results show that PST-Dox is superior to its parental counterparts, exhibiting a greater cytotoxicity by the induction of apoptosis against a wide variety of cancers by enhanced cellular uptake of Dox from the nanoparticle conjugates. Also, PST-Dox nanoparticles were non-toxic to normal lymphocytes with limited immunostimulatory effects up to certain doses. Elucidation of molecular mechanism by whole genome microarray in cancer cells and lymphocytes revealed that a large number of genes were dysregulated specifically in cancer cells. Specifically, a unique target gene EGR1, contextually determined translational activation of P53 in the cancerous and non-cancerous cells. Most of the key downregulated genes were tyrosine kinases, indicating the potential inhibitory action of PST-Dox on tyrosine kinase oncogenic pathways. Western blotting of proteins corresponding to the genes that were altered at the genomic level was very well correlated in the majority of them, except in a few that demonstrated post-transcriptional modifications. The important findings and highly disciplined approaches highlighted in the present study will speed up the therapeutic potential of this augmented nanoparticle formulation for more robust clinical studies and testing in several cancers. PMID:25864443

  15. Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

    PubMed Central

    Yang, Lun; Chen, Jian; He, Lin

    2009-01-01

    Identifying genetic factors responsible for serious adverse drug reaction (SADR) is of critical importance to personalized medicine. However, genome-wide association studies are hampered due to the lack of case-control samples, and the selection of candidate genes is limited by the lack of understanding of the underlying mechanisms of SADRs. We hypothesize that drugs causing the same type of SADR might share a common mechanism by targeting unexpectedly the same SADR-mediating protein. Hence we propose an approach of identifying the common SADR-targets through constructing and mining an in silico chemical-protein interactome (CPI), a matrix of binding strengths among 162 drug molecules known to cause at least one type of SADR and 845 proteins. Drugs sharing the same SADR outcome were also found to possess similarities in their CPI profiles towards this 845 protein set. This methodology identified the candidate gene of sulfonamide-induced toxic epidermal necrolysis (TEN): all nine sulfonamides that cause TEN were found to bind strongly to MHC I (Cw*4), whereas none of the 17 control drugs that do not cause TEN were found to bind to it. Through an insight into the CPI, we found the Y116S substitution of MHC I (B*5703) enhances the unexpected binding of abacavir to its antigen presentation groove, which explains why B*5701, not B*5703, is the risk allele of abacavir-induced hypersensitivity. In conclusion, SADR targets and the patient-specific off-targets could be identified through a systematic investigation of the CPI, generating important hypotheses for prospective experimental validation of the candidate genes. PMID:19629158

  16. Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

    PubMed Central

    Cheng, Feixiong; Jia, Peilin; Wang, Quan; Zhao, Zhongming

    2014-01-01

    The human kinome is gaining importance through its promising cancer therapeutic targets, yet no general model to address the kinase inhibitor resistance has emerged. Here, we constructed a systems biology-based framework to catalogue the human kinome, including 538 kinase genes, in the broader context of the human interactome. Specifically, we constructed three networks: a kinase-substrate interaction network containing 7,346 pairs connecting 379 kinases to 36,576 phosphorylation sites in 1,961 substrates, a protein-protein interaction network (PPIN) containing 92,699 pairs, and an atomic resolution PPIN containing 4,278 pairs. We identified the conserved regulatory phosphorylation motifs (e.g., Ser/Thr-Pro) using a sequence logo analysis. We found the typical anticancer target selection strategy that uses network hubs as drug targets, might lead to a high adverse drug reaction risk. Furthermore, we found the distinct network centrality of kinases creates a high anticancer drug resistance risk by feedback or crosstalk mechanisms within cellular networks. This notion is supported by the systematic network and pathway analyses that anticancer drug resistance genes are significantly enriched as hubs and heavily participate in multiple signaling pathways. Collectively, this comprehensive human kinome interactome map sheds light on anticancer drug resistance mechanisms and provides an innovative resource for rational kinase inhibitor design. PMID:25003367

  17. The Cellular Interactome of the Coronavirus Infectious Bronchitis Virus Nucleocapsid Protein and Functional Implications for Virus Biology

    PubMed Central

    Munday, Diane; Bickerton, Erica; Britton, Paul; Rodgers, Mark A.; Whitehouse, Adrian; Zhou, En-Min

    2013-01-01

    The coronavirus nucleocapsid (N) protein plays a multifunctional role in the virus life cycle, from regulation of replication and transcription and genome packaging to modulation of host cell processes. These functions are likely to be facilitated by interactions with host cell proteins. The potential interactome of the infectious bronchitis virus (IBV) N protein was mapped using stable isotope labeling with amino acids in cell culture (SILAC) coupled to a green fluorescent protein-nanotrap pulldown methodology and liquid chromatography-tandem mass spectrometry. The addition of the SILAC label allowed discrimination of proteins that were likely to specifically bind to the N protein over background binding. Overall, 142 cellular proteins were selected as potentially binding to the N protein, many as part of larger possible complexes. These included ribosomal proteins, nucleolar proteins, translation initiation factors, helicases, and hnRNPs. The association of selected cellular proteins with IBV N protein was confirmed by immunoblotting, cosedimentation, and confocal microscopy. Further, the localization of selected proteins in IBV-infected cells as well as their activity during virus infection was assessed by small interfering RNA-mediated depletion, demonstrating the functional importance of cellular proteins in the biology of IBV. This interactome not only confirms previous observations made with other coronavirus and IBV N proteins with both overexpressed proteins and infectious virus but also provides novel data that can be exploited to understand the interaction between the virus and the host cell. PMID:23637410

  18. Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy.

    PubMed

    Cheng, Feixiong; Jia, Peilin; Wang, Quan; Zhao, Zhongming

    2014-06-15

    The human kinome is gaining importance through its promising cancer therapeutic targets, yet no general model to address the kinase inhibitor resistance has emerged. Here, we constructed a systems biology-based framework to catalogue the human kinome, including 538 kinase genes, in the broader context of the human interactome. Specifically, we constructed three networks: a kinase-substrate interaction network containing 7,346 pairs connecting 379 kinases to 36,576 phosphorylation sites in 1,961 substrates, a protein-protein interaction network (PPIN) containing 92,699 pairs, and an atomic resolution PPIN containing 4,278 pairs. We identified the conserved regulatory phosphorylation motifs (e.g., Ser/Thr-Pro) using a sequence logo analysis. We found the typical anticancer target selection strategy that uses network hubs as drug targets, might lead to a high adverse drug reaction risk. Furthermore, we found the distinct network centrality of kinases creates a high anticancer drug resistance risk by feedback or crosstalk mechanisms within cellular networks. This notion is supported by the systematic network and pathway analyses that anticancer drug resistance genes are significantly enriched as hubs and heavily participate in multiple signaling pathways. Collectively, this comprehensive human kinome interactome map sheds light on anticancer drug resistance mechanisms and provides an innovative resource for rational kinase inhibitor design. PMID:25003367

  19. Dynamics of spatiotemporally propagating transport barriers

    Microsoft Academic Search

    P. H. Diamond; V. B. Lebedev; D. E. Newman; B. A. Carreras

    1995-01-01

    A simple dynamic model of spatiotemporally propagating transport barriers and transition fronts from low (L) to high (H) confinement regimes is presented. The model introduces spatial coupling (via transport) into the coupled evolution equations for flow shear and fluctuation intensity, thus coupling the supercritical L to H bifurcation instability to turbulent transport. Hence, fast spatiotemporal front propagation and evolutionary behavior

  20. Scalable spatio-temporal knowledge harvesting

    Microsoft Academic Search

    Yafang Wang; Bin Yang; Spyros Zoupanos; Marc Spaniol; Gerhard Weikum

    2011-01-01

    Knowledge harvesting enables the automated construction of large knowledge bases. In this work, we made a first attempt to harvest spatio-temporal knowledge from news archives to construct trajectories of individual entities for spatio-temporal entity tracking. Our approach consists of an entity extraction and disambiguation module and a fact generation module which produce pertinent trajectory records from textual sources. The evaluation

  1. Spatiotemporal firing patterns in the cerebellum

    Microsoft Academic Search

    Freek E. Hoebeek; Laurens W. J. Bosman; Martijn Schonewille; Laurens Witter; Sebastiaan K. Koekkoek; Chris I. De Zeeuw

    2011-01-01

    Neurons are generally considered to communicate information by increasing or decreasing their firing rate. However, in principle, they could in addition convey messages by using specific spatiotemporal patterns of spiking activities and silent intervals. Here, we review expanding lines of evidence that such spatiotemporal coding occurs in the cerebellum, and that the olivocerebellar system is optimally designed to generate and

  2. A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case

    PubMed Central

    2015-01-01

    Background Computational pharmacology can uniquely address some issues in the process of drug development by providing a macroscopic view and a deeper understanding of drug action. Specifically, network-assisted approach is promising for the inference of drug repurposing. However, the drug-target associations coming from different sources and various assays have much noise, leading to an inflation of the inference errors. To reduce the inference errors, it is necessary and critical to create a comprehensive and weighted data set of drug-target associations. Results In this study, we created a weighted and integrated drug-target interactome (WinDTome) to provide a comprehensive resource of drug-target associations for computational pharmacology. We first collected drug-target interactions from six commonly used drug-target centered data sources including DrugBank, KEGG, TTD, MATADOR, PDSP Ki Database, and BindingDB. Then, we employed the record linkage method to normalize drugs and targets to the unique identifiers by utilizing the public data sources including PubChem, Entrez Gene, and UniProt. To assess the reliability of the drug-target associations, we assigned two scores (Score_S and Score_R) to each drug-target association based on their data sources and publication references. Consequently, the WinDTome contains 546,196 drug-target associations among 303,018 compounds and 4,113 genes. To assess the application of the WinDTome, we designed a network-based approach for drug repurposing using mental disorder schizophrenia (SCZ) as a case. Starting from 41 known SCZ drugs and their targets, we inferred a total of 264 potential SCZ drugs through the associations of drug-target with Score_S higher than two in WinDTome and human protein-protein interactions. Among the 264 SCZ-related drugs, 39 drugs have been investigated in clinical trials for SCZ treatment and 74 drugs for the treatment of other mental disorders, respectively. Compared with the results using other Score_S cutoff values, single data source, or the data from STITCH, the inference of 264 SCZ-related drugs had the highest performance. Conclusions The WinDTome generated in this study contains comprehensive drug-target associations with confidence scores. Its application to the SCZ drug repurposing demonstrated that the WinDTome is promising to serve as a useful resource for drug repurposing. PMID:26100720

  3. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins.

    PubMed

    Bish, Rebecca; Cuevas-Polo, Nerea; Cheng, Zhe; Hambardzumyan, Dolores; Munschauer, Mathias; Landthaler, Markus; Vogel, Christine

    2015-01-01

    DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1?, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely conserved across eukaryotes. PMID:26184334

  4. Spatiotemporal Thinking in the Geosciences

    NASA Astrophysics Data System (ADS)

    Shipley, T. F.; Manduca, C. A.; Ormand, C. J.; Tikoff, B.

    2011-12-01

    Reasoning about spatial relations is a critical skill for geoscientists. Within the geosciences different disciplines may reason about different sorts of relationships. These relationships may span vastly different spatial and temporal scales (from the spatial alignment in atoms in crystals to the changes in the shape of plates). As part of work in a research center on spatial thinking in STEM education, we have been working to classify the spatial skills required in geology, develop tests for each spatial skill, and develop the cognitive science tools to promote the critical spatial reasoning skills. Research in psychology, neurology and linguistics supports a broad classification of spatial skills along two dimensions: one versus many objects (which roughly translates to object- focused and navigation focused skills) and static versus dynamic spatial relations. The talk will focus on the interaction of space and time in spatial cognition in the geosciences. We are working to develop measures of skill in visualizing spatiotemporal changes. A new test developed to measure visualization of brittle deformations will be presented. This is a skill that has not been clearly recognized in the cognitive science research domain and thus illustrates the value of interdisciplinary work that combines geosciences with cognitive sciences. Teaching spatiotemporal concepts can be challenging. Recent theoretical work suggests analogical reasoning can be a powerful tool to aid student learning to reason about temporal relations using spatial skills. Recent work in our lab has found that progressive alignment of spatial and temporal scales promotes accurate reasoning about temporal relations at geological time scales.

  5. Spatiotemporal structures in aging and rejuvenating glasses

    PubMed Central

    Peter G., Wolynes

    2009-01-01

    Complex spatiotemporal structures develop during the process of aging glasses after cooling and of rejuvenating glasses on heating. The key to understanding these structures is the interplay between the activated reconfiguration events that generate mobility and the transport of mobility. These effects are both accounted for by combining the random first-order transition theory of activated events with mode coupling theory in an inhomogeneous setting. The predicted modifications by mobility transport of the time course of the aging regime are modest. In contrast, the rejuvenation process is strongly affected through the propagation of fronts of enhanced mobility originating from the initial reconfiguration events. The structures in a rejuvenating glass resemble flames. An analysis along the lines of combustion theory provides an estimate of the front propagation speed. Heterogeneous rejuvenation naturally should occur for glasses with free surfaces. The analogy with combustion also provides a way of looking at the uptake of diluents by glasses described by case II and super case II diffusion. PMID:19188612

  6. Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome*

    PubMed Central

    Bounab, Yacine; Hesse, Anne-Marie-; Iannascoli, Bruno; Grieco, Luca; Couté, Yohann; Niarakis, Anna; Roncagalli, Romain; Lie, Eunkyung; Lam, Kong-Peng; Demangel, Caroline; Thieffry, Denis; Garin, Jérôme; Malissen, Bernard; Daëron, Marc

    2013-01-01

    We report the first proteomic analysis of the SLP76 interactome in resting and activated primary mouse mast cells. This was made possible by a novel genetic approach used for the first time here. It consists in generating knock-in mice that express signaling molecules bearing a C-terminal tag that has a high affinity for a streptavidin analog. Tagged molecules can be used as molecular baits to affinity-purify the molecular complex in which they are engaged, which can then be studied by mass spectrometry. We examined first SLP76 because, although this cytosolic adapter is critical for both T cell and mast cell activation, its role is well known in T cells but not in mast cells. Tagged SLP76 was expressed in physiological amounts and fully functional in mast cells. We unexpectedly found that SLP76 is exquisitely sensitive to mast cell granular proteases, that Zn2+-dependent metalloproteases are especially abundant in mast cells and that they were responsible for SLP76 degradation. Adding a Zn2+ chelator fully protected SLP76 in mast cell lysates, thereby enabling an efficient affinity-purification of this adapter with its partners. Label-free quantitative mass spectrometry analysis of affinity-purified SLP76 interactomes uncovered both partners already described in T cells and novel partners seen in mast cells only. Noticeably, molecules inducibly recruited in both cell types primarily concur to activation signals, whereas molecules recruited in activated mast cells only are mostly associated with inhibition signals. The transmembrane adapter LAT2, and the serine/threonine kinase with an exchange factor activity Bcr were the most recruited molecules. Biochemical and functional validations established the unexpected finding that Bcr is recruited by SLP76 and positively regulates antigen-induced mast cell activation. Knock-in mice expressing tagged molecules with a normal tissue distribution and expression therefore provide potent novel tools to investigate signalosomes and to uncover novel signaling molecules in mast cells. PMID:23820730

  7. Bayesian spatio-temporal analysis and geospatial risk factors of human monocytic ehrlichiosis.

    PubMed

    Raghavan, Ram K; Neises, Daniel; Goodin, Douglas G; Andresen, Daniel A; Ganta, Roman R

    2014-01-01

    Variations in spatio-temporal patterns of Human Monocytic Ehrlichiosis (HME) infection in the state of Kansas, USA were examined and the relationship between HME relative risk and various environmental, climatic and socio-economic variables were evaluated. HME data used in the study was reported to the Kansas Department of Health and Environment between years 2005-2012, and geospatial variables representing the physical environment [National Land cover/Land use, NASA Moderate Resolution Imaging Spectroradiometer (MODIS)], climate [NASA MODIS, Prediction of Worldwide Renewable Energy (POWER)], and socio-economic conditions (US Census Bureau) were derived from publicly available sources. Following univariate screening of candidate variables using logistic regressions, two Bayesian hierarchical models were fit; a partial spatio-temporal model with random effects and a spatio-temporal interaction term, and a second model that included additional covariate terms. The best fitting model revealed that spatio-temporal autocorrelation in Kansas increased steadily from 2005-2012, and identified poverty status, relative humidity, and an interactive factor, 'diurnal temperature range x mixed forest area' as significant county-level risk factors for HME. The identification of significant spatio-temporal pattern and new risk factors are important in the context of HME prevention, for future research in the areas of ecology and evolution of HME, and as well as climate change impacts on tick-borne diseases. PMID:24992684

  8. Spatiotemporal control of nanooptical excitations

    PubMed Central

    Aeschlimann, Martin; Bauer, Michael; Bayer, Daniela; Brixner, Tobias; Cunovic, Stefan; Dimler, Frank; Fischer, Alexander; Pfeiffer, Walter; Rohmer, Martin; Schneider, Christian; Steeb, Felix; Strüber, Christian; Voronine, Dmitri V.

    2010-01-01

    The most general investigation and exploitation of light-induced processes require simultaneous control over spatial and temporal properties of the electromagnetic field on a femtosecond time and nanometer length scale. Based on the combination of polarization pulse shaping and time-resolved two-photon photoemission electron microscopy, we demonstrate such control over nanoscale spatial and ultrafast temporal degrees of freedom of an electromagnetic excitation in the vicinity of a nanostructure. The time-resolved cross-correlation measurement of the local photoemission yield reveals the switching of the nanolocalized optical near-field distribution with a lateral resolution well below the diffraction limit and a temporal resolution on the femtosecond time scale. In addition, successful adaptive spatiotemporal control demonstrates the flexibility of the method. This flexible simultaneous control of temporal and spatial properties of nanophotonic excitations opens new possibilities to tailor and optimize the light–matter interaction in spectroscopic methods as well as in nanophotonic applications. PMID:20212153

  9. Facial Expression Recognition Using Spatiotemporal Boosted Discriminatory

    E-print Network

    Bowden, Richard

    Facial Expression Recognition Using Spatiotemporal Boosted Discriminatory Classifiers Stephen Moore approach to facial expression recognition in video sequences. Low cost contour features are introduced information to build boosted classifiers for frontal facial expression recognition in video sequences. Facial

  10. Anomalous Video Event Detection Using Spatiotemporal Context

    E-print Network

    Tsaftaris, Sotirios

    . Keywords: Video surveillance, anomaly detection, data mining, clustering, context 1. Introduction DiscoveryAnomalous Video Event Detection Using Spatiotemporal Context Fan Jianga, , Junsong Yuanc , Sotirios anomalous video event detection approaches that ana- lyze object trajectories only, we propose a context

  11. Generating spatiotemporal datasets on the WWW

    Microsoft Academic Search

    Yannis Theodoridis; Mario A. Nascimento

    2000-01-01

    Efficient storage, indexing and retrieval of time-evolving spatial data are some of the tasks that a Spatiotemporal Database Management System (STDBMS) must support. Aiming at designers of indexing methods and access structures, in this article we review the GSTD algorithm for generating spatiotemporal datasets according to several user-defined parameters, and introduce a WWW-based environment for generating and visualizing such datasets.

  12. Spatiotemporal features for asynchronous event-based data

    PubMed Central

    Lagorce, Xavier; Ieng, Sio-Hoi; Clady, Xavier; Pfeiffer, Michael; Benosman, Ryad B.

    2015-01-01

    Bio-inspired asynchronous event-based vision sensors are currently introducing a paradigm shift in visual information processing. These new sensors rely on a stimulus-driven principle of light acquisition similar to biological retinas. They are event-driven and fully asynchronous, thereby reducing redundancy and encoding exact times of input signal changes, leading to a very precise temporal resolution. Approaches for higher-level computer vision often rely on the reliable detection of features in visual frames, but similar definitions of features for the novel dynamic and event-based visual input representation of silicon retinas have so far been lacking. This article addresses the problem of learning and recognizing features for event-based vision sensors, which capture properties of truly spatiotemporal volumes of sparse visual event information. A novel computational architecture for learning and encoding spatiotemporal features is introduced based on a set of predictive recurrent reservoir networks, competing via winner-take-all selection. Features are learned in an unsupervised manner from real-world input recorded with event-based vision sensors. It is shown that the networks in the architecture learn distinct and task-specific dynamic visual features, and can predict their trajectories over time. PMID:25759637

  13. Proteomic Profiling of the TRAF3 Interactome Network Reveals a New Role for the ER-to-Golgi Transport Compartments in Innate Immunity

    Microsoft Academic Search

    Wendy J. van Zuylen; Priscilla Doyon; Jean-François Clément; Kashif Aziz Khan; Lisa M. DAmbrosio; Florence Dô; Myriam St-Amant-Verret; Tasheen Wissanji; Gregory Emery; Anne-Claude Gingras; Sylvain Meloche; Marc J. Servant

    2012-01-01

    Tumor Necrosis Factor receptor-associated factor-3 (TRAF3) is a central mediator important for inducing type I interferon (IFN) production in response to intracellular double-stranded RNA (dsRNA). Here, we report the identification of Sec16A and p115, two proteins of the ER-to-Golgi vesicular transport system, as novel components of the TRAF3 interactome network. Notably, in non-infected cells, TRAF3 was found associated with markers

  14. Hierarchical Bayesian space-time interpolation versus spatio-temporal BME approach

    NASA Astrophysics Data System (ADS)

    Hussain, I.; Pilz, J.; Spoeck, G.

    2010-03-01

    The restrictions of the analysis of natural processes which are observed at any point in space or time to a purely spatial or purely temporal domain may cause loss of information and larger prediction errors. Moreover, the arbitrary combinations of purely spatial and purely temporal models may not yield valid models for the space-time domain. For such processes the variation can be characterized by sophisticated spatio-temporal modeling. In the present study the composite spatio-temporal Bayesian maximum entropy (BME) method and transformed hierarchical Bayesian space-time interpolation are used in order to predict precipitation in Pakistan during the monsoon period. Monthly average precipitation data whose time domain is the monsoon period for the years 1974-2000 and whose spatial domain are various regions in Pakistan are considered. The prediction of space-time precipitation is applicable in many sectors of industry and economy in Pakistan especially; the agricultural sector. Mean field maps and prediction error maps for both methods are estimated and compared. In this paper it is shown that the transformed hierarchical Bayesian model is providing more accuracy and lower prediction error compared to the spatio-temporal Bayesian maximum entropy method; additionally, the transformed hierarchical Bayesian model also provides predictive distributions.

  15. Interactome analysis reveals that FAM161A, deficient in recessive retinitis pigmentosa, is a component of the Golgi-centrosomal network.

    PubMed

    Di Gioia, Silvio Alessandro; Farinelli, Pietro; Letteboer, Stef J F; Arsenijevic, Yvan; Sharon, Dror; Roepman, Ronald; Rivolta, Carlo

    2015-06-15

    Defects in FAM161A, a protein of unknown function localized at the cilium of retinal photoreceptor cells, cause retinitis pigmentosa, a form of hereditary blindness. By using different fragments of this protein as baits to screen cDNA libraries of human and bovine retinas, we defined a yeast two-hybrid-based FAM161A interactome, identifying 53 bona fide partners. In addition to statistically significant enrichment in ciliary proteins, as expected, this interactome revealed a substantial bias towards proteins from the Golgi apparatus, the centrosome and the microtubule network. Validation of interaction with key partners by co-immunoprecipitation and proximity ligation assay confirmed that FAM161A is a member of the recently recognized Golgi-centrosomal interactome, a network of proteins interconnecting Golgi maintenance, intracellular transport and centrosome organization. Notable FAM161A interactors included AKAP9, FIP3, GOLGA3, KIFC3, KLC2, PDE4DIP, NIN and TRIP11. Furthermore, analysis of FAM161A localization during the cell cycle revealed that this protein followed the centrosome during all stages of mitosis, likely reflecting a specific compartmentalization related to its role at the ciliary basal body during the G0 phase. Altogether, these findings suggest that FAM161A's activities are probably not limited to ciliary tasks but also extend to more general cellular functions, highlighting possible novel mechanisms for the molecular pathology of retinal disease. PMID:25749990

  16. Spatiotemporal model for the progression of transgressive dunes

    NASA Astrophysics Data System (ADS)

    Yizhaq, Hezi; Ashkenazy, Yosef; Levin, Noam; Tsoar, Haim

    2013-10-01

    Transgressive dune fields, which are active sand areas surrounded by vegetation, exist on many coasts. In some regions like in Fraser Island in Australia, small dunes shrink while large ones grow, although both experience the same climatic conditions. We propose a general mathematical model for the spatiotemporal dynamics of vegetation cover on sand dunes and focus on the dynamics of transgressive dunes. Among other possibilities, the model predicts growth parallel to the wind with shrinkage perpendicular to the wind, where, depending on geometry and size, a transgressive dune can initially grow although eventually shrink. The larger is the initial area the slower its stabilization process. The model’s predictions are supported by field observations from Fraser Island in Australia.

  17. BME analysis of spatiotemporal particulate matter distributions in North Carolina

    NASA Astrophysics Data System (ADS)

    Christakos, George; Serre, Marc L.

    Spatiotemporal maps of particulate matter (PM) concentrations contribute considerably to the understanding of the underlying natural processes and the adequate assessment of the PM health effects. These maps should be derived using an approach that combines rigorous mathematical formulation with sound science. To achieve such a task, the PM 10 distribution in the state of North Carolina is studied using the Bayesian maximum entropy (BME) mapping method. This method is based on a realistic representation of the spatiotemporal domain, which can integrate rigorously and efficiently various forms of physical knowledge and sources of uncertainty. BME offers a complete characterization of PM 10 concentration patterns in terms of multi-point probability distributions and allows considerable flexibility regarding the choice of the appropriate concentration estimates. The PM 10 maps show significant variability both spatially and temporally, a finding that may be associated with geographical characteristics, climatic changes, seasonal patterns, and random fluctuations. The inherently spatiotemporal nature of PM 10 variation is demonstrated by means of theoretical considerations as well as in terms of the more accurate PM 10 predictions of composite space/time analysis compared to spatial estimation. It is shown that the study of PM 10 distributions in North Carolina can be improved by properly incorporating uncertain data into the mapping process, whereas more informative estimates are generated by considering soft data at the estimation points. Uncertainty maps illustrate the significance of stochastic PM 10 characterization in space/time, and identify limitations associated with inadequate interpolation techniques. Stochastic PM 10 analysis has important applications in the optimization of monitoring networks in space and time, environmental risk assessment, health management and administration, etc.

  18. Formally grounding spatio-temporal thinking.

    PubMed

    Klippel, Alexander; Wallgrün, Jan Oliver; Yang, Jinlong; Li, Rui; Dylla, Frank

    2012-08-01

    To navigate through daily life, humans use their ability to conceptualize spatio-temporal information, which ultimately leads to a system of categories. Likewise, the spatial sciences rely heavily on conceptualization and categorization as means to create knowledge when they process spatio-temporal data. In the spatial sciences and in related branches of artificial intelligence, an approach has been developed for processing spatio-temporal data on the level of coarse categories: qualitative spatio-temporal representation and reasoning (QSTR). Calculi developed in QSTR allow for the meaningful processing of and reasoning with spatio-temporal information. While qualitative calculi are widely acknowledged in the cognitive sciences, there is little behavioral assessment whether these calculi are indeed cognitively adequate. This is an astonishing conundrum given that these calculi are ubiquitous, are often intended to improve processes at the human-machine interface, and are on several occasions claimed to be cognitively adequate. We have systematically evaluated several approaches to formally characterize spatial relations from a cognitive-behavioral perspective for both static and dynamically changing spatial relations. This contribution will detail our framework, which is addressing the question how formal characterization of space can help us understand how people think with, in, and about space. PMID:22806649

  19. Learning of Spatiotemporal Behavior in Cellular Neural Networks

    E-print Network

    Learning of Spatiotemporal Behavior in Cellular Neural Networks Samuel Xavier-de-Souza, Johan A In this paper the problem of learning spatiotemporal behavior with cellu- lar neural networks is analyzed. As a consequence, it does not force the desired spatiotemporal behavior to be learned in its original speed

  20. Spatio-temporal Feature Recogntion using Randomised Ferns

    E-print Network

    Paris-Sud XI, Université de

    Spatio-temporal Feature Recogntion using Randomised Ferns Olusegun Oshin, Andrew Gilbert, John Bayesian classifier of Ferns to the spatio-temporal domain and learn clas- sifiers that duplicate video sequence. We extend a Naive Bayesian classifier called Ferns [1] to the spatio-temporal domain

  1. Spatiotemporal electromagnetic soliton and spatial ring formation in nonlinear metamaterials

    SciTech Connect

    Zhang Jinggui; Wen Shuangchun; Xiang Yuanjiang; Wang Youwen; Luo Hailu [Key Laboratory for Micro/Nano Optoelectronic Devices of Ministry of Education, School of Computer and Communication, Hunan University, Changsha 410082 (China)

    2010-02-15

    We present a systematic investigation of ultrashort electromagnetic pulse propagation in metamaterials (MMs) with simultaneous cubic electric and magnetic nonlinearity. We predict that spatiotemporal electromagnetic solitons may exist in the positive-index region of a MM with focusing nonlinearity and anomalous group velocity dispersion (GVD), as well as in the negative-index region of the MM with defocusing nonlinearity and normal GVD. The experimental circumstances for generating and manipulating spatiotemporal electromagnetic solitons can be created by elaborating appropriate MMs. In addition, we find that, in the negative-index region of a MM, a spatial ring may be formed as the electromagnetic pulse propagates for focusing nonlinearity and anomalous GVD; while the phenomenon of temporal splitting of the electromagnetic pulse may appear for the same case except for the defocusing nonlinearity. Finally, we demonstrate that the nonlinear magnetization makes the sign of effective electric nonlinear effect switchable due to the combined action of electric and magnetic nonlinearity, exerting a significant influence on the propagation of electromagnetic pulses.

  2. Mercury Toolset for Spatiotemporal Metadata

    NASA Astrophysics Data System (ADS)

    Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce; Rhyne, B. Timothy; Lindsley, Chris

    2010-06-01

    Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily)harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

  3. Mercury Toolset for Spatiotemporal Metadata

    NASA Technical Reports Server (NTRS)

    Wilson, Bruce E.; Palanisamy, Giri; Devarakonda, Ranjeet; Rhyne, B. Timothy; Lindsley, Chris; Green, James

    2010-01-01

    Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily) harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

  4. A Spatio-temporal Model of African Animal Trypanosomosis Risk

    PubMed Central

    Dicko, Ahmadou H.; Percoma, Lassane; Sow, Adama; Adam, Yahaya; Mahama, Charles; Sidibé, Issa; Dayo, Guiguigbaza-Kossigan; Thévenon, Sophie; Fonta, William; Sanfo, Safietou; Djiteye, Aligui; Salou, Ernest; Djohan, Vincent; Cecchi, Giuliano; Bouyer, Jérémy

    2015-01-01

    Background African animal trypanosomosis (AAT) is a major constraint to sustainable development of cattle farming in sub-Saharan Africa. The habitat of the tsetse fly vector is increasingly fragmented owing to demographic pressure and shifts in climate, which leads to heterogeneous risk of cyclical transmission both in space and time. In Burkina Faso and Ghana, the most important vectors are riverine species, namely Glossina palpalis gambiensis and G. tachinoides, which are more resilient to human-induced changes than the savannah and forest species. Although many authors studied the distribution of AAT risk both in space and time, spatio-temporal models allowing predictions of it are lacking. Methodology/Principal Findings We used datasets generated by various projects, including two baseline surveys conducted in Burkina Faso and Ghana within PATTEC (Pan African Tsetse and Trypanosomosis Eradication Campaign) national initiatives. We computed the entomological inoculation rate (EIR) or tsetse challenge using a range of environmental data. The tsetse apparent density and their infection rate were separately estimated and subsequently combined to derive the EIR using a “one layer-one model” approach. The estimated EIR was then projected into suitable habitat. This risk index was finally validated against data on bovine trypanosomosis. It allowed a good prediction of the parasitological status (r2 = 67%), showed a positive correlation but less predictive power with serological status (r2 = 22%) aggregated at the village level but was not related to the illness status (r2 = 2%). Conclusions/Significance The presented spatio-temporal model provides a fine-scale picture of the dynamics of AAT risk in sub-humid areas of West Africa. The estimated EIR was high in the proximity of rivers during the dry season and more widespread during the rainy season. The present analysis is a first step in a broader framework for an efficient risk management of climate-sensitive vector-borne diseases. PMID:26154506

  5. Self-reconstructing spatiotemporal light bullets.

    PubMed

    Gražulevi?i?t?, I; Tamošauskas, G; Jukna, V; Couairon, A; Faccio, D; Dubietis, A

    2014-12-15

    We show that spatiotemporal light bullets generated by self-focusing and filamentation of 100 fs, 1.8 ?m pulses in a dielectric medium with anomalous group velocity dispersion (sapphire) are extremely robust to external perturbations. We present the experimental results supported by the numerical simulations that demonstrate complete spatiotemporal self-reconstruction of the light bullet after hitting an obstacle, which blocks its intense core carrying the self-compressed pulse, in nonlinear as well as in linear (free-space) propagation regimes. PMID:25607009

  6. Spatiotemporal characterization of ultrashort optical vortex pulses

    E-print Network

    Miranda, Miguel; Rudawski, Piotr; Guo, Chen; Harth, Anne; L'Huillier, Anne; Arnold, Cord L

    2015-01-01

    Generation of few-cycle optical vortex pulses is challenging due to the large spectral bandwidths, as most vortex generation techniques are designed for monochromatic light. In this work, we use a spiral phase plate to generate few-cycle optical vortices from an ultrafast titanium:sapphire oscillator, and characterize them in the spatiotemporal domain using a recently introduced technique based on spatially resolved Fourier transform spectrometry. The performance of this simple approach to the generation of optical vortices is analyzed from a wavelength dependent perspective, as well as in the spatiotemporal domain, allowing us to completely characterize ultrashort vortex pulses in space, frequency, and time.

  7. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway.

    PubMed

    Xing, Mengtan; Yang, Mingrui; Huo, Wei; Feng, Feng; Wei, Leizhen; Jiang, Wenxia; Ning, Shaokai; Yan, Zhenxin; Li, Wen; Wang, Qingsong; Hou, Mei; Dong, Chunxia; Guo, Rong; Gao, Ge; Ji, Jianguo; Zha, Shan; Lan, Li; Liang, Huanhuan; Xu, Dongyi

    2015-01-01

    Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku. The crystal structure of PAXX is similar to those of XRCC4 and XLF. Importantly, PAXX-deficient cells are sensitive to DSB-causing agents. Moreover, epistasis analysis demonstrates that PAXX functions together with XLF in response to ionizing radiation-induced complex DSBs, whereas they function redundantly in response to Topo2 inhibitor-induced simple DSBs. Consistently, PAXX and XLF coordinately promote the ligation of complex but not simple DNA ends in vitro. Altogether, our data identify PAXX as a new NHEJ factor and provide insight regarding the organization of NHEJ factors responding to diverse types of DSB ends. PMID:25670504

  8. Mutant p53 interactome identifies nardilysin as a p53R273H-specific binding partner that promotes invasion

    PubMed Central

    Coffill, Cynthia R; Muller, Patricia A J; Oh, Hue Kian; Neo, Suat Peng; Hogue, Kelly A; Cheok, Chit Fang; Vousden, Karen H; Lane, David P; Blackstock, Walter P; Gunaratne, Jayantha

    2012-01-01

    The invasiveness of tumour cells depends on changes in cell shape, polarity and migration. Mutant p53 induces enhanced tumour metastasis in mice, and human cells overexpressing p53R273H have aberrant polarity and increased invasiveness, demonstrating the ‘gain of function' of mutant p53 in carcinogenesis. We hypothesize that p53R273H interacts with mutant p53-specific binding partners that control polarity, migration or invasion. Here we analyze the p53R273H interactome using stable isotope labelling by amino acids in cell culture and quantitative mass spectrometry, and identify at least 15 new potential mutant p53-specific binding partners. The interaction of p53R273H with one of them—nardilysin (NRD1)—promotes an invasive response to heparin binding–epidermal growth factor-like growth factor that is p53R273H-dependant but does not require Rab coupling protein or p63. Advanced proteomics has thus allowed the detection of a new mechanism of p53-driven invasion. PMID:22653443

  9. The Cellular EJC Interactome Reveals Higher Order mRNP Structure and an EJC-SR Protein Nexus

    PubMed Central

    Singh, Guramrit; Kucukural, Alper; Cenik, Can; Leszyk, John D.; Shaffer, Scott A.; Weng, Zhiping; Moore, Melissa J.

    2012-01-01

    SUMMARY In addition to sculpting eukaryotic transcripts by removing introns, pre-mRNA splicing greatly impacts protein composition of the emerging mRNP. The exon junction complex (EJC), deposited upstream of exon-exon junctions after splicing, is a major constituent of spliced mRNPs. Here we report comprehensive analysis of the endogenous human EJC protein and RNA interactomes. We confirm that the major “canonical” EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions and that the majority of exon junctions carry an EJC. Unexpectedly, we find that endogenous EJCs multimerize with one another and with numerous SR proteins to form megadalton sized complexes in which SR proteins are super-stoichiometric to EJC core factors. This tight physical association may explain known functional parallels between EJCs and SR proteins. Further, their protection of long mRNA stretches from nuclease digestion suggests that endogenous EJCs and SR proteins cooperate to promote mRNA packaging and compaction. PMID:23084401

  10. AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions

    PubMed Central

    Scholz, Bastian; Kowarz, Eric; Rössler, Tanja; Ahmad, Khalil; Steinhilber, Dieter; Marschalek, Rolf

    2015-01-01

    AF4/AFF1 and AF5/AFF4 are the molecular backbone to assemble “super-elongation complexes” (SECs) that have two main functions: (1) control of transcriptional elongation by recruiting the positive transcription elongation factor b (P-TEFb = CyclinT1/CDK9) that is usually stored in inhibitory 7SK RNPs; (2) binding of different histone methyltransferases, like DOT1L, NSD1 and CARM1. This way, transcribed genes obtain specific histone signatures (e.g. H3K79me2/3, H3K36me2) to generate a transcriptional memory system. Here we addressed several questions: how is P-TEFb recruited into SEC, how is the AF4 interactome composed, and what is the function of the naturally occuring AF4N protein variant which exhibits only the first 360 amino acids of the AF4 full-length protein. Noteworthy, shorter protein variants are a specific feature of all AFF protein family members. Here, we demonstrate that full-length AF4 and AF4N are both catalyzing the transition of P-TEFb from 7SK RNP to their N-terminal domain. We have also mapped the protein-protein interaction network within both complexes. In addition, we have first evidence that the AF4N protein also recruits TFIIH and the tumor suppressor MEN1. This indicate that AF4N may have additional functions in transcriptional initiation and in MEN1-dependend transcriptional processes.

  11. Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system.

    PubMed

    Binai, Nadine A; Marino, Fabio; Soendergaard, Peter; Bache, Nicolai; Mohammed, Shabaz; Heck, Albert J R

    2015-02-01

    Here, we explore applications of a LC system using disposable solid-phase extraction (SPE) cartridges and very short LC-MS/MS gradients that allows for rapid analyses in less than 10 min analysis time. The setup consists of an autosampler harboring two sets of 96 STAGE tips that function as precolumns and a short RP analytical column running 6.5 min gradients. This system combines efficiently with several proteomics workflows such as offline prefractionation methods, including 1D gel electrophoresis and strong-cation exchange chromatography. It also enables the analysis of interactomes obtained by affinity purification with an analysis time of approximately 1 h. In a typical shotgun proteomics experiment involving 36 SCX fractions of an AspN digested cell lysate, we detected over 3600 protein groups with an analysis time of less than 5.5 h. This innovative fast LC system reduces proteome analysis time while maintaining sufficient proteomic detail. This has particular relevance for the use of proteomics within a clinical environment, where large sample numbers and fast turnover times are essential. PMID:25485597

  12. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway

    PubMed Central

    Xing, Mengtan; Yang, Mingrui; Huo, Wei; Feng, Feng; Wei, Leizhen; Jiang, Wenxia; Ning, Shaokai; Yan, Zhenxin; Li, Wen; Wang, Qingsong; Hou, Mei; Dong, Chunxia; Guo, Rong; Gao, Ge; Ji, Jianguo; Zha, Shan; Lan, Li; Liang, Huanhuan; Xu, Dongyi

    2015-01-01

    Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku. The crystal structure of PAXX is similar to those of XRCC4 and XLF. Importantly, PAXX-deficient cells are sensitive to DSB-causing agents. Moreover, epistasis analysis demonstrates that PAXX functions together with XLF in response to ionizing radiation-induced complex DSBs, whereas they function redundantly in response to Topo2 inhibitor-induced simple DSBs. Consistently, PAXX and XLF coordinately promote the ligation of complex but not simple DNA ends in vitro. Altogether, our data identify PAXX as a new NHEJ factor and provide insight regarding the organization of NHEJ factors responding to diverse types of DSB ends. PMID:25670504

  13. TCTEX1D4 Interactome in Human Testis: Unraveling the Function of Dynein Light Chain in Spermatozoa

    PubMed Central

    Freitas, Maria João; Korrodi-Gregório, Luís; Morais-Santos, Filipa; da Cruz e Silva, Edgar

    2014-01-01

    Abstract Studies were designed to identify the TCTEX1D4 interactome in human testis, with the purpose of unraveling putative protein complexes essential to male reproduction and thus novel TCTEX1D4 functions. TCTEX1D4 is a dynein light chain that belongs to the DYNT1/TCTEX1 family. In spermatozoa, it appears to be important to sperm motility, intraflagellar transport, and acrosome reaction. To contribute to the knowledge on TCTEX1D4 function in testis and spermatozoa, a yeast two-hybrid assay was performed in testis, which allowed the identification of 40 novel TCTEX1D4 interactors. Curiously, another dynein light chain, TCTEX1D2, was identified and its existence demonstrated for the first time in human spermatozoa. Immunofluorescence studies proved that TCTEX1D2 is an intra-acrosomal protein also present in the midpiece, suggesting a role in cargo movement in human spermatozoa. Further, an in silico profile of TCTEX1D4 revealed that most TCTEX1D4 interacting proteins were not previously characterized and the ones described present a very broad nature. This reinforces TCTEX1D4 as a dynein light chain that is capable of interacting with a variety of functionally different proteins. These observations collectively contribute to a deeper molecular understanding of the human spermatozoa function. PMID:24606217

  14. Interaction proteomics of canonical Caspr2 (CNTNAP2) reveals the presence of two Caspr2 isoforms with overlapping interactomes.

    PubMed

    Chen, Ning; Koopmans, Frank; Gordon, Aaron; Paliukhovich, Iryna; Klaassen, Remco V; van der Schors, Roel C; Peles, Elior; Verhage, Matthijs; Smit, August B; Li, Ka Wan

    2015-07-01

    Autism is a human developmental brain disorder characterized by impaired social interaction and communication. Contactin-associated protein-like 2 (Caspr2, CNTNAP2) is a known genetic risk factor of autism. However, how this protein might contribute to pathology is unclear. In this study, we demonstrate that Caspr2 is abundantly present in lipid raft and in the synaptic membrane but is highly depleted in the postsynaptic density. The Caspr2 protein level in hippocampus is present at a constant level during synapse formation and myelination from P0 to P84. Interaction proteomics revealed the interactors of Caspr2, including CNTN2, KCNAs, members of the ADAM family (ADAM22, ADAM23 and ADAM11), members of LGI family and MAGUKs (DLGs and MPPs). Interestingly, a short form of Caspr2 was detected, which lacks most of the extracellular domains, however, is still associated with ADAM22 and to a lesser extent LGI1 and Kv1 channels. The comprehensive Caspr2 interactome revealed here might aid in understanding the molecular mechanisms underlying autism. This article is part of a Special Issue titled Neuroproteomics: Applications in Neuroscience and Neurology. PMID:25707359

  15. Propagation of epileptic spikes reconstructed from spatiotemporal magnetoencephalographic and electroencephalographic source analysis

    PubMed Central

    Tanaka, Naoaki; Hämäläinen, Matti S; Ahlfors, Seppo P.; Liu, Hesheng; Madsen, Joseph R.; Bourgeois, Blaise F.; Lee, Jong Woo; Dworetzky, Barbara A.; Belliveau, John W.; Stufflebeam, Steven M.

    2009-01-01

    The purpose of this study is to assess the accuracy of spatiotemporal source analysis of magnetoencephalography (MEG) and scalp electroencephalography (EEG) for representing the propagation of frontotemporal spikes in patients with partial epilepsy. This study focuses on frontotemporal spikes, which are typically characterized by a preceding anterior temporal peak followed by an ipsilateral inferior frontal peak. Ten patients with frontotemporal spikes on MEG/EEG were studied. We analyzed the propagation of temporal to frontal epileptic spikes on both MEG and EEG independently by using a cortically-constrained minimum norm estimate (MNE). Spatiotemporal source distribution of each spike was obtained on the cortical surface derived from the patient’s MRI. All patients underwent an extraoperative intracranial EEG (IEEG) recording covering temporal and frontal lobes after presurgical evaluation. We extracted source waveforms of MEG and EEG from the source distribution of interictal spikes at the sites corresponding to the location of intracranial electrodes. The time differences of the ipsilateral temporal and frontal peaks as obtained by MEG, EEG and IEEG were statistically compared in each patient. In all patients, MEG and IEEG showed similar time differences between temporal and frontal peaks. The time differences of EEG spikes were significantly smaller than those of IEEG in nine of ten patients. Spatiotemporal analysis of MEG spikes models the time course of frontotemporal spikes as observed on IEEG more adequately than EEG in our patients. Spatiotemporal source analysis may be useful for planning epilepsy surgery, by predicting the pattern of IEEG spikes. PMID:20006721

  16. Interactive visualization of uncertain spatial and spatio-temporal data under different scenarios: an air quality example

    Microsoft Academic Search

    Edzer J. Pebesma; Kor De Jong; David Briggs

    2007-01-01

    This paper introduces a method for visually exploring spatio?temporal data or predictions that come as probability density functions, e.g. output of statistical models or Monte Carlo simulations, under different scenarios. For a given moment in time, we can explore the probability dimension by looking at maps with cumulative or exceedance probability while varying the attribute level that is exceeded, or

  17. Application of kinetic theory models in spatiotemporal flows for polymer solutions, liquid crystals and polymer melts using the CONNFFESSIT approach

    Microsoft Academic Search

    C. C. Hua; J. D. Schieber

    1996-01-01

    Three kinetic theory models are used to predict the spatiotemporal stress and velocity fields that arise in the startup of Couette flow. The models considered do not have analytic closed-form expressions for the stress tensor. Nevertheless, using a combined finite-element and Brownian dynamics technique (CONNFFESSIT), numerical solutions can be found. To describe the dynamics for dilute polymer solutions, a dumbbell

  18. Spatiotemporal dynamics and optical vortices in a photorefractive phase-conjugate resonator

    NASA Technical Reports Server (NTRS)

    Liu, Siuying Raymond; Indebetouw, Guy

    1992-01-01

    A truncated modal expansion approach is used to study the spatiotemporal dynamics of a phase-conjugate resonator as a function of Bragg detuning. The numerical results reveal a rich variety of behaviors. Emphasis is given to the spatial distribution of optical vortices, their trajectories and their relationship to the beam's spatial coherence. The limitations of the model are discussed and experimental results are presented for comparison with the model's predictions and assessment of its soundness.

