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  1. Spatiotemporal evolution of Calophaca (fabaceae) reveals multiple dispersals in central Asian mountains.

    Science.gov (United States)

    Zhang, Ming-Li; Wen, Zhi-Bin; Fritsch, Peter W; Sanderson, Stewart C

    2015-01-01

    The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried out in order to confirm its taxonomic status and reconstruct its evolutionary history. We employed BEAST Bayesian inference for dating, and S-DIVA and BBM for ancestral area reconstruction, to study its spatiotemporal evolution. Our results show that Calophacais monophyletic and nested within Caragana. The divergence time of Calophaca is estimated at ca. 8.0 Ma, most likely driven by global cooling and aridification, influenced by rapid uplift of the Qinghai Tibet Plateau margins. According to ancestral area reconstructions, the genus most likely originated in the Pamir Mountains, a global biodiversity hotspot and hypothesized Tertiary refugium of many Central Asian plant lineages. Dispersals from this location are inferred to the western Tianshan Mountains, then northward to the Tarbagatai Range, eastward to East Asia, and westward to the Caucasus, Russia, and Europe. The spatiotemporal evolution of Calophaca provides a case contributing to an understanding of the flora and biodiversity of the Central Asian mountains and adjacent regions.

  2. Zebrafish con/disp1 reveals multiple spatiotemporal requirements for Hedgehog-signaling in craniofacial development

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    Schwend Tyler

    2009-11-01

    Full Text Available Abstract Background The vertebrate head skeleton is derived largely from cranial neural crest cells (CNCC. Genetic studies in zebrafish and mice have established that the Hedgehog (Hh-signaling pathway plays a critical role in craniofacial development, partly due to the pathway's role in CNCC development. Disruption of the Hh-signaling pathway in humans can lead to the spectral disorder of Holoprosencephaly (HPE, which is often characterized by a variety of craniofacial defects including midline facial clefting and cyclopia 12. Previous work has uncovered a role for Hh-signaling in zebrafish dorsal neurocranium patterning and chondrogenesis, however Hh-signaling mutants have not been described with respect to the ventral pharyngeal arch (PA skeleton. Lipid-modified Hh-ligands require the transmembrane-spanning receptor Dispatched 1 (Disp1 for proper secretion from Hh-synthesizing cells to the extracellular field where they act on target cells. Here we study chameleon mutants, lacking a functional disp1(con/disp1. Results con/disp1 mutants display reduced and dysmorphic mandibular and hyoid arch cartilages and lack all ceratobranchial cartilage elements. CNCC specification and migration into the PA primorida occurs normally in con/disp1 mutants, however disp1 is necessary for post-migratory CNCC patterning and differentiation. We show that disp1 is required for post-migratory CNCC to become properly patterned within the first arch, while the gene is dispensable for CNCC condensation and patterning in more posterior arches. Upon residing in well-formed pharyngeal epithelium, neural crest condensations in the posterior PA fail to maintain expression of two transcription factors essential for chondrogenesis, sox9a and dlx2a, yet continue to robustly express other neural crest markers. Histology reveals that posterior arch residing-CNCC differentiate into fibrous-connective tissue, rather than becoming chondrocytes. Treatments with Cyclopamine, to

  3. Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons.

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    Oddo, Calogero M; Mazzoni, Alberto; Spanne, Anton; Enander, Jonas M D; Mogensen, Hannes; Bengtsson, Fredrik; Camboni, Domenico; Micera, Silvestro; Jörntell, Henrik

    2017-04-04

    Investigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models.

  4. Single Turnover at Molecular Polymerization Catalysts Reveals Spatiotemporally Resolved Reactions.

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    Easter, Quinn T; Blum, Suzanne A

    2017-10-23

    Multiple active individual molecular ruthenium catalysts have been pinpointed within growing polynorbornene, thereby revealing information on the reaction dynamics and location that is unavailable through traditional ensemble experiments. This is the first single-turnover imaging of a molecular catalyst by fluorescence microscopy and allows detection of individual monomer reactions at an industrially important molecular ruthenium ring-opening metathesis polymerization (ROMP) catalyst under synthetically relevant conditions (e.g. unmodified industrial catalyst, ambient pressure, condensed phase, ca. 0.03 m monomer). These results further establish the key fundamentals of this imaging technique for characterizing the reactivity and location of active molecular catalysts even when they are the minor components. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

    DEFF Research Database (Denmark)

    Frelat, Romain; Lindegren, Martin; Dencker, Tim Spaanheden

    2017-01-01

    it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered...... by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii...

  6. Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster

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    Kim Man-Sun

    2012-05-01

    Full Text Available Abstract Background Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a “spatiotemporal network motif,” a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts. Results On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns. Conclusions Taken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.

  7. Widespread Micropollutant Monitoring in the Hudson River Estuary Reveals Spatiotemporal Micropollutant Clusters and Their Sources.

    Science.gov (United States)

    Carpenter, Corey M G; Helbling, Damian E

    2018-06-05

    The objective of this study was to identify sources of micropollutants in the Hudson River Estuary (HRE). We collected 127 grab samples at 17 sites along the HRE over 2 years and screened for up to 200 micropollutants. We quantified 168 of the micropollutants in at least one of the samples. Atrazine, gabapentin, metolachlor, and sucralose were measured in every sample. We used data-driven unsupervised methods to cluster the micropollutants on the basis of their spatiotemporal occurrence and normalized-concentration patterns. Three major clusters of micropollutants were identified: ubiquitous and mixed-use (core micropollutants), sourced from sewage treatment plant outfalls (STP micropollutants), and derived from diffuse upstream sources (diffuse micropollutants). Each of these clusters was further refined into subclusters that were linked to specific sources on the basis of relationships identified through geospatial analysis of watershed features. Evaluation of cumulative loadings of each subcluster revealed that the Mohawk River and Rondout Creek are major contributors of most core micropollutants and STP micropollutants and the upper HRE is a major contributor of diffuse micropollutants. These data provide the first comprehensive evaluation of micropollutants in the HRE and define distinct spatiotemporal micropollutant clusters that are linked to sources and conserved across surface water systems around the world.

  8. Spatiotemporal dynamics of word retrieval in speech production revealed by cortical high-frequency band activity.

    Science.gov (United States)

    Riès, Stephanie K; Dhillon, Rummit K; Clarke, Alex; King-Stephens, David; Laxer, Kenneth D; Weber, Peter B; Kuperman, Rachel A; Auguste, Kurtis I; Brunner, Peter; Schalk, Gerwin; Lin, Jack J; Parvizi, Josef; Crone, Nathan E; Dronkers, Nina F; Knight, Robert T

    2017-06-06

    Word retrieval is core to language production and relies on complementary processes: the rapid activation of lexical and conceptual representations and word selection, which chooses the correct word among semantically related competitors. Lexical and conceptual activation is measured by semantic priming. In contrast, word selection is indexed by semantic interference and is hampered in semantically homogeneous (HOM) contexts. We examined the spatiotemporal dynamics of these complementary processes in a picture naming task with blocks of semantically heterogeneous (HET) or HOM stimuli. We used electrocorticography data obtained from frontal and temporal cortices, permitting detailed spatiotemporal analysis of word retrieval processes. A semantic interference effect was observed with naming latencies longer in HOM versus HET blocks. Cortical response strength as indexed by high-frequency band (HFB) activity (70-150 Hz) amplitude revealed effects linked to lexical-semantic activation and word selection observed in widespread regions of the cortical mantle. Depending on the subsecond timing and cortical region, HFB indexed semantic interference (i.e., more activity in HOM than HET blocks) or semantic priming effects (i.e., more activity in HET than HOM blocks). These effects overlapped in time and space in the left posterior inferior temporal gyrus and the left prefrontal cortex. The data do not support a modular view of word retrieval in speech production but rather support substantial overlap of lexical-semantic activation and word selection mechanisms in the brain.

  9. A Tracking Analyst for large 3D spatiotemporal data from multiple sources (case study: Tracking volcanic eruptions in the atmosphere)

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    Gad, Mohamed A.; Elshehaly, Mai H.; Gračanin, Denis; Elmongui, Hicham G.

    2018-02-01

    This research presents a novel Trajectory-based Tracking Analyst (TTA) that can track and link spatiotemporally variable data from multiple sources. The proposed technique uses trajectory information to determine the positions of time-enabled and spatially variable scatter data at any given time through a combination of along trajectory adjustment and spatial interpolation. The TTA is applied in this research to track large spatiotemporal data of volcanic eruptions (acquired using multi-sensors) in the unsteady flow field of the atmosphere. The TTA enables tracking injections into the atmospheric flow field, the reconstruction of the spatiotemporally variable data at any desired time, and the spatiotemporal join of attribute data from multiple sources. In addition, we were able to create a smooth animation of the volcanic ash plume at interactive rates. The initial results indicate that the TTA can be applied to a wide range of multiple-source data.

  10. Spatiotemporal multiple coherence resonances and calcium waves in a coupled hepatocyte system

    International Nuclear Information System (INIS)

    Bao-Hua, Wang; Qi-Shao, Lu; Shu-Juan, Lü; Xiu-Feng, Lang

    2009-01-01

    Spatiotemporal multiple coherence resonances for calcium activities induced by weak Gaussian white noise in coupled hepatocytes are studied. It is shown that bi-resonances in hepatocytes are induced by the interplay and competition between noise and coupling of cells, in other words, the cell in network can be excited either by noise or by its neighbour via gap junction which can transfer calcium ions between cells. Furthermore, the intercellular annular calcium waves induced by noise are observed, in which the wave length decreases with noise intensity augmenting but increases monotonically with coupling strength increasing. And for a fixed noise level, there is an optimal coupling strength that makes the coherence resonance reach maximum. (general)

  11. Geophysical Factor Resolving of Rainfall Mechanism for Super Typhoons by Using Multiple Spatiotemporal Components Analysis

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    Huang, Chien-Lin; Hsu, Nien-Sheng

    2016-04-01

    This study develops a novel methodology to resolve the geophysical cause of typhoon-induced rainfall considering diverse dynamic co-evolution at multiple spatiotemporal components. The multi-order hidden patterns of complex hydrological process in chaos are detected to understand the fundamental laws of rainfall mechanism. The discovered spatiotemporal features are utilized to develop a state-of-the-art descriptive statistical model for mechanism validation, modeling and further prediction during typhoons. The time series of hourly typhoon precipitation from different types of moving track, atmospheric field and landforms are respectively precede the signal analytical process to qualify each type of rainfall cause and to quantify the corresponding affected degree based on the measured geophysical atmospheric-hydrological variables. This study applies the developed methodology in Taiwan Island which is constituted by complex diverse landform formation. The identified driving-causes include: (1) cloud height to ground surface; (2) co-movement effect induced by typhoon wind field with monsoon; (3) stem capacity; (4) interaction between typhoon rain band and terrain; (5) structural intensity variance of typhoon; and (6) integrated cloudy density of rain band. Results show that: (1) for the central maximum wind speed exceeding 51 m/sec, Causes (1) and (3) are the primary ones to generate rainfall; (2) for the typhoon moving toward the direction of 155° to 175°, Cause (2) is the primary one; (3) for the direction of 90° to 155°, Cause (4) is the primary one; (4) for the typhoon passing through mountain chain which above 3500 m, Cause (5) is the primary one; and (5) for the moving speed lower than 18 km/hr, Cause (6) is the primary one. Besides, the multiple geophysical component-based precipitation modeling can achieve 81% of average accuracy and 0.732 of average correlation coefficient (CC) within average 46 hours of duration, that improve their predictability.

  12. Spatio-temporal analyses of impacts of multiple climatic hazards in a savannah ecosystem of Ghana

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    Gerald A.B. Yiran, PhD

    2016-01-01

    Full Text Available Ghana’s savannah ecosystem has been subjected to a number of climatic hazards of varying severity. This paper presents a spatial, time-series analysis of the impacts of multiple hazards on the ecosystem and human livelihoods over the period 1983–2012, using the Upper East Region of Ghana as a case study. Our aim is to understand the nature of hazards (their frequency, magnitude and duration and how they cumulatively affect humans. Primary data were collected using questionnaires, focus group discussions, in-depth interviews and personal observations. Secondary data were collected from documents and reports. Calculations of the standard precipitation index (SPI and crop failure index used rainfall data from 4 weather stations (Manga, Binduri, Vea and Navrongo and crop yield data of 5 major crops (maize, sorghum, millet, rice and groundnuts respectively. Temperature and windstorms were analysed from the observed weather data. We found that temperatures were consistently high and increasing. From the SPI, drought frequency varied spatially from 9 at Binduri to 13 occurrences at Vea; dry spells occurred at least twice every year and floods occurred about 6 times on average, with slight spatial variations, during 1988–2012, a period with consistent data from all stations. Impacts from each hazard varied spatio-temporally. Within the study period, more 70% of years recorded severe crop losses with greater impacts when droughts and floods occur in the same year, especially in low lying areas. The effects of crop losses were higher in districts with no/little irrigation (Talensi, Nabdam, Garu-Tempane, Kassena-Nankana East. Frequency and severity of diseases and sicknesses such as cerebrospinal meningitis, heat rashes, headaches and malaria related to both dry and wet conditions have increased steadily over time. Other impacts recorded with spatio-temporal variations included destruction to housing, displacement, injury and death of people. These

  13. The spatiotemporal pattern of Src activation at lipid rafts revealed by diffusion-corrected FRET imaging.

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    Shaoying Lu

    2008-07-01

    Full Text Available Genetically encoded biosensors based on fluorescence resonance energy transfer (FRET have been widely applied to visualize the molecular activity in live cells with high spatiotemporal resolution. However, the rapid diffusion of biosensor proteins hinders a precise reconstruction of the actual molecular activation map. Based on fluorescence recovery after photobleaching (FRAP experiments, we have developed a finite element (FE method to analyze, simulate, and subtract the diffusion effect of mobile biosensors. This method has been applied to analyze the mobility of Src FRET biosensors engineered to reside at different subcompartments in live cells. The results indicate that the Src biosensor located in the cytoplasm moves 4-8 folds faster (0.93+/-0.06 microm(2/sec than those anchored on different compartments in plasma membrane (at lipid raft: 0.11+/-0.01 microm(2/sec and outside: 0.18+/-0.02 microm(2/sec. The mobility of biosensor at lipid rafts is slower than that outside of lipid rafts and is dominated by two-dimensional diffusion. When this diffusion effect was subtracted from the FRET ratio images, high Src activity at lipid rafts was observed at clustered regions proximal to the cell periphery, which remained relatively stationary upon epidermal growth factor (EGF stimulation. This result suggests that EGF induced a Src activation at lipid rafts with well-coordinated spatiotemporal patterns. Our FE-based method also provides an integrated platform of image analysis for studying molecular mobility and reconstructing the spatiotemporal activation maps of signaling molecules in live cells.

  14. Phenology Data Products to Support Assessment and Forecasting of Phenology on Multiple Spatiotemporal Scales

    Science.gov (United States)

    Gerst, K.; Enquist, C.; Rosemartin, A.; Denny, E. G.; Marsh, L.; Moore, D. J.; Weltzin, J. F.

    2014-12-01

    The USA National Phenology Network (USA-NPN; www.usanpn.org) serves science and society by promoting a broad understanding of plant and animal phenology and the relationships among phenological patterns and environmental change. The National Phenology Database maintained by USA-NPN now has over 3.7 million records for plants and animals for the period 1954-2014, with the majority of these observations collected since 2008 as part of a broad, national contributory science strategy. These data have been used in a number of science, conservation and resource management applications, including national assessments of historical and potential future trends in phenology, regional assessments of spatio-temporal variation in organismal activity, and local monitoring for invasive species detection. Customizable data downloads are freely available, and data are accompanied by FGDC-compliant metadata, data-use and data-attribution policies, vetted and documented methodologies and protocols, and version control. While users are free to develop custom algorithms for data cleaning, winnowing and summarization prior to analysis, the National Coordinating Office of USA-NPN is developing a suite of standard data products to facilitate use and application by a diverse set of data users. This presentation provides a progress report on data product development, including: (1) Quality controlled raw phenophase status data; (2) Derived phenometrics (e.g. onset, duration) at multiple scales; (3) Data visualization tools; (4) Tools to support assessment of species interactions and overlap; (5) Species responsiveness to environmental drivers; (6) Spatially gridded phenoclimatological products; and (7) Algorithms for modeling and forecasting future phenological responses. The prioritization of these data products is a direct response to stakeholder needs related to informing management and policy decisions. We anticipate that these products will contribute to broad understanding of plant

  15. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    Science.gov (United States)

    Aksoy, B.; Rehman, A.; Bayraktar, H.; Alaca, B. E.

    2017-04-01

    Micropatterns are generated on a vast selection of polymeric substrates for various applications ranging from stretchable electronics to cellular mechanobiological systems. When these patterned substrates are exposed to external loading, strain field is primarily affected by the presence of microfabricated structures and similarly by fabrication-related defects. The capturing of such nonhomogeneous strain fields is of utmost importance in cases where study of the mechanical behavior with a high spatial resolution is necessary. Image-based non-contact strain measurement techniques are favorable and have recently been extended to scanning tunneling microscope and scanning electron microscope images for the characterization of mechanical properties of metallic materials, e.g. steel and aluminum, at the microscale. A similar real-time analysis of strain heterogeneity in elastomers is yet to be achieved during the entire loading sequence. The available measurement methods for polymeric materials mostly depend on cross-head displacement or precalibrated strain values. Thus, they suffer either from the lack of any real-time analysis, spatiotemporal distribution or high resolution in addition to a combination of these factors. In this work, these challenges are addressed by integrating a tensile stretcher with an inverted optical microscope and developing a subpixel particle tracking algorithm. As a proof of concept, the patterns with a critical dimension of 200 µm are generated on polydimethylsiloxane substrates and strain distribution in the vicinity of the patterns is captured with a high spatiotemporal resolution. In the field of strain measurement, there is always a tradeoff between minimum measurable strain value and spatial resolution. Current noncontact techniques on elastomers can deliver a strain resolution of 0.001% over a minimum length of 5 cm. More importantly, inhomogeneities within this quite large region cannot be captured. The proposed technique can

  16. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    International Nuclear Information System (INIS)

    Aksoy, B; Alaca, B E; Rehman, A; Bayraktar, H

    2017-01-01

    Micropatterns are generated on a vast selection of polymeric substrates for various applications ranging from stretchable electronics to cellular mechanobiological systems. When these patterned substrates are exposed to external loading, strain field is primarily affected by the presence of microfabricated structures and similarly by fabrication-related defects. The capturing of such nonhomogeneous strain fields is of utmost importance in cases where study of the mechanical behavior with a high spatial resolution is necessary. Image-based non-contact strain measurement techniques are favorable and have recently been extended to scanning tunneling microscope and scanning electron microscope images for the characterization of mechanical properties of metallic materials, e.g. steel and aluminum, at the microscale. A similar real-time analysis of strain heterogeneity in elastomers is yet to be achieved during the entire loading sequence. The available measurement methods for polymeric materials mostly depend on cross-head displacement or precalibrated strain values. Thus, they suffer either from the lack of any real-time analysis, spatiotemporal distribution or high resolution in addition to a combination of these factors. In this work, these challenges are addressed by integrating a tensile stretcher with an inverted optical microscope and developing a subpixel particle tracking algorithm. As a proof of concept, the patterns with a critical dimension of 200 µ m are generated on polydimethylsiloxane substrates and strain distribution in the vicinity of the patterns is captured with a high spatiotemporal resolution. In the field of strain measurement, there is always a tradeoff between minimum measurable strain value and spatial resolution. Current noncontact techniques on elastomers can deliver a strain resolution of 0.001% over a minimum length of 5 cm. More importantly, inhomogeneities within this quite large region cannot be captured. The proposed technique can

  17. Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics.

    Science.gov (United States)

    Börlin, Christoph S; Lang, Verena; Hamacher-Brady, Anne; Brady, Nathan R

    2014-09-10

    Autophagy is a vesicle-mediated pathway for lysosomal degradation, essential under basal and stressed conditions. Various cellular components, including specific proteins, protein aggregates, organelles and intracellular pathogens, are targets for autophagic degradation. Thereby, autophagy controls numerous vital physiological and pathophysiological functions, including cell signaling, differentiation, turnover of cellular components and pathogen defense. Moreover, autophagy enables the cell to recycle cellular components to metabolic substrates, thereby permitting prolonged survival under low nutrient conditions. Due to the multi-faceted roles for autophagy in maintaining cellular and organismal homeostasis and responding to diverse stresses, malfunction of autophagy contributes to both chronic and acute pathologies. We applied a systems biology approach to improve the understanding of this complex cellular process of autophagy. All autophagy pathway vesicle activities, i.e. creation, movement, fusion and degradation, are highly dynamic, temporally and spatially, and under various forms of regulation. We therefore developed an agent-based model (ABM) to represent individual components of the autophagy pathway, subcellular vesicle dynamics and metabolic feedback with the cellular environment, thereby providing a framework to investigate spatio-temporal aspects of autophagy regulation and dynamic behavior. The rules defining our ABM were derived from literature and from high-resolution images of autophagy markers under basal and activated conditions. Key model parameters were fit with an iterative method using a genetic algorithm and a predefined fitness function. From this approach, we found that accurate prediction of spatio-temporal behavior required increasing model complexity by implementing functional integration of autophagy with the cellular nutrient state. The resulting model is able to reproduce short-term autophagic flux measurements (up to 3

  18. Stable isotope analysis of precipitation samples obtained via crowdsourcing reveals the spatiotemporal evolution of Superstorm Sandy.

    Directory of Open Access Journals (Sweden)

    Stephen P Good

    Full Text Available 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 δ(18O, > 160‰ for δ(2H 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.

  19. Stable isotope analysis of precipitation samples obtained via crowdsourcing reveals the spatiotemporal evolution of Superstorm Sandy.

    Science.gov (United States)

    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 δ(18)O, > 160‰ for δ(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.

  20. iRaster: a novel information visualization tool to explore spatiotemporal patterns in multiple spike trains.

    Science.gov (United States)

    Somerville, J; Stuart, L; Sernagor, E; Borisyuk, R

    2010-12-15

    Over the last few years, simultaneous recordings of multiple spike trains have become widely used by neuroscientists. Therefore, it is important to develop new tools for analysing multiple spike trains in order to gain new insight into the function of neural systems. This paper describes how techniques from the field of visual analytics can be used to reveal specific patterns of neural activity. An interactive raster plot called iRaster has been developed. This software incorporates a selection of statistical procedures for visualization and flexible manipulations with multiple spike trains. For example, there are several procedures for the re-ordering of spike trains which can be used to unmask activity propagation, spiking synchronization, and many other important features of multiple spike train activity. Additionally, iRaster includes a rate representation of neural activity, a combined representation of rate and spikes, spike train removal and time interval removal. Furthermore, it provides multiple coordinated views, time and spike train zooming windows, a fisheye lens distortion, and dissemination facilities. iRaster is a user friendly, interactive, flexible tool which supports a broad range of visual representations. This tool has been successfully used to analyse both synthetic and experimentally recorded datasets. In this paper, the main features of iRaster are described and its performance and effectiveness are demonstrated using various types of data including experimental multi-electrode array recordings from the ganglion cell layer in mouse retina. iRaster is part of an ongoing research project called VISA (Visualization of Inter-Spike Associations) at the Visualization Lab in the University of Plymouth. The overall aim of the VISA project is to provide neuroscientists with the ability to freely explore and analyse their data. The software is freely available from the Visualization Lab website (see www.plymouth.ac.uk/infovis). Copyright © 2010

  1. Neurog1 Genetic Inducible Fate Mapping (GIFM) Reveals the Existence of Complex Spatiotemporal Cyto-Architectures in the Developing Cerebellum.

    Science.gov (United States)

    Obana, Edwin A; Lundell, Travis G; Yi, Kevin J; Radomski, Kryslaine L; Zhou, Qiong; Doughty, Martin L

    2015-06-01

    Neurog1 is a pro-neural basic helix-loop-helix (bHLH) transcription factor expressed in progenitor cells located in the ventricular zone and subsequently the presumptive white matter tracts of the developing mouse cerebellum. We used genetic inducible fate mapping (GIFM) with a transgenic Neurog1-CreER allele to characterize the contributions of Neurog1 lineages to cerebellar circuit formation in mice. GIFM reveals Neurog1-expressing progenitors are fate-mapped to become Purkinje cells and all GABAergic interneuron cell types of the cerebellar cortex but not glia. The spatiotemporal sequence of GIFM is unique to each neuronal cell type. GIFM on embryonic days (E) 10.5 to E12.5 labels Purkinje cells with different medial-lateral settling patterns depending on the day of tamoxifen delivery. GIFM on E11.5 to P7 labels interneurons and the timing of tamoxifen administration correlates with the final inside-to-outside resting position of GABAergic interneurons in the cerebellar cortex. Proliferative status and long-term BrdU retention of GIFM lineages reveals Purkinje cells express Neurog1 around the time they become post-mitotic. In contrast, GIFM labels mitotic and post-mitotic interneurons. Neurog1-CreER GIFM reveals a correlation between the timing of Neurog1 expression and the spatial organization of GABAergic neurons in the cerebellar cortex with possible implications for cerebellar circuit assembly.

  2. Spatio-temporal dynamics of ocean conditions and forage taxa reveal regional structuring of seabird–prey relationships.

    Science.gov (United States)

    Santora, Jarrod A; Schroeder, Isaac D; Field, John C; Wells, Brian K; Sydeman, William J

    Studies of predator–prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator–prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990–2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of four hydrographic measurements yielded an index that partitioned “warm/weak upwelling” and “cool/strong upwelling” years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification, weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish co-varied strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially variable associations indicative of the dynamic nature of “predator–habitat” relationships. Quantification of spatially explicit demographic responses, and their variability through time, demonstrate the possibility of delineating specific critical areas where the

  3. Spatiotemporal fusion of multiple-satellite aerosol optical depth (AOD) products using Bayesian maximum entropy method

    Science.gov (United States)

    Tang, Qingxin; Bo, Yanchen; Zhu, Yuxin

    2016-04-01

    Merging multisensor aerosol optical depth (AOD) products is an effective way to produce more spatiotemporally complete and accurate AOD products. A spatiotemporal statistical data fusion framework based on a Bayesian maximum entropy (BME) method was developed for merging satellite AOD products in East Asia. The advantages of the presented merging framework are that it not only utilizes the spatiotemporal autocorrelations but also explicitly incorporates the uncertainties of the AOD products being merged. The satellite AOD products used for merging are the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 5.1 Level-2 AOD products (MOD04_L2) and the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Deep Blue Level 2 AOD products (SWDB_L2). The results show that the average completeness of the merged AOD data is 95.2%,which is significantly superior to the completeness of MOD04_L2 (22.9%) and SWDB_L2 (20.2%). By comparing the merged AOD to the Aerosol Robotic Network AOD records, the results show that the correlation coefficient (0.75), root-mean-square error (0.29), and mean bias (0.068) of the merged AOD are close to those (the correlation coefficient (0.82), root-mean-square error (0.19), and mean bias (0.059)) of the MODIS AOD. In the regions where both MODIS and SeaWiFS have valid observations, the accuracy of the merged AOD is higher than those of MODIS and SeaWiFS AODs. Even in regions where both MODIS and SeaWiFS AODs are missing, the accuracy of the merged AOD is also close to the accuracy of the regions where both MODIS and SeaWiFS have valid observations.

  4. Spatio-temporal hotspots of satellite-tracked arctic foxes reveal a large detection range in a mammalian predator.

    Science.gov (United States)

    Lai, Sandra; Bêty, Joël; Berteaux, Dominique

    2015-01-01

    The scale at which animals perceive their environment is a strong fitness determinant, yet few empirical estimates of animal detection ranges exist, especially in mammalian predators. Using daily Argos satellite tracking of 26 adult arctic foxes (Vulpes lagopus) during a single winter in the High Canadian Arctic, we investigated the detection range of arctic foxes by detecting hotspots of fox activity on the sea ice. While maintaining territories in the tundra, these solitary foragers occasionally used the sea ice where they sometimes formed spatio-temporal hotspots, likely scavenging on marine mammal carcasses. We detected 35 movements by 13 individuals forming five hotspots. Foxes often traveled more than 10 km, and up to 40 km, to reach hotspots, which lasted one-two weeks and could gather up to 12 individuals. The likelihood of a fox joining a hotspot was neither influenced by its distance from the hotspot nor by the distance of its home range to the coast. Observed traveling distances may indicate a high detection range in arctic foxes, and our results suggest their ability to detect food sources on the sea ice from their terrestrial home range. While revealing a wide knowledge gap regarding resource detection abilities in mammalian predators, our study provides estimates of detection range useful for interpreting and modeling animal movements. It also allows a better understanding of foraging behavior and navigation capacity in terrestrial predators.

  5. Spatiotemporal mechanical variation reveals critical role for rho kinase during primitive streak morphogenesis.

    Science.gov (United States)

    Henkels, Julia; Oh, Jaeho; Xu, Wenwei; Owen, Drew; Sulchek, Todd; Zamir, Evan

    2013-02-01

    Large-scale morphogenetic movements during early embryo development are driven by complex changes in biochemical and biophysical factors. Current models for amniote primitive streak morphogenesis and gastrulation take into account numerous genetic pathways but largely ignore the role of mechanical forces. Here, we used atomic force microscopy (AFM) to obtain for the first time precise biomechanical properties of the early avian embryo. Our data reveal that the primitive streak is significantly stiffer than neighboring regions of the epiblast, and that it is stiffer than the pre-primitive streak epiblast. To test our hypothesis that these changes in mechanical properties are due to a localized increase of actomyosin contractility, we inhibited actomyosin contractility via the Rho kinase (ROCK) pathway using the small-molecule inhibitor Y-27632. Our results using several different assays show the following: (1) primitive streak formation was blocked; (2) the time-dependent increase in primitive streak stiffness was abolished; and (3) convergence of epiblast cells to the midline was inhibited. Taken together, our data suggest that actomyosin contractility is necessary for primitive streak morphogenesis, and specifically, ROCK plays a critical role. To better understand the underlying mechanisms of this fundamental process, future models should account for the findings presented in this study.

  6. Spatiotemporal evolution of Calophaca (Fabaceae) reveals multiple dispersals in the Central Asian mountains and adjacent regions

    Science.gov (United States)

    Ming-Li Zhang; Zhi-Bin Wen; Peter W. Fritsch; Stewart C. Sanderson

    2015-01-01

    The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried...

  7. The influence of weather and lemmings on spatiotemporal variation in the abundance of multiple avian guilds in the arctic.

    Directory of Open Access Journals (Sweden)

    Barry G Robinson

    Full Text Available 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

  8. Precipitation-productivity Relation in Grassland in Northern China: Investigations at Multiple Spatiotemporal Scales

    Science.gov (United States)

    Hu, Z.

    2017-12-01

    Climate change is predicted to cause dramatic variability in precipitation regime, not only in terms of change in annual precipitation amount, but also in precipitation seasonal distribution and precipitation event characteristics (high frenquency extrem precipitation, larger but fewer precipitation events), which combined to influence productivity of grassland in arid and semiarid regions. In this study, combining remote sensing products with in-situ measurements of aboveground net primary productivity (ANPP) and gross primary productivity (GPP) data from eddy covariance system in grassland of northern China, we quantified the effects of spatio-temporal vairation in precipitation on productivity from local sites to region scale. We found that, for an individual precipitation event, the duration of GPP-response to the individual precipitation event and the maximum absolute GPP response induced by the individual precipitation event increased linearly with the size of precipitation events. Comparison of the productivity-precipitation relationships between multi-sites determined that the predominant characteristics of precipitation events (PEC) that affected GPP differed remarkably between the water-limited temperate steppe and the temperature-limited alpine meadow. The number of heavy precipitation events (>10 mm d-1) was the most important PEC to impact GPP in the temperate steppe through affecting soil moisture at different soil profiles, while precipitation interval was the factor that affected GPP most in the alpine meadow via its effects on temperature. At the region scale, shape of ANPP-precipitation relationship varies with distinct spatial scales, and besides annual precipitation, precipitation seasonal distribution also has comparable impacts on spatial variation in ANPP. Temporal variability in ANPP was lower at both the dry and wet end, and peaked at a precipitation of 243.1±3.5mm, which is the transition region between typical steppe and desert steppe

  9. Multiple-Parameter Estimation Method Based on Spatio-Temporal 2-D Processing for Bistatic MIMO Radar

    Directory of Open Access Journals (Sweden)

    Shouguo Yang

    2015-12-01

    Full Text Available A novel spatio-temporal 2-dimensional (2-D processing method that can jointly estimate the transmitting-receiving azimuth and Doppler frequency for bistatic multiple-input multiple-output (MIMO radar in the presence of spatial colored noise and an unknown number of targets is proposed. In the temporal domain, the cross-correlation of the matched filters’ outputs for different time-delay sampling is used to eliminate the spatial colored noise. In the spatial domain, the proposed method uses a diagonal loading method and subspace theory to estimate the direction of departure (DOD and direction of arrival (DOA, and the Doppler frequency can then be accurately estimated through the estimation of the DOD and DOA. By skipping target number estimation and the eigenvalue decomposition (EVD of the data covariance matrix estimation and only requiring a one-dimensional search, the proposed method achieves low computational complexity. Furthermore, the proposed method is suitable for bistatic MIMO radar with an arbitrary transmitted and received geometrical configuration. The correction and efficiency of the proposed method are verified by computer simulation results.

  10. Whole brain white matter changes revealed by multiple diffusion metrics in multiple sclerosis: A TBSS study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yaou, E-mail: asiaeurope80@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Duan, Yunyun, E-mail: xiaoyun81.love@163.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); He, Yong, E-mail: yong.h.he@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Yu, Chunshui, E-mail: csyuster@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Wang, Jun, E-mail: jun_wang@bnu.edu.cn [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Huang, Jing, E-mail: sainthj@126.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Ye, Jing, E-mail: jingye.2007@yahoo.com.cn [Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Parizel, Paul M., E-mail: paul.parizel@ua.ac.be [Department of Radiology, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Edegem, 8 Belgium (Belgium); Li, Kuncheng, E-mail: kunchengli55@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Shu, Ni, E-mail: nshu55@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China)

    2012-10-15

    Objective: To investigate whole brain white matter changes in multiple sclerosis (MS) by multiple diffusion indices, we examined patients with diffusion tensor imaging and utilized tract-based spatial statistics (TBSS) method to analyze the data. Methods: Forty-one relapsing-remitting multiple sclerosis (RRMS) patients and 41 age- and gender-matched normal controls were included in this study. Diffusion weighted images were acquired by employing a single-shot echo planar imaging sequence on a 1.5 T MR scanner. Voxel-wise analyses of multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were performed with TBSS. Results: The MS patients had significantly decreased FA (9.11%), increased MD (8.26%), AD (3.48%) and RD (13.17%) in their white matter skeletons compared with the controls. Through TBSS analyses, we found abnormal diffusion changes in widespread white matter regions in MS patients. Specifically, decreased FA, increased MD and increased RD were involved in whole-brain white matter, while several regions exhibited increased AD. Furthermore, white matter regions with significant correlations between the diffusion metrics and the clinical variables (the EDSS scores, disease durations and white matter lesion loads) in MS patients were identified. Conclusion: Widespread white matter abnormalities were observed in MS patients revealed by multiple diffusion metrics. The diffusion changes and correlations with clinical variables were mainly attributed to increased RD, implying the predominant role of RD in reflecting the subtle pathological changes in MS.

  11. Whole brain white matter changes revealed by multiple diffusion metrics in multiple sclerosis: A TBSS study

    International Nuclear Information System (INIS)

    Liu, Yaou; Duan, Yunyun; He, Yong; Yu, Chunshui; Wang, Jun; Huang, Jing; Ye, Jing; Parizel, Paul M.; Li, Kuncheng; Shu, Ni

    2012-01-01

    Objective: To investigate whole brain white matter changes in multiple sclerosis (MS) by multiple diffusion indices, we examined patients with diffusion tensor imaging and utilized tract-based spatial statistics (TBSS) method to analyze the data. Methods: Forty-one relapsing-remitting multiple sclerosis (RRMS) patients and 41 age- and gender-matched normal controls were included in this study. Diffusion weighted images were acquired by employing a single-shot echo planar imaging sequence on a 1.5 T MR scanner. Voxel-wise analyses of multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were performed with TBSS. Results: The MS patients had significantly decreased FA (9.11%), increased MD (8.26%), AD (3.48%) and RD (13.17%) in their white matter skeletons compared with the controls. Through TBSS analyses, we found abnormal diffusion changes in widespread white matter regions in MS patients. Specifically, decreased FA, increased MD and increased RD were involved in whole-brain white matter, while several regions exhibited increased AD. Furthermore, white matter regions with significant correlations between the diffusion metrics and the clinical variables (the EDSS scores, disease durations and white matter lesion loads) in MS patients were identified. Conclusion: Widespread white matter abnormalities were observed in MS patients revealed by multiple diffusion metrics. The diffusion changes and correlations with clinical variables were mainly attributed to increased RD, implying the predominant role of RD in reflecting the subtle pathological changes in MS

  12. Characteristics of juvenile survivors reveal spatio-temporal differences in early life stage survival of Baltic cod

    DEFF Research Database (Denmark)

    Huwer, Bastian; Hinrichsen, H.H.; Böttcher, U.

    2014-01-01

    with previous modeling studies on the survival chances of early-stage larvae and with general spatio-temporal patterns of larval prey availability suggests that differences in survival are related to food availability during the early larval stage. Results are discussed in relation to the recruitment process...

  13. Analysis of Relations between Spatiotemporal Movement Regulation and Performance of Discrete Actions Reveals Functionality in Skilled Climbing.

    Science.gov (United States)

    Orth, Dominic; Kerr, Graham; Davids, Keith; Seifert, Ludovic

    2017-01-01

    In this review of research on climbing expertise, we focus on different measures of climbing performance, including spatiotemporal measures related to fluency and activity states (i.e., discrete actions), adopted by climbers for achieving overall performance goals of getting to the end of a route efficiently and safely. Currently, a broad range of variables have been reported, however, many of these fail to capture how climbers adapt to a route whilst climbing. We argue that spatiotemporal measures should be considered concurrently with evaluation of activity states (such as reaching or exploring) in order gain a more comprehensive picture of how climbers successfully adapt to a route. Spatial and temporal movement measures taken at the hip are a traditional means of assessing efficiency of climbing behaviors. More recently, performatory and exploratory actions of the limbs have been used in combination with spatiotemporal indicators, highlighting the influence of limb states on climbing efficiency and skill transfer. However, only a few studies have attempted to combine spatiotemporal and activity state measures taken during route climbing. This review brings together existing approaches for observing climbing skill at performance outcome (i.e., spatiotemporal assessments) and process (i.e., limb activity states) levels of analysis. Skill level is associated with a spatially efficient route progression and lower levels of immobility. However, more difficult hold architecture designs require significantly greater mobility and more complex movement patterning to maintain performance. Different forms of functional, or goal-supportive, movement variability, including active recovery and hold exploration, have been implicated as important adaptations to physiological and environmental dynamics that emerge during the act of climbing. Indeed, recently it has also been shown that, when climbing on new routes, efficient exploration can improve the transfer of skill. This

  14. Analysis of Relations between Spatiotemporal Movement Regulation and Performance of Discrete Actions Reveals Functionality in Skilled Climbing

    Directory of Open Access Journals (Sweden)

    Dominic Orth

    2017-10-01

    Full Text Available In this review of research on climbing expertise, we focus on different measures of climbing performance, including spatiotemporal measures related to fluency and activity states (i.e., discrete actions, adopted by climbers for achieving overall performance goals of getting to the end of a route efficiently and safely. Currently, a broad range of variables have been reported, however, many of these fail to capture how climbers adapt to a route whilst climbing. We argue that spatiotemporal measures should be considered concurrently with evaluation of activity states (such as reaching or exploring in order gain a more comprehensive picture of how climbers successfully adapt to a route. Spatial and temporal movement measures taken at the hip are a traditional means of assessing efficiency of climbing behaviors. More recently, performatory and exploratory actions of the limbs have been used in combination with spatiotemporal indicators, highlighting the influence of limb states on climbing efficiency and skill transfer. However, only a few studies have attempted to combine spatiotemporal and activity state measures taken during route climbing. This review brings together existing approaches for observing climbing skill at performance outcome (i.e., spatiotemporal assessments and process (i.e., limb activity states levels of analysis. Skill level is associated with a spatially efficient route progression and lower levels of immobility. However, more difficult hold architecture designs require significantly greater mobility and more complex movement patterning to maintain performance. Different forms of functional, or goal-supportive, movement variability, including active recovery and hold exploration, have been implicated as important adaptations to physiological and environmental dynamics that emerge during the act of climbing. Indeed, recently it has also been shown that, when climbing on new routes, efficient exploration can improve the transfer

  15. Multiple skeletal muscle metastases revealing a cardiac intimal sarcoma

    Energy Technology Data Exchange (ETDEWEB)

    Crombe, Amandine [Institut Bergonie, Department of Radiology, Bordeaux (France); Lintingre, Pierre-Francois; Dallaudiere, Benjamin [Clinique du Sport de Bordeaux-Merignac, Department of Musculoskeletal Radiology, Merignac (France); Le Loarer, Francois [Institut Bergonie, Department of Pathology, Bordeaux (France); Lachatre, Denis [Dupuytren University Hospital, Department of Radiology, Limoges (France)

    2018-01-15

    We report the case of a 59-year-old female with progressive bilateral painful swelling of the thighs. MRI revealed multiple intramuscular necrotic masses with similar morphologic patterns. Whole-body CT and 18-FDG PET-CT scans demonstrated additional hypermetabolic muscular masses and a lobulated lesion within the left atrial cavity. As biopsy of a muscular mass was compatible with a poorly differentiated sarcoma with MDM2 oncogene amplification, two diagnoses were discussed: a dedifferentiated liposarcoma with muscle and heart metastases or a primary cardiac sarcoma, mainly a cardiac intimal sarcoma, with muscular metastases, which was finally confirmed by array-comparative genomic hybridization (aCGH) in a sarcoma reference center. This case emphasizes the potential for intimal sarcoma to disseminate in skeletal muscle prior to any other organ and the need for a genomic approach in addition to classical radiopathologic analyses to distinguish primary from secondary locations facing simultaneous tumors of the heart and skeletal muscles with MDM2 amplification. (orig.)