  19. Experimental observation of a skewed X-type spatiotemporal correlation of ultrabroadband twin beams.

    PubMed

    Jedrkiewicz, O; Gatti, A; Brambilla, E; Di Trapani, P

    2012-12-14

    This work presents the experimental observation of the nonfactorable near-field spatiotemporal correlation of ultrabroadband twin beams generated by parametric down-conversion, in an interferometric-type experiment using sum frequency generation, where both the temporal and the spatial degrees of freedom of parametric down-conversion light are controlled with high resolution. The revealed correlation is skewed in space-time in accordance with the X structure predicted by the theory. PMID:23368318

  20. Spatio-temporal patterns of forest carbon dioxide exchange based on global eddy covariance measurements

    Microsoft Academic Search

    XingChang Wang; ChuanKuan Wang; GuiRui Yu

    2008-01-01

    Spatio-temporal patterns and driving mechanisms of forest carbon dioxide (CO2) exchange are the key issues on terrestrial ecosystem carbon cycles, which are the basis for developing and validating ecosystem\\u000a carbon cycle models, assessing and predicting the role of forests in global carbon balance. Eddy covariance (EC) technique,\\u000a an important method for measuring energy and material exchanges between terrestrial ecosystems and

  1. Methods for generating non-separable spatiotemporal covariance models with potential environmental applications

    Microsoft Academic Search

    A. Kolovos; G. Christakos; D. T. Hristopulos; M. L. Serre

    2004-01-01

    Environmental processes (e.g., groundwater contaminants, air pollution patterns, air–water and air–soil energy exchanges) are characterized by variability and uncertainty. Spatiotemporal random fields are used to represent correlations between fluctuations in the composite space–time domain. Modelling the effects of fluctuations with suitable covariance functions can improve our ability to characterize and predict space–time variations in various natural systems (e.g., environmental media,

  2. A general science-based framework for dynamical spatio-temporal models

    Microsoft Academic Search

    Christopher K. Wikle; Mevin B. Hooten

    2010-01-01

    Spatio-temporal statistical models are increasingly being used across a wide variety of scientific disciplines to describe\\u000a and predict spatially-explicit processes that evolve over time. Correspondingly, in recent years there has been a significant\\u000a amount of research on new statistical methodology for such models. Although descriptive models that approach the problem from\\u000a the second-order (covariance) perspective are important, and innovative work

  3. Spatiotemporal transformations of ultrashort terahertz pulses

    E-print Network

    Ku?el, Petr

    Spatiotemporal transformations of ultrashort terahertz pulses Petr Kuzel, Maxim A. Khazan, and Jan-cycle terahertz pulses emitted by large-aperture emitters. The spatial transformations of the beams are connected the temporal waveform and the spectrum of the pulses are altered as a result of these spa- tial transformations

  4. Spatiotemporal chaos in Easter Island ecology.

    PubMed

    Sprott, J C

    2012-10-01

    This paper demonstrates that a recently proposed spatiotemporal model for the ecology of Easter Island admits periodic and chaotic attractors, not previously reported. Such behavior may more realistically depict the population dynamics of general ecosystems and illustrates the power of simple models to produce the kind of complex behavior that is ubiquitous in such systems. PMID:22980451

  5. Specifications for Efficient Indexing in Spatiotemporal Databases

    Microsoft Academic Search

    Yannis Theodoridis; Timos K. Sellis; Apostolos N. Papadopoulos; Yannis Manolopoulos

    1998-01-01

    A new issue that arises in modern applications involves the efficient manipulation of (static or moving) spatial objects, and the relationships among them. As a result, modern database systems should be able to efficiently support that type of data. Towards this goal, appropriate extensions of multidimensional access methods can be exploited in order to index and retrieve spatiotemporal objects, satisfying

  6. On the Generation of Spatiotemporal Datasets

    Microsoft Academic Search

    Yannis Theodoridis; Jefferson R. O. Silva; Mario A. Nascimento

    1999-01-01

    An efficient benchmarking environment for spatiotemporal access methods should at least include modules for generating synthetic datasets, storing datasets (real datasets included), collecting and running access structures, and visualizing experimental results. Focusing on the dataset repository module, a collection of synthetic data that would simulate a variety of real life scenarios is required. Several algorithms have been implemented in the

  7. Cortical spatiotemporal plasticity in visual category learning

    E-print Network

    Regier, Terry

    -110 School of Computer Science Machine Learning Department Carnegie Mellon University Pittsburgh, PA 15213 behavioral experiments, magnetoencephalographic (MEG) imaging, and statistical machine learning methods. FromCortical spatiotemporal plasticity in visual category learning Yang Xu August 2013 CMU-ML-13

  8. Working with Spatio-Temporal Data Type

    NASA Astrophysics Data System (ADS)

    Raza, A.

    2012-07-01

    Several aspects of spatiotemporal databases have been explored in past decades, ranging from basic data structure to query processing and indexing. But today, operational temporal GIS does not exist. The key impediments have been the complexity of integrating space and time and the lack of standards. OpenGIS standards for simple feature access (spatial type) do exist, but unlike the spatial type, standards for spatiotemporal data type do not exist. This paper explores a new approach to modeling space and time to provide the basis for implementing a temporal GIS. This approach is based on the concept of data types in databases. A data type provides constructors, accessors, and operators. Most commercial and open source databases provide data types to deal with the spatial component of a GIS, called spatial type. Oracle Spatial, DB2 Spatial Extender and Informix Spatial DataBlade, ST_Geometry for PostgreSQL and Oracle from Esri, PostGIS for PostgreSQL, etc., are some examples. This new spatiotemporal data type is called spatiotemporal type (STT). This STT is implemented in PostgreSQL, an open source relational database management system. The STT is an extension of Esri's ST_Geometry type for PostgreSQL, in which each spatial object has a life span. Constructors, accessors, and relational functions are provided to create STT and support spatial, spatiotemporal, and temporal queries. Some functions are extended based on OpenGIS standards for the spatial type. Examples are provided to demonstrate the application of these functions. The paper concludes with limitations and challenges of implementing STT.

  9. Spatio-temporal prediction for West African monsoon Anestis Antoniadisa

    E-print Network

    . It explains why we fit our model with real data in this study : Reynolds climatological data on eighteen years : +33 (0)4 76 63 12 63. 1 hal-00551303,version1-3Jan2011 #12;comparisons with precipitation data. Global of the data is concerned, require considerable computational resources, it will be run in a grid

  10. Spatio-temporal patterns of schistosomiasis japonica in lake and marshland areas in China: the effect of snail habitats.

    PubMed

    Hu, Yi; Gao, Jie; Chi, Meina; Luo, Can; Lynn, Henry; Sun, Liqian; Tao, Bo; Wang, Decheng; Zhang, Zhijie; Jiang, Qingwu

    2014-09-01

    The progress of the integrated control policy for schistosomiasis implemented since 2005 in China, which is aiming at reducing the roles of bovines and humans as infection sources, may be challenged by persistent presence of infected snails in lake and marshland areas. Based on annual parasitologic data for schistosomiasis during 2004-2011 in Xingzi County, a spatio-temporal kriging model was used to investigate the spatio-temporal pattern of schistosomiasis risk. Results showed that environmental factors related to snail habitats can explain the spatio-temporal variation of schistosomiasis. Predictive maps of schistosomiasis risk illustrated that clusters of the disease fluctuated during 2004-2008; there was an extensive outbreak in 2008 and attenuated disease occurrences afterwards. An area with an annually constant cluster of schistosomiasis was identified. Our study suggests that targeting snail habitats located within high-risk areas for schistosomiasis would be an economic and sustainable way of schistosomiasis control in the future. PMID:24980498

  11. Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

    PubMed Central

    Huang, Shao-shan Carol; Clarke, David C.; Gosline, Sara J. C.; Labadorf, Adam; Chouinard, Candace R.; Gordon, William; Lauffenburger, Douglas A.; Fraenkel, Ernest

    2013-01-01

    Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study each of these stages individually, but do not capture the connections between them. Here we present an approach for building a network of physical links among these data that can be used to prioritize targets for pharmacological intervention. Our method recovers the critical missing links between proteomic and transcriptional data by relating changes in chromatin accessibility to changes in expression and then uses these links to connect proteomic and transcriptome data. We applied our approach to integrate epigenomic, phosphoproteomic and transcriptome changes induced by the variant III mutation of the epidermal growth factor receptor (EGFRvIII) in a cell line model of glioblastoma multiforme (GBM). To test the relevance of the network, we used small molecules to target highly connected nodes implicated by the network model that were not detected by the experimental data in isolation and we found that a large fraction of these agents alter cell viability. Among these are two compounds, ICG-001, targeting CREB binding protein (CREBBP), and PKF118–310, targeting ?-catenin (CTNNB1), which have not been tested previously for effectiveness against GBM. At the level of transcriptional regulation, we used chromatin immunoprecipitation sequencing (ChIP-Seq) to experimentally determine the genome-wide binding locations of p300, a transcriptional co-regulator highly connected in the network. Analysis of p300 target genes suggested its role in tumorigenesis. We propose that this general method, in which experimental measurements are used as constraints for building regulatory networks from the interactome while taking into account noise and missing data, should be applicable to a wide range of high-throughput datasets. PMID:23408876

  12. Analysis of the Bovine Intracellular Enteric Pathogen Interactome Each year the beef and dairy industries lose more than $330 million because of enteric diseases that cause the death of more than

    E-print Network

    Analysis of the Bovine Intracellular Enteric Pathogen Interactome Each year the beef and dairy weight gain. Understanding how cattle respond to enteric pathogens during acute infection is crucial have developed an in vivo bovine ligated ileal loop model to study bovine response to enteric pathogens

  13. Spatiotemporal dynamics of multimode optical solitons.

    PubMed

    Wright, Logan G; Renninger, William H; Christodoulides, Demetrios N; Wise, Frank W

    2015-02-01

    As optical fiber communications and fiber lasers approach fundamental limits there is considerable interest in multimode fibers. In nonlinear science, they represent an exciting environment for complex nonlinear waves. As in single-mode fiber, solitons may be particularly important. Multimode solitons consist of synchronized, non-dispersive pulses in multiple spatial modes, which interact via the Kerr nonlinearity of the fiber. They are expected to exhibit novel spatiotemporal characteristics, dynamics and, like single-mode solitons, may provide a convenient intuitive tool for understanding more complex nonlinear phenomena in multimode fibers. Here we explore experimentally and numerically basic properties and spatiotemporal behaviors of these solitons: their formation, fission, and Raman dynamics. PMID:25836204

  14. Spatiotemporal video segmentation based on graphical models.

    PubMed

    Wang, Yang; Loe, Kia-Fock; Tan, Tele; Wu, Jian-Kang

    2005-07-01

    This paper proposes a probabilistic framework for spatiotemporal segmentation of video sequences. Motion information, boundary information from intensity segmentation, and spatial connectivity of segmentation are unified in the video segmentation process by means of graphical models. A Bayesian network is presented to model interactions among the motion vector field, the intensity segmentation field, and the video segmentation field. The notion of the Markov random field is used to encourage the formation of continuous regions. Given consecutive frames, the conditional joint probability density of the three fields is maximized in an iterative way. To effectively utilize boundary information from the intensity segmentation, distance transformation is employed in local objective functions. Experimental results show that the method is robust and generates spatiotemporally coherent segmentation results. Moreover, the proposed video segmentation approach can be viewed as the compromise of previous motion based approaches and region merging approaches. PMID:16028557

  15. Spatiotemporal bessel beams: theory and experiments.

    PubMed

    Dallaire, Michaël; McCarthy, Nathalie; Piché, Michel

    2009-09-28

    We describe a family of dispersion-free and diffraction-free optical beams consisting in two-dimensional wave packets with a spatiotemporal Bessel (STB) profile propagating in media with anomalous dispersion. We also describe quasi-invariant optical beams with a spatiotemporal Bessel-Gauss (STBG) profile; these wave packets have finite dimensions and energy, conditions to be representative of physical beams. The paper provides a detailed account of the properties of STB and STBG beams, including their spatially resolved frequency spectrum, their far-field behaviour and a comparison of the propagation of STBG beams with that of Gaussian wave packets. An experimental setup based on a folded pulse shaper has allowed to generate STBG beams using the ultrashort pulses from a Ti:sapphire laser. The analysis of the spatially resolved frequency spectrum and of the spatial and temporal profiles obtained experimentally shows good agreement with theory. PMID:19907605

  16. Interactome Analyses of Mature ?-Secretase Complexes Reveal Distinct Molecular Environments of Presenilin (PS) Paralogs and Preferential Binding of Signal Peptide Peptidase to PS2*

    PubMed Central

    Jeon, Amy Hye Won; Böhm, Christopher; Chen, Fusheng; Huo, Hairu; Ruan, Xueying; Ren, Carl He; Ho, Keith; Qamar, Seema; Mathews, Paul M.; Fraser, Paul E.; Mount, Howard T. J.; St George-Hyslop, Peter; Schmitt-Ulms, Gerold

    2013-01-01

    ?-Secretase plays a pivotal role in the production of neurotoxic amyloid ?-peptides (A?) in Alzheimer disease (AD) and consists of a heterotetrameric core complex that includes the aspartyl intramembrane protease presenilin (PS). The human genome codes for two presenilin paralogs. To understand the causes for distinct phenotypes of PS paralog-deficient mice and elucidate whether PS mutations associated with early-onset AD affect the molecular environment of mature ?-secretase complexes, quantitative interactome comparisons were undertaken. Brains of mice engineered to express wild-type or mutant PS1, or HEK293 cells stably expressing PS paralogs with N-terminal tandem-affinity purification tags served as biological source materials. The analyses revealed novel interactions of the ?-secretase core complex with a molecular machinery that targets and fuses synaptic vesicles to cellular membranes and with the H+-transporting lysosomal ATPase macrocomplex but uncovered no differences in the interactomes of wild-type and mutant PS1. The catenin/cadherin network was almost exclusively found associated with PS1. Another intramembrane protease, signal peptide peptidase, predominantly co-purified with PS2-containing ?-secretase complexes and was observed to influence A? production. PMID:23589300

  17. A comprehensive protein–protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1

    PubMed Central

    DeMille, Desiree; Bikman, Benjamin T.; Mathis, Andrew D.; Prince, John T.; Mackay, Jordan T.; Sowa, Steven W.; Hall, Tacie D.; Grose, Julianne H.

    2014-01-01

    Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein–protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase–deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis. PMID:24850888

  18. Probabilistic Spatio-Temporal Video Object Segmentation Incorporating Shape Information

    Microsoft Academic Search

    Rakib Ahmed; Gour C. Karmakar; Laurence S. Dooley

    2006-01-01

    From a video object segmentation perspective, using a joint spatio-temporal strategy is superior to processing with priority in either the spatial or temporal domains, as it considers a video sequence as a spatio-temporal grouping of pixels. However, existing spatio-temporal object segmentation techniques consider only pixel features, which tend to limit their performance in being able to segment arbitrary shaped objects.

  19. Closest pair queries in spatio-temporal databases

    Microsoft Academic Search

    Chin-wan Chung; Sunghee Choi; Yong-jin Choi

    2005-01-01

    In recent years, spatio-temporal databases have been studied intensively. This paper proposes how to process k closest pair queries in spatio-temporal databases for the flrst time. A spatio-temporal k closest pair query continuously searches the k closest pairs between a set of spatial objects and a set of moving objects for a specifled time interval of the query. To maintain

  20. The immersive spatiotemporal hallucination model of dreaming

    Microsoft Academic Search

    Jennifer M. Windt

    2010-01-01

    The paper proposes a minimal definition of dreaming in terms of immersive spatiotemporal hallucination (ISTH) occurring in\\u000a sleep or during sleep–wake transitions and under the assumption of reportability. I take these conditions to be both necessary\\u000a and sufficient for dreaming to arise. While empirical research results may, in the future, allow for an extension of the concept\\u000a of dreaming beyond

  1. Hirarchical Bayesian Spatio-Temporal Interpolation including Covariates

    NASA Astrophysics Data System (ADS)

    Hussain, Ijaz; Mohsin, Muhammad; Spoeck, Gunter; Pilz, Juergen

    2010-05-01

    The space-time interpolation of precipitation has significant contribution to river control,reservoir operations, forestry interest and flash flood watches etc. The changes in environmental covariates and spatial covariates make space-time estimation of precipitation a challenging task. In our earlier paper [1], we used transformed hirarchical Bayesian sapce-time interpolation method for predicting the amount of precipiation. In present paper, we modified the [2] method to include covarites which varaies with respect to space-time. The proposed method is applied to estimating space-time monthly precipitation in the monsoon periods during 1974 - 2000. The 27-years monthly average data of precipitation, temperature, humidity and wind speed are obtained from 51 monitoring stations in Pakistan. The average monthly precipitation is used response variable and temperature, humidity and wind speed are used as time varying covariates. Moreovere the spatial covarites elevation, latitude and longitude of same monitoring stations are also included. The cross-validation method is used to compare the results of transformed hierarchical Bayesian spatio-temporal interpolation with and without including environmental and spatial covariates. The software of [3] is modified to incorprate enviornmental covariates and spatil covarites. It is observed that the transformed hierarchical Bayesian method including covarites provides more accuracy than the transformed hierarchical Bayesian method without including covarites. Moreover, the five potential monitoring cites are selected based on maximum entropy sampaling design approach. References [1] I.Hussain, J.Pilz,G. Spoeck and H.L.Yu. Spatio-Temporal Interpolation of Precipitation during Monsoon Periods in Pakistan. submitted in Advances in water Resources,2009. [2] N.D. Le, W. Sun, and J.V. Zidek, Bayesian multivariate spatial interpolation with data missing by design. Journal of the Royal Statistical Society. Series B (Methodological), 501-510, 1997. [3] N.D. Le, and J.V. Zidek, Statistical analysis of environmental space-time processes, Springer Verlag, (2006), PP. 272-294

  2. Spatiotemporal coupling in dispersive nonlinear planar waveguides

    NASA Astrophysics Data System (ADS)

    Ryan, Andrew T.; Agrawal, Govind P.

    1995-12-01

    The multidimensional nonlinear Schrodinger equation governs the spatial and temporal evolution of an optical field inside a nonlinear dispersive medium. Although spatial (diffractive) and temporal (dispersive) effects can be studied independently in a linear medium, they become mutually coupled in a nonlinear medium. We present the results of numerical simulations showing this spatiotemporal coupling for ultrashort pulses propagating in dispersive Kerr media. We investigate how spatiotemporal coupling affects the behavior of the optical field in each of the four regimes defined by the type of group-velocity dispersion (normal or anomalous) and the type of nonlinearity (focusing or defocusing). We show that dispersion, through spatiotemporal coupling, can either enhance or suppress self-focusing and self-defocusing. Similarly, we demonstrate that diffraction can either enhance or suppress pulse compression or broadening. We also discuss how these effects can be controlled with optical phase modulation, such as that provided by a lens (spatial phase modulation) or frequency chirping (temporal phase modulation). Copyright (c) 1995 Optical Society of America

  3. Spatiotemporal transcriptome of the human brain

    PubMed Central

    Kang, Hyo Jung; Kawasawa, Yuka Imamura; Cheng, Feng; Zhu, Ying; Xu, Xuming; Li, Mingfeng; Sousa, André M. M.; Pletikos, Mihovil; Meyer, Kyle A.; Sedmak, Goran; Guennel, Tobias; Shin, Yurae; Johnson, Matthew B.; Krsnik, Željka; Mayer, Simone; Fertuzinhos, Sofia; Umlauf, Sheila; Lisgo, Steven N.; Vortmeyer, Alexander; Weinberger, Daniel R.; Mane, Shrikant; Hyde, Thomas M.; Huttner, Anita; Reimers, Mark; Kleinman, Joel E.; Šestan, Nenad

    2012-01-01

    Summary Here we report the generation and analysis of genome-wide exon-level transcriptome data from 16 brain regions comprising the cerebellar cortex, mediodorsal nucleus of the thalamus, striatum, amygdala, hippocampus, and 11 areas of the neocortex. The dataset was generated from 1,340 tissue samples collected from one or both hemispheres of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genotyping of 2.5 million SNPs and assessed copy number variations for all donors. Approximately 86% of protein-coding genes were found to be expressed using stringent criteria, and over 90% of these were differentially regulated at the whole transcript or exon level across regions and/or time. The majority of these spatiotemporal differences occurred before birth, followed by an increase in the similarity among regional transcriptomes during postnatal lifespan. Genes were organized into functionally distinct co-expression networks, and sex differences were present in gene expression and exon usage. Finally, we demonstrate how these results can be used to profile trajectories of genes associated with neurodevelopmental processes, cell types, neurotransmitter systems, autism, and schizophrenia, as well as to discover associations between SNPs and spatiotemporal gene expression. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of human neurodevelopment. PMID:22031440

  4. Bayesian spatiotemporal modelling for the assessment of short-term exposure to particle pollution in urban areas

    PubMed Central

    Pirani, Monica; Gulliver, John; Fuller, Gary W; Blangiardo, Marta

    2014-01-01

    This paper describes a Bayesian hierarchical approach to predict short-term concentrations of particle pollution in an urban environment, with application to inhalable particulate matter (PM10) in Greater London. We developed and compared several spatiotemporal models that differently accounted for factors affecting the spatiotemporal properties of particle concentrations. We considered two main source contributions to ambient measurements: (i) the long-range transport of the secondary fraction of particles, which temporal variability was described by a latent variable derived from rural concentrations; and (ii) the local primary component of particles (traffic- and non-traffic-related) captured by the output of the dispersion model ADMS-Urban, which site-specific effect was described by a Bayesian kriging. We also assessed the effect of spatiotemporal covariates, including type of site, daily temperature to describe the seasonal changes in chemical processes affecting local PM10 concentrations that are not considered in local-scale dispersion models and day of the week to account for time-varying emission rates not available in emissions inventories. The evaluation of the predictive ability of the models, obtained via a cross-validation approach, revealed that concentration estimates in urban areas benefit from combining the city-scale particle component and the long-range transport component with covariates that account for the residual spatiotemporal variation in the pollution process. PMID:24280683

  5. Spatiotemporal Modeling of Precipitation in the Upper Shiyang River Watershed Spatiotemporal Modeling of Monthly Precipitation in the Upper Shiyang3

    E-print Network

    of Hongyashan Lake reservoir (lowest rainfall) demonstrated near-similar15 spatiotemporal patterns. The greatest precipitation, elevated temperatures, and high evaporative6 demand (Ma et al., 2005). Oases

  6. Spatio-temporal population estimates for risk management

    NASA Astrophysics Data System (ADS)

    Cockings, Samantha; Martin, David; Smith, Alan; Martin, Rebecca

    2013-04-01

    Accurate estimation of population at risk from hazards and effective emergency management of events require not just appropriate spatio-temporal modelling of hazards but also of population. While much recent effort has been focused on improving the modelling and predictions of hazards (both natural and anthropogenic), there has been little parallel advance in the measurement or modelling of population statistics. Different hazard types occur over diverse temporal cycles, are of varying duration and differ significantly in their spatial extent. Even events of the same hazard type, such as flood events, vary markedly in their spatial and temporal characteristics. Conceptually and pragmatically then, population estimates should also be available for similarly varying spatio-temporal scales. Routine population statistics derived from traditional censuses or surveys are usually static representations in both space and time, recording people at their place of usual residence on census/survey night and presenting data for administratively defined areas. Such representations effectively fix the scale of population estimates in both space and time, which is unhelpful for meaningful risk management. Over recent years, the Pop24/7 programme of research, based at the University of Southampton (UK), has developed a framework for spatio-temporal modelling of population, based on gridded population surfaces. Based on a data model which is fully flexible in terms of space and time, the framework allows population estimates to be produced for any time slice relevant to the data contained in the model. It is based around a set of origin and destination centroids, which have capacities, spatial extents and catchment areas, all of which can vary temporally, such as by time of day, day of week, season. A background layer, containing information on features such as transport networks and landuse, provides information on the likelihood of people being in certain places at specific times. Unusual patterns associated with special events can also be modelled and the framework is fully volume preserving. Outputs from the model are gridded population surfaces for the specified time slice, either for total population or by sub-groups (e.g. age). Software to implement the models (SurfaceBuilder247) has been developed and pre-processed layers for typical time slices for England and Wales in 2001 and 2006 are available for UK academic purposes. The outputs and modelling framework from the Pop24/7 programme provide significant opportunities for risk management applications. For estimates of mid- to long-term cumulative population exposure to hazards, such as in flood risk mapping, populations can be produced for numerous time slices and integrated with flood models. For applications in emergency response/ management, time-specific population models can be used as seeds for agent-based models or other response/behaviour models. Estimates for sub-groups of the population also permit exploration of vulnerability through space and time. This paper outlines the requirements for effective spatio-temporal population models for risk management. It then describes the Pop24/7 framework and illustrates its potential for risk management through presentation of examples from natural and anthropogenic hazard applications. The paper concludes by highlighting key challenges for future research in this area.

  7. targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

    PubMed Central

    Raman, Karthik; Yeturu, Kalidas; Chandra, Nagasuma

    2008-01-01

    Background Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes. PMID:19099550

  8. Gestural Interaction with Spatiotemporal Linked Open Data Gestural Interaction with Spatiotemporal

    E-print Network

    Köbben, Barend

    - grated into an exhibit. We present a set of gestures that visitors to a science fair can use to explore Information Science to the pub- lic, for example in an exhibition, in a science museum or science center for complex spatiotemporal data is a contribution towards Linked Open Science [14] to support transparency

  9. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

    PubMed Central

    Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

    2010-01-01

    Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. PMID:20706207

  10. Mapping the miRNA interactome by crosslinking ligation and sequencing of hybrids (CLASH)

    PubMed Central

    Helwak, Aleksandra; Tollervey, David

    2014-01-01

    RNA-RNA interactions play critical roles in many cellular processes but studying them is difficult and laborious. Here, we describe an experimental procedure, termed crosslinking ligation and sequencing of hybrids (CLASH), which allows high-throughput identification of sites of RNA-RNA interaction. During CLASH, a tagged bait protein is UV crosslinked in vivo to stabilise RNA interactions and purified under denaturing conditions. RNAs associated with the bait protein are partially truncated, and the ends of RNA-duplexes are ligated together. Following linker addition, cDNA library preparation and high-throughput sequencing, the ligated duplexes give rise to chimeric cDNAs, which unambiguously identify RNA-RNA interaction sites independent of bioinformatic predictions. This protocol is optimized for studying miRNA targets bound by Argonaute proteins, but should be easily adapted for other RNA-binding proteins and classes of RNA. The protocol requires around 5 days to complete, excluding the time required for high-throughput sequencing and bioinformatic analyses. PMID:24577361

  11. cytoHubba: identifying hub objects and sub-networks from complex interactome

    PubMed Central

    2014-01-01

    Background Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. Results We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network. Conclusions CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010. PMID:25521941

  12. Asynchronous Visualization of Spatiotemporal Information for Multiple Moving Targets

    ERIC Educational Resources Information Center

    Wang, Huadong

    2013-01-01

    In the modern information age, the quantity and complexity of spatiotemporal data is increasing both rapidly and continuously. Sensor systems with multiple feeds that gather multidimensional spatiotemporal data will result in information clusters and overload, as well as a high cognitive load for users of these systems. To meet future…

  13. Spatio-Temporal and Context Reasoning in Smart Homes

    E-print Network

    Marsland, Stephen

    Spatio-Temporal and Context Reasoning in Smart Homes Sook-Ling Chua, Stephen Marsland, and Hans W intelligence has a wide range of applications, includ- ing smart homes. Smart homes can support. In this paper, we discuss spatio-temporal and context-based reasoning in smart homes and some methods by which

  14. A pattern matching language for spatio-temporal databases

    Microsoft Academic Search

    Tsz S. Cheng; Shashi K. Gadia

    1994-01-01

    We propose a pattern matching language for spatio-temporal databases. The matching process in time dimension is based upon the evolutionary nature of time, but in spatial dimension it is based on placement, shape and sizes of regions. The concept of pattern matching introduced in this paper is independent of the choice of the underlying model for spatio-temporal databases. In particular,

  15. Spatiotemporal Data Mining, Analysis, and Visualization of Human Activity Data

    ERIC Educational Resources Information Center

    Li, Xun

    2012-01-01

    This dissertation addresses the research challenge of developing efficient new methods for discovering useful patterns and knowledge in large volumes of electronically collected spatiotemporal activity data. I propose to analyze three types of such spatiotemporal activity data in a methodological framework that integrates spatial analysis, data…

  16. Spatio-temporal modelling of corrosion in an industrial furnace

    E-print Network

    Little, John

    Spatio-temporal modelling of corrosion in an industrial furnace John Little, Michael Goldstein-scale industrial furnace subject to corrosion will be considered. A suitable Bayesian spatio-temporal dynamic of paper In Section 2, we introduce the motivating example - an industrial furnace used in the oil refining

  17. Quantification and classification of locomotion patterns by spatiotemporal morphable models

    E-print Network

    Poggio, Tomaso

    Quantification and classification of locomotion patterns by spatio­temporal morphable models M; Quantification and classification of locomotion patterns by spatio­temporal morphable models M. A. Giese and T on the linear weights that deter­ mine the contributions of the examples to the linear com­ bination, complex

  18. Origin of transient and intermittent dynamics in spatiotemporal chaotic systems.

    PubMed

    Rempel, Erico L; Chian, Abraham C-L

    2007-01-01

    Nonattracting chaotic sets (chaotic saddles) are shown to be responsible for transient and intermittent dynamics in an extended system exemplified by a nonlinear regularized long-wave equation, relevant to plasma and fluid studies. As the driver amplitude is increased, the system undergoes a transition from quasiperiodicity to temporal chaos, then to spatiotemporal chaos. The resulting intermittent time series of spatiotemporal chaos displays random switching between laminar and bursty phases. We identify temporally and spatiotemporally chaotic saddles which are responsible for the laminar and bursty phases, respectively. Prior to the transition to spatiotemporal chaos, a spatiotemporally chaotic saddle is responsible for chaotic transients that mimic the dynamics of the post-transition attractor. PMID:17358476

  19. Deconstructing spatiotemporal chaos using local symbolic dynamics.

    PubMed

    Pethel, Shawn D; Corron, Ned J; Bollt, Erik

    2007-11-23

    We find that the global symbolic dynamics of a diffusively coupled map lattice is well approximated by a very small local model for weak to moderate coupling strengths. A local symbolic model is a truncation of the full symbolic model to one that considers only a single element and a few neighbors. Using interval analysis, we give rigorous results for a range of coupling strengths and different local model widths. Examples are presented of extracting a local symbolic model from data and of controlling spatiotemporal chaos. PMID:18233220

  20. Subwavelength ultrasonic circulator based on spatiotemporal modulation

    NASA Astrophysics Data System (ADS)

    Fleury, Romain; Sounas, Dimitrios L.; Alù, Andrea

    2015-05-01

    Enabling efficient nonreciprocal acoustic devices is challenging, yet very desirable for a variety of applications, including acoustic imaging, underwater communications, energy concentration and harvesting, signal processing, and noise control. We discuss the theory and design of a fully linear compact acoustic circulator based on spatiotemporal modulation of the effective acoustic index, providing a compact and practical way to realize large sound circulation at any desired frequency. Our proposal enables tunable isolation levels of over 40 dB, with insertion losses as low as 0.3 dB, in a noise-free, integrable, frequency scalable device whose total size does not exceed ? /6 .

  1. Spatiotemporal temperature profiling of corneal surface during LTK

    NASA Astrophysics Data System (ADS)

    Papaioannou, Thanassis; Maguen, Ezra I.; Grundfest, Warren S.

    2002-06-01

    Accurate prediction of LTK treatments requires refined thermal corneal models which necessitate precise input parameters. The overall objective of this study was to provide detailed information on the spatiotemporal temperature profile of the corneal surface, during in-vitro thermal keratoplasty. LTK was performed in-vitro on freshly harvested porcine eyes (N equals 16) with the Sunrise Technologies corneal shaping system (Model SUN 1000). Spatiotemporal thermal imaging of the irradiated corneas were obtained with a short wave Inframetrics thermal camera (Model PM290). Images were obtained at 8-bits resolution, with ~100 microns spatial and ~17 msec temporal resolution respectively. Treatment pattern consisted of eight spots at 6 mm zone, while lasing was conducted at settings of either 100 mJ and 15 pulses (N equals 8), or 260 mJ and 7 pulses (N equals 8). Temporal and spatial variation of the corneal surface temperatures were calculated at locations of importance to LTK. At the laser spot, temperature profiles consisted of transients coinciding approximately with the laser pulses. Maximum transient temperatures observed were 98.0+/- 4.6 degree(s)C for the high and 56.3+/- 2.6 degree(s)C for the low energy respectively. These temperature transients were superimposed on an envelope of lower-slowly varying temperatures. The maximum temperatures observed for this temperature envelope, were 51.8+/- 3.4 degree(s)C for the high and 35.4+/- 3.4 degree(s)C for the low energy respectively. The evolution of either the maximum temperature transients or the lower temperature envelope, followed exponential growth of the form: T equals A * exp(B*t). Maximum temperatures at locations 0.5 mm and 1 mm away from the laser spot, reached 25.7 degree(s)C and 23.3 degree(s)C for the low energy, and 34 degree(s)C and 25.6 degree(s)C for the high energy settings respectively. Temperature decay constants were approximately 2 to 3 sec, while the spatial temperature profile at the laser spot extended more than 2 mm at 2.5 sec post irradiation. The data obtained may help to refine corneal thermal modeling during LTK, and thus improve predictability of current or future-modified-treatments.

  2. Searching for Cellular Partners of Hantaviral Nonstructural Protein NSs: Y2H Screening of Mouse cDNA Library and Analysis of Cellular Interactome

    PubMed Central

    Parviainen, Ville; Vaheri, Antti; Renkonen, Risto; Bouloy, Michele; Plyusnin, Alexander

    2012-01-01

    Hantaviruses (Bunyaviridae) are negative-strand RNA viruses with a tripartite genome. The small (S) segment encodes the nucleocapsid protein and, in some hantaviruses, also the nonstructural protein (NSs). The aim of this study was to find potential cellular partners for the hantaviral NSs protein. Toward this aim, yeast two-hybrid (Y2H) screening of mouse cDNA library was performed followed by a search for potential NSs protein counterparts via analyzing a cellular interactome. The resulting interaction network was shown to form logical, clustered structures. Furthermore, several potential binding partners for the NSs protein, for instance ACBD3, were identified and, to prove the principle, interaction between NSs and ACBD3 proteins was demonstrated biochemically. PMID:22506017

  3. The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome

    PubMed Central

    Niepel, Mario; Molloy, Kelly R.; Williams, Rosemary; Farr, Julia C.; Meinema, Anne C.; Vecchietti, Nicholas; Cristea, Ileana M.; Chait, Brian T.; Rout, Michael P.; Strambio-De-Castillia, Caterina

    2013-01-01

    The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance. PMID:24152732

  4. CUTOFF: A spatio-temporal imputation method

    NASA Astrophysics Data System (ADS)

    Feng, Lingbing; Nowak, Gen; O'Neill, T. J.; Welsh, A. H.

    2014-11-01

    Missing values occur frequently in many different statistical applications and need to be dealt with carefully, especially when the data are collected spatio-temporally. We propose a method called CUTOFF imputation that utilizes the spatio-temporal nature of the data to accurately and efficiently impute missing values. The main feature of this method is that the estimate of a missing value is produced by incorporating similar observed temporal information from the value's nearest spatial neighbors. Extensions to this method are also developed to expand the method's ability to accommodate other data generating processes. We develop a cross-validation procedure that optimally chooses parameters for CUTOFF, which can be used by other imputation methods as well. We analyze some rainfall data from 78 gauging stations in the Murray-Darling Basin in Australia using the CUTOFF imputation method and compare its performance to four well-studied competing imputation methods, namely, k-nearest neighbors, singular value decomposition, multiple imputation and random forest. Empirical results show that our method captures the temporal patterns well and is effective at imputing large gaps in the data. Compared to the competing methods, CUTOFF is more accurate and much faster. We analyze further examples to demonstrate CUTOFF's applications to two different data sets and provide extra evidence of its validity and usefulness. We implement a simulation study based on the Murray-Darling Basin data to evaluate the method; the results show that our method performs well in both accuracy and computational efficiency.

  5. A simple approach for predicting protein-protein interactions.

    PubMed

    Rashid, Mamoon; Ramasamy, Sumathy; Raghava, Gajendra P S

    2010-11-01

    The availability of an increased number of fully sequenced genomes demands functional interpretation of the genomic information. Despite high throughput experimental techniques and in silico methods of predicting protein-protein interaction (PPI); the interactome of most organisms is far from completion. Thus, predicting the interactome of an organism is one of the major challenges in the post-genomic era. This manuscript describes Support Vector Machine (SVM) based models that have been developed for discriminating interacting and non-interacting pairs of proteins from their amino acid sequence. We have developed SVM models using various types of sequence compositions e.g. amino acid, dipeptide, biochemical property, split amino acid and pseudo amino acid composition. We also developed SVM models using evolutionary information in the form of Position Specific Scoring Matrix (PSSM) composition. We achieved maximum Matthews's correlation coefficient (MCC) of 1.00, 0.52 and 0.74 for Escherichia coli, Saccharomyces cerevisiae, and Helicobacter pylori, using dipeptide based SVM model at default threshold. It was observed that the performance of a prediction model depends on the dataset used for training and testing. In case of E. coli MCC decreased from 1.0 to 0.67 when evaluated on a new dataset. In order to understand PPI in different cellular environment, we developed species-specific and general models. It was observed that species-specific models are more accurate than general models. We conclude that the primary amino acid sequence based descriptors could be used to differentiate interacting from non-interacting protein pairs. Some amino acids tend to be favored in interacting pairs than non-interacting ones. Finally, a web server has been developed for predicting protein-protein interactions. PMID:20887258

  6. Predicting Wave Glider Speed from Environmental Measurements

    E-print Network

    Sukhatme, Gaurav S.

    Predicting Wave Glider Speed from Environmental Measurements Ryan N. Smith, Jnaneshwar Das, Graham spatiotemporal resolutions. This paper focuses on the newly developed Wave Glider platform from Liquid Robotics ocean waves, the Liquid Robotics Wave Glider (see Fig. 1) provides a persistent ocean presence

  7. Controlling spatiotemporal chaos in one- and two-dimensional coupled logistic map lattices

    SciTech Connect

    Astakhov, V.V.; Anishchenko, V.S.; Strelkova, G.I.; Shabunin, A.V. [Laboratory of Nonlinear Dynamics, Saratov State University, Saratov (Russia)

    1996-06-01

    A method of control of spatiotemporal chaos in lattices of coupled maps is proposed in this work. Forms of spatiotemporal perturbations of a system parameter are analytically determined for one- and two-dimensional logistic map lattices with different kinds of coupling to stabilize chosen spatiotemporal states previously unstable. The results are illustrated by numerical simulation. Controlled transition from the regime of spatiotemporal chaos to the previously chosen regular spatiotemporal patterns is demonstrated. {copyright} {ital 1996 American Institute of Physics.}

  8. A Spatio-Temporal Downscaler for Output From Numerical Models.

    PubMed

    Berrocal, Veronica J; Gelfand, Alan E; Holland, David M

    2010-06-01

    Often, in environmental data collection, data arise from two sources: numerical models and monitoring networks. The first source provides predictions at the level of grid cells, while the second source gives measurements at points. The first is characterized by full spatial coverage of the region of interest, high temporal resolution, no missing data but consequential calibration concerns. The second tends to be sparsely collected in space with coarser temporal resolution, often with missing data but, where recorded, provides, essentially, the true value. Accommodating the spatial misalignment between the two types of data is of fundamental importance for both improved predictions of exposure as well as for evaluation and calibration of the numerical model. In this article we propose a simple, fully model-based strategy to downscale the output from numerical models to point level. The static spatial model, specified within a Bayesian framework, regresses the observed data on the numerical model output using spatially-varying coefficients which are specified through a correlated spatial Gaussian process.As an example, we apply our method to ozone concentration data for the eastern U.S. and compare it to Bayesian melding (Fuentes and Raftery 2005) and ordinary kriging (Cressie 1993; Chilès and Delfiner 1999). Our results show that our method outperforms Bayesian melding in terms of computing speed and it is superior to both Bayesian melding and ordinary kriging in terms of predictive performance; predictions obtained with our method are better calibrated and predictive intervals have empirical coverage closer to the nominal values. Moreover, our model can be easily extended to accommodate for the temporal dimension. In this regard, we consider several spatio-temporal versions of the static model. We compare them using out-of-sample predictions of ozone concentration for the eastern U.S. for the period May 1-October 15, 2001. For the best choice, we present a summary of the analysis. Supplemental material, including color versions of Figures 4, 5, 6, 7, and 8, and MCMC diagnostic plots, are available online. PMID:21113385

  9. Spatio-temporal interpolation of daily temperatures for global land areas at 1 km resolution

    NASA Astrophysics Data System (ADS)

    Kilibarda, Milan; Hengl, Tomislav; Heuvelink, Gerard B. M.; Gräler, Benedikt; Pebesma, Edzer; Per?ec Tadi?, Melita; Bajat, Branislav

    2014-03-01

    Combined Global Surface Summary of Day and European Climate Assessment and Dataset daily meteorological data sets (around 9000 stations) were used to build spatio-temporal geostatistical models and predict daily air temperature at ground resolution of 1 km for the global land mass. Predictions in space and time were made for the mean, maximum, and minimum temperatures using spatio-temporal regression-kriging with a time series of Moderate Resolution Imaging Spectroradiometer (MODIS) 8 day images, topographic layers (digital elevation model and topographic wetness index), and a geometric temperature trend as covariates. The accuracy of predicting daily temperatures was assessed using leave-one-out cross validation. To account for geographical point clustering of station data and get a more representative cross-validation accuracy, predicted values were aggregated to blocks of land of size 500×500 km. Results show that the average accuracy for predicting mean, maximum, and minimum daily temperatures is root-mean-square error (RMSE) =±2°C for areas densely covered with stations and between ±2°C and ±4°C for areas with lower station density. The lowest prediction accuracy was observed at high altitudes (>1000 m) and in Antarctica with an RMSE around 6°C. The model and predictions were built for the year 2011 only, but the same methodology could be extended for the whole range of the MODIS land surface temperature images (2001 to today), i.e., to produce global archives of daily temperatures (a next-generation http://WorldClim.org repository) and to feed various global environmental models.

  10. Systemic risk and spatiotemporal dynamics of the US housing market.

    PubMed

    Meng, Hao; Xie, Wen-Jie; Jiang, Zhi-Qiang; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H Eugene

    2014-01-01

    Housing markets play a crucial role in economies and the collapse of a real-estate bubble usually destabilizes the financial system and causes economic recessions. We investigate the systemic risk and spatiotemporal dynamics of the US housing market (1975-2011) at the state level based on the Random Matrix Theory (RMT). We identify richer economic information in the largest eigenvalues deviating from RMT predictions for the housing market than for stock markets and find that the component signs of the eigenvectors contain either geographical information or the extent of differences in house price growth rates or both. By looking at the evolution of different quantities such as eigenvalues and eigenvectors, we find that the US housing market experienced six different regimes, which is consistent with the evolution of state clusters identified by the box clustering algorithm and the consensus clustering algorithm on the partial correlation matrices. We find that dramatic increases in the systemic risk are usually accompanied by regime shifts, which provide a means of early detection of housing bubbles. PMID:24413626

  11. Spatiotemporal hydrological patterns in the landscape: Water quality implications

    NASA Astrophysics Data System (ADS)

    Walter, M.; Lyon, S.; Steenhuis, T. S.; Seifert, S. L.

    2006-05-01

    Linking spatiotemporally varying hydrologic processes and streamwater quality remains an important research challenge and a critical knowledge gap for improving management strategies. Indeed, the very term "nonpoint source pollution" implies that we cannot generally identify specific flowpaths connecting streams with their surrounding watersheds. Areas where the soil is saturated to the surface play important roles in terrestrial biogeochemistry and watershed hydrology, especially in humid, well-vegetated areas, like the northeastern US. In this talk we present an overview of our work to identify and predict the spatial and temporal distributions of surface saturation and to improve our understanding of how these areas impact water quality. We are finding that areas especially prone to saturation, i.e., hydrologically sensitive areas, account for a disproportionately large fraction of storm runoff and nutrient loss. We suggest targeting these areas when developing water quality protection strategies and will present some recent examples. As our understanding of the relevant hydrological and biogeochemical processes controlling water quality improves, we are making simultaneous improvements in the tools available for environmental-protection professionals, taking advantage of new technologies. At the same time, technological advances in areas like molecular biogeochemistry and nanotechnology are providing exciting new opportunities to investigate landscape hydrological and transport dynamics.

  12. Systemic risk and spatiotemporal dynamics of the US housing market

    NASA Astrophysics Data System (ADS)

    Meng, Hao; Xie, Wen-Jie; Jiang, Zhi-Qiang; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H. Eugene

    2014-01-01

    Housing markets play a crucial role in economies and the collapse of a real-estate bubble usually destabilizes the financial system and causes economic recessions. We investigate the systemic risk and spatiotemporal dynamics of the US housing market (1975-2011) at the state level based on the Random Matrix Theory (RMT). We identify richer economic information in the largest eigenvalues deviating from RMT predictions for the housing market than for stock markets and find that the component signs of the eigenvectors contain either geographical information or the extent of differences in house price growth rates or both. By looking at the evolution of different quantities such as eigenvalues and eigenvectors, we find that the US housing market experienced six different regimes, which is consistent with the evolution of state clusters identified by the box clustering algorithm and the consensus clustering algorithm on the partial correlation matrices. We find that dramatic increases in the systemic risk are usually accompanied by regime shifts, which provide a means of early detection of housing bubbles.

  13. Ambient Air Pollution and Preeclampsia: A Spatiotemporal Analysis

    PubMed Central

    Figueras, Francesc; Basagaña, Xavier; Beelen, Rob; Martinez, David; Cirach, Marta; Schembari, Anna; Hoek, Gerard; Brunekreef, Bert; Nieuwenhuijsen, Mark J

    2013-01-01

    Background: Available evidence concerning the association between air pollution and preeclampsia is limited, and specific associations with early- and late-onset preeclampsia have not been assessed. Objectives: We investigated the association, if any, between preeclampsia (all, early-, and late-onset) and exposure to nitrogen dioxide, nitrogen oxides, particulate matter with aerodynamic diameter ? 2.5 ?m (PM2.5; fine particles), ? 10 ?m, and 2.5–10 ?m, and PM2.5 light absorption (a proxy for elemental carbon) during the entire pregnancy and during the first, second, and third trimesters. Methods: This study was based on 8,398 pregnancies (including 103 cases of preeclampsia) among women residing in Barcelona, Spain (2000–2005). We applied a spatiotemporal exposure assessment framework using land use regression models to predict ambient pollutant levels during each week of pregnancy at the geocoded residence address of each woman at the time of birth. Logistic and conditional logistic regression models were used to estimate unadjusted and adjusted associations. Results: We found positive associations for most of our evaluated outcome–exposure pairs, with the strongest associations observed for preeclampsia and late-onset preeclampsia in relation to the third-trimester exposure to fine particulate pollutants, and for early-onset preeclampsia in relation to the first-trimester exposure to fine particulate pollutants. Among our investigated associations, those of first- and third-trimester exposures to PM2.5 and third-trimester exposure to PM2.5 absorbance and all preeclampsia, and third-trimester PM2.5 exposure and late-onset preeclampsia attained statistical significance. Conclusion: We observed increased risk of preeclampsia associated with exposure to fine particulate air pollution. Our findings, in combination with previous evidence suggesting distinct pathogenic mechanisms for early- and late-onset preeclampsia, support additional research on this topic. Citation: Dadvand P, Figueras F, Basagaña X, Beelen R, Martinez D, Cirach M, Schembari A, Hoek G, Brunekreef B, Nieuwenhuijsen MJ. 2013. Ambient air pollution and preeclampsia: a spatiotemporal analysis. Environ Health Perspect 121:1365–1371;?http://dx.doi.org/10.1289/ehp.1206430 PMID:24021707

  14. Initial spatio-temporal domain expansion of the Modelfest database

    NASA Astrophysics Data System (ADS)

    Carney, Thom; Mozaffari, Sahar; Sun, Sean; Johnson, Ryan; Shirvastava, Sharona; Shen, Priscilla; Ly, Emma

    2013-03-01

    The first Modelfest group publication appeared in the SPIE Human Vision and Electronic Imaging conference proceedings in 1999. "One of the group's goals is to develop a public database of test images with threshold data from multiple laboratories for designing and testing HVS (Human Vision Models)." After extended discussions the group selected a set of 45 static images thought to best meet that goal and collected psychophysical detection data which is available on the WEB and presented in the 2000 SPIE conference proceedings. Several groups have used these datasets to test spatial modeling ideas. Further discussions led to the preliminary stimulus specification for extending the database into the temporal domain which was published in the 2002 conference proceeding. After a hiatus of 12 years, some of us have collected spatio-temporal thresholds on an expanded stimulus set of 41 video clips; the original specification included 35 clips. The principal change involved adding one additional spatial pattern beyond the three originally specified. The stimuli consisted of 4 spatial patterns, Gaussian Blob, 4 c/d Gabor patch, 11.3 c/d Gabor patch and a 2D white noise patch. Across conditions the patterns were temporally modulated over a range of approximately 0-25 Hz as well as temporal edge and pulse modulation conditions. The display and data collection specifications were as specified by the Modelfest groups in the 2002 conference proceedings. To date seven subjects have participated in this phase of the data collection effort, one of which also participated in the first phase of Modelfest. Three of the spatio-temporal stimuli were identical to conditions in the original static dataset. Small differences in the thresholds were evident and may point to a stimulus limitation. The temporal CSF peaked between 4 and 8 Hz for the 0 c/d (Gaussian blob) and 4 c/d patterns. The 4 c/d and 11.3 c/d Gabor temporal CSF was low pass while the 0 c/d pattern was band pass. This preliminary expansion of the Modelfest dataset needs the participation of additional laboratories to evaluate the impact of different methods on threshold estimates and increase the subject base. We eagerly await the addition of new data from interested researchers. It remains to be seen how accurately general HVS models will predict thresholds across both Modelfest datasets.

  15. Perturbation of the heparin/heparin-sulfate interactome of human breast cancer cells modulates pro-tumourigenic effects associated with PI3K/Akt and MAPK/ERK signalling.

    PubMed

    Chen, Yunliang; Scully, Michael; Dawson, Gloria; Goodwin, Christopher; Xia, Min; Lu, Xinjie; Kakkar, Ajay

    2013-06-01

    Heparansulfate-proteoglycans (HSPGs) interact via their polyanionic heparansulfate (HS) side chains with a variety of proteins on the cell surface or within the extracellular matrix membrane. The large number of heparin/HS binding proteins form a highly interconnected functional network, which has been termed as the heparin/HS interactome and is functionally linked to physiological and pathological processes. The aim of this study was to investigate the global effect of these protein-HSPG interactions on the tumourigenicity of two breast cancer cell lines (MCF-7 and MDA-MB-231). Cancer cells were cultured in serum-free medium and treated with a concentration of heparin which was capable of modulating HS/ligand interaction. Microarray analysis of MCF-7 cells cultured under these conditions showed that expression of 105 of 1,357 genes potentially related to the pathogenesis of breast neoplasm was significantly altered by heparin treatment. The changes in gene expression correlated with a less tumourigenic phenotype, including reduction of cell adhesive, invasive and migratory properties. These effects were associated with an inhibition of the PI3K/Akt and Raf/MEK/ERK signalling pathways. The modulatory effect of heparin on HS-associated activity was confirmed with one example of heparin/HS interactomes, transforming growth factor ? (TGF?). The innate TGF? activity of MCF-7 cells was reduced by heparin treatment, with specific interruption of the TGF?-Smad signalling pathway. The pro-tumourigenic contribution of the heparin/HS interactomes was verified in cells in which HSPG synthesis was blocked using ?-xyloside. In conclusion, the interaction between cell surface HPSGs and innate heparin/HS interactomes makes a significant contribution to the tumourigenicity. PMID:23571852

  16. Non-invertible transformations and spatiotemporal randomness

    E-print Network

    J. A. Gonzalez; A. J. Moreno; L. E. Guerrero

    2006-02-12

    We generalize the exact solution to the Bernoulli shift map. Under certain conditions, the generalized functions can produce unpredictable dynamics. We use the properties of the generalized functions to show that certain dynamical systems can generate random dynamics. For instance, the chaotic Chua's circuit coupled to a circuit with a non-invertible I-V characteristic can generate unpredictable dynamics. In general, a nonperiodic time-series with truncated exponential behavior can be converted into unpredictable dynamics using non-invertible transformations. Using a new theoretical framework for chaos and randomness, we investigate some classes of coupled map lattices. We show that, in some cases, these systems can produce completely unpredictable dynamics. In a similar fashion, we explain why some wellknown spatiotemporal systems have been found to produce very complex dynamics in numerical simulations. We discuss real physical systems that can generate random dynamics.

  17. Spatiotemporal smoothing of single trial MEG data.

    PubMed

    Ventrucci, Massimo; Miller, Claire née Ferguson; Gross, Joachim; Schoffelen, Jan-Mathijs; Bowman, Adrian W

    2011-09-15

    In MEG experiments an electromagnetic field is measured at a very high temporal resolution in many sensors located in a helmet-shaped dewar, producing a very large dataset. Filtering techniques are commonly used to reduce the noise in the data. In this paper, spatiotemporal smoothing across space and time simultaneously is used, not simply as a pre-processing step, but as the central focus of a modelling technique intended to estimate the structure of the spatial and temporal response to stimulus. A particular advantage of this approach is the ability to study responses from individual replicates, rather than averages. The benefits of this form of smoothing are discussed and simulation used to evaluate its performance. The methods are illustrated on an application with real data. PMID:21704077

  18. Spatiotemporal complexity of the aortic sinus vortex

    NASA Astrophysics Data System (ADS)

    Moore, Brandon; Dasi, Lakshmi Prasad

    2014-07-01

    The aortic sinus vortex is a classical flow structure of significant importance to aortic valve dynamics and the initiation and progression of calcific aortic valve disease. We characterize the spatiotemporal characteristics of aortic sinus vortex dynamics in relation to the viscosity of blood analog solution as well as heart rate. High-resolution time-resolved (2 kHz) particle image velocimetry was conducted to capture 2D particle streak videos and 2D instantaneous velocity and streamlines along the sinus midplane using a physiological but rigid aorta model fitted with a porcine bioprosthetic heart valve. Blood analog fluids used include a water-glycerin mixture and saline to elucidate the sensitivity of vortex dynamics to viscosity. Experiments were conducted to record 10 heart beats for each combination of blood analog and heart rate condition. Results show that the topological characteristics of the velocity field vary in timescales as revealed using time bin-averaged vectors and corresponding instantaneous streamlines. There exist small timescale vortices and a large timescale main vortex. A key flow structure observed is the counter vortex at the upstream end of the sinus adjacent to the base (lower half) of the leaflet. The spatiotemporal complexity of vortex dynamics is shown to be profoundly influenced by strong leaflet flutter during systole with a peak frequency of 200 Hz and peak amplitude of 4 mm observed in the saline case. While fluid viscosity influences the length and timescales as well as the introduction of leaflet flutter, heart rate influences the formation of counter vortex at the upstream end of the sinus. Higher heart rates are shown to reduce the strength of the counter vortex that can greatly influence the directionality and strength of shear stresses along the base of the leaflet. This study demonstrates the impact of heart rate and blood analog viscosity on aortic sinus hemodynamics.

  19. Study on spatio-temporal properties of rainfall 

    E-print Network

    Choi, Janghwoan

    2007-04-25

    This dissertation describes spatio-temporal properties of rainfall. Rainfall in space was modeled by a precipitation areal reduction factor (ARF) using a NEXRAD image. The storms are represented as ellipses, which are determined by maximizing...

  20. VIDEO DENOISING USING A SPATIOTEMPORAL STATISTICAL MODEL OF WAVELET COEFFICIENTS

    E-print Network

    Wang, Zhou

    VIDEO DENOISING USING A SPATIOTEMPORAL STATISTICAL MODEL OF WAVELET COEFFICIENTS Gijesh Varghese1 signal processing, video denoising, statistical image modeling, image restoration, motion estima- tion 1 been developed for the denoising of still images, and has achieved superior performance [8

  1. Transition to turbulence via spatiotemporal intermittency in stimulated Raman backscattering

    SciTech Connect

    Skoric, M.M.; Jovanovic, M.S.; Rajkovic, M.R. [Vinca Institute of Nuclear Sciences, P.O. Box 522, 11001 Belgrade (Yugoslavia)]|[Department of Physics, University of Nis, P.O. Box 91, 18001 Nis (Yugoslavia)

    1996-04-01

    The spatiotemporal evolution of stimulated Raman backscattering in a bounded, uniform, weakly dissipative plasma is studied. The nonlinear model of a three-wave interaction involves a quadratic coupling of slowly varying complex amplitudes of the laser pump, the backscattered and the electron plasma wave. The corresponding set of coupled partial differential equations with nonlinear phase detuning that is taken into account is solved numerically in space time with fixed nonzero source boundary conditions. The study of the above open, convective, weakly confined system reveals a quasiperiodic transition to spatiotemporal chaos via spatiotemporal intermittency. In the analysis of transitions a dual scheme borrowed from fields of nonlinear dynamics and statistical physics is applied. An introduction of a nonlinear three-wave interaction to a growing family of paradigmatic equations which exhibit a route to turbulence via spatiotemporal intermittency is outlined in this work. {copyright} {ital 1996 The American Physical Society.}

  2. Modelling pandemic influenza progression using Spatiotemporal Epidemiological Modeller (STEM)

    E-print Network

    Zhang, Hui, S.M. Massachusetts Institute of Technology

    2009-01-01

    The purpose of this project is to incorporate a Poisson disease model into the Spatiotemporal Epidemiological Modeler (STEM) and visualize the disease spread on Google Earth. It is done through developing a Poisson disease ...

  3. A LANGUAGE FOR MODULAR SPATIO-TEMPORAL SIMULATION (R824766)

    EPA Science Inventory

    Creating an effective environment for collaborative spatio-temporal model development will require computational systems that provide support for the user in three key areas: (1) Support for modular, hierarchical model construction and archiving/linking of simulation modules; (2)...

  4. Role Based Access Control with Spatiotemporal Context for Mobile Applications

    Microsoft Academic Search

    Subhendu Aich; Samrat Mondal; Shamik Sural; Arun Kumar Majumdar

    2009-01-01

    Role based access control (RBAC) is an established paradigm in resource protection. However, with the proliferation of mobile\\u000a computing, it is being frequently observed that the RBAC access decision is directly influenced by the spatiotemporal context\\u000a of both the subjects and the objects in the system. Currently, there are only a few models (STRBAC, GSTRBAC) in place which\\u000a specify spatiotemporal

  5. Spatiotemporal information systems in soil and environmental sciences

    Microsoft Academic Search

    George Christakos

    1998-01-01

    This work is concerned with spatiotemporal information systems and their application in soil and environmental sciences. Issues investigated in this work include developments in the space\\/time modelling of natural variations, composite spatiotemporal mapping, and the incorporation of various sources of information into space\\/time analysis. Theoretical models, simulation examples, as well as real-world case studies are discussed. The models can process

  6. Spatiotemporal variation in reproductive parameters of yellow-bellied marmots

    Microsoft Academic Search

    Arpat Ozgul; Madan K. Oli; Lucretia E. Olson; Daniel T. Blumstein; Kenneth B. Armitage

    2007-01-01

    Spatiotemporal variation in reproductive rates is a common phenomenon in many wildlife populations, but the population dynamic\\u000a consequences of spatial and temporal variability in different components of reproduction remain poorly understood. We used\\u000a 43 years (1962–2004) of data from 17 locations and a capture–mark–recapture (CMR) modeling framework to investigate the spatiotemporal\\u000a variation in reproductive parameters of yellow-bellied marmots (Marmota flaviventris), and

  7. Vector zonal operations for spatio-temporal analysis

    E-print Network

    Xu, Tingting

    2008-11-19

    Vector Zonal Operations for Spatiotemporal Analysis Tingting Xu Department of Geography University of Kansas Conventional Zonal Operations Zonal operations take a zone and value raster layer as inputs and calculate a value for each cell... temporal resolution • NEXRAD Tool Spatiotemporal Vector Zone Calculate daily sub-watershed precipitation for non-point source pollution models + 24 hours (daily) time Area Weight Precipitation ? ? = == 9 1 9 1 * i i i ii a ap p Antecedent...

  8. A New Shape Function Based Spatiotemporal Interpolation Method

    Microsoft Academic Search

    Lixin Li; Youming Li; Reinhard Piltner

    2004-01-01

    \\u000a In this paper we propose a new spatiotemporal interpolation method for 3-D space and 1-D time geographic data. Similarly to\\u000a the existing ST (space-time) product and the tetrahedral spatiotemporal interpolation methods, this new method is also based\\u000a on shape functions. However, instead of only manipulating the time dimension as in the ST product and the tetrahedral methods,\\u000a our new method

  9. Spatiotemporal patterns of induced resistance and susceptibility linking diverse plant parasites.

    PubMed

    Mouttet, Raphaëlle; Kaplan, Ian; Bearez, Philippe; Amiens-Desneux, Edwige; Desneux, Nicolas

    2013-12-01

    Induced defenses mediate interactions between parasites sharing the same host plant, but the outcomes of these interactions are challenging to predict because of spatiotemporal variation in plant responses and differences in defense pathways elicited by herbivores or pathogens. Dissecting these mediating factors necessitates an approach that encompasses a diversity of parasitic feeding styles and tracks interactions over space and time. We tested indirect plant-mediated relationships across three tomato (Solanum lycopersicum) consumers: (1) the fungal pathogen-powdery mildew, Oidium neolycopersici; (2) a sap-feeding insect-silverleaf whitefly, Bemisia tabaci; and (3) a chewing insect-the leaf miner, Tuta absoluta. Further, we evaluated insect/pathogen responses on local vs. systemic leaves and over short (1 day) vs. long (4 days) time scales. Overall, we documented: (1) a bi-directional negative effect between O. neolycopersici and B. tabaci; (2) an asymmetrical negative effect of B. tabaci on T. absoluta; and (3) an asymmetrical positive effect of T. absoluta on O. neolycopersici. Spatiotemporal patterns varied depending on the species pair (e.g., whitefly effects on leaf miner performance were highly localized to the induced leaf, whereas effects on pathogen growth were both local and systemic). These results highlight the context-dependent effects of induced defenses on a diverse community of tomato parasites. Notably, the outcomes correspond to those predicted by phytohormonal theory based on feeding guild differences with key implications for the recent European invasion by T. absoluta. PMID:23851986

  10. Spatio-temporal change modeling with array data

    NASA Astrophysics Data System (ADS)

    Lu, Meng; Pebesma, Edzer

    2015-04-01

    Spatio-temporal change modeling of our ecosystems is critical for environmental conservation. Open access to remote sensing satellite image archives provides new opportunities for change modeling, such as near real-time change monitoring with long term image time series. Newly developed time series analysis methods allow the detection of quantitative changes in trend and seasonality for each pixel of the image. A drawback of pure time series analysis is that spatial dependence is neglected. There are several spatio-temporal statistical approaches to incorporate spatial context. One method is to build hierarchical models with spatial effects for time series parameters. Other methods include representing regression parameters as spatially correlated random fields, or integrating spatial autoregressive models to time series analysis. Apart from spatio-temporal statistical modeling, the results can be further improved by qualification of detected change points with their spatio-temporal neighbors. Spatio-temporal modeling approaches are typically complex and large in scale, and call for new data management and analysis tools. Remote sensing satellite images, which are continuous and regular in space and time, can naturally be represented as three- or four-dimensional arrays for spatio-temporal data management and analysis. The developed spatio-temporal statistical algorithms can be flexibly applied within array partitions that span the relevant array-based dimensions. This study investigates the potential of array-based Data Data Management and Analytic Software (DMAS) for fast data access, data integration and large-scale complex spatio-temporal analysis. A study case is developed in near-real time deforestation monitoring in Amazonian rainforest with long-term 250 m, 8-day resolution MODIS image time series. A novel spatio-temporal change modeling process is being developed and implemented in DMAS to realize rapid and automated analysis of satellite image time series for forest disturbance detection. The study expects results that improve over a pure time series analysis approach, and that is practically applicable to massive complex spatio-temporal data.

  11. Deformation localization in orogens: Spatiotemporal expression and thermodynamic constraint

    NASA Astrophysics Data System (ADS)

    Patton, R. L.; Watkinson, A. John

    2013-05-01

    Orogens are spatiotemporal expressions of instabilities in materials under load, constrained by thermodynamics, and preserved in the cold outer shell of the planet. Their pressure-temperature-time histories are consistent with the predictions of differential grade-2 (DG-2) materials in pure shear. We place the statistically invariant shear localization mechanism of these materials in a coherent thermodynamic context using an analysis of strained elastic materials. This prototype system exhibits non-classical thermodynamic symmetry-breaking, where the potentials are all functions of a single variable and the distinction between heat and work fades from view. Consequently, internal energy must be described by a monotonically decreasing function of the entropy in order for heat capacity and absolute temperature to be positive. The entropy itself exhibits an inverse dependence on length. These constraints are satisfied by the overall shape and slope of the distributed deformation threshold ?D for DG-2 materials, and its noted 1/length correlation with naturally observed folds as a function of thermomechanical competence ?/?. We predict that temperature in this non-linear elastic material will vary in proportion to the slope of ?D, being high at low competence, and low at high competence. Similar constraints apply to a self-gravitating body, where the energy function varies inversely with radius. Assigning zero pressure at the surface of the body, we also predict that pressure, the tensor trace of its stress-energy density, will vary inversely with radius. Thus, the body force of gravity will be expressed in this elastic self-gravitating system through the interplay of elastic and thermal lengths. Deformation localization in DG-2 materials arises due to the dynamic rescaling of lengths in response to a spike in the intrinsic energy ?I at ?/? = ½. While the intrinsic ?I and localization ?L thresholds are monotonically decreasing for ?/? > ½, they exhibit positive slopes at lower competence, signaling a return to classical thermodynamics and Joule heating in this transitional domain. Numerous structural and tectonic observations can be correlated using this remarkably simple model, beginning with the thickness and mechanical character of the brittle crust and oceanic lithosphere. In effect, this model projects the kinematic theory of plate tectonics into four-dimensional spacetime.

  12. Spatiotemporal correlations in Earth's temperature field from fractional stochastic-diffusive energy balance models

    NASA Astrophysics Data System (ADS)

    Rypdal, Kristoffer; Rypdal, Martin; Fredriksen, Hege-Beate

    2015-04-01

    In the Earth temperature field, spatiotemporal long-range dependence is usually explained as a result of nonlinear cross-scale coupling and cascading. In this contribution we challenge that paradigm, demonstrating that the observed correlation structure can arise from simple, linear, conceptual models. A two-dimensional stochastic-diffusive energy balance model (EBM) formulated on a sphere by G. R. North et al., J. Climate, 24:5850-5862, 2011, is explored and generalized. We compute instantaneous and frequency-dependent spatial autocorrelation functions, and local temporal power spectral densities for local sites and for spatially averaged signal up to the global scale. On time scales up to the relaxation time scale given by the effective heat capacities of the ocean mixed layer and land surface, respectively, we obtain scaling features reminiscent of what can be derived from the observed temperature field. On longer time scales, however, the EBM predicts a transition to a white-noise scaling, which is not reflected in the observed records. We propose and explore a fractional generalization (FEBM), which can be considered as a spatiotemporal version of the zero-dimensional, long-memory EBM of M. Rypdal and K. Rypdal, J. Climate, 27:5240-5258, 2014. The fractional equation introduces a power-law (rather than exponential) impulse response representing the delayed action due to the slow heat exchange between the mixed layer and the deep ocean. It is demonstrated that this generalized model describes qualitatively the main spatiotemporal correlation characteristics of the temperature field derived from instrumental data and from a 500 yr control run of the Nor-ESM model. For instance, the FEBM implies temporal power-law spectra where the spectral exponent for globally averaged temperature is twice that of local temperatures, and spatial autocorrelation lengths increases with time scale, in good agreement with the Nor-ESM simulations. It also reproduces the long-time response to a step-function forcing in the Nor-ESM model.

  13. Automatic spatiotemporal matching of detected pleural thickenings

    NASA Astrophysics Data System (ADS)

    Chaisaowong, Kraisorn; Keller, Simon Kai; Kraus, Thomas

    2014-01-01

    Pleural thickenings can be found in asbestos exposed patient's lung. Non-invasive diagnosis including CT imaging can detect aggressive malignant pleural mesothelioma in its early stage. In order to create a quantitative documentation of automatic detected pleural thickenings over time, the differences in volume and thickness of the detected thickenings have to be calculated. Physicians usually estimate the change of each thickening via visual comparison which provides neither quantitative nor qualitative measures. In this work, automatic spatiotemporal matching techniques of the detected pleural thickenings at two points of time based on the semi-automatic registration have been developed, implemented, and tested so that the same thickening can be compared fully automatically. As result, the application of the mapping technique using the principal components analysis turns out to be advantageous than the feature-based mapping using centroid and mean Hounsfield Units of each thickening, since the resulting sensitivity was improved to 98.46% from 42.19%, while the accuracy of feature-based mapping is only slightly higher (84.38% to 76.19%).

  14. Nonlinear Schrödinger equation with spatiotemporal perturbations.

    PubMed

    Mertens, Franz G; Quintero, Niurka R; Bishop, A R

    2010-01-01

    We investigate the dynamics of solitons of the cubic nonlinear Schrödinger equation (NLSE) with the following perturbations: nonparametric spatiotemporal driving of the form f(x,t)=a exp[iK(t)x], damping, and a linear term which serves to stabilize the driven soliton. Using the time evolution of norm, momentum and energy, or, alternatively, a Lagrangian approach, we develop a collective-coordinate-theory which yields a set of ordinary differential equations (ODEs) for our four collective coordinates. These ODEs are solved analytically and numerically for the case of a constant, spatially periodic force f(x). The soliton position exhibits oscillations around a mean trajectory with constant velocity. This means that the soliton performs, on the average, a unidirectional motion although the spatial average of the force vanishes. The amplitude of the oscillations is much smaller than the period of f(x). In order to find out for which regions the above solutions are stable, we calculate the time evolution of the soliton momentum P(t) and the soliton velocity V(t): This is a parameter representation of a curve P(V) which is visited by the soliton while time evolves. Our conjecture is that the soliton becomes unstable, if this curve has a branch with negative slope. This conjecture is fully confirmed by our simulations for the perturbed NLSE. Moreover, this curve also yields a good estimate for the soliton lifetime: the soliton lives longer, the shorter the branch with negative slope is. PMID:20365492

  15. Spatio-temporal variability of lowland river properties and effects on metabolic rate estimates

    E-print Network

    VILLAMIZAR AMAYA, SANDRA ROCIO

    2013-01-01

    type = "dissolved oxygen"; y_units = " mg/l"} if(SENSOR_NUMdissolved oxygen (DO) spatiotemporal behavior observed using the mobile sensordissolved oxygen (DO) spatiotemporal behavior observed using the mobile sensor

  16. Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus

    PubMed Central

    Milanesi, Luciano

    2014-01-01

    Hepatitis C virus infection is one of the most common and chronic in the world, and hepatitis associated with HCV infection is a major risk factor for the development of cirrhosis and hepatocellular carcinoma (HCC). The rapidly growing number of viral-host and host protein-protein interactions is enabling more and more reliable network-based analyses of viral infection supported by omics data. The study of molecular interaction networks helps to elucidate the mechanistic pathways linking HCV molecular activities and the host response that modulates the stepwise hepatocarcinogenic process from preneoplastic lesions (cirrhosis and dysplasia) to HCC. Simulating the impact of HCV-host molecular interactions throughout the host protein-protein interaction (PPI) network, we ranked the host proteins in relation to their network proximity to viral targets. We observed that the set of proteins in the neighborhood of HCV targets in the host interactome is enriched in key players of the host response to HCV infection. In opposition to HCV targets, subnetworks of proteins in network proximity to HCV targets are significantly enriched in proteins reported as differentially expressed in preneoplastic and neoplastic liver samples by two independent studies. Using multi-objective optimization, we extracted subnetworks that are simultaneously “guilt-by-association” with HCV proteins and enriched in proteins differentially expressed. These subnetworks contain established, recently proposed and novel candidate proteins for the regulation of the mechanisms of liver cells response to chronic HCV infection. PMID:25461596

  17. Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

    PubMed Central

    Chen, Jian; Jegga, Anil G.; Luo, Heng; Shi, Leming; Wan, Chunling; Guo, Xizhi; Qin, Shengying; He, Guang; Feng, Guoyin; He, Lin

    2011-01-01

    In the era of personalized medical practice, understanding the genetic basis of patient-specific adverse drug reaction (ADR) is a major challenge. Clozapine provides effective treatments for schizophrenia but its usage is limited because of life-threatening agranulocytosis. A recent high impact study showed the necessity of moving clozapine to a first line drug, thus identifying the biomarkers for drug-induced agranulocytosis has become important. Here we report a methodology termed as antithesis chemical-protein interactome (CPI), which utilizes the docking method to mimic the differences in the drug-protein interactions across a panel of human proteins. Using this method, we identified HSPA1A, a known susceptibility gene for CIA, to be the off-target of clozapine. Furthermore, the mRNA expression of HSPA1A-related genes (off-target associated systems) was also found to be differentially expressed in clozapine treated leukemia cell line. Apart from identifying the CIA causal genes we identified several novel candidate genes which could be responsible for agranulocytosis. Proteins related to reactive oxygen clearance system, such as oxidoreductases and glutathione metabolite enzymes, were significantly enriched in the antithesis CPI. This methodology conducted a multi-dimensional analysis of drugs' perturbation to the biological system, investigating both the off-targets and the associated off-systems to explore the molecular basis of an adverse event or the new uses for old drugs. PMID:21483481

  18. Quantitative proteomics of the yeast Hsp70/Hsp90 interactomes during DNA damage reveals chaperone-dependent regulation of ribonucleotide reductase

    PubMed Central

    Truman, Andrew W.; Kristjansdottir, Kolbrun; Wolfgeher, Donald; Ricco, Natalia; Mayampurath, Anoop; Volchenboum, Samuel L.; Clotet, Josep; Kron, Stephen J.

    2015-01-01

    The highly conserved molecular chaperones Hsp90 and Hsp70 are indispensible for folding and maturation of a significant fraction of the proteome, including many proteins involved in signal transduction and stress response. To examine the dynamics of chaperone-client interactions after DNA damage, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to characterize interactomes of the yeast Hsp70 isoform Ssa1 and Hsp90 isoform Hsp82 before and after exposure to methyl methanesulfonate. Of 256 proteins identified and quantified via 16O/18O labeling and LC-MS/MS, 142 are novel Hsp70/90 interactors. Nearly all interactions remained unchanged or decreased after DNA damage, but 5 proteins increased interactions with Ssa1 and/or Hsp82, including the ribonucleotide reductase (RNR) subunit Rnr4. Inhibiting Hsp70 or 90 chaperone activity destabilized Rnr4 in yeast and its vertebrate homolog hRMM2 in breast cancer cells. In turn, pre-treatment of cancer cells with chaperone inhibitors sensitized cells to the RNR inhibitor gemcitabine, suggesting a novel chemotherapy strategy. All MS data have been deposited in the ProteomeXchange with identifier PXD001284. PMID:25452130

  19. Spatio-temporal data clustering based on type-2 fuzzy sets and cloud models

    Microsoft Academic Search

    Kun Qin; Mengran Wu; Lingqiao Kong; Yao Liu

    2010-01-01

    The time series remote sensing data and meteorological satellite data offer new opportunities for understanding the earth system. Spatio-temporal data clustering becomes a kind of idea tool to explore huge data space of spatio-temporal data. Because there are many uncertainties in the huge spatio-temporal data, including fuzziness and randomness, the spatio-temporal clustering methods with uncertainties are needed. Based on type-2

  20. SeTPR*-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared

    E-print Network

    He, Zhen

    existing spatiotemporal index for updates takes around 6 ms to process an individual update when indexing 1 algorithms for the fast batch processing of queries and updates for spatiotemporal indexes. Another situationSeTPR*-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared Execution THI NGUYEN, ZHEN

  1. A general science-based framework for dynamical spatio-temporal models

    USGS Publications Warehouse

    Wikle, C.K.; Hooten, M.B.

    2010-01-01

    Spatio-temporal statistical models are increasingly being used across a wide variety of scientific disciplines to describe and predict spatially-explicit processes that evolve over time. Correspondingly, in recent years there has been a significant amount of research on new statistical methodology for such models. Although descriptive models that approach the problem from the second-order (covariance) perspective are important, and innovative work is being done in this regard, many real-world processes are dynamic, and it can be more efficient in some cases to characterize the associated spatio-temporal dependence by the use of dynamical models. The chief challenge with the specification of such dynamical models has been related to the curse of dimensionality. Even in fairly simple linear, first-order Markovian, Gaussian error settings, statistical models are often over parameterized. Hierarchical models have proven invaluable in their ability to deal to some extent with this issue by allowing dependency among groups of parameters. In addition, this framework has allowed for the specification of science based parameterizations (and associated prior distributions) in which classes of deterministic dynamical models (e. g., partial differential equations (PDEs), integro-difference equations (IDEs), matrix models, and agent-based models) are used to guide specific parameterizations. Most of the focus for the application of such models in statistics has been in the linear case. The problems mentioned above with linear dynamic models are compounded in the case of nonlinear models. In this sense, the need for coherent and sensible model parameterizations is not only helpful, it is essential. Here, we present an overview of a framework for incorporating scientific information to motivate dynamical spatio-temporal models. First, we illustrate the methodology with the linear case. We then develop a general nonlinear spatio-temporal framework that we call general quadratic nonlinearity and demonstrate that it accommodates many different classes of scientific-based parameterizations as special cases. The model is presented in a hierarchical Bayesian framework and is illustrated with examples from ecology and oceanography. ?? 2010 Sociedad de Estad??stica e Investigaci??n Operativa.

  2. Prediction model of potential hepatocarcinogenicity of rat hepatocarcinogens using a large-scale toxicogenomics database

    SciTech Connect

    Uehara, Takeki, E-mail: takeki.uehara@shionogi.co.jp [Drug Developmental Research Laboratories, Shionogi and Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825 (Japan); Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085 (Japan); Minowa, Yohsuke; Morikawa, Yuji [Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085 (Japan); Kondo, Chiaki; Maruyama, Toshiyuki; Kato, Ikuo [Drug Developmental Research Laboratories, Shionogi and Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825 (Japan); Nakatsu, Noriyuki; Igarashi, Yoshinobu; Ono, Atsushi [Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085 (Japan); Hayashi, Hitomi [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Harumi-cho, Fuchu, Tokyo 183-8509 (Japan); Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Gifu (Japan); Mitsumori, Kunitoshi [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Harumi-cho, Fuchu, Tokyo 183-8509 (Japan); Yamada, Hiroshi [Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085 (Japan); Ohno, Yasuo [National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501 (Japan); Urushidani, Tetsuro [Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085 (Japan); Department of Pathophysiology, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kodo, Kyotanabe, Kyoto 610-0395 (Japan)

    2011-09-15

    The present study was performed to develop a robust gene-based prediction model for early assessment of potential hepatocarcinogenicity of chemicals in rats by using our toxicogenomics database, TG-GATEs (Genomics-Assisted Toxicity Evaluation System developed by the Toxicogenomics Project in Japan). The positive training set consisted of high- or middle-dose groups that received 6 different non-genotoxic hepatocarcinogens during a 28-day period. The negative training set consisted of high- or middle-dose groups of 54 non-carcinogens. Support vector machine combined with wrapper-type gene selection algorithms was used for modeling. Consequently, our best classifier yielded prediction accuracies for hepatocarcinogenicity of 99% sensitivity and 97% specificity in the training data set, and false positive prediction was almost completely eliminated. Pathway analysis of feature genes revealed that the mitogen-activated protein kinase p38- and phosphatidylinositol-3-kinase-centered interactome and the v-myc myelocytomatosis viral oncogene homolog-centered interactome were the 2 most significant networks. The usefulness and robustness of our predictor were further confirmed in an independent validation data set obtained from the public database. Interestingly, similar positive predictions were obtained in several genotoxic hepatocarcinogens as well as non-genotoxic hepatocarcinogens. These results indicate that the expression profiles of our newly selected candidate biomarker genes might be common characteristics in the early stage of carcinogenesis for both genotoxic and non-genotoxic carcinogens in the rat liver. Our toxicogenomic model might be useful for the prospective screening of hepatocarcinogenicity of compounds and prioritization of compounds for carcinogenicity testing. - Highlights: >We developed a toxicogenomic model to predict hepatocarcinogenicity of chemicals. >The optimized model consisting of 9 probes had 99% sensitivity and 97% specificity. >This model enables us to detect genotoxic as well as non-genotoxic hepatocarcinogens.

  3. Experimental study of spatiotemporally localized surface gravity water waves.

    PubMed

    Chabchoub, A; Akhmediev, N; Hoffmann, N P

    2012-07-01

    We present experimental results on the study of spatiotemporally localized surface wave events on deep water that can be modeled using the Peregrine breather solution of the nonlinear Schrödinger equation. These are often considered as prototypes of oceanic rogue waves that can focus wave energy into a single wave packet. For small steepness values of the carrier gravity waves the Peregrine breathers are relatively wide, thus providing an excellent agreement between the theory and experimental results. For larger steepnesses the focusing leads to temporally and spatially shorter events. Nevertheless, agreement between measurements and the Peregrine breather theory remains reasonably good, with discrepancies of modulation gradients and spatiotemporal symmetries being tolerable. Lifetimes and travel distances of the spatiotemporally localized wave events determined from the experiment are in good agreement with the theory. PMID:23005529

  4. RST: a connectionist architecture to deal with spatiotemporal relationships.

    PubMed

    Chappelier, J C; Grumbach, A

    1998-05-15

    In the past decade, connectionism has proved its efficiency in the field of static pattern recognition. The next challenge is to deal with spatiotemporal problems. This article presents a new connectionist architecture, RST (réseau spatio temporel [spatio temporal network]), with such spatiotemporal capacities. It aims at taking into account at the architecture level both spatial relationships (e.g., as between neighboring pixels in an image) and temporal relationships (e.g., as between consecutive images in a video sequence). Concerning the spatial aspect, the network is embedded in actual space (two) or three-dimensional-, the metrics of which directly influence its structure through a connection distribution function. For the temporal aspect, we looked toward biology and used a leaky-integrator neuron model with a refractory period and postsynaptic potentials. The propagation of activity by spatiotemporal synchronized waves enables RST to perform motion detection and localization in sequences of video images. PMID:9573411

  5. Control of spatiotemporal patterns in the Gray-Scott model

    NASA Astrophysics Data System (ADS)

    Kyrychko, Y. N.; Blyuss, K. B.; Hogan, S. J.; Schöll, E.

    2009-12-01

    This paper studies the effects of a time-delayed feedback control on the appearance and development of spatiotemporal patterns in a reaction-diffusion system. Different types of control schemes are investigated, including single-species, diagonal, and mixed control. This approach helps to unveil different dynamical regimes, which arise from chaotic state or from traveling waves. In the case of spatiotemporal chaos, the control can either stabilize uniform steady states or lead to bistability between a trivial steady state and a propagating traveling wave. Furthermore, when the basic state is a stable traveling pulse, the control is able to advance stationary Turing patterns or yield the above-mentioned bistability regime. In each case, the stability boundary is found in the parameter space of the control strength and the time delay, and numerical simulations suggest that diagonal control fails to control the spatiotemporal chaos.

  6. Application of Geostatistical Methods and Machine Learning for spatio-temporal Earthquake Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Schaefer, A. M.; Daniell, J. E.; Wenzel, F.

    2014-12-01

    Earthquake clustering tends to be an increasingly important part of general earthquake research especially in terms of seismic hazard assessment and earthquake forecasting and prediction approaches. The distinct identification and definition of foreshocks, aftershocks, mainshocks and secondary mainshocks is taken into account using a point based spatio-temporal clustering algorithm originating from the field of classic machine learning. This can be further applied for declustering purposes to separate background seismicity from triggered seismicity. The results are interpreted and processed to assemble 3D-(x,y,t) earthquake clustering maps which are based on smoothed seismicity records in space and time. In addition, multi-dimensional Gaussian functions are used to capture clustering parameters for spatial distribution and dominant orientations. Clusters are further processed using methodologies originating from geostatistics, which have been mostly applied and developed in mining projects during the last decades. A 2.5D variogram analysis is applied to identify spatio-temporal homogeneity in terms of earthquake density and energy output. The results are mitigated using Kriging to provide an accurate mapping solution for clustering features. As a case study, seismic data of New Zealand and the United States is used, covering events since the 1950s, from which an earthquake cluster catalogue is assembled for most of the major events, including a detailed analysis of the Landers and Christchurch sequences.

  7. The role of climate and socioeconomic factors on the spatiotemporal variability of cholera in Nigeria

    NASA Astrophysics Data System (ADS)

    Abdussalam, Auwal; Thornes, John; Leckebusch, Gregor

    2015-04-01

    Nigeria has a number of climate-sensitive infectious diseases; one of the most important of these diseases that remains a threat to public health is cholera. This study investigates the influences of both meteorological and socioeconomic factors on the spatiotemporal variability of cholera in Nigeria. A stepwise multiple regression models are used to estimate the influence of the year-to-year variations of cholera cases and deaths for individual states in the country and as well for three groups of states that are classified based on annual rainfall amount. Specifically, seasonal mean maximum and minimum temperatures and annual rainfall totals were analysed with annual aggregate count of cholera cases and deaths, taking into account of the socioeconomic factors that are potentially enhancing vulnerability such as: absolute poverty, adult literacy, access to pipe borne water and population density. Result reveals that the most important explanatory meteorological and socioeconomic variables in explaining the spatiotemporal variability of the disease are rainfall totals, seasonal mean maximum temperature, absolute poverty, and accessibility to pipe borne water. The influences of socioeconomic factors appeared to be more pronounced in the northern part of the country, and vice-versa in the case of meteorological factors. Also, cross validated models output suggests a strong possibility of disease prediction, which will help authorities to put effective control measures in place which depend on prevention, and or efficient response.

  8. Spatiotemporal Analysis of Hepatitis C Virus Infection

    PubMed Central

    Shulla, Ana; Randall, Glenn

    2015-01-01

    Hepatitis C virus (HCV) entry, translation, replication, and assembly occur with defined kinetics in distinct subcellular compartments. It is unclear how HCV spatially and temporally regulates these events within the host cell to coordinate its infection. We have developed a single molecule RNA detection assay that facilitates the simultaneous visualization of HCV (+) and (?) RNA strands at the single cell level using high-resolution confocal microscopy. We detect (+) strand RNAs as early as 2 hours post-infection and (?) strand RNAs as early as 4 hours post-infection. Single cell levels of (+) and (?) RNA vary considerably with an average (+):(?) RNA ratio of 10 and a range from 1–35. We next developed microscopic assays to identify HCV (+) and (?) RNAs associated with actively translating ribosomes, replication, virion assembly and intracellular virions. (+) RNAs display a defined temporal kinetics, with the majority of (+) RNAs associated with actively translating ribosomes at early times of infection, followed by a shift to replication and then virion assembly. (?) RNAs have a strong colocalization with NS5A, but not NS3, at early time points that correlate with replication compartment formation. At later times, only ~30% of the replication complexes appear to be active at a given time, as defined by (?) strand colocalization with either (+) RNA, NS3, or NS5A. While both (+) and (?) RNAs colocalize with the viral proteins NS3 and NS5A, only the plus strand preferentially colocalizes with the viral envelope E2 protein. These results suggest a defined spatiotemporal regulation of HCV infection with highly varied replication efficiencies at the single cell level. This approach can be applicable to all plus strand RNA viruses and enables unprecedented sensitivity for studying early events in the viral life cycle. PMID:25822891

  9. Moment analysis for spatiotemporal fractional dispersion

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Benson, David A.; Baeumer, Boris

    2008-04-01

    The evolution of the first five nonnegative integer-order spatial moments (corresponding to the mass, mean, variance, skewness, and kurtosis) are investigated systematically for spatiotemporal nonlocal, fractional dispersion. Three commonly used fractional-order transport equations, including the time fractional advection-dispersion equation (Time-FADE), the fractal mobile-immobile (MIM) equation, and the fully fractional advection-dispersion equation (FFADE), are considered. Analytical solutions verify our numerical results and reveal the anomalous evolution of the moments. Following Adams and Gelhar's (1992) work on the classical ADE, we find that a simultaneous analysis of all moments is critical in discriminating between different nonlocal models. The evolution of dispersion among the subdiffusive to superdiffusive rates is then further explored numerically by a non-Markovian random walk particle-tracking method that can be used for any heterogeneous boundary or initial value problem in three dimensions. Both the analytical and the numerical results also show the similarity (at the early time) and the difference (at the late time) of moment growth for solutes in different phases (mobile versus total) described by the MIM models. Further simulations of the 1-D bromide snapshots measured at the MADE experiments, using all three models with parameters fitted by the observed zeroth to fourth moments, indicate that (1) both the time and space nonlocality strongly affect the solute transport at the MADE site, (2) all five spatial moments should be considered in transport model selection and calibration because those up to the variance cannot effectively discriminate between nonlocal models, and (3) the log concentration should be used when evaluating the plume leading edge and the effects of space nonlocality.

  10. Stabilization of spatiotemporal solitons in Kerr media by dispersive coupling.

    PubMed

    Kartashov, Yaroslav V; Malomed, Boris A; Konotop, Vladimir V; Lobanov, Valery E; Torner, Lluis

    2015-03-15

    We introduce a mechanism to stabilize spatiotemporal solitons in Kerr nonlinear media, based on the dispersion of linear coupling between the field components forming the soliton states. Specifically, we consider solitons in a two-core guiding structure with inter-core coupling dispersion (CD). We show that CD profoundly affects properties of the solitons, causing the complete stabilization of the otherwise highly unstable spatiotemporal solitons in Kerr media with focusing nonlinearity. We also find that the presence of CD stimulates the formation of bound states, which, however, are unstable. PMID:25768178

  11. Spatiotemporal focusing dynamics in plasmas at X-ray wavelength

    NASA Astrophysics Data System (ADS)

    Sharma, A.; Tibai, Z.; Hebling, J.; Mishra, S. K.

    2014-03-01

    Using a finite curvature beam, we investigate here the spatiotemporal focusing dynamics of a laser pulse in plasmas at X-ray wavelength. We trace the dependence of curvature parameter on the focusing of laser pulse and recognize that the self-focusing in plasma is more intense for the X-ray laser pulse with curved wavefront than with flat wavefront. The simulation results demonstrate that spatiotemporal focusing dynamics in plasmas can be controlled with the appropriate choice of beam-plasma parameters to explore the high intensity effects in X-ray regime.

  12. Spatiotemporal focusing dynamics in plasmas at X-ray wavelength

    SciTech Connect

    Sharma, A., E-mail: a-physics2001@yahoo.com; Tibai, Z. [Institute of Physics, University of Pecs, Pecs–7624 (Hungary)] [Institute of Physics, University of Pecs, Pecs–7624 (Hungary); Hebling, J. [Institute of Physics, University of Pecs, Pecs–7624 (Hungary) [Institute of Physics, University of Pecs, Pecs–7624 (Hungary); Szentagothai Research Centre, University of Pecs, Pecs-7624 (Hungary); Mishra, S. K. [Institute for Plasma Research, Gandhinagar (India)] [Institute for Plasma Research, Gandhinagar (India)

    2014-03-15

    Using a finite curvature beam, we investigate here the spatiotemporal focusing dynamics of a laser pulse in plasmas at X-ray wavelength. We trace the dependence of curvature parameter on the focusing of laser pulse and recognize that the self-focusing in plasma is more intense for the X-ray laser pulse with curved wavefront than with flat wavefront. The simulation results demonstrate that spatiotemporal focusing dynamics in plasmas can be controlled with the appropriate choice of beam-plasma parameters to explore the high intensity effects in X-ray regime.

  13. Toward understanding the multiple spatiotemporal dynamics of chlorophyll fluorescence.

    PubMed

    Iwai, Masakazu; Yokono, Makio; Nakano, Akihiko

    2015-06-01

    Dynamic reorganization of photosystems I and II is suggested to occur in chloroplast thylakoid membranes to maintain the efficiency of photosynthesis under fluctuating light conditions. To directly observe the process in action, live-cell imaging techniques are necessary. Using live-cell imaging, we have shown that the fine thylakoid structures in the moss Physcomitrella patens are flexible in time. However, the spatiotemporal resolution of a conventional confocal microscopy limits more precise visualization of entire thylakoid structures and understanding of the structural dynamics. Here, we discuss the issues related to observing chlorophyll fluorescence at multiple spatiotemporal scales in vivo and in vitro. PMID:26176900

  14. Spatio-Temporal Continuity and Physical Object Identity

    E-print Network

    Smythe, Thomas W.

    SpatioTemporal Continuity and Physical Object Identity Thomas W. Smythe I One important answer to the question of how we are to identify material objects as identical through time is that material objects must preserve spatio-temporal (s... at the same spot or position. It is the purpose of this paper to investigate this common conception. In order to see how closely s-t continuity is re­ lated to the numerical identity of material objects through time I shall try to defend the contrary view...

  15. Time reversal and the spatio-temporal matched filter

    SciTech Connect

    Lehman, S K; Poggio, A J; Kallman, J S; Meyer, A W; Candy, J V

    2004-03-08

    It is known that focusing of an acoustic field by a time-reversal mirror (TRM) is equivalent to a spatio-temporal matched filter under conditions where the Green's function of the field satisfies reciprocity and is time invariant, i.e. the Green's function is independent of the choice of time origin. In this letter, it is shown that both reciprocity and time invariance can be replaced by a more general constraint on the Green's function that allows a TRM to implement the spatio-temporal matched filter even when conditions are time varying.