  16. INFORMATION MINING OF SPATIO-TEMPORAL EVOLUTION OF LAKES BASED ON MULTIPLE DYNAMIC MEASUREMENTS

    Directory of Open Access Journals (Sweden)

    W. Feng

    2017-09-01

    Full Text Available Lakes are important water resources and integral parts of the natural ecosystem, and it is of great significance to study the evolution of lakes. The area of each lake increased and decreased at the same time in natural condition, only but the net change of lakes’ area is the result of the bidirectional evolution of lakes. In this paper, considering the effects of net fragmentation, net attenuation, swap change and spatial invariant part in lake evolution, a comprehensive evaluation indexes of lake dynamic evolution were defined,. Such degree contains three levels of measurement: 1 the swap dynamic degree (SDD reflects the space activity of lakes in the study period. 2 the attenuation dynamic degree (ADD reflects the net attenuation of lakes into non-lake areas. 3 the fragmentation dynamic degree (FDD reflects the trend of lakes to be divided and broken into smaller lakes. Three levels of dynamic measurement constitute the three-dimensional "Swap - attenuation – fragmentation" dynamic evolution measurement system of lakes. To show its effectiveness, the dynamic measurement was applied to lakes in Jianghan Plain, the middle Yangtze region of China for a more detailed analysis of lakes from 1984 to 2014. In combination with spatial-temporal location characteristics of lakes, the hidden information in lake evolution in the past 30 years can be revealed.

  17. Spatiotemporal maps reveal regional differences in the effects on gut motility for Lactobacillus reuteri and rhamnosus strains.

    Science.gov (United States)

    Wu, R Y; Pasyk, M; Wang, B; Forsythe, P; Bienenstock, J; Mao, Y-K; Sharma, P; Stanisz, A M; Kunze, W A

    2013-03-01

    Commensal bacteria such as probiotics that are neuroactive acutely affect the amplitudes of intestinal migrating motor complexes (MMCs). What is lacking for an improved understanding of these motility effects are region specific measurements of velocity and frequency. We have combined intraluminal pressure recordings with spatiotemporal diameter maps to analyze more completely effects of different strains of beneficial bacteria on motility. Intraluminal peak pressure (PPr) was measured and video recordings made of mouse ex vivo jejunum and colon segments before and after intraluminal applications of Lactobacillus rhamnosus (JB-1) or Lactobacillus reuteri (DSM 17938). Migrating motor complex frequency and velocity were calculated. JB-1 decreased jejunal frequencies by 56% and 34% in colon. Jejunal velocities increased 171%, but decreased 31% in colon. Jejunal PPr decreased by 55% and in colon by 21%. DSM 17938 increased jejunal frequencies 63% and in colon 75%; jejunal velocity decreased 57%, but increased in colon 146%; jejunal PPr was reduced 26% and 12% in colon. TRAM-34 decreased frequency by 71% and increased velocity 200% for jejunum, but increased frequency 46% and velocity 50% for colon; PPr was decreased 59% for jejunum and 39% for colon. The results show that probiotics and other beneficial bacteria have strain and region-specific actions on gut motility that can be successfully discriminated using spatiotemporal mapping of diameter changes. Effects are not necessarily the same in colon and jejunum. Further research is needed on the detailed effects of the strains on enteric neuron currents for each gut region. © 2013 Blackwell Publishing Ltd.

  18. Atypical Functional Brain Activation during a Multiple Object Tracking Task in Girls with Turner Syndrome: Neurocorrelates of Reduced Spatiotemporal Resolution

    Science.gov (United States)

    Beaton, Elliott A.; Stoddard, Joel; Lai, Song; Lackey, John; Shi, Jianrong; Ross, Judith L.; Simon, Tony J.

    2010-01-01

    Turner syndrome is associated with spatial and numerical cognitive impairments. We hypothesized that these nonverbal cognitive impairments result from limits in spatial and temporal processing, particularly as it affects attention. To examine spatiotemporal attention in girls with Turner syndrome versus typically developing controls, we used a…

  19. Biosensor reveals multiple sources for mitochondrial NAD⁺.

    Science.gov (United States)

    Cambronne, Xiaolu A; Stewart, Melissa L; Kim, DongHo; Jones-Brunette, Amber M; Morgan, Rory K; Farrens, David L; Cohen, Michael S; Goodman, Richard H

    2016-06-17

    Nicotinamide adenine dinucleotide (NAD(+)) is an essential substrate for sirtuins and poly(adenosine diphosphate-ribose) polymerases (PARPs), which are NAD(+)-consuming enzymes localized in the nucleus, cytosol, and mitochondria. Fluctuations in NAD(+) concentrations within these subcellular compartments are thought to regulate the activity of NAD(+)-consuming enzymes; however, the challenge in measuring compartmentalized NAD(+) in cells has precluded direct evidence for this type of regulation. We describe the development of a genetically encoded fluorescent biosensor for directly monitoring free NAD(+) concentrations in subcellular compartments. We found that the concentrations of free NAD(+) in the nucleus, cytoplasm, and mitochondria approximate the Michaelis constants for sirtuins and PARPs in their respective compartments. Systematic depletion of enzymes that catalyze the final step of NAD(+) biosynthesis revealed cell-specific mechanisms for maintaining mitochondrial NAD(+) concentrations. Copyright © 2016, American Association for the Advancement of Science.

  20. Psychiatric disorders revealing multiple sclerosis after 20 years of evolvement

    Directory of Open Access Journals (Sweden)

    Aicha Slassi Sennou

    2014-01-01

    Full Text Available Previous research indicates that the onset of psychiatric disorders is sometimes associated with multiple sclerosis (MS evolving several years later. However, information on why this might occur, and on the outcomes of such patients, is still lacking. We aim to discuss these limitations with the current paper. We describe a 51-year-old female who demonstrated severe anxiety disorder and depression years before developing MS neurological symptoms. The patient was treated for these psychiatric disorders over 20 years. In the last 3 years of her treatment, the patient demonstrated a choreic-type of movement disorder in all her limbs. This disorder is consistent with relapsing-remitting MS. Clinical and magnetic resonance imaging (MRI examinations demonstrated aspects of MS, without MS being diagnosed conclusively. The visual evoked potential indicated a diagnosis of conduction abnormalities. The established diagnosis was slow relapsing MS. The patient underwent methylprednisolone bolus (1 g/day. This case-study suggests that health professionals should conduct a full neurological assessment when they find atypical psychiatric symptoms in a patient. This would make sure that patients receive a better standard of care, and thus experience a better quality of life.

  1. Phylogenetic analysis reveals multiple introductions of Cynodon species in Australia.

    Science.gov (United States)

    Jewell, M; Frère, C H; Harris-Shultz, K; Anderson, W F; Godwin, I D; Lambrides, C J

    2012-11-01

    The distinction between native and introduced flora within isolated land masses presents unique challenges. The geological and colonisation history of Australia, the world's largest island, makes it a valuable system for studying species endemism, introduction, and phylogeny. Using this strategy we investigated Australian cosmopolitan grasses belonging to the genus Cynodon. While it is believed that seven species of Cynodon are present in Australia, no genetic analyses have investigated the origin, diversity and phylogenetic history of Cynodon within Australia. To address this gap, 147 samples (92 from across Australia and 55 representing global distribution) were sequenced for a total of 3336bp of chloroplast DNA spanning six genes. Data showed the presence of at least six putatively introduced Cynodon species (C. transvaalensis, C. incompletus, C. hirsutus, C. radiatus, C. plectostachyus and C. dactylon) in Australia and suggested multiple recent introductions. C. plectostachyus, a species often confused with C. nlemfuensis, was not previously considered to be present in Australia. Most significantly, we identified two common haplotypes that formed a monophyletic clade diverging from previously identified Cynodon species. We hypothesise that these two haplotypes may represent a previously undescribed species of Cynodon. We provide further evidence that two Australian native species, Brachyachne tenella and B. convergens belong in the genus Cynodon and, therefore, argue for the taxonomic revision of the genus Cynodon. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Cdc42 and RhoA reveal different spatio-temporal dynamics upon local stimulation with Semaphorin-3A

    Directory of Open Access Journals (Sweden)

    Federico eIseppon

    2015-08-01

    Full Text Available Small RhoGTPases, such as Cdc42 and RhoA, are key players in integrating external cues and intracellular signaling pathways that regulate growth cone (GC motility. Indeed, Cdc42 is involved in actin polymerization and filopodia formation, whereas RhoA induces GC collapse and neurite retraction through actomyosin contraction. In this study we employed Förster Resonance Energy Transfer (FRET microscopy to study the spatio-temporal dynamics of Cdc42 and RhoA in GCs in response to local Semaphorin-3A stimulation obtained with lipid vesicles filled with Semaphorin-3A and positioned near the selected GC using optical tweezers. We found that Cdc42 and RhoA were activated at the leading edge of NG108-15 neuroblastoma cells during spontaneous cycles of protrusion and retraction, respectively. The release of Semaphorin-3A brought to a progressive activation of RhoA within 30 seconds from the stimulus in the central region of the GC that collapsed and retracted. In contrast, the same stimulation evoked waves of Cdc42 activation propagating away from the stimulated region. A more localized stimulation obtained with Sema3A coated beads placed on the GC, led to Cdc42 active waves that propagated in a retrograde manner with a mean period of 70 seconds, and followed by GC retraction. Therefore, Semaphorin-3A activates both Cdc42 and RhoA with a complex and different spatial-temporal dynamics.

  3. Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants

    Energy Technology Data Exchange (ETDEWEB)

    Huang Qihong; Jin Xidong; Gaillard, Elias T.; Knight, Brian L.; Pack, Franklin D.; Stoltz, James H.; Jayadev, Supriya; Blanchard, Kerry T

    2004-05-18

    Microarray technology continues to gain increased acceptance in the drug development process, particularly at the stage of toxicology and safety assessment. In the current study, microarrays were used to investigate gene expression changes associated with hepatotoxicity, the most commonly reported clinical liability with pharmaceutical agents. Acetaminophen, methotrexate, methapyrilene, furan and phenytoin were used as benchmark compounds capable of inducing specific but different types of hepatotoxicity. The goal of the work was to define gene expression profiles capable of distinguishing the different subtypes of hepatotoxicity. Sprague-Dawley rats were orally dosed with acetaminophen (single dose, 4500 mg/kg for 6, 24 and 72 h), methotrexate (1 mg/kg per day for 1, 7 and 14 days), methapyrilene (100 mg/kg per day for 3 and 7 days), furan (40 mg/kg per day for 1, 3, 7 and 14 days) or phenytoin (300 mg/kg per day for 14 days). Hepatic gene expression was assessed using toxicology-specific gene arrays containing 684 target genes or expressed sequence tags (ESTs). Principal component analysis (PCA) of gene expression data was able to provide a clear distinction of each compound, suggesting that gene expression data can be used to discern different hepatotoxic agents and toxicity endpoints. Gene expression data were applied to the multiplicity-adjusted permutation test and significantly changed genes were categorized and correlated to hepatotoxic endpoints. Repression of enzymes involved in lipid oxidation (acyl-CoA dehydrogenase, medium chain, enoyl CoA hydratase, very long-chain acyl-CoA synthetase) were associated with microvesicular lipidosis. Likewise, subsets of genes associated with hepatotocellular necrosis, inflammation, hepatitis, bile duct hyperplasia and fibrosis have been identified. The current study illustrates that expression profiling can be used to: (1) distinguish different hepatotoxic endpoints; (2) predict the development of toxic endpoints; and

  4. A Unified Spatiotemporal Modeling Approach for Predicting Concentrations of Multiple Air Pollutants in the Multi-Ethnic Study of Atherosclerosis and Air Pollution

    Science.gov (United States)

    Olives, Casey; Kim, Sun-Young; Sheppard, Lianne; Sampson, Paul D.; Szpiro, Adam A.; Oron, Assaf P.; Lindström, Johan; Vedal, Sverre; Kaufman, Joel D.

    2014-01-01

    Background: Cohort studies of the relationship between air pollution exposure and chronic health effects require predictions of exposure over long periods of time. Objectives: We developed a unified modeling approach for predicting fine particulate matter, nitrogen dioxide, oxides of nitrogen, and black carbon (as measured by light absorption coefficient) in six U.S. metropolitan regions from 1999 through early 2012 as part of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air). Methods: We obtained monitoring data from regulatory networks and supplemented those data with study-specific measurements collected from MESA Air community locations and participants’ homes. In each region, we applied a spatiotemporal model that included a long-term spatial mean, time trends with spatially varying coefficients, and a spatiotemporal residual. The mean structure was derived from a large set of geographic covariates that was reduced using partial least-squares regression. We estimated time trends from observed time series and used spatial smoothing methods to borrow strength between observations. Results: Prediction accuracy was high for most models, with cross-validation R2 (R2CV) > 0.80 at regulatory and fixed sites for most regions and pollutants. At home sites, overall R2CV ranged from 0.45 to 0.92, and temporally adjusted R2CV ranged from 0.23 to 0.92. Conclusions: This novel spatiotemporal modeling approach provides accurate fine-scale predictions in multiple regions for four pollutants. We have generated participant-specific predictions for MESA Air to investigate health effects of long-term air pollution exposures. These successes highlight modeling advances that can be adopted more widely in modern cohort studies. Citation: Keller JP, Olives C, Kim SY, Sheppard L, Sampson PD, Szpiro AA, Oron AP, Lindström J, Vedal S, Kaufman JD. 2015. A unified spatiotemporal modeling approach for predicting concentrations of multiple air pollutants in the Multi

  5. Mapping the spatiotemporal evolution of solute transport in articular cartilage explants reveals how cartilage recovers fluid within the contact area during sliding.

    Science.gov (United States)

    Graham, Brian T; Moore, Axel C; Burris, David L; Price, Christopher

    2018-04-11

    The interstitial fluid within articular cartilage shields the matrix from mechanical stresses, reduces friction and wear, enables biochemical processes, and transports solutes into and out of the avascular extracellular matrix. The balanced competition between fluid exudation and recovery under load is thus critical to the mechanical and biological functions of the tissue. We recently discovered that sliding alone can induce rapid solute transport into buried cartilage contact areas via a phenomenon termed tribological rehydration. In this study, we use in situ confocal microscopy measurements to track the spatiotemporal propagation of a small neutral solute into the buried contact area to clarify the fluid mechanics underlying the tribological rehydration phenomenon. Sliding experiments were interrupted by periodic static loading to enable scanning of the entire contact area. Spatiotemporal patterns of solute transport combined with tribological data suggested pressure driven flow through the extracellular matrix from the contact periphery rather than into the surface via a fluid film. Interestingly, these testing interruptions also revealed dynamic, repeatable and history-independent fluid loss and recovery processes consistent with those observed in vivo. Unlike the migrating contact area, which preserves hydration by moving faster than interstitial fluid can flow, our results demonstrate that the stationary contact area can maintain and actively recover hydration through a dynamic competition between load-induced exudation and sliding-induced recovery. The results demonstrate that sliding contributes to the recovery of fluid and solutes by cartilage within the contact area while clarifying the means by which it occurs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes.

    Science.gov (United States)

    Hohmann, Nora; Koch, Marcus A

    2017-10-23

    Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Footprints of adaptive introgression in the

  7. Monitoring and identification of spatiotemporal landscape changes in multiple remote sensing images by using a stratified conditional Latin hypercube sampling approach and geostatistical simulation.

    Science.gov (United States)

    Lin, Yu-Pin; Chu, Hone-Jay; Huang, Yu-Long; Tang, Chia-Hsi; Rouhani, Shahrokh

    2011-06-01

    This study develops a stratified conditional Latin hypercube sampling (scLHS) approach for multiple, remotely sensed, normalized difference vegetation index (NDVI) images. The objective is to sample, monitor, and delineate spatiotemporal landscape changes, including spatial heterogeneity and variability, in a given area. The scLHS approach, which is based on the variance quadtree technique (VQT) and the conditional Latin hypercube sampling (cLHS) method, selects samples in order to delineate landscape changes from multiple NDVI images. The images are then mapped for calibration and validation by using sequential Gaussian simulation (SGS) with the scLHS selected samples. Spatial statistical results indicate that in terms of their statistical distribution, spatial distribution, and spatial variation, the statistics and variograms of the scLHS samples resemble those of multiple NDVI images more closely than those of cLHS and VQT samples. Moreover, the accuracy of simulated NDVI images based on SGS with scLHS samples is significantly better than that of simulated NDVI images based on SGS with cLHS samples and VQT samples, respectively. However, the proposed approach efficiently monitors the spatial characteristics of landscape changes, including the statistics, spatial variability, and heterogeneity of NDVI images. In addition, SGS with the scLHS samples effectively reproduces spatial patterns and landscape changes in multiple NDVI images.

  8. A novel dendrochronological approach reveals drivers of carbon sequestration in tree species of riparian forests across spatiotemporal scales.

    Science.gov (United States)

    Rieger, Isaak; Kowarik, Ingo; Cherubini, Paolo; Cierjacks, Arne

    2017-01-01

    Aboveground carbon (C) sequestration in trees is important in global C dynamics, but reliable techniques for its modeling in highly productive and heterogeneous ecosystems are limited. We applied an extended dendrochronological approach to disentangle the functioning of drivers from the atmosphere (temperature, precipitation), the lithosphere (sedimentation rate), the hydrosphere (groundwater table, river water level fluctuation), the biosphere (tree characteristics), and the anthroposphere (dike construction). Carbon sequestration in aboveground biomass of riparian Quercus robur L. and Fraxinus excelsior L. was modeled (1) over time using boosted regression tree analysis (BRT) on cross-datable trees characterized by equal annual growth ring patterns and (2) across space using a subsequent classification and regression tree analysis (CART) on cross-datable and not cross-datable trees. While C sequestration of cross-datable Q. robur responded to precipitation and temperature, cross-datable F. excelsior also responded to a low Danube river water level. However, CART revealed that C sequestration over time is governed by tree height and parameters that vary over space (magnitude of fluctuation in the groundwater table, vertical distance to mean river water level, and longitudinal distance to upstream end of the study area). Thus, a uniform response to climatic drivers of aboveground C sequestration in Q. robur was only detectable in trees of an intermediate height class and in taller trees (>21.8m) on sites where the groundwater table fluctuated little (≤0.9m). The detection of climatic drivers and the river water level in F. excelsior depended on sites at lower altitudes above the mean river water level (≤2.7m) and along a less dynamic downstream section of the study area. Our approach indicates unexploited opportunities of understanding the interplay of different environmental drivers in aboveground C sequestration. Results may support species-specific and

  9. Spatiotemporal Characterization of Land Subsidence and Uplift (2009–2010 over Wuhan in Central China Revealed by TerraSAR-X InSAR Analysis

    Directory of Open Access Journals (Sweden)

    Lin Bai

    2016-04-01

    Full Text Available The effects of ground deformation pose a significant geo-hazard to the environment and infrastructure in Wuhan, the most populous city in Central China, in the eastern Jianghan Plain at the intersection of the Yangtze and Han rivers. Prior to this study, however, rates and patterns of region-wide ground deformation in Wuhan were little known. Here we employ multi-temporal SAR interferometry to detect and characterize spatiotemporal variations of ground deformation in major metropolitan areas in Wuhan. A total of twelve TerraSAR-X images acquired during 2009–2010 are used in the InSAR time series analysis. InSAR-derived results are validated by levelling survey measurements and reveal a distinct subsidence pattern within six zones in major commercial and industrial areas, with a maximum subsidence rate up to −67.3 mm/year. A comparison analysis between subsiding patterns and urban developments as well as geological conditions suggests that land subsidence in Wuhan is mainly attributed to anthropogenic activities, natural compaction of soft soil, and karst dissolution of subsurface carbonate rocks. However, anthropogenic activities related to intensive municipal construction and industrial production have more significant impacts on the measured subsidence than natural factors. Moreover, remarkable signals of secular land uplift are found along both banks of the Yangtze River, especially along the southern bank, with deformation rates ranging mostly from +5 mm/year to +17.5 mm/year. A strong temporal correlation is highlighted between the detected displacement evolutions and the water level records of the Yangtze River, inferring that this previously unknown deformation phenomenon is likely related to seasonal fluctuations in water levels of the Yangtze River.

  10. Multiple remote sensing data sources to assess spatio-temporal patterns of fire incidence over Campos Amazônicos Savanna Vegetation Enclave (Brazilian Amazon).

    Science.gov (United States)

    Alves, Daniel Borini; Pérez-Cabello, Fernando

    2017-12-01

    Fire activity plays an important role in the past, present and future of Earth system behavior. Monitoring and assessing spatial and temporal fire dynamics have a fundamental relevance in the understanding of ecological processes and the human impacts on different landscapes and multiple spatial scales. This work analyzes the spatio-temporal distribution of burned areas in one of the biggest savanna vegetation enclaves in the southern Brazilian Amazon, from 2000 to 2016, deriving information from multiple remote sensing data sources (Landsat and MODIS surface reflectance, TRMM pluviometry and Vegetation Continuous Field tree cover layers). A fire scars database with 30 m spatial resolution was generated using a Landsat time series. MODIS daily surface reflectance was used for accurate dating of the fire scars. TRMM pluviometry data were analyzed to dynamically establish time limits of the yearly dry season and burning periods. Burned area extent, frequency and recurrence were quantified comparing the results annually/seasonally. Additionally, Vegetation Continuous Field tree cover layers were used to analyze fire incidence over different types of tree cover domains. In the last seventeen years, 1.03millionha were burned within the study area, distributed across 1432 fire occurrences, highlighting 2005, 2010 and 2014 as the most affected years. Middle dry season fires represent 86.21% of the total burned areas and 32.05% of fire occurrences, affecting larger amount of higher density tree surfaces than other burning periods. The results provide new insights into the analysis of burned areas of the neotropical savannas, spatially and statistically reinforcing important aspects linked to the seasonality patterns of fire incidence in this landscape. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. A novel mouse model for multiple myeloma (MOPC315.BM that allows noninvasive spatiotemporal detection of osteolytic disease.

    Directory of Open Access Journals (Sweden)

    Peter O Hofgaard

    Full Text Available Multiple myeloma (MM is a lethal human cancer characterized by a clonal expansion of malignant plasma cells in bone marrow. Mouse models of human MM are technically challenging and do not always recapitulate human disease. Therefore, new mouse models for MM are needed. Mineral-oil induced plasmacytomas (MOPC develop in the peritoneal cavity of oil-injected BALB/c mice. However, MOPC typically grow extramedullary and are considered poor models of human MM. Here we describe an in vivo-selected MOPC315 variant, called MOPC315.BM, which can be maintained in vitro. When injected i.v. into BALB/c mice, MOPC315.BM cells exhibit tropism for bone marrow. As few as 10(4 MOPC315.BM cells injected i.v. induced paraplegia, a sign of spinal cord compression, in all mice within 3-4 weeks. MOPC315.BM cells were stably transfected with either firefly luciferase (MOPC315.BM.Luc or DsRed (MOPC315.BM.DsRed for studies using noninvasive imaging. MOPC315.BM.Luc cells were detected in the tibiofemoral region already 1 hour after i.v. injection. Bone foci developed progressively, and as of day 5, MM cells were detected in multiple sites in the axial skeleton. Additionally, the spleen (a hematopoietic organ in the mouse was invariably affected. Luminescent signals correlated with serum myeloma protein concentration, allowing for easy tracking of tumor load with noninvasive imaging. Affected mice developed osteolytic lesions. The MOPC315.BM model employs a common strain of immunocompetent mice (BALB/c and replicates many characteristics of human MM. The model should be suitable for studies of bone marrow tropism, development of osteolytic lesions, drug testing, and immunotherapy in MM.

  12. Collective synchronization of self/non-self discrimination in T cell activation, across multiple spatio-temporal scales

    Science.gov (United States)

    Altan-Bonnet, Gregoire

    The immune system is a collection of cells whose function is to eradicate pathogenic infections and malignant tumors while protecting healthy tissues. Recent work has delineated key molecular and cellular mechanisms associated with the ability to discriminate self from non-self agents. For example, structural studies have quantified the biophysical characteristics of antigenic molecules (those prone to trigger lymphocyte activation and a subsequent immune response). However, such molecular mechanisms were found to be highly unreliable at the individual cellular level. We will present recent efforts to build experimentally validated computational models of the immune responses at the collective cell level. Such models have become critical to delineate how higher-level integration through nonlinear amplification in signal transduction, dynamic feedback in lymphocyte differentiation and cell-to-cell communication allows the immune system to enforce reliable self/non-self discrimination at the organism level. In particular, we will present recent results demonstrating how T cells tune their antigen discrimination according to cytokine cues, and how competition for cytokine within polyclonal populations of cells shape the repertoire of responding clones. Additionally, we will present recent theoretical and experimental results demonstrating how competition between diffusion and consumption of cytokines determine the range of cell-cell communications within lymphoid organs. Finally, we will discuss how biochemically explicit models, combined with quantitative experimental validation, unravel the relevance of new feedbacks for immune regulations across multiple spatial and temporal scales.

  13. Cerebral and subdural abscess with spatio-temporal multiplicity 12 years after initial craniotomy for acute subdural hematoma. Case report.

    Science.gov (United States)

    Wakui, Daisuke; Nagashima, Goro; Takada, Tatsuro; Ueda, Toshihiro; Itoh, Hidemichi; Tanaka, Yuichiro; Hashimoto, Takuo

    2012-01-01

    A 34-year-old man presented with a case of subdural empyema and cerebral abscess that developed 12 years after initial neurosurgical intervention for a traffic accident in 1998. Under a diagnosis of acute subdural hematoma and cerebral contusion, several neurosurgical procedures were performed at another hospital, including hematoma removal by craniotomy, external decompression, duraplasty, and cranioplasty. The patient experienced an epileptic seizure, and was referred to our hospital in March 2010. Magnetic resonance imaging revealed a cerebral abscess extending to the subdural space just under the previous surgical field. Surgical intervention was refused and antimicrobial treatment was initiated, but proved ineffective. Surgical removal of artificial dura and cranium with subdural empyema, and resection of a cerebral abscess were performed on May 12, 2010. No organism was recovered from the surgical samples. Meropenem and vancomycin were selected as perioperative antimicrobial agents. No recurrence of infection has been observed. Postneurosurgical subdural empyema and cerebral abscess are recently emerging problems. Infections of neurosurgical sites containing implanted materials occur in 6% of cases, usually within several months of the surgery. Subdural empyema and cerebral abscess developing 12 years after neurosurgical interventions are extremely rare. The long-term clinical course suggests less pathogenic organisms as a cause of infection, and further investigations to develop appropriate antimicrobial selection and adequate duration of antimicrobial administration for these cases are needed.

  14. On the potentials of multiple climate variables in assessing the spatio-temporal characteristics of hydrological droughts over the Volta Basin.

    Science.gov (United States)

    Ndehedehe, Christopher E; Awange, Joseph L; Corner, Robert J; Kuhn, Michael; Okwuashi, Onuwa

    2016-07-01

    Multiple drought episodes over the Volta basin in recent reports may lead to food insecurity and loss of revenue. However, drought studies over the Volta basin are rather generalised and largely undocumented due to sparse ground observations and unsuitable framework to determine their space-time occurrence. In this study, we examined the utility of standardised indicators (standardised precipitation index (SPI), standardised runoff index (SRI), standardised soil moisture index (SSI), and multivariate standardised drought index (MSDI)) and Gravity Recovery and Climate Experiment (GRACE) derived terrestrial water storage to assess hydrological drought characteristics over the basin. In order to determine the space-time patterns of hydrological drought in the basin, Independent Component Analysis (ICA), a higher order statistical technique was employed. The results show that SPI and SRI exhibit inconsistent behaviour in observed wet years presupposing a non-linear relationship that reflects the slow response of river discharge to precipitation especially after a previous extreme dry period. While the SPI and SSI show a linear relationship with a correlation of 0.63, the correlation between the MSDIs derived from combining precipitation/river discharge and precipitation/soil moisture indicates a significant value of 0.70 and shows an improved skill in hydrological drought monitoring over the Volta basin during the study period. The ICA-derived spatio-temporal hydrological drought patterns show Burkina Faso and the Lake Volta areas as predominantly drought zones. Further, the statistically significant negative correlations of pacific decadal oscillations (0.39 and 0.25) with temporal evolutions of drought in Burkina Faso and Ghana suggest the possible influence of low frequency large scale oscillations in the observed wet and dry regimes over the basin. Finally, our approach in drought assessment over the Volta basin contributes to a broad framework for hydrological

  15. [Exome sequencing revealed Allan-Herndon-Dudley syndrome underlying multiple disabilities].

    Science.gov (United States)

    Arvio, Maria; Philips, Anju K; Ahvenainen, Minna; Somer, Mirja; Kalscheuer, Vera; Järvelä, Irma

    2014-01-01

    Normal function of the thyroid gland is the cornerstone of a child's mental development and physical growth. We describe a Finnish family, in which the diagnosis of three brothers became clear after investigations that lasted for more than 30 years. Two of the sons have already died. DNA analysis of the third one, a 16-year-old boy, revealed in exome sequencing of the complete X chromosome a mutation in the SLC16A2 gene, i.e. MCT8, coding for a thyroid hormone transport protein. Allan-Herndon-Dudley syndrome was thus shown to be the cause of multiple disabilities.

  16. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.

    Directory of Open Access Journals (Sweden)

    Xiaoke Ma

    2015-06-01

    Full Text Available Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which exhibits differential activity compared to the network of the baseline/healthy condition. We describe the iMDM algorithm to identify both unique and shared gene modules across multiple differential co-expression networks, termed M-DMs (multiple differential modules. We applied iMDM to a time-course RNA-Seq dataset generated using a murine heart failure model generated on two genotypes. We showed that iMDM achieves higher accuracy in inferring gene modules compared to using single or multiple co-expression networks. We found that condition-specific M-DMs exhibit differential activities, mediate different biological processes, and are enriched for genes with known cardiovascular phenotypes. By analyzing M-DMs that are present in multiple conditions, we revealed dynamic changes in pathway activity and connectivity across heart failure conditions. We further showed that module dynamics were correlated with the dynamics of disease phenotypes during the development of heart failure. Thus, pathway dynamics is a powerful measure for understanding pathogenesis. iMDM provides a principled way to dissect the dynamics of gene pathways and its relationship to the dynamics of disease phenotype. With the exponential growth of omics data, our method can aid in generating systems-level insights into disease progression.

  17. Distinct spatio-temporal profiles of beta-oscillations within visual and sensorimotor areas during action recognition as revealed by MEG.

    Science.gov (United States)

    Pavlidou, Anastasia; Schnitzler, Alfons; Lange, Joachim

    2014-05-01

    The neural correlates of action recognition have been widely studied in visual and sensorimotor areas of the human brain. However, the role of neuronal oscillations involved during the process of action recognition remains unclear. Here, we were interested in how the plausibility of an action modulates neuronal oscillations in visual and sensorimotor areas. Subjects viewed point-light displays (PLDs) of biomechanically plausible and implausible versions of the same actions. Using magnetoencephalography (MEG), we examined dynamic changes of oscillatory activity during these action recognition processes. While both actions elicited oscillatory activity in visual and sensorimotor areas in several frequency bands, a significant difference was confined to the beta-band (∼20 Hz). An increase of power for plausible actions was observed in left temporal, parieto-occipital and sensorimotor areas of the brain, in the beta-band in successive order between 1650 and 2650 msec. These distinct spatio-temporal beta-band profiles suggest that the action recognition process is modulated by the degree of biomechanical plausibility of the action, and that spectral power in the beta-band may provide a functional interaction between visual and sensorimotor areas in humans. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments

    International Nuclear Information System (INIS)

    Wang, Mengcen; Qian, Yuan; Liu, Xiaoyu; Wei, Peng; Deng, Man; Wang, Lei; Wu, Huiming; Zhu, Guonian

    2017-01-01

    Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3–11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted. - Highlights: • Multiple spectroscopic analyses were applied to investigate agrochemicals transformation in environment. • Three novel compounds were isolated and identified as triafamone metabolites. • The fate and transformation pathway of triafamone in rice paddy were revealed. • Long-term consumption of the triafamone-containing brown rice is relatively safe. • Elucidation of environmental impacts by exposure to these triazine or oxazolidinedione metabolites is warranted. - Triafamone rapidly dissipates in agricultural environments

  19. Proteomic profiling in multiple sclerosis clinical courses reveals potential biomarkers of neurodegeneration.

    Directory of Open Access Journals (Sweden)

    Maria Liguori

    Full Text Available The aim of our project was to perform an exploratory analysis of the cerebrospinal fluid (CSF proteomic profiles of Multiple Sclerosis (MS patients, collected in different phases of their clinical course, in order to investigate the existence of peculiar profiles characterizing the different MS phenotypes. The study was carried out on 24 Clinically Isolated Syndrome (CIS, 16 Relapsing Remitting (RR MS, 11 Progressive (Pr MS patients. The CSF samples were analysed using the Matrix Assisted Laser Desorption Ionisation Time Of Flight (MALDI-TOF mass spectrometer in linear mode geometry and in delayed extraction mode (m/z range: 1000-25000 Da. Peak lists were imported for normalization and statistical analysis. CSF data were correlated with demographic, clinical and MRI parameters. The evaluation of MALDI-TOF spectra revealed 348 peak signals with relative intensity ≥ 1% in the study range. The peak intensity of the signals corresponding to Secretogranin II and Protein 7B2 were significantly upregulated in RRMS patients compared to PrMS (p<0.05, whereas the signals of Fibrinogen and Fibrinopeptide A were significantly downregulated in CIS compared to PrMS patients (p<0.04. Additionally, the intensity of the Tymosin β4 peak was the only signal to be significantly discriminated between the CIS and RRMS patients (p = 0.013. Although with caution due to the relatively small size of the study populations, and considering that not all the findings remained significant after adjustment for multiple comparisons, in our opinion this mass spectrometry evaluation confirms that this technique may provide useful and important information to improve our understanding of the complex pathogenesis of MS.

  20. Monoclonal antibodies reveal multiple forms of expression of human microsomal epoxide hydrolase

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Hongying; Takagi, Akira [Department of Microbiology, Faculty of Medicine, Saitama Medical University, Moroyama-cho, Iruma-gun, Saitama 350-0495 (Japan); Kayano, Hidekazu [Department of Pathology, Faculty of Medicine, Saitama Medical University, Moroyama-cho, Iruma-gun, Saitama 350-0495 (Japan); Koyama, Isamu [Department of Digestive and General Surgery, Saitama International Medical Center, Faculty of Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama 350-1298 (Japan); Morisseau, Christophe; Hammock, Bruce D. [Department of Entomology and Cancer Center, University of California, Davis, One Shields Avenue, Davis, CA 95616-8584 (United States); Akatsuka, Toshitaka, E-mail: akatsuka@saitama-med.ac.jp [Department of Microbiology, Faculty of Medicine, Saitama Medical University, Moroyama-cho, Iruma-gun, Saitama 350-0495 (Japan)

    2012-04-01

    In a previous study, we developed five kinds of monoclonal antibodies against different portions of human mEH: three, anti-N-terminal; one, anti-C-terminal; one, anti-conformational epitope. Using them, we stained the intact and the permeabilized human cells of various kinds and performed flow cytometric analysis. Primary hepatocytes and peripheral blood mononuclear cells (PBMC) showed remarkable differences. On the surface, hepatocytes exhibited 4 out of 5 epitopes whereas PBMC did not show any of the epitopes. mEH was detected inside both cell types, but the most prominent expression was observed for the conformational epitope in the hepatocytes and the two N-terminal epitopes in PBMC. These differences were also observed between hepatocyte-derived cell lines and mononuclear cell-derived cell lines. In addition, among each group, there were several differences which may be related to the cultivation, the degree of differentiation, or the original cell subsets. We also noted that two glioblastoma cell lines reveal marked expression of the conformational epitope on the surface which seemed to correlate with the brain tumor-associated antigen reported elsewhere. Several cell lines also underwent selective permeabilization before flow cytometric analysis, and we noticed that the topological orientation of mEH on the ER membrane in those cells was in accordance with the previous report. However, the orientation on the cell surface was inconsistent with the report and had a great variation between the cells. These findings show the multiple mode of expression of mEH which may be possibly related to the multiple roles that mEH plays in different cells. -- Highlights: ► We examine expression of five mEH epitopes in human cells. ► Remarkable differences exist between hepatocytes and PBMC. ► mEH expression in cell lines differs depending on several factors. ► Some glioblastoma cell lines reveal marked surface expression of mEH. ► Topology of mEH on the cell

  1. Spatiotemporal analysis of putative notochordal cell markers reveals CD24 and keratins 8, 18, and 19 as notochord-specific markers during early human intervertebral disc development.

    Science.gov (United States)

    Rodrigues-Pinto, Ricardo; Berry, Andrew; Piper-Hanley, Karen; Hanley, Neil; Richardson, Stephen M; Hoyland, Judith A

    2016-08-01

    In humans, the nucleus pulposus (NP) is composed of large vacuolated notochordal cells in the fetus but, soon after birth, becomes populated by smaller, chondrocyte-like cells. Although animal studies indicate that notochord-derived cells persist in the adult NP, the ontogeny of the adult human NP cell population is still unclear. As such, identification of unique notochordal markers is required. This study was conducted to determine the spatiotemporal expression of putative human notochordal markers to aid in the elucidation of the ontogeny of adult human NP cells. Human embryos and fetuses (3.5-18 weeks post-conception (WPC)) were microdissected to isolate the spine anlagens (notochord and somites/sclerotome). Morphology of the developing IVD was assessed using hematoxylin and eosin. Expression of keratin (KRT) 8, KRT18, KRT19, CD24, GAL3, CD55, BASP1, CTGF, T, CD90, Tie2, and E-cadherin was assessed using immunohistochemistry. KRT8, KRT18, KRT19 were uniquely expressed by notochordal cells at all spine levels at all stages studied; CD24 was expressed at all stages except 3.5 WPC. While GAL3, CD55, BASP1, CTGF, and T were expressed by notochordal cells at specific stages, they were also co-expressed by sclerotomal cells. CD90, Tie2, and E-cadherin expression was not detectable in developing human spine cells at any stage. This study has identified, for the first time, the consistent expression of KRT8, KRT18, KRT19, and CD24 as human notochord-specific markers during early IVD development. Thus, we propose that these markers can be used to help ascertain the ontogeny of adult human NP cells. © 2016 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc. J Orthop Res 34:1327-1340, 2016. © 2016 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc.

  2. Spatiotemporal analysis of putative notochordal cell markers reveals CD24 and keratins 8, 18, and 19 as notochord‐specific markers during early human intervertebral disc development

    Science.gov (United States)

    Rodrigues‐Pinto, Ricardo; Berry, Andrew; Piper‐Hanley, Karen; Hanley, Neil; Richardson, Stephen M.