  16. Time reversal and the spatio-temporal matched filter (L)

    NASA Astrophysics Data System (ADS)

    Chambers, D. H.; Candy, J. V.; Lehman, S. K.; Kallman, J. S.; Poggio, A. J.; Meyer, A. W.

    2004-09-01

    It is known that focusing of an acoustic field by a time-reversal mirror (TRM) is equivalent to a spatio-temporal matched filter under conditions where the Green's function of the field satisfies reciprocity and is time invariant, i.e., the Green's function is independent of the choice of time origin. In this letter, it is shown that both reciprocity and time invariance can be replaced by a more general constraint on the Green's function that allows a TRM to implement the spatio-temporal matched filter even when conditions are time varying.

  17. Real-time spatio-temporal analysis of dynamic scenes

    Microsoft Academic Search

    Tobias Warden; Ubbo Visser

    We propose a set of tools for spatio-temporal real-time analysis of dynamic scenes. It is designed to improve the grounding\\u000a situation of autonomous agents in (simulated) physical domains. We introduce a knowledge processing pipeline ranging from\\u000a relevance-driven compilation of a qualitative scene description to a knowledge-based detection of complex event and action\\u000a sequences, conceived as a spatio-temporal pattern-matching problem. A

  18. Spatiotemporal evolution of dielectric driven cogenerated dust density waves

    SciTech Connect

    Sarkar, Sanjib; Bose, M. [Department of Physics, Jadavpur University, Kolkata 700032 (India)] [Department of Physics, Jadavpur University, Kolkata 700032 (India); Mukherjee, S. [FCIPT, Institute for Plasma Research, Gandhinagar 382428 (India)] [FCIPT, Institute for Plasma Research, Gandhinagar 382428 (India); Pramanik, J. [Kharagpur College, Kharagpur 721305, West Bengal (India)] [Kharagpur College, Kharagpur 721305, West Bengal (India)

    2013-06-15

    An experimental observation of spatiotemporal evolution of dust density waves (DDWs) in cogenerated dusty plasma in the presence of modified field induced by glass plate is reported. Various DDWs, such as vertical, oblique, and stationary, were detected simultaneously for the first time. Evolution of spatiotemporal complexity like bifurcation in propagating wavefronts is also observed. As dust concentration reaches extremely high value, the DDW collapses. Also, the oblique and nonpropagating mode vanishes when we increase the number of glass plates, while dust particles were trapped above each glass plates showing only vertical DDWs.

  19. Light-Activated Proteolysis for the Spatiotemporal Control of Proteins.

    PubMed

    Delacour, Quentin; Li, Chenge; Plamont, Marie-Aude; Billon-Denis, Emmanuelle; Aujard, Isabelle; Le Saux, Thomas; Jullien, Ludovic; Gautier, Arnaud

    2015-07-17

    The regulation of proteolysis is an efficient way to control protein function in cells. Here, we present a general strategy enabling to increase the spatiotemporal resolution of conditional proteolysis by using light activation as trigger. Our approach relies on the auxin-inducible degradation system obtained by transposing components of the plant auxin-dependent degradation pathway in mammalian cells. We developed a photoactivatable auxin that acts as a photoactivatable inducer of degradation. Upon local and short light illumination, auxin is released in cells and triggers the degradation of a protein of interest with spatiotemporal control. PMID:25938742

  20. Male reproductive strategy explains spatiotemporal segregation in brown bears.

    PubMed

    Steyaert, Sam M J G; Kindberg, Jonas; Swenson, Jon E; Zedrosser, Andreas

    2013-07-01

    Spatiotemporal segregation is often explained by the risk for offspring predation or by differences in physiology, predation risk vulnerability or competitive abilities related to size dimorphism. Most large carnivores are size dimorphic and offspring predation is often intraspecific and related to nonparental infanticide (NPI). NPI can be a foraging strategy, a strategy to reduce competition, or a male reproductive strategy. Spatiotemporal segregation is widespread among large carnivores, but its nature remains poorly understood. We evaluated three hypotheses to explain spatiotemporal segregation in the brown bear, a size-dimorphic large carnivore in which NPI is common; the 'NPI - foraging/competition hypothesis', i.e. NPI as a foraging strategy or a strategy to reduce competition, the 'NPI - sexual selection hypothesis', i.e. infanticide as a male reproductive strategy and the 'body size hypothesis', i.e. body-size-related differences in physiology, predation risk vulnerability or competitive ability causes spatiotemporal segregation. To test these hypotheses, we quantified spatiotemporal segregation among adult males, lone adult females and females with cubs-of-the-year, based on GPS-relocation data (2006-2010) and resource selection functions in a Scandinavian population. We found that spatiotemporal segregation was strongest between females with cubs-of-the-year and adult males during the mating season. During the mating season, females with cubs-of-the-year selected their resources, in contrast to adult males, in less rugged landscapes in relative close proximity to certain human-related variables, and in more open habitat types. After the mating season, females with cubs-of-the-year markedly shifted their resource selection towards a pattern more similar to that of their conspecifics. No strong spatiotemporal segregation was apparent between females with cubs-of-the-year and conspecifics during the mating and the postmating season. The 'NPI - sexual selection hypothesis' best explained spatiotemporal segregation in our study system. We suggest that females with cubs-of-the-year alter their resource selection to avoid infanticidal males. In species exhibiting NPI as a male reproductive strategy, female avoidance of infanticidal males is probably more common than observed or reported, and may come with a fitness cost if females trade safety for optimal resources. PMID:23461483

  1. Phenomenal Permanence and the Development of Predictive Tracking in Infancy

    ERIC Educational Resources Information Center

    Bertenthal, Bennett I.; Longo, Matthew R.; Kenny, Sarah

    2007-01-01

    The perceived spatiotemporal continuity of objects depends on the way they appear and disappear as they move in the spatial layout. This study investigated whether infants' predictive tracking of a briefly occluded object is sensitive to the manner by which the object disappears and reappears. Five-, 7-, and 9-month-old infants were shown a ball…

  2. PSO2004/FU5766 Improved wind power prediction

    E-print Network

    PSO2004/FU5766 Improved wind power prediction Spatio-temporal modelling of short-term wind power of wind power generation in power systems. The quality of the forecast is very important, and a reliable estimate of the uncertainty of the forecast is known to be essential. Today the forecasts of wind power

  3. Asymmetric spatiotemporal chaos induced by a polypoid mass in the excised larynx

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Jiang, Jack J.

    2008-12-01

    In this paper, asymmetric spatiotemporal chaos induced by a polypoid mass simulating the laryngeal pathology of a vocal polyp is experimentally observed using high-speed imaging in an excised larynx. Spatiotemporal analysis reveals that the normal vocal folds show spatiotemporal correlation and symmetry. Normal vocal fold vibrations are dominated mainly by the first vibratory eigenmode. However, pathological vocal folds with a polypoid mass show broken symmetry and spatiotemporal irregularity. The spatial correlation is decreased. The pathological vocal folds spread vibratory energy across a large number of eigenmodes and induce asymmetric spatiotemporal chaos. High-order eigenmodes show complicated dynamics. Spatiotemporal analysis provides a valuable biomedical application for investigating the spatiotemporal chaotic dynamics of pathological vocal fold systems with a polypoid mass and may represent a valuable clinical tool for the detection of laryngeal mass lesion using high-speed imaging.

  4. The GLIMS Glacier Database: a spatio-temporal database

    E-print Network

    Raup, Bruce H.

    complex geospatial objects. MapServer is a flexible and easy tool for serving data on the WebThe GLIMS Glacier Database: a spatio-temporal database implemented using Open Source tools Bruce small budgets). Capable, and fast! Runs on Linux, where we can take advantage of our stock of Linux

  5. Spatiotemporal clustering of synchronized bursting events in neuronal networks

    Microsoft Academic Search

    Uri Barkan; David Horn

    2006-01-01

    in vitro neuronal networks display Synchronized Bursting Events (SBEs), with characteristic temporal width of 100-500 ms and frequency of once every few sec- onds. We analyze such data using preprocessing by SVD for dimensional reduction, after which we apply quantum clustering to sort out the SBEs into dieren t groups. Each SBE is described within a spatiotemporal template, allowing us

  6. Spatio-temporal evaluation matrices for geospatial data

    NASA Astrophysics Data System (ADS)

    Triglav, Joc; Petrovi?, Dušan; Stopar, Bojan

    2011-02-01

    The global geospatial community is investing substantial effort in providing tools for geospatial data-quality information analysis and systematizing the criteria for geospatial data quality. The importance of these activities is increasing, especially in the last decade, which has witnessed an enormous expansion of geospatial data use in general and especially among mass users. Although geospatial data producers are striving to define and present data-quality standards to users and users increasingly need to assess the fitness for use of the data, the success of these activities is still far from what is expected or required. As a consequence, neglect or misunderstanding of data quality among users results in misuse or risks. This paper presents an aid in spatio-temporal quality evaluation through the use of spatio-temporal evaluation matrices (STEM) and the index of spatio-temporal anticipations (INSTANT) matrices. With the help of these two simple tools, geospatial data producers can systematically categorize and visualize the granularity of their spatio-temporal data, and users can present their requirements in the same way using business intelligence principles and a Web 2.0 approach. The basic principles and some examples are presented in the paper, and potential further applied research activities are briefly described.

  7. Spatiotemporal Analysis of Face Profiles: Detection, Segmentation, and Registration

    Microsoft Academic Search

    Behzad Dariush; Sing Bang Kang; Keith Waters

    1998-01-01

    We use a two-image approach to construct a 3D human facial model for multimedia applications. The images used are those of faces at direct frontal and side views. The selection of the side view from a sequence of facial images is automatically done by applying a spatiotemporal approach to face profile analysis. The extracted side profile is then segmented based

  8. Spatio-temporal Pattern Formation in Reaction-Diffusion Systems

    E-print Network

    Mocenni, Chiara

    Spatio-temporal Pattern Formation in Reaction-Diffusion Systems Chiara Mocenni January 15, 2013 #12 without diffusion By nondimensionalization and discarding diffusion, we have the following system is the wave number. #12;Diffusion-Driven Instability c = f (c) c Rn (R) #12;Diffusion-Driven Instability c

  9. SPATIO-TEMPORAL REGISTRATION OF EMBRYO IMAGES L. Guignard

    E-print Network

    Paris-Sud XI, Université de

    SPATIO-TEMPORAL REGISTRATION OF EMBRYO IMAGES L. Guignard C. Godin U.-M. Fiuza L. Hufnagel P. Stitching together sequences captured from different embryos may help producing a sequence covering is to describe cell and/or embryo shapes through development, to analyze their dy- namics and variability within

  10. SPATIOTEMPORAL VARIATION IN SURVIVAL OF MALE YELLOW-BELLIED MARMOTS

    E-print Network

    Grether, Gregory

    SPATIOTEMPORAL VARIATION IN SURVIVAL OF MALE YELLOW-BELLIED MARMOTS NATALIA BORREGO,a ARPAT OZGUL variation in age-specific survival rates of male yellow-bellied marmots (Marmota flaviventris) in Colorado in survival rates. Our results suggest that male marmots of different ages respond differentially to temporal

  11. Spatio-Temporal Signal Recovery from Political Tweets in Indonesia

    E-print Network

    Davulcu, Hasan

    Spatio-Temporal Signal Recovery from Political Tweets in Indonesia Anisha Mazumder, Arun Das activity in the provinces of Indonesia. Based on analysis of radical/counter radical sentiments expressed in tweets by Twitter users, we create a Heat Map of Indonesia which visually demonstrates the degree

  12. Spatio-Temporal Saliency Perception via Hypercomplex Frequency Spectral Contrast

    PubMed Central

    Li, Ce; Xue, Jianru; Zheng, Nanning; Lan, Xuguang; Tian, Zhiqiang

    2013-01-01

    Salient object perception is the process of sensing the salient information from the spatio-temporal visual scenes, which is a rapid pre-attention mechanism for the target location in a visual smart sensor. In recent decades, many successful models of visual saliency perception have been proposed to simulate the pre-attention behavior. Since most of the methods usually need some ad hoc parameters or high-cost preprocessing, they are difficult to rapidly detect salient object or be implemented by computing parallelism in a smart sensor. In this paper, we propose a novel spatio-temporal saliency perception method based on spatio-temporal hypercomplex spectral contrast (HSC). Firstly, the proposed HSC algorithm represent the features in the HSV (hue, saturation and value) color space and features of motion by a hypercomplex number. Secondly, the spatio-temporal salient objects are efficiently detected by hypercomplex Fourier spectral contrast in parallel. Finally, our saliency perception model also incorporates with the non-uniform sampling, which is a common phenomenon of human vision that directs visual attention to the logarithmic center of the image/video in natural scenes. The experimental results on the public saliency perception datasets demonstrate the effectiveness of the proposed approach compared to eleven state-of-the-art approaches. In addition, we extend the proposed model to moving object extraction in dynamic scenes, and the proposed algorithm is superior to the traditional algorithms. PMID:23482090

  13. Fast Spatio-Temporal Data Mining from Large Geophysical Datasets

    NASA Technical Reports Server (NTRS)

    Stolorz, P.; Mesrobian, E.; Muntz, R.; Santos, J. R.; Shek, E.; Yi, J.; Mechoso, C.; Farrara, J.

    1995-01-01

    Use of the UCLA CONQUEST (CONtent-based Querying in Space and Time) is reviewed for performance of automatic cyclone extraction and detection of spatio-temporal blocking conditions on MPP. CONQUEST is a data analysis environment for knowledge and data mining to aid in high-resolution modeling of climate modeling.

  14. Location, Location, Location: Development of Spatiotemporal Sequence Learning in Infancy

    ERIC Educational Resources Information Center

    Kirkham, Natasha Z.; Slemmer, Jonathan A.; Richardson, Daniel C.; Johnson, Scott P.

    2007-01-01

    We investigated infants' sensitivity to spatiotemporal structure. In Experiment 1, circles appeared in a statistically defined spatial pattern. At test 11-month-olds, but not 8-month-olds, looked longer at a novel spatial sequence. Experiment 2 presented different color/shape stimuli, but only the location sequence was violated during test;…

  15. Spatio-temporal wavelet transforms for motion tracking

    Microsoft Academic Search

    Jean-Pierre Leduc; Fernando Mujica; Romain Murenzi; Mark Smith

    1997-01-01

    This paper addresses the problem of detecting and tracking moving objects in digital image sequences. The main goal is to detect and select mobile objects in a scene, construct the trajectories, and eventually reconstruct the target objects or their signatures. It is assumed that the image sequences are acquired from imaging sensors. The method is based on spatio-temporal continuous wavelet

  16. Spatio-temporal Information Ranking in VANET Applications

    E-print Network

    Wolfson, Ouri E.

    Spatio-temporal Information Ranking in VANET Applications PIOTR SZCZUREK, BO XU, JIE LIN, AND OURI WOLFSON University of Illinois at Chicago Vehicular ad-hoc networks (VANETs) is a promising approach ranking in VANETs. In this method, mobile nodes such as vehicles judge the relevance of incoming

  17. Spatiotemporal surface solitons in two-dimensional photonic lattices

    E-print Network

    with respect to the ratio of group velocity dis- persion and coupling constant. The slowly varying normalizedSpatiotemporal surface solitons in two-dimensional photonic lattices Dumitru Mihalache,1 Dumitru lattices and demon- strate the existence of two-dimensional surface light bullets localized in the lattice

  18. Localized and nonspreading spatiotemporal Wannier wave packets in photonic crystals.

    PubMed

    Longhi, Stefano

    2005-01-01

    A general analysis of undistorted propagation of localized wave packets in photonic crystals based on a Wannier-function expansion technique is presented. Different kinds of propagating and stationary spatiotemporal localized waves are found from an asymptotic analysis of the Wannier function envelope equation. PMID:15697743

  19. Spatiotemporal characteristics of calcium dynamics in astrocytes Minchul Kang1

    E-print Network

    Othmer, Hans

    are 10­15 times more numerous than neurons, make up about half of the total brain weight. AstrocytesSpatiotemporal characteristics of calcium dynamics in astrocytes Minchul Kang1 and Hans G. Othmer2 Cai 2+ waves in networks of astrocytes in vivo are well documented, propagation in vivo is much more

  20. Finding Spatio-Temporal Patterns in Large Sensor Datasets

    ERIC Educational Resources Information Center

    McGuire, Michael Patrick

    2010-01-01

    Spatial or temporal data mining tasks are performed in the context of the relevant space, defined by a spatial neighborhood, and the relevant time period, defined by a specific time interval. Furthermore, when mining large spatio-temporal datasets, interesting patterns typically emerge where the dataset is most dynamic. This dissertation is…

  1. Spatiotemporal dynamics in Rayleigh band of photonic quantum ring laser

    Microsoft Academic Search

    D. K. Kim; O'Dae Kwon

    2006-01-01

    Spatiotemporal dynamic analysis is used to analyze the carrier-field interactions on photonic quantum ring laser devices in a three dimensional toroidal whispering gallery cavity. We observe quantum wires-like carrier re-distributions instantly and naturally formed in the quantum well plane within the Rayleigh cavity.

  2. SPATIOTEMPORAL INFORMATION FUSION FOR HUMAN ACTION RECOGNITION IN VIDEOS

    E-print Network

    Tziritas, Georgios

    applications like video retrieval and archival, security surveil- lance, medical diagnosis, sports analysisSPATIOTEMPORAL INFORMATION FUSION FOR HUMAN ACTION RECOGNITION IN VIDEOS Emmanuel Ramasso, Denis particularly for video retrieval and archival. Usual approaches focus on proba- bilistic methods and assume

  3. Spatiotemporal information during unsupervised learning enhances viewpoint invariant object recognition.

    PubMed

    Tian, Moqian; Grill-Spector, Kalanit

    2015-05-01

    Recognizing objects is difficult because it requires both linking views of an object that can be different and distinguishing objects with similar appearance. Interestingly, people can learn to recognize objects across views in an unsupervised way, without feedback, just from the natural viewing statistics. However, there is intense debate regarding what information during unsupervised learning is used to link among object views. Specifically, researchers argue whether temporal proximity, motion, or spatiotemporal continuity among object views during unsupervised learning is beneficial. Here, we untangled the role of each of these factors in unsupervised learning of novel three-dimensional (3-D) objects. We found that after unsupervised training with 24 object views spanning a 180° view space, participants showed significant improvement in their ability to recognize 3-D objects across rotation. Surprisingly, there was no advantage to unsupervised learning with spatiotemporal continuity or motion information than training with temporal proximity. However, we discovered that when participants were trained with just a third of the views spanning the same view space, unsupervised learning via spatiotemporal continuity yielded significantly better recognition performance on novel views than learning via temporal proximity. These results suggest that while it is possible to obtain view-invariant recognition just from observing many views of an object presented in temporal proximity, spatiotemporal information enhances performance by producing representations with broader view tuning than learning via temporal association. Our findings have important implications for theories of object recognition and for the development of computational algorithms that learn from examples. PMID:26024454

  4. Intelligence and Spatiotemporal Patterns of Event-Related Desynchronization (ERD).

    ERIC Educational Resources Information Center

    Neubauer, Aljoscha; And Others

    1995-01-01

    The relationship between psychometric intelligence, determined by Raven's Advanced Progressive Matrices, and spatiotemporal patterns of cortical activation, determined by quantifying event-related desynchronization, was studied in 17 college students. Findings support the hypothesis of a more efficient use of the brain in higher IQ individuals.…

  5. VIDEO ANOMALY DETECTION IN SPATIOTEMPORAL CONTEXT , Junsong Yuan2

    E-print Network

    Tsaftaris, Sotirios

    VIDEO ANOMALY DETECTION IN SPATIOTEMPORAL CONTEXT Fan Jiang1 , Junsong Yuan2 , Sotirios A are detected as anomalies. Experiments on real traffic video prove that the detected video anomalies are defined as anomaly. Despite the success of clustering-based approaches for anomaly detection

  6. Modeling spatiotemporal covariance for magnetoencephalography or electroencephalography source analysis

    Microsoft Academic Search

    Sergey M. Plis; J. S. George; S. C. Jun; J. Paré-Blagoev; D. M. Ranken; C. C. Wood; D. M. Schmidt

    2007-01-01

    We propose a new model to approximate spatiotemporal noise covariance for use in neural electromagnetic source analysis, which better captures temporal variability in background activity. As with other existing formalisms, our model employs a Kronecker product of matrices representing temporal and spatial covariance. In our model, spatial components are allowed to have differing temporal covariances. Variability is represented as a

  7. Nonlinear Dynamics and Spatiotemporal Instabilities in Semiconductor Laser Arrays

    Microsoft Academic Search

    Lutfur Rahman

    1993-01-01

    By coupling several semiconductor lasers to form a laser array, a compact high power source of coherent radiation can be obtained. In addition to their technological importance, these devices also serve as useful paradigms for the study of spatiotemporal complexity in coupled nonlinear oscillators. In this thesis, we investigate the nature and origin of dynamical instabilities in semiconductor laser arrays

  8. Toward Understanding Tornado Formation Through Spatiotemporal Data Mining

    E-print Network

    McGovern, Amy

    Toward Understanding Tornado Formation Through Spatiotemporal Data Mining Amy McGovern and Derek H. Rosendahl and Rodger A. Brown 1 Motivation Tornadoes, which are one of the most feared natural phenomena produce tornadoes. There are no obvious clues within any of the routinely observed data to indicate which

  9. The Truncated Tornado in TMBB: A Spatiotemporal Uncertainty Model for

    E-print Network

    Bae, Wan

    The Truncated Tornado in TMBB: A Spatiotemporal Uncertainty Model for Moving Objects Shayma and system performance. In this paper, we propose an uncertainty model called the Truncated Tornado model as a significant advance in minimizing uncertainty re- gion sizes. The Truncated Tornado model removes uncertainty

  10. Spatiotemporal dynamics of neocortical excitation and inhibition during human sleep

    E-print Network

    Destexhe, Alain

    Spatiotemporal dynamics of neocortical excitation and inhibition during human sleep Adrien of excitatory and inhibitory cells has not been attempted in human neocortex, particularly during the sleep cells) from fast-spiking cells resulted in well-defined clusters that each showed unique intrinsic

  11. Collapse-driven spatiotemporal dynamics of filament formation

    E-print Network

    Porras, M A; Faccio, D; Parola, A; Trapani, P D; Couairon, Arnaud; Faccio, Daniele; Parola, Alberto; Porras, Miguel A.; Trapani, Paolo Di

    2006-01-01

    The transition from spatial to spatiotemporal dynamics in Kerr-driven beam collapse is modelled as the instability of the Townes profile. Coupled axial and conical radiation, temporal splitting and X waves appear as the effect of Y-shaped unstable modes, whose growth is experimentally detected.

  12. Cubic map algebra functions for spatio-temporal analysis

    USGS Publications Warehouse

    Mennis, J.; Viger, R.; Tomlin, C.D.

    2005-01-01

    We propose an extension of map algebra to three dimensions for spatio-temporal data handling. This approach yields a new class of map algebra functions that we call "cube functions." Whereas conventional map algebra functions operate on data layers representing two-dimensional space, cube functions operate on data cubes representing two-dimensional space over a third-dimensional period of time. We describe the prototype implementation of a spatio-temporal data structure and selected cube function versions of conventional local, focal, and zonal map algebra functions. The utility of cube functions is demonstrated through a case study analyzing the spatio-temporal variability of remotely sensed, southeastern U.S. vegetation character over various land covers and during different El Nin??o/Southern Oscillation (ENSO) phases. Like conventional map algebra, the application of cube functions may demand significant data preprocessing when integrating diverse data sets, and are subject to limitations related to data storage and algorithm performance. Solutions to these issues include extending data compression and computing strategies for calculations on very large data volumes to spatio-temporal data handling.

  13. Spatiotemporal interactions between audition and touch depend on hand posture

    Microsoft Academic Search

    Daniel Sanabria; Salvador Soto-Faraco; Charles Spence

    2005-01-01

    We report two experiments designed to assess the consequences of posture change on audiotactile spatiotemporal interactions. In Experiment 1, participants had to discriminate the direction of an auditory stream (consisting of the sequential presentation of two tones from different spatial positions) while attempting to ignore a task-irrelevant tactile stream (consisting of the sequential presentation of two vibrations, one to each

  14. Locally Regularized Spatiotemporal Modeling and Model Comparison for Functional MRI

    E-print Network

    Rotstein, Horacio G.

    Locally Regularized Spatiotemporal Modeling and Model Comparison for Functional MRI Patrick L fMRI data analysis as a spatio- temporal system identification problem and address issues of model to iden- tifying appropriate statistical models for fMRI studies. © 2001 Academic Press Key Words

  15. Phosphoinositide-specific Phospholipase C ? 1b (PI-PLC?1b) Interactome: Affinity Purification-Mass Spectrometry Analysis of PI-PLC?1b with Nuclear Protein*

    PubMed Central

    Piazzi, Manuela; Blalock, William L.; Bavelloni, Alberto; Faenza, Irene; D'Angelo, Antonietta; Maraldi, Nadir M.; Cocco, Lucio

    2013-01-01

    Two isoforms of inositide-dependent phospholipase C ?1 (PI-PLC?1) are generated by alternative splicing (PLC?1a and PLC?1b). Both isoforms are present within the nucleus, but in contrast to PLC?1a, the vast majority of PLC?1b is nuclear. In mouse erythroid leukemia cells, PI-PLC?1 is involved in the regulation of cell division and the balance between cell proliferation and differentiation. It has been demonstrated that nuclear localization is crucial for the enzymatic function of PI-PLC?1, although the mechanism by which this nuclear import occurs has never been fully characterized. The aim of this study was to characterize both the mechanism of nuclear localization and the molecular function of nuclear PI-PLC?1 by identifying its interactome in Friend's erythroleukemia isolated nuclei, utilizing a procedure that coupled immuno-affinity purification with tandem mass spectrometry analysis. Using this procedure, 160 proteins were demonstrated to be in association with PI-PLC?1b, some of which have been previously characterized, such as the splicing factor SRp20 (Srsf3) and Lamin B (Lmnb1). Co-immunoprecipitation analysis of selected proteins confirmed the data obtained via mass spectrometry. Of particular interest was the identification of the nuclear import proteins Kpna2, Kpna4, Kpnb1, Ran, and Rangap1, as well as factors involved in hematological malignancies and several anti-apoptotic proteins. These data give new insight into possible mechanisms of nuclear trafficking and functioning of this critical signaling molecule. PMID:23665500

  16. Spatiotemporal evolution of erythema migrans, the hallmark rash of Lyme disease.

    PubMed

    Vig, Dhruv K; Wolgemuth, Charles W

    2014-02-01

    To elucidate pathogen-host interactions during early Lyme disease, we developed a mathematical model that explains the spatiotemporal dynamics of the characteristic first sign of the disease, a large (?5-cm diameter) rash, known as an erythema migrans. The model predicts that the bacterial replication and dissemination rates are the primary factors controlling the speed that the rash spreads, whereas the rate that active macrophages are cleared from the dermis is the principle determinant of rash morphology. In addition, the model supports the clinical observations that antibiotic treatment quickly clears spirochetes from the dermis and that the rash appearance is not indicative of the efficacy of the treatment. The quantitative agreement between our results and clinical data suggest that this model could be used to develop more efficient drug treatments and may form a basis for modeling pathogen-host interactions in other emerging infectious diseases. PMID:24507617

  17. Kinetics of the active medium of a He-Sr{sup +} recombination laser: 1. Spatiotemporal characteristics

    SciTech Connect

    Chebotarev, G D; Latush, E L; Prutsakov, O O; Fesenko, A A [Southern Federal University, Faculty of Physics, Department of Quantum Radiophysics, Rostov-on-Don (Russian Federation)

    2008-04-30

    A self-consistent mathematical model of a He-Sr{sup +} recombination laser is developed and used to study the establishment of a repetitively pulsed regime in the active medium. The spatiotemporal characteristics are analysed in the stationary regime under different excitation conditions, the contraction of a repetitively pulsed discharge in helium is investigated and the discharge decontraction upon addition of strontium vapour, which is fundamentally important for metal vapour lasers is studied. Numerical simulations are shown to be a convenient tool for investigating the kinetics of the active medium of a He-Sr{sup +} laser, which enables predicting the optimal excitation conditions and calculating the limiting lasing characteristics. (lasers and amplifiers)

  18. Bayesian spatiotemporal modeling for blending in situ observations with satellite precipitation estimates

    NASA Astrophysics Data System (ADS)

    Jin, Baisuo; Wu, Yuehua; Miao, Baiqi; Wang, Xiaolan L.; Guo, Pengfei

    2014-02-01

    This study has developed a methodology for blending in situ gauge precipitation measurements with satellite precipitation estimates in a region, which uses a Bayesian spatiotemporal model. A fast and simple procedure is proposed for implementing the proposed methodology, which consists of four steps that use kriging, expectation-maximization, and Sampson-Guttorp methods in turn. The evaluation study has confirmed that the use of the new method has helped to improve the quality of the prediction when the available gauge stations are very sparse. For example, for the training sets of size 20, 40, and 70 and the evaluation sets of size more than 850 located in southwestern Canada, the 10 year (1994-2003) root-mean-square errors of the proposed method are respectively 1.278, 1.236, and 1.168. Moreover, the proposed methodology can be easily extended to blend in situ gauge observations with satellite estimates for other types of climate data.

  19. Quantifying Uncertainty in Spatio-temporal Forest Composition Changes Inferred from Fossil Pollen Records

    NASA Astrophysics Data System (ADS)

    Dawson, A.; Paciorek, C. J.; McLachlan, J. S.; Goring, S. J.; Williams, J. W.; Jackson, S. T.

    2014-12-01

    Understanding past compositional changes in vegetation provides insight about ecosystem dynamics in response to changing environments. Past vegetation reconstructions rely predominantly on fossil pollen data from sedimentary lake cores, which acts as a proxy record for the surrounding vegetation. Stratigraphic changes in these pollen records allow us to infer changes in composition and species distributions. Pollen records collected from a network of sites allow us to make inference about the spatio-temporal changes in vegetation over thousands of years. However, the complexity of the relationship between pollen deposits and surrounding vegetation, as well as the spatially sparse set of fossil pollen sites are important sources of uncertainty. In addition, uncertainty arises from the carbon dating and age-depth modelling processes. To reconstruct vegetation composition including uncertainty for the Upper Midwestern USA, we build a Bayesian hierarchical model that links vegetation composition to fossil pollen data via a dispersal model. In the calibration phase, we estimate the relationship between vegetation and pollen for the settlement era using Public Land Survey data and a network of pollen records. In the prediction phase, parameter estimates obtained during the calibration phase are used to estimate latent species distributions and relative abundances over the last 2500 years. We account for additional uncertainty in the pollen records by: allowing expert palynologists to identify pre-settlement pollen samples to be included in our calibration data, and through the incorporation of age uncertainty obtained from the Bayesian age-depth model BACON in our prediction data. Resulting spatio-temporal composition and abundance estimates will be used to improve forecasting capabilities of ecosystem models.

  20. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly-made proteins with complex topologies

    PubMed Central

    Yam, Alice Y.; Xia, Yu; Jill Lin, Hen-Tzu; Burlingame, Alma; Gerstein, Mark; Frydman, Judith

    2008-01-01

    Folding within the crowded cellular milieu often requires assistance from molecular chaperones that prevent inappropriate interactions leading to aggregation and toxicity. The contribution of individual chaperones to folding the proteome remains elusive. We here demonstrate that the eukaryotic chaperonin TRiC/CCT (TCP1-Ring Complex or Chaperonin Containing TCP1) has broad binding specificity in vitro similar to the prokaryotic chaperonin GroEL. However, in vivo TRiC substrate selection is not based solely on intrinsic determinants; instead, specificity is dictated by factors present during protein biogenesis. The identification of cellular substrates revealed that TRiC interacts with folding intermediates of a subset of structurally and functionally diverse polypeptides. Bioinformatics analysis revealed an enrichment in multidomain proteins and regions of beta strand propensity that are predicted to be slow-folding and aggregation-prone. Thus, TRiC may have evolved to protect complex protein topologies within its central cavity during biosynthesis and folding. PMID:19011634

  1. Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective

    PubMed Central

    Zanzoni, Andreas; Chapple, Charles E.; Brun, Christine

    2015-01-01

    Moonlighting proteins are a subset of multifunctional proteins characterized by their multiple, independent, and unrelated biological functions. We recently set up a large-scale identification of moonlighting proteins using a protein-protein interaction (PPI) network approach. We established that 3% of the current human interactome is composed of predicted moonlighting proteins. We found that disease-related genes are over-represented among those candidates. Here, by comparing moonlighting candidates to non-candidates as groups, we further show that (i) they are significantly involved in more than one disease, (ii) they contribute to complex rather than monogenic diseases, (iii) the diseases in which they are involved are phenotypically different according to their annotations, finally, (iv) they are enriched for diseases pairs showing statistically significant comorbidity patterns based on Medicare records. Altogether, our results suggest that some observed comorbidities between phenotypically different diseases could be due to a shared protein involved in unrelated biological processes.

  2. A novel multiresolution spatiotemporal saliency detection model and its applications in image and video compression.

    PubMed

    Guo, Chenlei; Zhang, Liming

    2010-01-01

    Salient areas in natural scenes are generally regarded as areas which the human eye will typically focus on, and finding these areas is the key step in object detection. In computer vision, many models have been proposed to simulate the behavior of eyes such as SaliencyToolBox (STB), Neuromorphic Vision Toolkit (NVT), and others, but they demand high computational cost and computing useful results mostly relies on their choice of parameters. Although some region-based approaches were proposed to reduce the computational complexity of feature maps, these approaches still were not able to work in real time. Recently, a simple and fast approach called spectral residual (SR) was proposed, which uses the SR of the amplitude spectrum to calculate the image's saliency map. However, in our previous work, we pointed out that it is the phase spectrum, not the amplitude spectrum, of an image's Fourier transform that is key to calculating the location of salient areas, and proposed the phase spectrum of Fourier transform (PFT) model. In this paper, we present a quaternion representation of an image which is composed of intensity, color, and motion features. Based on the principle of PFT, a novel multiresolution spatiotemporal saliency detection model called phase spectrum of quaternion Fourier transform (PQFT) is proposed in this paper to calculate the spatiotemporal saliency map of an image by its quaternion representation. Distinct from other models, the added motion dimension allows the phase spectrum to represent spatiotemporal saliency in order to perform attention selection not only for images but also for videos. In addition, the PQFT model can compute the saliency map of an image under various resolutions from coarse to fine. Therefore, the hierarchical selectivity (HS) framework based on the PQFT model is introduced here to construct the tree structure representation of an image. With the help of HS, a model called multiresolution wavelet domain foveation (MWDF) is proposed in this paper to improve coding efficiency in image and video compression. Extensive tests of videos, natural images, and psychological patterns show that the proposed PQFT model is more effective in saliency detection and can predict eye fixations better than other state-of-the-art models in previous literature. Moreover, our model requires low computational cost and, therefore, can work in real time. Additional experiments on image and video compression show that the HS-MWDF model can achieve higher compression rate than the traditional model. PMID:19709976

  3. Nature of spatiotemporal light bullets in bulk Kerr media.

    PubMed

    Majus, D; Tamošauskas, G; Gražulevi?i?t?, I; Garejev, N; Lotti, A; Couairon, A; Faccio, D; Dubietis, A

    2014-05-16

    We present a detailed experimental investigation which uncovers the nature of light bullets generated from self-focusing in a bulk dielectric medium with Kerr nonlinearity in the anomalous group velocity dispersion regime. By high dynamic range measurements of three-dimensional intensity profiles, we demonstrate that the light bullets consist of a sharply localized high-intensity core, which carries the self-compressed pulse and contains approximately 25% of the total energy, and a ring-shaped spatiotemporal periphery. Subdiffractive propagation along with dispersive broadening of the light bullets in free space after they exit the nonlinear medium indicate a strong space-time coupling within the bullet. This finding is confirmed by measurements of a spatiotemporal energy density flux that exhibits the same features as a stationary, polychromatic Bessel beam, thus highlighting the nature of the light bullets. PMID:24877940

  4. Spatiotemporal Chaotic unjamming and jamming in granular avalanches

    E-print Network

    Ziwei Wang; Jie Zhang

    2014-10-23

    We have investigated the spatiotemporal chaotic dynamics of unjamming and jamming of particles in a toy-model system -- a rotating drum partially filled with bidisperse disks to create avalanches. The magnitudes of the first Lyapunov vector $\\delta u(t)$ and velocity $v(t)$ of particles are directly measured for the first time to yield insights into their spatial correlation $C_{\\delta u,v}$, which is stronger near the unjamming but is weaker near the jamming transition, consistent with the recent work of Banigan et al., Nature Phys. $\\bf{9}$, 288, (2013). $v(t)$ shows rich dynamics: it grows exponentially for unstable particles and keeps increasing despite stochastic interactions; after the maximum, it decays with large fluctuations. Hence the spatiotemporal chaotic dynamics of avalanche particles are entangled, causing temporal correlations of macroscopic quantities of the system. We propose a simple model for these observations.

  5. Kalman filter control of a model of spatiotemporal cortical dynamics

    PubMed Central

    Schiff, Steven J; Sauer, Tim

    2007-01-01

    Recent advances in Kalman filtering to estimate system state and parameters in nonlinear systems have offered the potential to apply such approaches to spatiotemporal nonlinear systems. We here adapt the nonlinear method of unscented Kalman filtering to observe the state and estimate parameters in a computational spatiotemporal excitable system that serves as a model for cerebral cortex. We demonstrate the ability to track spiral wave dynamics, and to use an observer system to calculate control signals delivered through applied electrical fields. We demonstrate how this strategy can control the frequency of such a system, or quench the wave patterns, while minimizing the energy required for such results. These findings are readily testable in experimental applications, and have the potential to be applied to the treatment of human disease. PMID:18310806

  6. Identification of nonlinear spatiotemporal systems via partitioned filtering

    NASA Astrophysics Data System (ADS)

    Voss, H. U.; Sitz, A.; Kurths, J.

    2003-04-01

    The problem of simultaneous estimation of parameters and unobserved states from noisy time series and spatiotemporal data sets of nonlinear dynamical systems is considered. It is examined how the recently developed statistical method of unscented Kalman filtering can be utilized in solving this problem. Due to its recursive and derivative-free structure, this method minimizes the cost function in a computationally efficient and robust way. However, for spatiotemporal systems this problem is determined by its computational complexity, rendering the straightforward application of recursive filtering infeasible. An approximate solution is proposed by means of nonlinear state space filtering along with a state partition technique. The method is demonstrated on the application to one component of simulated chaotic data of a two-component reaction diffusion system, yielding estimates of both the unobserved state component and the diffusion constant.

  7. Proteomic profiling of the TRAF3 interactome network reveals a new role for the ER-to-Golgi transport compartments in innate immunity.

    PubMed

    van Zuylen, Wendy J; Doyon, Priscilla; Clément, Jean-François; Khan, Kashif Aziz; D'Ambrosio, Lisa M; Dô, Florence; St-Amant-Verret, Myriam; Wissanji, Tasheen; Emery, Gregory; Gingras, Anne-Claude; Meloche, Sylvain; Servant, Marc J

    2012-01-01

    Tumor Necrosis Factor receptor-associated factor-3 (TRAF3) is a central mediator important for inducing type I interferon (IFN) production in response to intracellular double-stranded RNA (dsRNA). Here, we report the identification of Sec16A and p115, two proteins of the ER-to-Golgi vesicular transport system, as novel components of the TRAF3 interactome network. Notably, in non-infected cells, TRAF3 was found associated with markers of the ER-Exit-Sites (ERES), ER-to-Golgi intermediate compartment (ERGIC) and the cis-Golgi apparatus. Upon dsRNA and dsDNA sensing however, the Golgi apparatus fragmented into cytoplasmic punctated structures containing TRAF3 allowing its colocalization and interaction with Mitochondrial AntiViral Signaling (MAVS), the essential mitochondria-bound RIG-I-like Helicase (RLH) adaptor. In contrast, retention of TRAF3 at the ER-to-Golgi vesicular transport system blunted the ability of TRAF3 to interact with MAVS upon viral infection and consequently decreased type I IFN response. Moreover, depletion of Sec16A and p115 led to a drastic disorganization of the Golgi paralleled by the relocalization of TRAF3, which under these conditions was unable to associate with MAVS. Consequently, upon dsRNA and dsDNA sensing, ablation of Sec16A and p115 was found to inhibit IRF3 activation and anti-viral gene expression. Reciprocally, mild overexpression of Sec16A or p115 in Hec1B cells increased the activation of IFN?, ISG56 and NF-?B -dependent promoters following viral infection and ectopic expression of MAVS and Tank-binding kinase-1 (TBK1). In line with these results, TRAF3 was found enriched in immunocomplexes composed of p115, Sec16A and TBK1 upon infection. Hence, we propose a model where dsDNA and dsRNA sensing induces the formation of membrane-bound compartments originating from the Golgi, which mediate the dynamic association of TRAF3 with MAVS leading to an optimal induction of innate immune responses. PMID:22792062

  8. Proteomic Profiling of the TRAF3 Interactome Network Reveals a New Role for the ER-to-Golgi Transport Compartments in Innate Immunity

    PubMed Central

    Khan, Kashif Aziz; D'Ambrosio, Lisa M.; Dô, Florence; St-Amant-Verret, Myriam; Wissanji, Tasheen; Emery, Gregory; Gingras, Anne-Claude; Meloche, Sylvain; Servant, Marc J.

    2012-01-01

    Tumor Necrosis Factor receptor-associated factor-3 (TRAF3) is a central mediator important for inducing type I interferon (IFN) production in response to intracellular double-stranded RNA (dsRNA). Here, we report the identification of Sec16A and p115, two proteins of the ER-to-Golgi vesicular transport system, as novel components of the TRAF3 interactome network. Notably, in non-infected cells, TRAF3 was found associated with markers of the ER-Exit-Sites (ERES), ER-to-Golgi intermediate compartment (ERGIC) and the cis-Golgi apparatus. Upon dsRNA and dsDNA sensing however, the Golgi apparatus fragmented into cytoplasmic punctated structures containing TRAF3 allowing its colocalization and interaction with Mitochondrial AntiViral Signaling (MAVS), the essential mitochondria-bound RIG-I-like Helicase (RLH) adaptor. In contrast, retention of TRAF3 at the ER-to-Golgi vesicular transport system blunted the ability of TRAF3 to interact with MAVS upon viral infection and consequently decreased type I IFN response. Moreover, depletion of Sec16A and p115 led to a drastic disorganization of the Golgi paralleled by the relocalization of TRAF3, which under these conditions was unable to associate with MAVS. Consequently, upon dsRNA and dsDNA sensing, ablation of Sec16A and p115 was found to inhibit IRF3 activation and anti-viral gene expression. Reciprocally, mild overexpression of Sec16A or p115 in Hec1B cells increased the activation of IFN?, ISG56 and NF-?B -dependent promoters following viral infection and ectopic expression of MAVS and Tank-binding kinase-1 (TBK1). In line with these results, TRAF3 was found enriched in immunocomplexes composed of p115, Sec16A and TBK1 upon infection. Hence, we propose a model where dsDNA and dsRNA sensing induces the formation of membrane-bound compartments originating from the Golgi, which mediate the dynamic association of TRAF3 with MAVS leading to an optimal induction of innate immune responses. PMID:22792062

  9. Three dimensional electromagnetic wavepackets in a plasma: Spatiotemporal modulational instability

    SciTech Connect

    Borhanian, J.; Hosseini Faradonbe, F. [Department of Physics, Faculty of Science, University of Mohaghegh Ardabili, P. O. Box 179, Ardabil (Iran, Islamic Republic of)] [Department of Physics, Faculty of Science, University of Mohaghegh Ardabili, P. O. Box 179, Ardabil (Iran, Islamic Republic of)

    2014-04-15

    The nonlinear interaction of an intense electromagnetic beam with relativistic collisionless unmagnetized plasma is investigated by invoking the reductive perturbation technique, resting on the model of three-dimensional nonlinear Schrödinger (NLS) equation with cubic nonlinearity which incorporates the effects of self-focusing, self-phase modulation, and diffraction on wave propagation. Relying on the derived NLS equation, the occurrence of spatiotemporal modulational instability is investigated in detail.

  10. Spatiotemporal causal modeling for the management of Dengue Fever

    NASA Astrophysics Data System (ADS)

    Yu, Hwa-Lung; Huang, Tailin; Lee, Chieh-Han

    2015-04-01

    Increasing climatic extremes have caused growing concerns about the health effects and disease outbreaks. The association between climate variation and the occurrence of epidemic diseases play an important role on a country's public health systems. Part of the impacts are direct casualties associated with the increasing frequency and intensity of typhoons, the proliferation of disease vectors and the short-term increase of clinic visits on gastro-intestinal discomforts, diarrhea, dermatosis, or psychological trauma. Other impacts come indirectly from the influence of disasters on the ecological and socio-economic systems, including the changes of air/water quality, living environment and employment condition. Previous risk assessment studies on dengue fever focus mostly on climatic and non-climatic factors and their association with vectors' reproducing pattern. The public-health implication may appear simple. Considering the seasonal changes and regional differences, however, the causality of the impacts is full of uncertainties. Without further investigation, the underlying dengue fever risk dynamics may not be assessed accurately. The objective of this study is to develop an epistemic framework for assessing dynamic dengue fever risk across space and time. The proposed framework integrates cross-departmental data, including public-health databases, precipitation data over time and various socio-economic data. We explore public-health issues induced by typhoon through literature review and spatiotemporal analytic techniques on public health databases. From those data, we identify relevant variables and possible causal relationships, and their spatiotemporal patterns derived from our proposed spatiotemporal techniques. Eventually, we create a spatiotemporal causal network and a framework for modeling dynamic dengue fever risk.

  11. Spatiotemporal energy models for the perception of motion

    Microsoft Academic Search

    E. H. Adelson; J. R. Bergen

    1985-01-01

    A motion sequence may be represented as a single pattern in x-y-t space; a velocity of motion corresponds to a three-dimensional orientation in this space. Motion information can be extracted by a system that responds to the oriented spatiotemporal energy. We discuss a class of models for human motion mechanisms in which the first stage consists of linear filters that

  12. Time reversal and the spatio-temporal matched filter

    Microsoft Academic Search

    S K Lehman; A J Poggio; J S Kallman; A W Meyer; J V Candy

    2004-01-01

    It is known that focusing of an acoustic field by a time-reversal mirror (TRM) is equivalent to a spatio-temporal matched filter under conditions where the Green's function of the field satisfies reciprocity and is time invariant, i.e. the Green's function is independent of the choice of time origin. In this letter, it is shown that both reciprocity and time invariance

  13. Spatiotemporal energy models for the perception of motion

    Microsoft Academic Search

    Edward H. Adelson; James R. Bergen

    2002-01-01

    A motion sequence may be represented as a single pattern in x-y-t space; a velocity of motion corresponds to a three-dimensional orientation in this space. Motion sinformation can be extracted by a system that responds to the oriented spatiotemporal energy. We discuss a class of models for human motion mechanisms in which the first stage consists of linear filters that

  14. Spatio-temporal Filtering for Fetal QRS Enhancement

    Microsoft Academic Search

    M. Kotas; J. Je?ewski; A. Matonia; T. Kupka

    \\u000a We propose a new approach to maternal ECG suppression and fetal QRS detection in the multi-channel maternal abdominal bioelectric\\u000a signals. First, a single-channel method based on template subtraction is applied to suppress the maternal ECG in the respective\\u000a channels. Then we use spatial or spatio-temporal filtering to enhance the fetal QRS complexes. Finally, the QRS detection\\u000a is performed. In the

  15. Spatio-Temporal Measurements of Short Wind Water Waves

    Microsoft Academic Search

    Roland Rocholz; Bernd Jähne

    2010-01-01

    Spatio-temporal measurements of wind-driven short-gravity capillary waves are reported for a wide range of experimental conditions, including wind, rain and surface slicks. The experiments were conducted in the Hamburg linear wind\\/wave flume in cooperation with the Institute of Oceanography at the University of Hamburg, Germany. Both components of the slope field were measured optically at a fetch of 14.4 m

  16. Spatio-temporal variability of the North Sea cod recruitment in relation to temperature and zooplankton.

    PubMed

    Nicolas, Delphine; Rochette, Sébastien; Llope, Marcos; Licandro, Priscilla

    2014-01-01

    The North Sea cod (Gadus morhua, L.) stock has continuously declined over the past four decades linked with overfishing and climate change. Changes in stock structure due to overfishing have made the stock largely dependent on its recruitment success, which greatly relies on environmental conditions. Here we focus on the spatio-temporal variability of cod recruitment in an effort to detect changes during the critical early life stages. Using International Bottom Trawl Survey (IBTS) data from 1974 to 2011, a major spatio-temporal change in the distribution of cod recruits was identified in the late 1990s, characterized by a pronounced decrease in the central and southeastern North Sea stock. Other minor spatial changes were also recorded in the mid-1980s and early 1990s. We tested whether the observed changes in recruits distribution could be related with direct (i.e. temperature) and/or indirect (i.e. changes in the quantity and quality of zooplankton prey) effects of climate variability. The analyses were based on spatially-resolved time series, i.e. sea surface temperature (SST) from the Hadley Center and zooplankton records from the Continuous Plankton Recorder Survey. We showed that spring SST increase was the main driver for the most recent decrease in cod recruitment. The late 1990s were also characterized by relatively low total zooplankton biomass, particularly of energy-rich zooplankton such as the copepod Calanus finmarchicus, which have further contributed to the decline of North Sea cod recruitment. Long-term spatially-resolved observations were used to produce regional distribution models that could further be used to predict the abundance of North Sea cod recruits based on temperature and zooplankton food availability. PMID:24551103

  17. Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver

    PubMed Central

    Schwen, Lars Ole; Krauss, Markus; Niederalt, Christoph; Gremse, Felix; Kiessling, Fabian; Schenk, Andrea; Preusser, Tobias; Kuepfer, Lars

    2014-01-01

    The liver is the central organ for detoxification of xenobiotics in the body. In pharmacokinetic modeling, hepatic metabolization capacity is typically quantified as hepatic clearance computed as degradation in well-stirred compartments. This is an accurate mechanistic description once a quasi-equilibrium between blood and surrounding tissue is established. However, this model structure cannot be used to simulate spatio-temporal distribution during the first instants after drug injection. In this paper, we introduce a new spatially resolved model to simulate first pass perfusion of compounds within the naive liver. The model is based on vascular structures obtained from computed tomography as well as physiologically based mass transfer descriptions obtained from pharmacokinetic modeling. The physiological architecture of hepatic tissue in our model is governed by both vascular geometry and the composition of the connecting hepatic tissue. In particular, we here consider locally distributed mass flow in liver tissue instead of considering well-stirred compartments. Experimentally, the model structure corresponds to an isolated perfused liver and provides an ideal platform to address first pass effects and questions of hepatic heterogeneity. The model was evaluated for three exemplary compounds covering key aspects of perfusion, distribution and metabolization within the liver. As pathophysiological states we considered the influence of steatosis and carbon tetrachloride-induced liver necrosis on total hepatic distribution and metabolic capacity. Notably, we found that our computational predictions are in qualitative agreement with previously published experimental data. The simulation results provide an unprecedented level of detail in compound concentration profiles during first pass perfusion, both spatio-temporally in liver tissue itself and temporally in the outflowing blood. We expect our model to be the foundation of further spatially resolved models of the liver in the future. PMID:24625393

  18. Spatiotemporal distributions of tsunami sources and discovered periodicities

    NASA Astrophysics Data System (ADS)

    Levin, B. W.; Sasorova, E. V.

    2014-09-01

    Both spatial and spatiotemporal distributions of the sources of tsunamigenic earthquakes of tectonic origin over the last 112 years have been analyzed. This analysis has been made using tsunami databases published by the Institute of Computational Mathematics and Mathematical Geophysics (Siberian Branch, Russian Academy of Sciences) and the National Aeronautics and Space Administration (United States), as well as earthquake catalogs published by the National Earthquake Information Center (United States). It has been found that the pronounced activation of seismic processes and an increase in the total energy of tsunamigenic earthquakes were observed at the beginning of both the 20th (1905-1920) and 21st (2004-2011) centuries. Studying the spatiotemporal periodicity of such events on the basis of an analysis of the two-dimensional distributions of the sources of tectonic tsunamis has made it possible to determine localized latitudinal zones with a total lack of such events (90°-75° N, 45°-90° S, and 35°-25° N) and regions with a periodic occurrence of tsunamis mainly within the middle (65°-35° N and 25°-40° S) and subequatorial (15° N-20° S) latitudes of the Northern and Southern hemispheres. The objective of this work is to analyze the spatiotemporal distributions of sources of tsunamigenic earthquakes and the effect of the periodic occurrence of such events on the basis of data taken from global tsunami catalogs.

  19. Spatiotemporal Variations in the Fire Regimes of Whitebark Pine (Pinus albicaulis Engelm.) Forests, Western Montana, USA,

    E-print Network

    Grissino-Mayer, Henri D.

    Spatiotemporal Variations in the Fire Regimes of Whitebark Pine (Pinus albicaulis Engelm.) Forests Change Research Group at the University of Tennessee. #12;v Abstract Whitebark pine (Pinus albicaulis

  20. Structure-based algorithms for protein-protein interaction prediction

    E-print Network

    Hosur, Raghavendra

    2012-01-01

    Protein-protein interactions (PPIs) play a central role in all biological processes. Akin to the complete sequencing of genomes, complete descriptions of interactomes is a fundamental step towards a deeper understanding ...

  1. Spatiotemporal Dynamics of Dengue Epidemics, Southern Vietnam

    PubMed Central

    Cuong, Hoang Quoc; Vu, Nguyen Thanh; Cazelles, Bernard; Boni, Maciej F.; Thai, Khoa T.D.; Rabaa, Maia A.; Quang, Luong Chan; Simmons, Cameron P.; Huu, Tran Ngoc

    2013-01-01

    An improved understanding of heterogeneities in dengue virus transmission might provide insights into biological and ecologic drivers and facilitate predictions of the magnitude, timing, and location of future dengue epidemics. To investigate dengue dynamics in urban Ho Chi Minh City and neighboring rural provinces in Vietnam, we analyzed a 10-year monthly time series of dengue surveillance data from southern Vietnam. The per capita incidence of dengue was lower in Ho Chi Minh City than in most rural provinces; annual epidemics occurred 1–3 months later in Ho Chi Minh City than elsewhere. The timing and the magnitude of annual epidemics were significantly more correlated in nearby districts than in remote districts, suggesting that local biological and ecologic drivers operate at a scale of 50–100 km. Dengue incidence during the dry season accounted for 63% of variability in epidemic magnitude. These findings can aid the targeting of vector-control interventions and the planning for dengue vaccine implementation. PMID:23735713

  2. SPATIOTEMPORAL MODELING SEPARABILITY NONSEPARABILITY IRISH WIND DATA EXTENDING THE MODEL CONCLUSIONS MODELOS ESPACO-TEMPORAIS N ~AO

    E-print Network

    Liu, I-Shih

    SPATIOTEMPORAL MODELING SEPARABILITY NONSEPARABILITY IRISH WIND DATA EXTENDING THE MODEL SEPARABILITY NONSEPARABILITY IRISH WIND DATA EXTENDING THE MODEL CONCLUSIONS 1 SPATIOTEMPORAL MODELING Introduction Covariance modeling 2 SEPARABILITY Properties and definition 3 NONSEPARABILITY Mixture approach

  3. Spatiotemporal Patterns of Evapotranspiration in Response to Multiple Environmental Factors Simulated by the Community Land Model

    SciTech Connect

    Shi, Xiaoying; Mao, Jiafu; Thornton, P.; Huang, Maoyi

    2013-04-25

    Spatiotemporal patterns of evapotranspiration (ET) over the period from 1982 to 2008 are investigated and attributed to multiple environmental factors using the Community Land Model version 4 (CLM4). Our results show that CLM4 captures the spatial distribution and interannual variability of ET well when compared to observation-based estimates. We find that climate dominates the predicted variability in ET. Elevated atmospheric CO2 concentration also plays an important role in modulating the trend of predicted ET over most land areas, and replaces climate to function as the dominant factor controlling ET changes over the North America, South America and Asia regions. Compared to the effect of climate and CO2 concentration, the roles of other factors such as nitrogen deposition, land use change and aerosol deposition are less pronounced and regionally dependent. The aerosol deposition contribution is the third most important factor for trends of ET over Europe, while it has the smallest impact over other regions. As ET is a dominant component of the terrestrial water cycle, our results suggest that environmental factors like elevated CO2, nitrogen and aerosol depositions, and land use change, in addition to climate, could have significant impact on future projections of water resources and water cycle dynamics at global and regional scales.

  4. Spatiotemporal Patterns of Urban Human Mobility

    NASA Astrophysics Data System (ADS)

    Hasan, Samiul; Schneider, Christian M.; Ukkusuri, Satish V.; González, Marta C.

    2013-04-01

    The modeling of human mobility is adopting new directions due to the increasing availability of big data sources from human activity. These sources enclose digital information about daily visited locations of a large number of individuals. Examples of these data include: mobile phone calls, credit card transactions, bank notes dispersal, check-ins in internet applications, among several others. In this study, we consider the data obtained from smart subway fare card transactions to characterize and model urban mobility patterns. We present a simple mobility model for predicting peoples' visited locations using the popularity of places in the city as an interaction parameter between different individuals. This ingredient is sufficient to reproduce several characteristics of the observed travel behavior such as: the number of trips between different locations in the city, the exploration of new places and the frequency of individual visits of a particular location. Moreover, we indicate the limitations of the proposed model and discuss open questions in the current state of the art statistical models of human mobility.

  5. Spatiotemporal wavelet analysis for functional MRI Chris Long,a,* Emery N. Brown,b,c

    E-print Network

    Manoach, Dara S.

    Spatiotemporal wavelet analysis for functional MRI Chris Long,a,* Emery N. Brown,b,c Dara Manoach in their statistical formulations. To address these issues, we present a novel spatiotemporal wavelet procedure that uses a stimulus-convolved hemodynamic signal plus correlated noise model. The wavelet fits, computed

  6. Improving spatiotemporal resolution of USPIO-enhanced dynamic imaging of rat kidneys

    E-print Network

    Moura, José

    Improving spatiotemporal resolution of USPIO-enhanced dynamic imaging of rat kidneys Ying Suna spatiotemporal resolution of ultra-small superparamagnetic iron oxide (USPIO)-enhanced dynamic MRI of rat kidneys possible using USPIO-enhanced dynamic imaging of rat kidneys, and prove valuable for early detection

  7. Scale-free model for spatio-temporal distribution of outbreaks of avian influenza

    E-print Network

    Tse, Chi K. "Michael"

    Scale-free model for spatio-temporal distribution of outbreaks of avian influenza Michael Small influenza outbreaks among wild and domestic birds, we show that this model is not appropriate. We find the global spatio-temporal distribution of avian influenza cases in both wild and domestic birds and find

  8. Intro Temporal Tests Declustering Methods Tests on SCEC data Spatiotemporal Test Discussion Testing for Poisson Behavior

    E-print Network

    Stark, Philip B.

    Intro Temporal Tests Declustering Methods Tests on SCEC data Spatiotemporal Test Discussion Testing Seismological Society of America Annual Meeting San Diego, CA #12;Intro Temporal Tests Declustering Methods Tests on SCEC data Spatiotemporal Test Discussion Quake Physics versus Quake Statistics · Distribution

  9. A hypercube-based data structure for spatio-temporal exploration and analysis

    E-print Network

    1 A hypercube-based data structure for spatio-temporal exploration and analysis Pierre Marchand database (MDDB) approach to support spatio-temporal data exploration and analysis (STEA). MDDB STEA can be achieved. We thus propose a new data structure which implements a spatio- temporal

  10. A SURF-based Spatio-Temporal Feature for Feature-fusion-based

    E-print Network

    Yanai, Keiji

    A SURF-based Spatio-Temporal Feature for Feature-fusion-based Action Recognition #12;1. Background to ­ sparse Spatio-Temporal (ST) features SURF-based new ST feature using Delauney triangulation ­ temporally motion features and intermediate ST features SURF-based new ST features Temporally-dense sampling

  11. TELEGEOMATIC SYSTEM AND REAL TIME SPATIO-TEMPORAL DATABASE Sylvie SERVIGNE *, Tullio TANZI**, Guillaume NOEL*

    E-print Network

    Servigne, Sylvie

    TELEGEOMATIC SYSTEM AND REAL TIME SPATIO-TEMPORAL DATABASE Sylvie SERVIGNE *, Tullio TANZI processing systems able to exploit spatio- temporal and real time data. These data are issued from sensors spatio-temporal and real time data. These data are issued from sensors and fixed or mobile systems

  12. A Spatiotemporal Saliency Model for Video Surveillance Tong Yubing Faouzi Alaya Cheikh

    E-print Network

    Paris-Sud XI, Université de

    A Spatiotemporal Saliency Model for Video Surveillance Tong Yubing · Faouzi Alaya Cheikh · Fahad sequences and propose a novel spatiotemporal saliency model devoted for video surveillance applications. Com models, the proposed model is more correlated to visual saliency per- ception of surveillance videos

  13. Spatiotemporal variation in range-wide Golden-cheeked Warbler breeding habitat

    E-print Network

    Weckerly, Floyd "Butch" - Department of Biology, Texas State University

    Spatiotemporal variation in range-wide Golden-cheeked Warbler breeding habitat ADAM DUARTE,1. Spatiotemporal variation in range-wide Golden-cheeked Warbler breeding habitat. Ecosphere 4(12):152. http quantified the degree of change in range-wide breeding habitat for the Golden-cheeked Warbler (Setophaga

  14. Spatiotemporal mapping of visual attention CerCo, UPS, Universit de Toulouse III, Toulouse, France, &

    E-print Network

    VanRullen, Rufin

    mapping of exogenous attention revealed a significant enhancement zone from 150 to 430 ms, extending up across time. Our results represent the first detailed spatiotemporal maps of both endogenousSpatiotemporal mapping of visual attention CerCo, UPS, Université de Toulouse III, Toulouse, France

  15. Enhancement of peak intensity in a filament core with spatiotemporally focused femtosecond laser pulses

    SciTech Connect

    Zeng Bin; Chu Wei; Li Guihua; Zhang Haisu; Ni Jielei [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China); Graduate School of Chinese Academy of Sciences, Beijing 100080 (China); Gao Hui; Liu Weiwei [Institute of Modern Optics, Nankai University, Tianjin, 300071 (China); Yao Jinping; Cheng Ya; Xu Zhizhan [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China); Chin, See Leang [Center for Optics, Photonics and Laser (COPL) and Department of Physics, Engineering Physics and Optics, Universite Laval, Quebec City, QC, G1V 0A6 (Canada)

    2011-12-15

    We demonstrate that the peak intensity in the filament core, which is inherently limited by the intensity clamping effect during femtosecond laser filamentation, can be significantly enhanced using spatiotemporally focused femtosecond laser pulses. In addition, the filament length obtained by spatiotemporally focused femtosecond laser pulses is {approx}25 times shorter than that obtained by a conventional focusing scheme, resulting in improved high spatial resolution.

  16. A Spatio-Temporal Memory Based on SOMs with Activity Diffusion Neil R. Eulianoa

    E-print Network

    Slatton, Clint

    A Spatio-Temporal Memory Based on SOMs with Activity Diffusion Neil R. Eulianoa and Jose CEngineering Laboratory, University of Florida Gainesville, FL 32611 This paper discusses the use of the biologically inspired concept of activity diffusion to create a spatio-temporal memory in the SOM and neural gas

  17. Data Repository Spatiotemporal trends in erosion rates across a pronounced rainfall

    E-print Network

    Bookhagen, Bodo

    Data Repository Spatiotemporal trends in erosion rates across a pronounced rainfall gradient. Bookhagen and M.R. Strecker: Spatiotemporal trends in erosion rates Note that the overall rainfall pattern is similar; however, the steep rainfall gradient is more accurately captured by the TRMM 2B31 (A) data. 5

  18. The spatiotemporal organization of cerebellar network activity resolved by two-photon imaging of multiple single neurons

    PubMed Central

    Gandolfi, Daniela; Pozzi, Paolo; Tognolina, Marialuisa; Chirico, Giuseppe; Mapelli, Jonathan; D'Angelo, Egidio

    2014-01-01

    In order to investigate the spatiotemporal organization of neuronal activity in local microcircuits, techniques allowing the simultaneous recording from multiple single neurons are required. To this end, we implemented an advanced spatial-light modulator two-photon microscope (SLM-2PM). A critical issue for cerebellar theory is the organization of granular layer activity in the cerebellum, which has been predicted by single-cell recordings and computational models. With SLM-2PM, calcium signals could be recorded from different network elements in acute cerebellar slices including granule cells (GrCs), Purkinje cells (PCs) and molecular layer interneurons. By combining WCRs with SLM-2PM, the spike/calcium relationship in GrCs and PCs could be extrapolated toward the detection of single spikes. The SLM-2PM technique made it possible to monitor activity of over tens to hundreds neurons simultaneously. GrC activity depended on the number of spikes in the input mossy fiber bursts. PC and molecular layer interneuron activity paralleled that in the underlying GrC population revealing the spread of activity through the cerebellar cortical network. Moreover, circuit activity was increased by the GABA-A receptor blocker, gabazine, and reduced by the AMPA and NMDA receptor blockers, NBQX and APV. The SLM-2PM analysis of spatiotemporal patterns lent experimental support to the time-window and center-surround organizing principles of the granular layer. PMID:24782707

  19. Traffic dynamics in empirical probe vehicle data studied with three-phase theory: Spatiotemporal reconstruction of traffic phases and generation of jam warning messages

    NASA Astrophysics Data System (ADS)

    Kerner, Boris S.; Rehborn, Hubert; Schäfer, Ralf-Peter; Klenov, Sergey L.; Palmer, Jochen; Lorkowski, Stefan; Witte, Nikolaus

    2013-01-01

    Empirical and theoretical analyses of the spatiotemporal dynamics of traffic flow reconstructed from randomly distributed probe vehicle data are presented. For the empirical analysis, probe vehicle data generated by TomTom’s navigation devices in the commercial TomTom’s HD-traffic service as well as road detector data measured at the same road section are used. A stochastic microscopic (car-following) three-phase model is further developed for simulations of a real empirical complex spatiotemporal traffic dynamics measured over a three-lane long road stretch with several different bottlenecks. Physical features and limitations of simulations of real spatiotemporal traffic dynamics are revealed. Phase transition points between free flow (F), synchronized flow (S), and wide moving jam (J) are identified along trajectories of empirical and simulated probe vehicles randomly distributed in traffic flow. As predicted by three-phase theory, the empirical probe vehicle data shows that traffic breakdown is an F?S transition and wide moving jams emerge only in synchronized flow, i.e., due to S?J transitions. Through the use of the simulations, it has been found that already about 2% of probe vehicle data allows us to reconstruct traffic dynamics in space and time with an accuracy that is high enough for most applications like the generation of jam warning messages studied in the article.

  20. Spatiotemporal Patterns of Japanese Encephalitis in China, 2002–2010

    PubMed Central

    Sun, Hai-Long; Li, Yi-Xing; Zou, Wen; Wang, Yong; Liu, Qi-Yong; Li, Shen-Long; Yin, Wen-Wu; Huang, Liu-Yu; Clements, Archie C. A.; Bi, Peng; Li, Cheng-Yi

    2013-01-01

    Objective The aim of the study is to examine the spatiotemporal pattern of Japanese Encephalitis (JE) in mainland China during 2002–2010. Specific objectives of the study were to quantify the temporal variation in incidence of JE cases, to determine if clustering of JE cases exists, to detect high risk spatiotemporal clusters of JE cases and to provide evidence-based preventive suggestions to relevant stakeholders. Methods Monthly JE cases at the county level in mainland China during 2002–2010 were obtained from the China Information System for Diseases Control and Prevention (CISDCP). For the purpose of the analysis, JE case counts for nine years were aggregated into four temporal periods (2002; 2003–2005; 2006; and 2007–2010). Local Indicators of Spatial Association and spatial scan statistics were performed to detect and evaluate local high risk space-time clusters. Results JE incidence showed a decreasing trend from 2002 to 2005 but peaked in 2006, then fluctuated over the study period. Spatial cluster analysis detected high value clusters, mainly located in Southwestern China. Similarly, we identified a primary spatiotemporal cluster of JE in Southwestern China between July and August, with the geographical range of JE transmission increasing over the past years. Conclusion JE in China is geographically clustered and its spatial extent dynamically changed during the last nine years in mainland China. This indicates that risk factors for JE infection are likely to be spatially heterogeneous. The results may assist national and local health authorities in the development/refinement of a better preventive strategy and increase the effectiveness of public health interventions against JE transmission. PMID:23819000

  1. Refined estimate of China's CO2 emissions in spatiotemporal distributions

    NASA Astrophysics Data System (ADS)

    Liu, M.-M.; Wang, H.-K.; Wang, H.-M.; Oda, T.; Zhao, Y.; Yang, X.-H.; Zhang, R.-R.; Zhang, B.; Bi, J.; Chen, J.-M.

    2013-07-01

    Being the largest contributor to the global source of fossil-fuel CO2 emissions, China's emissions need to be accurately quantified and well understood. Previous studies have usually focused on the amount of national emissions and rarely discussed their spatiotemporal distributions, which are also crucial for both carbon flux and carbon management. In this study, we calculated China's CO2 emissions from fossil fuel use and industrial processes using provincial statistics and then mapped those emissions at 0.25° resolution on monthly basis. Several key steps have been implemented to gain a better understanding of the spatiotemporal distributions, including (1) development and application of China's CO2 emission inventories using provincial statistics; (2) separate calculations of emissions from large point sources and accurate identification of their geographical locations; (3) development of 1 km×1 km gridded population and GDP data for China from 2000 to 2009 and application of them as dynamic spatial proxies to allocate emissions; and (4) monthly variation curves of CO2 emissions from various sectors were developed for each province and applied to our inventory. China's total CO2 emission from fossil fuel and industrial process have increased from 3.6 billion tons in 2000 to 8.6 billion tons in 2009, which may be off by 14-18% and are enough to skew global totals. And the resulting spatiotemporal distributions of our inventories also differed greatly in several ways from those derived using national statistics and population-based approach for the various economic development levels, industrial and energy structures, and even large point emissions sources within China and each province.

  2. Refined estimate of China's CO2 emissions in spatiotemporal distributions

    NASA Astrophysics Data System (ADS)

    Liu, M.; Wang, H.; Wang, H.; Oda, T.; Zhao, Y.; Yang, X.; Zang, R.; Zang, B.; Bi, J.; Chen, J.

    2013-11-01

    Being the largest contributor to the global source of fossil-fuel CO2 emissions, China's emissions need to be accurately quantified and well understood. Previous studies have usually focused on the amount of national emissions and rarely discussed their spatiotemporal distributions, which are also crucial for both carbon flux and carbon management. In this study, we calculated China's CO2 emissions from fossil fuel use and industrial processes using provincial statistics and then mapped those emissions at 0.25° resolution on a monthly basis. Several key steps have been implemented to gain a better understanding of the spatiotemporal distributions, including (1) development and application of China's CO2 emission inventories using provincial statistics; (2) separate calculations of emissions from large point sources and accurate identification of their geographical locations; (3) development of 1 km × 1 km gridded population and GDP (gross domestic product) data for China from 2000 to 2009 and application of them as dynamic spatial proxies to allocate emissions; and (4) monthly variation curves of CO2 emissions from various sectors that were developed for each province and applied to our inventory. China's total CO2 emission from fossil fuels and industrial processes has increased from 3.6 billion tons in 2000 to 8.6 billion tons in 2009, which may be off by 14-18% and is enough to skew global totals. The resulting spatiotemporal distributions of our inventories also differed greatly in several ways from those derived using a national statistics and population-based approach for the various economic development levels, industrial and energy structures, and even large point emission sources within China and each province.

  3. Spatiotemporal modelling of ozone distribution in the State of California

    NASA Astrophysics Data System (ADS)

    Bogaert, P.; Christakos, G.; Jerrett, M.; Yu, H.-L.

    This paper is concerned with the spatiotemporal mapping of monthly 8-h average ozone ( O3) concentrations over California during a 15-years period. The basic methodology of our analysis is based on the spatiotemporal random field (S/TRF) theory. We use a S/TRF decomposition model with a dominant seasonal O3 component that may change significantly from site to site. O3 seasonal patterns are estimated and separated from stochastic fluctuations. By means of Bayesian Maximum Entropy (BME) analysis, physically meaningful and sufficiently detailed space-time maps of the seasonal O3 patterns are generated across space and time. During the summer and winter months the seasonal O3 concentration maps exhibit clear and progressively changing geographical patterns over time, suggesting the existence of relationships in accordance with the typical physiographic and climatologic features of California. BME mapping accuracy can be superior to that of other techniques commonly used by EPA; its framework can rigorously assimilate useful data sources that were previously unaccounted for; the generated maps offer valuable assessments of the spatiotemporal O3 patterns that can be helpful in the identification of physical mechanisms and their interrelations, the design of human exposure and population health models, and in risk assessment. As they focus on the seasonal patterns, the maps are not contingent on short-time and locally prevalent weather conditions, which are of no interest in a global and non-forecasting framework. Moreover, the maps offer valuable insight about the space-time O3 concentration patterns and are, thus, helpful for disentangling the influence of explanatory factors or even for identifying some influential ones that could have been otherwise overlooked.

  4. Spatio-temporal dynamics in the origin of genetic information

    NASA Astrophysics Data System (ADS)

    Kim, Pan-Jun; Jeong, Hawoong

    2005-04-01

    We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations, we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work, we also find that ‘hypercycle hybrid’ protects the hypercycle from its environment during the growth process. There is little selective advantage for one hypercycle to maintain coexistence with others. This brings the possibility of the outcompetition between hypercycles resulting in the negative effect on information diversity. To enrich the information in hypercycles, symbiosis with parasites is suggested. It is shown that symbiosis with parasites can play an important role in the prebiotic immunology.

  5. Spatiotemporal Dynamics of Phosphorylation in Lipid Second Messenger Signaling*

    PubMed Central

    Antal, Corina E.; Newton, Alexandra C.

    2013-01-01

    The plasma membrane serves as a dynamic interface that relays information received at the cell surface into the cell. Lipid second messengers coordinate signaling on this platform by recruiting and activating kinases and phosphatases. Specifically, diacylglycerol and phosphatidylinositol 3,4,5-trisphosphate activate protein kinase C and Akt, respectively, which then phosphorylate target proteins to transduce downstream signaling. This review addresses how the spatiotemporal dynamics of protein kinase C and Akt signaling can be monitored using genetically encoded reporters and provides information on how the coordination of signaling at protein scaffolds or membrane microdomains affords fidelity and specificity in phosphorylation events. PMID:23788531

  6. Spatiotemporal dynamics of dendritic spines in the living brain

    PubMed Central

    Chen, Chia-Chien; Lu, Ju; Zuo, Yi

    2014-01-01

    Dendritic spines are ubiquitous postsynaptic sites of most excitatory synapses in the mammalian brain, and thus may serve as structural indicators of functional synapses. Recent works have suggested that neuronal coding of memories may be associated with rapid alterations in spine formation and elimination. Technological advances have enabled researchers to study spine dynamics in vivo during development as well as under various physiological and pathological conditions. We believe that better understanding of the spatiotemporal patterns of spine dynamics will help elucidate the principles of experience-dependent circuit modification and information processing in the living brain. PMID:24847214

  7. Cellular automata model simulating complex spatiotemporal structure of wide jams.

    PubMed

    Li, Xiao-Bai; Jiang, Rui; Wu, Qing-Song

    2003-07-01

    According to the empirical observation of highway traffic, inside wide moving jams there is a complex spatiotemporal structure: jam is not compact and relatively large values of the time and the distance headway are visible. We present a cellular automata model by introducing "jam headway" and "jammed status" to simulate that complex structure. Using computer simulations, the fundamental diagram, the space-time plots, the time series of the density in the jams, and the 1-min average data of this model are analyzed. It is shown that compared to other existing models, this model can display the experimental characteristics of the wide moving jams. PMID:12935210

  8. Spontaneous bursting: From temporal to spatio-temporal intermittency

    SciTech Connect

    Platt, N.; Hammel, S.M. [Code B44, Nonlinear Dynamics and Wavelets Group, Naval Surface Warfare Center, 10901 New Hampshire Ave, Silver Spring, Maryland, 20903-5640 (United States)

    1996-06-01

    A simple model for temporal bursting is introduced. This model invokes either dynamic or random forcing of a bifurcation parameter of some simple dynamical system in a way that makes the bifurcation parameter spend suitable amounts of time below and above the bifurcation threshold. This model is extended to coupled map lattices to produce spontaneous spatio-temporal burstings. It models physical systems which are embedded in a random background that is statistically homogeneous in space and time. An application of this model to optical turbulence is discussed. {copyright} {ital 1996 American Institute of Physics.}

  9. Spatio-temporal variability of soil respiration of forest ecosystems in China: influencing factors and evaluation model.

    PubMed

    Zheng, Ze-Mei; Yu, Gui-Rui; Sun, Xiao-Min; Li, Sheng-Gong; Wang, Yue-Si; Wang, Ying-Hong; Fu, Yu-Ling; Wang, Qiu-Feng

    2010-10-01

    Understanding the influencing factors of the spatio-temporal variability of soil respiration (R (s)) across different ecosystems as well as the evaluation model of R (s) is critical to the accurate prediction of future changes in carbon exchange between ecosystems and the atmosphere. R (s) data from 50 different forest ecosystems in China were summarized and the influences of environmental variables on the spatio-temporal variability of R (s) were analyzed. The results showed that both the mean annual air temperature and precipitation were weakly correlated with annual R (s), but strongly with soil carbon turnover rate. R (s) at a reference temperature of 0°C was only significantly and positively correlated with soil organic carbon (SOC) density at a depth of 20 cm. We tested a global-scale R (s) model which predicted monthly mean R (s) (R (s,monthly)) from air temperature and precipitation. Both the original model and the reparameterized model poorly explained the monthly variability of R (s) and failed to capture the inter-site variability of R (s). However, the residual of R (s,monthly) was strongly correlated with SOC density. Thus, a modified empirical model (TPS model) was proposed, which included SOC density as an additional predictor of R (s). The TPS model explained monthly and inter-site variability of R (s) for 56% and 25%, respectively. Moreover, the simulated annual R (s) of TPS model was significantly correlated with the measured value. The TPS model driven by three variables easy to be obtained provides a new tool for R (s) prediction, although a site-specific calibration is needed for using at a different region. PMID:20571797

  10. Event Detection using Twitter: A Spatio-Temporal Approach

    PubMed Central

    Cheng, Tao; Wicks, Thomas

    2014-01-01

    Background Every day, around 400 million tweets are sent worldwide, which has become a rich source for detecting, monitoring and analysing news stories and special (disaster) events. Existing research within this field follows key words attributed to an event, monitoring temporal changes in word usage. However, this method requires prior knowledge of the event in order to know which words to follow, and does not guarantee that the words chosen will be the most appropriate to monitor. Methods This paper suggests an alternative methodology for event detection using space-time scan statistics (STSS). This technique looks for clusters within the dataset across both space and time, regardless of tweet content. It is expected that clusters of tweets will emerge during spatio-temporally relevant events, as people will tweet more than expected in order to describe the event and spread information. The special event used as a case study is the 2013 London helicopter crash. Results and Conclusion A spatio-temporally significant cluster is found relating to the London helicopter crash. Although the cluster only remains significant for a relatively short time, it is rich in information, such as important key words and photographs. The method also detects other special events such as football matches, as well as train and flight delays from Twitter data. These findings demonstrate that STSS is an effective approach to analysing Twitter data for event detection. PMID:24893168

  11. Sparse Spatio-temporal Inference of Electromagnetic Brain Sources

    NASA Astrophysics Data System (ADS)

    Stahlhut, Carsten; Attias, Hagai T.; Wipf, David; Hansen, Lars K.; Nagarajan, Srikantan S.

    The electromagnetic brain activity measured via MEG (or EEG) can be interpreted as arising from a collection of current dipoles or sources located throughout the cortex. Because the number of candidate locations for these sources is much larger than the number of sensors, source reconstruction involves solving an inverse problem that is severely underdetermined. Bayesian graphical models provide a powerful means of incorporating prior assumptions that narrow the solution space and lead to tractable posterior distributions over the unknown sources given the observed data. In particular, this paper develops a hierarchical, spatio-temporal Bayesian model that accommodates the principled computation of sparse spatial and smooth temporal M/EEG source reconstructions consistent with neurophysiological assumptions in a variety of event-related imaging paradigms. The underlying methodology relies on the notion of automatic relevance determination (ARD) to express the unknown sources via a small collection of spatio-temporal basis functions. Experiments with several data sets provide evidence that the proposed model leads to improved source estimates. The underlying methodology is also well-suited for estimation problems that arise from other brain imaging modalities such as functional or diffusion weighted MRI.

  12. Spatio-temporal Granger causality: a new framework

    PubMed Central

    Luo, Qiang; Lu, Wenlian; Cheng, Wei; Valdes-Sosa, Pedro A.; Wen, Xiaotong; Ding, Mingzhou; Feng, Jianfeng

    2015-01-01

    That physiological oscillations of various frequencies are present in fMRI signals is the rule, not the exception. Herein, we propose a novel theoretical framework, spatio-temporal Granger causality, which allows us to more reliably and precisely estimate the Granger causality from experimental datasets possessing time-varying properties caused by physiological oscillations. Within this framework, Granger causality is redefined as a global index measuring the directed information flow between two time series with time-varying properties. Both theoretical analyses and numerical examples demonstrate that Granger causality is a monotonically increasing function of the temporal resolution used in the estimation. This is consistent with the general principle of coarse graining, which causes information loss by smoothing out very fine-scale details in time and space. Our results confirm that the Granger causality at the finer spatio-temporal scales considerably outperforms the traditional approach in terms of an improved consistency between two resting-state scans of the same subject. To optimally estimate the Granger causality, the proposed theoretical framework is implemented through a combination of several approaches, such as dividing the optimal time window and estimating the parameters at the fine temporal and spatial scales. Taken together, our approach provides a novel and robust framework for estimating the Granger causality from fMRI, EEG, and other related data. PMID:23643924

  13. Generalized spatiotemporal myocardial strain analysis for DENSE and SPAMM imaging.

    PubMed

    Young, Alistair A; Li, Bo; Kirton, Robert S; Cowan, Brett R

    2012-06-01

    Displacement encoding using stimulated echoes (DENSE) and spatial modulation of magnetization (SPAMM) are MRI techniques for quantifying myocardial displacement and strain. However, DENSE has not been compared against SPAMM in phantoms exhibiting nonhomogeneous strain, and interobserver variability has not been compared between DENSE and SPAMM. To perform these comparisons, there is a need for a generalized analysis framework for the evaluation of myocardial strain. A spatiotemporal mathematical model was used to represent myocardial geometry and motion. The model was warped to each frame using tissue displacement maps calculated from either automated phase unwrapping (DENSE) or nonrigid registration (SPAMM). Strain and motion were then calculated from the model using standard methods. DENSE and SPAMM results were compared in a deformable gel phantom exhibiting known nonhomogeneous strain, and interobserver errors were determined in 19 healthy human volunteers. Nonhomogeneous strain in the phantom was accurately quantified using both DENSE and SPAMM. In the healthy volunteers, DENSE produced better interobserver errors than SPAMM for radial strain (-0.009 ± 0.069 vs. 0.029 ± 0.152, respectively, bias ± 95% confidence interval). In conclusion, generalized spatiotemporal modeling enables robust myocardial strain analysis for DENSE or SPAMM. PMID:22135133

  14. Spatiotemporal variation in reproductive parameters of yellow-bellied marmots.

    PubMed

    Ozgul, Arpat; Oli, Madan K; Olson, Lucretia E; Blumstein, Daniel T; Armitage, Kenneth B

    2007-11-01

    Spatiotemporal variation in reproductive rates is a common phenomenon in many wildlife populations, but the population dynamic consequences of spatial and temporal variability in different components of reproduction remain poorly understood. We used 43 years (1962-2004) of data from 17 locations and a capture-mark-recapture (CMR) modeling framework to investigate the spatiotemporal variation in reproductive parameters of yellow-bellied marmots (Marmota flaviventris), and its influence on the realized population growth rate. Specifically, we estimated and modeled breeding probabilities of two-year-old females (earliest age of first reproduction), >2-year-old females that have not reproduced before (subadults), and >2-year-old females that have reproduced before (adults), as well as the litter sizes of two-year old and >2-year-old females. Most reproductive parameters exhibited spatial and/or temporal variation. However, reproductive parameters differed with respect to their relative influence on the realized population growth rate (lambda). Litter size had a stronger influence than did breeding probabilities on both spatial and temporal variations in lambda. Our analysis indicated that lambda was proportionately more sensitive to survival than recruitment. However, the annual fluctuation in litter size, abetted by the breeding probabilities, accounted for most of the temporal variation in lambda. PMID:17687571

  15. Deep Spatiotemporal Feature Learning with Application to Image Classification

    SciTech Connect

    Karnowski, Thomas Paul [ORNL; Arel, Itamar [ORNL; Rose, Derek C [ORNL

    2010-01-01

    Deep machine learning is an emerging framework for dealing with complex high-dimensionality data in a hierarchical fashion which draws some inspiration from biological sources. Despite the notable progress made in the field, there remains a need for an architecture that can represent temporal information with the same ease that spatial information is discovered. In this work, we present new results using a recently introduced deep learning architecture called Deep Spatio-Temporal Inference Network (DeSTIN). DeSTIN is a discriminative deep learning architecture that combines concepts from unsupervised learning for dynamic pattern representation together with Bayesian inference. In DeSTIN the spatiotemporal dependencies that exist within the observations are modeled inherently in an unguided manner. Each node models the inputs by means of clustering and simple dynamics modeling while it constructs a belief state over the distribution of sequences using Bayesian inference. We demonstrate that information from the different layers of this hierarchical system can be extracted and utilized for the purpose of pattern classification. Earlier simulation results indicated that the framework is highly promising, consequently in this work we expand DeSTIN to a popular problem, the MNIST data set of handwritten digits. The system as a preprocessor to a neural network achieves a recognition accuracy of 97.98% on this data set. We further show related experimental results pertaining to automatic cluster adaptation and termination.

  16. Spatiotemporal chaotic unjamming and jamming in granular avalanches

    PubMed Central

    Wang, Ziwei; Zhang, Jie

    2015-01-01

    We have investigated the spatiotemporal chaotic dynamics of unjamming and jamming of particles in a model experiment – a rotating drum partially filled with bidisperse disks to create avalanches. The magnitudes of the first Lyapunov vector ?u(t) and velocity v(t) of particles are directly measured for the first time to yield insights into their spatial correlation C?u,v, which is on statistical average slightly larger near the unjamming than the value near the jamming transition. These results are consistent with the recent work of Banigan et al (Nature Phys. 2013), and it is for the first time to validate their theoretical models in a real scenario. v(t) shows rich dynamics: it grows exponentially for unstable particles and keeps increasing despite stochastic interactions; after the maximum, it decays with large fluctuations. Hence the spatiotemporal chaotic dynamics of avalanche particles are entangled, causing temporal correlations of macroscopic quantities of the system. We propose a simple model for these observations. PMID:25634753

  17. Spatiotemporal chaotic unjamming and jamming in granular avalanches.

    PubMed

    Wang, Ziwei; Zhang, Jie

    2015-01-01

    We have investigated the spatiotemporal chaotic dynamics of unjamming and jamming of particles in a model experiment - a rotating drum partially filled with bidisperse disks to create avalanches. The magnitudes of the first Lyapunov vector ?u(t) and velocity v(t) of particles are directly measured for the first time to yield insights into their spatial correlation C?u,v, which is on statistical average slightly larger near the unjamming than the value near the jamming transition. These results are consistent with the recent work of Banigan et al (Nature Phys. 2013), and it is for the first time to validate their theoretical models in a real scenario. v(t) shows rich dynamics: it grows exponentially for unstable particles and keeps increasing despite stochastic interactions; after the maximum, it decays with large fluctuations. Hence the spatiotemporal chaotic dynamics of avalanche particles are entangled, causing temporal correlations of macroscopic quantities of the system. We propose a simple model for these observations. PMID:25634753

  18. BICAR: A New Algorithm for Multiresolution Spatiotemporal Data Fusion

    PubMed Central

    Brown, Kevin S.; Grafton, Scott T.; Carlson, Jean M.

    2012-01-01

    We introduce a method for spatiotemporal data fusion and demonstrate its performance on three constructed data sets: one entirely simulated, one with temporal speech signals and simulated spatial images, and another with recorded music time series and astronomical images defining the spatial patterns. Each case study is constructed to present specific challenges to test the method and demonstrate its capabilities. Our algorithm, BICAR (Bidirectional Independent Component Averaged Representation), is based on independent component analysis (ICA) and extracts pairs of temporal and spatial sources from two data matrices with arbitrarily different spatiotemporal resolution. We pair the temporal and spatial sources using a physical transfer function that connects the dynamics of the two. BICAR produces a hierarchy of sources ranked according to reproducibility; we show that sources which are more reproducible are more similar to true (known) sources. BICAR is robust to added noise, even in a “worst case” scenario where all physical sources are equally noisy. BICAR is also relatively robust to misspecification of the transfer function. BICAR holds promise as a useful data-driven assimilation method in neuroscience, earth science, astronomy, and other signal processing domains. PMID:23209693

  19. Spatiotemporal Variations of Reference Crop Evapotranspiration in Northern Xinjiang, China

    PubMed Central

    Lv, Xin; Lin, Hai-rong

    2014-01-01

    To set up a reasonable crop irrigation system in the context of global climate change in Northern Xinjiang, China, reference crop evapotranspiration (ET0) was analyzed by means of spatiotemporal variations. The ET0 values from 1962 to 2010 were calculated by Penman-Monteith formula, based on meteorological data of 22 meteorological observation stations in the study area. The spatiotemporal variations of ET0 were analyzed by Mann-Kendall test, Morlet wavelet analysis, and ArcGIS spatial analysis. The results showed that regional average ET0 had a decreasing trend and there was an abrupt change around 1983. The trend of regional average ET0 had a primary period about 28 years, in which there were five alternating stages (high-low-high-low-high). From the standpoint of spatial scale, ET0 gradually increased from the northeast and southwest toward the middle; the southeast and west had slightly greater variation, with significant regional differences. From April to October, the ET0 distribution significantly influenced the distribution characteristic of annual ET0. Among them sunshine hours and wind speed were two of principal climate factors affecting ET0. PMID:25254259

  20. Spatiotemporal continuous wavelets applied to missile warhead detection and tracking

    NASA Astrophysics Data System (ADS)

    Mujica, Fernando; Leduc, Jean-Pierre; Smith, Mark J. T.; Murenzi, Romain

    1997-01-01

    This paper addresses the problem of tracking a ballistic missile warhead. In this scenario, the ballistic missile is assumed to be fragmented into many pieces. The goal of the algorithm presented here is to track the warhead that is among the fragments. It is assumed that images are acquired from an optical sensor located in the interceptor nose cone. This imagery is used by the algorithm to steer the course of interception. The algorithm proposed in this paper is based on continuous spatio-temporal wavelet transforms (CWTs). Two different energy densities of the CWT are used to perform velocity detection and filtering. Additional post-processing is applied to discriminate among objects traveling at similar velocities. Particular attention is given to achieving robust performance on noisy sensor data and under conditions of temporary occlusions. First we introduce the spatio-temporal CWT and stress the relationships with classical orientation filters. Then we describe the CWT- based algorithm for target tracking, and present results on synthetically generated sequences.

  1. Stochastic spatio-temporal modelling with PCRaster Python

    NASA Astrophysics Data System (ADS)

    Karssenberg, D.; Schmitz, O.; de Jong, K.

    2012-04-01

    PCRaster Python is a software framework for building spatio-temporal models of land surface processes (Karssenberg, Schmitz, Salamon, De Jong, & Bierkens, 2010; PCRaster, 2012). Building blocks of models are spatial operations on raster maps, including a large suite of operations for water and sediment routing. These operations, developed in C++, are available to model builders as Python functions. Users create models by combining these functions in a Python script. As construction of large iterative models is often difficult and time consuming for non-specialists in programming, the software comes with a set of Python framework classes that provide control flow for static modelling, temporal modelling, stochastic modelling using Monte Carlo simulation, and data assimilation techniques including the Ensemble Kalman filter and the Particle Filter. A framework for integrating model components with different time steps and spatial discretization is currently available as a prototype (Schmitz, de Jong, & Karssenberg, in review). The software includes routines for visualisation of stochastic spatio-temporal data for prompt, interactive, visualisation of model inputs and outputs. Visualisation techniques include animated maps, time series, probability distributions, and animated maps with exceedance probabilities. The PCRaster Python software is used by researchers from a large range of disciplines, including hydrology, ecology, sedimentology, and land use change studies. Applications include global scale hydrological modelling and error propagation in large-scale land use change models. The software runs on MS Windows and Linux operating systems, and OS X (under development).