    2016-01-01

    ABSTRACT In humans, the nucleus pulposus (NP) is composed of large vacuolated notochordal cells in the fetus but, soon after birth, becomes populated by smaller, chondrocyte‐like cells. Although animal studies indicate that notochord‐derived cells persist in the adult NP, the ontogeny of the adult human NP cell population is still unclear. As such, identification of unique notochordal markers is required. This study was conducted to determine the spatiotemporal expression of putative human notochordal markers to aid in the elucidation of the ontogeny of adult human NP cells. Human embryos and fetuses (3.5–18 weeks post‐conception (WPC)) were microdissected to isolate the spine anlagens (notochord and somites/sclerotome). Morphology of the developing IVD was assessed using hematoxylin and eosin. Expression of keratin (KRT) 8, KRT18, KRT19, CD24, GAL3, CD55, BASP1, CTGF, T, CD90, Tie2, and E‐cadherin was assessed using immunohistochemistry. KRT8, KRT18, KRT19 were uniquely expressed by notochordal cells at all spine levels at all stages studied; CD24 was expressed at all stages except 3.5 WPC. While GAL3, CD55, BASP1, CTGF, and T were expressed by notochordal cells at specific stages, they were also co‐expressed by sclerotomal cells. CD90, Tie2, and E‐cadherin expression was not detectable in developing human spine cells at any stage. This study has identified, for the first time, the consistent expression of KRT8, KRT18, KRT19, and CD24 as human notochord‐specific markers during early IVD development. Thus, we propose that these markers can be used to help ascertain the ontogeny of adult human NP cells. © 2016 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc. J Orthop Res 34:1327–1340, 2016. PMID:26910849

  3. How Do Multiple-Star Systems Form? VLA Study Reveals "Smoking Gun"

    Science.gov (United States)

    2006-12-01

    system, all the antennas could provide data for us. In addition, we improved the level of detail by using the Pie Town, NM, antenna of the Very Long Baseline Array, as part of an expanded system," Lim said. The implementation and improvement of the 43 GHz receiving system was a collaborative program among the German Max Planck Institute, the Mexican National Autonomous University, and the U.S. National Radio Astronomy Observatory. Two popular theoretical models for the formation of multiple-star systems are, first, that the two protostars and their surrounding dusty disks fragment from a larger parent disk, and, second, that the protostars form independently and then one captures the other into a mutual orbit. "Our new study shows that the disks of the two main protostars are aligned with each other, and also are aligned with the larger, surrounding disk. In addition, their orbital motion resembles the rotation of the larger disk. This is a 'smoking gun' supporting the fragmentation model," Lim said. However, the new study also revealed a third young star with a dust disk. "The disk of this one is misaligned with those of the other two, so it may be the result of either fragmentation or capture," Takakuwa said. The misalignment of the third disk could have come through gravitational interactions with the other two, larger, protostars, the scientists said. They plan further observations to try to resolve the question. "We have a very firm indication that two of these protostars and their dust disks formed from the same, larger disk-like cloud, then broke out from it in a fragmentation process. That strongly supports one theoretical model for how multiple-star systems are formed. The misalignment of the third protostar and its disk leaves open the possibility that it could have formed elsewhere and been captured, and we'll continue to work on reconstructing the history of this fascinating system," Lim summarized. The National Radio Astronomy Observatory is a facility of

  4. Human mast cell tryptase: Multiple cDNAs and genes reveal a multigene serine protease family

    International Nuclear Information System (INIS)

    Vanderslice, P.; Ballinger, S.M.; Tam, E.K.; Goldstein, S.M.; Craik, C.S.; Caughey, G.H.

    1990-01-01

    Three different cDNAs and a gene encoding human skin mast cell tryptase have been cloned and sequenced in their entirety. The deduced amino acid sequences reveal a 30-amino acid prepropeptide followed by a 245-amino acid catalytic domain. The C-terminal undecapeptide of the human preprosequence is identical in dog tryptase and appears to be part of a prosequence unique among serine proteases. The differences among the three human tryptase catalytic domains include the loss of a consensus N-glycosylation site in one cDNA, which may explain some of the heterogeneity in size and susceptibility to deglycosylation seen in tryptase preparations. All three tryptase cDNAs are distinct from a recently reported cDNA obtained from a human lung mast cell library. A skin tryptase cDNA was used to isolate a human tryptase gene, the exons of which match one of the skin-derived cDNAs. The organization of the ∼1.8-kilobase-pair tryptase gene is unique and is not closely related to that of any other mast cell or leukocyte serine protease. The 5' regulatory regions of the gene share features with those of other serine proteases, including mast cell chymase, but are unusual in being separated from the protein-coding sequence by an intron. High-stringency hybridization of a human genomic DNA blot with a fragment of the tryptase gene confirms the presence of multiple tryptase genes. These findings provide genetic evidence that human mast cell tryptases are the products of a multigene family

  5. Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition.

    Science.gov (United States)

    Kohrs, F; Heyer, R; Bissinger, T; Kottler, R; Schallert, K; Püttker, S; Behne, A; Rapp, E; Benndorf, D; Reichl, U

    2017-08-01

    Complex microbial communities are the functional core of anaerobic digestion processes taking place in biogas plants (BGP). So far, however, a comprehensive characterization of the microbiomes involved in methane formation is technically challenging. As an alternative, enriched communities from laboratory-scale experiments can be investigated that have a reduced number of organisms and are easier to characterize by state of the art mass spectrometric-based (MS) metaproteomic workflows. Six parallel laboratory digesters were inoculated with sludge from a full-scale BGP to study the development of enriched microbial communities under defined conditions. During the first three month of cultivation, all reactors (R1-R6) were functionally comparable regarding biogas productions (375-625 NL L reactor volume -1 d -1 ), methane yields (50-60%), pH values (7.1-7.3), and volatile fatty acids (VFA, 1 gNH 3 L -1 ) showed an increase to pH 7.5-8.0, accumulation of acetate (>10 mM), and decreasing biogas production (<125 NL L reactor volume -1 d -1 ). Tandem MS (MS/MS)-based proteotyping allowed the identification of taxonomic abundances and biological processes. Although all reactors showed similar performances, proteotyping and terminal restriction fragment length polymorphisms (T-RFLP) fingerprinting revealed significant differences in the composition of individual microbial communities, indicating multiple steady-states. Furthermore, cellulolytic enzymes and cellulosomal proteins of Clostridium thermocellum were identified to be specific markers for the thermophilic reactors (R3, R4). Metaproteins found in R3 indicated hydrogenothrophic methanogenesis, whereas metaproteins of acetoclastic methanogenesis were identified in R4. This suggests not only an individual evolution of microbial communities even for the case that BGPs are started at the same initial conditions under well controlled environmental conditions, but also a high compositional variance of microbiomes under

  6. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment

    Directory of Open Access Journals (Sweden)

    Hao Yang

    2018-01-01

    Full Text Available Bryostatin 1 (henceforth bryostatin is in clinical trials for the treatment of Alzheimer’s disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer immunotherapy and other therapeutic indications. Yet nothing is known about the conformation of bryostatin bound to its protein kinase C (PKC target in a membrane microenvironment. As a result, efforts to design more efficacious, better tolerated, or more synthetically accessible ligands have been limited to structures that do not include PKC or membrane effects known to influence PKC–ligand binding. This problem extends more generally to many membrane-associated proteins in the human proteome. Here, we use rotational-echo double-resonance (REDOR solid-state NMR to determine the conformations of PKC modulators bound to the PKCδ-C1b domain in the presence of phospholipid vesicles. The conformationally limited PKC modulator phorbol diacetate (PDAc is used as an initial test substrate. While unanticipated partitioning of PDAc between an immobilized protein-bound state and a mobile state in the phospholipid assembly was observed, a single conformation in the bound state was identified. In striking contrast, a bryostatin analogue (bryolog was found to exist exclusively in a protein-bound state, but adopts a distribution of conformations as defined by three independent distance measurements. The detection of multiple PKCδ-C1b-bound bryolog conformers in a functionally relevant phospholipid complex reveals the inherent dynamic nature of cellular systems that is not captured with single-conformation static structures. These results indicate that binding, selectivity, and function of PKC modulators, as well as the design of new modulators, are best addressed using a dynamic multistate model, an analysis potentially applicable to other membrane-associated proteins.

  7. Canonical correlation analysis of multiple sensory directed metabolomics data blocks reveals corresponding parts between data blocks.

    NARCIS (Netherlands)

    Doeswijk, T. G.; Hageman, J.A.; Westerhuis, J.A.; Tikunov, Y.; Bovy, A.; van Eeuwijk, F.A.

    2011-01-01

    Multiple analytical platforms are frequently used in metabolomics studies. The resulting multiple data blocks contain, in general, similar parts of information which can be disclosed by chemometric methods. The metabolites of interest, however, are usually just a minor part of the complete data

  8. Multifractal fluctuations in joint angles during infant spontaneous kicking reveal multiplicativity-driven coordination

    International Nuclear Information System (INIS)

    Stephen, Damian G.; Hsu, Wen-Hao; Young, Diana; Saltzman, Elliot L.; Holt, Kenneth G.; Newman, Dava J.; Weinberg, Marc; Wood, Robert J.; Nagpal, Radhika; Goldfield, Eugene C.

    2012-01-01

    Previous research has considered infant spontaneous kicking as a form of exploration. According to this view, spontaneous kicking provides information about motor degrees of freedom and may shape multijoint coordinations for more complex movement patterns such as gait. Recent work has demonstrated that multifractal, multiplicative fluctuations in exploratory movements index energy flows underlying perceptual-motor information. If infant spontaneous kicking is exploratory and occasions an upstream flow of information from the motor periphery, we expected not only that multiplicativity of fluctuations at the hip should promote multiplicativity of fluctuations at more distal joints (i.e., reflecting downstream effects of neural control) but also that multiplicativity at more distal joints should promote multiplicativity at the hip. Multifractal analysis demonstrated that infant spontaneous kicking in four typically developing infants for evidence of multiplicative fluctuations in multiple joint angles along the leg (i.e., hip, knee, and ankle) exhibited multiplicativity. Vector autoregressive modeling demonstrated that only one leg exhibited downstream effects but that both legs exhibited upstream effects. These results confirm the exploratory aspect of infant spontaneous kicking and suggest chaotic dynamics in motor coordination. They also resonate with existing models of chaos-controlled robotics and noise-based interventions for rehabilitating motor coordination in atypically developing patients.

  9. Latest Holocene Climate Variability revealed by a high-resolution multiple Proxy Record off Lisbon (Portugal)

    Science.gov (United States)

    Abrantes, F.; Lebreiro, S.; Ferreira, A.; Gil, I.; Jonsdottir, H.; Rodrigues, T.; Kissel, C.; Grimalt, J.

    2003-04-01

    The North Atlantic Oscillation (NAO) is known to have a major influence on the wintertime climate of the Atlantic basin and surrounding countries, determining precipitation and wind conditions at mid-latitudes. A comparison of Hurrel's NAO index to the mean winter (January-March) discharge of the Iberian Tagus River reveals a good negative correlation to negative NAO, while the years of largest upwelling anomalies, as referred in the literature, appear to be in good agreement with positive NAO. On this basis, a better understanding of the long-term variability of the NAO and Atlantic climate variability can be gained from high-resolution climate records from the Lisbon area. Climate variability of the last 2,000 years is assessed through a multiple proxy study of sedimentary sequences recovered from the Tagus prodelta deposition center, off Lisbon (Western Iberia). Physical properties, XRF and magnetic properties from core logging, grain size, δ18O, TOC, CaCO3, total alkenones, n-alkanes, alkenone SST, diatoms, benthic and planktonic foraminiferal assemblage compositions and fluxes are the proxies employed. The age model for site D13902 is based on AMS C-14 dates from mollusc and planktonic foraminifera shells, the reservoir correction for which was obtained by dating 3 pre-bomb, mollusc shells from the study area. Preliminary results indicate a Little Ice Age (LIA - 1300 - 1600 AD) alkenone derived SSTs around 15 degC followed by a sharp and rapid increase towards 19 degC. In spite the strong variability observed for most records, this low temperature interval is marked by a general increase in organic carbon, total alkenone concentration, diatom and foraminiferal abundances, as well as an increase in the sediment fine fraction and XRF determined Fe content, pointing to important river input and higher productivity. The Medieval Warm Period (1080 - 1300 AD) is characterized by 17-18 degC SSTs, increased mean grain size, but lower magnetic susceptibility and Fe

  10. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  11. Spatiotemporal Wave Patterns: Information Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mikhail Rabinovich; Lev Tsimring

    2006-01-20

    Pattern formation has traditionally been studied in non-equilibrium physics from the viewpoint of describing the basic structures and their interactions. While this is still an important area of research, the emphasis in the last few years has shifted towards analysis of specific properties of patterns in various complex media. For example, diverse and unexpected phenomena occur in neuro-like media that are characterized by highly non-trivial local dynamics. We carried out an active research program on analysis of spatio-temporal patterns in various physical systems (convection, oscillating fluid layer, soap film), as well as in neuro-like media, with an emphasis on informational aspects of the dynamics. Nonlinear nonequilibrium media and their discrete analogs have a unique ability to represent, memorize, and process the information contained in spatio-temporal patterns. Recent neurophysiological experiments demonstrated a certain universality of spatio-temporal representation of information by neural ensembles. Information processing is also revealed in the spatio-temporal dynamics of cellular patterns in nonequilibrium media. It is extremely important for many applications to study the informational aspects of these dynamics, including the origins and mechanisms of information generation, propagation and storage. Some of our results are: the discovery of self-organization of periodically oscillatory patterns in chaotic heterogeneous media; the analysis of the propagation of the information along a chaotic media as function of the entropy of the signal; the analysis of wave propagation in discrete non-equilibrium media with autocatalytic properties, which simulates the calcium dynamics in cellular membranes. Based on biological experiments we suggest the mechanism by which the spatial sensory information is transferred into the spatio-temporal code in the neural media. We also found a new mechanism of self-pinning in cellular structures and the related phenomenon

  12. Non-invasive imaging provides spatiotemporal information on disease progression and response to therapy in a murine model of multiple myeloma.

    Directory of Open Access Journals (Sweden)

    Simone S Riedel

    Full Text Available Multiple myeloma (MM is a B-cell malignancy, where malignant plasma cells clonally expand in the bone marrow of older people, causing significant morbidity and mortality. Typical clinical symptoms include increased serum calcium levels, renal insufficiency, anemia, and bone lesions. With standard therapies, MM remains incurable; therefore, the development of new drugs or immune cell-based therapies is desirable. To advance the goal of finding a more effective treatment for MM, we aimed to develop a reliable preclinical MM mouse model applying sensitive and reproducible methods for monitoring of tumor growth and metastasis in response to therapy.A mouse model was created by intravenously injecting bone marrow-homing mouse myeloma cells (MOPC-315.BM that expressed luciferase into BALB/c wild type mice. The luciferase in the myeloma cells allowed in vivo tracking before and after melphalan treatment with bioluminescence imaging (BLI. Homing of MOPC-315.BM luciferase+ myeloma cells to specific tissues was examined by flow cytometry. Idiotype-specific myeloma protein serum levels were measured by ELISA. In vivo measurements were validated with histopathology.Strong bone marrow tropism and subsequent dissemination of MOPC-315.BM luciferase(+ cells in vivo closely mimicked the human disease. In vivo BLI and later histopathological analysis revealed that 12 days of melphalan treatment slowed tumor progression and reduced MM dissemination compared to untreated controls. MOPC-315.BM luciferase(+ cells expressed CXCR4 and high levels of CD44 and α4β1 in vitro which could explain the strong bone marrow tropism. The results showed that MOPC-315.BM cells dynamically regulated homing receptor expression and depended on interactions with surrounding cells.This study described a novel MM mouse model that facilitated convenient, reliable, and sensitive tracking of myeloma cells with whole body BLI in living animals. This model is highly suitable for monitoring

  13. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates.

    Science.gov (United States)

    Bouts, Mark J R J; Westmoreland, Susan V; de Crespigny, Alex J; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M; Wu, Ona; D'Arceuil, Helen E

    2015-12-15

    Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by combining quantitative T2 and diffusion MRI indices into MRI 'tissue signatures', (2) to evaluate temporal differences in these signatures between transient (n = 2) and permanent (n = 2) middle cerebral artery occlusion, and (3) to correlate histopathology findings in the chronic stroke period to the acute and subacute MRI derived tissue signatures. An improved iterative self-organizing data analysis algorithm was used to combine T2, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) maps across seven successive timepoints (1, 2, 3, 24, 72, 144, 240 h) which revealed five temporal MRI signatures, that were different from the normal tissue pattern (P MRI signatures associated with specific tissue fates may further aid in assessing and monitoring the efficacy of novel pharmaceutical treatments for stroke in a pre-clinical and clinical setting.

  15. Multiple long bone cysts revealed by MRI in trichorhinophalangeal syndrome type II predisposing to pathological fractures

    Energy Technology Data Exchange (ETDEWEB)

    Konala, Praveen; Cassar-Pullicino, Victor N. [The Robert Jones and Agnes Hunt Orthopaedic Hospital, Department of Radiology, Oswestry (United Kingdom); Kiely, Nigel [The Robert Jones and Agnes Hunt Orthopaedic Hospital, Department of Orthopaedic Surgery, Oswestry (United Kingdom); Noakes, Charlotte [Oxford University Hospital, The Oxford Genetics Laboratories, Oxford (United Kingdom); Blair, Edward [Oxford University Hospital, Department of Clinical Genetics, Oxford (United Kingdom)

    2017-07-15

    Trichorhinophalangeal syndrome type II is a rare genetic disorder with the few published case reports mainly reporting the radiographic skeletal manifestations. There are no published imaging reports of long bone cysts involving multiple bones in this condition. We report a unique case of bone cysts involving multiple long bones detected with MRI in a patient with trichorhinophalangeal syndrome type II complicated by a subsequent pathological fracture. It is possible that the bone cysts are a previously undescribed feature of this syndrome; however, the evidence is insufficient to establish a definite association. Chromosomal abnormality identified in this patient is consistent with trichorhinophalangeal syndrome type II with no unusual features. Although the nature of these bone cysts is unclear, they are one of the causes of the known increased fracture risk observed in this syndrome. (orig.)

  16. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  17. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes

    Directory of Open Access Journals (Sweden)

    Elvezia Maria Paraboschi

    2015-09-01

    Full Text Available Abnormalities in RNA metabolism and alternative splicing (AS are emerging as important players in complex disease phenotypes. In particular, accumulating evidence suggests the existence of pathogenic links between multiple sclerosis (MS and altered AS, including functional studies showing that an imbalance in alternatively-spliced isoforms may contribute to disease etiology. Here, we tested whether the altered expression of AS-related genes represents a MS-specific signature. A comprehensive comparative analysis of gene expression profiles of publicly-available microarray datasets (190 MS cases, 182 controls, followed by gene-ontology enrichment analysis, highlighted a significant enrichment for differentially-expressed genes involved in RNA metabolism/AS. In detail, a total of 17 genes were found to be differentially expressed in MS in multiple datasets, with CELF1 being dysregulated in five out of seven studies. We confirmed CELF1 downregulation in MS (p = 0.0015 by real-time RT-PCRs on RNA extracted from blood cells of 30 cases and 30 controls. As a proof of concept, we experimentally verified the unbalance in alternatively-spliced isoforms in MS of the NFAT5 gene, a putative CELF1 target. In conclusion, for the first time we provide evidence of a consistent dysregulation of splicing-related genes in MS and we discuss its possible implications in modulating specific AS events in MS susceptibility genes.

  18. Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories.

    Science.gov (United States)

    Avigdor, Bracha Erlanger; Cimino-Mathews, Ashley; DeMarzo, Angelo M; Hicks, Jessica L; Shin, James; Sukumar, Saraswati; Fetting, John; Argani, Pedram; Park, Ben H; Wheelan, Sarah J

    2017-12-21

    Heterogeneity within and among tumors in a metastatic cancer patient is a well-established phenomenon that may confound treatment and accurate prognosis. Here, we used whole-exome sequencing to survey metastatic breast cancer tumors from 5 patients in a rapid autopsy program to construct the origin and genetic development of metastases. Metastases were obtained from 5 breast cancer patients using a rapid autopsy protocol and subjected to whole-exome sequencing. Metastases were evaluated for sharing of somatic mutations, correlation of copy number variation and loss of heterozygosity, and genetic similarity scores. Pathological features of the patients' disease were assessed by immunohistochemical analyses. Our data support a monoclonal origin of metastasis in 3 cases, but in 2 cases, metastases arose from at least 2 distinct subclones in the primary tumor. In the latter 2 cases, the primary tumor presented with mixed histologic and pathologic features, suggesting early divergent evolution within the primary tumor with maintenance of metastatic capability in multiple lineages. We used genetic and histopathological evidence to demonstrate that metastases can be derived from a single or multiple independent clones within a primary tumor. This underscores the complexity of breast cancer clonal evolution and has implications for how best to determine and implement therapies for early- and late-stage disease.

  19. Multiple Spectral Ratio Analyses Reveal Earthquake Source Spectra of Small Earthquakes and Moment Magnitudes of Microearthquakes

    Science.gov (United States)

    Uchide, T.; Imanishi, K.

    2016-12-01

    Spectral studies for macroscopic earthquake source parameters are helpful for characterizing earthquake rupture process and hence understanding earthquake source physics and fault properties. Those studies require us mute wave propagation path and site effects in spectra of seismograms to accentuate source effect. We have recently developed the multiple spectral ratio method [Uchide and Imanishi, BSSA, 2016] employing many empirical Green's function (EGF) events to reduce errors from the choice of EGF events. This method helps us estimate source spectra more accurately as well as moment ratios among reference and EGF events, which are useful to constrain the seismic moment of microearthquakes. First, we focus on earthquake source spectra. The source spectra have generally been thought to obey the omega-square model with single corner-frequency. However recent studies imply the existence of another corner frequency for some earthquakes. We analyzed small shallow inland earthquakes (3.5 multiple spectral ratio analyses. For 20000 microearthquakes in Fukushima Hamadori and northern Ibaraki prefecture area, we found that the JMA magnitudes (Mj) based on displacement or velocity amplitude are systematically below Mw. The slope of the Mj-Mw relation is 0.5 for Mj 5. We propose a fitting curve for the obtained relationship as Mw = (1/2)Mj + (1/2)(Mjγ + Mcorγ)1/γ+ c, where Mcor is a corner magnitude, γ determines the sharpness of the corner, and c denotes an offset. We obtained Mcor = 4.1, γ = 5.6, and c = -0.47 to fit the observation. The parameters are useful for characterizing the Mj-Mw relationship. This non-linear relationship affects the b-value of the Gutenberg-Richter law. Quantitative discussions on b-values are affected by the definition of magnitude to use.

  20. Microstructural abnormalities in the trigeminal nerves of patients with trigeminal neuralgia revealed by multiple diffusion metrics

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yaou [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Beijing Key laboratory of MRI and Brain Informatics, Beijing (China); Li, Jiping [Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Butzkueven, Helmut [Department of Medicine, University of Melbourne, Parkville 3010 (Australia); Duan, Yunyun; Zhang, Mo [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Shu, Ni [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Li, Yongjie [Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Zhang, Yuqing, E-mail: yuqzhang@sohu.com [Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Li, Kuncheng, E-mail: kunchengli55@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China)

    2013-05-15

    Objective: To investigate microstructural tissue changes of trigeminal nerve (TGN) in patients with unilateral trigeminal neuralgia (TN) by multiple diffusion metrics, and correlate the diffusion indexes with the clinical variables. Methods: 16 patients with TN and 6 healthy controls (HC) were recruited into our study. All participants were imaged with a 3.0 T system with three-dimension time-of-flight (TOF) magnetic resonance angiography and fluid attenuated inversion recovery (FLAIR) DTI-sequence. We placed regions of interest over the root entry zone of the TGN and measured fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). The mean values of FA, MD, AD and RD were compared between the affected and unaffected sides in the same patient, and to HC values. The correlation between the side-to-side diffusion metric difference and clinical variables (disease duration and visual analogy scale, VAS) was further explored. Results: Compared with the unaffected side and HC, the affected side showed significantly decreased FA and increased RD; however, no significant changes of AD were found. A trend toward significantly increased MD was identified on the affected side comparing with the unaffected side. We also found the significant correlation between the FA reduction and VAS of pain (r = −0.55, p = 0.03). Conclusion: DTI can quantitatively assess the microstructural abnormalities of the affected TGN in patients with TN. Our results suggest demyelination without significant axonal injury is the essential pathological basis of the affected TGN by multiple diffusion metrics. The correlation between FA reduction and VAS suggests FA as a potential objective MRI biomarker to correlate with clinical severity.

  1. Microstructural abnormalities in the trigeminal nerves of patients with trigeminal neuralgia revealed by multiple diffusion metrics

    International Nuclear Information System (INIS)

    Liu, Yaou; Li, Jiping; Butzkueven, Helmut; Duan, Yunyun; Zhang, Mo; Shu, Ni; Li, Yongjie; Zhang, Yuqing; Li, Kuncheng

    2013-01-01

    Objective: To investigate microstructural tissue changes of trigeminal nerve (TGN) in patients with unilateral trigeminal neuralgia (TN) by multiple diffusion metrics, and correlate the diffusion indexes with the clinical variables. Methods: 16 patients with TN and 6 healthy controls (HC) were recruited into our study. All participants were imaged with a 3.0 T system with three-dimension time-of-flight (TOF) magnetic resonance angiography and fluid attenuated inversion recovery (FLAIR) DTI-sequence. We placed regions of interest over the root entry zone of the TGN and measured fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). The mean values of FA, MD, AD and RD were compared between the affected and unaffected sides in the same patient, and to HC values. The correlation between the side-to-side diffusion metric difference and clinical variables (disease duration and visual analogy scale, VAS) was further explored. Results: Compared with the unaffected side and HC, the affected side showed significantly decreased FA and increased RD; however, no significant changes of AD were found. A trend toward significantly increased MD was identified on the affected side comparing with the unaffected side. We also found the significant correlation between the FA reduction and VAS of pain (r = −0.55, p = 0.03). Conclusion: DTI can quantitatively assess the microstructural abnormalities of the affected TGN in patients with TN. Our results suggest demyelination without significant axonal injury is the essential pathological basis of the affected TGN by multiple diffusion metrics. The correlation between FA reduction and VAS suggests FA as a potential objective MRI biomarker to correlate with clinical severity

  2. Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events.

    Science.gov (United States)

    Armour, Christine M; Smith, Amanda; Hartley, Taila; Chardon, Jodi Warman; Sawyer, Sarah; Schwartzentruber, Jeremy; Hennekam, Raoul; Majewski, Jacek; Bulman, Dennis E; Suri, Mohnish; Boycott, Kym M

    2016-07-01

    In 1987 Fitzsimmons and Guilbert described identical male twins with progressive spastic paraplegia, brachydactyly with cone shaped epiphyses, short stature, dysarthria, and "low-normal" intelligence. In subsequent years, four other patients, including one set of female identical twins, a single female child, and a single male individual were described with the same features, and the eponym Fitzsimmons syndrome was adopted (OMIM #270710). We performed exome analysis of the patient described in 2009, and one of the original twins from 1987, the only patients available from the literature. No single genetic etiology exists that explains Fitzsimmons syndrome; however, multiple different genetic causes were identified. Specifically, the twins described by Fitzsimmons had heterozygous mutations in the SACS gene, the gene responsible for autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS), as well as a heterozygous mutation in the TRPS1, the gene responsible in Trichorhinophalangeal syndrome type 1 (TRPS1 type 1) which includes brachydactyly as a feature. A TBL1XR1 mutation was identified in the patient described in 2009 as contributing to his cognitive impairment and autistic features with no genetic cause identified for his spasticity or brachydactyly. The findings show that these individuals have multiple different etiologies giving rise to a similar phenotype, and that "Fitzsimmons syndrome" is in fact not one single syndrome. Over time, we anticipate that continued careful phenotyping with concomitant genome-wide analysis will continue to identify the causes of many rare syndromes, but it will also highlight that previously delineated clinical entities are, in fact, not syndromes at all. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development

    Science.gov (United States)

    Benitez, Cecil M.; Qu, Kun; Sugiyama, Takuya; Pauerstein, Philip T.; Liu, Yinghua; Tsai, Jennifer; Gu, Xueying; Ghodasara, Amar; Arda, H. Efsun; Zhang, Jiajing; Dekker, Joseph D.; Tucker, Haley O.; Chang, Howard Y.; Kim, Seung K.

    2014-01-01

    The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. PMID:25330008

  4. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.

    Directory of Open Access Journals (Sweden)

    Cecil M Benitez

    2014-10-01

    Full Text Available The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus.

  5. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  6. Novel multiplex PCR reveals multiple trypanosomatid species infecting North American bumble bees (Hymenoptera: Apidae: Bombus).

    Science.gov (United States)

    Tripodi, Amber D; Szalanski, Allen L; Strange, James P

    2018-03-01

    Crithidia bombi and Crithidia expoeki (Trypanosomatidae) are common parasites of bumble bees (Bombus spp.). Crithidia bombi was described in the 1980s, and C. expoeki was recently discovered using molecular tools. Both species have cosmopolitan distributions among their bumble bee hosts, but there have been few bumble bee studies that have identified infections to species since the original description of C. expoeki in 2010. Morphological identification of species is difficult due to variability within each stage of their complex lifecycles, although they can be easily differentiated through DNA sequencing. However, DNA sequencing can be expensive, particularly with many samples to diagnose. In order to reliably and inexpensively distinguish Crithidia species for a large-scale survey, we developed a multiplex PCR protocol using species-specific primers with a universal trypanosomatid primer set to detect unexpected relatives. We applied this method to 356 trypanosomatid-positive bumble bees from North America as a first-look at the distribution and host range of each parasite in the region. Crithidia bombi was more common (90.2%) than C. expoeki (21.3%), with most C. expoeki-positive samples existing as co-infections with C. bombi (13.8%). This two-step detection method also revealed that 2.2% samples were positive for trypanosmatids that were neither C. bombi nor C. expoeki. Sequencing revealed that two individuals were positive for C. mellificae, one for Lotmaria passim, and three for two unclassified trypanosomatids. This two-step method is effective in diagnosing known bumble bee infecting Crithidia species, and allowing for the discovery of unknown potential symbionts. Published by Elsevier Inc.

  7. Multiple surveys employing a new sample-processing protocol reveal the genetic diversity of placozoans in Japan.

    Science.gov (United States)

    Miyazawa, Hideyuki; Nakano, Hiroaki

    2018-03-01

    Placozoans, flat free-living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest-branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S rRNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, "ethanol-treated substrate sampling," for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine-jima, Chichi-jima, and Haha-jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine-jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.

  8. Phylogenetic and molecular epidemiological studies reveal evidence of multiple past recombination events between infectious laryngotracheitis viruses.

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    Sang-Won Lee

    Full Text Available In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field.

  9. A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility.

    Science.gov (United States)

    Bush, W S; McCauley, J L; DeJager, P L; Dudek, S M; Hafler, D A; Gibson, R A; Matthews, P M; Kappos, L; Naegelin, Y; Polman, C H; Hauser, S L; Oksenberg, J; Haines, J L; Ritchie, M D

    2011-07-01

    Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also increases power to detect weak main effects. We conducted a knowledge-driven interaction analysis of a GWAS of 931 multiple sclerosis (MS) trios to discover gene-gene interactions within established biological contexts. We identify heterogeneous signals, including a gene-gene interaction between CHRM3 (muscarinic cholinergic receptor 3) and MYLK (myosin light-chain kinase) (joint P=0.0002), an interaction between two phospholipase C-β isoforms, PLCβ1 and PLCβ4 (joint P=0.0098), and a modest interaction between ACTN1 (actinin alpha 1) and MYH9 (myosin heavy chain 9) (joint P=0.0326), all localized to calcium-signaled cytoskeletal regulation. Furthermore, we discover a main effect (joint P=5.2E-5) previously unidentified by single-locus analysis within another related gene, SCIN (scinderin), a calcium-binding cytoskeleton regulatory protein. This work illustrates that knowledge-driven interaction analysis of GWAS data is a feasible approach to identify new genetic effects. The results of this study are among the first gene-gene interactions and non-immune susceptibility loci for MS. Further, the implicated genes cluster within inter-related biological mechanisms that suggest a neurodegenerative component to MS.

  10. Benznidazole biotransformation and multiple targets in Trypanosoma cruzi revealed by metabolomics.

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    Andrea Trochine

    2014-05-01

    Full Text Available The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, involves administration of benznidazole (Bzn. Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active, although its mode of action is not fully understood. In the present work we used a non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn.Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols trypanothione, homotrypanothione and cysteine were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment. These metabolites included reduction products, fragments and covalent adducts of reduced Bzn linked to each of the major low molecular weight thiols: trypanothione, glutathione, γ-glutamylcysteine, glutathionylspermidine, cysteine and ovothiol A. Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI, were found within the parasites, but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected.Our data is indicative of a major role of the thiol binding capacity of Bzn reduction products in the mechanism of Bzn toxicity against T. cruzi.

  11. Genetic analysis of yeast RPA1 reveals its multiple functions in DNA metabolism

    International Nuclear Information System (INIS)

    Umezu, K.; Sugawara, N.; Chen, C.; Haber, J.E.; Kolodner, R.D.

    1998-01-01

    Replication protein A (RPA) is a single-stranded DNA-binding protein identified as an essential factor for SV40 DNA replication in vitro. To understand the in vivo functions of RPA, we mutagenized the Saccharomyces cerevisiae RFA1 gene and identified 19 ultraviolet light (UV) irradiation- and methyl methane sulfonate (MMS)-sensitive mutants and 5 temperature-sensitive mutants. The UV- and MMS-sensitive mutants showed up to 10 4 to 10 5 times increased sensitivity to these agents. Some of the UV- and MMSsensitive mutants were killed by an HO-induced double-strand break atMAT. Physical analysis of recombination in one UV- and MMS-sensitive rfa1 mutant demonstrated that it was defective for mating type switching and single-strand annealing recombination. Two temperature-sensitive mutants were characterized in detail, and at the restrictive temperature were found to have an arrest phenotype and DNA content indicative of incomplete DNA replication. DNA sequence analysis indicated that most of the mutations altered amino acids that were conserved between yeast, human, and Xenopus RPA1. Taken together, we conclude that RPA1 has multiple roles in vivo and functions in DNA replication, repair, and recombination, like the single-stranded DNA-binding proteins of bacteria and phages. (author)

  12. Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis.

    Science.gov (United States)

    Stewart, Philip E; Carroll, James A; Olano, L Rennee; Sturdevant, Daniel E; Rosa, Patricia A

    2016-02-15

    The saprophyte Leptospira biflexa is an excellent model for studying the physiology of the medically important Leptospira genus, the pathogenic members of which are more recalcitrant to genetic manipulation and have significantly slower in vitro growth. However, relatively little is known regarding the proteome of L. biflexa, limiting its utility as a model for some studies. Therefore, we have generated a proteomic map of both soluble and membrane-associated proteins of L. biflexa during exponential growth and in stationary phase. Using these data, we identified abundantly produced proteins in each cellular fraction and quantified the transcript levels from a subset of these genes using quantitative reverse transcription-PCR (RT-PCR). These proteins should prove useful as cellular markers and as controls for gene expression studies. We also observed a significant number of L. biflexa membrane-associated proteins with multiple isoforms, each having unique isoelectric focusing points. L. biflexa cell lysates were examined for several posttranslational modifications suggested by the protein patterns. Methylation and acetylation of lysine residues were predominately observed in the proteins of the membrane-associated fraction, while phosphorylation was detected mainly among soluble proteins. These three posttranslational modification systems appear to be conserved between the free-living species L. biflexa and the pathogenic species Leptospira interrogans, suggesting an important physiological advantage despite the varied life cycles of the different species. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Logic programming reveals alteration of key transcription factors in multiple myeloma.

    Science.gov (United States)

    Miannay, Bertrand; Minvielle, Stéphane; Roux, Olivier; Drouin, Pierre; Avet-Loiseau, Hervé; Guérin-Charbonnel, Catherine; Gouraud, Wilfried; Attal, Michel; Facon, Thierry; Munshi, Nikhil C; Moreau, Philippe; Campion, Loïc; Magrangeas, Florence; Guziolowski, Carito

    2017-08-23

    Innovative approaches combining regulatory networks (RN) and genomic data are needed to extract biological information for a better understanding of diseases, such as cancer, by improving the identification of entities and thereby leading to potential new therapeutic avenues. In this study, we confronted an automatically generated RN with gene expression profiles (GEP) from a cohort of multiple myeloma (MM) patients and normal individuals using global reasoning on the RN causality to identify key-nodes. We modeled each patient by his or her GEP, the RN and the possible automatically detected repairs needed to establish a coherent flow of the information that explains the logic of the GEP. These repairs could represent cancer mutations leading to GEP variability. With this reasoning, unmeasured protein states can be inferred, and we can simulate the impact of a protein perturbation on the RN behavior to identify therapeutic targets. We showed that JUN/FOS and FOXM1 activities are altered in almost all MM patients and identified two survival markers for MM patients. Our results suggest that JUN/FOS-activation has a strong impact on the RN in view of the whole GEP, whereas FOXM1-activation could be an interesting way to perturb an MM subgroup identified by our method.

  14. Multiple severe typhoons in recent history revealed by coral boulders of northwestern Luzon, Philippines

    Science.gov (United States)

    Gong, Shou-Yeh; Wu, Tso-Ren; Liu, Sze-Chieh; Shen, Chuan-Chou; Siringan, Fernando; Lin, Han-Wei

    2017-04-01

    Meter-sized coral boulders occurred on Holocene reef flat at Pasuquin, Ilocos Norte and Cabugao, Ilocos Sur, Philippines. Boulders larger than 3 meters were located and measured by field survey and UAV photogrammetry. Boulders now distributed 45-140 m away from edge of Holocene reef flat, and above highest high tide. The lithology of those boulders is the same as the underlying Holocene coral reef at the sites, hence believed to be broken from reef edge locally. Fossil corals in those boulders mostly appeal not in upward-growing attitude but overturned or tilted. Several tens of photos were taken around selected boulders from different angles, and 3D models were established from the photos. Dimension and volumes were calculated from 3D models. Boulder volumes can be estimated much more accurately this way than simply multiple X, Y, and Z as many previous studies did. The volumes of boulders larger than 3 m in length vary from 10-52.6 m3. Assuming 2.1 g/cm3 for wet density, weights of boulders are estimated to range from 21-110 metric tons. Boulders of such size and weight obviously can't be moved by normal waves, and likely dislodged by Extreme Wave Event (EWE). Small and well-preserved corals were found in depressions on boulder surface and interpreted to represent timing of final displacement. Corals found on seven boulders at Pasuquin were 230Th dated to be 1782, 1904, 1946, 1957, 1978 and 2003 AD respectively. No tsunami was reported in historical records in northern Luzon for those years, but several documented typhoons could be responsible for displacement of each of those boulders. Another Porites boulder at Cabugao was dated to be tilted five times from 673-838 AD, averaging one EWE every 33 years. Such frequent occurrence of EWE is unlikely resulted from tsunami. Therefore, those coral boulders at Pasuquin and Cabugao are interpreted to be displaced by severe typhoons.

  15. Whole exome sequencing reveals concomitant mutations of multiple FA genes in individual Fanconi anemia patients.

    Science.gov (United States)

    Chang, Lixian; Yuan, Weiping; Zeng, Huimin; Zhou, Quanquan; Wei, Wei; Zhou, Jianfeng; Li, Miaomiao; Wang, Xiaomin; Xu, Mingjiang; Yang, Fengchun; Yang, Yungui; Cheng, Tao; Zhu, Xiaofan

    2014-05-15

    Fanconi anemia (FA) is a rare inherited genetic syndrome with highly variable clinical manifestations. Fifteen genetic subtypes of FA have been identified. Traditional complementation tests for grouping studies have been used generally in FA patients and in stepwise methods to identify the FA type, which can result in incomplete genetic information from FA patients. We diagnosed five pediatric patients with FA based on clinical manifestations, and we performed exome sequencing of peripheral blood specimens from these patients and their family members. The related sequencing data were then analyzed by bioinformatics, and the FANC gene mutations identified by exome sequencing were confirmed by PCR re-sequencing. Homozygous and compound heterozygous mutations of FANC genes were identified in all of the patients. The FA subtypes of the patients included FANCA, FANCM and FANCD2. Interestingly, four FA patients harbored multiple mutations in at least two FA genes, and some of these mutations have not been previously reported. These patients' clinical manifestations were vastly different from each other, as were their treatment responses to androstanazol and prednisone. This finding suggests that heterozygous mutation(s) in FA genes could also have diverse biological and/or pathophysiological effects on FA patients or FA gene carriers. Interestingly, we were not able to identify de novo mutations in the genes implicated in DNA repair pathways when the sequencing data of patients were compared with those of their parents. Our results indicate that Chinese FA patients and carriers might have higher and more complex mutation rates in FANC genes than have been conventionally recognized. Testing of the fifteen FANC genes in FA patients and their family members should be a regular clinical practice to determine the optimal care for the individual patient, to counsel the family and to obtain a better understanding of FA pathophysiology.

  16. Multiple Measures Reveal Antiretroviral Adherence Successes and Challenges in HIV-Infected Ugandan Children

    Science.gov (United States)

    Haberer, Jessica E.; Kiwanuka, Julius; Nansera, Denis; Ragland, Kathleen; Mellins, Claude; Bangsberg, David R.

    2012-01-01

    Background Adherence to HIV antiretroviral therapy (ART) among children in developing settings is poorly understood. Methodology/Principal Findings To understand the level, distribution, and correlates of ART adherence behavior, we prospectively determined monthly ART adherence through multiple measures and six-monthly HIV RNA levels among 121 Ugandan children aged 2–10 years for one year. Median adherence levels were 100% by three-day recall, 97.4% by 30-day visual analog scale, 97.3% by unannounced pill count/liquid formulation weights, and 96.3% by medication event monitors (MEMS). Interruptions in MEMS adherence of ≥48 hours were seen in 57.0% of children; 36.3% had detectable HIV RNA at one year. Only MEMS correlated significantly with HIV RNA levels (r = −0.25, p = 0.04). Multivariable regression found the following to be associated with liquid formulation use (AOR 1.4, 95%CI 1.0–2.0; p = 0.04), and caregiver’s alcohol use (AOR 3.1, 95%CI 1.8–5.2; passets (AOR 0.7, 95%CI 0.6–0.9; p = 0.0007) were protective against these interruptions. Conclusions/Significance Adherence success depends on a well-established medication taking routine, including caregiver support and adequate education on medication changes. Caregiver-reported depression and shame may reflect fear of poor outcomes, functioning as motivation for the child to adhere. Further research is needed to better understand and build on these key influential factors for adherence intervention development. PMID:22590600

  17. Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data.