  2. Target detection and recognition improvements by use of spatiotemporal fusion.

    PubMed

    Chen, Hai-Wen; Sutha, Surachai; Olson, Teresa

    2004-01-10

    We developed spatiotemporal fusion techniques for improving target detection and automatic target recognition. We also investigated real IR (infrared) sensor clutter noise. The sensor noise was collected by an IR (256 x 256) sensor looking at various scenes (trees, grass, roads, buildings, etc.). More than 95% of the sensor pixels showed near-stationary sensor clutter noise that was uncorrelated between pixels as well as across time frames. However, in a few pixels (covering the grass near the road) the sensor noise showed nonstationary properties (with increasing or decreasing mean across time frames). The natural noise extracted from the IR sensor, as well as the computer-generated noise with Gaussian and Rayleigh distributions, was used to test and compare different spatiotemporal fusion strategies. Finally, we proposed two advanced detection schemes: the double-thresholding the reverse-thresholding techniques. These techniques may be applied to complicated clutter situations (e.g., very-high clutter or nonstationary clutter situations) where the traditional constant-false-alarm-ratio technique may fail. PMID:14735959

  3. Localizable and photoactivatable fluorophore for spatiotemporal two-photon bioimaging.

    PubMed

    Zhou, Liyi; Zhang, Xiaobing; Lv, Yifan; Yang, Chao; Lu, Danqing; Wu, Yuan; Chen, Zhuo; Liu, Qiaoling; Tan, Weihong

    2015-06-01

    Photoactivatable probe-based fluorescent imaging has become an efficient and attractive technique for spatiotemporal microscopic studies of biological events. However, almost all previously reported photoactivatable organic probes have been based on hydrosoluble precursors, which have produced water-soluble active fluorophores able to readily diffuse away from the photocleavage site, thereby dramatically reducing spatial resolution. Hydroxyphenylquinazolinone (HPQ), a small organic dye known for its classic luminescence mechanism through excited-state intramolecular proton transfer (ESIPT), shows strong light emission in the solid state, but no emission in solution. In this work, HPQ was employed as a precursor to develop a localizable, photoactivatable two-photon probe (PHPQ) for spatiotemporal bioimaging applications. After photocleavage, PHPQ releases a precipitating HPQ fluorophore which shows both one-photon and two-photon excited yellow-green fluorescence, thereby producing a localizable fluorescence signal that affords high spatial resolution for bioimaging, with more than 200-fold one-photon and 150-fold two-photon fluorescence enhancement. PMID:25903256

  4. A unified framework for gesture recognition and spatiotemporal gesture segmentation.

    PubMed

    Alon, Jonathan; Athitsos, Vassilis; Yuan, Quan; Sclaroff, Stan

    2009-09-01

    Within the context of hand gesture recognition, spatiotemporal gesture segmentation is the task of determining, in a video sequence, where the gesturing hand is located and when the gesture starts and ends. Existing gesture recognition methods typically assume either known spatial segmentation or known temporal segmentation, or both. This paper introduces a unified framework for simultaneously performing spatial segmentation, temporal segmentation, and recognition. In the proposed framework, information flows both bottom-up and top-down. A gesture can be recognized even when the hand location is highly ambiguous and when information about when the gesture begins and ends is unavailable. Thus, the method can be applied to continuous image streams where gestures are performed in front of moving, cluttered backgrounds. The proposed method consists of three novel contributions: a spatiotemporal matching algorithm that can accommodate multiple candidate hand detections in every frame, a classifier-based pruning framework that enables accurate and early rejection of poor matches to gesture models, and a subgesture reasoning algorithm that learns which gesture models can falsely match parts of other longer gestures. The performance of the approach is evaluated on two challenging applications: recognition of hand-signed digits gestured by users wearing short-sleeved shirts, in front of a cluttered background, and retrieval of occurrences of signs of interest in a video database containing continuous, unsegmented signing in American Sign Language (ASL). PMID:19574627

  5. Spatiotemporal regulation of chemical reactions by active cytoskeletal remodeling

    PubMed Central

    Chaudhuri, Abhishek; Bhattacharya, Bhaswati; Gowrishankar, Kripa; Mayor, Satyajit; Rao, Madan

    2011-01-01

    Efficient and reproducible construction of signaling and sorting complexes, both on the surface and within the living cell, is contingent on local regulation of biochemical reactions by the cellular milieu. We propose that in many cases this spatiotemporal regulation can be mediated by interaction with components of the dynamic cytoskeleton. We show how the interplay between active contractility and remodeling of the cytoskeleton can result in transient focusing of passive molecules to form clusters, leading to a dramatic increase in the reaction efficiency and output levels. The dynamic cytoskeletal elements that drive focusing behave as quasienzymes catalyzing the chemical reaction. These ideas are directly applicable to the cortical actin-dependent clustering of cell surface proteins such as lipid-tethered GPI-anchored proteins, Ras proteins, as well as many proteins that have domains that confer the ability to interact with the actin cytoskeleton. In general such cytoskeletal driven clustering of proteins could be a cellular mechanism to spatiotemporally regulate and amplify local chemical reaction rates in a variety of contexts such as signaling, transcription, sorting, and endocytosis. PMID:21873247

  6. Exploring spatiotemporal network transitions in task functional MRI.

    PubMed

    Scott, Gregory; Hellyer, Peter J; Hampshire, Adam; Leech, Robert

    2015-04-01

    A critical question for cognitive neuroscience regards how transitions between cognitive states emerge from the dynamic activity of functional brain networks. Here we combine a simple data reorganization with spatial independent component analysis (ICA), enabling a spatiotemporal ICA (stICA) which captures the consistent evolution of networks during the onset and offset of a task. The technique was applied to functional magnetic resonance imaging (MRI) (FMRI) datasets involving alternating between rest and task, and to simple synthetic data. Starting and finishing time-points of periods of interest (anchors) were defined at task block onsets and offsets. For each subject, the 10 volumes following each anchor were extracted and concatenated spatially, producing a single 3D sample. Samples for all anchors and subjects were concatenated along the fourth dimension. This 4D dataset was decomposed using ICA into spatiotemporal components. One component exhibited the transition with task onset from a default mode network (DMN) becoming less active to a frontoparietal control network becoming more active. We observed other changes with relevance to understanding network dynamics, for example, the DMN showed a changing spatial distribution, shifting to an anterior/superior pattern of deactivation during task from a posterior/inferior pattern during rest. By anchoring analyses to periods associated with the onsets and offsets of task, our approach reveals novel aspects of the dynamics of network activity accompanying these transitions. Importantly, these findings were observed without specifying a priori either the spatial networks or the task time courses. PMID:25504834

  7. Multiple movement modes by large herbivores at multiple spatiotemporal scales

    PubMed Central

    Fryxell, John M.; Hazell, Megan; Börger, Luca; Dalziel, Ben D.; Haydon, Daniel T.; Morales, Juan M.; McIntosh, Therese; Rosatte, Rick C.

    2008-01-01

    Recent theory suggests that animals should switch facultatively among canonical movement modes as a complex function of internal state, landscape characteristics, motion capacity, and navigational capacity. We tested the generality of this paradigm for free-ranging elk (Cervus elaphus) over 5 orders of magnitude in time (minutes to years) and space (meters to 100 km). At the coarsest spatiotemporal scale, elk shifted from a dispersive to a home-ranging phase over the course of 1–3 years after introduction into a novel environment. At intermediate spatiotemporal scales, elk continued to alternate between movement modes. During the dispersive phase, elk alternated between encamped and exploratory modes, possibly linked to changes in motivational goals from foraging to social bonding. During the home-ranging phase, elk movements were characterized by a complex interplay between attraction to preferred habitat types and memory of previous movements across the home-range. At the finest temporal and spatial scale, elk used area-restricted search while browsing, interspersed with less sinuous paths when not browsing. Encountering a patch of high-quality food plants triggered the switch from one mode to the next, creating biphasic movement dynamics that were reinforced by local resource heterogeneity. These patterns suggest that multiphasic structure is fundamental to the movement patterns of elk at all temporal and spatial scales tested. PMID:19060190

  8. Multiple dipole modeling of spatio-temporal MEG (magnetoencephalogram) data

    SciTech Connect

    Mosher, J.C. (TRW Defense Systems Group, Redondo Beach, CA (USA). Systems Engineering and Development Div. University of Southern California, Los Angeles, CA (USA). Signal and Image Processing Inst.); Lewis, P.S. (Los Alamos National Lab., NM (USA)); Leahy, R. (University of Southern California, Los Angeles, CA (USA). Signal and Image Processing Inst.); Singh, M. (University of Southern Californi

    1990-01-01

    An array of SQUID biomagentometers may be used to measure the spatio-temporal neuromagnetic field produced by the brain in response to a given sensory stimulus. A popular model for the neural activity that produces these fields is a set of current dipoles. We present here a common linear algebraic framework for three common spatio-temporal dipole models: moving and rotating dipoles, rotating dipoles with fixed location, and dipoles with fixed orientation and location. Our intent here is not to argue the merits of one model over another, but rather show how each model may be solved efficiently, and within the same framework as the others. In all cases, we assume that the location, orientation, and magnitude of the dipoles are unknown. We present the parameter estimation problem for these three models in a common framework, and show how, in each case, the problem may be decomposed into the estimation of the dipole locations using nonlinear minimization followed by linear estimation of the associated moment time series. Numerically efficient means of calculating the cost function are presented, and problems of model order selection and missing moments are also investigated. The methods described are demonstrated in a simulated application to a three dipole problem. 21 refs., 2 figs., 1 tab.

  9. The Hippo Signaling Pathway Interactome

    PubMed Central

    Kwon, Young; Vinayagam, Arunachalam; Sun, Xiaoyun; Dephoure, Noah; Gygi, Steven P.; Hong, Pengyu; Perrimon, Norbert

    2014-01-01

    The Hippo pathway controls metazoan organ growth by regulating cell proliferation and apoptosis. Many components have been identified, but our knowledge of the composition and structure of this pathway is still incomplete. Using existing pathway components as baits, we generated by mass spectrometry a high-confidence Drosophila Hippo protein-protein interaction network (Hippo-PPIN) consisting of 153 proteins and 204 interactions. Depletion of 67% of the proteins by RNA interference regulated the transcriptional coactivator Yorkie (Yki) either positively or negatively. We selected for further characterization a new member of the alpha-arrestin family, Leash, and show that it promotes degradation of Yki through the lysosomal pathway. Given the importance of the Hippo pathway in tumor development, the Hippo-PPIN will contribute to our understanding of this network in both normal growth and cancer. PMID:24114784

  10. Disordered interactome of human papillomavirus.

    PubMed

    Xue, Bin; Ganti, Ketaki; Rabionet, Alejandro; Banks, Lawrence; Uversky, Vladimir N

    2014-01-01

    Intrinsically disordered proteins (IDPs) and proteins with long intrinsically disordered protein regions (IDPRs) lack ordered structure but are involved in a multitude of biological processes, where they often serve as major regulators and controllers of various functions of their binding partners. Furthermore, IDPs/IDPRs are often related to the pathogenesis of various diseases, including cancer. Intrinsic disorder confers multiple functional advantages to its carriers. As a result, due to their functional versatility and structural plasticity, IDPs and IDPRs are common in various proteomes, including proteomes of different pathological organisms. Viruses are "well-educated" users of various aspects of intrinsic disorder for their advantage. These small but highly efficient invaders broadly use intrinsic disorder to overrun the host organism's defense system, as well as to seize and overrun host systems and pathways forcing them to work for the virus needs, to ensure accommodation of viruses to their variable and often hostile habitats, and to promote and support the economic usage of the viral genetic material. Human papillomaviruses (HPVs), with their tiny proteomes (the entire HPV genome includes just eight open reading frames), intricate life cycle, and ability to either cause benign papillomas/warts or promote the development of carcinomas of the genital tract, head and neck and epidermis, attracted considerable attention of researchers. This review analyzes the plentitude and demeanor of intrinsic disorder in proteins from HPVs and their cellular targets. PMID:23713779

  11. Predictive Modeling-Based Data Collection in Wireless Sensor Networks

    Microsoft Academic Search

    Lidan Wang; Amol Deshpande

    2008-01-01

    We address the problem of designing practical, energy-efficient protocols for data collection in wireless sensor networks\\u000a using predictive modeling. Prior work has suggested several approaches to capture and exploit the rich spatio-temporal correlations\\u000a prevalent in WSNs during data collection. Although shown to be effective in reducing the data collection cost, those approaches\\u000a use simplistic corelation models and further, ignore many

  12. Spatiotemporal dynamics of a digital phase-locked loop based coupled map lattice system.

    PubMed

    Banerjee, Tanmoy; Paul, Bishwajit; Sarkar, B C

    2014-03-01

    We explore the spatiotemporal dynamics of a coupled map lattice (CML) system, which is realized with a one dimensional array of locally coupled digital phase-locked loops (DPLLs). DPLL is a nonlinear feedback-controlled system widely used as an important building block of electronic communication systems. We derive the phase-error equation of the spatially extended system of coupled DPLLs, which resembles a form of the equation of a CML system. We carry out stability analysis for the synchronized homogeneous solutions using the circulant matrix formalism. It is shown through extensive numerical simulations that with the variation of nonlinearity parameter and coupling strength the system shows transitions among several generic features of spatiotemporal dynamics, viz., synchronized fixed point solution, frozen random pattern, pattern selection, spatiotemporal intermittency, and fully developed spatiotemporal chaos. We quantify the spatiotemporal dynamics using quantitative measures like average quadratic deviation and spatial correlation function. We emphasize that instead of using an idealized model of CML, which is usually employed to observe the spatiotemporal behaviors, we consider a real world physical system and establish the existence of spatiotemporal chaos and other patterns in this system. We also discuss the importance of the present study in engineering application like removal of clock-skew in parallel processors. PMID:24697378

  13. Spatiotemporal dynamics of a digital phase-locked loop based coupled map lattice system

    SciTech Connect

    Banerjee, Tanmoy, E-mail: tbanerjee@phys.buruniv.ac.in; Paul, Bishwajit; Sarkar, B. C. [Department of Physics, University of Burdwan, Burdwan, West Bengal 713 104 (India)] [Department of Physics, University of Burdwan, Burdwan, West Bengal 713 104 (India)

    2014-03-15

    We explore the spatiotemporal dynamics of a coupled map lattice (CML) system, which is realized with a one dimensional array of locally coupled digital phase-locked loops (DPLLs). DPLL is a nonlinear feedback-controlled system widely used as an important building block of electronic communication systems. We derive the phase-error equation of the spatially extended system of coupled DPLLs, which resembles a form of the equation of a CML system. We carry out stability analysis for the synchronized homogeneous solutions using the circulant matrix formalism. It is shown through extensive numerical simulations that with the variation of nonlinearity parameter and coupling strength the system shows transitions among several generic features of spatiotemporal dynamics, viz., synchronized fixed point solution, frozen random pattern, pattern selection, spatiotemporal intermittency, and fully developed spatiotemporal chaos. We quantify the spatiotemporal dynamics using quantitative measures like average quadratic deviation and spatial correlation function. We emphasize that instead of using an idealized model of CML, which is usually employed to observe the spatiotemporal behaviors, we consider a real world physical system and establish the existence of spatiotemporal chaos and other patterns in this system. We also discuss the importance of the present study in engineering application like removal of clock-skew in parallel processors.

  14. Spatiotemporal dynamics of a digital phase-locked loop based coupled map lattice system

    NASA Astrophysics Data System (ADS)

    Banerjee, Tanmoy; Paul, Bishwajit; Sarkar, B. C.

    2014-03-01

    We explore the spatiotemporal dynamics of a coupled map lattice (CML) system, which is realized with a one dimensional array of locally coupled digital phase-locked loops (DPLLs). DPLL is a nonlinear feedback-controlled system widely used as an important building block of electronic communication systems. We derive the phase-error equation of the spatially extended system of coupled DPLLs, which resembles a form of the equation of a CML system. We carry out stability analysis for the synchronized homogeneous solutions using the circulant matrix formalism. It is shown through extensive numerical simulations that with the variation of nonlinearity parameter and coupling strength the system shows transitions among several generic features of spatiotemporal dynamics, viz., synchronized fixed point solution, frozen random pattern, pattern selection, spatiotemporal intermittency, and fully developed spatiotemporal chaos. We quantify the spatiotemporal dynamics using quantitative measures like average quadratic deviation and spatial correlation function. We emphasize that instead of using an idealized model of CML, which is usually employed to observe the spatiotemporal behaviors, we consider a real world physical system and establish the existence of spatiotemporal chaos and other patterns in this system. We also discuss the importance of the present study in engineering application like removal of clock-skew in parallel processors.

  15. Association rule mining based on spatio-temporal processes of spatial distribution patterns

    NASA Astrophysics Data System (ADS)

    Zhang, Xuewu; Su, Fenzhen; Shi, Yishao; He, Yawen

    2008-12-01

    Spatial distribution pattern is an arrangement of two or more spatial objects according to some spatial relations, such as spatial direction, topological and distance relations. In the real world, spatial objects and spatial distribution pattern all vary continuously along the time-line. Traditional spatial and non-spatial data dissevers this continuous spatio-temporal process. Under analyzing relations among spatial object, its attributes and spatial distribution pattern, we brought metaspatio- temporal process, spatio-temporal process and spatial distribution pattern spatio-temporal process. Rainfall in Eastern China has a typical spatial distribution pattern, being composed of the northern rain area and the southern rain area. Through constructing spatio-temporal process transactions, the association rules can be extracted from spatiotemporal process data set by the Apriori algorithm. The result of the spaio-temporal process association rule mining is consistent with the analysis of the theory. Finally, it is concluded that the spatio-temporal process can describe change of a spatial object in a defined time range, and change trend of one entity can be forecasted through varying trend of others based on the valuable spatio-temporal process association rules.

  16. The response of the Limulus retina to moving stimuli: a prediction by Fourier synthesis

    PubMed Central

    1978-01-01

    The Limulus retina responds as a linear system to light stimuli which vary moderately about a mean level. The dynamics of such a system may conveniently be summarized by means of a spatiotemporal transfer function, which describes the response of the system to moving sinusoidal gratings. The response of the system to an arbitrary stimulus may then be calculated by adding together the system's responses to suitably weighted sinusoidal stimuli. We have measured such a spatiotemporal transfer function for the Limulus eye. We have then accurately predicted, in a parameter-free calculation, the eye's response to various stimulus patterns which move across it at several different velocities. PMID:690594

  17. Sedimentological constraints to the spatio-temporal evolution of the first Cenozoic Antarctic glaciation

    NASA Astrophysics Data System (ADS)

    Stocchi, P.; Galeotti, S.; De Boer, B.; Escutia, C.; DeConto, R.; Houben, A. J.; Passchier, S.; Vermeersen, B. L.; Van de Wal, R.; Brinkhuis, H.

    2012-12-01

    Glacial Isostatic Adjustement (GIA) modeling of solid Earth and gravitational perturbations induced by the Antarctic glaciation across the Eocene/Oligocene transition (EOT; ~34 Ma) predicts a relative sea level (rsl) rise over-ice proximal marine marginal settings. Accordingly, available sedimentary records from the Ross Sea (CIROS1, CRP-3), Prydz Bay (ODP 739, 1166) and Wilkes Land (IOPD U1356, U1360) provide evidence for progressively deeper depositional environments across the late Eocene towards the Oligocene isotope event-1 (Oi-1; 33.7 Ma, which marks a major glacial advancement episode. Since bathymetric changes at these near-field sites are controlled by GIA, the analysis and inter-site comparison of their sedimentary records provide insights into the spatio-temporal evolution of the nascent Antarctic Ice Sheet. In this work we simulate the inception of the Antarctic glaciation by means of a thermomechanical ice sheet-shelf model dynamically coupled to a sea level model based on the gravitationally self-consistent Sea Level Equation (SLE). We generate a set of ice-sheet and rsl scenarios according to (i) different values for the Earth rheological parameters, (ii) initial topographic/bathymetric conditions and (iii) precipitation/temperature patterns. By comparing the observations with the modeling solutions we find that the initial undeformed topography/bathymetry, and consequently its deformations driven by the GIA described by the SLE, are important conditions for a realistic development of the Antarctic ice-sheet.

  18. Stable isotope analysis of precipitation samples obtained via crowdsourcing reveals the spatiotemporal evolution of Superstorm Sandy.

    PubMed

    Good, Stephen P; Mallia, Derek V; Lin, John C; Bowen, Gabriel J

    2014-01-01

    Extra-tropical cyclones, such as 2012 Superstorm Sandy, pose a significant climatic threat to the northeastern United Sates, yet prediction of hydrologic and thermodynamic processes within such systems is complicated by their interaction with mid-latitude water patterns as they move poleward. Fortunately, the evolution of these systems is also recorded in the stable isotope ratios of storm-associated precipitation and water vapor, and isotopic analysis provides constraints on difficult-to-observe cyclone dynamics. During Superstorm Sandy, a unique crowdsourced approach enabled 685 precipitation samples to be obtained for oxygen and hydrogen isotopic analysis, constituting the largest isotopic sampling of a synoptic-scale system to date. Isotopically, these waters span an enormous range of values (> 21‰ for ?(18)O, > 160‰ for ?(2)H) and exhibit strong spatiotemporal structure. Low isotope ratios occurred predominantly in the west and south quadrants of the storm, indicating robust isotopic distillation that tracked the intensity of the storm's warm core. Elevated values of deuterium-excess (> 25‰) were found primarily in the New England region after Sandy made landfall. Isotope mass balance calculations and Lagrangian back-trajectory analysis suggest that these samples reflect the moistening of dry continental air entrained from a mid-latitude trough. These results demonstrate the power of rapid-response isotope monitoring to elucidate the structure and dynamics of water cycling within synoptic-scale systems and improve our understanding of storm evolution, hydroclimatological impacts, and paleo-storm proxies. PMID:24618882

  19. A linear merging methodology for high-resolution precipitation products using spatiotemporal regression

    SciTech Connect

    Turlapaty, Anish C. [Mississippi State University (MSU); Younan, Nicolas H. [Mississippi State University (MSU); Anantharaj, Valentine G [ORNL

    2012-01-01

    Currently, the only viable option for a global precipitation product is the merger of several precipitation products from different modalities. In this article, we develop a linear merging methodology based on spatiotemporal regression. Four highresolution precipitation products (HRPPs), obtained through methods including the Climate Prediction Center's Morphing (CMORPH), Geostationary Operational Environmental Satellite-Based Auto-Estimator (GOES-AE), GOES-Based Hydro-Estimator (GOES-HE) and Self-Calibrating Multivariate Precipitation Retrieval (SCAMPR) algorithms, are used in this study. The merged data are evaluated against the Arkansas Red Basin River Forecast Center's (ABRFC's) ground-based rainfall product. The evaluation is performed using the Heidke skill score (HSS) for four seasons, from summer 2007 to spring 2008, and for two different rainfall detection thresholds. It is shown that the merged data outperform all the other products in seven out of eight cases. A key innovation of this machine learning method is that only 6% of the validation data are used for the initial training. The sensitivity of the algorithm to location, distribution of training data, selection of input data sets and seasons is also analysed and presented.

  20. A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis.

    PubMed

    Geng, Yu; Wu, Rui; Wee, Choon Wei; Xie, Fei; Wei, Xueliang; Chan, Penny Mei Yeen; Tham, Cliff; Duan, Lina; Dinneny, José R

    2013-06-01

    Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point-specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment. PMID:23898029

  1. Spatio-temporal distribution of dengue fever under scenarios of climate change in the southern Taiwan

    NASA Astrophysics Data System (ADS)

    Lee, Chieh-Han; Yu, Hwa-Lung

    2014-05-01

    Dengue fever has been recognized as the most important widespread vector-borne infectious disease in recent decades. Over 40% of the world's population is risk from dengue and about 50-100 million people are infected world wide annually. Previous studies have found that dengue fever is highly correlated with climate covariates. Thus, the potential effects of global climate change on dengue fever are crucial to epidemic concern, in particular, the transmission of the disease. This present study investigated the nonlinearity of time-delayed impact of climate on spatio-temporal variations of dengue fever in the southern Taiwan during 1998 to 2011. A distributed lag nonlinear model (DLNM) is used to assess the nonlinear lagged effects of meteorology. The statistically significant meteorological factors are considered, including weekly minimum temperature and maximum 24-hour rainfall. The relative risk and the distribution of dengue fever then predict under various climate change scenarios. The result shows that the relative risk is similar for different scenarios. In addition, the impact of rainfall on the incidence risk is higher than temperature. Moreover, the incidence risk is associated to spatially population distribution. The results can be served as practical reference for environmental regulators for the epidemic prevention under climate change scenarios.

  2. A novel spatiotemporal muscle activity imaging approach based on the Extended Kalman Filter.

    PubMed

    Wang, Jing; Zhang, Yingchun; Zhu, Xiangjun; Zhou, Ping; Liu, Chenguang; Rymer, William Z

    2012-01-01

    A novel spatiotemporal muscle activity imaging (sMAI) approach has been developed using the Extended Kalman Filter (EKF) to reconstruct internal muscle activities from non-invasive multi-channel surface electromyogram (sEMG) recordings. A distributed bioelectric dipole source model is employed to describe the internal muscle activity space, and a linear relationship between the muscle activity space and the sEMG measurement space is then established. The EKF is employed to recursively solve the ill-posed inverse problem in the sMAI approach, in which the weighted minimum norm (WMN) method is utilized to calculate the initial state and a new nonlinear method is developed based on the propagating features of muscle activities to predict the recursive state. A series of computer simulations was conducted to test the performance of the proposed sMAI approach. Results show that the localization error rapidly decreases over 35% and the overlap ratio rapidly increases over 45% compared to the results achieved using the WMN method only. The present promising results demonstrate the feasibility of utilizing the proposed EKF-based sMAI approach to accurately reconstruct internal muscle activities from non-invasive sEMG recordings. PMID:23367354

  3. Understanding the spatio-temporal variability of phytoplankton biomass distribution in a microtidal Mediterranean estuary

    NASA Astrophysics Data System (ADS)

    Artigas, M. L.; Llebot, C.; Ross, O. N.; Neszi, N. Z.; Rodellas, V.; Garcia-Orellana, J.; Masqué, P.; Piera, J.; Estrada, M.; Berdalet, E.

    2014-03-01

    Understanding the spatio-temporal variability of phytoplankton in aquaculture zones is necessary for the prevention and/or prediction of harmful algal bloom events. Synoptic cruises, time series analyses of physical and biological parameters, and 3D modeling were combined to investigate the variability of phytoplankton biomass in Alfacs Bay at basin scale. This microtidal estuary located in the NW Mediterranean is an important area of shellfish and finfish exploitation, which is regularly affected by toxic outbreaks. Observations showed the existence of a preferential phytoplankton accumulation area on the NE interior of the bay. This pattern can be observed throughout the year, and we show that it is directly linked to the physical forcing in the bay, in particular, the interplay between freshwater input and wind-induced turbulence. Both drivers affect the strength of the estuarine circulation, explaining nearly 75% of the variability in phytoplankton biomass. More cells are retained when stratification is weakened and the estuarine circulation reduced, while flushing rates are higher during times of increased stratification and stronger estuarine flow. This has been confirmed by using a 3D hydrodynamic model with Eulerian tracers. Nutrients, while important to support phytoplankton populations, have been found to play only a secondary role in explaining this variability at basin scale.

  4. Spatio-Temporal Analysis of Human Faces Using Multi-resolution Subdivision Surfaces

    Microsoft Academic Search

    Jan Neumann; Yiannis Aloimonos

    2001-01-01

    We demonstrate a method to automatically extract spatio-temporal descriptions of human faces from synchronized and calibrated\\u000a multi-view sequences. The head is modeled by a time-varying multi-resolution subdivision surface that is fitted to the observed\\u000a person using spatio-temporal multi-view stereo information, as well as contour constraints. The stereo data is utilized by\\u000a computing the normalized correlation between corresponding spatio-temporal image trajectories

  5. A computational approach to mechanistic and predictive toxicology of pesticides.

    PubMed

    Kongsbak, Kristine; Vinggaard, Anne Marie; Hadrup, Niels; Audouze, Karine

    2014-01-01

    Emerging challenges of managing and interpreting large amounts of complex biological data have given rise to the growing field of computational biology. We investigated the applicability of an integrated systems toxicology approach on five selected pesticides to get an overview of their modes of action in humans, to group them according to their modes of action, and to hypothesize on their potential effects on human health. We extracted human proteins associated to prochloraz, tebuconazole, epoxiconazole, procymidone, and mancozeb and enriched each protein set by using a high confidence human protein interactome. Then, we explored modes of action of the chemicals, by integrating protein-disease information to the resulting protein networks. The dominating human adverse effects affected were reproductive disorders followed by adrenal diseases. Our results indicated that prochloraz, tebuconazole, and procymidone exerted their effects mainly via interference with steroidogenesis and nuclear receptors. Prochloraz was associated to a large number of human diseases, and together with tebuconazole showed several significant associations to Testicular Dysgenesis Syndrome. Mancozeb showed a differential mode of action, involving inflammatory processes. This method provides an efficient way of overviewing data and grouping chemicals according to their mode of action and potential human adverse effects. Such information is valuable when dealing with predictions of mixture effects of chemicals and may contribute to the development of adverse outcome pathways. PMID:24037280

  6. Spatio-temporal modeling with GIS and remote sensing for schistosomiasis control in Sichuan, China

    NASA Astrophysics Data System (ADS)

    Xu, Bing

    Schistosomiasis is a water-borne parasitic disease endemic in tropical and subtropical areas. Its transmission requires certain kind of snail as the intermediate host. Some efforts have been made to mapping snail habitats with remote sensing and schistosomiasis transmission modeling. However, the modeling is limited to isolated residential groups and does not include spatial interaction among those groups. Remotely sensed data are only used in snail habitat classification, not in estimation of snail abundance that is an important parameter in schistosomiasis transmission modeling. This research overcomes the above two problems using innovative geographic information system (GIS) and remote sensing technology. A mountainous environment near Xichang, China, is chosen as the test site. Environmental and epidemiological data are stored in a GIS to support modeling. Snail abundance is estimated from land-cover and land-use fractions derived from high spatial resolution IKONOS satellite data. Spatial interaction is determined in consideration of neighborhoods, group areas, relative slopes among groups, and natural barriers. Land-cover and land-use information extracted from 4 m high resolution IKONOS data is used as reference in scaling up to the regional level. The scale-up is done with coarser resolution satellite data including Landsat Thematic Mapper (TM), EO-1 Advanced Land Imager (ALI) and Hyperion data all at 30 m resolution. Snail abundance is estimated by regressing snail survey data with land-cover and land-use fractions. An R2 of 0.87 is obtained between the average snail density predicted and that surveyed at the group level. With such a model, a snail density map is generated for all residential groups in the study area. A spatio-temporal model of schistosomiasis transmission is finally built to incorporate the spatial interaction caused by miracidia and cercaria migration. Comparing the model results with and without spatial interaction has revealed a number of advantages of the spatio-temporal model. Particularly, with the inclusion of spatial interaction, more effective control of schistosomiasis transmission over the whole study area can be achieved.

  7. Spatiotemporal correlation structure of the Earth's surface temperature

    NASA Astrophysics Data System (ADS)

    Fredriksen, Hege-Beate; Rypdal, Kristoffer; Rypdal, Martin

    2015-04-01

    We investigate the spatiotemporal temperature variability for several gridded instrumental and climate model data sets. The temporal variability is analysed by estimating the power spectral density and studying the differences between local and global temperatures, land and sea, and among local temperature records at different locations. The spatiotemporal correlation structure is analysed through cross-spectra that allow us to compute frequency-dependent spatial autocorrelation functions (ACFs). Our results are then compared to theoretical spectra and frequency-dependent spatial ACFs derived from a fractional stochastic-diffusive energy balance model (FEBM). From the FEBM we expect both local and global temperatures to have a long-range persistent temporal behaviour, and the spectral exponent (?) is expected to increase by a factor of two when going from local to global scales. Our comparison of the average local spectrum and the global spectrum shows good agreement with this model, although the FEBM has so far only been studied for a pure land planet and a pure ocean planet, respectively, with no seasonal forcing. Hence it cannot capture the substantial variability among the local spectra, in particular between the spectra for land and sea, and for equatorial and non-equatorial temperatures. Both models and observation data show that land temperatures in general have a low persistence, while sea surface temperatures show a higher, and also more variable degree of persistence. Near the equator the spectra deviate from the power-law shape expected from the FEBM. Instead we observe large variability at time scales of a few years due to ENSO, and a flat spectrum at longer time scales, making the spectrum more reminiscent of that of a red noise process. From the frequency-dependent spatial ACFs we observe that the spatial correlation length increases with increasing time scale, which is also consistent with the FEBM. One consequence of this is that longer-lasting structures must also be wider in space. The spatial correlation length is also observed to be longer for land than for sea. The climate model simulations studied are mainly CMIP5 control runs of length 500-1000 yr. On time scales up to several centuries we do not observe that the difference between the local and global spectral exponents vanish. This also follows from the FEBM and shows that the dynamics is spatiotemporal (not just temporal) even on these time scales.

  8. Spatio-temporal prediction of daily temperatures using time-series of MODIS LST images

    Microsoft Academic Search

    Tomislav Hengl; Gerard B. M. Heuvelink; Melita Per?ec Tadi?; Edzer J. Pebesma

    2012-01-01

    A computational framework to generate daily temperature maps using time-series of publicly available MODIS MOD11A2 product\\u000a Land Surface Temperature (LST) images (1 km resolution; 8-day composites) is illustrated using temperature measurements from\\u000a the national network of meteorological stations (159) in Croatia. The input data set contains 57,282 ground measurements of\\u000a daily temperature for the year 2008. Temperature was modeled as a

  9. Spatiotemporal prediction applying fuzzy logic in a sequence of satellite images

    Microsoft Academic Search

    Tania Mezzadri-Centeno; Gilles Selleron

    2002-01-01

    Spatial evolutions of anthropized ecosystems and the progressive transformation of spaces in the course of time emerge more and more as a special interest issue in researches about the environment. This evolution constitutes one of the major concerns in the domain of environmental space management. The landscape evolution of a region area and the perspectives for a future state rises

  10. Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization.

    PubMed

    Wang, Hua; Huang, Heng; Ding, Chris; Nie, Feiping

    2013-04-01

    Protein interactions are central to all the biological processes and structural scaffolds in living organisms, because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Several high-throughput methods, for example, yeast two-hybrid system and mass spectrometry method, can help determine protein interactions, which, however, suffer from high false-positive rates. Moreover, many protein interactions predicted by one method are not supported by another. Therefore, computational methods are necessary and crucial to complete the interactome expeditiously. In this work, we formulate the problem of predicting protein interactions from a new mathematical perspective--sparse matrix completion, and propose a novel nonnegative matrix factorization (NMF)-based matrix completion approach to predict new protein interactions from existing protein interaction networks. Through using manifold regularization, we further develop our method to integrate different biological data sources, such as protein sequences, gene expressions, protein structure information, etc. Extensive experimental results on four species, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, and Caenorhabditis elegans, have shown that our new methods outperform related state-of-the-art protein interaction prediction methods. PMID:23509857

  11. Optimizing Spatio-Temporal Sampling Designs of Synchronous, Static, or Clustered Measurements

    NASA Astrophysics Data System (ADS)

    Helle, Kristina; Pebesma, Edzer

    2010-05-01

    When sampling spatio-temporal random variables, the cost of a measurement may differ according to the setup of the whole sampling design: static measurements, i.e. repeated measurements at the same location, synchronous measurements or clustered measurements may be cheaper per measurement than completely individual sampling. Such "grouped" measurements may however not be as good as individually chosen ones because of redundancy. Often, the overall cost rather than the total number of measurements is fixed. A sampling design with grouped measurements may allow for a larger number of measurements thus outweighing the drawback of redundancy. The focus of this paper is to include the tradeoff between the number of measurements and the freedom of their location in sampling design optimisation. For simple cases, optimal sampling designs may be fully determined. To predict e.g. the mean over a spatio-temporal field having known covariance, the optimal sampling design often is a grid with density determined by the sampling costs [1, Ch. 15]. For arbitrary objective functions sampling designs can be optimised relocating single measurements, e.g. by Spatial Simulated Annealing [2]. However, this does not allow to take advantage of lower costs when using grouped measurements. We introduce a heuristic that optimises an arbitrary objective function of sampling designs, including static, synchronous, or clustered measurements, to obtain better results at a given sampling budget. Given the cost for a measurement, either within a group or individually, the algorithm first computes affordable sampling design configurations. The number of individual measurements as well as kind and number of grouped measurements are determined. Random locations and dates are assigned to the measurements. Spatial Simulated Annealing is used on each of these initial sampling designs (in parallel) to improve them. In grouped measurements either the whole group is moved or single measurements within the group, e.g. static measurements may be moved to another location or the sampling times may be rearranged. After several optimisation steps, the objective functions of the sampling designs are compared. Only for the best ones optimisation is pursued. After several iterations the sampling designs are selected again. Thus more and more of the low performing sampling designs are deleted and computational effort is concentrated on the most promising candidates. The use case is optimisation of a monitoring sampling design for a river. We use a flow model to simulate the spread of a pollutant that enters the system at different locations with known, location-dependent probabilities and at random times. The objective function to be minimised is the amount of pollution that is not detected. Keywords: spatio-temporal sampling design, static sample, synchronous sample, spatial simulated annealing, cost function References [1] Jaap de Gruijter, Dick Brus, Marc Bierkens, and Martin Knotters. Sampling for Natural Ressource Monitoring. Springer, 2006. [2] J. W. van Groenigen. Spatial simulated annealing for optimizing sampling, In: GeoENV I Geostatistics for environmental applications, pages 351 - 361, 1997.

  12. Decomposition of the complex system into nonlinear spatio-temporal modes: algorithm and application to climate data mining

    NASA Astrophysics Data System (ADS)

    Feigin, Alexander; Gavrilov, Andrey; Loskutov, Evgeny; Mukhin, Dmitry

    2015-04-01

    Proper decomposition of the complex system into well separated "modes" is a way to reveal and understand the mechanisms governing the system behaviour as well as discover essential feedbacks and nonlinearities. The decomposition is also natural procedure that provides to construct adequate and concurrently simplest models of both corresponding sub-systems, and of the system in whole. In recent works two new methods of decomposition of the Earth's climate system into well separated modes were discussed. The first method [1-3] is based on the MSSA (Multichannel Singular Spectral Analysis) [4] for linear expanding vector (space-distributed) time series and makes allowance delayed correlations of the processes recorded in spatially separated points. The second one [5-7] allows to construct nonlinear dynamic modes, but neglects delay of correlations. It was demonstrated [1-3] that first method provides effective separation of different time scales, but prevent from correct reduction of data dimension: slope of variance spectrum of spatio-temporal empirical orthogonal functions that are "structural material" for linear spatio-temporal modes, is too flat. The second method overcomes this problem: variance spectrum of nonlinear modes falls essentially sharply [5-7]. However neglecting time-lag correlations brings error of mode selection that is uncontrolled and increases with growth of mode time scale. In the report we combine these two methods in such a way that the developed algorithm allows constructing nonlinear spatio-temporal modes. The algorithm is applied for decomposition of (i) multi hundreds years globally distributed data generated by the INM RAS Coupled Climate Model [8], and (ii) 156 years time series of SST anomalies distributed over the globe [9]. We compare efficiency of different methods of decomposition and discuss the abilities of nonlinear spatio-temporal modes for construction of adequate and concurrently simplest ("optimal") models of climate systems. 1. Feigin A.M., Mukhin D., Gavrilov A., Volodin E.M., and Loskutov E.M. (2013) "Separation of spatial-temporal patterns ("climatic modes") by combined analysis of really measured and generated numerically vector time series", AGU 2013 Fall Meeting, Abstract NG33A-1574. 2. Alexander Feigin, Dmitry Mukhin, Andrey Gavrilov, Evgeny Volodin, and Evgeny Loskutov (2014) "Approach to analysis of multiscale space-distributed time series: separation of spatio-temporal modes with essentially different time scales", Geophysical Research Abstracts, Vol. 16, EGU2014-6877. 3. Dmitry Mukhin, Dmitri Kondrashov, Evgeny Loskutov, Andrey Gavrilov, Alexander Feigin, and Michael Ghil (2014) "Predicting critical transitions in ENSO models, Part II: Spatially dependent models", Journal of Climate (accepted, doi: 10.1175/JCLI-D-14-00240.1). 4. Ghil, M., R. M. Allen, M. D. Dettinger, K. Ide, D. Kondrashov, et al. (2002) "Advanced spectral methods for climatic time series", Rev. Geophys. 40(1), 3.1-3.41. 5. Dmitry Mukhin, Andrey Gavrilov, Evgeny M Loskutov and Alexander M Feigin (2014) "Nonlinear Decomposition of Climate Data: a New Method for Reconstruction of Dynamical Modes", AGU 2014 Fall Meeting, Abstract NG43A-3752. 6. Andrey Gavrilov, Dmitry Mukhin, Evgeny Loskutov, and Alexander Feigin (2015) "Empirical decomposition of climate data into nonlinear dynamic modes", Geophysical Research Abstracts, Vol. 17, EGU2015-627. 7. Dmitry Mukhin, Andrey Gavrilov, Evgeny Loskutov, Alexander Feigin, and Juergen Kurths (2015) "Reconstruction of principal dynamical modes from climatic variability: nonlinear approach", Geophysical Research Abstracts, Vol. 17, EGU2015-5729. 8. http://83.149.207.89/GCM_DATA_PLOTTING/GCM_INM_DATA_XY_en.htm. 9. http://iridl.ldeo.columbia.edu/SOURCES/.KAPLAN/.EXTENDED/.v2/.ssta/.

  13. Spatiotemporal clustering and temporal order in the excitable BZ reaction

    NASA Astrophysics Data System (ADS)

    Hastings, Harold M.; Sobel, Sabrina G.; Lemus, Arely; Yuen, Fiona; Peralta, Catalina; Cammalleri, Carolyn; Chabrel, Johan; Chaterpaul, Stephen; Frank, Claudia; Hilaire, Christian; Lang, Daniel; Ravinovitch, Daniel; Zaharakis, Alex

    2005-08-01

    The prototype experimental example of "spontaneous" pattern formation in an unstirred chemical medium is the oscillatory Belousov-Zhabotinsky (BZ) reaction: target patterns of outward-moving concentric rings are readily observed when the reaction is run in a thin layer in a Petri dish. In many experimental runs, new target centers appeared to form closer to pre-existing target centers than expected in a randomized model. Here we describe a simple direct test for the presence of temporal order in the spatiotemporal dynamics of target nucleation, and apply this test to detect significant temporal order in target formation in the ferroin-catalyzed BZ reaction. We also describe how mixing heterogeneity can generate temporal order, even in the absence of heterogeneous physical nucleating centers.

  14. Spatiotemporal clustering and temporal order in the excitable BZ reaction.

    PubMed

    Hastings, Harold M; Sobel, Sabrina G; Lemus, Arely; Yuen, Fiona; Peralta, Catalina; Cammalleri, Carolyn; Chabrel, Johan; Chaterpaul, Stephen; Frank, Claudia; Hilaire, Christian; Lang, Daniel; Ravinovitch, Daniel; Zaharakis, Alex

    2005-08-01

    The prototype experimental example of "spontaneous" pattern formation in an unstirred chemical medium is the oscillatory Belousov-Zhabotinsky (BZ) reaction: target patterns of outward-moving concentric rings are readily observed when the reaction is run in a thin layer in a Petri dish. In many experimental runs, new target centers appeared to form closer to pre-existing target centers than expected in a randomized model. Here we describe a simple direct test for the presence of temporal order in the spatiotemporal dynamics of target nucleation, and apply this test to detect significant temporal order in target formation in the ferroin-catalyzed BZ reaction. We also describe how mixing heterogeneity can generate temporal order, even in the absence of heterogeneous physical nucleating centers. PMID:16122321

  15. Inferring Synaptic Connectivity from Spatio-Temporal Spike Patterns

    PubMed Central

    Van Bussel, Frank; Kriener, Birgit; Timme, Marc

    2011-01-01

    Networks of well-known dynamical units but unknown interaction topology arise across various fields of biology, including genetics, ecology, and neuroscience. The collective dynamics of such networks is often sensitive to the presence (or absence) of individual interactions, but there is usually no direct way to probe for their existence. Here we present an explicit method for reconstructing interaction networks of leaky integrate-and-fire neurons from the spike patterns they exhibit in response to external driving. Given the dynamical parameters are known, the approach works well for networks in simple collective states but is also applicable to networks exhibiting complex spatio-temporal spike patterns. In particular, stationarity of spiking time series is not required. PMID:21344004

  16. Passive spatiotemporal geometry reconstruction of human faces at high fidelity.

    PubMed

    Beeler, Thabo

    2015-01-01

    Creating photo-real digital human faces remains one of the biggest challenges in computer graphics. A core component of the challenge comes from the high complexity of the human face, and the difficult task of building realistic faces is aggravated by human perception. Based on the work of his doctorial thesis, the author and his colleagues developed a fully passive and markerless system that reconstructs facial geometry at the skin pore level and at a full frame rate, achieving the highest spatiotemporal resolution to date. Passive capture setups are simpler than active ones and only require cameras and static illumination. The author's research has already been implemented in production systems and used by the commercial videogame and entertainment industries. PMID:26010791

  17. Theranostic agents for intracellular gene delivery with spatiotemporal imaging

    PubMed Central

    Knipe, Jennifer M.; Peters, Jonathan T.; Peppas, Nicholas A.

    2013-01-01

    Gene therapy is the modification of gene expression to treat a disease. However, efficient intracellular delivery and monitoring of gene therapeutic agents is an ongoing challenge. Use of theranostic agents with suitable targeted, controlled delivery and imaging modalities has the potential to greatly advance gene therapy. Inorganic nanoparticles including magnetic nanoparticles, gold nanoparticles, and quantum dots have been shown to be effective theranostic agents for the delivery and spatiotemporal tracking of oligonucleotides in vitro and even a few cases in vivo. Major concerns remain to be addressed including cytotoxicity, particularly of quantum dots; effective dosage of nanoparticles for optimal theranostic effect; development of real-time in vivo imaging; and further improvement of gene therapy efficacy. PMID:23606894

  18. Spatiotemporal dynamics of excitons in monolayer and bulk WS2

    NASA Astrophysics Data System (ADS)

    He, Jiaqi; He, Dawei; Wang, Yongsheng; Cui, Qiannan; Ceballos, Frank; Zhao, Hui

    2015-05-01

    Spatiotemporal dynamics of excitons in monolayer and bulk WS2 at room temperature is studied by transient absorption microscopy in the reflection geometry. Excitons are formed from photocarriers injected by a tightly focused 390 nm pump pulse, and monitored by detecting different reflection of a time-delayed and spatially scanned 620 nm probe pulse. We obtain exciton lifetimes of 22 +/- 1 and 110 +/- 10 ps in monolayer and bulk WS2, respectively. Both lifetimes are independent of the exciton density, showing the absence of multi-exciton recombination processes. Exciton diffusion coefficients of 60 +/- 20 and 3.5 +/- 0.5 cm2 s-1 are obtained in monolayer and bulk samples, respectively. These results provide a foundation for understanding excitons in this new material and its optoelectronic applications.

  19. Clinical gait data analysis based on Spatio-Temporal features

    E-print Network

    Katiyar, Rohit

    2010-01-01

    Analysing human gait has found considerable interest in recent computer vision research. So far, however, contributions to this topic exclusively dealt with the tasks of person identification or activity recognition. In this paper, we consider a different application for gait analysis and examine its use as a means of deducing the physical well-being of people. The proposed method is based on transforming the joint motion trajectories using wavelets to extract spatio-temporal features which are then fed as input to a vector quantiser; a self-organising map for classification of walking patterns of individuals with and without pathology. We show that our proposed algorithm is successful in extracting features that successfully discriminate between individuals with and without locomotion impairment.