    Science.gov (United States)

    Miannay, Bertrand; Minvielle, Stéphane; Magrangeas, Florence; Guziolowski, Carito

    2018-03-21

    The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distance measures among significantly measured species. Only a small number of them include the directionality and underlying logic existing in biological networks. In this study we approach the GEP-networks integration problem by considering the network logic, however our approach does not require a prior species selection according to their gene expression level. We start by modeling the biological network representing its underlying logic using Logic Programming. This model points to reachable network discrete states that maximize a notion of harmony between the molecular species active or inactive possible states and the directionality of the pathways reactions according to their activator or inhibitor control role. Only then, we confront these network states with the GEP. From this confrontation independent graph components are derived, each of them related to a fixed and optimal assignment of active or inactive states. These components allow us to decompose a large-scale network into subgraphs and their molecular species state assignments have different degrees of similarity when compared to the same GEP. We apply our method to study the set of possible states derived from a subgraph from the NCI-PID Pathway Interaction Database. This graph links Multiple Myeloma (MM) genes to known receptors for this blood cancer. We discover that the NCI-PID MM graph had 15 independent components, and when confronted to 611 MM GEPs, we find 1 component as being more specific to represent the difference between cancer and healthy profiles.

  18. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

    Science.gov (United States)

    Kangaspeska, Sara; Hultsch, Susanne; Edgren, Henrik; Nicorici, Daniel; Murumägi, Astrid; Kallioniemi, Olli

    2012-01-01

    RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

  19. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

    Directory of Open Access Journals (Sweden)

    Sara Kangaspeska

    Full Text Available RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60% of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

  20. Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process

    International Nuclear Information System (INIS)

    Chandran, Uma R; Ma, Changqing; Dhir, Rajiv; Bisceglia, Michelle; Lyons-Weiler, Maureen; Liang, Wenjing; Michalopoulos, George; Becich, Michael; Monzon, Federico A

    2007-01-01

    Prostate cancer is characterized by heterogeneity in the clinical course that often does not correlate with morphologic features of the tumor. Metastasis reflects the most adverse outcome of prostate cancer, and to date there are no reliable morphologic features or serum biomarkers that can reliably predict which patients are at higher risk of developing metastatic disease. Understanding the differences in the biology of metastatic and organ confined primary tumors is essential for developing new prognostic markers and therapeutic targets. Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors. The metastatic samples are highly heterogenous in expression; however, differential expression analysis shows that 415 genes are upregulated and 364 genes are downregulated at least 2 fold in every patient with metastasis. The expression profile of metastatic samples reveals changes in expression of a unique set of genes representing both the androgen ablation related pathways and other metastasis related gene networks such as cell adhesion, bone remodelling and cell cycle. The differentially expressed genes include metabolic enzymes, transcription factors such as Forkhead Box M1 (FoxM1) and cell adhesion molecules such as Osteopontin (SPP1). We hypothesize that these genes have a role in the biology of metastatic disease and that they represent potential therapeutic targets for prostate cancer

  1. Multiple measures reveal antiretroviral adherence successes and challenges in HIV-infected Ugandan children.

    Directory of Open Access Journals (Sweden)

    Jessica E Haberer

    Full Text Available Adherence to HIV antiretroviral therapy (ART among children in developing settings is poorly understood.To understand the level, distribution, and correlates of ART adherence behavior, we prospectively determined monthly ART adherence through multiple measures and six-monthly HIV RNA levels among 121 Ugandan children aged 2-10 years for one year. Median adherence levels were 100% by three-day recall, 97.4% by 30-day visual analog scale, 97.3% by unannounced pill count/liquid formulation weights, and 96.3% by medication event monitors (MEMS. Interruptions in MEMS adherence of ≥ 48 hours were seen in 57.0% of children; 36.3% had detectable HIV RNA at one year. Only MEMS correlated significantly with HIV RNA levels (r = -0.25, p = 0.04. Multivariable regression found the following to be associated with <90% MEMS adherence: hospitalization of child (adjusted odds ratio [AOR] 3.0, 95% confidence interval [CI] 1.6-5.5; p = 0.001, liquid formulation use (AOR 1.4, 95%CI 1.0-2.0; p = 0.04, and caregiver's alcohol use (AOR 3.1, 95%CI 1.8-5.2; p<0.0001. Child's use of co-trimoxazole (AOR 0.5, 95%CI 0.4-0.9; p = 0.009, caregiver's use of ART (AOR 0.6, 95%CI 0.4-0.9; p = 0.03, possible caregiver depression (AOR 0.6, 95%CI 0.4-0.8; p = 0.001, and caregiver feeling ashamed of child's HIV status (AOR 0.5, 95%CI 0.3-0.6; p<0.0001 were protective against <90% MEMS adherence. Change in drug manufacturer (AOR 4.1, 95%CI 1.5-11.5; p = 0.009 and caregiver's alcohol use (AOR 5.5, 95%CI 2.8-10.7; p<0.0001 were associated with ≥ 48-hour interruptions by MEMS, while second-line ART (AOR 0.3, 95%CI 0.1-0.99; p = 0.049 and increasing assets (AOR 0.7, 95%CI 0.6-0.9; p = 0.0007 were protective against these interruptions.Adherence success depends on a well-established medication taking routine, including caregiver support and adequate education on medication changes. Caregiver-reported depression and shame may reflect fear of poor outcomes, functioning as motivation for

  2. Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    Yener Bülent

    2007-10-01

    Full Text Available Abstract Background Recently, we demonstrated that human mesenchymal stem cells (hMSC stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (Stem Cells Dev 14(6: 1608–20, 2005. Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM proteins (collagen I, vitronectin, or laminin-5 or osteogenic media supplements (OS media. Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST, with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants. Results Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST. Conclusion The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.

  3. Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes.

    Directory of Open Access Journals (Sweden)

    Wayne Chadwick

    Full Text Available The central nervous system normally functions at O(2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O(2-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O(2 tensions compared to the cell culture standard of 20% O(2, to investigate their ability to sense and translate this O(2 information to transcriptional activity. Variance of ambient O(2 tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O(2 tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O(2 tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O(2 tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional 'programs' may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.

  4. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

    Science.gov (United States)

    Zai, Xiaodong; Yang, Qiaoling; Yin, Ying; Li, Ruihua; Qian, Mengying; Zhao, Taoran; Li, Yaohui; Zhang, Jun; Fu, Ling; Xu, Junjie; Chen, Wei

    2017-01-01

    Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic

  5. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses

    Directory of Open Access Journals (Sweden)

    Xiaodong Zai

    2017-11-01

    Full Text Available Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular

  6. Use of Multi-class Empirical Orthogonal Function for Identification of Hydrogeological Parameters and Spatiotemporal Pattern of Multiple Recharges in Groundwater Modeling

    Science.gov (United States)

    Huang, C. L.; Hsu, N. S.; Yeh, W. W. G.; Hsieh, I. H.

    2017-12-01

    This study develops an innovative calibration method for regional groundwater modeling by using multi-class empirical orthogonal functions (EOFs). The developed method is an iterative approach. Prior to carrying out the iterative procedures, the groundwater storage hydrographs associated with the observation wells are calculated. The combined multi-class EOF amplitudes and EOF expansion coefficients of the storage hydrographs are then used to compute the initial gauss of the temporal and spatial pattern of multiple recharges. The initial guess of the hydrogeological parameters are also assigned according to in-situ pumping experiment. The recharges include net rainfall recharge and boundary recharge, and the hydrogeological parameters are riverbed leakage conductivity, horizontal hydraulic conductivity, vertical hydraulic conductivity, storage coefficient, and specific yield. The first step of the iterative algorithm is to conduct the numerical model (i.e. MODFLOW) by the initial guess / adjusted values of the recharges and parameters. Second, in order to determine the best EOF combination of the error storage hydrographs for determining the correction vectors, the objective function is devised as minimizing the root mean square error (RMSE) of the simulated storage hydrographs. The error storage hydrograph are the differences between the storage hydrographs computed from observed and simulated groundwater level fluctuations. Third, adjust the values of recharges and parameters and repeat the iterative procedures until the stopping criterion is reached. The established methodology was applied to the groundwater system of Ming-Chu Basin, Taiwan. The study period is from January 1st to December 2ed in 2012. Results showed that the optimal EOF combination for the multiple recharges and hydrogeological parameters can decrease the RMSE of the simulated storage hydrographs dramatically within three calibration iterations. It represents that the iterative approach that

  7. Multiple roles of integrin-linked kinase in epidermal development, maturation and pigmentation revealed by molecular profiling.

    Directory of Open Access Journals (Sweden)

    David Judah

    Full Text Available Integrin-linked kinase (ILK is an important scaffold protein that mediates a variety of cellular responses to integrin stimulation by extracellular matrix proteins. Mice with epidermis-restricted inactivation of the Ilk gene exhibit pleiotropic phenotypic defects, including impaired hair follicle morphogenesis, reduced epidermal adhesion to the basement membrane, compromised epidermal integrity, as well as wasting and failure to thrive leading to perinatal death. To better understand the underlying molecular mechanisms that cause such a broad range of alterations, we investigated the impact of Ilk gene inactivation on the epidermis transcriptome. Microarray analysis showed over 700 differentially regulated mRNAs encoding proteins involved in multiple aspects of epidermal function, including keratinocyte differentiation and barrier formation, inflammation, regeneration after injury, and fundamental epidermal developmental pathways. These studies also revealed potential effects on genes not previously implicated in ILK functions, including those important for melanocyte and melanoblast development and function, regulation of cytoskeletal dynamics, and homeobox genes. This study shows that ILK is a critical regulator of multiple aspects of epidermal function and homeostasis, and reveals the previously unreported involvement of ILK not only in epidermal differentiation and barrier formation, but also in melanocyte genesis and function.

  8. Multiple roles of integrin-linked kinase in epidermal development, maturation and pigmentation revealed by molecular profiling.

    Science.gov (United States)

    Judah, David; Rudkouskaya, Alena; Wilson, Ryan; Carter, David E; Dagnino, Lina

    2012-01-01

    Integrin-linked kinase (ILK) is an important scaffold protein that mediates a variety of cellular responses to integrin stimulation by extracellular matrix proteins. Mice with epidermis-restricted inactivation of the Ilk gene exhibit pleiotropic phenotypic defects, including impaired hair follicle morphogenesis, reduced epidermal adhesion to the basement membrane, compromised epidermal integrity, as well as wasting and failure to thrive leading to perinatal death. To better understand the underlying molecular mechanisms that cause such a broad range of alterations, we investigated the impact of Ilk gene inactivation on the epidermis transcriptome. Microarray analysis showed over 700 differentially regulated mRNAs encoding proteins involved in multiple aspects of epidermal function, including keratinocyte differentiation and barrier formation, inflammation, regeneration after injury, and fundamental epidermal developmental pathways. These studies also revealed potential effects on genes not previously implicated in ILK functions, including those important for melanocyte and melanoblast development and function, regulation of cytoskeletal dynamics, and homeobox genes. This study shows that ILK is a critical regulator of multiple aspects of epidermal function and homeostasis, and reveals the previously unreported involvement of ILK not only in epidermal differentiation and barrier formation, but also in melanocyte genesis and function.

  9. Hierarchical Spatio-Temporal Probabilistic Graphical Model with Multiple Feature Fusion for Binary Facial Attribute Classification in Real-World Face Videos.

    Science.gov (United States)

    Demirkus, Meltem; Precup, Doina; Clark, James J; Arbel, Tal

    2016-06-01

    Recent literature shows that facial attributes, i.e., contextual facial information, can be beneficial for improving the performance of real-world applications, such as face verification, face recognition, and image search. Examples of face attributes include gender, skin color, facial hair, etc. How to robustly obtain these facial attributes (traits) is still an open problem, especially in the presence of the challenges of real-world environments: non-uniform illumination conditions, arbitrary occlusions, motion blur and background clutter. What makes this problem even more difficult is the enormous variability presented by the same subject, due to arbitrary face scales, head poses, and facial expressions. In this paper, we focus on the problem of facial trait classification in real-world face videos. We have developed a fully automatic hierarchical and probabilistic framework that models the collective set of frame class distributions and feature spatial information over a video sequence. The experiments are conducted on a large real-world face video database that we have collected, labelled and made publicly available. The proposed method is flexible enough to be applied to any facial classification problem. Experiments on a large, real-world video database McGillFaces [1] of 18,000 video frames reveal that the proposed framework outperforms alternative approaches, by up to 16.96 and 10.13%, for the facial attributes of gender and facial hair, respectively.

  10. A stream cipher based on a spatiotemporal chaotic system

    International Nuclear Information System (INIS)

    Li Ping; Li Zhong; Halang, Wolfgang A.; Chen Guanrong

    2007-01-01

    A stream cipher based on a spatiotemporal chaotic system is proposed. A one-way coupled map lattice consisting of logistic maps is served as the spatiotemporal chaotic system. Multiple keystreams are generated from the coupled map lattice by using simple algebraic computations, and then are used to encrypt plaintext via bitwise XOR. These make the cipher rather simple and efficient. Numerical investigation shows that the cryptographic properties of the generated keystream are satisfactory. The cipher seems to have higher security, higher efficiency and lower computation expense than the stream cipher based on a spatiotemporal chaotic system proposed recently

  11. Noninvasive pulsed focused ultrasound allows spatiotemporal control of targeted homing for multiple stem cell types in murine skeletal muscle and the magnitude of cell homing can be increased through repeated applications.

    Science.gov (United States)

    Burks, Scott R; Ziadloo, Ali; Kim, Saejeong J; Nguyen, Ben A; Frank, Joseph A

    2013-11-01

    Stem cells are promising therapeutics for cardiovascular diseases, and i.v. injection is the most desirable route of administration clinically. Subsequent homing of exogenous stem cells to pathological loci is frequently required for therapeutic efficacy and is mediated by chemoattractants (cell adhesion molecules, cytokines, and growth factors). Homing processes are inefficient and depend on short-lived pathological inflammation that limits the window of opportunity for cell injections. Noninvasive pulsed focused ultrasound (pFUS), which emphasizes mechanical ultrasound-tissue interactions, can be precisely targeted in the body and is a promising approach to target and maximize stem cell delivery by stimulating chemoattractant expression in pFUS-treated tissue prior to cell infusions. We demonstrate that pFUS is nondestructive to murine skeletal muscle tissue (no necrosis, hemorrhage, or muscle stem cell activation) and initiates a largely M2-type macrophage response. We also demonstrate that local upregulation of chemoattractants in pFUS-treated skeletal muscle leads to enhance homing, permeability, and retention of human mesenchymal stem cells (MSC) and human endothelial precursor cells (EPC). Furthermore, the magnitude of MSC or EPC homing was increased when pFUS treatments and cell infusions were repeated daily. This study demonstrates that pFUS defines transient "molecular zip codes" of elevated chemoattractants in targeted muscle tissue, which effectively provides spatiotemporal control and tunability of the homing process for multiple stem cell types. pFUS is a clinically translatable modality that may ultimately improve homing efficiency and flexibility of cell therapies for cardiovascular diseases. © AlphaMed Press.

  12. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages.

    Directory of Open Access Journals (Sweden)

    Julia Naumann

    Full Text Available Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG from Illumina transcriptome data from one of the "strangest plants in the world", Hydnora visseri (Hydnoraceae. A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the "temporal specialization hypothesis" (TSH implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

  13. Spatiotemporal representation of cardiac vectorcardiogram (VCG signals

    Directory of Open Access Journals (Sweden)

    Yang Hui

    2012-03-01

    Full Text Available Abstract Background Vectorcardiogram (VCG signals monitor both spatial and temporal cardiac electrical activities along three orthogonal planes of the body. However, the absence of spatiotemporal resolution in conventional VCG representations is a major impediment for medical interpretation and clinical usage of VCG. This is especially so because time-domain features of 12-lead ECG, instead of both spatial and temporal characteristics of VCG, are widely used for the automatic assessment of cardiac pathological patterns. Materials and methods We present a novel representation approach that captures critical spatiotemporal heart dynamics by displaying the real time motion of VCG cardiac vectors in a 3D space. Such a dynamic display can also be realized with only one lead ECG signal (e.g., ambulatory ECG through an alternative lag-reconstructed ECG representation from nonlinear dynamics principles. Furthermore, the trajectories are color coded with additional dynamical properties of space-time VCG signals, e.g., the curvature, speed, octant and phase angles to enhance the information visibility. Results In this investigation, spatiotemporal VCG signal representation is used to characterize various spatiotemporal pathological patterns for healthy control (HC, myocardial infarction (MI, atrial fibrillation (AF and bundle branch block (BBB. The proposed color coding scheme revealed that the spatial locations of the peak of T waves are in the Octant 6 for the majority (i.e., 74 out of 80 of healthy recordings in the PhysioNet PTB database. In contrast, the peak of T waves from 31.79% (117/368 of MI subjects are found to remain in Octant 6 and the rest (68.21% spread over all other octants. The spatiotemporal VCG signal representation is shown to capture the same important heart characteristics as the 12-lead ECG plots and more. Conclusions Spatiotemporal VCG signal representation is shown to facilitate the characterization of space-time cardiac

  14. Indeterminacy and Spatiotemporal Data

    DEFF Research Database (Denmark)

    Pfoser, D.; Tryfona, N.; Jensen, Christian Søndergaard

    2005-01-01

    For some spatiotemporal applications, it can be assumed that the modeled world is precise and bounded, and that our record of it is precise. While these simplifying assumptions are sufficient in applications like a land information system, they are unnecessarily crude for many other applications...

  15. Spatio-Temporal Rule Mining

    DEFF Research Database (Denmark)

    Gidofalvi, Gyozo; Pedersen, Torben Bach

    2005-01-01

    Recent advances in communication and information technology, such as the increasing accuracy of GPS technology and the miniaturization of wireless communication devices pave the road for Location-Based Services (LBS). To achieve high quality for such services, spatio-temporal data mining techniques...... are needed. In this paper, we describe experiences with spatio-temporal rule mining in a Danish data mining company. First, a number of real world spatio-temporal data sets are described, leading to a taxonomy of spatio-temporal data. Second, the paper describes a general methodology that transforms...... the spatio-temporal rule mining task to the traditional market basket analysis task and applies it to the described data sets, enabling traditional association rule mining methods to discover spatio-temporal rules for LBS. Finally, unique issues in spatio-temporal rule mining are identified and discussed....

  16. Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics.

    Science.gov (United States)

    Huang, Chien-Hsun; Zhang, Caifei; Liu, Mian; Hu, Yi; Gao, Tiangang; Qi, Ji; Ma, Hong

    2016-11-01

    Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Protein expression profiling of inflammatory mediators in human temporal lobe epilepsy reveals co-activation of multiple chemokines and cytokines

    Directory of Open Access Journals (Sweden)

    Kan Anne A

    2012-08-01

    Full Text Available Abstract Mesial temporal lobe epilepsy (mTLE is a chronic and often treatment-refractory brain disorder characterized by recurrent seizures originating from the hippocampus. The pathogenic mechanisms underlying mTLE remain largely unknown. Recent clinical and experimental evidence supports a role of various inflammatory mediators in mTLE. Here, we performed protein expression profiling of 40 inflammatory mediators in surgical resection material from mTLE patients with and without hippocampal sclerosis, and autopsy controls using a multiplex bead-based immunoassay. In mTLE patients we identified 21 upregulated inflammatory mediators, including 10 cytokines and 7 chemokines. Many of these upregulated mediators have not previously been implicated in mTLE (for example, CCL22, IL-7 and IL-25. Comparing the three patient groups, two main hippocampal expression patterns could be distinguished, pattern I (for example, IL-10 and IL-25 showing increased expression in mTLE + HS patients compared to mTLE-HS and controls, and pattern II (for example, CCL4 and IL-7 showing increased expression in both mTLE groups compared to controls. Upregulation of a subset of inflammatory mediators (for example, IL-25 and IL-7 could not only be detected in the hippocampus of mTLE patients, but also in the neocortex. Principle component analysis was used to cluster the inflammatory mediators into several components. Follow-up analyses of the identified components revealed that the three patient groups could be discriminated based on their unique expression profiles. Immunocytochemistry showed that IL-25 IR (pattern I and CCL4 IR (pattern II were localized in astrocytes and microglia, whereas IL-25 IR was also detected in neurons. Our data shows co-activation of multiple inflammatory mediators in hippocampus and neocortex of mTLE patients, indicating activation of multiple pro- and anti-epileptogenic immune pathways in this disease.

  18. Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

    Science.gov (United States)

    Shinde, Mansi Y.; Sidoli, Simone; Kulej, Katarzyna; Mallory, Michael J.; Radens, Caleb M.; Reicherter, Amanda L.; Myers, Rebecca L.; Barash, Yoseph; Lynch, Kristen W.; Garcia, Benjamin A.; Klein, Peter S.

    2017-01-01

    Glycogen synthase kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. In vitro kinase assays and genetic and pharmacological manipulations of GSK-3 have identified more than 100 putative GSK-3 substrates in diverse cell types. Many more have been predicted on the basis of a recurrent GSK-3 consensus motif ((pS/pT)XXX(S/T)), but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. Using stable isotope labeling of amino acids in culture (SILAC) and MS techniques to analyze the repertoire of GSK-3–dependent phosphorylation in mouse embryonic stem cells (ESCs), we found that ∼2.4% of (pS/pT)XXX(S/T) sites are phosphorylated in a GSK-3–dependent manner. A comparison of WT and Gsk3a;Gsk3b knock-out (Gsk3 DKO) ESCs revealed prominent GSK-3–dependent phosphorylation of multiple splicing factors and regulators of RNA biosynthesis as well as proteins that regulate transcription, translation, and cell division. Gsk3 DKO reduced phosphorylation of the splicing factors RBM8A, SRSF9, and PSF as well as the nucleolar proteins NPM1 and PHF6, and recombinant GSK-3β phosphorylated these proteins in vitro. RNA-Seq of WT and Gsk3 DKO ESCs identified ∼190 genes that are alternatively spliced in a GSK-3–dependent manner, supporting a broad role for GSK-3 in regulating alternative splicing. The MS data also identified posttranscriptional regulation of protein abundance by GSK-3, with ∼47 proteins (1.4%) whose levels increased and ∼78 (2.4%) whose levels decreased in the absence of GSK-3. This study provides the first unbiased analysis of the GSK-3 phosphoproteome and strong evidence that GSK-3 broadly regulates alternative splicing. PMID:28916722

  19. Multiple Object Permanence Tracking: Maintenance, Retrieval and Transformation of Dynamic Object Representations

    OpenAIRE

    Saiki, Jun

    2008-01-01

    Multiple object permanence tracking (MOPT) task revealed that our ability of maintaining and transforming multiple representations of complex feature-bound objects is limited to handle only 1-2 objects. Often reported capacity of 3-5 objects likely reflects memory for partial representations of objects and simple cases such as just color and their locations. Also, performance in multiple object tracking (MOT) task is likely mediated by spatiotemporal indices, not by feature-bound object repre...

  20. The Immersive Virtual Reality Experience: A Typology of Users Revealed Through Multiple Correspondence Analysis Combined with Cluster Analysis Technique.

    Science.gov (United States)

    Rosa, Pedro J; Morais, Diogo; Gamito, Pedro; Oliveira, Jorge; Saraiva, Tomaz

    2016-03-01

    Immersive virtual reality is thought to be advantageous by leading to higher levels of presence. However, and despite users getting actively involved in immersive three-dimensional virtual environments that incorporate sound and motion, there are individual factors, such as age, video game knowledge, and the predisposition to immersion, that may be associated with the quality of virtual reality experience. Moreover, one particular concern for users engaged in immersive virtual reality environments (VREs) is the possibility of side effects, such as cybersickness. The literature suggests that at least 60% of virtual reality users report having felt symptoms of cybersickness, which reduces the quality of the virtual reality experience. The aim of this study was thus to profile the right user to be involved in a VRE through head-mounted display. To examine which user characteristics are associated with the most effective virtual reality experience (lower cybersickness), a multiple correspondence analysis combined with cluster analysis technique was performed. Results revealed three distinct profiles, showing that the PC gamer profile is more associated with higher levels of virtual reality effectiveness, that is, higher predisposition to be immersed and reduced cybersickness symptoms in the VRE than console gamer and nongamer. These findings can be a useful orientation in clinical practice and future research as they help identify which users are more predisposed to benefit from immersive VREs.

  1. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  2. Spatiotemporal drought forecasting using nonlinear models

    Science.gov (United States)

    Vasiliades, Lampros; Loukas, Athanasios

    2010-05-01

    Spatiotemporal data mining is the extraction of unknown and implicit knowledge, structures, spatiotemporal relationships, or patterns not explicitly stored in spatiotemporal databases. As one of data mining techniques, forecasting is widely used to predict the unknown future based upon the patterns hidden in the current and past data. In order to achieve spatiotemporal forecasting, some mature analysis tools, e.g., time series and spatial statistics are extended to the spatial dimension and the temporal dimension, respectively. Drought forecasting plays an important role in the planning and management of natural resources and water resource systems in a river basin. Early and timelines forecasting of a drought event can help to take proactive measures and set out drought mitigation strategies to alleviate the impacts of drought. Despite the widespread application of nonlinear mathematical models, comparative studies on spatiotemporal drought forecasting using different models are still a huge task for modellers. This study uses a promising approach, the Gamma Test (GT), to select the input variables and the training data length, so that the trial and error workload could be greatly reduced. The GT enables to quickly evaluate and estimate the best mean squared error that can be achieved by a smooth model on any unseen data for a given selection of inputs, prior to model construction. The GT is applied to forecast droughts using monthly Standardized Precipitation Index (SPI) timeseries at multiple timescales in several precipitation stations at Pinios river basin in Thessaly region, Greece. Several nonlinear models have been developed efficiently, with the aid of the GT, for 1-month up to 12-month ahead forecasting. Several temporal and spatial statistical indices were considered for the performance evaluation of the models. The predicted results show reasonably good agreement with the actual data for short lead times, whereas the forecasting accuracy decreases with

  3. Spatiotemporal optical solitons

    International Nuclear Information System (INIS)

    Malomed, Boris A; Mihalache, Dumitru; Wise, Frank; Torner, Lluis

    2005-01-01

    In the course of the past several years, a new level of understanding has been achieved about conditions for the existence, stability, and generation of spatiotemporal optical solitons, which are nondiffracting and nondispersing wavepackets propagating in nonlinear optical media. Experimentally, effectively two-dimensional (2D) spatiotemporal solitons that overcome diffraction in one transverse spatial dimension have been created in quadratic nonlinear media. With regard to the theory, fundamentally new features of light pulses that self-trap in one or two transverse spatial dimensions and do not spread out in time, when propagating in various optical media, were thoroughly investigated in models with various nonlinearities. Stable vorticity-carrying spatiotemporal solitons have been predicted too, in media with competing nonlinearities (quadratic-cubic or cubic-quintic). This article offers an up-to-date survey of experimental and theoretical results in this field. Both achievements and outstanding difficulties are reviewed, and open problems are highlighted. Also briefly described are recent predictions for stable 2D and 3D solitons in Bose-Einstein condensates supported by full or low-dimensional optical lattices. (review article)

  4. Spatiotemporal patterns formed by deformed adhesive in peeling

    International Nuclear Information System (INIS)

    Yamazaki, Yoshihiro; Toda, Akihiko

    2007-01-01

    Dynamical properties of peeling an adhesive tape are investigated experimentally as an analogy of sliding friction. An adhesive tape is peeled by pulling an elastic spring connected to the tape. Controlling its spring constant k and pulling speed V, peel force is measured and spatiotemporal patterns formed on the peeled tape by deformed adhesive are observed. It is found that there exist two kinds of adhesive state in peeling front. The emergence of multiple states is caused by the stability of a characteristic structure (tunnel structure) formed by deformed adhesive. Tunnel structures are distributed spatiotemporally on adhesive tape after peeling. Based on the spatiotemporal distribution, a morphology-dynamical phase diagram is constructed on k-V space and is divided into the four regions: (A) uniform pattern with tunnel structure, (B) uniform pattern without tunnel structure, (C) striped pattern with oscillatory peeling, and (D) spatiotemporally coexistent pattern

  5. Spatiotemporal Modeling of Community Risk

    Science.gov (United States)

    2016-03-01

    Ertugay, and Sebnem Duzgun, “Exploratory and Inferential Methods for Spatio-Temporal Analysis of Residential Fire Clustering in Urban Areas,” Fire ...response in communities.”26 In “Exploratory and Inferential Methods for Spatio-temporal Analysis of Residential Fire Clustering in Urban Areas,” Ceyhan...of fire resources spread across the community. Spatiotemporal modeling shows that actualized risk is dynamic and relatively patterned. Though

  6. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

  7. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

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

    International Nuclear Information System (INIS)

    Skoric, M.M.; Jovanovic, M.S.; Rajkovic, M.R.

    1996-01-01

    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 1996 The American Physical Society

  9. Multiple endocrine neoplasia phenocopy revealed as a co-occurring neuroendocrine tumor and familial hypocalciuric hypercalcemia type 3

    DEFF Research Database (Denmark)

    Hovden, Silje; Jespersen, Marie Louise; Nissen, Peter H

    2016-01-01

    Familial hypocalciuric hypercalcemia type 3 should be considered as differential diagnosis in patients with suspected primary hyperparathyroidism and/or suspected multiple neoplasia syndrome, as correct diagnosis will spare the patients for going through multiple futile parathyroidectomies...... and for the worry of being diagnosed with a cancer susceptibility syndrome....

  10. Direct sampling during multiple sediment density flows reveals dynamic sediment transport and depositional environment in Monterey submarine canyon

    Science.gov (United States)

    Maier, K. L.; Gales, J. A.; Paull, C. K.; Gwiazda, R.; Rosenberger, K. J.; McGann, M.; Lundsten, E. M.; Anderson, K.; Talling, P.; Xu, J.; Parsons, D. R.; Barry, J.; Simmons, S.; Clare, M. A.; Carvajal, C.; Wolfson-Schwehr, M.; Sumner, E.; Cartigny, M.

    2017-12-01

    Sediment density flows were directly sampled with a coupled sediment trap-ADCP-instrument mooring array to evaluate the character and frequency of turbidity current events through Monterey Canyon, offshore California. This novel experiment aimed to provide links between globally significant sediment density flow processes and their resulting deposits. Eight to ten Anderson sediment traps were repeatedly deployed at 10 to 300 meters above the seafloor on six moorings anchored at 290 to 1850 meters water depth in the Monterey Canyon axial channel during 6-month deployments (October 2015 - April 2017). Anderson sediment traps include a funnel and intervalometer (discs released at set time intervals) above a meter-long tube, which preserves fine-scale stratigraphy and chronology. Photographs, multi-sensor logs, CT scans, and grain size analyses reveal layers from multiple sediment density flow events that carried sediment ranging from fine sand to granules. More sediment accumulation from sediment density flows, and from between flows, occurred in the upper canyon ( 300 - 800 m water depth) compared to the lower canyon ( 1300 - 1850 m water depth). Sediment accumulated in the traps during sediment density flows is sandy and becomes finer down-canyon. In the lower canyon where sediment directly sampled from density flows are clearly distinguished within the trap tubes, sands have sharp basal contacts, normal grading, and muddy tops that exhibit late-stage pulses. In at least two of the sediment density flows, the simultaneous low velocity and high backscatter measured by the ADCPs suggest that the trap only captured the collapsing end of a sediment density flow event. In the upper canyon, accumulation between sediment density flow events is twice as fast compared to the lower canyon; it is characterized by sub-cm-scale layers in muddy sediment that appear to have accumulated with daily to sub-daily frequency, likely related to known internal tidal dynamics also measured

  11. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    Directory of Open Access Journals (Sweden)

    Jörger Katharina M

    2012-12-01

    Full Text Available Abstract Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH. In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC, statistical parsimony, Bayesian Species Delineation (BPP and Automatic Barcode Gap Discovery (ABGD. The secondary species hypothesis (SSH is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’, resulting in the discovery of a radiation of (at least 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically

  12. A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway.

    Science.gov (United States)

    Salašová, Alena; Yokota, Chika; Potěšil, David; Zdráhal, Zbyněk; Bryja, Vítězslav; Arenas, Ernest

    2017-07-11

    Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson's disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson's disease patients. Co-immunoprecipitation and tandem mass spectrometry was performed in a mouse substantia nigra cell line (SN4741) and human HEK293T cell line in order to identify novel LRRK2 binding partners. Inhibition of the WNT/β-catenin reporter, TOPFlash, was used as a read-out of WNT/PCP pathway activation. The capacity of LRRK2 to regulate WNT/PCP signaling in vivo was tested in Xenopus laevis' early development. Our proteomic analysis identified that LRRK2 interacts with proteins involved in WNT/PCP signaling such as the PDZ domain-containing protein GIPC1 and Integrin-linked kinase (ILK) in dopaminergic cells in vitro and in the mouse ventral midbrain in vivo. Moreover, co-immunoprecipitation analysis revealed that LRRK2 binds to two core components of the WNT/PCP signaling pathway, PRICKLE1 and CELSR1, as well as to FLOTILLIN-2 and CULLIN-3, which regulate WNT secretion and inhibit WNT/β-catenin signaling, respectively. We also found that PRICKLE1 and LRRK2 localize in signalosomes and act as dual regulators of WNT/PCP and β-catenin signaling. Accordingly, analysis of the function of LRRK2 in vivo, in X. laevis revelaed that LRKK2 not only inhibits WNT/β-catenin pathway, but induces a classical WNT/PCP phenotype in vivo. Our study shows for the first time that LRRK2 activates the WNT

  13. Analysis of Brassica oleracea early stage abiotic stress responses reveals tolerance in multiple crop types and for multiple sources of stress.

    Science.gov (United States)

    Beacham, Andrew M; Hand, Paul; Pink, David Ac; Monaghan, James M

    2017-12-01

    Brassica oleracea includes a number of important crop types such as cabbage, cauliflower, broccoli and kale. Current climate conditions and weather patterns are causing significant losses in these crops, meaning that new cultivars with improved tolerance of one or more abiotic stress types must be sought. In this study, genetically fixed B. oleracea lines belonging to a Diversity Fixed Foundation Set (DFFS) were assayed for their response to seedling stage-imposed drought, flood, salinity, heat and cold stress. Significant (P ≤ 0.05) variation in stress tolerance response was found for each stress, for each of four measured variables (relative fresh weight, relative dry weight, relative leaf number and relative plant height). Lines tolerant to multiple stresses were found to belong to several different crop types. There was no overall correlation between the responses to the different stresses. Abiotic stress tolerance was identified in multiple B. oleracea crop types, with some lines exhibiting resistance to multiple stresses. For each stress, no one crop type appeared significantly more or less tolerant than others. The results are promising for the development of more environmentally robust lines of different B. oleracea crops by identifying tolerant material and highlighting the relationship between responses to different stresses. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  14. Circular RNA profiling reveals that circular RNAs from ANXA2 can be used as new biomarkers for multiple sclerosis.

    Science.gov (United States)

    Iparraguirre, Leire; Muñoz-Culla, Maider; Prada-Luengo, Iñigo; Castillo-Triviño, Tamara; Olascoaga, Javier; Otaegui, David

    2017-09-15

    Multiple sclerosis is an autoimmune disease, with higher prevalence in women, in whom the immune system is dysregulated. This dysregulation has been shown to correlate with changes in transcriptome expression as well as in gene-expression regulators, such as non-coding RNAs (e.g. microRNAs). Indeed, some of these have been suggested as biomarkers for multiple sclerosis even though few biomarkers have reached the clinical practice. Recently, a novel family of non-coding RNAs, circular RNAs, has emerged as a new player in the complex network of gene-expression regulation. MicroRNA regulation function through a 'sponge system' and a RNA splicing regulation function have been proposed for the circular RNAs. This regulating role together with their high stability in biofluids makes them seemingly good candidates as biomarkers. Given the dysregulation of both protein-coding and non-coding transcriptome that have been reported in multiple sclerosis patients, we hypothesised that circular RNA expression may also be altered. Therefore, we carried out expression profiling of 13.617 circular RNAs in peripheral blood leucocytes from multiple sclerosis patients and healthy controls finding 406 differentially expressed (P-value  1.5) and demonstrate after validation that, circ_0005402 and circ_0035560 are underexpressed in multiple sclerosis patients and could be used as biomarkers of the disease. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. A spatiotemporal mixed model to assess the influence of environmental and socioeconomic factors on the incidence of hand, foot and mouth disease

    Directory of Open Access Journals (Sweden)

    Lianfa Li

    2018-02-01

    Full Text Available Abstract Background As a common infectious disease, hand, foot and mouth disease (HFMD is affected by multiple environmental and socioeconomic factors, and its pathogenesis is complex. Furthermore, the transmission of HFMD is characterized by strong spatial clustering and autocorrelation, and the classical statistical approach may be biased without consideration of spatial autocorrelation. In this paper, we propose to embed spatial characteristics into a spatiotemporal additive model to improve HFMD incidence assessment. Methods Using incidence data (6439 samples from 137 monitoring district for Shandong Province, China, along with meteorological, environmental and socioeconomic spatial and spatiotemporal covariate data, we proposed a spatiotemporal mixed model to estimate HFMD incidence. Geo-additive regression was used to model the non-linear effects of the covariates on the incidence risk of HFMD in univariate and multivariate models. Furthermore, the spatial effect was constructed to capture spatial autocorrelation at the sub-regional scale, and clusters (hotspots of high risk were generated using spatiotemporal scanning statistics as a predictor. Linear and non-linear effects were compared to illustrate the usefulness of non-linear associations. Patterns of spatial effects and clusters were explored to illustrate the variation of the HFMD incidence across geographical sub-regions. To validate our approach, 10-fold cross-validation was conducted. Results The results showed that there were significant non-linear associations of the temporal index, spatiotemporal meteorological factors and spatial environmental and socioeconomic factors with HFMD incidence. Furthermore, there were strong spatial autocorrelation and clusters for the HFMD incidence. Spatiotemporal meteorological parameters, the normalized difference vegetation index (NDVI, the temporal index, spatiotemporal clustering and spatial effects played important roles as predictors in

  16. Mercury Toolset for Spatiotemporal Metadata

    Science.gov (United States)

    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.

  17. Mercury Toolset for Spatiotemporal Metadata

    Science.gov (United States)

    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.

  18. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

    Science.gov (United States)

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

  19. Genome-wide mRNA and miRNA expression profiling reveal multiple regulatory networks in colorectal cancer

    DEFF Research Database (Denmark)

    Vishnubalaji, R; Hamam, R; Abdulla, M-H

    2015-01-01

    Despite recent advances in cancer management, colorectal cancer (CRC) remains the third most common cancer and a major health-care problem worldwide. MicroRNAs have recently emerged as key regulators of cancer development and progression by targeting multiple cancer-related genes; however, such r...

  20. Control and characterization of spatio-temporal disorder in ...

    Indian Academy of Sciences (India)

    characterizing the type of spatio-temporal disorder that is embodied in this disordered ... The results from this experiment will shed light on the more general questions ... sponds to only odd or even multiples of the common frequency, ω0. Thus ...

  1. Spatiotemporal Data Organization and Application Research

    Science.gov (United States)

    Tan, C.; Yan, S.

    2017-09-01

    Organization and management of spatiotemporal data is a key support technology for intelligence in all fields of the smart city. The construction of a smart city cannot be realized without spatiotemporal data. Oriented to support intelligent applications this paper proposes an organizational model for spatiotemporal data, and details the construction of a spatiotemporal big data calculation, analysis, and service framework for highly efficient management and intelligent application of spatiotemporal data for the entire data life cycle.

  2. Multiple giant coronary aneurysms arising from coronary istula to the pulmonary artery revealed in aorta CT angiography

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Eun Ju; Lee, Ki Nam [Dept. of Radiology, Dong A University Hospital, Dong-A University College of Medicine, Busan (Korea, Republic of); Lee, Jong Min [Dept. of Radiology, Kyungpook National University Hospital, Kyungpook National University College of Medicine, Daegu (Korea, Republic of)

    2015-12-15

    Coronary fistula is a rare coronary abnormality through which blood drains into the cardiac chamber, great vessel or other vessels. In addition, giant aneurysm arising from coronary fistula is rare pathologic manifestation. Herein, we presented a rare case of multiple giant coronary artery aneurysms arising from coronary to pulmonary artery fistula in a 79-year-old woman presenting with sudden loss of consciousness. The aneurysms were detected using thoracic computed tomography angiography and consequently confirmed by invasive coronary angiography.

  3. Spatiotemporal chaos from bursting dynamics

    International Nuclear Information System (INIS)

    Berenstein, Igal; De Decker, Yannick

    2015-01-01

    In this paper, we study the emergence of spatiotemporal chaos from mixed-mode oscillations, by using an extended Oregonator model. We show that bursting dynamics consisting of fast/slow mixed mode oscillations along a single attractor can lead to spatiotemporal chaotic dynamics, although the spatially homogeneous solution is itself non-chaotic. This behavior is observed far from the Hopf bifurcation and takes the form of a spatiotemporal intermittency where the system locally alternates between the fast and the slow phases of the mixed mode oscillations. We expect this form of spatiotemporal chaos to be generic for models in which one or several slow variables are coupled to activator-inhibitor type of oscillators

  4. The gene order on Human Chromosome 15 and Chicken Chromosome 10 reveal multiple inter- and intrachromosomal rearrangements

    NARCIS (Netherlands)

    Crooijmans, R.P.M.A.; Dijkhof, R.J.M.; Veenendaal, T.; Poel, van der J.J.; Groenen, M.A.M.

    2001-01-01

    Comparative mapping between the human and chicken genomes has revealed a striking conservation of synteny between the genomes of these two species, but the results have been based on low-resolution comparative maps. To address this conserved synteny in much more detail, a high-resolution

  5. An integrated data model to estimate spatiotemporal occupancy, abundance, and colonization dynamics

    Science.gov (United States)

    Williams, Perry J.; Hooten, Mevin B.; Womble, Jamie N.; Esslinger, George G.; Bower, Michael R.; Hefley, Trevor J.

    2017-01-01

    Ecological invasions and colonizations occur dynamically through space and time. Estimating the distribution and abundance of colonizing species is critical for efficient management or conservation. We describe a statistical framework for simultaneously estimating spatiotemporal occupancy and abundance dynamics of a colonizing species. Our method accounts for several issues that are common when modeling spatiotemporal ecological data including multiple levels of detection probability, multiple data sources, and computational limitations that occur when making fine-scale inference over a large spatiotemporal domain. We apply the model to estimate the colonization dynamics of sea otters (Enhydra lutris) in Glacier Bay, in southeastern Alaska.

  6. Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China

    Directory of Open Access Journals (Sweden)

    Mingjun Sun

    2017-12-01

    Full Text Available Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2 was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2 and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS-single-nucleotide polymorphism (SNP-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.

  7. A hybrid spatiotemporal drought forecasting model for operational use

    Science.gov (United States)

    Vasiliades, L.; Loukas, A.

    2010-09-01

    Drought forecasting plays an important role in the planning and management of natural resources and water resource systems in a river basin. Early and timelines forecasting of a drought event can help to take proactive measures and set out drought mitigation strategies to alleviate the impacts of drought. Spatiotemporal data mining is the extraction of unknown and implicit knowledge, structures, spatiotemporal relationships, or patterns not explicitly stored in spatiotemporal databases. As one of data mining techniques, forecasting is widely used to predict the unknown future based upon the patterns hidden in the current and past data. This study develops a hybrid spatiotemporal scheme for integrated spatial and temporal forecasting. Temporal forecasting is achieved using feed-forward neural networks and the temporal forecasts are extended to the spatial dimension using a spatial recurrent neural network model. The methodology is demonstrated for an operational meteorological drought index the Standardized Precipitation Index (SPI) calculated at multiple timescales. 48 precipitation stations and 18 independent precipitation stations, located at Pinios river basin in Thessaly region, Greece, were used for the development and spatiotemporal validation of the hybrid spatiotemporal scheme. Several quantitative temporal and spatial statistical indices were considered for the performance evaluation of the models. Furthermore, qualitative statistical criteria based on contingency tables between observed and forecasted drought episodes were calculated. The results show that the lead time of forecasting for operational use depends on the SPI timescale. The hybrid spatiotemporal drought forecasting model could be operationally used for forecasting up to three months ahead for SPI short timescales (e.g. 3-6 months) up to six months ahead for large SPI timescales (e.g. 24 months). The above findings could be useful in developing a drought preparedness plan in the region.

  8. An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.

    Directory of Open Access Journals (Sweden)

    Shaun Mahony

    2014-03-01

    Full Text Available Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.

  9. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development

    DEFF Research Database (Denmark)

    Venø, Morten T; Hansen, Thomas B; Venø, Susanne T

    2015-01-01

    BACKGROUND: Recently, thousands of circular RNAs (circRNAs) have been discovered in various tissues and cell types from human, mouse, fruit fly and nematodes. However, expression of circRNAs across mammalian brain development has never been examined. RESULTS: Here we profile the expression of circ......RNA in five brain tissues at up to six time-points during fetal porcine development, constituting the first report of circRNA in the brain development of a large animal. An unbiased analysis reveals a highly complex regulation pattern of thousands of circular RNAs, with a distinct spatio-temporal expression...... are functionally conserved between mouse and human. Furthermore, we observe that "hot-spot" genes produce multiple circRNA isoforms, which are often differentially expressed across porcine brain development. A global comparison of porcine circRNAs reveals that introns flanking circularized exons are longer than...

  10. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

    Directory of Open Access Journals (Sweden)

    Cécile Troupin

    2016-12-01

    Full Text Available The natural evolution of rabies virus (RABV provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

  11. Transcriptome Analysis Reveals Novel Entry Mechanisms and a Central Role of SRC in Host Defense during High Multiplicity Mycobacterial Infection.

    Directory of Open Access Journals (Sweden)

    Jay Zhang

    Full Text Available Mycobacterium tuberculosis (MTB infects an estimated one-third of the global population and is one of the main causes of mortality from an infectious agent. The characteristics of macrophages challenged by MTB with a high multiplicity of infection (MOI, which mimics both clinical disseminated infection and granuloma formation, are distinct from macrophages challenged with a low MOI. To better understand the cross talk between macrophage host cells and mycobacteria, we compared the transcription patterns of mouse macrophages infected with bacille Calmette-Guérin, H37Ra and M. smegmatis. Attention was focused on the changes in the abundance of transcripts related to immune system function. From the results of a transcriptome profiling study with a high mycobacterial MOI, we defined a pathogen-specific host gene expression pattern. The present study suggests that two integrins, ITGA5 and ITGAV, are novel cell surface receptors mediating mycobacterium entry into macrophages challenged with high MOI. Our results indicate that SRC likely plays a central role in regulating multiple unique signaling pathways activated by MTB infection. The integrated results increase our understanding of the molecular networks behind the host innate immune response and identify important targets that might be useful for the development of tuberculosis therapy.

  12. Spatiotemporal resonances in mixing of open viscous fluids

    DEFF Research Database (Denmark)

    Okkels, Fridolin; Tabeling, Patrick

    2004-01-01

    In this Letter, we reveal a new dynamical phenomenon, called "spatiotemporal resonance," which is expected to take place in a broad range of viscous, periodically forced, open systems. The observation originates from a numerical and theoretical analysis of a micromixer, and is supported...

  13. Secondary Instabilities and Spatiotemporal Chaos in Parametric Surface Waves

    International Nuclear Information System (INIS)

    Zhang, W.; Vinals, J.

    1995-01-01

    A 2D model is introduced to study the onset of parametric surface waves, their secondary instabilities, and the transition to spatiotemporal chaos. We obtain the stability boundary of a periodic standing wave above onset against Eckhaus, zigzag, and transverse amplitude modulations (TAM), as a function of the control parameter var-epsilon and the wavelength of the pattern. The Eckhaus and TAM boundaries cross at a finite value of var-epsilon, thus explaining the finite threshold for the TAM observed experimentally. At larger values of var-epsilon, a numerical solution reveals a transition to spatiotemporal chaotic states mediated by the TAM instability

  14. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance

    KAUST Repository

    Sheen, Patricia

    2017-10-11

    Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear.We genotyped and sequenced the complete genomes of 68 M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion.These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.

  15. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance

    KAUST Repository

    Sheen, Patricia; Requena, David; Gushiken, Eduardo; Gilman, Robert H.; Antiparra, Ricardo; Lucero, Bryan; Lizá rraga, Pilar; Cieza, Basilio; Roncal, Elisa; Grandjean, Louis; Pain, Arnab; McNerney, Ruth; Clark, Taane G.; Moore, David; Zimic, Mirko

    2017-01-01

    Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear.We genotyped and sequenced the complete genomes of 68 M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion.These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.

  16. Genetic analysis of the isolated Faroe Islands reveals SORCS3 as a potential multiple sclerosis risk gene

    DEFF Research Database (Denmark)

    Binzer, Stefanie; Stenager, Egon; Binzer, Michael

    2016-01-01

    BACKGROUND: In search of the missing heritability in multiple sclerosis (MS), additional approaches adding to the genetic discoveries of large genome-wide association studies are warranted. OBJECTIVE: The objective of this research paper is to search for rare genetic MS risk variants...... in the genetically homogenous population of the isolated Faroe Islands. METHODS: Twenty-nine Faroese MS cases and 28 controls were genotyped with the HumanOmniExpressExome-chip. The individuals make up 1596 pair-combinations in which we searched for identical-by-descent shared segments using the PLINK...... of neurotrophin factors and involvement in glutamate homeostasis. Although additional work is needed to scrutinise the genetic effect of the SORCS3-covering haplotype, this study suggests that SORCS3 may also be important in MS pathogenesis....

  17. MULTIPLE SHELLS AROUND G79.29+0.46 REVEALED FROM NEAR-IR TO MILLIMETER DATA

    International Nuclear Information System (INIS)

    Jimenez-Esteban, F. M.; Rizzo, J. R.; Palau, Aina

    2010-01-01

    Aiming to perform a study of the warm dust and gas in the luminous blue variable star G79.29+0.46 and its associated nebula, we present infrared Spitzer imaging and spectroscopy, and new CO J = 2 → 1 and 4 → 3 maps obtained with the IRAM 30 m radio telescope and the Submillimeter Telescope, respectively. We have analyzed the nebula detecting multiple shells of dust and gas connected to the star. Using Infrared Spectrograph-Spitzer spectra, we have compared the properties of the central object, the nebula, and their surroundings. These spectra show a rich variety of solid-state features (amorphous silicates, polycyclic aromatic hydrocarbons, and CO 2 ices) and narrow emission lines, superimposed on a thermal continuum. We have also analyzed the physical conditions of the nebula, which point to the existence of a photo-dissociation region.

  18. LUT REVEALS AN ALGOL-TYPE ECLIPSING BINARY WITH THREE ADDITIONAL STELLAR COMPANIONS IN A MULTIPLE SYSTEM

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, L.-Y.; Zhou, X.; Qian, S.-B.; Li, L.-J.; Liao, W.-P.; Tian, X.-M.; Wang, Z.-H. [Yunnan Observatories, Chinese Academy of Sciences (CAS), P.O. Box 110, 650011 Kunming (China); Hu, J.-Y., E-mail: zhuly@ynao.ac.cn [National Astronomical Observatories, Chinese Academy of Sciences, 100012 Beijing (China)

    2016-04-15

    A complete light curve of the neglected eclipsing binary Algol V548 Cygni in the UV band was obtained with the Lunar-based Ultraviolet Telescope in 2014 May. Photometric solutions are obtained using the Wilson–Devinney method. It is found that solutions with and without third light are quite different. The mass ratio without third light is determined to be q = 0.307, while that derived with third light is q = 0.606. It is shown that V548 Cygni is a semi-detached binary where the secondary component is filling the critical Roche lobe. An analysis of all available eclipse times suggests that there are three cyclic variations in the O–C diagram that are interpreted by the light travel-time effect via the presence of three additional stellar companions. This is in agreement with the presence of a large quantity of third light in the system. The masses of these companions are estimated as m sin i′ ∼ 1.09, 0.20, and 0.52 M{sub ⊙}. They are orbiting the central binary with orbital periods of about 5.5, 23.3, and 69.9 years, i.e., in 1:4:12 resonance orbit. Their orbital separations are about 4.5, 13.2, and 26.4 au, respectively. Our photometric solutions suggest that they contribute about 32.4% to the total light of the multiple system. No obvious long-term changes in the orbital period were found, indicating that the contributions of the mass transfer and the mass loss due to magnetic braking to the period variations are comparable. The detection of three possible additional stellar components orbiting a typical Algol in a multiple system make V548 Cygni a very interesting binary to study in the future.

  19. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia

    Science.gov (United States)

    Kerr, Peter J.; Cattadori, Isabella M.; Fitch, Adam; Geber, Adam; Liu, June; Sim, Derek G.; Boag, Brian; Ghedin, Elodie

    2017-01-01

    The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954–1955) and between 2008–2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms. PMID:28253375

  20. Flow cytometric analysis reveals the high levels of platelet activation parameters in circulation of multiple sclerosis patients.

    Science.gov (United States)

    Morel, Agnieszka; Rywaniak, Joanna; Bijak, Michał; Miller, Elżbieta; Niwald, Marta; Saluk, Joanna

    2017-06-01

    The epidemiological studies confirm an increased risk of cardiovascular disease in multiple sclerosis, especially prothrombotic events directly associated with abnormal platelet activity. The aim of our study was to investigate the level of blood platelet activation in the circulation of patients with chronic phase of multiple sclerosis (SP MS) and their reactivity in response to typical platelets' physiological agonists. We examined 85 SP MS patients diagnosed according to the revised McDonald's criteria and 50 healthy volunteers as a control group. The platelet activation and reactivity were assessed using flow cytometry analysis of the following: P-selectin expression (CD62P), activation of GP IIb/IIIa complex (PAC-1 binding), and formation of platelet microparticles (PMPs) and platelet aggregates (PA) in agonist-stimulated (ADP, collagen) and unstimulated whole blood samples. Furthermore, we measured the level of soluble P-selectin (sP-selectin) in plasma using ELISA method, to evaluate the in vivo level of platelet activation, both in healthy and SP MS subjects. We found a statistically significant increase in P-selectin expression, GP IIb/IIIa activation, and formation of PMPs and PA, as well as in unstimulated and agonist-stimulated (ADP, collagen) platelets in whole blood samples from patients with SP MS in comparison to the control group. We also determined the higher sP-selectin level in plasma of SP MS subjects than in the control group. Based on the obtained results, we might conclude that during the course of SP MS platelets are chronically activated and display hyperreactivity to physiological agonists, such as ADP or collagen.

  1. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

    Directory of Open Access Journals (Sweden)

    Peter J Kerr

    2017-03-01

    Full Text Available The co-evolution of myxoma virus (MYXV and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955 and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release Lausanne strain. Inferred virulence ranged from highly virulent (grade 1 to highly attenuated (grade 5. Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.

  2. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

    Science.gov (United States)

    Kerr, Peter J; Cattadori, Isabella M; Rogers, Matthew B; Fitch, Adam; Geber, Adam; Liu, June; Sim, Derek G; Boag, Brian; Eden, John-Sebastian; Ghedin, Elodie; Read, Andrew F; Holmes, Edward C

    2017-03-01

    The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955) and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.

  3. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence.

    Directory of Open Access Journals (Sweden)

    Cristina Aguado

    2014-03-01

    Full Text Available In recent years different types of structural variants (SVs have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies.

  4. Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Torrealdea Javier

    2011-07-01

    Full Text Available Abstract Background The relapsing-remitting dynamics is a hallmark of autoimmune diseases such as Multiple Sclerosis (MS. Although current understanding of both cellular and molecular mechanisms involved in the pathogenesis of autoimmune diseases is significant, how their activity generates this prototypical dynamics is not understood yet. In order to gain insight about the mechanisms that drive these relapsing-remitting dynamics, we developed a computational model using such biological knowledge. We hypothesized that the relapsing dynamics in autoimmunity can arise through the failure in the mechanisms controlling cross-regulation between regulatory and effector T cells with the interplay of stochastic events (e.g. failure in central tolerance, activation by pathogens that are able to trigger the immune system. Results The model represents five concepts: central tolerance (T-cell generation by the thymus, T-cell activation, T-cell memory, cross-regulation (negative feedback between regulatory and effector T-cells and tissue damage. We enriched the model with reversible and irreversible tissue damage, which aims to provide a comprehensible link between autoimmune activity and clinical relapses and active lesions in the magnetic resonances studies in patients with Multiple Sclerosis. Our analysis shows that the weakness in this negative feedback between effector and regulatory T-cells, allows the immune system to generate the characteristic relapsing-remitting dynamics of autoimmune diseases, without the need of additional environmental triggers. The simulations show that the timing at which relapses appear is highly unpredictable. We also introduced targeted perturbations into the model that mimicked immunotherapies that modulate effector and regulatory populations. The effects of such therapies happened to be highly dependent on the timing and/or dose, and on the underlying dynamic of the immune system. Conclusion The relapsing dynamic in MS

  5. Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

    Science.gov (United States)

    Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

    2018-01-01

    Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

  6. Rainfall spatiotemporal variability relation to wetlands hydroperiods

    Science.gov (United States)

    Serrano-Hidalgo, Carmen; Guardiola-Albert, Carolina; Fernandez-Naranjo, Nuria

    2017-04-01

    Doñana natural space (Southwestern Spain) is one of the largest protected wetlands in Europe. The wide marshes present in this natural space have such ecological value that this wetland has been declared a Ramsar reserve in 1982. Apart from the extensive marsh, there are also small lagoons and seasonally flooded areas which are likewise essential to maintain a wide variety of valuable habitats. Hydroperiod, the length of time each point remains flooded along an annual cycle, is a critical ecological parameter that shapes aquatic plants and animals distribution and determines available habitat for many of the living organisms in the marshes. Recently, there have been published two different works estimating the hydroperiod of Doñana lagoons with Landsat Time Series images (Cifuentes et al., 2015; Díaz-Delgado et al., 2016). In both works the flooding cycle hydroperiod in Doñana marshes reveals a flooding regime mainly driven by rainfall, evapotranspiration, topography and local hydrological management actions. The correlation found between rainfall and hydroperiod is studied differently in both works. While in one the rainfall is taken from one raingauge (Cifuentes et al., 2015), the one performed by Díaz-Delgado (2016) uses annual rainfall maps interpolated with the inverse of the distance method. The rainfall spatiotemporal variability in this area can be highly significant; however the amount of this importance has not been quantified at the moment. In the present work the geostatistical tool known as spatiotemporal variogram is used to study the rainfall spatiotemporal variability. The spacetime package implemented in R (Pebesma, 2012) facilities its computation from a high rainfall data base of more than 100 raingauges from 1950 to 2016. With the aid of these variograms the rainfall spatiotemporal variability is quantified. The principal aim of the present work is the study of the relation between the rainfall spatiotemporal variability and the

  7. An evaluation of space time cube representation of spatiotemporal patterns.

    Science.gov (United States)

    Kristensson, Per Ola; Dahlbäck, Nils; Anundi, Daniel; Björnstad, Marius; Gillberg, Hanna; Haraldsson, Jonas; Mårtensson, Ingrid; Nordvall, Mathias; Ståhl, Josefine

    2009-01-01

    Space time cube representation is an information visualization technique where spatiotemporal data points are mapped into a cube. Information visualization researchers have previously argued that space time cube representation is beneficial in revealing complex spatiotemporal patterns in a data set to users. The argument is based on the fact that both time and spatial information are displayed simultaneously to users, an effect difficult to achieve in other representations. However, to our knowledge the actual usefulness of space time cube representation in conveying complex spatiotemporal patterns to users has not been empirically validated. To fill this gap, we report on a between-subjects experiment comparing novice users' error rates and response times when answering a set of questions using either space time cube or a baseline 2D representation. For some simple questions, the error rates were lower when using the baseline representation. For complex questions where the participants needed an overall understanding of the spatiotemporal structure of the data set, the space time cube representation resulted in on average twice as fast response times with no difference in error rates compared to the baseline. These results provide an empirical foundation for the hypothesis that space time cube representation benefits users analyzing complex spatiotemporal patterns.

  8. Contrasting Responses of the Humboldt Current Ecosystem between the Holocene and MIS5e Interglacials Revealed from Multiple Sediment Records

    Science.gov (United States)

    Salvatteci, R.; Schneider, R. R.; Blanz, T.; Martinez, P.; Crosta, X.

    2016-12-01

    The Humboldt Current Ecosystem (HCE) off Peru yields about 10% of the global fish catch, producing more fish per unit area than any other region in the world. The high productivity is maintained by the upwelling of cold, nutrient-rich water from the oxygen minimum zone (OMZ), driven by strong trade winds. However, the potential impacts of climate change on upwelling dynamics and oceanographic conditions in the near future are uncertain, threatening local and global economies. Here, we unravel the response of the HCE to contrasting climatic conditions during the last two interglacials (i.e. Holocene and MIS5e) providing an independent insight about the relation between climatic factors and upwelling and productivity dynamics. For this purpose, we used multiple cores to reconstruct past changes in OMZ and upwelling intensity, productivity and fish biomass variability. Chronologies for the Holocene were obtained by multiple 14C ages and laminae correlations among cores, while for the MIS5e they were mainly done by correlation of prominent features in several proxies with other published records. We used a multiproxy approach including alkenones to reconstruct sea surface temperatures, δ15N as a proxy for water column denitrification, redox sensitive metals as proxies for sediment redox conditions, and diatom and fish debris assemblages to reconstruct ecological changes. The results show a very different response of the HCE to climate conditions during the last 2 interglacials, likely driven by changes in Tropical Pacific dynamics. During the Holocene we find that 1) the Late Holocene exhibits higher multi-centennial scale variability compared to the Early Holocene, 2) increased upwelling and a weak OMZ during the mid-Holocene, and 3) long term increase in productivity (diatoms and fishes) from the Early to the Late Holocene. During the MIS5e we find an 1) intense OMZ, 2) strong water column stratification, 3) high siliceous biomass, and 4) low fish biomass compared

  9. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics.

    Directory of Open Access Journals (Sweden)

    Jennifer L Anderson

    Full Text Available Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio, neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate, the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F(2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome.

  10. Transcriptome and proteomic analyses reveal multiple differences associated with chloroplast development in the spaceflight-induced wheat albino mutant mta.

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    Kui Shi

    Full Text Available Chloroplast development is an integral part of plant survival and growth, and occurs in parallel with chlorophyll biosynthesis. However, little is known about the mechanisms underlying chloroplast development in hexaploid wheat. Here, we obtained a spaceflight-induced wheat albino mutant mta. Chloroplast ultra-structural observation showed that chloroplasts of mta exhibit abnormal morphology and distribution compared to wild type. Photosynthetic pigments content was also significantly decreased in mta. Transcriptome and chloroplast proteome profiling of mta and wild type were done to identify differentially expressed genes (DEGs and proteins (DEPs, respectively. In total 4,588 DEGs including 1,980 up- and 2,608 down-regulated, and 48 chloroplast DEPs including 15 up- and 33 down-regulated were identified in mta. Classification of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. Besides, transcription factors such as PIF3, GLK and MYB which might participate in those pathways were also identified. The correlation analysis between DEGs and DEPs revealed that the transcript-to-protein in abundance was functioned into photosynthesis and chloroplast relevant groups. Real time qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in mta. Together, our results suggest that the molecular mechanism for albino leaf color formation in mta is a thoroughly regulated and complicated process. The combined analysis of transcriptome and proteome afford comprehensive information for further research on chloroplast development mechanism in wheat. And spaceflight provides a potential means for mutagenesis in crop breeding.

  11. Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar (Coleoptera: Curculionidae Reveals Multiple Protease-Like Transcripts.

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    Arnubio Valencia

    Full Text Available The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

  12. A high-density ERP study reveals latency, amplitude, and topographical differences in multiple sclerosis patients versus controls.

    LENUS (Irish Health Repository)

    Whelan, R

    2012-02-01

    OBJECTIVE: To quantify latency, amplitude and topographical differences in event-related potential (ERP) components between multiple sclerosis (MS) patients and controls and to compare ERP findings with results from the paced auditory serial addition test (PASAT). METHODS: Fifty-four subjects (17 relapsing remitting (RRMS) patients, 16 secondary progressive (SPMS) patients, and 21 controls) completed visual and auditory oddball tasks while data were recorded from 134 EEG channels. Latency and amplitude differences, calculated using composite mean amplitude measures, were tested using an ANOVA. Topographical differences were tested using statistical parametric mapping (SPM). RESULTS: In the visual modality, P2, P3 amplitudes and N2 latency were significantly different across groups. In the auditory modality, P2, N2, and P3 latencies and N1 amplitude were significantly different across groups. There were no significant differences between RRMS and SPMS patients on any ERP component. There were topographical differences between MS patients and controls for both early and late components for the visual modality, but only in the early components for the auditory modality. PASAT score correlated significantly with auditory P3 latency for MS patients. CONCLUSIONS: There were significant ERP differences between MS patients and controls. SIGNIFICANCE: The present study indicated that both early sensory and later cognitive ERP components are impaired in MS patients relative to controls.

  13. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

    Science.gov (United States)

    Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

    2014-11-01

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts.

    Science.gov (United States)

    Valencia, Arnubio; Wang, Haichuan; Soto, Alberto; Aristizabal, Manuel; Arboleda, Jorge W; Eyun, Seong-Il; Noriega, Daniel D; Siegfried, Blair

    2016-01-01

    The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

  15. Deletion of GLUT1 and GLUT3 Reveals Multiple Roles for Glucose Metabolism in Platelet and Megakaryocyte Function

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    Trevor P. Fidler

    2017-07-01

    Full Text Available Anucleate platelets circulate in the blood to facilitate thrombosis and diverse immune functions. Platelet activation leading to clot formation correlates with increased glycogenolysis, glucose uptake, glucose oxidation, and lactic acid production. Simultaneous deletion of glucose transporter (GLUT 1 and GLUT3 (double knockout [DKO] specifically in platelets completely abolished glucose uptake. In DKO platelets, mitochondrial oxidative metabolism of non-glycolytic substrates, such as glutamate, increased. Thrombosis and platelet activation were decreased through impairment at multiple activation nodes, including Ca2+ signaling, degranulation, and integrin activation. DKO mice developed thrombocytopenia, secondary to impaired pro-platelet formation from megakaryocytes, and increased platelet clearance resulting from cytosolic calcium overload and calpain activation. Systemic treatment with oligomycin, inhibiting mitochondrial metabolism, induced rapid clearance of platelets, with circulating counts dropping to zero in DKO mice, but not wild-type mice, demonstrating an essential role for energy metabolism in platelet viability. Thus, substrate metabolism is essential for platelet production, activation, and survival.

  16. A Multiplexed Assay That Monitors Effects of Multiple Compound Treatment Times Reveals Candidate Immune-Enhancing Compounds.

    Science.gov (United States)

    Zhao, Ziyan; Henowitz, Liza; Zweifach, Adam

    2018-05-01

    We previously developed a flow cytometry assay that monitored lytic granule exocytosis in cytotoxic T lymphocytes stimulated by contacting beads coated with activating anti-CD3 antibodies. That assay was multiplexed in that responses of cells that did or did not receive the activating stimulus were distinguished via changes in light scatter accompanying binding of cells to beads, allowing us to discriminate compounds that activate responses on their own from compounds that enhance responses in cells that received the activating stimulus, all within a single sample. Here we add a second dimension of multiplexing by developing means to assess in a single sample the effects of treating cells with test compounds for different times. Bar-coding cells before adding them to test wells lets us determine compound treatment time while also monitoring activation status and response amplitude at the point of interrogation. This multiplexed assay is suitable for screening 96-well plates. We used it to screen compounds from the National Cancer Institute, identifying several compounds that enhance anti-LAMP1 responses. Multiple-treatment-time (MTT) screening enabled by bar-coding and read via high-throughput flow cytometry may be a generally useful method for facilitating the discovery of compounds of interest.

  17. Capture-based next-generation sequencing reveals multiple actionable mutations in cancer patients failed in traditional testing.

    Science.gov (United States)

    Xie, Jing; Lu, Xiongxiong; Wu, Xue; Lin, Xiaoyi; Zhang, Chao; Huang, Xiaofang; Chang, Zhili; Wang, Xinjing; Wen, Chenlei; Tang, Xiaomei; Shi, Minmin; Zhan, Qian; Chen, Hao; Deng, Xiaxing; Peng, Chenghong; Li, Hongwei; Fang, Yuan; Shao, Yang; Shen, Baiyong

    2016-05-01

    Targeted therapies including monoclonal antibodies and small molecule inhibitors have dramatically changed the treatment of cancer over past 10 years. Their therapeutic advantages are more tumor specific and with less side effects. For precisely tailoring available targeted therapies to each individual or a subset of cancer patients, next-generation sequencing (NGS) has been utilized as a promising diagnosis tool with its advantages of accuracy, sensitivity, and high throughput. We developed and validated a NGS-based cancer genomic diagnosis targeting 115 prognosis and therapeutics relevant genes on multiple specimen including blood, tumor tissue, and body fluid from 10 patients with different cancer types. The sequencing data was then analyzed by the clinical-applicable analytical pipelines developed in house. We have assessed analytical sensitivity, specificity, and accuracy of the NGS-based molecular diagnosis. Also, our developed analytical pipelines were capable of detecting base substitutions, indels, and gene copy number variations (CNVs). For instance, several actionable mutations of EGFR,PIK3CA,TP53, and KRAS have been detected for indicating drug susceptibility and resistance in the cases of lung cancer. Our study has shown that NGS-based molecular diagnosis is more sensitive and comprehensive to detect genomic alterations in cancer, and supports a direct clinical use for guiding targeted therapy.

  18. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms.

    Directory of Open Access Journals (Sweden)

    Marlena M Wilson

    Full Text Available Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes.

  19. A comprehensive molecular phylogeny of dalytyphloplanida (platyhelminthes: rhabdocoela reveals multiple escapes from the marine environment and origins of symbiotic relationships.

    Directory of Open Access Journals (Sweden)

    Niels Van Steenkiste

    Full Text Available In this study we elaborate the phylogeny of Dalytyphloplanida based on complete 18S rDNA (156 sequences and partial 28S rDNA (125 sequences, using a Maximum Likelihood and a Bayesian Inference approach, in order to investigate the origin of a limnic or limnoterrestrial and of a symbiotic lifestyle in this large group of rhabditophoran flatworms. The results of our phylogenetic analyses and ancestral state reconstructions indicate that dalytyphloplanids have their origin in the marine environment and that there was one highly successful invasion of the freshwater environment, leading to a large radiation of limnic and limnoterrestrial dalytyphloplanids. This monophyletic freshwater clade, Limnotyphloplanida, comprises the taxa Dalyelliidae, Temnocephalida, and most Typhloplanidae. Temnocephalida can be considered ectosymbiotic Dalyelliidae as they are embedded within this group. Secondary returns to brackish water and marine environments occurred relatively frequently in several dalyeliid and typhloplanid taxa. Our phylogenies also show that, apart from the Limnotyphloplanida, there have been only few independent invasions of the limnic environment, and apparently these were not followed by spectacular speciation events. The distinct phylogenetic positions of the symbiotic taxa also suggest multiple origins of commensal and parasitic life strategies within Dalytyphloplanida. The previously established higher-level dalytyphloplanid clades are confirmed in our topologies, but many of the traditional families are not monophyletic. Alternative hypothesis testing constraining the monophyly of these families in the topologies and using the approximately unbiased test, also statistically rejects their monophyly.

  20. Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution.

    Science.gov (United States)

    Sekigami, Yuka; Kobayashi, Takuya; Omi, Ai; Nishitsuji, Koki; Ikuta, Tetsuro; Fujiyama, Asao; Satoh, Noriyuki; Saiga, Hidetoshi

    2017-01-01

    Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis ( Ci ), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi ( Hr ) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution. Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1 , 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a , 11/12/13.b and HoxX . To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr , distinct from their arrangement in Ci . We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1 , 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci , we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution. The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci

  1. Spatiotemporal Data Mining: A Computational Perspective

    Directory of Open Access Journals (Sweden)

    Shashi Shekhar

    2015-10-01

    Full Text Available Explosive growth in geospatial and temporal data as well as the emergence of new technologies emphasize the need for automated discovery of spatiotemporal knowledge. Spatiotemporal data mining studies the process of discovering interesting and previously unknown, but potentially useful patterns from large spatiotemporal databases. It has broad application domains including ecology and environmental management, public safety, transportation, earth science, epidemiology, and climatology. The complexity of spatiotemporal data and intrinsic relationships limits the usefulness of conventional data science techniques for extracting spatiotemporal patterns. In this survey, we review recent computational techniques and tools in spatiotemporal data mining, focusing on several major pattern families: spatiotemporal outlier, spatiotemporal coupling and tele-coupling, spatiotemporal prediction, spatiotemporal partitioning and summarization, spatiotemporal hotspots, and change detection. Compared with other surveys in the literature, this paper emphasizes the statistical foundations of spatiotemporal data mining and provides comprehensive coverage of computational approaches for various pattern families. ISPRS Int. J. Geo-Inf. 2015, 4 2307 We also list popular software tools for spatiotemporal data analysis. The survey concludes with a look at future research needs.

  2. The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus.

    Science.gov (United States)

    Porretta, Daniele; Mastrantonio, Valentina; Mona, Stefano; Epis, Sara; Montagna, Matteo; Sassera, Davide; Bandi, Claudio; Urbanelli, Sandra

    2013-03-01

    In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent-based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of 'bridges' among populations. Our study highlights the importance of species-specific ecology in affecting responses to Pleistocene glacial-interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes. © 2013 Blackwell Publishing Ltd.

  3. Ecological Momentary Assessment of Pain, Fatigue, Depressive, and Cognitive Symptoms Reveals Significant Daily Variability in Multiple Sclerosis.

    Science.gov (United States)

    Kratz, Anna L; Murphy, Susan L; Braley, Tiffany J

    2017-11-01

    To describe the daily variability and patterns of pain, fatigue, depressed mood, and cognitive function in persons with multiple sclerosis (MS). Repeated-measures observational study of 7 consecutive days of home monitoring, including ecological momentary assessment (EMA) of symptoms. Multilevel mixed models were used to analyze data. General community. Ambulatory adults (N=107) with MS recruited through the University of Michigan and surrounding community. Not applicable. EMA measures of pain, fatigue, depressed mood, and cognitive function rated on a 0 to 10 scale, collected 5 times a day for 7 days. Cognitive function and depressed mood exhibited more stable within-person patterns than pain and fatigue, which varied considerably within person. All symptoms increased in intensity across the day (all Pfatigue showing the most substantial increase. Notably, this diurnal increase varied by sex and age; women showed a continuous increase from wake to bedtime, whereas fatigue plateaued after 7 pm for men (wake-bed B=1.04, P=.004). For the oldest subgroup, diurnal increases were concentrated to the middle of the day compared with younger subgroups, which showed an earlier onset of fatigue increase and sustained increases until bed time (wake-3 pm B=.04, P=.01; wake-7 pm B=.03, P=.02). Diurnal patterns of cognitive function varied by education; those with advanced college degrees showed a more stable pattern across the day, with significant differences compared with those with bachelor-level degrees in the evening (wake-7 pm B=-.47, P=.02; wake-bed B=-.45, P=.04). Findings suggest that chronic symptoms in MS are not static, even over a short time frame; rather, symptoms-fatigue and pain in particular-vary dynamically across and within days. Incorporation of EMA methods should be considered in the assessment of these chronic MS symptoms to enhance assessment and treatment strategies. Copyright © 2017 American Congress of Rehabilitation Medicine. Published by Elsevier

  4. Multiple cooling episodes in the Central Tarim (Northwest China) revealed by apatite fission track analysis and vitrinite reflectance data

    Science.gov (United States)

    Chang, Jian; Qiu, Nansheng; Song, Xinying; Li, Huili

    2016-06-01

    Apatite fission track and vitrinite reflectance are integrated for the first time to study the cooling history in the Central Tarim, northwest China. The paleo-temperature profiles from vitrinite reflectance data of the Z1 and Z11 wells showed a linear relationship with depth, suggesting an approximately 24.8 °C/km paleo-geothermal gradient and 2700-3900 m of erosion during the Early Mesozoic. The measured apatite fission track ages from well Z2 in the Central Tarim range from 39 to 159 Ma and effectively record the Meso-Cenozoic cooling events that occurred in Central Tarim. Moreover, two cooling events at 190-140 Ma in the Early Jurassic-Early Cretaceous and 80-45 Ma in the Late Cretaceous-Paleocene revealed by measured AFT data and thermal modeling results are related to the collisions of the Qiangtang-Lhasa terranes and the Greater India Plate with the southern margin of the Eurasian Plate, respectively. This study provides new insights into the tectonic evolution of the Tarim Basin (and more broadly Central Asia) and for hydrocarbon generation and exploration in the Central Tarim.

  5. Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants.

    Science.gov (United States)

    Guo, Shengye; Li, Xingyu; He, Pengfei; Ho, Honhing; Wu, Yixin; He, Yueqiu

    2015-06-01

    Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain's plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for developing a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

  6. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

    Directory of Open Access Journals (Sweden)

    Wu Shi-Fang

    2011-07-01

    Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

  7. Comparative Genomic Hybridization of Human Malignant Gliomas Reveals Multiple Amplification Sites and Nonrandom Chromosomal Gains and Losses

    Science.gov (United States)

    Schròck, Evelin; Thiel, Gundula; Lozanova, Tanka; du Manoir, Stanislas; Meffert, Marie-Christine; Jauch, Anna; Speicher, Michael R.; Nürnberg, Peter; Vogel, Siegfried; Janisch, Werner; Donis-Keller, Helen; Ried, Thomas; Witkowski, Regine; Cremer, Thomas

    1994-01-01

    Nine human malignant gliomas (2 astrocytomas grade III and 7 glioblastomas) were analyzed using comparative genomic hybridization (CGH). In addition to the amplification of the EGFR gene at 7p12 in 4 of 9 cases, six new amplification sites were mapped to 1q32, 4q12, 7q21.1, 7q21.2-3, 12p, and 22q12. Nonrandom chromosomal gains and losses were identified with overrepresentation of chromosome 7 and underrepresentation of chromosome 10 as the most frequent events (1 of 2 astrocytomas, 7 of 7 glioblastomas). Gain of a part or the whole chromosome 19 and losses of chromosome bands 9pter-23 and 22q13 were detected each in five cases. Loss of chromosome band 17p13 and gain of chromosome 20 were revealed each in three cases. The validity of the CGH data was confirmed using interphase cytogenetics with YAC clones, chromosome painting in tumor metaphase spreads, and DNA fingerprinting. A comparison of CGH data with the results of chromosome banding analyses indicates that metaphase spreads accessible in primary tumor cell cultures may not represent the clones predominant in the tumor tissue ImagesFigure 1Figure 4Figure 6 PMID:8203461

  8. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor; Pittius, Nicolaas Gey van; Naicker, Brendon; Michel, Anita

    2017-04-01

    Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment, and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness, which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples. These isolates were previously identified during an NTM survey and were all found, using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. A polyphasic approach that included phenotypic characterization, antibiotic susceptibility profiling, mycolic acid profiling and phylogenetic analysis of four gene loci, 16S rRNA, hsp65, sodA and rpoB, was employed to characterize these isolates. Sequence data analysis of the four gene loci revealed that these isolates belong to a unique species of the genus Mycobacterium. This evidence was further supported by several differences in phenotypic characteristics between the isolates and the closely related species. We propose the name Mycobacterium malmesburyense sp. nov. for this novel species. The type strain is WCM 7299T (=ATCC BAA-2759T=CIP 110822T).

  9. Surface plasmon resonance imaging reveals multiple binding modes of Agrobacterium transformation mediator VirE2 to ssDNA.

    Science.gov (United States)

    Kim, Sanghyun; Zbaida, David; Elbaum, Michael; Leh, Hervé; Nogues, Claude; Buckle, Malcolm

    2015-07-27

    VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein-protein interactions. In order to isolate the protein-DNA interactions, imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1-VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1-VirE2 followed the Langmuir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. HYDRA: Revealing heterogeneity of imaging and genetic patterns through a multiple max-margin discriminative analysis framework.

    Science.gov (United States)

    Varol, Erdem; Sotiras, Aristeidis; Davatzikos, Christos

    2017-01-15

    Multivariate pattern analysis techniques have been increasingly used over the past decade to derive highly sensitive and specific biomarkers of diseases on an individual basis. The driving assumption behind the vast majority of the existing methodologies is that a single imaging pattern can distinguish between healthy and diseased populations, or between two subgroups of patients (e.g., progressors vs. non-progressors). This assumption effectively ignores the ample evidence for the heterogeneous nature of brain diseases. Neurodegenerative, neuropsychiatric and neurodevelopmental disorders are largely characterized by high clinical heterogeneity, which likely stems in part from underlying neuroanatomical heterogeneity of various pathologies. Detecting and characterizing heterogeneity may deepen our understanding of disease mechanisms and lead to patient-specific treatments. However, few approaches tackle disease subtype discovery in a principled machine learning framework. To address this challenge, we present a novel non-linear learning algorithm for simultaneous binary classification and subtype identification, termed HYDRA (Heterogeneity through Discriminative Analysis). Neuroanatomical subtypes are effectively captured by multiple linear hyperplanes, which form a convex polytope that separates two groups (e.g., healthy controls from pathologic samples); each face of this polytope effectively defines a disease subtype. We validated HYDRA on simulated and clinical data. In the latter case, we applied the proposed method independently to the imaging and genetic datasets of the Alzheimer's Disease Neuroimaging Initiative (ADNI 1) study. The imaging dataset consisted of T1-weighted volumetric magnetic resonance images of 123 AD patients and 177 controls. The genetic dataset consisted of single nucleotide polymorphism information of 103 AD patients and 139 controls. We identified 3 reproducible subtypes of atrophy in AD relative to controls: (1) diffuse and extensive

  11. Multiple episodes of mineralization revealed by Re-Os molybdenite geochronology in the Lala Fe-Cu deposit, SW China

    Science.gov (United States)

    Zhu, Zhimin; Tan, Hongqi; Liu, Yingdong; Li, Chao

    2018-03-01

    The Lala Fe-Cu deposit is one of the largest iron oxide-copper-gold (IOCG) deposits in the Kangdian copper belt, southwest China. The paragenetic sequence of the Lala deposit includes six hydrothermal stages: pre-ore pervasive Na alteration (I); magnetite stage with K-feldspar and apatite (II); polymetallic disseminated/massive magnetite-sulfide stage (III); banded magnetite-sulfide stage (IV); sulfide vein stage (V); and late quartz-carbonate vein stage (VI). Fifteen molybdenite separates from stages III to VI were analyzed for Re-Os dating. Our new Re-Os data, together with previous studies, identify four distinct hydrothermal events at the Lala deposit. Molybdenite from the stage III disseminated to massive chalcopyrite-magnetite ores yielded a weighted average Re-Os age of 1306 ± 8 Ma (MSWD = 1.1, n = 6) which represents the timing of main ore formation. Molybdenite from the stage IV-banded magnetite-chalcopyrite ores yielded a weighted average Re-Os age of 1086 ± 8 Ma (MSWD = 2.2, n = 7), i.e., a second ore-forming event. Molybdenite from the stage V sulfide veins yielded a weighted average Re-Os age of 988 ± 8 Ma (MSWD = 1.3, n = 7) which represents the timing of a third hydrothermal event. Molybdenite from the quartz-carbonate veins (stage VI) yielded a weighted average Re-Os age at 835 ± 4 Ma (MSWD = 0.66, n = 10) and documented the timing of a late hydrothermal event. Our results indicate that the Lala deposit formed during multiple, protracted mineralization events over several hundred million years. The first three Mesoproterozoic mineralization events are coeval with intra-continental rifting (breakup of the supercontinent Nuna) and share a temporal link to other IOCG-style deposits within the Kangdian Copper Belt, and the last Neoproterozoic hydrothermal event is coeval with the Sibao orogeny which culminated with the amalgamation of the Yangtze Block with the Cathaysia Block at 860-815 Ma.