  20. Spatiotemporal reconstruction of list-mode PET data

    SciTech Connect

    Nichols, Thomas E.; Qi, Jinyi; Asma, Evren; Leahy, Richard M.

    2002-03-01

    We describe a method for computing a continuous time estimate of tracer density using list-mode positron emission tomography data. The rate function in each voxel is modeled as an inhomogeneous Poisson process whose rate function can be represented using a cubic B-spline basis. The rate functions are estimated by maximizing the likelihood of the arrival times of detected photon pairs over the control vertices of the spline, modified by quadratic spatial and temporal smoothness penalties and a penalty term to enforce nonnegativity. Randoms rate functions are estimated by assuming independence between the spatial and temporal randoms distributions. Similarly, scatter rate functions are estimated by assuming spatiotemporal independence and that the temporal distribution of the scatter is proportional to the temporal distribution of the trues. A quantitative evaluation was performed using simulated data and the method is also demonstrated in a human study using 11C-raclopride.

  1. Spatio-temporal characteristics of Trichel pulse at low pressure

    NASA Astrophysics Data System (ADS)

    He, Shoujie; Jing, Ha

    2014-01-01

    Trichel pulses are investigated using a needle-to-plane electrode geometry at low pressure. The evolution of current and voltage, the spatio-temporal discharge images of Trichel pulse are measured. The rising time and duration time in a pulse are about 10 ?s and several tens of microseconds, respectively. One period of pulse can be divided into three stages: the stage preceding cathode breakdown, cathode glow formation, and discharge decaying process. Besides a cathode glow and a dark space, an anode glow is also observed. The emission spectra mainly originate from the C3?u ? B3?g transition for nitrogen. In addition, the capacitances in parallel connected with the discharge cell have important influence on the pulsing frequency.

  2. Spatio-Temporal Structure of Hooded Gull Flocks

    PubMed Central

    Yomosa, Makoto; Mizuguchi, Tsuyoshi; Hayakawa, Yoshinori

    2013-01-01

    We analyzed the spatio-temporal structure of hooded gull flocks with a portable stereo camera system. The 3-dimensional positions of individuals were reconstructed from pairs of videos. The motions of each individual were analyzed, and both gliding and flapping motions were quantified based on the velocity time series. We analyzed the distributions of the nearest neighbor’s position in terms of coordinates based on each individual’s motion. The obtained results were consistent with the aerodynamic interaction between individuals. We characterized the leader-follower relationship between individuals by a delay time to mimic the direction of a motion. A relation between the delay time and a relative position was analyzed quantitatively, which suggested the basic properties of the formation flight that maintains order in the flock. PMID:24339960

  3. Spatiotemporal dynamics of excitons in monolayer and bulk WS2.

    PubMed

    He, Jiaqi; He, Dawei; Wang, Yongsheng; Cui, Qiannan; Ceballos, Frank; Zhao, Hui

    2015-05-21

    Spatiotemporal dynamics of excitons in monolayer and bulk WS2 at room temperature is studied by transient absorption microscopy in the reflection geometry. Excitons are formed from photocarriers injected by a tightly focused 390 nm pump pulse, and monitored by detecting different reflection of a time-delayed and spatially scanned 620 nm probe pulse. We obtain exciton lifetimes of 22 ± 1 and 110 ± 10 ps in monolayer and bulk WS2, respectively. Both lifetimes are independent of the exciton density, showing the absence of multi-exciton recombination processes. Exciton diffusion coefficients of 60 ± 20 and 3.5 ± 0.5 cm(2) s(-1) are obtained in monolayer and bulk samples, respectively. These results provide a foundation for understanding excitons in this new material and its optoelectronic applications. PMID:25947347

  4. Spatio-temporal characteristics of Trichel pulse at low pressure

    SciTech Connect

    He, Shoujie, E-mail: hedajingdian@126.com [College of Physics Science and Technology, Hebei University, Baoding (China)] [College of Physics Science and Technology, Hebei University, Baoding (China); Jing, Ha [Institute of Science, Hebei Agriculture University, Baoding (China)] [Institute of Science, Hebei Agriculture University, Baoding (China)

    2014-01-15

    Trichel pulses are investigated using a needle-to-plane electrode geometry at low pressure. The evolution of current and voltage, the spatio-temporal discharge images of Trichel pulse are measured. The rising time and duration time in a pulse are about 10??s and several tens of microseconds, respectively. One period of pulse can be divided into three stages: the stage preceding cathode breakdown, cathode glow formation, and discharge decaying process. Besides a cathode glow and a dark space, an anode glow is also observed. The emission spectra mainly originate from the C{sup 3}?{sub u} ? B{sup 3}?{sub g} transition for nitrogen. In addition, the capacitances in parallel connected with the discharge cell have important influence on the pulsing frequency.

  5. A spatio-temporal extension to the map cube operator

    NASA Astrophysics Data System (ADS)

    Alzate, Juan C.; Moreno, Francisco J.; Echeverri, Jaime

    2012-09-01

    OLAP (On Line Analytical Processing) is a set of techniques and operators to facilitate the data analysis usually stored in a data warehouse. In this paper, we extend the functionality of an OLAP operator known as Map Cube with the definition and incorporation of a function that allows the formulation of spatio-temporal queries. For example, consider a data warehouse about crimes that includes data about the places where the crimes were committed. Suppose we want to find and visualize the trajectory (a trajectory is just the path that an object follows through space as a function of time) of the crimes of a suspect beginning with his oldest crime and ending with his most recent one. In order to meet this requirement, we extend the Map Cube operator.

  6. Spatiotemporal positioning of multipotent modules in diverse biological networks.

    PubMed

    Chen, Yinying; Wang, Zhong; Wang, Yongyan

    2014-07-01

    A biological network exhibits a modular organization. The modular structure dependent on functional module is of great significance in understanding the organization and dynamics of network functions. A huge variety of module identification methods as well as approaches to analyze modularity and dynamics of the inter- and intra-module interactions have emerged recently, but they are facing unexpected challenges in further practical applications. Here, we discuss recent progress in understanding how such a modular network can be deconstructed spatiotemporally. We focus particularly on elucidating how various deciphering mechanisms operate to ensure precise module identification and assembly. In this case, a system-level understanding of the entire mechanism of module construction is within reach, with important implications for reasonable perspectives in both constructing a modular analysis framework and deconstructing different modular hierarchical structures. PMID:24413666

  7. IIS – Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools

    PubMed Central

    Carazzolle, Marcelo Falsarella; de Carvalho, Lucas Miguel; Slepicka, Hugo Henrique; Vidal, Ramon Oliveira; Pereira, Gonçalo Amarante Guimarães; Kobarg, Jörg; Vaz Meirelles, Gabriela

    2014-01-01

    Background High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. Results We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. Conclusions We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/. PMID:24949626

  8. SPATIO-TEMPORAL COMPLEXITY OF THE AORTIC SINUS VORTEX

    PubMed Central

    Moore, Brandon; Dasi, Lakshmi Prasad

    2014-01-01

    The aortic sinus vortex is a classical flow structure of significant importance to aortic valve dynamics and the initiation and progression of calific aortic valve disease. We characterize the spatio-temporal characteristics of aortic sinus voxtex dynamics in relation to the viscosity of blood analog solution as well as heart rate. High resolution time-resolved (2KHz) particle image velocimetry was conducted to capture 2D particle streak videos and 2D instantaneous velocity and streamlines along the sinus midplane using a physiological but rigid aorta model fitted with a porcine bioprosthetic heart valve. Blood analog fluids used include a water-glycerin mixture and saline to elucidate the sensitivity of vortex dynamics to viscosity. Experiments were conducted to record 10 heart beats for each combination of blood analog and heart rate condition. Results show that the topological characteristics of the velocity field vary in time-scales as revealed using time bin averaged vectors and corresponding instantaneous streamlines. There exist small time-scale vortices and a large time-scale main vortex. A key flow structure observed is the counter vortex at the upstream end of the sinus adjacent to the base (lower half) of the leaflet. The spatio-temporal complexity of vortex dynamics is shown to be profoundly influenced by strong leaflet flutter during systole with a peak frequency of 200Hz and peak amplitude of 4 mm observed in the saline case. While fluid viscosity influences the length and time-scales as well as the introduction of leaflet flutter, heart rate influences the formation of counter vortex at the upstream end of the sinus. Higher heart rates are shown to reduce the strength of the counter vortex that can greatly influence the directionality and strength of shear stresses along the base of the leaflet. This study demonstrates the impact of heart rate and blood analog viscosity on aortic sinus hemodynamics. PMID:25067881

  9. BioenergyKDF: Enabling Spatiotemporal Data Synthesis and Research Collaboration

    SciTech Connect

    Myers, Aaron T [ORNL; Movva, Sunil [ORNL; Karthik, Rajasekar [ORNL; Bhaduri, Budhendra L [ORNL; White, Devin A [ORNL; Thomas, Neil [ORNL; Chase, Adrian S Z [ORNL

    2014-01-01

    The Bioenergy Knowledge Discovery Framework (BioenergyKDF) is a scalable, web-based collaborative environment for scientists working on bioenergy related research in which the connections between data, literature, and models can be explored and more clearly understood. The fully-operational and deployed system, built on multiple open source libraries and architectures, stores contributions from the community of practice and makes them easy to find, but that is just its base functionality. The BioenergyKDF provides a national spatiotemporal decision support capability that enables data sharing, analysis, modeling, and visualization as well as fosters the development and management of the U.S. bioenergy infrastructure, which is an essential component of the national energy infrastructure. The BioenergyKDF is built on a flexible, customizable platform that can be extended to support the requirements of any user community especially those that work with spatiotemporal data. While there are several community data-sharing software platforms available, some developed and distributed by national governments, none of them have the full suite of capabilities available in BioenergyKDF. For example, this component-based platform and database independent architecture allows it to be quickly deployed to existing infrastructure and to connect to existing data repositories (spatial or otherwise). As new data, analysis, and features are added; the BioenergyKDF will help lead research and support decisions concerning bioenergy into the future, but will also enable the development and growth of additional communities of practice both inside and outside of the Department of Energy. These communities will be able to leverage the substantial investment the agency has made in the KDF platform to quickly stand up systems that are customized to their data and research needs.

  10. Spatiotemporal conceptual platform for querying archaeological information systems

    NASA Astrophysics Data System (ADS)

    Partsinevelos, Panagiotis; Sartzetaki, Mary; Sarris, Apostolos

    2015-04-01

    Spatial and temporal distribution of archaeological sites has been shown to associate with several attributes including marine, water, mineral and food resources, climate conditions, geomorphological features, etc. In this study, archeological settlement attributes are evaluated under various associations in order to provide a specialized query platform in a geographic information system (GIS). Towards this end, a spatial database is designed to include a series of archaeological findings for a secluded geographic area of Crete in Greece. The key categories of the geodatabase include the archaeological type (palace, burial site, village, etc.), temporal information of the habitation/usage period (pre Minoan, Minoan, Byzantine, etc.), and the extracted geographical attributes of the sites (distance to sea, altitude, resources, etc.). Most of the related spatial attributes are extracted with readily available GIS tools. Additionally, a series of conceptual data attributes are estimated, including: Temporal relation of an era to a future one in terms of alteration of the archaeological type, topologic relations of various types and attributes, spatial proximity relations between various types. These complex spatiotemporal relational measures reveal new attributes towards better understanding of site selection for prehistoric and/or historic cultures, yet their potential combinations can become numerous. Therefore, after the quantification of the above mentioned attributes, they are classified as of their importance for archaeological site location modeling. Under this new classification scheme, the user may select a geographic area of interest and extract only the important attributes for a specific archaeological type. These extracted attributes may then be queried against the entire spatial database and provide a location map of possible new archaeological sites. This novel type of querying is robust since the user does not have to type a standard SQL query but graphically select an area of interest. In addition, according to the application at hand, novel spatiotemporal attributes and relations can be supported, towards the understanding of historical settlement patterns.

  11. Toxic Releases and Risk Disparity: A Spatiotemporal Model of Industrial Ecology and Social Empowerment

    PubMed Central

    Aoyagi, Hannah; Ogunseitan, Oladele A.

    2015-01-01

    Information-based regulations (IBRs) are founded on the theoretical premise that public participation in accomplishing policy goals is empowered by open access to information. Since its inception in 1988, the Toxics Release Inventory (TRI) has provided the framework and regulatory impetus for the compilation and distribution of data on toxic releases associated with industrial development, following the tenets of IBR. As TRI emissions are reputed to disproportionately affect low-income communities, we investigated how demographic characteristics are related to change in TRI emissions and toxicity risks between 1989 and 2002, and we sought to identify factors that predict these changes. We used local indicators of spatial association (LISA) maps and spatial regression techniques to study risk disparity in the Los Angeles urban area. We also surveyed 203 individuals in eight communities in the same region to measure the levels of awareness of TRI, attitudes towards air pollution, and general environmental risk. We discovered, through spatial lag models, that changes in gross and toxic emissions are related to community ethnic composition, poverty level, home ownership, and base 1989 emissions (R-square = 0.034–0.083). We generated a structural equation model to explain the determinants of social empowerment to act on the basis of environmental information. Hierarchical confirmatory factor analysis (HCFA) supports the theoretical model that individual empowerment is predicted by risk perception, worry, and awareness (Chi-square = 63.315, p = 0.022, df = 42). This study provides strong evidence that spatiotemporal changes in regional-scale environmental risks are influenced by individual-scale empowerment mediated by IBRs. PMID:26042368

  12. "Smoking-Gun" Observables of Magnetic Reconnection: Spatiotemporal Evolution of Electron Characteristics Throughout the Diffusion Region

    NASA Astrophysics Data System (ADS)

    Shuster, J. R.; Chen, L. J.; Bessho, N.; Li, G.; Torbert, R. B.; Wang, S.; Argall, M. R.; Daughton, W. S.

    2014-12-01

    Electron distribution functions can provide "smoking-gun" evidence for the detection of electron diffusion regions in collisionless magnetic reconnection. Knowledge of the spatiotemporal evolution of electron distributions during reconnection is significantly lacking, and will further elucidate the outstanding questions of how, where, and when electrons are energized during reconnection. Based on spacecraft observations and PIC simulations of symmetric reconnection, electrons in the inflow region are known to exhibit a temperature anisotropy Te// > Te?. Studies of exhaust electrons have reported hot and isotropic electrons, while others have reported anisotropic exhaust structures. Electron distributions in the vicinity of the X-line have a triangular, 3D velocity space structure with distinct striations corresponding to the number of times electrons reflect within the electron current layer. Here, we report the spatial and temporal evolution of electron distributions from the vicinity of the X-line to the end of the electron outflow jet, with the discovery that the discrete striations swirl and rotate as electrons re-magnetize, forming arc and ring structures. Highly structured, time-dependent electron anisotropy develops in the exhaust distributions only near or after the peak reconnection rate, explaining the previous discrepancy concerning the degree of electron anisotropy in the exhaust, and suggesting a technique to infer the evolution stage of reconnection using spacecraft measurements. We also present a theory for predicting the spacing of the striations of electron distributions in the vicinity of the X-line based on local measurements, which could be directly tested by spacecraft observations. Electron data from Cluster magnetotail reconnection inflows and exhausts exhibit many anisotropic structures as predicted by simulation. Observed distributions near the reconnection mid-plane (Bx ~ 0 nT) are often highly structured with populations exhibiting Te? > Te// in addition to lower energy field-aligned beams. Our work advances the understanding of electron distribution evolution, setting a foundation to successfully interpret the high resolution electron data anticipated from NASA's upcoming Magnetospheric Multi-Scale Mission.

  13. In Situ Spatiotemporal Mapping of Flow Fields around Seeded Stem Cells at the Subcellular Length Scale

    PubMed Central

    Song, Min Jae; Dean, David; Knothe Tate, Melissa L.

    2010-01-01

    A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (?-PIV) for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD) predicts flow regimes within 12% of ?-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our ?-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms. PMID:20862249

  14. Detection of Dynamic Spatiotemporal Response to Periodic Chemical Stimulation in a Xenopus Embryonic Tissue

    PubMed Central

    Messner, William C.; LeDuc, Philip R.; Davidson, Lance A.

    2011-01-01

    Embryonic development is guided by a complex and integrated set of stimuli that results in collective system-wide organization that is both time and space regulated. These regulatory interactions result in the emergence of highly functional units, which are correlated to frequency-modulated stimulation profiles. We have determined the dynamic response of vertebrate embryonic tissues to highly controlled, time-varying localized chemical stimulation using a microfluidic system with feedback control. Our approach has enabled localized spatiotemporal manipulation of the steroid hormone dexamethasone (DEX) in Animal Cap (AC) tissues isolated from gastrulating Xenopus embryos. Using this approach we investigated cell-scale responses to precisely controlled stimulation by tracking the redistribution of a GFP-tagged DEX-reporter constructed from the human glucocorticoid receptor (GR). We exposed defined regions of a single AC explant to different stimulation conditions—continuous stimulation, periodic stimulation, and no stimulation. We observed collective behavior of the GR transport into the nucleus was first-order. Furthermore, the dynamic response was well-modeled by a first-order differential equation with a single time derivative. The model predicted that responses to periodic stimulations closely matched the results of the frequency-based experiments. We find that stimulation with localized bursts versus continuous stimulation can result in highly distinct responses. This finding is critical as controlled space and time exposure to growth factors is a hallmark of complex processes in embryonic development. These complex responses to cellular signaling and transport machinery were similar to emergent behaviors in other complex systems, suggesting that even within a complex embryonic tissue, the overall system can converge toward a predictive first-order response. PMID:21305055

  15. Toxic releases and risk disparity: a spatiotemporal model of industrial ecology and social empowerment.

    PubMed

    Aoyagi, Hannah; Ogunseitan, Oladele A

    2015-01-01

    Information-based regulations (IBRs) are founded on the theoretical premise that public participation in accomplishing policy goals is empowered by open access to information. Since its inception in 1988, the Toxics Release Inventory (TRI) has provided the framework and regulatory impetus for the compilation and distribution of data on toxic releases associated with industrial development, following the tenets of IBR. As TRI emissions are reputed to disproportionately affect low-income communities, we investigated how demographic characteristics are related to change in TRI emissions and toxicity risks between 1989 and 2002, and we sought to identify factors that predict these changes. We used local indicators of spatial association (LISA) maps and spatial regression techniques to study risk disparity in the Los Angeles urban area. We also surveyed 203 individuals in eight communities in the same region to measure the levels of awareness of TRI, attitudes towards air pollution, and general environmental risk. We discovered, through spatial lag models, that changes in gross and toxic emissions are related to community ethnic composition, poverty level, home ownership, and base 1989 emissions (R-square = 0.034-0.083). We generated a structural equation model to explain the determinants of social empowerment to act on the basis of environmental information. Hierarchical confirmatory factor analysis (HCFA) supports the theoretical model that individual empowerment is predicted by risk perception, worry, and awareness (Chi-square = 63.315, p = 0.022, df = 42). This study provides strong evidence that spatiotemporal changes in regional-scale environmental risks are influenced by individual-scale empowerment mediated by IBRs. PMID:26042368

  16. Mediated Spatiotemporal Fusion of Multiple Cardiac Magnetic Resonance Datasets for Patient-specific Perfusion Analysis

    E-print Network

    Magee, Derek

    ). This paper de- scribes the crucial component of this framework designed to establish a reliable correlationMediated Spatiotemporal Fusion of Multiple Cardiac Magnetic Resonance Datasets for Patient. Introduction Cardiovascular Magnetic Resonance (CMR) imaging provides diagnostic information for the assessment

  17. SPATIOTEMPORAL FORECASTING OF HOME PRICES: A GIS APPLICATION M.A. Kaboudan

    E-print Network

    Fernandez, Thomas

    calculations to estimate model coefficients and restrictions formal statistical models impose are totally be useful in modelling and forecasting spatiotemporal data. Statistical challenges that emanate from statistical complications encountered when analysing or modelling spatial data. When spatial data is taken

  18. Towards Duplicate Detection for Situation Awareness Based on Spatio-Temporal Relations

    E-print Network

    Hochreiter, Sepp

    Towards Duplicate Detection for Situation Awareness Based on Spatio-Temporal Relations Norbert, Altenbergerstr. 69, 4040 Linz, Austria Abstract. Systems supporting situation awareness typically integrate detection methods exist, a recent survey revealed that the character- istics of situation awareness

  19. CVPR 2006 Submission #795. CONFIDENTIAL REVIEW COPY. DO NOT DISTRIBUTE. Spatiotemporal Contour Tracking of Microtubules

    E-print Network

    California at Santa Barbara, University of

    COPY. DO NOT DISTRIBUTE. Spatiotemporal Contour Tracking of Microtubules Anonymous CVPR submission Address Line2 Paper ID 795 Abstract Microtubules (MTs), one of three major cytoskeletal components, serve. Introduction Microtubules (MTs) are cylindrical, cytoskeletal protein polymers found in essentially all

  20. Characterization of high spatiotemporal rainfall events in the upper washita river basin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transport phenomena at the watershed scale are driven by spatially distributed hydrological processes in which variable rainfall duration and intensity plays a fundamental role. Characterization of these rainfall phenomena using high spatiotemporal resolution is essential when using models to assess...

  1. Kronecker PCA based spatio-temporal modeling of video for dismount classification

    NASA Astrophysics Data System (ADS)

    Greenewald, Kristjan H.; Hero, Alfred O.

    2014-06-01

    We consider the application of KronPCA spatio-temporal modeling techniques1, 2 to the extraction of spatiotemporal features for video dismount classification. KronPCA performs a low-rank type of dimensionality reduction that is adapted to spatio-temporal data and is characterized by the T frame multiframe mean ? and covariance ? of p spatial features. For further regularization and improved inverse estimation, we also use the diagonally corrected KronPCA shrinkage methods we presented in.1 We apply this very general method to the modeling of the multivariate temporal behavior of HOG features extracted from pedestrian bounding boxes in video, with gender classification in a challenging dataset chosen as a specific application. The learned covariances for each class are used to extract spatiotemporal features which are then classified, achieving competitive classification performance.

  2. Complex spatiotemporal haemodynamic response following sensory stimulation in the awake rat

    E-print Network

    Reber, Paul J.

    Keywords: fMRI Neurovascular coupling Anaesthesia Haemodynamic Optical imaging Detailed understanding of neurovascular coupling or the haemodynamic response function. In this study we therefore measured spatiotemporal and therefore reflect neurovascular or cerebrovascular processes. These hitherto unreported hyperemic response

  3. Quasiperiodicity route to spatiotemporal chaos in one-dimensional pattern-forming systems

    NASA Astrophysics Data System (ADS)

    Clerc, Marcel G.; Verschueren, Nicolas

    2013-11-01

    We propose a route to spatiotemporal chaos for one-dimensional stationary patterns, which is a natural extension of the quasiperiodicity route for low-dimensional chaos to extended systems. This route is studied through a universal model of pattern formation. The model exhibits a scenario where stationary patterns become spatiotemporally chaotic through two successive bifurcations. First, the pattern undergoes a subcritical Andronov-Hopf bifurcation leading to an oscillatory pattern. Subsequently, a secondary bifurcation gives rise to an oscillation with an incommensurable frequency with respect to the former one. This last bifurcation is responsible for the spatiotemporally chaotic behavior. The Lyapunov spectrum enables us to identify the complex behavior observed as spatiotemporal chaos, and also from the larger Lyapunov exponents characterize the above instabilities.

  4. Validation of spatiotemporally dense springtime land surface phenology with intensive and upscale in situ

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Land surface phenology (LSP) developed using temporally and spatially optimized remote sensing data, is particularly promising for use in detailed ecosystem monitoring and modeling efforts. Validating spatiotemporally dense LSP using compatible (intensively collected) in situ phenological data is t...

  5. Spatiotemporal perspective on the decay of turbulence in wall-bounded flows Paul Manneville*

    E-print Network

    Paris-Sud XI, Université de

    to that occurring at a thermodynamic first-order phase transition. The approach, apt to deal with the large that a genuinely spatiotemporal dynamics is expected. A different angle of attack was proposed long ago by Pomeau

  6. Hostparasitoid persistence over variable spatio-temporally susceptible habitats: bottomup effects of ephemeral resources

    E-print Network

    de Aguiar, Marcus A. M.

    1665 Host­parasitoid persistence over variable spatio-temporally susceptible habitats: bottom fluctuations and environmental stochasticity affected the density of migrants, patch habitat connectivity habitat to breed species) on a random basis, rather than undergoing constant replenishment of resources

  7. Recognizing human actions by fusing spatio-temporal appearance and motion descriptors

    Microsoft Academic Search

    Lamberto Ballan; Marco Bertini; Alberto Del Bimbo; Lorenzo Seidenari; Giuseppe Serra

    2009-01-01

    In this paper we propose a new method for human action cat- egorization by using an effective combination of a new 3D gradient descriptor with an optic flow descriptor, to represent spatio-temporal interest points. These points are used to rep- resent video sequences using a bag of spatio-temporal visual words, following the successful results achieved in object and scene classification.

  8. Human Action Recognition and Localization using Spatio-temporal Descriptors and Tracking

    Microsoft Academic Search

    Lamberto Ballan; Marco Bertini; Alberto Del Bimbo; Lorenzo Seidenari; Giuseppe Serra

    2009-01-01

    In this paper we propose a system for human action tracking and recognition using a robust particle lter-based visual tracker and a novel descriptor, to represent spatio-temporal interest points, based on an eective combination of a new 3D gradient descriptor with an optic ow descriptor. These points are used to represent video sequences using a bag of spatio-temporal visual words,

  9. Concepts and Applications of Spatiotemporal Interoperability in Environmental and Emergency Management

    Microsoft Academic Search

    Ulrich Raape; Ingo Simonis; Thomas Schulze

    2005-01-01

    Interoperability of Systems and Services is gaining importance, but is mostly limited to a specific domain, e.g. the geospatial or modeling & simulation (M&S) domains. Spatiotemporal Interoperability describes an approach to exploit the synergies of coupling OGC-compliant services and HLA-based simulations in a standardized manner. The paper describes the current status of the Distributed spAtiotemporaL Interoperability Architecture (DALI), potential aplications

  10. Spatiotemporal mechanisms for simple image feature perception in normal and amblyopic vision.

    PubMed

    Song, Shuang; Levi, Dennis M

    2010-01-01

    We used the method of image classification to investigate the spatiotemporal mechanisms for simple feature perception in normal and amblyopic vision. In the first experiment, we estimated the spatiotemporal mechanism for detecting a luminance increment of a bright bar embedded in spatiotemporal noise for normal and amblyopic observers. The normal template is characterized by a temporal summation zone surrounded by symmetric spatial inhibition zones and followed by a temporal inhibition zone. The abnormal amblyopic template lacks inhibition but shows normal temporal summation. Neither blurring the stimuli in space nor varying the target signal-to-noise ratios caused any significant change in the normal or amblyopic template. However, decreasing the fundamental frequency of the stimuli restored the normal template in the amblyopic eye. Furthermore, the normal periphery demonstrates a spatiotemporal template similar to that of the amblyopic eye. The second experiment mapped the spatiotemporal interaction dynamics of flankers in an orientation discrimination task. For normal peripheral vision, assimilation of the perceived target orientation into the flanker orientation (i.e., crowding) occurs at flanker locations adjacent to the target in space and around or before the target presentation in time. Cueing the target may influence the spatiotemporal interaction map, but the strongest crowding never coincides with the target presentation. The amblyopic spatiotemporal interaction map is similar to that of the normal periphery, except that in general the spatiotemporal interaction is more widely distributed around and after the target presentation. Distant flankers induced "anti-crowding" (repulsion) of perceived orientation in both normal and amblyopic vision. PMID:21106686

  11. Spatio-temporal ranging behaviour and its relevance to foraging strategies in wide-ranging wolverines

    Microsoft Academic Search

    Roel May; Jiska van Dijk; Arild Landa; Roy Andersen; Reidar Andersen

    2010-01-01

    Conservation of carnivores in an increasingly changing environment is greatly helped by understanding the decision-making processes underlying habitat patch choice. Foraging theory may give us insight into spatio-temporal search patterns and consequent foraging decisions that carnivores make in heterogeneous and fluctuating environments. Constraints placed on central-place foragers in particular are likely to influence both foraging decisions and related spatio-temporal movement

  12. Geovisualization Approaches for Spatio-temporal Crime Scene Analysis - Towards 4D Crime Mapping

    Microsoft Academic Search

    Markus Wolff; Hartmut Asche

    2009-01-01

    This paper presents a set of methods and techniques for analysis and multidimensional visualisation of crime scenes in a German\\u000a city. As a first step the approach implies spatio-temporal analysis of crime scenes. Against this background a GIS-based application\\u000a is developed that facilitates discovering initial trends in spatio-temporal crime scene distributions even for a GIS untrained\\u000a user. Based on these

  13. Spatio-temporal foraging patterns of a giant zooplanktivore, the leatherback turtle

    Microsoft Academic Search

    Sabrina Fossette; Victoria J. Hobson; Charlotte Girard; Beatriz Calmettes; Philippe Gaspar; Jean-Yves Georges; Graeme C. Hays

    2010-01-01

    Understanding food web functioning through the study of natural bio-indicators may constitute a valuable and original approach. In the context of jellyfish proliferation in many overexploited marine ecosystems studying the spatio-temporal foraging patterns of the giant “jellyvore” leatherback turtle turns out to be particularly relevant. Here we analyzed long-term tracking data to assess spatio-temporal foraging patterns in 21 leatherback turtles

  14. Localized nonlinear matter waves in Bose-Einstein condensates with spatially and spatiotemporally modulated nonlinearities

    NASA Astrophysics Data System (ADS)

    Wang, Deng-Shan; Song, Shu-Wei; Liu, W. M.

    2012-12-01

    The novel phenomena arising from Bose-Einstein condensates with spatially and spatiotemporally modulated nonlinearities in external potential is reviewed from a theoretical viewpoint. We first present theoretical analysis and numerical studies of the localized nonlinear matter waves in one-dimensional single and two-component BECs with spatially and spatiotemporally modulated nonlinearities, respectively. It is shown that the spatially or spatiotemporally modulated nonlinearity can support stable novel localized nonlinear matter waves such as the breathing solitons and moving solitons. Then the quasi-two-dimensional BEC with spatially modulated nonlinearity is investigated and we show that all of the BECs, similar to the linear harmonic oscillator, can have an arbitrary number of localized nonlinear matter waves with discrete energies. Their properties are determined by the principal quantum number and secondary quantum number. Moreover, we investigate the quantized vortices in a rotating BEC with spatiotemporally modulated interaction in harmonic and anharmonic potentials, respectively. The exact quantized vortex and giant vortex solutions are constructed explicitly by similarity transformation. Their stability behavior is examined by numerical simulation, which shows that a new series of stable vortex states which are defined by radial and angular quantum numbers, can be supported by the spatiotemporally modulated interaction in this system. We find that there exist stable quantized vortices with large topological charges in repulsive condensates with spatiotemporally modulated interaction.

  15. Blind prediction of natural video quality.

    PubMed

    Saad, Michele A; Bovik, Alan C; Charrier, Christophe

    2014-03-01

    We propose a blind (no reference or NR) video quality evaluation model that is nondistortion specific. The approach relies on a spatio-temporal model of video scenes in the discrete cosine transform domain, and on a model that characterizes the type of motion occurring in the scenes, to predict video quality. We use the models to define video statistics and perceptual features that are the basis of a video quality assessment (VQA) algorithm that does not require the presence of a pristine video to compare against in order to predict a perceptual quality score. The contributions of this paper are threefold. 1) We propose a spatio-temporal natural scene statistics (NSS) model for videos. 2) We propose a motion model that quantifies motion coherency in video scenes. 3) We show that the proposed NSS and motion coherency models are appropriate for quality assessment of videos, and we utilize them to design a blind VQA algorithm that correlates highly with human judgments of quality. The proposed algorithm, called video BLIINDS, is tested on the LIVE VQA database and on the EPFL-PoliMi video database and shown to perform close to the level of top performing reduced and full reference VQA algorithms. PMID:24723532

  16. Metabolic-stress-induced rearrangement of the 14-3-3? interactome promotes autophagy via a ULK1- and AMPK-regulated 14-3-3? interaction with phosphorylated Atg9.

    PubMed

    Weerasekara, Vajira K; Panek, David J; Broadbent, David G; Mortenson, Jeffrey B; Mathis, Andrew D; Logan, Gideon N; Prince, John T; Thomson, David M; Thompson, J Will; Andersen, Joshua L

    2014-12-01

    14-3-3? promotes cell survival via dynamic interactions with a vast network of binding partners, many of which are involved in stress regulation. We show here that hypoxia (low glucose and oxygen) triggers a rearrangement of the 14-3-3? interactome to favor an interaction with the core autophagy regulator Atg9A. Our data suggest that the localization of mammalian Atg9A to autophagosomes requires phosphorylation on the C terminus of Atg9A at S761, which creates a 14-3-3? docking site. Under basal conditions, this phosphorylation is maintained at a low level and is dependent on both ULK1 and AMPK. However, upon induction of hypoxic stress, activated AMPK bypasses the requirement for ULK1 and mediates S761 phosphorylation directly, resulting in an increase in 14-3-3? interactions, recruitment of Atg9A to LC3-positive autophagosomes, and enhanced autophagosome production. These data suggest a novel mechanism whereby the level of autophagy induction can be modulated by AMPK/ULK1-mediated phosphorylation of mammalian Atg9A. PMID:25266655

  17. Metabolic-Stress-Induced Rearrangement of the 14-3-3? Interactome Promotes Autophagy via a ULK1- and AMPK-Regulated 14-3-3? Interaction with Phosphorylated Atg9

    PubMed Central

    Weerasekara, Vajira K.; Panek, David J.; Broadbent, David G.; Mortenson, Jeffrey B.; Mathis, Andrew D.; Logan, Gideon N.; Prince, John T.; Thomson, David M.; Thompson, J. Will

    2014-01-01

    14-3-3? promotes cell survival via dynamic interactions with a vast network of binding partners, many of which are involved in stress regulation. We show here that hypoxia (low glucose and oxygen) triggers a rearrangement of the 14-3-3? interactome to favor an interaction with the core autophagy regulator Atg9A. Our data suggest that the localization of mammalian Atg9A to autophagosomes requires phosphorylation on the C terminus of Atg9A at S761, which creates a 14-3-3? docking site. Under basal conditions, this phosphorylation is maintained at a low level and is dependent on both ULK1 and AMPK. However, upon induction of hypoxic stress, activated AMPK bypasses the requirement for ULK1 and mediates S761 phosphorylation directly, resulting in an increase in 14-3-3? interactions, recruitment of Atg9A to LC3-positive autophagosomes, and enhanced autophagosome production. These data suggest a novel mechanism whereby the level of autophagy induction can be modulated by AMPK/ULK1-mediated phosphorylation of mammalian Atg9A. PMID:25266655

  18. Matrix Factorization-Based Prediction of Novel Drug Indications by Integrating Genomic Space

    PubMed Central

    Dai, Wen; Liu, Xi; Gao, Yibo; Chen, Lin; Gao, Kuo; Jiang, Yongshi; Yang, Yiping; Chen, Jianxin

    2015-01-01

    There has been rising interest in the discovery of novel drug indications because of high costs in introducing new drugs. Many computational techniques have been proposed to detect potential drug-disease associations based on the creation of explicit profiles of drugs and diseases, while seldom research takes advantage of the immense accumulation of interaction data. In this work, we propose a matrix factorization model based on known drug-disease associations to predict novel drug indications. In addition, genomic space is also integrated into our framework. The introduction of genomic space, which includes drug-gene interactions, disease-gene interactions, and gene-gene interactions, is aimed at providing molecular biological information for prediction of drug-disease associations. The rationality lies in our belief that association between drug and disease has its evidence in the interactome network of genes. Experiments show that the integration of genomic space is indeed effective. Drugs, diseases, and genes are described with feature vectors of the same dimension, which are retrieved from the interaction data. Then a matrix factorization model is set up to quantify the association between drugs and diseases. Finally, we use the matrix factorization model to predict novel indications for drugs.

  19. Spatio-Temporal Controls of Stream Water Nitrogen Export in a Rapidly Developing Watershed in the Northern Rockies

    NASA Astrophysics Data System (ADS)

    Gardner, K. K.; McGlynn, B. L.

    2007-12-01

    Human alteration of the patterns of land use/land cover (LULC) on the earths surface is one of the most profound impacts on the functioning of natural ecosystems. At the watershed scale, we expect that not only the amount and type of landscape alteration, but also its spatial distribution and the corresponding watershed characteristics, hydrologic conditions, and biological season will dictate the spatio-temporal patterns of streamwater nitrogen (N). We conducted six synoptic sampling events (50 sites) and weekly streamwater sampling (7 sites) in the West Fork Watershed, a 212 km2 mountainous watershed in Southwestern Montana, which drains the rapidly developing Big Sky resort community. Synoptic sampling campaigns captured each season and a range of hydrological conditions and biologic activity. Samples were analyzed for inorganic and organic forms of nitrogen. We performed exploratory multiple regression analysis to determine the explanatory variables for spatio-temporal streamwater nitrogen (N) patterns. Variables considered included DEM derived hydrologic features (e.g. stream order, upland travel time, slope, aspect, riparian area, riparian buffer ratios, and watershed area), geology, forest cover, and septic locations. These variables were used in generalized least squares with a spatial correlation model based on weighted stream distance to predict streamwater nitrate concentrations. We found greatest correlation (adj r2 =0.90) in the winter with variables including number of septic locations, upland fertilization, and geology. This suggests nitrogen loading to the watershed was more conservatively transported through the uplands and stream network in the winter. In the late summer, however, transport and related biological variables became more important, and included travel time weighted septic loading locations, riparian hillslope buffer ratios, and stream order (adj. r2 =0.21). Here, we present the results of our exploratory statistical analysis as a first step toward modeling the impact of watershed location and spatial distribution of LULC change on the spatial, seasonal, and speciation patterns of streamwater N.

  20. The influence of weather and lemmings on spatiotemporal variation in the abundance of multiple avian guilds in the arctic.

    PubMed

    Robinson, Barry G; Franke, Alastair; Derocher, Andrew E

    2014-01-01

    Climate change is occurring more rapidly in the Arctic than other places in the world, which is likely to alter the distribution and abundance of migratory birds breeding there. A warming climate can provide benefits to birds by decreasing spring snow cover, but increases in the frequency of summer rainstorms, another product of climate change, may reduce foraging opportunities for insectivorous birds. Cyclic lemming populations in the Arctic also influence bird abundance because Arctic foxes begin consuming bird eggs when lemmings decline. The complex interaction between summer temperature, precipitation, and the lemming cycle hinder our ability to predict how Arctic-breeding birds will respond to climate change. The main objective of this study was to investigate the relationship between annual variation in weather, spring snow cover, lemming abundance and spatiotemporal variation in the abundance of multiple avian guilds in a tundra ecosystem in central Nunavut, Canada: songbirds, shorebirds, gulls, loons, and geese. We spatially stratified our study area based on vegetation productivity, terrain ruggedness, and freshwater abundance, and conducted distance sampling to estimate strata-specific densities of each guild during the summers of 2010-2012. We also monitored temperature, rainfall, spring snow cover, and lemming abundance each year. Spatial variation in bird abundance matched what was expected based on previous ecological knowledge, but weather and lemming abundance also significantly influenced the abundance of some guilds. In particular, songbirds were less abundant during the cool, wet summer with moderate snow cover, and shorebirds and gulls declined with lemming abundance. The abundance of geese did not vary over time, possibly because benefits created by moderate spring snow cover were offset by increased fox predation when lemmings were scarce. Our study provides an example of a simple way to monitor the correlation between weather, spring snow cover, lemming abundance, and spatiotemporal variations in Arctic-breeding birds. PMID:24983471

  1. The Influence of Weather and Lemmings on Spatiotemporal Variation in the Abundance of Multiple Avian Guilds in the Arctic

    PubMed Central

    Robinson, Barry G.; Franke, Alastair; Derocher, Andrew E.

    2014-01-01

    Climate change is occurring more rapidly in the Arctic than other places in the world, which is likely to alter the distribution and abundance of migratory birds breeding there. A warming climate can provide benefits to birds by decreasing spring snow cover, but increases in the frequency of summer rainstorms, another product of climate change, may reduce foraging opportunities for insectivorous birds. Cyclic lemming populations in the Arctic also influence bird abundance because Arctic foxes begin consuming bird eggs when lemmings decline. The complex interaction between summer temperature, precipitation, and the lemming cycle hinder our ability to predict how Arctic-breeding birds will respond to climate change. The main objective of this study was to investigate the relationship between annual variation in weather, spring snow cover, lemming abundance and spatiotemporal variation in the abundance of multiple avian guilds in a tundra ecosystem in central Nunavut, Canada: songbirds, shorebirds, gulls, loons, and geese. We spatially stratified our study area based on vegetation productivity, terrain ruggedness, and freshwater abundance, and conducted distance sampling to estimate strata-specific densities of each guild during the summers of 2010–2012. We also monitored temperature, rainfall, spring snow cover, and lemming abundance each year. Spatial variation in bird abundance matched what was expected based on previous ecological knowledge, but weather and lemming abundance also significantly influenced the abundance of some guilds. In particular, songbirds were less abundant during the cool, wet summer with moderate snow cover, and shorebirds and gulls declined with lemming abundance. The abundance of geese did not vary over time, possibly because benefits created by moderate spring snow cover were offset by increased fox predation when lemmings were scarce. Our study provides an example of a simple way to monitor the correlation between weather, spring snow cover, lemming abundance, and spatiotemporal variations in Arctic-breeding birds. PMID:24983471

  2. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

    PubMed Central

    2011-01-01

    Background Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. Results The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We demonstrate it's usefulness using the example of a signaling cascade leading to formation of a morphological gradient of Fus3 within the cytoplasm of the mating yeast cell Saccharomyces cerevisiae. Conclusions STSE is an efficient and powerful novel platform, designed for computational handling and evaluation of microscopic images. It allows for an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. By providing the means to relate the simulation to the image data it allows for systematic, image driven model validation or rejection. STSE can be scripted and extended using the Python language. STSE should be considered rather as an API together with workflow guidelines and a collection of GUI tools than a stand alone application. The priority of the project is to provide an easy and intuitive way of extending and customizing software using the Python language. PMID:21527030

  3. Spatiotemporal evolution of dehydration reactions in subduction zones (Invited)

    NASA Astrophysics Data System (ADS)

    Padron-Navarta, J.

    2013-12-01

    Large-scale deep water cycling takes place through subduction zones in the Earth, making our planet unique in the solar system. This idiosyncrasy is the result of a precise but unknown balance between in-gassing and out-gassing fluxes of volatiles. Water is incorporated into hydrous minerals during seafloor alteration of the oceanic lithosphere. The cycling of volatiles is triggered by dehydration of these minerals that release fluids from the subducting slab to the mantle wedge and eventually to the crust or to the deep mantle. Whereas the loci of such reactions are reasonably well established, the mechanisms of fluid migration during dehydration reactions are still barely known. One of the challenges is that dehydration reactions are dynamic features evolving in time and space. Experimental data on low-temperature dehydration reactions (i.e. gypsum) and numerical models applied to middle-crust conditions point to a complex spatiotemporal evolution of the dehydration process. The extrapolation of these inferences to subduction settings has not yet been explored but it is essential to understand the dynamism of these settings. Here I propose an alternative approach to tackle this problem through the textural study of high-pressure terrains that experienced dehydration reactions. Spatiotemporal evolution of dehydration reactions should be recorded during mineral nucleation and growth through variations in time and space of the reaction rate. Insights on the fluid migration mechanism could be inferred therefore by noting changes in the texture of prograde assemblages. The dehydration of antigorite in serpentinite is a perfect candidate to test this approach as it releases a significant amount of fluid and produces a concomitant porosity. Unusual alternation of equilibrium and disequilibrium textures observed in Cerro del Almirez (Betic Cordillera, S Spain)[1, 2] attest for a complex fluid migration pattern for one of the most relevant reactions in subduction zones. This opens the possibility to correlate textural features recorded in high-pressure terrains with the physical fingerprint of dehydration reactions such as fluid flow rates and eventually seismicity or tremor. References [1] Padrón-Navarta, J. A., Tommasi, A., Garrido, C. J., López Sánchez-Vizcaíno, V., Gómez-Pugnaire, M. T., Jabaloy, A. & Vauchez, A. (2010). Fluid transfer into the wedge controlled by high-pressure hydrofracturing in the cold top-slab mantle. Earth and Planetary Science Letters 297, 271-286. [2] Padrón-Navarta, J. A., López Sánchez-Vizcaíno, V., Garrido, C. J. & Gómez-Pugnaire, M. T. (2011). Metamorphic Record of High-pressure Dehydration of Antigorite Serpentinite to Chlorite Harzburgite in a Subduction Setting (Cerro del Almirez, Nevado-Filábride Complex, Southern Spain). Journal of Petrology 52, 2047-2078.