  12. Evolutionary history of the fish genus Astyanax Baird & Girard (1854 (Actinopterygii, Characidae in Mesoamerica reveals multiple morphological homoplasies

    Directory of Open Access Journals (Sweden)

    Doadrio Ignacio

    2008-12-01

    colonization of Upper Mesoamerica apparently occurred by two independent routes, with lineage turnover over a large part of the region. Conclusion Our results support multiple, independent origins of morphological traits in Astyanax, whereby the morphotype associated with Bramocharax represents a recurrent trophic adaptation. Molecular clock estimates indicate that Astyanax was present in Mesoamerica during the Miocene (~8 Mya, which implies the existence of an incipient land-bridge connecting South America and Central America before the final closure of the Isthmus of Panama (~3.3 Mya.

  13. Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

    Science.gov (United States)

    Sturgis, James N; Niederman, Robert A

    2008-01-01

    Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

  14. Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates.

    Directory of Open Access Journals (Sweden)

    Andreas Tuerk

    2017-05-01

    Full Text Available Accuracy of transcript quantification with RNA-Seq is negatively affected by positional fragment bias. This article introduces Mix2 (rd. "mixquare", a transcript quantification method which uses a mixture of probability distributions to model and thereby neutralize the effects of positional fragment bias. The parameters of Mix2 are trained by Expectation Maximization resulting in simultaneous transcript abundance and bias estimates. We compare Mix2 to Cufflinks, RSEM, eXpress and PennSeq; state-of-the-art quantification methods implementing some form of bias correction. On four synthetic biases we show that the accuracy of Mix2 overall exceeds the accuracy of the other methods and that its bias estimates converge to the correct solution. We further evaluate Mix2 on real RNA-Seq data from the Microarray and Sequencing Quality Control (MAQC, SEQC Consortia. On MAQC data, Mix2 achieves improved correlation to qPCR measurements with a relative increase in R2 between 4% and 50%. Mix2 also yields repeatable concentration estimates across technical replicates with a relative increase in R2 between 8% and 47% and reduced standard deviation across the full concentration range. We further observe more accurate detection of differential expression with a relative increase in true positives between 74% and 378% for 5% false positives. In addition, Mix2 reveals 5 dominant biases in MAQC data deviating from the common assumption of a uniform fragment distribution. On SEQC data, Mix2 yields higher consistency between measured and predicted concentration ratios. A relative error of 20% or less is obtained for 51% of transcripts by Mix2, 40% of transcripts by Cufflinks and RSEM and 30% by eXpress. Titration order consistency is correct for 47% of transcripts for Mix2, 41% for Cufflinks and RSEM and 34% for eXpress. We, further, observe improved repeatability across laboratory sites with a relative increase in R2 between 8% and 44% and reduced standard deviation.

  15. Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).

    Science.gov (United States)

    Stervander, Martin; Alström, Per; Olsson, Urban; Ottosson, Ulf; Hansson, Bengt; Bensch, Staffan

    2016-09-01

    The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

    Energy Technology Data Exchange (ETDEWEB)

    Pincus, David; Ryan, Christopher J.; Smith, Richard D.; Brent, Roger; Resnekov, Orna; Hakimi, Mohamed Ali

    2013-03-12

    Cell signaling systems transmit information by post-­translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-­protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-­output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

  17. Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

    Directory of Open Access Journals (Sweden)

    Sharat K. Pradhan

    2017-04-01

    Full Text Available Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

  18. Multiple analytical approaches reveal distinct gene-environment interactions in smokers and non smokers in lung cancer.

    Directory of Open Access Journals (Sweden)

    Rakhshan Ihsan

    Full Text Available Complex disease such as cancer results from interactions of multiple genetic and environmental factors. Studying these factors singularly cannot explain the underlying pathogenetic mechanism of the disease. Multi-analytical approach, including logistic regression (LR, classification and regression tree (CART and multifactor dimensionality reduction (MDR, was applied in 188 lung cancer cases and 290 controls to explore high order interactions among xenobiotic metabolizing genes and environmental risk factors. Smoking was identified as the predominant risk factor by all three analytical approaches. Individually, CYP1A1*2A polymorphism was significantly associated with increased lung cancer risk (OR = 1.69;95%CI = 1.11-2.59,p = 0.01, whereas EPHX1 Tyr113His and SULT1A1 Arg213His conferred reduced risk (OR = 0.40;95%CI = 0.25-0.65,p<0.001 and OR = 0.51;95%CI = 0.33-0.78,p = 0.002 respectively. In smokers, EPHX1 Tyr113His and SULT1A1 Arg213His polymorphisms reduced the risk of lung cancer, whereas CYP1A1*2A, CYP1A1*2C and GSTP1 Ile105Val imparted increased risk in non-smokers only. While exploring non-linear interactions through CART analysis, smokers carrying the combination of EPHX1 113TC (Tyr/His, SULT1A1 213GG (Arg/Arg or AA (His/His and GSTM1 null genotypes showed the highest risk for lung cancer (OR = 3.73;95%CI = 1.33-10.55,p = 0.006, whereas combined effect of CYP1A1*2A 6235CC or TC, SULT1A1 213GG (Arg/Arg and betel quid chewing showed maximum risk in non-smokers (OR = 2.93;95%CI = 1.15-7.51,p = 0.01. MDR analysis identified two distinct predictor models for the risk of lung cancer in smokers (tobacco chewing, EPHX1 Tyr113His, and SULT1A1 Arg213His and non-smokers (CYP1A1*2A, GSTP1 Ile105Val and SULT1A1 Arg213His with testing balance accuracy (TBA of 0.6436 and 0.6677 respectively. Interaction entropy interpretations of MDR results showed non-additive interactions of tobacco chewing with

  19. The influence of spatiotemporal structure of noisy stimuli in decision making.

    Science.gov (United States)

    Insabato, Andrea; Dempere-Marco, Laura; Pannunzi, Mario; Deco, Gustavo; Romo, Ranulfo

    2014-04-01

    Decision making is a process of utmost importance in our daily lives, the study of which has been receiving notable attention for decades. Nevertheless, the neural mechanisms underlying decision making are still not fully understood. Computational modeling has revealed itself as a valuable asset to address some of the fundamental questions. Biophysically plausible models, in particular, are useful in bridging the different levels of description that experimental studies provide, from the neural spiking activity recorded at the cellular level to the performance reported at the behavioral level. In this article, we have reviewed some of the recent progress made in the understanding of the neural mechanisms that underlie decision making. We have performed a critical evaluation of the available results and address, from a computational perspective, aspects of both experimentation and modeling that so far have eluded comprehension. To guide the discussion, we have selected a central theme which revolves around the following question: how does the spatiotemporal structure of sensory stimuli affect the perceptual decision-making process? This question is a timely one as several issues that still remain unresolved stem from this central theme. These include: (i) the role of spatiotemporal input fluctuations in perceptual decision making, (ii) how to extend the current results and models derived from two-alternative choice studies to scenarios with multiple competing evidences, and (iii) to establish whether different types of spatiotemporal input fluctuations affect decision-making outcomes in distinctive ways. And although we have restricted our discussion mostly to visual decisions, our main conclusions are arguably generalizable; hence, their possible extension to other sensory modalities is one of the points in our discussion.

  20. Spatio-Temporal Variations and Source Apportionment of Water Pollution in Danjiangkou Reservoir Basin, Central China

    Directory of Open Access Journals (Sweden)

    Pan Chen

    2015-05-01

    Full Text Available Understanding the spatio-temporal variation and the potential source of water pollution could greatly improve our knowledge of human impacts on the environment. In this work, data of 11 water quality indices were collected during 2012–2014 at 10 monitoring sites in the mainstream and major tributaries of the Danjiangkou Reservoir Basin, Central China. The fuzzy comprehensive assessment (FCA, the cluster analysis (CA and the discriminant analysis (DA were used to assess the water pollution status and analyze its spatio-temporal variation. Ten sites were classified by the high pollution (HP region and the low pollution (LP region, while 12 months were divided into the wet season and the dry season. It was found that the HP region was mainly in the small tributaries with small drainage areas and low average annual discharges, and it was also found that most of these rivers went through urban areas with industrial and domestic sewages input into the water body. Principal component analysis/factor analysis (PCA/FA was applied to reveal potential pollution sources, whereas absolute principal component score-multiple linear regression (APCS-MLR was used to identify their contributions to each water quality variable. The study area was found as being generally affected by industrial and domestic sewage. Furthermore, the HP region was polluted by chemical industries, and the LP region was influenced by agricultural and livestock sewage.

  1. Spatio-temporal models of mental processes from fMRI.

    Science.gov (United States)

    Janoos, Firdaus; Machiraju, Raghu; Singh, Shantanu; Morocz, Istvan Ákos

    2011-07-15

    Understanding the highly complex, spatially distributed and temporally organized phenomena entailed by mental processes using functional MRI is an important research problem in cognitive and clinical neuroscience. Conventional analysis methods focus on the spatial dimension of the data discarding the information about brain function contained in the temporal dimension. This paper presents a fully spatio-temporal multivariate analysis method using a state-space model (SSM) for brain function that yields not only spatial maps of activity but also its temporal structure along with spatially varying estimates of the hemodynamic response. Efficient algorithms for estimating the parameters along with quantitative validations are given. A novel low-dimensional feature-space for representing the data, based on a formal definition of functional similarity, is derived. Quantitative validation of the model and the estimation algorithms is provided with a simulation study. Using a real fMRI study for mental arithmetic, the ability of this neurophysiologically inspired model to represent the spatio-temporal information corresponding to mental processes is demonstrated. Moreover, by comparing the models across multiple subjects, natural patterns in mental processes organized according to different mental abilities are revealed. Copyright © 2011 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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.

  3. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  4. Comparing infants' use of featural and spatiotemporal information when individuating objects in an event monitoring design

    DEFF Research Database (Denmark)

    Krøjgaard, Peter

    . The results obtained using this design reveal that infants are more successful using spatiotemporal object information than when using featural information. However, recent studies using the less cognitively demanding event monitoring design have revealed that even younger infants are capable of object...... in the present series of experiments in which infants' use of spatiotemporal and featural information is compared directly using the less demanding event monitoring design. The results are discussed in relation to existing empirical evidence......., to what extent infants rely on spatiotemporal or featural object information when individuating objects is currently under debate. Hitherto, infants' use of spatiotemporal and featural object information has only been compared directly using the rather cognitively demanding event mapping design...

  5. Integrative proteomics, genomics, and translational immunology approaches reveal mutated forms of Proteolipid Protein 1 (PLP1) and mutant-specific immune response in multiple sclerosis.

    Science.gov (United States)

    Qendro, Veneta; Bugos, Grace A; Lundgren, Debbie H; Glynn, John; Han, May H; Han, David K

    2017-03-01

    In order to gain mechanistic insights into multiple sclerosis (MS) pathogenesis, we utilized a multi-dimensional approach to test the hypothesis that mutations in myelin proteins lead to immune activation and central nervous system autoimmunity in MS. Mass spectrometry-based proteomic analysis of human MS brain lesions revealed seven unique mutations of PLP1; a key myelin protein that is known to be destroyed in MS. Surprisingly, in-depth genomic analysis of two MS patients at the genomic DNA and mRNA confirmed mutated PLP1 in RNA, but not in the genomic DNA. Quantification of wild type and mutant PLP RNA levels by qPCR further validated the presence of mutant PLP RNA in the MS patients. To seek evidence linking mutations in abundant myelin proteins and immune-mediated destruction of myelin, specific immune response against mutant PLP1 in MS patients was examined. Thus, we have designed paired, wild type and mutant peptide microarrays, and examined antibody response to multiple mutated PLP1 in sera from MS patients. Consistent with the idea of different patients exhibiting unique mutation profiles, we found that 13 out of 20 MS patients showed antibody responses against specific but not against all the mutant-PLP1 peptides. Interestingly, we found mutant PLP-directed antibody response against specific mutant peptides in the sera of pre-MS controls. The results from integrative proteomic, genomic, and immune analyses reveal a possible mechanism of mutation-driven pathogenesis in human MS. The study also highlights the need for integrative genomic and proteomic analyses for uncovering pathogenic mechanisms of human diseases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Spatio-Temporal Data Construction

    Directory of Open Access Journals (Sweden)

    Hai Ha Le

    2013-08-01

    Full Text Available On the route to a spatio-temporal geoscience information system, an appropriate data model for geo-objects in space and time has been developed. In this model, geo-objects are represented as sequences of geometries and properties with continuous evolution in each time interval. Because geomodeling software systems usually model objects at specific time instances, we want to interpolate the geometry and properties from two models of an object with only geometrical constraints (no physical or mechanical constraints. This process is called spatio-temporal data construction or morphological interpolation of intermediate geometries. This paper is strictly related to shape morphing, shape deformation, cross-parameterization and compatible remeshing and is only concerned with geological surfaces. In this study, two main sub-solutions construct compatible meshes and find trajectories in which vertices of the mesh evolve. This research aims to find an algorithm to construct spatio-temporal data with some constraints from the geosciences, such as cutting surfaces by faulting or fracturing phenomena and evolving boundaries attached to other surfaces. Another goal of this research is the implementation of the algorithm in a software product, namely a gOcad plug-in. The four main procedures of the algorithm are cutting the surfaces, setting up constraints, partitioning and calculating the parameterizations and trajectories. The software has been tested to construct data for a salt dome and other surfaces in regard to the geological processes of faulting, deposition and erosion. The result of this research is an algorithm and software for the construction of spatio-temporal data.

  7. Dynamic characterizers of spatiotemporal intermittency

    OpenAIRE

    Gupte, Neelima; Jabeen, Zahera

    2006-01-01

    Systems of coupled sine circle maps show regimes of spatiotemporally intermittent behaviour with associated scaling exponents which belong to the DP class, as well as regimes of spatially intermittent behaviour (with associated regular dynamical behaviour) which do not belong to the DP class. Both types of behaviour are seen along the bifurcation boundaries of the synchronized solutions, and contribute distinct signatures to the dynamical characterizers of the system, viz. the distribution of...

  8. Compressing spatio-temporal trajectories

    DEFF Research Database (Denmark)

    Gudmundsson, Joachim; Katajainen, Jyrki; Merrick, Damian

    2009-01-01

    such that the most common spatio-temporal queries can still be answered approximately after the compression has taken place. In the process, we develop an implementation of the Douglas–Peucker path-simplification algorithm which works efficiently even in the case where the polygonal path given as input is allowed...... to self-intersect. For a polygonal path of size n, the processing time is O(nlogkn) for k=2 or k=3 depending on the type of simplification....

  9. Visual representation of spatiotemporal structure

    Science.gov (United States)

    Schill, Kerstin; Zetzsche, Christoph; Brauer, Wilfried; Eisenkolb, A.; Musto, A.

    1998-07-01

    The processing and representation of motion information is addressed from an integrated perspective comprising low- level signal processing properties as well as higher-level cognitive aspects. For the low-level processing of motion information we argue that a fundamental requirement is the existence of a spatio-temporal memory. Its key feature, the provision of an orthogonal relation between external time and its internal representation, is achieved by a mapping of temporal structure into a locally distributed activity distribution accessible in parallel by higher-level processing stages. This leads to a reinterpretation of the classical concept of `iconic memory' and resolves inconsistencies on ultra-short-time processing and visual masking. The spatial-temporal memory is further investigated by experiments on the perception of spatio-temporal patterns. Results on the direction discrimination of motion paths provide evidence that information about direction and location are not processed and represented independent of each other. This suggests a unified representation on an early level, in the sense that motion information is internally available in form of a spatio-temporal compound. For the higher-level representation we have developed a formal framework for the qualitative description of courses of motion that may occur with moving objects.

  10. Tensor-based spatiotemporal saliency detection

    Science.gov (United States)

    Dou, Hao; Li, Bin; Deng, Qianqian; Zhang, LiRui; Pan, Zhihong; Tian, Jinwen

    2018-03-01

    This paper proposes an effective tensor-based spatiotemporal saliency computation model for saliency detection in videos. First, we construct the tensor representation of video frames. Then, the spatiotemporal saliency can be directly computed by the tensor distance between different tensors, which can preserve the complete temporal and spatial structure information of object in the spatiotemporal domain. Experimental results demonstrate that our method can achieve encouraging performance in comparison with the state-of-the-art methods.

  11. The World Spatiotemporal Analytics and Mapping Project (WSTAMP): Discovering, Exploring, and Mapping Spatiotemporal Patterns Across Heterogenous Space-Time Data

    Science.gov (United States)

    Morton, A.; Stewart, R.; Held, E.; Piburn, J.; Allen, M. R.; McManamay, R.; Sanyal, J.; Sorokine, A.; Bhaduri, B. L.

    2017-12-01

    Spatiotemporal (ST) analytics applied to major spatio-temporal data sources from major vendors such as USGS, NOAA, World Bank and World Health Organization have tremendous value in shedding light on the evolution of physical, cultural, and geopolitical landscapes on a local and global level. Especially powerful is the integration of these physical and cultural datasets across multiple and disparate formats, facilitating new interdisciplinary analytics and insights. Realizing this potential first requires an ST data model that addresses challenges in properly merging data from multiple authors, with evolving ontological perspectives, semantical differences, changing attributes, and content that is textual, numeric, categorical, and hierarchical. Equally challenging is the development of analytical and visualization approaches that provide a serious exploration of this integrated data while remaining accessible to practitioners with varied backgrounds. The WSTAMP project at the Oak Ridge National Laboratory has yielded two major results in addressing these challenges: 1) development of the WSTAMP database, a significant advance in ST data modeling that integrates 16000+ attributes covering 200+ countries for over 50 years from over 30 major sources and 2) a novel online ST exploratory and analysis tool providing an array of modern statistical and visualization techniques for analyzing these data temporally, spatially, and spatiotemporally under a standard analytic workflow. We report on these advances, provide an illustrative case study, and inform how others may freely access the tool.

  12. Placental gene-expression profiles of intrahepatic cholestasis of pregnancy reveal involvement of multiple molecular pathways in blood vessel formation and inflammation.

    Science.gov (United States)

    Du, QiaoLing; Pan, YouDong; Zhang, YouHua; Zhang, HaiLong; Zheng, YaJuan; Lu, Ling; Wang, JunLei; Duan, Tao; Chen, JianFeng

    2014-07-07

    Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-associated liver disease with potentially deleterious consequences for the fetus, particularly when maternal serum bile-acid concentration >40 μM. However, the etiology and pathogenesis of ICP remain elusive. To reveal the underlying molecular mechanisms for the association of maternal serum bile-acid level and fetal outcome in ICP patients, DNA microarray was applied to characterize the whole-genome expression profiles of placentas from healthy women and women diagnosed with ICP. Thirty pregnant women recruited in this study were categorized evenly into three groups: healthy group; mild ICP, with serum bile-acid concentration ranging from 10-40 μM; and severe ICP, with bile-acid concentration >40 μM. Gene Ontology analysis in combination with construction of gene-interaction and gene co-expression networks were applied to identify the core regulatory genes associated with ICP pathogenesis, which were further validated by quantitative real-time PCR and histological staining. The core regulatory genes were mainly involved in immune response, VEGF signaling pathway and G-protein-coupled receptor signaling, implying essential roles of immune response, vasculogenesis and angiogenesis in ICP pathogenesis. This implication was supported by the observed aggregated immune-cell infiltration and deficient blood vessel formation in ICP placentas. Our study provides a system-level insight into the placental gene-expression profiles of women with mild or severe ICP, and reveals multiple molecular pathways in immune response and blood vessel formation that might contribute to ICP pathogenesis.

  13. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  14. Estimating repetitive spatiotemporal patterns from resting-state brain activity data.

    Science.gov (United States)

    Takeda, Yusuke; Hiroe, Nobuo; Yamashita, Okito; Sato, Masa-Aki

    2016-06-01

    Repetitive spatiotemporal patterns in spontaneous brain activities have been widely examined in non-human studies. These studies have reported that such patterns reflect past experiences embedded in neural circuits. In human magnetoencephalography (MEG) and electroencephalography (EEG) studies, however, spatiotemporal patterns in resting-state brain activities have not been extensively examined. This is because estimating spatiotemporal patterns from resting-state MEG/EEG data is difficult due to their unknown onsets. Here, we propose a method to estimate repetitive spatiotemporal patterns from resting-state brain activity data, including MEG/EEG. Without the information of onsets, the proposed method can estimate several spatiotemporal patterns, even if they are overlapping. We verified the performance of the method by detailed simulation tests. Furthermore, we examined whether the proposed method could estimate the visual evoked magnetic fields (VEFs) without using stimulus onset information. The proposed method successfully detected the stimulus onsets and estimated the VEFs, implying the applicability of this method to real MEG data. The proposed method was applied to resting-state functional magnetic resonance imaging (fMRI) data and MEG data. The results revealed informative spatiotemporal patterns representing consecutive brain activities that dynamically change with time. Using this method, it is possible to reveal discrete events spontaneously occurring in our brains, such as memory retrieval. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Dynamic Response Genes in CD4+ T Cells Reveal a Network of Interactive Proteins that Classifies Disease Activity in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Sandra Hellberg

    2016-09-01

    Full Text Available Multiple sclerosis (MS is a chronic inflammatory disease of the CNS and has a varying disease course as well as variable response to treatment. Biomarkers may therefore aid personalized treatment. We tested whether in vitro activation of MS patient-derived CD4+ T cells could reveal potential biomarkers. The dynamic gene expression response to activation was dysregulated in patient-derived CD4+ T cells. By integrating our findings with genome-wide association studies, we constructed a highly connected MS gene module, disclosing cell activation and chemotaxis as central components. Changes in several module genes were associated with differences in protein levels, which were measurable in cerebrospinal fluid and were used to classify patients from control individuals. In addition, these measurements could predict disease activity after 2 years and distinguish low and high responders to treatment in two additional, independent cohorts. While further validation is needed in larger cohorts prior to clinical implementation, we have uncovered a set of potentially promising biomarkers.

  16. Anti-inflammatory mechanisms of IFN-γ studied in experimental autoimmune encephalomyelitis reveal neutrophils as a potential target in multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Nichole M Miller

    2015-08-01

    Full Text Available Multiple sclerosis (MS is an autoimmune disease of the central nervous system (CNS mediated by T helper (h1 and/or Th17 CD4 T cells that drive inflammatory lesion development along with demyelination and neuronal damage. Defects in immune regulatory mechanisms are thought to play a role in the pathogenesis of MS. While an early clinical trial indicated that IFN-γ administration was detrimental to MS, studies in the mouse model of MS, experimental autoimmune encephalomyelitis (EAE, indicated that IFN-γ exhibits a number of anti-inflammatory properties within the CNS. These mechanisms include inhibition of IL-17 production, induction of regulatory T cells, T cell apoptosis and regulation of chemokine production. Mice deficient in IFN-γ or its receptor were instrumental in deciphering the anti-inflammatory properties of IFN-γ in the CNS. In particular, they revealed that IFN-γ is a major regulator of neutrophil recruitment into the CNS, which by a variety of mechanisms including disruption of the blood-brain-barrier (BBB and production of reactive oxygen species are thought to contribute to the onset and progression of EAE. Neutrophils were also shown to be instrumental in EAE relapses. To date neutrophils have not been appreciated as a driver of MS, but more recently based largely on the strong EAE data this view is being reevaluated by some investigators in the field.

  17. Spatiotemporal chaos involving wave instability.

    Science.gov (United States)

    Berenstein, Igal; Carballido-Landeira, Jorge

    2017-01-01

    In this paper, we investigate pattern formation in a model of a reaction confined in a microemulsion, in a regime where both Turing and wave instability occur. In one-dimensional systems, the pattern corresponds to spatiotemporal intermittency where the behavior of the systems alternates in both time and space between stationary Turing patterns and traveling waves. In two-dimensional systems, the behavior initially may correspond to Turing patterns, which then turn into wave patterns. The resulting pattern also corresponds to a chaotic state, where the system alternates in both space and time between standing wave patterns and traveling waves, and the local dynamics may show vanishing amplitude of the variables.

  18. Noise tolerant spatiotemporal chaos computing.

    Science.gov (United States)

    Kia, Behnam; Kia, Sarvenaz; Lindner, John F; Sinha, Sudeshna; Ditto, William L

    2014-12-01

    We introduce and design a noise tolerant chaos computing system based on a coupled map lattice (CML) and the noise reduction capabilities inherent in coupled dynamical systems. The resulting spatiotemporal chaos computing system is more robust to noise than a single map chaos computing system. In this CML based approach to computing, under the coupled dynamics, the local noise from different nodes of the lattice diffuses across the lattice, and it attenuates each other's effects, resulting in a system with less noise content and a more robust chaos computing architecture.

  19. VISUALIZATION OF SPATIO-TEMPORAL RELATIONS IN MOVEMENT EVENT USING MULTI-VIEW

    Directory of Open Access Journals (Sweden)

    K. Zheng

    2017-09-01

    Full Text Available Spatio-temporal relations among movement events extracted from temporally varying trajectory data can provide useful information about the evolution of individual or collective movers, as well as their interactions with their spatial and temporal contexts. However, the pure statistical tools commonly used by analysts pose many difficulties, due to the large number of attributes embedded in multi-scale and multi-semantic trajectory data. The need for models that operate at multiple scales to search for relations at different locations within time and space, as well as intuitively interpret what these relations mean, also presents challenges. Since analysts do not know where or when these relevant spatio-temporal relations might emerge, these models must compute statistical summaries of multiple attributes at different granularities. In this paper, we propose a multi-view approach to visualize the spatio-temporal relations among movement events. We describe a method for visualizing movement events and spatio-temporal relations that uses multiple displays. A visual interface is presented, and the user can interactively select or filter spatial and temporal extents to guide the knowledge discovery process. We also demonstrate how this approach can help analysts to derive and explain the spatio-temporal relations of movement events from taxi trajectory data.

  20. Visualization of Spatio-Temporal Relations in Movement Event Using Multi-View

    Science.gov (United States)

    Zheng, K.; Gu, D.; Fang, F.; Wang, Y.; Liu, H.; Zhao, W.; Zhang, M.; Li, Q.

    2017-09-01

    Spatio-temporal relations among movement events extracted from temporally varying trajectory data can provide useful information about the evolution of individual or collective movers, as well as their interactions with their spatial and temporal contexts. However, the pure statistical tools commonly used by analysts pose many difficulties, due to the large number of attributes embedded in multi-scale and multi-semantic trajectory data. The need for models that operate at multiple scales to search for relations at different locations within time and space, as well as intuitively interpret what these relations mean, also presents challenges. Since analysts do not know where or when these relevant spatio-temporal relations might emerge, these models must compute statistical summaries of multiple attributes at different granularities. In this paper, we propose a multi-view approach to visualize the spatio-temporal relations among movement events. We describe a method for visualizing movement events and spatio-temporal relations that uses multiple displays. A visual interface is presented, and the user can interactively select or filter spatial and temporal extents to guide the knowledge discovery process. We also demonstrate how this approach can help analysts to derive and explain the spatio-temporal relations of movement events from taxi trajectory data.

  1. Nonlinear Spatio-Temporal Dynamics and Chaos in Semiconductors

    Science.gov (United States)

    Schöll, Eckehard

    2005-08-01

    Nonlinear transport phenomena are an increasingly important aspect of modern semiconductor research. This volume deals with complex nonlinear dynamics, pattern formation, and chaotic behavior in such systems. It bridges the gap between two well-established fields: the theory of dynamic systems and nonlinear charge transport in semiconductors. This unified approach helps reveal important electronic transport instabilities. The initial chapters lay a general framework for the theoretical description of nonlinear self-organized spatio-temporal patterns, such as current filaments, field domains, fronts, and analysis of their stability. Later chapters consider important model systems in detail: impact ionization induced impurity breakdown, Hall instabilities, superlattices, and low-dimensional structures. State-of-the-art results include chaos control, spatio-temporal chaos, multistability, pattern selection, activator-inhibitor kinetics, and global coupling, linking fundamental issues to electronic device applications. This book will be of great value to semiconductor physicists and nonlinear scientists alike.

  2. High Resolution Spatiotemporal Climate Reconstruction and Variability in East Asia during Little Ice Age

    Science.gov (United States)

    Lin, K. H. E.; Wang, P. K.; Lee, S. Y.; Liao, Y. C.; Fan, I. C.; Liao, H. M.

    2017-12-01

    The Little ice Age (LIA) is one of the most prominent epochs in paleoclimate reconstruction of the Common Era. While the signals of LIA were generally discovered across hemispheres, wide arrays of regional variability were found, and the reconstructed anomalies were sometimes inconsistent across studies by using various proxy data or historical records. This inconsistency is mainly attributed to limited data coverage at fine resolution that can assist high-resolution climate reconstruction in the continuous spatiotemporal trends. Qing dynasty (1644-1911 CE) of China existed in the coldest period of LIA. Owing to a long-standing tradition that acquired local officials to record odds and social or meteorological events, thousands of local chronicles were left. Zhang eds. (2004) took two decades to compile all these meteorological records in a compendium, for which we then digitized and coded all records into our REACHS database system for reconstructing climate. There were in total 1,435 points (sites) in our database for over 80,000 events in the period of time. After implementing two-rounds coding check for data quality control (accuracy rate 87.2%), multiple indexes were retrieved for reconstructing annually and seasonally resolved temperature and precipitation series for North, Central, and South China. The reconstruction methods include frequency count and grading, with usage of multiple regression models to test sensitivity and to calculate correlations among several reconstructed series. Validation was also conducted through comparison with instrumental data and with other reconstructed series in previous studies. Major research results reveal interannual (3-5 years), decadal (8-12 years), and interdecadal (≈30 years) variabilities with strong regional expressions across East China. Cooling effect was not homogenously distributed in space and time. Flood and drought conditions frequently repeated but the spatiotemporal pattern was variant, indicating likely

  3. SPATIOTEMPORAL CONTRAST SENSITIVITY OF EARLY VISION

    NARCIS (Netherlands)

    Hateren, J.H. van

    Based on the spatial and temporal statistics of natural images, a theory is developed that specifies spatiotemporal filters that maximize the flow of information through noisy channels of limited dynamic range. Sensitivities resulting from these spatiotemporal filters are very similar to the human

  4. Spatiotemporal Thinking in the Geosciences

    Science.gov (United States)

    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. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

    Directory of Open Access Journals (Sweden)

    Rajani Rai

    2015-11-01

    Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

  6. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).

    Science.gov (United States)

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

    2014-06-04

    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III in India during 1956–2007

    Directory of Open Access Journals (Sweden)

    Bhattacharya D

    2009-01-01

    Full Text Available Abstract Background Dengue virus type 1 (DENV-1 have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India between 2001–2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis. Results The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I → T, A → T and L → S at amino acid positions 59,114 and 155 respectively in the Indian DENV-1 sequences, sequenced in this study. Except two 1997–98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1–4 showing proximity to isolates from diverse geographic locations. Conclusion The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.

  8. Intact protein analysis of ubiquitin in cerebrospinal fluid by multiple reaction monitoring reveals differences in Alzheimer's disease and frontotemporal lobar degeneration.

    Science.gov (United States)

    Oeckl, Patrick; Steinacker, Petra; von Arnim, Christine A F; Straub, Sarah; Nagl, Magdalena; Feneberg, Emily; Weishaupt, Jochen H; Ludolph, Albert C; Otto, Markus

    2014-11-07

    The impairment of the ubiquitin-proteasome system (UPS) is thought to be an early event in neurodegeneration, and monitoring UPS alterations might serve as a disease biomarker. Our aim was to establish an alternate method to antibody-based assays for the selective measurement of free monoubiquitin in cerebrospinal fluid (CSF). Free monoubiquitin was measured with liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MS/MS) in CSF of patients with Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), behavioral variant of frontotemporal dementia (bvFTD), Creutzfeldt-Jakob disease (CJD), Parkinson's disease (PD), primary progressive aphasia (PPA), and progressive supranuclear palsy (PSP). The LC-MS/MS method showed excellent intra- and interassay precision (4.4-7.4% and 4.9-10.3%) and accuracy (100-107% and 100-106%). CSF ubiquitin concentration was increased compared with that of controls (33.0 ± 9.7 ng/mL) in AD (47.5 ± 13.1 ng/mL, p < 0.05) and CJD patients (171.5 ± 103.5 ng/mL, p < 0.001) but not in other neurodegenerative diseases. Receiver operating characteristic curve (ROC) analysis of AD vs control patients revealed an area under the curve (AUC) of 0.832, and the specificity and sensitivity were 75 and 75%, respectively. ROC analysis of AD and FTLD patients yielded an AUC of 0.776, and the specificity and sensitivity were 53 and 100%, respectively. In conclusion, our LC-MS/MS method may facilitate ubiquitin determination to a broader community and might help to discriminate AD, CJD, and FTLD patients.

  9. Spatiotemporal and plantar pressure patterns of 1000 healthy individuals aged 3-101 years.

    Science.gov (United States)

    McKay, Marnee J; Baldwin, Jennifer N; Ferreira, Paulo; Simic, Milena; Vanicek, Natalie; Wojciechowski, Elizabeth; Mudge, Anita; Burns, Joshua

    2017-10-01

    The purpose of this study was to establish normative reference values for spatiotemporal and plantar pressure parameters, and to investigate the influence of demographic, anthropometric and physical characteristics. In 1000 healthy males and females aged 3-101 years, spatiotemporal and plantar pressure data were collected barefoot with the Zeno™ walkway and Emed ® platform. Correlograms were developed to visualise the relationships between widely reported spatiotemporal and pressure variables with demographic (age, gender), anthropometric (height, mass, waist circumference) and physical characteristics (ankle strength, ankle range of motion, vibration perception) in children aged 3-9 years, adolescents aged 10-19 years, adults aged 20-59 years and older adults aged over 60 years. A comprehensive catalogue of 31 spatiotemporal and pressure variables were generated from 1000 healthy individuals. The key findings were that gait velocity was stable during adolescence and adulthood, while children and older adults walked at a comparable slower speed. Peak pressures increased during childhood to older adulthood. Children demonstrated highest peak pressures beneath the rearfoot whilst adolescents, adults and older adults demonstrated highest pressures at the forefoot. Main factors influencing spatiotemporal and pressure parameters were: increased age, height, body mass and waist circumference, as well as ankle dorsiflexion and plantarflexion strength. This study has established whole of life normative reference values of widely used spatiotemporal and plantar pressure parameters, and revealed changes to be expected across the lifespan. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Structured spatio-temporal shot-noise Cox point process models, with a view to modelling forest fires

    DEFF Research Database (Denmark)

    Møller, Jesper; Diaz-Avalos, Carlos

    Spatio-temporal Cox point process models with a multiplicative structure for the driving random intensity, incorporating covariate information into temporal and spatial components, and with a residual term modelled by a shot-noise process, are considered. Such models are flexible and tractable fo...... dataset consisting of 2796 days and 5834 spatial locations of fires. The model is compared with a spatio-temporal log-Gaussian Cox point process model, and likelihood-based methods are discussed to some extent....

  11. AN ADAPTIVE ORGANIZATION METHOD OF GEOVIDEO DATA FOR SPATIO-TEMPORAL ASSOCIATION ANALYSIS

    Directory of Open Access Journals (Sweden)

    C. Wu

    2015-07-01

    Full Text Available Public security incidents have been increasingly challenging to address with their new features, including large-scale mobility, multi-stage dynamic evolution, spatio-temporal concurrency and uncertainty in the complex urban environment, which require spatio-temporal association analysis among multiple regional video data for global cognition. However, the existing video data organizational methods that view video as a property of the spatial object or position in space dissever the spatio-temporal relationship of scattered video shots captured from multiple video channels, limit the query functions on interactive retrieval between a camera and its video clips and hinder the comprehensive management of event-related scattered video shots. GeoVideo, which maps video frames onto a geographic space, is a new approach to represent the geographic world, promote security monitoring in a spatial perspective and provide a highly feasible solution to this problem. This paper analyzes the large-scale personnel mobility in public safety events and proposes a multi-level, event-related organization method with massive GeoVideo data by spatio-temporal trajectory. This paper designs a unified object identify(ID structure to implicitly store the spatio-temporal relationship of scattered video clips and support the distributed storage management of massive cases. Finally, the validity and feasibility of this method are demonstrated through suspect tracking experiments.

  12. PARALLEL SPATIOTEMPORAL SPECTRAL CLUSTERING WITH MASSIVE TRAJECTORY DATA

    Directory of Open Access Journals (Sweden)

    Y. Z. Gu

    2017-09-01

    Full Text Available Massive trajectory data contains wealth useful information and knowledge. Spectral clustering, which has been shown to be effective in finding clusters, becomes an important clustering approaches in the trajectory data mining. However, the traditional spectral clustering lacks the temporal expansion on the algorithm and limited in its applicability to large-scale problems due to its high computational complexity. This paper presents a parallel spatiotemporal spectral clustering based on multiple acceleration solutions to make the algorithm more effective and efficient, the performance is proved due to the experiment carried out on the massive taxi trajectory dataset in Wuhan city, China.

  13. Multivariate spatiotemporal visualizations for mobile devices in Flyover Country

    Science.gov (United States)

    Loeffler, S.; Thorn, R.; Myrbo, A.; Roth, R.; Goring, S. J.; Williams, J.

    2017-12-01

    Visualizing and interacting with complex multivariate and spatiotemporal datasets on mobile devices is challenging due to their smaller screens, reduced processing power, and limited data connectivity. Pollen data require visualizing pollen assemblages spatially, temporally, and across multiple taxa to understand plant community dynamics through time. Drawing from cartography, information visualization, and paleoecology, we have created new mobile-first visualization techniques that represent multiple taxa across many sites and enable user interaction. Using pollen datasets from the Neotoma Paleoecology Database as a case study, the visualization techniques allow ecological patterns and trends to be quickly understood on a mobile device compared to traditional pollen diagrams and maps. This flexible visualization system can be used for datasets beyond pollen, with the only requirements being point-based localities and multiple variables changing through time or depth.

  14. Mortality in Danish Swine herds: Spatio-temporal clusters and risk factors

    DEFF Research Database (Denmark)

    Lopes Antunes, Ana Carolina; Ersbøll, Annette Kjær; Bihrmann, Kristine

    2017-01-01

    -temporal analysis included data description for spatial, temporal, and spatio-temporal cluster analysis for three age groups: weaners (up to 30 kg), sows and finishers. Logistic regression models were used to assess the potential factors associated with finisher and weaner herds being included within multiple...

  15. Spatiotemporal Signal Analysis via the Phase Velocity Transform

    International Nuclear Information System (INIS)

    Mattor, Nathan

    2000-01-01

    The phase velocity transform (PVT) is an integral transform that divides a function of space and time into components that propagate at uniform phase velocities without distortion. This paper examines the PVT as a method to analyze spatiotemporal fluctuation data. The transform is extended to systems with discretely sampled data on a periodic domain, and applied to data from eight azimuthally distributed probes on the Sustained Spheromak Physics Experiment (SSPX). This reveals features not shown by Fourier analysis, particularly regarding nonsinusoidal mode structure. (c) 2000 The American Physical Society

  16. Spatio-temporal Hotelling observer for signal detection from image sequences.

    Science.gov (United States)

    Caucci, Luca; Barrett, Harrison H; Rodriguez, Jeffrey J

    2009-06-22

    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.

  17. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers

    DEFF Research Database (Denmark)

    Gaasenbeek, Michelle; Howarth, Kimberley; Rowan, Andrew J

    2006-01-01

    Cancers with chromosomal instability (CIN) are held to be aneuploid/polyploid with multiple large-scale gains/deletions, but the processes underlying CIN are unclear and different types of CIN might exist. We investigated colorectal cancer cell lines using array-comparative genomic hybridization...

  18. Metabolomic analysis reveals key metabolites related to the rapid adaptation of Saccharomyce cerevisiae to multiple inhibitors of furfural, acetic acid, and phenol.

    Science.gov (United States)

    Wang, Xin; Li, Bing-Zhi; Ding, Ming-Zhu; Zhang, Wei-Wen; Yuan, Ying-Jin

    2013-03-01

    During hydrolysis of lignocellulosic biomass, a broad range of inhibitors are generated, which interfere with yeast growth and bioethanol production. In order to improve the strain tolerance to multiple inhibitors--acetic acid, furfural, and phenol (three representative lignocellulose-derived inhibitors) and uncover the underlying tolerant mechanism, an adaptation experiment was performed in which the industrial Saccharomyces cerevisiae was cultivated repeatedly in a medium containing multiple inhibitors. The adaptation occurred quickly, accompanied with distinct increase in growth rate, glucose utilization rate, furfural metabolism rate, and ethanol yield, only after the first transfer. A similar rapid adaptation was also observed for the lab strains of BY4742 and BY4743. The metabolomic analysis was employed to investigate the responses of the industrial S. cereviaise to three inhibitors during the adaptation. The results showed that higher levels of 2-furoic acid, 2, 3-butanediol, intermediates in glycolytic pathway, and amino acids derived from glycolysis, were discovered in the adapted strains, suggesting that enhanced metabolic activity in these pathways may relate to resistance against inhibitors. Additionally, through single-gene knockouts, several genes related to alanine metabolism, GABA shunt, and glycerol metabolism were verified to be crucial for the resistance to multiple inhibitors. This study provides new insights into the tolerance mechanism against multiple inhibitors, and guides for the improvement of tolerant ethanologenic yeast strains for lignocellulose-bioethanol fermentation.

  19. Elimination of spiral waves and spatiotemporal chaos by the pulse with a specific spatiotemporal configuration

    International Nuclear Information System (INIS)

    Yuan Guoyong; Yang Shiping; Wang Guangrui; Chen Shigang

    2008-01-01

    Spiral waves and spatiotemporal chaos are sometimes harmful and should be controlled. In this paper spiral waves and spatiotemporal chaos are successfully eliminated by the pulse with a very specific spatiotemporal configuration. The excited position D of spiral waves or spatiotemporal chaos is first recorded at an arbitrary time (t 0 ). When the system at the domain D enters a recovering state, the external pulse is injected into the domain. If the intensity and the working time of the pulse are appropriate, spiral waves and spatiotemporal chaos can finally be eliminated because counter-directional waves can be generated by the pulse. There are two advantages in the method. One is that the tip can be quickly eliminated together with the body of spiral wave, and the other is that the injected pulse may be weak and the duration can be very short so that the original system is nearly not affected, which is important for practical applications

  20. Spatiotemporal mapping of ground water pollution in a Greek lignite basin, using geostatistics

    International Nuclear Information System (INIS)

    Modis, K.

    2010-01-01

    An issue of significant interest in the mining industry in Greece is the occurrence of chemical pollutants in ground water. Ammonium, nitrites and nitrates concentrations have been monitored through an extensive sampling network in the Ptolemais lignite opencast mining area in Greece. Due to intensive mining efforts in the area, the surface topology is continuously altered, affecting the life span of the water boreholes and resulting in messy spatiotemporal distribution of data. This paper discussed the spatiotemporal mapping of ground water pollution in the Ptolemais lignite basin, using geostatistics. More specifically, the spatiotemporal distribution of ground water contamination was examined by the application of the bayesian maximum entropy theory which allows merging spatial and temporal estimations in a single model. The paper provided a description of the site and discussed the materials and methods, including samples and statistics; variography; and spatiotemporal mapping. It was concluded that in the case of the Ptolemais mining area, results revealed an underlying average yearly variation pattern of pollutant concentrations. Inspection of the produced spatiotemporal maps demonstrated a continuous increase in the risk of ammonium contamination, while risk for the other two pollutants appeared in hot spots. 18 refs., 1 tab., 7 figs.

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

    Directory of Open Access Journals (Sweden)

    Ram K Raghavan

    Full Text Available 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.

  2. Spatiotemporal mapping of ground water pollution in a Greek lignite basin, using geostatistics

    Energy Technology Data Exchange (ETDEWEB)

    Modis, K. [National Technical Univ. of Athens, Athens (Greece)

    2010-07-01

    An issue of significant interest in the mining industry in Greece is the occurrence of chemical pollutants in ground water. Ammonium, nitrites and nitrates concentrations have been monitored through an extensive sampling network in the Ptolemais lignite opencast mining area in Greece. Due to intensive mining efforts in the area, the surface topology is continuously altered, affecting the life span of the water boreholes and resulting in messy spatiotemporal distribution of data. This paper discussed the spatiotemporal mapping of ground water pollution in the Ptolemais lignite basin, using geostatistics. More specifically, the spatiotemporal distribution of ground water contamination was examined by the application of the bayesian maximum entropy theory which allows merging spatial and temporal estimations in a single model. The paper provided a description of the site and discussed the materials and methods, including samples and statistics; variography; and spatiotemporal mapping. It was concluded that in the case of the Ptolemais mining area, results revealed an underlying average yearly variation pattern of pollutant concentrations. Inspection of the produced spatiotemporal maps demonstrated a continuous increase in the risk of ammonium contamination, while risk for the other two pollutants appeared in hot spots. 18 refs., 1 tab., 7 figs.

  3. Dynamic decomposition of spatiotemporal neural signals.

    Directory of Open Access Journals (Sweden)

    Luca Ambrogioni

    2017-05-01

    Full Text Available Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals.

  4. Optimization of Spatiotemporal Apertures in Channel Sounding

    DEFF Research Database (Denmark)

    Pedersen, Troels; Pedersen, Claus; Yin, Xuefeng

    2008-01-01

    a spatiotemporal model which can describe parallel as well as switched sounding systems. The proposed model is applicable for arbitrary layouts of the spatial arrays. To simplify the derivations we investigate the special case of linear spatial arrays. However, the results obtained for linear arrays can......In this paper we investigate the impact of the spatio-temporal aperture of a channel sounding system equipped with antenna arrays at the transmitter and receiver on the accuracy of joint estimation of Doppler frequency and bi-direction. The contribution of this work is three-fold. Firstly, we state...... be generalized to arbitrary arrays. Secondly, we give the necessary and sufficient conditions for a spatio-temporal array to yield the minimum Cramér-Rao lower bound in the single-path case and Bayesian Cramér-Rao Lower Bound in the multipath case. The obtained conditions amount to an orthogonality condition...

  5. Spatio-Temporal Data Exchange Standards

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Schmidt, Albrecht

    2003-01-01

    We believe that research that concerns aspects of spatio-temporal data management may benefit from taking into account the various standards for spatio-temporal data formats. For example, this may contribute to rendering prototype software “open” and more readily useful. This paper thus identifies...... and briefly surveys standardization in relation to primarily the exchange and integration of spatio-temporal data. An overview of several data exchange languages is offered, along with reviews their potential for facilitating the collection of test data and the leveraging of prototypes. The standards, most...... of which are XML-based, lend themselves to the integration of prototypes into middleware architectures, e.g., as Web services....

  6. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Science.gov (United States)

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  7. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  8. Analysis of Spatiotemporal Statistical Properties of Rainfall in the Phoenix Metropolitan Area

    Science.gov (United States)

    Mascaro, G.

    2016-12-01

    The analysis of the rainfall statistical properties at multiple spatiotemporal scales is a necessary preliminary step to support modeling of urban hydrology, including flood prediction and simulation of impacts of land use changes. In this contribution, the rainfall statistical properties are analyzed in the Phoenix Metropolitan area and its surroundings ( 29600 km2) in Arizona using observations from 310 gauges of the Flood Control District of the Maricopa County network. Different techniques are applied to investigate the rainfall properties at temporal scales from 1 min to years and to quantify the associated spatial variability. Results reveal the following. The rainfall regime is characterized by high interannual variability, which is partially explained by teleconnections with El Niño Southern Oscillation, and marked seasonality, with two maxima in the monsoon season from July to September and in winter from November to March. Elevation has a significant control on seasonal rainfall accumulation, strength of thermal convective activity during the monsoon, and peak occurrence of the rainfall diurnal cycle present in summer. The spatial correlation of wintertime rainfall is high even at short aggregation times (cells).

  9. Integrating GIS and ABM to Explore Spatiotemporal Dynamics

    Science.gov (United States)

    Sun, M.; Jiang, Y.; Yang, C.

    2013-12-01

    Agent-based modeling as a methodology for the bottom-up exploration with the account of adaptive behavior and heterogeneity of system components can help discover the development and pattern of the complex social and environmental system. However, ABM is a computationally intensive process especially when the number of system components becomes large and the agent-agent/agent-environmental interaction is modeled very complex. Most of traditional ABM frameworks developed based on CPU do not have a satisfying computing capacity. To address the problem and as the emergence of advanced techniques, GPU computing with CUDA can provide powerful parallel structure to enable the complex simulation of spatiotemporal dynamics. In this study, we first develop a GPU-based ABM system. Secondly, in order to visualize the dynamics generated from the movement of agent and the change of agent/environmental attributes during the simulation, we integrate GIS into the ABM system. Advanced geovisualization technologies can be utilized for representing the spatiotemporal change events, such as proper 2D/3D maps with state-of-the-art symbols, space-time cube and multiple layers each of which presents pattern in one time-stamp, etc. Thirdly, visual analytics which include interactive tools (e.g. grouping, filtering, linking, etc.) is included in our ABM-GIS system to help users conduct real-time data exploration during the progress of simulation. Analysis like flow analysis and spatial cluster analysis can be integrated according to the geographical problem we want to explore.

  10. Collaborative simulation method with spatiotemporal synchronization process control

    Science.gov (United States)

    Zou, Yisheng; Ding, Guofu; Zhang, Weihua; Zhang, Jian; Qin, Shengfeng; Tan, John Kian

    2016-10-01

    When designing a complex mechatronics system, such as high speed trains, it is relatively difficult to effectively simulate the entire system's dynamic behaviors because it involves multi-disciplinary subsystems. Currently,a most practical approach for multi-disciplinary simulation is interface based coupling simulation method, but it faces a twofold challenge: spatial and time unsynchronizations among multi-directional coupling simulation of subsystems. A new collaborative simulation method with spatiotemporal synchronization process control is proposed for coupling simulating a given complex mechatronics system across multiple subsystems on different platforms. The method consists of 1) a coupler-based coupling mechanisms to define the interfacing and interaction mechanisms among subsystems, and 2) a simulation process control algorithm to realize the coupling simulation in a spatiotemporal synchronized manner. The test results from a case study show that the proposed method 1) can certainly be used to simulate the sub-systems interactions under different simulation conditions in an engineering system, and 2) effectively supports multi-directional coupling simulation among multi-disciplinary subsystems. This method has been successfully applied in China high speed train design and development processes, demonstrating that it can be applied in a wide range of engineering systems design and simulation with improved efficiency and effectiveness.

  11. CRISPR/Cas9 Mutagenesis of UL21 in Multiple Strains of Herpes Simplex Virus Reveals Differential Requirements for pUL21 in Viral Replication

    Directory of Open Access Journals (Sweden)

    Renée L. Finnen

    2018-05-01

    Full Text Available Studies from multiple laboratories using different strains or species of herpes simplex virus (HSV with deletions in UL21 have yielded conflicting results regarding the necessity of pUL21 in HSV infection. To resolve this discrepancy, we utilized CRISPR/Cas9 mutagenesis to isolate pUL21 deficient viruses in multiple HSV backgrounds, and performed a side-by-side comparison of the cell-to-cell spread and replication phenotypes of these viruses. These analyses confirmed previous studies implicating the involvement of pUL21 in cell-to-cell spread of HSV. Cell-to-cell spread of HSV-2 was more greatly affected by the lack of pUL21 than HSV-1, and strain-specific differences in the requirement for pUL21 in cell-to-cell spread were also noted. HSV-2 strain 186 lacking pUL21 was particularly crippled in both cell-to-cell spread and viral replication in non-complementing cells, in comparison to other HSV strains lacking pUL21, suggesting that the strict requirement for pUL21 by strain 186 may not be representative of the HSV-2 species as a whole. This work highlights CRISPR/Cas9 technology as a useful tool for rapidly constructing deletion mutants of alphaherpesviruses, regardless of background strain, and should find great utility whenever strain-specific differences need to be investigated.

  12. Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides.

    Science.gov (United States)

    Egan, Jan B; Shi, Chang-Xin; Tembe, Waibhav; Christoforides, Alexis; Kurdoglu, Ahmet; Sinari, Shripad; Middha, Sumit; Asmann, Yan; Schmidt, Jessica; Braggio, Esteban; Keats, Jonathan J; Fonseca, Rafael; Bergsagel, P Leif; Craig, David W; Carpten, John D; Stewart, A Keith

    2012-08-02

    The longitudinal evolution of a myeloma genome from diagnosis to plasma cell leukemia has not previously been reported. We used whole-genome sequencing (WGS) on 4 purified tumor samples and patient germline DNA drawn over a 5-year period in a t(4;14) multiple myeloma patient. Tumor samples were acquired at diagnosis, first relapse, second relapse, and end-stage secondary plasma cell leukemia (sPCL). In addition to the t(4;14), all tumor time points also shared 10 common single-nucleotide variants (SNVs) on WGS comprising shared initiating events. Interestingly, we observed genomic sequence variants that waxed and waned with time in progressive tumors, suggesting the presence of multiple independent, yet related, clones at diagnosis that rose and fell in dominance. Five newly acquired SNVs, including truncating mutations of RB1 and ZKSCAN3, were observed only in the final sPCL sample suggesting leukemic transformation events. This longitudinal WGS characterization of the natural history of a high-risk myeloma patient demonstrated tumor heterogeneity at diagnosis with shifting dominance of tumor clones over time and has also identified potential mutations contributing to myelomagenesis as well as transformation from myeloma to overt extramedullary disease such as sPCL.

  13. Proteomic Profiling of Cranial (Superior) Cervical Ganglia Reveals Beta-Amyloid and Ubiquitin Proteasome System Perturbations in an Equine Multiple System Neuropathy.

    Science.gov (United States)

    McGorum, Bruce C; Pirie, R Scott; Eaton, Samantha L; Keen, John A; Cumyn, Elizabeth M; Arnott, Danielle M; Chen, Wenzhang; Lamont, Douglas J; Graham, Laura C; Llavero Hurtado, Maica; Pemberton, Alan; Wishart, Thomas M

    2015-11-01

    Equine grass sickness (EGS) is an acute, predominantly fatal, multiple system neuropathy of grazing horses with reported incidence rates of ∼2%. An apparently identical disease occurs in multiple species, including but not limited to cats, dogs, and rabbits. Although the precise etiology remains unclear, ultrastructural findings have suggested that the primary lesion lies in the glycoprotein biosynthetic pathway of specific neuronal populations. The goal of this study was therefore to identify the molecular processes underpinning neurodegeneration in EGS. Here, we use a bottom-up approach beginning with the application of modern proteomic tools to the analysis of cranial (superior) cervical ganglion (CCG, a consistently affected tissue) from EGS-affected patients and appropriate control cases postmortem. In what appears to be the proteomic application of modern proteomic tools to equine neuronal tissues and/or to an inherent neurodegenerative disease of large animals (not a model of human disease), we identified 2,311 proteins in CCG extracts, with 320 proteins increased and 186 decreased by greater than 20% relative to controls. Further examination of selected proteomic candidates by quantitative fluorescent Western blotting (QFWB) and subcellular expression profiling by immunohistochemistry highlighted a previously unreported dysregulation in proteins commonly associated with protein misfolding/aggregation responses seen in a myriad of human neurodegenerative conditions, including but not limited to amyloid precursor protein (APP), microtubule associated protein (Tau), and multiple components of the ubiquitin proteasome system (UPS). Differentially expressed proteins eligible for in silico pathway analysis clustered predominantly into the following biofunctions: (1) diseases and disorders, including; neurological disease and skeletal and muscular disorders and (2) molecular and cellular functions, including cellular assembly and organization, cell

  14. Studies of HVC Plasticity in Adult Canaries Reveal Social Effects and Sex Differences as Well as Limitations of Multiple Markers Available to Assess Adult Neurogenesis.

    Science.gov (United States)

    Shevchouk, Olesya T; Ball, Gregory F; Cornil, Charlotte A; Balthazart, Jacques

    2017-01-01

    In songbirds, neurogenesis in the song control nucleus HVC is sensitive to the hormonal and social environment but the dynamics of this process is difficult to assess with a single exogenous marker of new neurons. We simultaneously used three independent markers to investigate HVC neurogenesis in male and female canaries. Males were castrated, implanted with testosterone and housed either alone (M), with a female (M-F) or with another male (M-M) while females were implanted with 17β-estradiol and housed with a male (F-M). All subjects received injections of the two thymidine analogues, BrdU and of EdU, respectively 21 and 10 days before brain collection. Cells containing BrdU or EdU or expressing doublecortin (DCX), which labels newborn neurons, were quantified. Social context and sex differentially affected total BrdU+, EdU+, BrdU+EdU- and DCX+ populations. M-M males had a higher density of BrdU+ cells in the ventricular zone adjacent to HVC and of EdU+ in HVC than M-F males. M birds had a higher ratio of BrdU+EdU- to EdU+ cells than M-F subjects suggesting higher survival of newer neurons in the former group. Total number of HVC DCX+ cells was lower in M-F than in M-M males. Sex differences were also dependent of the type of marker used. Several technical limitations associated with the use of these multiple markers were also identified. These results indicate that proliferation, recruitment and survival of new neurons can be independently affected by environmental conditions and effects can only be fully discerned through the use of multiple neurogenesis markers.

  15. A Multiple Decrement Life Table Reveals That Host Plant Resistance and Parasitism Are Major Causes of Mortality for the Wheat Stem Sawfly.

    Science.gov (United States)

    Buteler, Micaela; Peterson, Robert K D; Hofland, Megan L; Weaver, David K

    2015-12-01

    This study investigated the dynamics of parasitism, host plant resistance, pathogens, and predation on the demography of wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), developing in susceptible (hollow stem) and resistant (solid stem) wheat hosts. This study is also the first to investigate the prevalence and impact of cannibalism on wheat stem sawfly mortality. Wheat stem sawflies were sampled in two commercial wheat fields over 4 yr from the egg stage through adult emergence, and multiple decrement life tables were constructed and analyzed. Cannibalism, host plant resistance, or unknown factors were the most prevalent factors causing egg mortality. Summer mortality of prediapause larvae ranged from 28 to 84%, mainly due to parasitism by Bracon cephi (Gahan) and Bracon lissogaster Muesebeck, cannibalism, and host plant resistance. Winter mortality ranged from 6 to 54% of the overwintering larvae, mainly due to unknown factors or pathogens. Cannibalism is a major cause of irreplaceable mortality because it is absolute, with only a single survivor in every multiple infested stem. Subsequent to obligate cannibalism, mortality of feeding larvae due to host plant resistance was lower in hollow stem wheat than in solid stem wheat. Mortality from host plant resistance was largely irreplaceable. Irreplaceable mortality due to parasitoids was greater in hollow stem wheat than in solid stem wheat. Host plant resistance due to stem solidness and parasitism in hollow stems cause substantial mortality in populations of actively feeding larvae responsible for all crop losses. Therefore, enhancing these mortality factors is vital to effective integrated pest management of wheat stem sawfly. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Studies of HVC Plasticity in Adult Canaries Reveal Social Effects and Sex Differences as Well as Limitations of Multiple Markers Available to Assess Adult Neurogenesis.

    Directory of Open Access Journals (Sweden)

    Olesya T Shevchouk

    Full Text Available In songbirds, neurogenesis in the song control nucleus HVC is sensitive to the hormonal and social environment but the dynamics of this process is difficult to assess with a single exogenous marker of new neurons. We simultaneously used three independent markers to investigate HVC neurogenesis in male and female canaries. Males were castrated, implanted with testosterone and housed either alone (M, with a female (M-F or with another male (M-M while females were implanted with 17β-estradiol and housed with a male (F-M. All subjects received injections of the two thymidine analogues, BrdU and of EdU, respectively 21 and 10 days before brain collection. Cells containing BrdU or EdU or expressing doublecortin (DCX, which labels newborn neurons, were quantified. Social context and sex differentially affected total BrdU+, EdU+, BrdU+EdU- and DCX+ populations. M-M males had a higher density of BrdU+ cells in the ventricular zone adjacent to HVC and of EdU+ in HVC than M-F males. M birds had a higher ratio of BrdU+EdU- to EdU+ cells than M-F subjects suggesting higher survival of newer neurons in the former group. Total number of HVC DCX+ cells was lower in M-F than in M-M males. Sex differences were also dependent of the type of marker used. Several technical limitations associated with the use of these multiple markers were also identified. These results indicate that proliferation, recruitment and survival of new neurons can be independently affected by environmental conditions and effects can only be fully discerned through the use of multiple neurogenesis markers.

  17. DNA-based identifications reveal multiple introductions of the vegetable leafminer Liriomyza sativae (Diptera: Agromyzidae) into the Torres Strait Islands and Papua New Guinea.

    Science.gov (United States)

    Blacket, M J; Rice, A D; Semeraro, L; Malipatil, M B

    2015-10-01

    Leafmining flies (Diptera: Agromyzidae) can be serious economic pests of horticultural crops. Some genera such as Liriomyza are particularly problematic with numerous species, some of which are highly polyphagous (wide host range), which can only be confidently identified morphologically from adult males. In our study, DNA barcoding was employed to establish new locality records of the vegetable leafminer fly, Liriomyza sativae, from the islands of Torres Strait (Queensland, Australia) and the central highlands of Papua New Guinea (PNG). These records represent significant range extensions of this highly invasive plant pest. Specimens of immature leafminers (from leaf mines) were collected over a 5-year period during routine plant health surveys in ethanol or on FTA® filter paper cards, both methods proved effective at preserving and transporting insect DNA under tropical conditions, with FTA cards possessing some additional logistical benefits. Specimens were identified through sequencing two sections of the cytochrome oxidase I gene and the utility of each was assessed for the identification of species and intra-specific genetic lineages. Our study indicates that multiple haplotypes of L. sativae occur in PNG, while a different haplotype is present in the Torres Strait, with genetic regionalization between these areas apart from a single possible instance - one haplotype 'S.7' appears to be common between these two regions - interestingly this has also been the most common haplotype detected in previous studies of invasive L. sativae populations. The DNA barcoding methods employed here not only identified multiple introductions of L. sativae, but also appear generally applicable to the identification of other agromyzid leafminers (Phytomyzinae and Agromyzinae) and should decrease the likelihood of potentially co-amplifying internal hymenopteran parasitoids. Currently, L. sativae is still not recorded from the Australian mainland; however, further sampling of

  18. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    Science.gov (United States)

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  19. Mining Spatiotemporal Patterns of the Elder's Daily Movement

    Science.gov (United States)

    Chen, C. R.; Chen, C. F.; Liu, M. E.; Tsai, S. J.; Son, N. T.; Kinh, L. V.

    2016-06-01

    With rapid developments in wearable device technology, a vast amount of spatiotemporal data, such as people's movement and physical activities, are generated. Information derived from the data reveals important knowledge that can contribute a long-term care and psychological assessment of the elders' living condition especially in long-term care institutions. This study aims to develop a method to investigate the spatial-temporal movement patterns of the elders with their outdoor trajectory information. To achieve the goal, GPS based location data of the elderly subjects from long-term care institutions are collected and analysed with geographic information system (GIS). A GIS statistical model is developed to mine the elderly subjects' spatiotemporal patterns with the location data and represent their daily movement pattern at particular time. The proposed method first finds the meaningful trajectory and extracts the frequent patterns from the time-stamp location data. Then, a density-based clustering method is used to identify the major moving range and the gather/stay hotspot in both spatial and temporal dimensions. The preliminary results indicate that the major moving area of the elderly people encompasses their dorm and has a short moving distance who often stay in the same site. Subjects' outdoor appearance are corresponded to their life routine. The results can be useful for understanding elders' social network construction, risky area identification and medical care monitoring.

  20. Placing invasive species management in a spatiotemporal context.

    Science.gov (United States)

    Baker, Christopher M; Bode, Michael

    2016-04-01

    Invasive species are a worldwide issue, both ecologically and economically. A large body of work focuses on various aspects of invasive species control, including how to allocate control efforts to eradicate an invasive population as cost effectively as possible: There are a diverse range of invasive species management problems, and past mathematical analyses generally focus on isolated examples, making it hard to identify and understand parallels between the different contexts. In this study, we use a single spatiotemporal model to tackle the problem of allocating control effort for invasive species when suppressing an island invasive species, and for long-term spatial suppression projects. Using feral cat suppression as an illustrative example, we identify the optimal resource allocation for island and mainland suppression projects. Our results demonstrate how using a single model to solve different problems reveals similar characteristics of the solutions in different scenarios. As well as illustrating the insights offered by linking problems through a spatiotemporal model, we also derive novel and practically applicable results for our case studies. For temporal suppression projects on islands, we find that lengthy projects are more cost effective and that rapid control projects are only economically cost effective when population growth rates are high or diminishing returns on control effort are low. When suppressing invasive species around conservation assets (e.g., national parks or exclusion fences), we find that the size of buffer zones should depend on the ratio of the species growth and spread rate.

  1. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

    Science.gov (United States)

    Marcelletti, Simone; Scortichini, Marco

    2016-10-01

    A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

  2. Multiple Identified Neurons and Peripheral Nerves Innervating the Prothoracic Defense Glands in Stick Insects Reveal Evolutionary Conserved and Novel Elements of a Chemical Defense System

    Directory of Open Access Journals (Sweden)

    Johannes Strauß

    2017-11-01

    Full Text Available The defense glands in the dorsal prothorax are an important autapomorphic trait of stick insects (Phasmatodea. Here, we study the functional anatomy and neuronal innervation of the defense glands in Anisomorpha paromalus (Westwood, 1859 (Pseudophasmatinae, a species which sprays its defense secretions when disturbed or attacked. We use a neuroanatomical approach to identify the nerves innervating the gland muscles and the motoneurons with axons in the different nerves. The defense gland is innervated by nerves originating from two segments, the subesophageal ganglion (SOG, and the prothoracic ganglion. Axonal tracing confirms the gland innervation via the anterior subesophageal nerve, and two intersegmental nerves, the posterior subesophageal nerve, and the anterior prothoracic nerve. Axonal tracing of individual nerves reveals eight identified neuron types in the subesophageal or prothoracic ganglion. The strongest innervating nerve of the gland is the anterior subesophageal nerve, which also supplies dorsal longitudinal thorax muscles (neck muscles by separate nerve branches. Tracing of individual nerve branches reveals different sets of motoneurons innervating the defense gland (one ipsilateral and one contralateral subesophageal neuron or the neck muscle (ventral median neurons. The ipsilateral and contralateral subesophageal neurons have no homologs in related taxa like locusts and crickets, and thus evolved within stick insects with the differentiation of the defense glands. The overall innervation pattern suggests that the longitudinal gland muscles derived from dorsal longitudinal neck muscles. In sum, the innervating nerves for dorsal longitudinal muscles are conserved in stick insects, while the neuronal control system was specialized with conserved motoneurons for the persisting neck muscles, and evolutionarily novel subesophageal and prothoracic motoneurons innervating the defense gland.

  3. Analyzing Spatiotemporal Anomalies through Interactive Visualization

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2014-06-01

    Full Text Available As we move into the big data era, data grows not just in size, but also in complexity, containing a rich set of attributes, including location and time information, such as data from mobile devices (e.g., smart phones, natural disasters (e.g., earthquake and hurricane, epidemic spread, etc. We are motivated by the rising challenge and build a visualization tool for exploring generic spatiotemporal data, i.e., records containing time location information and numeric attribute values. Since the values often evolve over time and across geographic regions, we are particularly interested in detecting and analyzing the anomalous changes over time/space. Our analytic tool is based on geographic information system and is combined with spatiotemporal data mining algorithms, as well as various data visualization techniques, such as anomaly grids and anomaly bars superimposed on the map. We study how effective the tool may guide users to find potential anomalies through demonstrating and evaluating over publicly available spatiotemporal datasets. The tool for spatiotemporal anomaly analysis and visualization is useful in many domains, such as security investigation and monitoring, situation awareness, etc.

  4. Comparison of Spatiotemporal Fusion Models: A Review

    Directory of Open Access Journals (Sweden)

    Bin Chen

    2015-02-01

    Full Text Available Simultaneously capturing spatial and temporal dynamics is always a challenge for the remote sensing community. Spatiotemporal fusion has gained wide interest in various applications for its superiority in integrating both fine spatial resolution and frequent temporal coverage. Though many advances have been made in spatiotemporal fusion model development and applications in the past decade, a unified comparison among existing fusion models is still limited. In this research, we classify the models into three categories: transformation-based, reconstruction-based, and learning-based models. The objective of this study is to (i compare four fusion models (STARFM, ESTARFM, ISTAFM, and SPSTFM under a one Landsat-MODIS (L-M pair prediction mode and two L-M pair prediction mode using time-series datasets from the Coleambally irrigation area and Poyang Lake wetland; (ii quantitatively assess prediction accuracy considering spatiotemporal comparability, landscape heterogeneity, and model parameter selection; and (iii discuss the advantages and disadvantages of the three categories of spatiotemporal fusion models.

  5. Spatio-temporal modeling for residential burglary

    NARCIS (Netherlands)

    Mahfoud, M.; Bhulai, Sandjai; van der Mei, R.D.; Bhulai, Sandjai; Kardaras, Dimitris

    2017-01-01

    Spatio-temporal modeling is widely recognized as a promising means for predicting crime patterns. Despite their enormous potential, the available methods are still in their infancy. A lot of research focuses on crime hotspot detection and geographic crime clusters, while a systematic approach to

  6. Spatiotemporal complexity in coupled map lattices

    International Nuclear Information System (INIS)

    Kaneko, Kunihiko

    1986-01-01

    Some spatiotemporal patterns of couple map lattices are presented. The chaotic kink-like motions are shown for the phase motion of the coupled circle lattices. An extension of the couple map lattice approach to Hamiltonian dynamics is briefly reported. An attempt to characterize the high-dimensional attractor by the extension of the correlation dimension is discussed. (author)

  7. A Flexible Spatio-Temporal Model for Air Pollution with Spatial and Spatio-Temporal Covariates

    OpenAIRE

    Lindström, Johan; Szpiro, Adam A; Sampson, Paul D; Oron, Assaf P; Richards, Mark; Larson, Tim V; Sheppard, Lianne

    2013-01-01

    The development of models that provide accurate spatio-temporal predictions of ambient air pollution at small spatial scales is of great importance for the assessment of potential health effects of air pollution. Here we present a spatio-temporal framework that predicts ambient air pollution by combining data from several different monitoring networks and deterministic air pollution model(s) with geographic information system (GIS) covariates. The model presented in this paper has been implem...

  8. State estimation of spatio-temporal phenomena

    Science.gov (United States)

    Yu, Dan

    This dissertation addresses the state estimation problem of spatio-temporal phenomena which can be modeled by partial differential equations (PDEs), such as pollutant dispersion in the atmosphere. After discretizing the PDE, the dynamical system has a large number of degrees of freedom (DOF). State estimation using Kalman Filter (KF) is computationally intractable, and hence, a reduced order model (ROM) needs to be constructed first. Moreover, the nonlinear terms, external disturbances or unknown boundary conditions can be modeled as unknown inputs, which leads to an unknown input filtering problem. Furthermore, the performance of KF could be improved by placing sensors at feasible locations. Therefore, the sensor scheduling problem to place multiple mobile sensors is of interest. The first part of the dissertation focuses on model reduction for large scale systems with a large number of inputs/outputs. A commonly used model reduction algorithm, the balanced proper orthogonal decomposition (BPOD) algorithm, is not computationally tractable for large systems with a large number of inputs/outputs. Inspired by the BPOD and randomized algorithms, we propose a randomized proper orthogonal decomposition (RPOD) algorithm and a computationally optimal RPOD (RPOD*) algorithm, which construct an ROM to capture the input-output behaviour of the full order model, while reducing the computational cost of BPOD by orders of magnitude. It is demonstrated that the proposed RPOD* algorithm could construct the ROM in real-time, and the performance of the proposed algorithms on different advection-diffusion equations. Next, we consider the state estimation problem of linear discrete-time systems with unknown inputs which can be treated as a wide-sense stationary process with rational power spectral density, while no other prior information needs to be known. We propose an autoregressive (AR) model based unknown input realization technique which allows us to recover the input

  9. High Spatiotemporal Resolution Prostate MRI

    Science.gov (United States)

    2017-09-01

    Subtask 2.2: Construct, tune, and match multiple pairs of triangular coils 7-12 (9) Dr. Riederer; Mr. Hulshizer Subtask 2.3: Test modular triangular...the project or its direction. If not previously reported in writing , provide the following additional information or state, “Nothing to Report,” if...all technical aspects of the projects. Name: Akira Kawashima, M.D., Ph.D. Project Role: Co-Investigator Nearest person month worked: .22

  10. The Voronoi spatio-temporal data structure

    Science.gov (United States)

    Mioc, Darka

    2002-04-01

    Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal

  11. Systematic analysis of fly models with multiple drivers reveals different effects of ataxin-1 and huntingtin in neuron subtype-specific expression.

    Directory of Open Access Journals (Sweden)

    Risa Shiraishi

    Full Text Available The fruit fly, Drosophila melanogaster, is a commonly used model organism for neurodegenerative diseases. Its major advantages include a short lifespan and its susceptibility to manipulation using sophisticated genetic techniques. Here, we report the systematic comparison of fly models of two polyglutamine (polyQ diseases. We induced expression of the normal and mutant forms of full-length Ataxin-1 and Huntingtin exon 1 in cholinergic, dopaminergic, and motor neurons, and glial cells using cell type-specific drivers. We systematically analyzed their effects based on multiple phenotypes: eclosion rate, lifespan, motor performance, and circadian rhythms of spontaneous activity. This systematic assay system enabled us to quantitatively evaluate and compare the functional disabilities of different genotypes. The results suggest different effects of Ataxin-1 and Huntingtin on specific types of neural cells during development and in adulthood. In addition, we confirmed the therapeutic effects of LiCl and butyrate using representative models. These results support the usefulness of this assay system for screening candidate chemical compounds that modify the pathologies of polyQ diseases.

  12. Task-relevant information is prioritized in spatiotemporal contextual cueing.

    Science.gov (United States)

    Higuchi, Yoko; Ueda, Yoshiyuki; Ogawa, Hirokazu; Saiki, Jun

    2016-11-01

    Implicit learning of visual contexts facilitates search performance-a phenomenon known as contextual cueing; however, little is known about contextual cueing under situations in which multidimensional regularities exist simultaneously. In everyday vision, different information, such as object identity and location, appears simultaneously and interacts with each other. We tested the hypothesis that, in contextual cueing, when multiple regularities are present, the regularities that are most relevant to our behavioral goals would be prioritized. Previous studies of contextual cueing have commonly used the visual search paradigm. However, this paradigm is not suitable for directing participants' attention to a particular regularity. Therefore, we developed a new paradigm, the "spatiotemporal contextual cueing paradigm," and manipulated task-relevant and task-irrelevant regularities. In four experiments, we demonstrated that task-relevant regularities were more responsible for search facilitation than task-irrelevant regularities. This finding suggests our visual behavior is focused on regularities that are relevant to our current goal.

  13. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability

    Directory of Open Access Journals (Sweden)

    Xu Chunming

    2009-05-01

    Full Text Available Abstract Background Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. Results We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0 and its selfed progenies (S1 ruled out contamination (via seed or pollen or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs, including a MITE (mPing, and three LTR retrotransposons (Osr7, Osr23 and Tos17. AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of

  14. Anatomy of a turbidity current: Concentration and grain size structure of a deep-sea flow revealed by multiple-frequency acoustic profilers

    Science.gov (United States)

    Simmons, S.; Parsons, D. R.; Paull, C. K.; Barry, J.; Chaffey, M. R.; Gwiazda, R.; O'Reilly, T. C.; Maier, K. L.; Rosenberger, K. J.; Talling, P.; Xu, J.

    2017-12-01

    Turbidity currents are responsible for transporting large volumes of sediment to the deep ocean, yet remain poorly understood due to the limited number of field observations of these episodic, high energy events. As part of the Monterey Coordinated Canyon Experiment high resolution, sub-minute acoustic velocity and backscatter profiles were acquired with downward-looking acoustic Doppler current profilers (ADCPs) distributed along the canyon on moorings at depths ranging from 270 to 1,900 m over a period of 18 months. Additionally, three upward-looking ADCPs on different frequencies (300, 600 and 1200 kHz) profiled the water column above a seafloor instrument node (SIN) at 1850 m water depth. Traps on the moorings collected sediment carried by the flows at different heights above the seafloor and sediment cores were taken to determine the depositional record produced by the flows. Several sediment-laden turbidity flows were observed during the experiment, three of which ran out for more than 50 km to water depths of greater than 1,900 m and were observed on all of the moorings. Flow speeds of up to 6 m/s were observed and individual moorings, anchored by railroad wheels, moved up to 7.8 km down-canyon during these powerful events. We present results based on a novel analysis of the multiple-frequency acoustic data acquired by the ADCPs at the SIN integrated with grain size data from the sediment traps, close to the deepest mooring in the array where the flow thickened to the 70 m height of the ADCP above the bed. The analysis allows, for the first time, retrieval of the suspended sediment concentration and vertical distribution of grain size structure within a turbidity in spectacular detail. The details of the stratification and flow dynamics will be used to re-evaluate and discuss our existing models for these deep-sea flows.

  15. Urban Heat Islands of the World's Major Cities Revealed at Multiple Scales Using Both Station Observations and Complementary Remotely Sensed Data Products

    Science.gov (United States)

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

    2016-12-01

    Urban heat islands (UHIs) have long been studied using both ground-based observations of air temperature and remotely sensed data. In the rapidly urbanizing world, cross-comparison between various datasets will allow us to characterize and model UHI effects more generally. Here we analyze UHIs of the world's major cities using station observations from the Global Historical Climate Network (GHCN), surface air temperatures derived from Advanced Microwave Scanning Radiometers (AMSRs), and land surface temperatures (LST) estimated from Moderate-resolution Imaging Spectroradiometer (MODIS). We compute the two measurements of thermal time (accumulated diurnal degree-days or ADDD and nocturnal degree-days or ANDD) and the normalized difference accumulated thermal time index (NDATTI) to characterize urban and rural thermal differences and day-night dynamics over multiple growing seasons. Our preliminary results for 27 major cities and 83 urban-rural groupings in the USA and Canada indicate that daytime urban thermal accumulations from the passive microwave data (AMSRs) were generally lower than in adjacent rural areas, with only 18% of urban-rural groupings showing higher thermal accumulations in cities. In contrast, station observations and MODIS LST showed consistently higher ADDD in cities (82% and 93% for GHCN and MODIS data respectively). UHIs are more pronounced at night, with 55% (AMSR), 93% (GHCN) and 100% (MODIS) of urban-rural groupings showing higher ANDD in cities. Humidity appears to be a common factor driving the day-night thermal dynamics throughout all three datasets (Figure 1). Normalized day-night differences in thermal time metrics were consistently lower (>90% of urban-rural groupings) in urban than rural areas for both air temperature datasets (GHCN and AMSRs). With MODIS LST, only 70% of urban-rural groupings show lower NDATTI in cities. We will present results for the rest of the globe.

  16. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau.

    Science.gov (United States)

    Wang, Bin; Xie, Feng; Li, Jiannan; Wang, Gang; Li, Cheng; Jiang, Jianping

    2017-01-01

    The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  17. Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors

    Directory of Open Access Journals (Sweden)

    Aixin Li

    2017-09-01

    Full Text Available C-repeat binding factors (CBF are a subfamily of AP2 transcription factors that play critical roles in the regulation of plant cold tolerance and growth in low temperature. In the present work, we sought to perform a detailed investigation into global transcriptional regulation of plant hormone signaling associated genes in transgenic plants engineered with CBF genes. RNA samples from Arabidopsis thaliana plants overexpressing two CBF genes, CBF2 and CBF3, were subjected to Illumina HiSeq 2000 RNA sequencing (RNA-Seq. Our results showed that more than half of the hormone associated genes that were differentially expressed in CBF2 or CBF3 transgenic plants were related to auxin signal transduction and metabolism. Most of these alterations in gene expression could lead to repression of auxin signaling. Accordingly, the IAA content was significantly decreased in young tissues of plants overexpressing CBF2 and CBF3 compared with wild type. In addition, genes associated with the biosynthesis of Jasmonate (JA and Salicylic acid (SA, as well as the signal sensing of Brassinolide (BR and SA, were down-regulated, while genes associated with Gibberellin (GA deactivation were up-regulated. In general, overexpression of CBF2 and CBF3 negatively affects multiple plant hormone signaling pathways in Arabidopsis. The transcriptome analysis using CBF2 and CBF3 transgenic plants provides novel and integrated insights into the interaction between CBFs and plant hormones, particularly the modulation of auxin signaling, which may contribute to the improvement of crop yields under abiotic stress via molecular engineering using CBF genes.

  18. Proteomic analysis reveals the enhancement of human serum apolipoprotein A-1(APO A-1) in individuals infected with multiple dengue virus serotypes.