  4. A Bayesian spatiotemporal model for very large data sets.

    PubMed

    Harrison, L M; Green, G G R

    2010-04-15

    Functional MRI provides a unique perspective of neuronal organization; however, these data include many complex sources of spatiotemporal variability, which require spatial preprocessing and statistical analysis. For the latter, Bayesian models provide a promising alternative to classical inference, which uses results from Gaussian random field theory to assess the significance of spatially correlated statistic images. A Bayesian approach generalizes the application of these ideas in that (1) random fields are used to model all spatial parameters, not solely observation error, (2) their smoothness is optimized, and (3) a broader class of models can be compared. The main problem, however, is computational, due to the large number of voxels in a brain volume. Sampling methods are time-consuming; however, approximate inference using variational Bayes (VB) offers a principled and transparent way to specify assumptions necessary for computational tractability. Penny et al. (2005b) described such a scheme using a joint spatial prior and approximated the joint posterior density with one that factorized over voxels. However, a further computational bottleneck is encountered when evaluating the log model evidence used to compare models. This has lead to dividing a brain volume into slices and treating each independently. This amounts to approximating the spatial prior over a full volume with stacked 2D priors. That is, smoothness along the z-axis is not included in the model. Here we describe a VB scheme that approximates the zero mean joint spatial prior with a non-zero mean empirical prior that factors over voxels, thereby overcoming this problem. We do this by modifying the original VB algorithm of Penny et al. using the conditional form of a so-called conditional autoregressive (CAR) prior to update a marginal prior over voxels. We refer to this as a spatially-informed voxel-wise prior (SVP) and use them to spatially regularise general linear model (GLM) and autoregressive (AR) coefficients (over time to model serial correlations). This algorithm scales more favourably with the number of voxels providing a truly 3D spatiotemporal model over volumes containing tens of thousands of voxels. We compare the scaling of compute times with the number of voxels and performance with a joint prior applied to synthetic and single-subject data. PMID:20026230

  5. The use of regression and normalisation for the comparison of spatio-temporal gait data in children.

    PubMed

    Dixon, P C; Bowtell, M V; Stebbins, J

    2014-09-01

    Spatio-temporal parameters (STPs) are fundamental gait measures often used to compare children of different ages or gait ability. In the first case, non-dimensional normalisation (ND) of STPs using either leg-length or height is frequently conducted even though the process may not remove known inter-subject variability. STPs of children with and without disability can be compared through matched databases or using regression driven prediction. Unfortunately, database assignment is largely arbitrary and previous regressions have employed too few parameters to be successful. Therefore, the aims of this study were to test how well actual and ND STPs could be predicted from anthropometrics and speed and to assess if self-selected speed could be predicted from anthropometrics using multivariate regression in a cohort of eighty-nine typically developing children. Equations were validated on an extraneous dataset. We found that equations for actual step length, stride length, and cadence explained more than 84% of the variance compared to their ND counterparts. Moreover, only leg-length ND versions of these parameters were linearly proportional to speed. Prediction of single and double limb support times was weaker (R(2)=0.69 and 0.72, respectively) and we were unable to predict self-selected speed (R(2)<0.16) suggesting the use of anthropometrics is inappropriate for this purpose. Validation was successful for most STPs except in children lying near or outside the normal ranges and for gait speed. Clinically, regression could be used to quantify the difference between a patient's actual and theoretical STPs, allowing for monitoring of progress pre- and post intervention. PMID:25017327

  6. Testing the Spatio-temporal Transferability of a Hydrological Water Quality Model in Central Germany

    NASA Astrophysics Data System (ADS)

    Jomaa, Seifeddine; Jiang, Sanyuan; Rode, Michael

    2014-05-01

    Numerous studies have shown that the changes in land cover/use affect significantly the hydrological regime, which in turn influence the surface water quality. It is known that, at the catchment scale, hydrological modelling is a favourable tool for discharge and nutrients transport (such as Nitrogen and Phosphorus) predictions. The semi-distributed hydrological water quality HYPE (Hydrological Predictions for the Environment) model, has been evaluated for different catchments, and has been shown to reliably reproduce the measured data. The aim of this study was to test the spatio-temporal transferability of the HYPE model in Central Germany. First, the spatial transferability of the HYPE model was tested using two mesoscale catchments with different physiographical characteristics. To achieve our gaols, the Selke (463 km²) and Weida (99.5 km²) catchments, which are two small tributaries of the Elbe river basin were utilized. Second, the temporal transferability of the HYPE model was tested in the Weida catchment using different periods, where different patterns of nitrogen leaching were measured due to two considerable shifts in land use intensities and fertilizers application rates in 1990 and 1997. For Selke, the HYPE model reproduced reasonably well the discharge and IN monthly loads (with lowest NSE of 0.86 and 0.69 for discharge and IN loads, respectively). Also, results showed that only a NSE of 0.30 was obtained for the Weida catchment, in situations where the same best-optimized values from Selke was utilized, reflecting the controlling factors of land use and topography on the runoff generation. However, when the physiographical characteristics of the Weida catchment were considered during the calibration and validation phases (1997-2000 and 2001-2004, respectively, daily data), the HYPE model could reasonably predict the measured discharge and IN concentrations with similar performance as the Selke. In addition, the temporal transferability of the HYPE model was tested successfully in the Weida catchment by representing the dynamics of IN concentrations during the periods of 1983-2004 by adjusting land use intensities and fertilizers inputs in three different periods, respectively. The preliminary results of this study will be discussed and presented.

  7. Spatiotemporal Molecular Analysis of Cyanobacteria Blooms Reveals Microcystis-Aphanizomenon Interactions

    PubMed Central

    Miller, Todd R.; Beversdorf, Lucas; Chaston, Sheena D.; McMahon, Katherine D.

    2013-01-01

    Spatial and temporal variability in cyanobacterial community composition (CCC) within and between eutrophic lakes is not well-described using culture independent molecular methods. We analyzed CCC across twelve locations in four eutrophic lakes and within-lake locations in the Yahara Watershed, WI, on a weekly basis, for 5 months. Taxa were discriminated by length of MspI-digested cpcB/A intergenic spacer gene sequences and identified by comparison to a PCR-based clone library. CCC across all stations was spatially segregated by depth of sampling locations (ANOSIM R = 0.23, p < 0.001). Accordingly, CCC was correlated with thermal stratification, nitrate and soluble reactive phosphorus (SRP, R = 0.2-0.3). Spatial variability in CCC and temporal trends in taxa abundances were rarely correlative between sampling locations in the same lake indicating significant within lake spatiotemporal heterogeneity. Across all stations, a total of 37 bloom events were observed based on distinct increases in phycocyanin. Out of 97 taxa, a single Microcystis, and two different Aphanizomenon taxa were the dominant cyanobacteria detected during bloom events. The Microcystis and Aphanizomenon taxa rarely bloomed together and were significantly anti-correlated with each other at 9 of 12 stations with Pearson R values of -0.6 to -0.9 (p < 0.001). Of all environmental variables measured, nutrients, especially nitrate were significantly greater during periods of Aphanizomenon dominance while the nitrate+nitrite:SRP ratio was lower. This study shows significant spatial variability in CCC within and between lakes structured by depth of the sampling location. Furthermore, our study reveals specific genotypes involved in bloom formation. More in-depth characterization of these genotypes should lead to a better understanding of factors promoting bloom events in these lakes and more reliable bloom prediction models. PMID:24086400

  8. Spatiotemporal molecular analysis of cyanobacteria blooms reveals Microcystis--Aphanizomenon interactions.

    PubMed

    Miller, Todd R; Beversdorf, Lucas; Chaston, Sheena D; McMahon, Katherine D

    2013-01-01

    Spatial and temporal variability in cyanobacterial community composition (CCC) within and between eutrophic lakes is not well-described using culture independent molecular methods. We analyzed CCC across twelve locations in four eutrophic lakes and within-lake locations in the Yahara Watershed, WI, on a weekly basis, for 5 months. Taxa were discriminated by length of MspI-digested cpcB/A intergenic spacer gene sequences and identified by comparison to a PCR-based clone library. CCC across all stations was spatially segregated by depth of sampling locations (ANOSIM R = 0.23, p < 0.001). Accordingly, CCC was correlated with thermal stratification, nitrate and soluble reactive phosphorus (SRP, R = 0.2-0.3). Spatial variability in CCC and temporal trends in taxa abundances were rarely correlative between sampling locations in the same lake indicating significant within lake spatiotemporal heterogeneity. Across all stations, a total of 37 bloom events were observed based on distinct increases in phycocyanin. Out of 97 taxa, a single Microcystis, and two different Aphanizomenon taxa were the dominant cyanobacteria detected during bloom events. The Microcystis and Aphanizomenon taxa rarely bloomed together and were significantly anti-correlated with each other at 9 of 12 stations with Pearson R values of -0.6 to -0.9 (p < 0.001). Of all environmental variables measured, nutrients, especially nitrate were significantly greater during periods of Aphanizomenon dominance while the nitrate+nitrite:SRP ratio was lower. This study shows significant spatial variability in CCC within and between lakes structured by depth of the sampling location. Furthermore, our study reveals specific genotypes involved in bloom formation. More in-depth characterization of these genotypes should lead to a better understanding of factors promoting bloom events in these lakes and more reliable bloom prediction models. PMID:24086400

  9. Towards an purely data driven view on the global carbon cycle and its spatiotemporal variability

    NASA Astrophysics Data System (ADS)

    Zscheischler, Jakob; Mahecha, Miguel; Reichstein, Markus; Avitabile, Valerio; Carvalhais, Nuno; Ciais, Philippe; Gans, Fabian; Gruber, Nicolas; Hartmann, Jens; Herold, Martin; Jung, Martin; Landschützer, Peter; Laruelle, Goulven; Lauerwald, Ronny; Papale, Dario; Peylin, Philippe; Regnier, Pierre; Rödenbeck, Christian; Cuesta, Rosa Maria Roman; Valentini, Ricardo

    2015-04-01

    Constraining carbon (C) fluxes between the Earth's surface and the atmosphere at regional scale via observations is essential for understanding the Earth's carbon budget and predicting future atmospheric C concentrations. Carbon budgets have often been derived based on merging observations, statistical models and process-based models, for example in the Global Carbon Project (GCP). However, it would be helpful to derive global C budgets and fluxes at global scale as independent as possible from model assumptions to obtain an independent reference. Long-term in-situ measurements of land and ocean C stocks and fluxes have enabled the derivation of a new generation of data driven upscaled data products. Here, we combine a wide range of in-situ derived estimates of terrestrial and aquatic C fluxes for one decade. The data were produced and/or collected during the FP7 project GEOCARBON and include surface-atmosphere C fluxes from the terrestrial biosphere, fossil fuels, fires, land use change, rivers, lakes, estuaries and open ocean. By including spatially explicit uncertainties in each dataset we are able to identify regions that are well constrained by observations and areas where more measurements are required. Although the budget cannot be closed at the global scale, we provide, for the first time, global time-varying maps of the most important C fluxes, which are all directly derived from observations. The resulting spatiotemporal patterns of C fluxes and their uncertainties inform us about the needs for intensifying global C observation activities. Likewise, we provide priors for inversion exercises or to identify regions of high (and low) uncertainty of integrated C fluxes. We discuss the reasons for regions of high observational uncertainties, and for biases in the budget. Our data synthesis might also be used as empirical reference for other local and global C budgeting exercises.

  10. Convective rain cells: radar-derived spatio-temporal characteristics and synoptic patterns

    NASA Astrophysics Data System (ADS)

    Peleg, N.; Morin, E.

    2012-04-01

    In this study we present the spatiotemporal characteristics of convective rain cells over the Eastern Mediterranean (northern Israel) and their relationship to synoptic patterns. Information on rain cell features was extracted from high-resolution weather radar data for a total of 191,586 radar volume scans from 12 hydrological years. The convective rain cell features (i.e., cell area, rainfall intensity and cell orientation) were obtained using cell segmentation technique. Cell tracking algorithm was used to analyze the changes of those features over time. Convective rain cells were clustered into three synoptic types (two extratropical winter lows: deep Cyprus low and shallow low, and a tropical intrusion: Active Red Sea Trough) using several NCEP/NCAR parameters, and empirical distributions were computed for their spatial and temporal features. In the study region, it was found that the Active Red Sea Trough rain cells are larger, live for less time and possess lower rain intensities than the rain cells generated by the winter lows. The Cyprus low rain cells were found to be less intense and slightly larger on average than the shallow low rain cells. It was further discovered that the preferential orientation of the rain cells is associated with the direction and velocity of the wind. The effect of distance from the coastline was also examined. An increase in the number and area of the rain cells near the coastline was observed, presumably due to the sea breeze convection. The mean rainfall intensity was found to peak near the shore and decrease with distance inland. This information is of great importance for understanding rain patterns and can be further applied in exploring the hydrological responses of the basins in this region. The presented study is the first step in achieving the long-term goal: to develop a high space-time resolution weather generator for creating rainfall ensembles under different climatology scenarios. Those rainfall ensembles will be incorporated into hydrological models for simulating hydrological response under predicted climate changes.

  11. Landscape control of uranium and thorium in boreal streams - spatiotemporal variability and the role of wetlands

    NASA Astrophysics Data System (ADS)

    Lidman, F.; Mörth, C. M.; Laudon, H.

    2012-11-01

    The concentrations of uranium and thorium in ten partly nested streams in the boreal forest region were monitored over a two-year period. The investigated catchments ranged from small headwaters (0.1 km2) up to a fourth-order stream (67 km2). Considerable spatiotemporal variations were observed, with little or no correlation between streams. The fluxes of both uranium and thorium varied substantially between the subcatchments, ranging from 1.7 to 30 g km-2 a-1 for uranium and from 3.2 to 24 g km-2 a-1 for thorium. Airborne gamma spectrometry was used to measure the concentrations of uranium and thorium in surface soils throughout the catchment, suggesting that the concentrations of uranium and thorium in mineral soils are similar throughout the catchment. The fluxes of uranium and thorium were compared to a wide range of parameters characterising the investigated catchments and the chemistry of the stream water, e.g. soil concentrations of these elements, pH, TOC (total organic carbon), Al, Si and hydrogen carbonate, but it was concluded that the spatial variabilities in the fluxes of both uranium and thorium mainly were controlled by wetlands. The results indicate that there is a predictable and systematic accumulation of both uranium and thorium in boreal wetlands that is large enough to control the transport of these elements. On the landscape scale approximately 65-80% of uranium and 55-65% of thorium entering a wetland were estimated to be retained in the peat. Overall, accumulation in mires and other types of wetlands was estimated to decrease the fluxes of uranium and thorium from the boreal forest landscape by 30-40%, indicating that wetlands play an important role for the biogeochemical cycling of uranium and thorium in the boreal forest landscape. The atmospheric deposition of uranium and thorium was also quantified, and its contribution to boreal streams was found to be low compared to weathering.

  12. Spatio-Temporal Dynamics of Urban Expansion in Japan Using Gridded Land Use Data, Population Census Data and DMSP Data

    NASA Astrophysics Data System (ADS)

    Bagan, H.; Yamagata, Y.

    2014-12-01

    Integration of population data, land-use data, and satellite images can be used to identify and characterize the spatio-temporal extent and expansion trends of urban growth. We provided an idea to investigate the spatio-temporal urban growth using satellite images with population data. We analyze the urban expansion in Japan from 1990 to 2005 by using gridded land-use data, population census data, and DMSP satellite images of nighttime lights. First, we mapped the DMSP nighttime lights and land-use data onto a grid based on the standard 1 km2grid cell system of Japan to determine the proportional areas of DMSP nighttime lights and urban land use within each grid cell. Then, we investigated the relationships among population density, DMSP nighttime lights area, and urban area. A rapid expansion of the urban/built-up area around megacities was associated with population increases; in contrast, population density dropped steeply in rural areas and in small towns. Spatial correlation analysis showed a strong positive correlation between population density and urban land use (r= 0.59). In addition, correlation coefficients between population density and DMSP data increased as the DMSP nighttime lights brightness value increased. We then used census population data as the base population input, and performed a linear multiple regression analysis to predict population density from the combination of urban land-use area and DMSP data in Hokkaido, Japan. Visual and numerical evaluation of the results showed that the combination of urban land-use data and DMSP data could be used to predict the spatial distribution of population density. The results from this study indicated the high correlation between these data and suggested the potentials of population density prediction using DMSP data and land use data. References Bagan, H., and Y. Yamagata. Land-cover change analysis in 50 global cities by using a combination of Landsat data and analysis of grid cell. Environmental Research Letters, vol.9, no. 6, 064015. Jun. 2014. Bagan, H., and Y. Yamagata. Landsat analysis of urban growth: How Tokyo became the world's largest megacity during the last 40 years. Remote Sensing of Environment, vol.127, pp. 210-222. Dec. 2012.

  13. Spatiotemporal receptive field structures in retinogeniculate connections of cat

    PubMed Central

    Suematsu, Naofumi; Naito, Tomoyuki; Miyoshi, Tomomitsu; Sawai, Hajime; Sato, Hiromichi

    2013-01-01

    The spatial structure of the receptive field (RF) of cat lateral geniculate nucleus (LGN) neurons is significantly elliptical, which may provide a basis for the orientation tuning of LGN neurons, especially at high spatial frequency stimuli. However, the input mechanisms generating this elliptical RF structure are poorly defined. We therefore compared the spatiotemporal RF structures of pairs of retinal ganglion cells (RGCs) and LGN neurons that form monosynaptic connections based on the cross-correlation analysis of their firing activities. We found that the spatial RF structure of both RGCs and LGN neurons were comparably elliptical and oriented in a direction toward the area centralis. Additionally, the spatial RF structures of pairs with the same response sign were often overlapped and similarly oriented. We also found there was a small population of pairs with RF structures that had the opposite response sign and were spatially displaced and independently oriented. Finally, the temporal RF structure of an RGC was tightly correlated with that of its target LGN neuron, though the response duration of the LGN neuron was significantly longer. Our results suggest that the elliptical RF structure of an LGN neuron is mainly inherited from the primary projecting RGC and is affected by convergent inputs from multiple RGCs. We discuss how the convergent inputs may enhance the stimulus feature sensitivity of LGN neurons. PMID:24367299

  14. A Distributed Spatio-Temporal EEG/MEG Inverse Solver

    PubMed Central

    Hämäläinen, Matti S.; Golland, Polina

    2009-01-01

    We propose a novel ?1?2-norm inverse solver for estimating the sources of EEG/MEG signals. Developed based on the standard ?1-norm inverse solvers, this sparse distributed inverse solver integrates the ?1-norm spatial model with a temporal model of the source signals in order to avoid unstable activation patterns and “spiky” reconstructed signals often produced by the currently used sparse solvers. The joint spatio-temporal model leads to a cost function with an ?1?2-norm regularizer whose minimization can be reduced to a convex second-order cone programming (SOCP) problem and efficiently solved using the interior-point method. The efficient computation of the SOCP problem allows us to implement permutation tests for estimating statistical significance of the inverse solution. Validation with simulated and real MEG data shows that the proposed solver yields source time course estimates qualitatively similar to those obtained through dipole fitting, but without the need to specify the number of dipole sources in advance. Furthermore, the ?1?2-norm solver achieves fewer false positives and a better representation of the source locations than the conventional ?2 minimum-norm estimates. PMID:18603008

  15. A distributed spatio-temporal EEG/MEG inverse solver

    PubMed Central

    Ou, Wanmei; Hämäläinen, Matti S.; Golland, Polina

    2009-01-01

    We propose a novel ?1?2-norm inverse solver for estimating the sources of EEG/MEG signals. Based on the standard ?1-norm inverse solvers, this sparse distributed inverse solver integrates the ?1-norm spatial model with a temporal model of the source signals in order to avoid unstable activation patterns and “spiky” reconstructed signals often produced by the currently used sparse solvers. The joint spatio-temporal model leads to a cost function with an ?1?2-norm regularizer whose minimization can be reduced to a convex second-order cone programming (SOCP) problem and efficiently solved using the interior-point method. The efficient computation of the SOCP problem allows us to implement permutation tests for estimating statistical significance of the inverse solution. Validation with simulated and human MEG data shows that the proposed solver yields source time course estimates qualitatively similar to those obtained through dipole fitting, but without the need to specify the number of dipole sources in advance. Furthermore, the ?1?2-norm solver achieves fewer false positives and a better representation of the source locations than the conventional ?2 minimum-norm estimates. PMID:18979728

  16. Hierarchical spatiotemporal modeling for dynamic video trajectory analysis

    NASA Astrophysics Data System (ADS)

    Kim, Byung Hyung; Shin, Hak Chul; Rhee, Phill Kyu

    2011-10-01

    Normalcy decision in video security involves highly uncertain phenomena due to its inherited insufficient knowledge, intrinsic ambiguity in human cognition, measurement error, etc. This paper presents a hierarchical spatiotemporal trajectory modeling for dynamic trajectory analysis using sparse trajectory data. The trajectory data is assumed to be given by people detection and tracking methods, which are also challenging issues due to occlusion, noise, illumination changes, etc. The proposed method partitions the trajectory feature space into the attributes of trajectory position, direction, and speed. Inherent uncertainty of video trajectory is tackled by employing the uncertainty propagation model of a trajectory segment and Markov random field in analyzing the uncertainty attributes of object movement direction and speed. The proposed method can be used in online learning for incremental adaptation as well as offline learning for optimality guarantee. The method was evaluated using both synthetic trajectories and video streams of multiple people movements acquired from multiple video cameras developed by GE Global Research Center and KAL beta sites. Extensive experiments were performed using video sequences in real world and synthesized trajectories, which achieved very encouraging results.

  17. Spatiotemporal changes in the role of cytokinin during root development.

    PubMed

    Del Bianco, Marta; Giustini, Leonardo; Sabatini, Sabrina

    2013-07-01

    The root is a dynamic system whose structure is regulated by a complex network of interactions between hormones. The primary root meristem is specified in the embryo. After germination, the primary root meristem grows and then reaches a final size that will be maintained during the life of the plant. Subsequently, secondary structures such as lateral roots and root nodules form via the re-specification of differentiated cells. Cytokinin plays key roles in the regulation of root development. Down-regulation of the cytokinin response is required for the specification of a new stem cell niche, during both embryo and lateral root development. In the root meristem, cytokinin signalling regulates the longitudinal zonation of the meristem by controlling cell differentiation. Moreover, cytokinin regulates radial patterning of root vasculature by promoting protophloem cell identity and by spatially inhibiting protoxylem formation. In this review, an effort is made to describe the known details of the role of cytokinin during root development, taking into account also the interactions between cytokinin and other hormones. Attention is given on the dynamicity of cytokinin signalling output during different developmental events. Indeed, there is much evidence that the effects of cytokinin change as organs grow, underlining the importance of the spatiotemporal specificity of cytokinin signalling. PMID:23692218

  18. Spatio-temporal statistical models for river monitoring networks.

    PubMed

    Clement, L; Thas, O; Vanrolleghem, P A; Ottoy, J P

    2006-01-01

    When introducing new wastewater treatment plants (WWTP), investors and policy makers often want to know if there indeed is a beneficial effect of the installation of a WWTP on the river water quality. Such an effect can be established in time as well as in space. Since both temporal and spatial components affect the output of a monitoring network, their dependence structure has to be modelled. River water quality data typically come from a river monitoring network for which the spatial dependence structure is unidirectional. Thus the traditional spatio-temporal models are not appropriate, as they cannot take advantage of this directional information. In this paper, a state-space model is presented in which the spatial dependence of the state variable is represented by a directed acyclic graph, and the temporal dependence by a first-order autoregressive process. The state-space model is extended with a linear model for the mean to estimate the effect of the activation of a WWTP on the dissolved oxygen concentration downstream. PMID:16532730

  19. Spatiotemporal Analysis of Differential Akt Regulation in Plasma Membrane Microdomains

    PubMed Central

    Gao, Xinxin

    2008-01-01

    As a central kinase in the phosphatidylinositol 3-kinase pathway, Akt has been the subject of extensive research; yet, spatiotemporal regulation of Akt in different membrane microdomains remains largely unknown. To examine dynamic Akt activity in membrane microdomains in living cells, we developed a specific and sensitive fluorescence resonance energy transfer-based Akt activity reporter, AktAR, through systematic testing of different substrates and fluorescent proteins. Targeted AktAR reported higher Akt activity with faster activation kinetics within lipid rafts compared with nonraft regions of plasma membrane. Disruption of rafts attenuated platelet-derived growth factor (PDGF)-stimulated Akt activity in rafts without affecting that in nonraft regions. However, in insulin-like growth factor-1 (IGF)-1 stimulation, Akt signaling in nonraft regions is dependent on that in raft regions. As a result, cholesterol depletion diminishes Akt activity in both regions. Thus, Akt activities are differentially regulated in different membrane microdomains, and the overall activity of this oncogenic pathway is dependent on raft function. Given the increased abundance of lipid rafts in some cancer cells, the distinct Akt-activating characteristics of PDGF and IGF-1, in terms of both effectiveness and raft dependence, demonstrate the capabilities of different growth factor signaling pathways to transduce differential oncogenic signals across plasma membrane. PMID:18701703

  20. Spatiotemporal analysis of differential Akt regulation in plasma membrane microdomains.

    PubMed

    Gao, Xinxin; Zhang, Jin

    2008-10-01

    As a central kinase in the phosphatidylinositol 3-kinase pathway, Akt has been the subject of extensive research; yet, spatiotemporal regulation of Akt in different membrane microdomains remains largely unknown. To examine dynamic Akt activity in membrane microdomains in living cells, we developed a specific and sensitive fluorescence resonance energy transfer-based Akt activity reporter, AktAR, through systematic testing of different substrates and fluorescent proteins. Targeted AktAR reported higher Akt activity with faster activation kinetics within lipid rafts compared with nonraft regions of plasma membrane. Disruption of rafts attenuated platelet-derived growth factor (PDGF)-stimulated Akt activity in rafts without affecting that in nonraft regions. However, in insulin-like growth factor-1 (IGF)-1 stimulation, Akt signaling in nonraft regions is dependent on that in raft regions. As a result, cholesterol depletion diminishes Akt activity in both regions. Thus, Akt activities are differentially regulated in different membrane microdomains, and the overall activity of this oncogenic pathway is dependent on raft function. Given the increased abundance of lipid rafts in some cancer cells, the distinct Akt-activating characteristics of PDGF and IGF-1, in terms of both effectiveness and raft dependence, demonstrate the capabilities of different growth factor signaling pathways to transduce differential oncogenic signals across plasma membrane. PMID:18701703

  1. Reference Canopy Stomatal Conductance Explains Spatiotemporal Patterns of Tree Transpiration

    NASA Astrophysics Data System (ADS)

    Loranty, M. M.; Mackay, D. S.; Ewers, B. E.; Kruger, E. L.; Traver, E.

    2007-12-01

    Increased heterogeneity in patterns of whole tree transpiration (EC) with increasing atmospheric vapor pressure deficit (D) suggests a dynamic response of sap flow velocity (JS) to environmental drivers. We hypothesized that differences in reference stomatal conductance (GSref), stomatal conductance at D = 1kPa, would explain the spatiotemporal dynamics of JS. Using a coupled model of plant hydraulic and biochemical processes we tested this hypothesis with sap flux data for 106 aspen ( Populus tremuloides) and 108 sugar maple ( Acer saccharum) trees collected from plots using in 2-D cyclic sampling scheme during the summer of 2005 in northern Wisconsin. Inverse modeling is used to estimate GSref for each tree. For each species, trees from across the ranges of JS and diameter distributions are compared. GSref explained temporal variability in spatial patterns of EC We explore several possible mechanistic explanations for differences in GSref among trees. Topoedaphic factors are considered to determine if location within a stand has an effect. We also consider competition with neighboring individuals as a possible explanation. Variations in GSref in aspen were explained in part by competition for light between neighboring individuals, while competition for light was not a significant factor for sugar maple. Based on simulation analysis we identify possible biochemical feedbacks as drivers of the variability in plant hydraulics. Other factors examined included micro-topography within both sites.

  2. Spatiotemporal Dynamics of Wind Velocity from Mini-Sodar Measurements

    NASA Astrophysics Data System (ADS)

    Krasnenko, N. P.; Tarasenkov, M. V.; Shamanaeva, L. G.

    2015-03-01

    Mini-sodar measurements of wind velocity profiles in the 20-200 m layer have demonstrated the high efficiency of the use of mini-sodars in monitoring the fine structure of the atmospheric boundary layer (ABL) and in detecting jets and wind shear. An analysis of measurements of vertical profiles of the wind velocity and its vertical and horizontal components has shown that analytical approximations of the vertical profile of the horizontal wind velocity are possible for both neutral and unstable stratifications of the atmosphere. They are well described by a logarithmic law. The approximation constants are found and the errors associated with their use are estimated. The established physical trends and the obtained constants for the horizontal and vertical components of the wind velocity allow a description of their hourly and daily dynamics and can be recommended for use in ABL models intended for prognostic calculations (forecasting). The vector representation makes it possible to visualize the spatiotemporal dynamics of the wind field in the atmospheric boundary layer, in particular to estimate the shape and size of jets and wind shear in them.

  3. Stability and dynamics of spatio-temporal structures

    SciTech Connect

    Riecke, H.

    1993-03-01

    The main goal of the project supported in this grant is to contribute to the understanding of localized spatial and spatio-temporal structures far from thermodynamic equilibrium. Here we report on our progress in the study of two classes of systems. (1) We have started to investigate localized wave-pulses in binary-mixture convection. This work is based on our recently derived extension of the conventionally used complex Ginzburg-Landau equations. We are considering three regimes: Dispersion-less supercritical waves; strongly dispersive subcritical waves; and localized waves as bound states of fronts between dispersionless subcritical waves and the motionless conductive state. (2) We have completed our investigation of steady domain structures in which domains of structures with different wave numbers alternate, separated by domain walls. In particular, we have studied their regimes of existence and stability within the framework of a Ginzburg-Landau equation and have compared it to previous results. Those were based on a long-wavelength approximation, which misses certain aspects which turn out to be important for the stability of the domain structures in realistic situations. In addition, we give a description of our work on resonantly forced waves in two-dimensional anisotropic systems.

  4. Motion coordination of multiple autonomous vehicles in a spatiotemporal flowfield

    NASA Astrophysics Data System (ADS)

    Peterson, Cameron Kai

    The long-term goal of this research is to provide theoretically justified control strategies to operate autonomous vehicles in spatiotemporal flowfields. The specific objective of this dissertation is to use estimation and nonlinear control techniques to generate decentralized control algorithms that enable motion coordination for multiple autonomous vehicles while operating in a time-varying flowfield. A cooperating team of vehicles can benefit from sharing data and tasking responsibilities. Many existing control algorithms promote collaboration of autonomous vehicles. However, these algorithms often fail to account for the degradation of control performance caused by flowfields. This dissertation presents decentralized multivehicle coordination algorithms designed for operation in a spatially or temporally varying flowfield. Each vehicle is represented using a Newtonian particle traveling in a plane at constant speed relative to the flow and subject to a steering control. Initially, we assume the flowfield is known and describe algorithms that stabilize a circular formation in a time-varying spatially nonuniform flow of moderate intensity. These algorithms are extended by relaxing the assumption that the flow is known: the vehicles dynamically estimate the flow and use that estimate in the control. We propose a distributed estimation and control algorithm comprising a consensus filter to share information gleaned from noisy position measurements, and an information filter to reconstruct a spatially varying flowfield. The theoretical results are illustrated with numerical simulations of circular formation control and validated in outdoor unmanned aerial vehicle (UAV) flight tests.

  5. Spatiotemporal noise characterization for chirped-pulse amplification systems

    PubMed Central

    Ma, Jingui; Yuan, Peng; Wang, Jing; Wang, Yongzhi; Xie, Guoqiang; Zhu, Heyuan; Qian, Liejia

    2015-01-01

    Optical noise, the core of the pulse-contrast challenge for ultra-high peak power femtosecond lasers, exhibits spatiotemporal (ST) coupling induced by angular dispersion. Full characterization of such ST noise requires two-dimensional measurements in the ST domain. Thus far, all noise measurements have been made only in the temporal domain. Here we report the experimental characterization of the ST noise, which is made feasible by extending cross-correlation from the temporal domain to the ST domain. We experimentally demonstrate that the ST noise originates from the optical surface imperfections in the pulse stretcher/compressor and exhibits a linear ST coupling in the far-field plane. The contrast on the far-field axis, underestimated in the conventional measurements, is further improved by avoiding the far-field optics in the stretcher. These results enhance our understanding of the pulse contrast with respect to its ST-coupling nature and pave the way toward the design of high-contrast ultra-high peak power lasers. PMID:25648187

  6. Spatiotemporal Dynamics of Word Processing in the Human Cortex

    PubMed Central

    Marinkovi?, Ksenija

    2013-01-01

    Understanding language relies on concurrent activation of multiple areas within a distributed neural network. Hemodynamic measures (fMRI and PET) indicate their location and electromagnetic measures (MEG and EEG) reveal the timing of brain activity during language processing. Their combination can show the spatiotemporal characteristics (where and when) of the underlying neural network. Activity to written and spoken words starts in sensory-specific areas and progresses anteriorly via respective ventral (“what”) processing streams towards the simultaneously active supramodal regions. The process of understanding a word in its current context peaks about 400 ms after word onset. It is carried out mainly through interactions of the temporal and inferior prefrontal areas on the left during word reading, and bilateral temporo-prefrontal areas during speech processing. Neurophysiological evidence suggests that lexical access, semantic associations, and contextual integration may be simultaneous as the brain uses available information in a concurrent manner, with the final goal of rapidly comprehending verbal input. Because the same areas may participate in multiple stages of semantic or syntactic processing, it is crucial to consider both spatial and temporal aspects of their interactions to appreciate how the brain understands words. PMID:15070488

  7. Spatiotemporal noise characterization for chirped-pulse amplification systems

    NASA Astrophysics Data System (ADS)

    Ma, Jingui; Yuan, Peng; Wang, Jing; Wang, Yongzhi; Xie, Guoqiang; Zhu, Heyuan; Qian, Liejia

    2015-02-01

    Optical noise, the core of the pulse-contrast challenge for ultra-high peak power femtosecond lasers, exhibits spatiotemporal (ST) coupling induced by angular dispersion. Full characterization of such ST noise requires two-dimensional measurements in the ST domain. Thus far, all noise measurements have been made only in the temporal domain. Here we report the experimental characterization of the ST noise, which is made feasible by extending cross-correlation from the temporal domain to the ST domain. We experimentally demonstrate that the ST noise originates from the optical surface imperfections in the pulse stretcher/compressor and exhibits a linear ST coupling in the far-field plane. The contrast on the far-field axis, underestimated in the conventional measurements, is further improved by avoiding the far-field optics in the stretcher. These results enhance our understanding of the pulse contrast with respect to its ST-coupling nature and pave the way toward the design of high-contrast ultra-high peak power lasers.

  8. Identification of spatiotemporal patterns of biophysical droughts in Iran

    NASA Astrophysics Data System (ADS)

    Kamali, Bahareh; Abbaspour, Karim; Yang, Hong

    2015-04-01

    This study aims to identify historical patterns of meteorological, hydrological, and agricultural (inclusively biophysical) droughts in Iran over the last forty years. Standardized precipitation index (SPI), standardized runoff index (SRI), and soil moisture deficit index (SMDI) were used to represent the three types of droughts, respectively. Variables required for calculating the indices were obtained from a SWAT (Soil and Water Assessment Tool) model constructed for the country. The model was calibrated based on monthly runoff using the Sequential Uncertainty Fitting (SUFI-2) algorithm in SWAT-CUP. The indices were compared across temporal and spatial dimensions. Drought characteristics including number of events, start, end, duration and severity were derived to identify areas most prone to drought events. The results on provincial level show a variety of spatiotemporal patterns in different drought aspects over the country. The summary of analysis ranked drought events based on short-term severe droughts to multi-year duration events. Our analyses on three types of droughts provide a basis for further studies concerning drought impacts under future climate change and water resource management strategies in semi-arid areas.

  9. Automated Classification of Spatiotemporal Characteristics of Gastric Slow Wave Propagation

    PubMed Central

    Paskaranandavadivel, Niranchan; Gao, Jerry; Du, Peng; O'Grady, Gregory; Cheng, Leo K.

    2014-01-01

    Gastric contractions are underpinned by an electrical event called slow wave activity. High-resolution electrical mapping has recently been adapted to study gastric slow waves at a high spatiotemporal detail. As more slow wave data becomes available, it is becoming evident that the spatial organization of slow wave plays a key role in the initiation and maintenance of gastric dsyrhythmias in major gastric motility disorders. All of the existing slow wave signal processing techniques deal with the identification and partitioning of recorded wave events, but not the analysis of the slow wave spatial organization, which is currently performed visually. This manual analysis is time consuming and is prone to observer bias and error. We present an automated approach to classify spatial slow wave propagation patterns via the use of Pearson cross correlations. Slow wave propagations were grouped into classes based on their similarity to each other. The method was applied to high-resolution gastric slow wave recordings from four pigs. There were significant changes in the velocity of the gastric slow wave wavefront and the amplitude of the slow wave event when there was a change in direction to the slow wave wavefront during dsyrhythmias, which could be detected with the automated approach. PMID:24111441

  10. A spatio-temporal detective quantum efficiency and its application to fluoroscopic systems

    SciTech Connect

    Friedman, S. N.; Cunningham, I. A. [Sackler School of Medicine, Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978 (Israel); Imaging Research Laboratories, Robarts Research Institute and Lawson Health Research Institute, 100 Perth Drive, London, Ontario N6A 5K8 (Canada) and Department of Medical Biophysics, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B8 (Canada)

    2010-11-15

    Purpose: Fluoroscopic x-ray imaging systems are used extensively in spatio-temporal detection tasks and require a spatio-temporal description of system performance. No accepted metric exists that describes spatio-temporal fluoroscopic performance. The detective quantum efficiency (DQE) is a metric widely used in radiography to quantify system performance and as a surrogate measure of patient ''dose efficiency.'' It has been applied previously to fluoroscopic systems with the introduction of a temporal correction factor. However, the use of a temporally-corrected DQE does not provide system temporal information and it is only valid under specific conditions, many of which are not likely to be satisfied by suboptimal systems. The authors propose a spatio-temporal DQE that describes performance in both space and time and is applicable to all spatio-temporal quantum-based imaging systems. Methods: The authors define a spatio-temporal DQE (two spatial-frequency axes and one temporal-frequency axis) in terms of a small-signal spatio-temporal modulation transfer function (MTF) and spatio-temporal noise power spectrum (NPS). Measurements were made on an x-ray image intensifier-based bench-top system using continuous fluoroscopy with an RQA-5 beam at 3.9 {mu}R/frame and hardened 50 kVp beam (0.8 mm Cu filtration added) at 1.9 {mu}R/frame. Results: A zero-frequency DQE value of 0.64 was measured under both conditions. Nonideal performance was noted at both larger spatial and temporal frequencies; DQE values decreased by {approx}50% at the cutoff temporal frequency of 15 Hz. Conclusions: The spatio-temporal DQE enables measurements of decreased temporal system performance at larger temporal frequencies analogous to previous measurements of decreased (spatial) performance. This marks the first time that system performance and dose efficiency in both space and time have been measured on a fluoroscopic system using DQE and is the first step toward the generalized use of DQE on clinical fluoroscopic systems.

  11. Sensitivity of spatiotemporal gait parameters in measuring disease severity in Friedreich ataxia.

    PubMed

    Milne, Sarah C; Hocking, Darren R; Georgiou-Karistianis, Nellie; Murphy, Anna; Delatycki, Martin B; Corben, Louise A

    2014-12-01

    Friedreich ataxia (FRDA) is an autosomal recessive disease with gait ataxia being the main source of morbidity. Mobility progressively declines, from initial symptom onset at approximately 10-15 years of age to being unable to ambulate 10-15 years later. Here, we sought to investigate the relationship between spatiotemporal gait parameters and clinical markers of disease severity. Thirteen people with FRDA walked along an 8.3-m GAITRite® mat six times each at their preferred fast and slow speeds. Relationships between spatiotemporal gait parameters and a range of clinical and disease characteristics were examined. Significant correlations were found between spatiotemporal gait characteristics at each of the walking speeds and Friedreich Ataxia Rating Scale (FARS) score and disease duration. During the fast-walking condition, gait speed and cadence decreased with an increase in disease duration and the FARS score. GAA1 repeat expansion negatively correlated with double-support percentage of the gait cycle in all speed conditions demonstrating a relationship between the genetic mutation and compensatory strategies for impaired dynamic balance. In all speed conditions, there were correlations between a range of spatiotemporal gait characteristics and the timed 25-ft walk test, a well-established measure of gait mobility. These findings suggest that spatiotemporal gait parameters are a sensitive measure of gait decline in individuals with FRDA and should be considered for inclusion in intervention studies whilst participants are still ambulant. PMID:25022367

  12. Spatiotemporal analysis of aquifers salinization in coastal area of Yunlin, Taiwan

    NASA Astrophysics Data System (ADS)

    Chen, P.-C.; Tan, Y.-C.

    2012-04-01

    In the past, time and space characteristics often discussed separately. This study adopts regionalized variables theory, and describes the water quality in terms of its structure in time and space to assess the situation of Yunlin. This study applied the Quantum Bayesian Maximum Entropy Toolbox (QtBME), which is a spatiotemporal statistics function, can be applied to estimate and map a non-stationary and non-homogeneous spatiotemporal process under the platform of Quantum GIS (QGIS) software. Kernel smoothing method is used to divide the original process into a deterministic trend and a stationary and homogeneous spatiotemporal process, assuming that a spatiotemporal process can be divided into high and low frequency. The covariance model of the process of high frequency is selected objectively by particle swarm optimization (PSO) method and Akaike's information criterion (AIC). Bayesian maximum entropy method is then applied to spatiotemporal mapping of the variable of interest. In this study, QtBME estimated the situation of aquifers salinization at Yunlin coastal area in 1992 to 2010. Finally, one investigated the rainfall and aquifers salinization on the degree of impact.

  13. Spatio-temporal Hotelling observer for signal detection from image sequences

    PubMed Central

    Caucci, Luca; Barrett, Harrison H.; Rodríguez, Jeffrey J.

    2010-01-01

    Detection of signals in noisy images is necessary in many applications, including astronomy and medical imaging. The optimal linear observer for performing a detection task, called the Hotelling observer in the medical literature, can be regarded as a generalization of the familiar prewhitening matched filter. Performance on the detection task is limited by randomness in the image data, which stems from randomness in the object, randomness in the imaging system, and randomness in the detector outputs due to photon and readout noise, and the Hotelling observer accounts for all of these effects in an optimal way. If multiple temporal frames of images are acquired, the resulting data set is a spatio-temporal random process, and the Hotelling observer becomes a spatio-temporal linear operator. This paper discusses the theory of the spatio-temporal Hotelling observer and estimation of the required spatio-temporal covariance matrices. It also presents a parallel implementation of the observer on a cluster of Sony PLAYSTATION 3 gaming consoles. As an example, we consider the use of the spatio-temporal Hotelling observer for exoplanet detection. PMID:19550494

  14. Spatiotemporal Heterogeneity Analysis of Hemorrhagic Fever with Renal Syndrome in China Using Geographically Weighted Regression Models

    PubMed Central

    Li, Shujuan; Ren, Hongyan; Hu, Wensheng; Lu, Liang; Xu, Xinliang; Zhuang, Dafang; Liu, Qiyong

    2014-01-01

    Hemorrhagic fever with renal syndrome (HFRS) is an important public health problem in China. The identification of the spatiotemporal pattern of HFRS will provide a foundation for the effective control of the disease. Based on the incidence of HFRS, as well as environmental factors, and social-economic factors of China from 2005–2012, this paper identified the spatiotemporal characteristics of HFRS distribution and the factors that impact this distribution. The results indicate that the spatial distribution of HFRS had a significant, positive spatial correlation. The spatiotemporal heterogeneity was affected by the temperature, precipitation, humidity, NDVI of January, NDVI of August for the previous year, land use, and elevation in 2005–2009. However, these factors did not explain the spatiotemporal heterogeneity of HFRS incidences in 2010–2012. Spatiotemporal heterogeneity of provincial HFRS incidences and its relation to environmental factors would provide valuable information for hygiene authorities to design and implement effective measures for the prevention and control of HFRS in China. PMID:25429681

  15. Evaluation of spatial and spatiotemporal estimation methods in simulation of precipitation variability patterns

    NASA Astrophysics Data System (ADS)

    Bayat, Bardia; Zahraie, Banafsheh; Taghavi, Farahnaz; Nasseri, Mohsen

    2013-08-01

    Identification of spatial and spatiotemporal precipitation variations plays an important role in different hydrological applications such as missing data estimation. In this paper, the results of Bayesian maximum entropy (BME) and ordinary kriging (OK) are compared for modeling spatial and spatiotemporal variations of annual precipitation with and without incorporating elevation variations. The study area of this research is Namak Lake watershed located in the central part of Iran with an area of approximately 90,000 km2. The BME and OK methods have been used to model the spatial and spatiotemporal variations of precipitation in this watershed, and their performances have been evaluated using cross-validation statistics. The results of the case study have shown the superiority of BME over OK in both spatial and spatiotemporal modes. The results have shown that BME estimates are less biased and more accurate than OK. The improvements in the BME estimates are mostly related to incorporating hard and soft data in the estimation process, which resulted in more detailed and reliable results. Estimation error variance for BME results is less than OK estimations in the study area in both spatial and spatiotemporal modes.

  16. A network-based approach for predicting Hsp27 knock-out targets in mouse skeletal muscles.

    PubMed

    Kammoun, Malek; Picard, Brigitte; Henry-Berger, Joëlle; Cassar-Malek, Isabelle

    2013-01-01

    Thanks to genomics, we have previously identified markers of beef tenderness, and computed a bioinformatic analysis that enabled us to build an interactome in which we found Hsp27 at a crucial node. Here, we have used a network-based approach for understanding the contribution of Hsp27 to tenderness through the prediction of its interactors related to tenderness. We have revealed the direct interactors of Hsp27. The predicted partners of Hsp27 included proteins involved in different functions, e.g. members of Hsp families (Hsp20, Cryab, Hsp70a1a, and Hsp90aa1), regulators of apoptosis (Fas, Chuk, and caspase-3), translation factors (Eif4E, and Eif4G1), cytoskeletal proteins (Desmin) and antioxidants (Sod1). The abundances of 15 proteins were quantified by Western blotting in two muscles of HspB1-null mice and their controls. We observed changes in the amount of most of the Hsp27 predicted targets in mice devoid of Hsp27 mainly in the most oxidative muscle. Our study demonstrates the functional links between Hsp27 and its predicted targets. It suggests that Hsp status, apoptotic processes and protection against oxidative stress are crucial for post-mortem muscle metabolism, subsequent proteolysis, and therefore for beef tenderness. PMID:24688716

  17. A novel spatio-temporal scale based on ocean currents unravels environmental drivers of reproductive timing in a marine predator.

    PubMed

    Afán, Isabel; Chiaradia, André; Forero, Manuela G; Dann, Peter; Ramírez, Francisco

    2015-07-01

    Life-history strategies have evolved in response to predictable patterns of environmental features. In practice, linking life-history strategies and changes in environmental conditions requires comparable space-time scales between both processes, a difficult match in most marine system studies. We propose a novel spatio-temporal and dynamic scale to explore marine productivity patterns probably driving reproductive timing in the inshore little penguin (Eudyptula minor), based on monthly data on ocean circulation in the Southern Ocean, Australia. In contrast to what occurred when considering any other fixed scales, little penguin's highly variable laying date always occurred within the annual peak of ocean productivity that emerged from our newly defined dynamic scale. Additionally, local sea surface temperature seems to have triggered the onset of reproduction, acting as an environmental cue informing on marine productivity patterns at our dynamic scale. Chlorophyll-a patterns extracted from this scale revealed that environment factors in marine ecosystems affecting breeding decisions are related to a much wider region than foraging areas that are commonly used in current studies investigating the link between animals' life history and their environment. We suggest that marine productivity patterns may be more predictable than previously thought when environmental and biological data are examined at appropriate scales. PMID:26063848

  18. A Visual Language for the Evolution of Spatial Relationships and its Translation into a Spatio-Temporal Calculus

    E-print Network

    Erwig, Martin

    , animals, ..., storms, lakes, forests, etc. Hence, database systems, in particular, spatial and temporal can be used directly as a visual query interface to spatio-temporal databases, or it can provide languages. Key Words: Visual Predicate Specification, Visual Database Interface, Spatio-Temporal Queries

  19. A Visual Language for the Evolution of Spatial Relationships and its Translation into a SpatioTemporal Calculus

    E-print Network

    Erwig, Martin

    , animals, ..., storms, lakes, forests, etc. Hence, database systems, in particular, spatial and temporal can be used directly as a visual query interface to spatio­temporal databases, or it can provide languages. Key Words: Visual Predicate Specification, Visual Database Interface, Spatio­Temporal Queries

  20. R. Lukac and K. N. Plataniotis: Adaptive Spatiotemporal Video Demosaicking Using Bidirectional Multistage Spectral Filters Contributed Paper

    E-print Network

    Plataniotis, Konstantinos N.

    motion artifacts in the demosaicked video [5]-[7]. Existing spatiotemporal video demosaicking solutions inputs to follow varying spatiotemporal characteristics of the captured video, reduce demosaicking errors to compensate for local motion translations. Built on the efficient data-adaptive and spectral modeling concepts