    Science.gov (United States)

    Manchala, Nageswar Reddy; Dungdung, Ranjeet; Pilankatta, Rajendra

    2017-10-01

    Human serum protein profiling of the individual infected with multiple dengue virus serotypes for identifying the potential biomarkers and to investigate the cause for the severity of dengue virus infection. Dengue virus NS1-positive serum samples were pooled into two groups (S2 and S3) based on the molecular serotyping and number of heterotypic infections. The pooled serum samples were subjected to two-dimensional gel electrophoresis (2DGE) to identify the differentially expressed proteins. The peptide masses of upregulated protein were detected by matrix-assisted laser desorption-ionisation time-of-flight MALDI-TOF mass spectrometry and analysed by MASCOT search engine. The results were compared with the control group (S1). The commonly upregulated protein was validated by quantitative ELISA and compared with control as well as single serotypic infected samples. Based on 2DGE, total thirteen proteins were differentially upregulated in S2 and S3 groups as compared to control. Some of the upregulated proteins were involved in mediating the complement activation of immune response. The apolipoprotein A-1 (APO A-1) was upregulated in S2 and S3 groups. Upon validation, APO A-1 levels were increased in line with the number of heterotypic infection of dengue viruses. Heterotypic infection of dengue viruses upregulate the serum proteins involved in the complement pathway in the early phase of infection. There was a significant increase in the level of APO A-1 in three different serotypic infections of dengue virus as compared to control. Further, the role of APO-A1 can be explored in elucidating the mechanism of dengue pathogenesis. © 2017 John Wiley & Sons Ltd.

  19. Multiple sclerosis

    DEFF Research Database (Denmark)

    Stenager, E; Knudsen, L; Jensen, K

    1994-01-01

    In a cross-sectional study of 94 patients (42 males, 52 females) with definite multiple sclerosis (MS) in the age range 25-55 years, the correlation of neuropsychological tests with the ability to read TV-subtitles and with the use of sedatives is examined. A logistic regression analysis reveals...

  20. Behavioural mapping of a pelagic seabird: combining multiple sensors and a hidden Markov model reveals the distribution of at-sea behaviour

    Science.gov (United States)

    Dean, Ben; Freeman, Robin; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

    2013-01-01

    The use of miniature data loggers is rapidly increasing our understanding of the movements and habitat preferences of pelagic seabirds. However, objectively interpreting behavioural information from the large volumes of highly detailed data collected by such devices can be challenging. We combined three biologging technologies—global positioning system (GPS), saltwater immersion and time–depth recorders—to build a detailed picture of the at-sea behaviour of the Manx shearwater (Puffinus puffinus) during the breeding season. We used a hidden Markov model to explore discrete states within the combined GPS and immersion data, and found that behaviour could be organized into three principal activities representing (i) sustained direct flight, (ii) sitting on the sea surface, and (iii) foraging, comprising tortuous flight interspersed with periods of immersion. The additional logger data verified that the foraging activity corresponded well to the occurrence of diving. Applying this approach to a large tracking dataset revealed that birds from two different colonies foraged in local waters that were exclusive, but overlapped in one key area: the Irish Sea Front (ISF). We show that the allocation of time to each activity differed between colonies, with birds breeding furthest from the ISF spending the greatest proportion of time engaged in direct flight and the smallest proportion of time engaged in foraging activity. This type of analysis has considerable potential for application in future biologging studies and in other taxa. PMID:23034356

  1. Spatiotemporal profiles of receptive fields of neurons in the lateral posterior nucleus of the cat LP-pulvinar complex.

    Science.gov (United States)

    Piché, Marilyse; Thomas, Sébastien; Casanova, Christian

    2015-10-01

    The pulvinar is the largest extrageniculate thalamic visual nucleus in mammals. It establishes reciprocal connections with virtually all visual cortexes and likely plays a role in transthalamic cortico-cortical communication. In cats, the lateral posterior nucleus (LP) of the LP-pulvinar complex can be subdivided in two subregions, the lateral (LPl) and medial (LPm) parts, which receive a predominant input from the striate cortex and the superior colliculus, respectively. Here, we revisit the receptive field structure of LPl and LPm cells in anesthetized cats by determining their first-order spatiotemporal profiles through reverse correlation analysis following sparse noise stimulation. Our data reveal the existence of previously unidentified receptive field profiles in the LP nucleus both in space and time domains. While some cells responded to only one stimulus polarity, the majority of neurons had receptive fields comprised of bright and dark responsive subfields. For these neurons, dark subfields' size was larger than that of bright subfields. A variety of receptive field spatial organization types were identified, ranging from totally overlapped to segregated bright and dark subfields. In the time domain, a large spectrum of activity overlap was found, from cells with temporally coinciding subfield activity to neurons with distinct, time-dissociated subfield peak activity windows. We also found LP neurons with space-time inseparable receptive fields and neurons with multiple activity periods. Finally, a substantial degree of homology was found between LPl and LPm first-order receptive field spatiotemporal profiles, suggesting a high integration of cortical and subcortical inputs within the LP-pulvinar complex. Copyright © 2015 the American Physiological Society.

  2. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics.

    Science.gov (United States)

    Yoon, Sook Hee; Kim, Jaemin; Shin, Donghyun; Cho, Seoae; Kwak, Woori; Lee, Hak-Kyo; Park, Kyoung-Do; Kim, Heebal

    2017-04-01

    The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.

  3. Spatio-temporal flow maps for visualizing movement and contact patterns

    Directory of Open Access Journals (Sweden)

    Bing Ni

    2017-03-01

    Full Text Available The advanced telecom technologies and massive volumes of intelligent mobile phone users have yielded a huge amount of real-time data of people’s all-in-one telecommunication records, which we call telco big data. With telco data and the domain knowledge of an urban city, we are now able to analyze the movement and contact patterns of humans in an unprecedented scale. Flow map is widely used to display the movements of humans from one single source to multiple destinations by representing locations as nodes and movements as edges. However, it fails the task of visualizing both movement and contact data. In addition, analysts often need to compare and examine the patterns side by side, and do various quantitative analysis. In this work, we propose a novel spatio-temporal flow map layout to visualize when and where people from different locations move into the same places and make contact. We also propose integrating the spatiotemporal flow maps into existing spatiotemporal visualization techniques to form a suite of techniques for visualizing the movement and contact patterns. We report a potential application the proposed techniques can be applied to. The results show that our design and techniques properly unveil hidden information, while analysis can be achieved efficiently. Keywords: Spatio-temporal data, Flow map, Urban mobility

  4. Dynamic spatiotemporal analysis of indigenous dengue fever at street-level in Guangzhou city, China

    Science.gov (United States)

    Xia, Yao; Zhang, Yingtao; Huang, Xiaodong; Huang, Jiawei; Nie, Enqiong; Jing, Qinlong; Wang, Guoling; Yang, Zhicong; Hu, Wenbiao

    2018-01-01

    Background This study aimed to investigate the spatiotemporal clustering and socio-environmental factors associated with dengue fever (DF) incidence rates at street level in Guangzhou city, China. Methods Spatiotemporal scan technique was applied to identify the high risk region of DF. Multiple regression model was used to identify the socio-environmental factors associated with DF infection. A Poisson regression model was employed to examine the spatiotemporal patterns in the spread of DF. Results Spatial clusters of DF were primarily concentrated at the southwest part of Guangzhou city. Age group (65+ years) (Odd Ratio (OR) = 1.49, 95% Confidence Interval (CI) = 1.13 to 2.03), floating population (OR = 1.09, 95% CI = 1.05 to 1.15), low-education (OR = 1.08, 95% CI = 1.01 to 1.16) and non-agriculture (OR = 1.07, 95% CI = 1.03 to 1.11) were associated with DF transmission. Poisson regression results indicated that changes in DF incidence rates were significantly associated with longitude (β = -5.08, P<0.01) and latitude (β = -1.99, P<0.01). Conclusions The study demonstrated that social-environmental factors may play an important role in DF transmission in Guangzhou. As geographic range of notified DF has significantly expanded over recent years, an early warning systems based on spatiotemporal model with socio-environmental is urgently needed to improve the effectiveness and efficiency of dengue control and prevention. PMID:29561835

  5. Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales

    NARCIS (Netherlands)

    Bui Thi Minh Dieu,; Marks, H.; Zwart, M.P.; Vlak, J.M.

    2010-01-01

    Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple

  6. Multiple faulting events revealed by trench analysis of the seismogenic structure of the 1976 Ms7.1 Luanxian earthquake, Tangshan Region, China

    Science.gov (United States)

    Guo, Hui; Jiang, Wali; Xie, Xinsheng

    2017-10-01

    The Ms7.8 Tangshan earthquake occurred on 28 July 1976 at 03:42 CST. Approximately 15 h later, the Ms7.1 Luanxian earthquake occurred approximately 40 km northeast of the main shock. The two earthquakes formed different surface rupture zones. The surface rupture of the Tangshan earthquake was NNE-trending and more than 47 km long. The surface rupture of the Luanxian earthquake was more than 6 km long and consisted of two sections, forming a protruding arc to the west. The north and south sections were NE- and NW-trending and 2 km and 4 km long, respectively. A trench was excavated in Sanshanyuan Village across the NE-trending rupture of the Luanxian earthquake, at the macroscopic epicenter of the Luanxian earthquake. Analysis of this trench revealed that the surface rupture is connected to the underground active fault. The following major conclusions regarding Late Quaternary fault activity have been reached. (1) The Sanshanyuan trench indicated that its fault planes trend NE30° and dip SE or NW at angles of approximately 69-82°. (2) The fault experienced four faulting events prior to the Luanxian earthquake at 27.98 ka with an average recurrence interval of approximately 7.5 ka. (3) The Ms7.1 Luanxian earthquake resulted from the activity of the Luanxian Western fault and was triggered by the Ms7.8 Tangshan earthquake. The seismogenic faults of the 1976 Ms7.1 Luanxian earthquake and the 1976 Ms7.8 Tangshan earthquake are not the same fault. This example of an M7 earthquake triggered by a nearly M8 earthquake after more than 10 h on a nearby fault is a worthy topic of research for the future prediction of strong earthquakes.

  7. Analysis of integrated multiple 'omics' datasets reveals the mechanisms of initiation and determination in the formation of tuberous roots in Rehmannia glutinosa.

    Science.gov (United States)

    Li, Mingjie; Yang, Yanhui; Li, Xinyu; Gu, Li; Wang, Fengji; Feng, Fajie; Tian, Yunhe; Wang, Fengqing; Wang, Xiaoran; Lin, Wenxiong; Chen, Xinjian; Zhang, Zhongyi

    2015-09-01

    All tuberous roots in Rehmannia glutinosa originate from the expansion of fibrous roots (FRs), but not all FRs can successfully transform into tuberous roots. This study identified differentially expressed genes and proteins associated with the expansion of FRs, by comparing the tuberous root at expansion stages (initiated tuberous root, ITRs) and FRs at the seedling stage (initiated FRs, IFRs). The role of miRNAs in the expansion of FRs was also explored using the sRNA transcriptome and degradome to identify miRNAs and their target genes that were differentially expressed between ITRs and FRs at the mature stage (unexpanded FRs, UFRs, which are unable to expand into ITRs). A total of 6032 genes and 450 proteins were differentially expressed between ITRs and IFRs. Integrated analyses of these data revealed several genes and proteins involved in light signalling, hormone response, and signal transduction that might participate in the induction of tuberous root formation. Several genes related to cell division and cell wall metabolism were involved in initiating the expansion of IFRs. Of 135 miRNAs differentially expressed between ITRs and UFRs, there were 27 miRNAs whose targets were specifically identified in the degradome. Analysis of target genes showed that several miRNAs specifically expressed in UFRs were involved in the degradation of key genes required for the formation of tuberous roots. As far as could be ascertained, this is the first time that the miRNAs that control the transition of FRs to tuberous roots in R. glutinosa have been identified. This comprehensive analysis of 'omics' data sheds new light on the mechanisms involved in the regulation of tuberous roots formation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development

    Directory of Open Access Journals (Sweden)

    Kyle J. Beauchemin

    2016-08-01

    Full Text Available To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ. Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS. Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO archive (GSE74243. Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org.

  9. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development.

    Science.gov (United States)

    Beauchemin, Kyle J; Wells, Julie M; Kho, Alvin T; Philip, Vivek M; Kamir, Daniela; Kohane, Isaac S; Graber, Joel H; Bult, Carol J

    2016-01-01

    To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org).

  10. High-resolution stratigraphy and multiple luminescence dating techniques to reveal the paleoseismic history of the central Dead Sea fault (Yammouneh fault, Lebanon)

    Science.gov (United States)

    Le Béon, Maryline; Tseng, Ya-Chu; Klinger, Yann; Elias, Ata; Kunz, Alexander; Sursock, Alexandre; Daëron, Mathieu; Tapponnier, Paul; Jomaa, Rachid

    2018-07-01

    Continuous sedimentation and detailed stratigraphy are key parameters for a complete paleo-earthquake record. Here, we present a new paleoseismological study across the main strike-slip fault branch of the Dead Sea fault in Lebanon. We aim to expand the current knowledge on local paleoseismicity and seismic behavior of strike-slip plate boundary faults and to explore the limitations of paleoseismology and dating methods. The trench, dug in the Jbab el-Homr basin, reveals a succession of remarkable, very thin (0.1 to 5 cm) palustrine and lacustrine layers, ruptured by at least 17 earthquakes. Absolute ages of 4 samples are obtained from three luminescence-dating techniques targeting fine-grain minerals. Blue-green stimulated luminescence (BGSL) on quartz and post-infrared infrared-stimulated luminescence at 225 °C on polymineral aliquots led to consistent ages, while ages from infrared-stimulated luminescence at 50 °C on polymineral aliquots appeared underestimated. The quartz BGSL ages are 26.9 ± 2.3 ka at 0.50 m depth and 30.8 ± 2.9 ka at 3.65 m depth. During this time period of 3.9 ka ([0; 9.1 ka]), 14 surface-rupturing events occurred with a mean return time of 280 years ([0; 650 years]) and probable clustering. This return time is much shorter than the 1127 ± 135 years return time previously determined at the Yammouneh site, located 30 km south. Although fault segmentation and temporal variations in the earthquake cycle remain possible causes for such different records, we argue that the high-resolution stratigraphy in Jbab is the main factor, enabling us to record small deformations related to smaller-magnitude events that may have been missed in the rougher strata of Yammouneh. Indeed, focusing only on larger events of Jbab, we obtain a mean return time of 720 years ([0; 1670 years]) that is compatible with the Yammouneh record.

  11. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism

    Directory of Open Access Journals (Sweden)

    Witold Uhrynowski

    2017-05-01

    Full Text Available Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland, an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the

  12. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism.

    Science.gov (United States)

    Uhrynowski, Witold; Decewicz, Przemyslaw; Dziewit, Lukasz; Radlinska, Monika; Krawczyk, Pawel S; Lipinski, Leszek; Adamska, Dorota; Drewniak, Lukasz

    2017-01-01

    Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance ( hmr ) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained

  13. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism

    Science.gov (United States)

    Uhrynowski, Witold; Decewicz, Przemyslaw; Dziewit, Lukasz; Radlinska, Monika; Krawczyk, Pawel S.; Lipinski, Leszek; Adamska, Dorota; Drewniak, Lukasz

    2017-01-01

    Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained

  14. Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species

    Directory of Open Access Journals (Sweden)

    Kotewong Rattanawadee

    2010-11-01

    Full Text Available Abstract Background Many species of marine shrimp in the Family Penaeidae, viz. Penaeus (Litopenaeus vannamei, Penaeus monodon, Penaeus (Fenneropenaeus chinensis, and Penaeus (Marsupenaeus japonicus, are animals of economic importance in the aquaculture industry. Yet information about their DNA and protein sequences is lacking. In order to predict their collective proteome, we combined over 270,000 available EST and cDNA sequences from the 4 shrimp species with all protein sequences of Drosophila melanogaster and Caenorhabditis elegans. EST data from 4 other crustaceans, the crab Carcinus maenas, the lobster Homarus americanus (Decapoda, the water flea Daphnia pulex, and the brine shrimp Artemia franciscana were also used. Findings Similarity searches from EST collections of the 4 shrimp species matched 64% of the protein sequences of the fruit fly, but only 45% of nematode proteins, indicating that the shrimp proteome content is more similar to that of an insect than a nematode. Combined results with 4 additional non-shrimp crustaceans increased matching to 78% of fruit fly and 56% of nematode proteins, suggesting that present shrimp EST collections still lack sequences for many conserved crustacean proteins. Analysis of matching data revealed the presence of 4 EST groups from shrimp, namely sequences for proteins that are both fruit fly-like and nematode-like, fruit fly-like only, nematode-like only, and non-matching. Gene ontology profiles of proteins for the 3 matching EST groups were analyzed. For non-matching ESTs, a small fraction matched protein sequences from other species in the UniProt database, including other crustacean-specific proteins. Conclusions Shrimp ESTs indicated that the shrimp proteome is comprised of sub-populations of proteins similar to those common to both insect and nematode models, those present specifically in either model, or neither. Combining small EST collections from related species to compensate for their

  15. A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation.

    Directory of Open Access Journals (Sweden)

    Andrea D Coviello

    Full Text Available Sex hormone-binding globulin (SHBG is a glycoprotein responsible for the transport and biologic availability of sex steroid hormones, primarily testosterone and estradiol. SHBG has been associated with chronic diseases including type 2 diabetes (T2D and with hormone-sensitive cancers such as breast and prostate cancer. We performed a genome-wide association study (GWAS meta-analysis of 21,791 individuals from 10 epidemiologic studies and validated these findings in 7,046 individuals in an additional six studies. We identified twelve genomic regions (SNPs associated with circulating SHBG concentrations. Loci near the identified SNPs included SHBG (rs12150660, 17p13.1, p = 1.8 × 10(-106, PRMT6 (rs17496332, 1p13.3, p = 1.4 × 10(-11, GCKR (rs780093, 2p23.3, p = 2.2 × 10(-16, ZBTB10 (rs440837, 8q21.13, p = 3.4 × 10(-09, JMJD1C (rs7910927, 10q21.3, p = 6.1 × 10(-35, SLCO1B1 (rs4149056, 12p12.1, p = 1.9 × 10(-08, NR2F2 (rs8023580, 15q26.2, p = 8.3 × 10(-12, ZNF652 (rs2411984, 17q21.32, p = 3.5 × 10(-14, TDGF3 (rs1573036, Xq22.3, p = 4.1 × 10(-14, LHCGR (rs10454142, 2p16.3, p = 1.3 × 10(-07, BAIAP2L1 (rs3779195, 7q21.3, p = 2.7 × 10(-08, and UGT2B15 (rs293428, 4q13.2, p = 5.5 × 10(-06. These genes encompass multiple biologic pathways, including hepatic function, lipid metabolism, carbohydrate metabolism and T2D, androgen and estrogen receptor function, epigenetic effects, and the biology of sex steroid hormone-responsive cancers including breast and prostate cancer. We found evidence of sex-differentiated genetic influences on SHBG. In a sex-specific GWAS, the loci 4q13.2-UGT2B15 was significant in men only (men p = 2.5 × 10(-08, women p = 0.66, heterogeneity p = 0.003. Additionally, three loci showed strong sex-differentiated effects: 17p13.1-SHBG and Xq22.3-TDGF3 were stronger in men, whereas 8q21.12-ZBTB10 was stronger in women. Conditional analyses identified additional signals at the SHBG gene that together almost double the proportion

  16. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis.

    Science.gov (United States)

    Castro, Juan C; Maddox, J Dylan; Cobos, Marianela; Requena, David; Zimic, Mirko; Bombarely, Aureliano; Imán, Sixto A; Cerdeira, Luis A; Medina, Andersson E

    2015-11-24

    Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with

  17. Distillation and Visualization of Spatiotemporal Structures in Turbulent Flow Fields

    International Nuclear Information System (INIS)

    Hege, Hans-Christian; Hotz, Ingrid; Kasten, Jens

    2011-01-01

    Although turbulence suggests randomness and disorder, organized motions that cause spatiotemporal 'coherent structures' are of particular interest. Revealing such structures in numerically given turbulent or semi-turbulent flows is of interest both for practically working engineers and theoretically oriented physicists. However, as long as there is no common agreement about the mathematical definition of coherent structures, extracting such structures is a vaguely defined task. Instead of searching for a general definition, the data visualization community takes a pragmatic approach and provides various tool chains implemented in flexible software frameworks that allow the user to extract distinct flow field structures. Thus physicists or engineers can select those flow structures which might advance their insight best. We present different approaches to distill important features from turbulent flows and discuss the necessary steps to be taken on the example of Lagrangian coherent structures.

  18. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  19. Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging.

    Directory of Open Access Journals (Sweden)

    Karin Gorzolka

    Full Text Available MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific localizations. Oligosaccharides were observed in the endosperm and in parts of the developed embryo. Lipids in the endosperm co-localized in dependency on their fatty acid compositions with changes in the distributions of diacyl phosphatidylcholines during germination. 26 potentially antifungal hordatines were detected in the embryo with tissue-specific localizations of their glycosylated, hydroxylated, and O-methylated derivates. In order to reveal spatio-temporal patterns in local metabolite compositions, multiple MSI data sets from a time series were analyzed in one batch. This requires a new preprocessing strategy to achieve comparability between data sets as well as a new strategy for unsupervised clustering. The resulting spatial segmentation for each time point sample is visualized in an interactive cluster map and enables simultaneous interactive exploration of all time points. Using this new analysis approach and visualization tool germination-dependent developments of metabolite patterns with single MS position accuracy were discovered. This is the first study that presents metabolite profiling of a cereals' germination process over time by MALDI MSI with the identification of a large number of peaks of agronomically and industrially important compounds such as oligosaccharides, lipids and antifungal agents. Their detailed localization as well as the MS cluster analyses for on-tissue metabolite profile mapping revealed important information for the understanding of the germination process, which is of high scientific interest.

  20. Spatiotemporal distribution and national measurement of the global carbonate carbon sink.

    Science.gov (United States)

    Li, Huiwen; Wang, Shijie; Bai, Xiaoyong; Luo, Weijun; Tang, Hong; Cao, Yue; Wu, Luhua; Chen, Fei; Li, Qin; Zeng, Cheng; Wang, Mingming

    2018-06-21

    The magnitudes, spatial distributions and contributions to global carbon budget of the global carbonate carbon sink (CCS) still remain uncertain, allowing the problem of national measurement of CCS remain unresolved which will directly influence the fairness of global carbon markets and emission trading. Here, based on high spatiotemporal resolution ecological, meteorological raster data and chemical field monitoring data, combining highly reliable machine learning algorithm with the thermodynamic dissolution equilibrium model, we estimated the new CCS of 0.89 ± 0.23 petagrams of carbon per year (Pg C yr -1 ), amounting to 74.50% of global net forest sink and accounting for 28.75% of terrestrial sinks or 46.81% of the missing sink. Our measurement for 142 nations of CCS showed that Russia, Canada, China and the USA contribute over half of the global CCS. We also presented the first global fluxes maps of the CCS with spatial resolution of 0.05°, exhibiting two peaks in equatorial regions (10°S to 10°N) and low latitudes (10°N to 35°N) in Northern Hemisphere. By contrast, there are no peaks in Southern Hemisphere. The greatest average carbon sink flux (CCSF), i.e., 2.12 tC ha -1  yr -1 , for 2000 to 2014 was contributed by tropical rainforest climate near the equator, and the smallest average CCSF was presented in tropical arid zones, showing a magnitude of 0.26 tC ha -1  yr -1 . This research estimated the magnitudes, spatial distributions, variations and contributions to the global carbon budget of the CCS in a higher spatiotemporal representativeness and expandability way, which, via multiple mechanisms, introduced an important sink in the terrestrial carbon sink system and the global missing sink and that can help us further reveal and support our understanding of global rock weathering carbon sequestration, terrestrial carbon sink system and global carbon cycle dynamics which make our understanding of global change more comprehensive

  1. Spatio-temporal scaling effects on longshore sediment transport pattern along the nearshore zone

    Science.gov (United States)

    Khorram, Saeed; Ergil, Mustafa

    2018-03-01

    A measure of uncertainties, entropy has been employed in such different applications as coastal engineering probability inferences. Entropy sediment transport integration theories present novel visions in coastal analyses/modeling the application and development of which are still far-reaching. Effort has been made in the present paper to propose a method that needs an entropy-power index for spatio-temporal patterns analyses. Results have shown that the index is suitable for marine/hydrological ecosystem components analyses based on a beach area case study. The method makes use of six Makran Coastal monthly data (1970-2015) and studies variables such as spatio-temporal patterns, LSTR (long-shore sediment transport rate), wind speed, and wave height all of which are time-dependent and play considerable roles in terrestrial coastal investigations; the mentioned variables show meaningful spatio-temporal variability most of the time, but explanation of their combined performance is not easy. Accordingly, the use of an entropy-power index can show considerable signals that facilitate the evaluation of water resources and will provide an insight regarding hydrological parameters' interactions at scales as large as beach areas. Results have revealed that an STDDPI (entropy based spatio-temporal disorder dynamics power index) can simulate wave, long-shore sediment transport rate, and wind when granulometry, concentration, and flow conditions vary.

  2. EXTRACTING SPATIOTEMPORAL OBJECTS FROM RASTER DATA TO REPRESENT PHYSICAL FEATURES AND ANALYZE RELATED PROCESSES

    Directory of Open Access Journals (Sweden)

    J. A. Zollweg

    2017-10-01

    Full Text Available Numerous ground-based, airborne, and orbiting platforms provide remotely-sensed data of remarkable spatial resolution at short time intervals. However, this spatiotemporal data is most valuable if it can be processed into information, thereby creating meaning. We live in a world of objects: cars, buildings, farms, etc. On a stormy day, we don’t see millions of cubes of atmosphere; we see a thunderstorm ‘object’. Temporally, we don’t see the properties of those individual cubes changing, we see the thunderstorm as a whole evolving and moving. There is a need to represent the bulky, raw spatiotemporal data from remote sensors as a small number of relevant spatiotemporal objects, thereby matching the human brain’s perception of the world. This presentation reveals an efficient algorithm and system to extract the objects/features from raster-formatted remotely-sensed data. The system makes use of the Python object-oriented programming language, SciPy/NumPy for matrix manipulation and scientific computation, and export/import to the GeoJSON standard geographic object data format. The example presented will show how thunderstorms can be identified and characterized in a spatiotemporal continuum using a Python program to process raster data from NOAA’s High-Resolution Rapid Refresh v2 (HRRRv2 data stream.

  3. Extracting Spatiotemporal Objects from Raster Data to Represent Physical Features and Analyze Related Processes

    Science.gov (United States)

    Zollweg, J. A.

    2017-10-01

    Numerous ground-based, airborne, and orbiting platforms provide remotely-sensed data of remarkable spatial resolution at short time intervals. However, this spatiotemporal data is most valuable if it can be processed into information, thereby creating meaning. We live in a world of objects: cars, buildings, farms, etc. On a stormy day, we don't see millions of cubes of atmosphere; we see a thunderstorm `object'. Temporally, we don't see the properties of those individual cubes changing, we see the thunderstorm as a whole evolving and moving. There is a need to represent the bulky, raw spatiotemporal data from remote sensors as a small number of relevant spatiotemporal objects, thereby matching the human brain's perception of the world. This presentation reveals an efficient algorithm and system to extract the objects/features from raster-formatted remotely-sensed data. The system makes use of the Python object-oriented programming language, SciPy/NumPy for matrix manipulation and scientific computation, and export/import to the GeoJSON standard geographic object data format. The example presented will show how thunderstorms can be identified and characterized in a spatiotemporal continuum using a Python program to process raster data from NOAA's High-Resolution Rapid Refresh v2 (HRRRv2) data stream.

  4. Structured Spatio-temporal shot-noise Cox point process models, with a view to modelling forest fires

    DEFF Research Database (Denmark)

    Møller, Jesper; Diaz-Avalos, Carlos

    2010-01-01

    Spatio-temporal Cox point process models with a multiplicative structure for the driving random intensity, incorporating covariate information into temporal and spatial components, and with a residual term modelled by a shot-noise process, are considered. Such models are flexible and tractable fo...... data set consisting of 2796 days and 5834 spatial locations of fires. The model is compared with a spatio-temporal log-Gaussian Cox point process model, and likelihood-based methods are discussed to some extent....

  5. Energy prediction using spatiotemporal pattern networks

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Zhanhong; Liu, Chao; Akintayo, Adedotun; Henze, Gregor P.; Sarkar, Soumik

    2017-11-01

    This paper presents a novel data-driven technique based on the spatiotemporal pattern network (STPN) for energy/power prediction for complex dynamical systems. Built on symbolic dynamical filtering, the STPN framework is used to capture not only the individual system characteristics but also the pair-wise causal dependencies among different sub-systems. To quantify causal dependencies, a mutual information based metric is presented and an energy prediction approach is subsequently proposed based on the STPN framework. To validate the proposed scheme, two case studies are presented, one involving wind turbine power prediction (supply side energy) using the Western Wind Integration data set generated by the National Renewable Energy Laboratory (NREL) for identifying spatiotemporal characteristics, and the other, residential electric energy disaggregation (demand side energy) using the Building America 2010 data set from NREL for exploring temporal features. In the energy disaggregation context, convex programming techniques beyond the STPN framework are developed and applied to achieve improved disaggregation performance.

  6. What Is Spatio-Temporal Data Warehousing?

    Science.gov (United States)

    Vaisman, Alejandro; Zimányi, Esteban

    In the last years, extending OLAP (On-Line Analytical Processing) systems with spatial and temporal features has attracted the attention of the GIS (Geographic Information Systems) and database communities. However, there is no a commonly agreed definition of what is a spatio-temporal data warehouse and what functionality such a data warehouse should support. Further, the solutions proposed in the literature vary considerably in the kind of data that can be represented as well as the kind of queries that can be expressed. In this paper we present a conceptual framework for defining spatio-temporal data warehouses using an extensible data type system. We also define a taxonomy of different classes of queries of increasing expressive power, and show how to express such queries using an extension of the tuple relational calculus with aggregated functions.

  7. Statistical methods for spatio-temporal systems

    CERN Document Server

    Finkenstadt, Barbel

    2006-01-01

    Statistical Methods for Spatio-Temporal Systems presents current statistical research issues on spatio-temporal data modeling and will promote advances in research and a greater understanding between the mechanistic and the statistical modeling communities.Contributed by leading researchers in the field, each self-contained chapter starts with an introduction of the topic and progresses to recent research results. Presenting specific examples of epidemic data of bovine tuberculosis, gastroenteric disease, and the U.K. foot-and-mouth outbreak, the first chapter uses stochastic models, such as point process models, to provide the probabilistic backbone that facilitates statistical inference from data. The next chapter discusses the critical issue of modeling random growth objects in diverse biological systems, such as bacteria colonies, tumors, and plant populations. The subsequent chapter examines data transformation tools using examples from ecology and air quality data, followed by a chapter on space-time co...

  8. Cryptanalysis on an image block encryption algorithm based on spatiotemporal chaos

    International Nuclear Information System (INIS)

    Wang Xing-Yuan; He Guo-Xiang

    2012-01-01

    An image block encryption scheme based on spatiotemporal chaos has been proposed recently. In this paper, we analyse the security weakness of the proposal. The main problem of the original scheme is that the generated keystream remains unchanged for encrypting every image. Based on the flaws, we demonstrate a chosen plaintext attack for revealing the equivalent keys with only 6 pairs of plaintext/ciphertext used. Finally, experimental results show the validity of our attack. (general)

  9. Spatiotemporal patterns and predictability of cyberattacks.

    Directory of Open Access Journals (Sweden)

    Yu-Zhong Chen

    Full Text Available 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.

  10. BioenergyKDF: Enabling Spatiotemporal Data Synthesis and Research Collaboration

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Spatio-temporal dependencies between hospital beds, physicians and health expenditure using visual variables and data classification in statistical table

    Science.gov (United States)

    Medyńska-Gulij, Beata; Cybulski, Paweł

    2016-06-01

    This paper analyses the use of table visual variables of statistical data of hospital beds as an important tool for revealing spatio-temporal dependencies. It is argued that some of conclusions from the data about public health and public expenditure on health have a spatio-temporal reference. Different from previous studies, this article adopts combination of cartographic pragmatics and spatial visualization with previous conclusions made in public health literature. While the significant conclusions about health care and economic factors has been highlighted in research papers, this article is the first to apply visual analysis to statistical table together with maps which is called previsualisation.

  12. Spatio-temporal dependencies between hospital beds, physicians and health expenditure using visual variables and data classification in statistical table

    Directory of Open Access Journals (Sweden)

    Medyńska-Gulij Beata

    2016-06-01

    Full Text Available This paper analyses the use of table visual variables of statistical data of hospital beds as an important tool for revealing spatio-temporal dependencies. It is argued that some of conclusions from the data about public health and public expenditure on health have a spatio-temporal reference. Different from previous studies, this article adopts combination of cartographic pragmatics and spatial visualization with previous conclusions made in public health literature. While the significant conclusions about health care and economic factors has been highlighted in research papers, this article is the first to apply visual analysis to statistical table together with maps which is called previsualisation.

  13. A spatio-temporal analysis of suicide in El Salvador.

    Science.gov (United States)

    Carcach, Carlos

    2017-04-20

    In 2012, international statistics showed El Salvador's suicide rate as 40th in the world and the highest in Latin America. Over the last 15 years, national statistics show the suicide death rate declining as opposed to an increasing rate of homicide. Though completed suicide is an important social and health issue, little is known about its prevalence, incidence, etiology and spatio-temporal behavior. The primary objective of this study was to examine completed suicide and homicide using the stream analogy to lethal violence within a spatio-temporal framework. A Bayesian model was applied to examine the spatio-temporal evolution of the tendency of completed suicide over homicide in El Salvador. Data on numbers of suicides and homicides at the municipal level were obtained from the Instituto de Medicina Legal (IML) and population counts, from the Dirección General de Estadística y Censos (DIGESTYC), for the period of 2002 to 2012. Data on migration were derived from the 2007 Population Census, and inequality data were obtained from a study by Damianović, Valenzuela and Vera. The data reveal a stable standardized rate of total lethal violence (completed suicide plus homicide) across municipalities over time; a decline in suicide; and a standardized suicide rate decreasing with income inequality but increasing with social isolation. Municipalities clustered in terms of both total lethal violence and suicide standardized rates. Spatial effects for suicide were stronger among municipalities located in the north-east and center-south sides of the country. New clusters of municipalities with large suicide standardized rates were detected in the north-west, south-west and center-south regions, all of which are part of time-stable clusters of homicide. Prevention efforts to reduce income inequality and mitigate the negative effects of weak relational systems should focus upon municipalities forming time-persistent clusters with a large rate of death by suicide. In

  14. A spatio-temporal analysis of suicide in El Salvador

    Directory of Open Access Journals (Sweden)

    Carlos Carcach

    2017-04-01

    Full Text Available Abstract Background In 2012, international statistics showed El Salvador’s suicide rate as 40th in the world and the highest in Latin America. Over the last 15 years, national statistics show the suicide death rate declining as opposed to an increasing rate of homicide. Though completed suicide is an important social and health issue, little is known about its prevalence, incidence, etiology and spatio-temporal behavior. The primary objective of this study was to examine completed suicide and homicide using the stream analogy to lethal violence within a spatio-temporal framework. Methods A Bayesian model was applied to examine the spatio-temporal evolution of the tendency of completed suicide over homicide in El Salvador. Data on numbers of suicides and homicides at the municipal level were obtained from the Instituto de Medicina Legal (IML and population counts, from the Dirección General de Estadística y Censos (DIGESTYC, for the period of 2002 to 2012. Data on migration were derived from the 2007 Population Census, and inequality data were obtained from a study by Damianović, Valenzuela and Vera. Results The data reveal a stable standardized rate of total lethal violence (completed suicide plus homicide across municipalities over time; a decline in suicide; and a standardized suicide rate decreasing with income inequality but increasing with social isolation. Municipalities clustered in terms of both total lethal violence and suicide standardized rates. Conclusions Spatial effects for suicide were stronger among municipalities located in the north-east and center-south sides of the country. New clusters of municipalities with large suicide standardized rates were detected in the north-west, south-west and center-south regions, all of which are part of time-stable clusters of homicide. Prevention efforts to reduce income inequality and mitigate the negative effects of weak relational systems should focus upon municipalities forming time

  15. Unsupervised Learning of Spatiotemporal Features by Video Completion

    OpenAIRE

    Nallabolu, Adithya Reddy

    2017-01-01

    In this work, we present an unsupervised representation learning approach for learning rich spatiotemporal features from videos without the supervision from semantic labels. We propose to learn the spatiotemporal features by training a 3D convolutional neural network (CNN) using video completion as a surrogate task. Using a large collection of unlabeled videos, we train the CNN to predict the missing pixels of a spatiotemporal hole given the remaining parts of the video through minimizing per...

  16. UNDERSTANDING SEVERE WEATHER PROCESSES THROUGH SPATIOTEMPORAL RELATIONAL RANDOM FORESTS

    Data.gov (United States)

    National Aeronautics and Space Administration — UNDERSTANDING SEVERE WEATHER PROCESSES THROUGH SPATIOTEMPORAL RELATIONAL RANDOM FORESTS AMY MCGOVERN, TIMOTHY SUPINIE, DAVID JOHN GAGNE II, NATHANIEL TROUTMAN,...

  17. Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa.

    Directory of Open Access Journals (Sweden)

    Jantien A Backer

    2016-12-01

    Full Text Available In 2014-2016, Guinea, Sierra Leone and Liberia in West Africa experienced the largest and longest Ebola epidemic since the discovery of the virus in 1976. During the epidemic, incidence data were collected and published at increasing resolution. To monitor the epidemic as it spread within and between districts, we develop an analysis method that exploits the full spatiotemporal resolution of the data by combining a local model for time-varying effective reproduction numbers with a gravity-type model for spatial dispersion of the infection. We test this method in simulations and apply it to the weekly incidences of confirmed and probable cases per district up to June 2015, as reported by the World Health Organization. Our results indicate that, of the newly infected cases, only a small percentage, between 4% and 10%, migrates to another district, and a minority of these migrants, between 0% and 23%, leave their country. The epidemics in the three countries are found to be similar in estimated effective reproduction numbers, and in the probability of importing infection into a district. The countries might have played different roles in cross-border transmissions, although a sensitivity analysis suggests that this could also be related to underreporting. The spatiotemporal analysis method can exploit available longitudinal incidence data at different geographical locations to monitor local epidemics, determine the extent of spatial spread, reveal the contribution of local and imported cases, and identify sources of introductions in uninfected areas. With good quality data on incidence, this data-driven method can help to effectively control emerging infections.

  18. Spatiotemporal conceptual platform for querying archaeological information systems

    Science.gov (United States)

    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

  19. New type of chimera and mutual synchronization of spatiotemporal structures in two coupled ensembles of nonlocally interacting chaotic maps

    Science.gov (United States)

    Bukh, Andrei; Rybalova, Elena; Semenova, Nadezhda; Strelkova, Galina; Anishchenko, Vadim

    2017-11-01

    We study numerically the dynamics of a network made of two coupled one-dimensional ensembles of discrete-time systems. The first ensemble is represented by a ring of nonlocally coupled Henon maps and the second one by a ring of nonlocally coupled Lozi maps. We find that the network of coupled ensembles can realize all the spatio-temporal structures which are observed both in the Henon map ensemble and in the Lozi map ensemble while uncoupled. Moreover, we reveal a new type of spatiotemporal structure, a solitary state chimera, in the considered network. We also establish and describe the effect of mutual synchronization of various complex spatiotemporal patterns in the system of two coupled ensembles of Henon and Lozi maps.

  20. Spatiotemporal Variability and Change of the South China Spring Precipitation during 1961–2012

    Directory of Open Access Journals (Sweden)

    Hong-Lan Liu

    2015-01-01

    Full Text Available We analyze precipitation data from 47 meteorological stations spanning between 1961 and 2012 and NCEP/NCAR reanalysis to understand spatiotemporal variability and change of spring precipitation of South China and their relations to atmospheric circulations. Empirical orthogonal function (EOF analysis and rotated EOF (REOF are used to reveal dominant spatial structures of precipitation anomaly and Mann-Kendall testing method to determine the temporal locations of abrupt changes during the analyzed time span. We find that the first spatial mode of the spring precipitation of the South China has a domain uniform structure; the second is dominated by a spatial dipole; and the third contains six variability centers. 1980s was the decade of the largest amount of precipitation while 1960s the decade of the smallest amount of precipitation. The spring precipitation also appeared to have a decreasing trend since 2000. We also find that spring precipitation of the South China has experienced a few abrupt changes: sudden increment at 1964, sudden decrement at 2002, and sudden increment at 1995. In addition to these abrupt changes, the precipitation could also be characterized by variability of multiple temporal scales, with dominant periodicities of 4 years, 8 years, and 14 years. The South China spring precipitation is also closely tied to the atmospheric circulations: when Aleutian Low strengthens, westerly weakens, and the center of the Western Pacific subtropical high shifts southeastward in the early spring; and the South China precipitation tends to be abundant (positive anomaly. In contrast, when Ural ridge strengthens, the southern branch of the East Asian trough weakens and the Western Pacific subtropical high shifts northwestward in the early spring, the South China precipitation tends to be reduced (negative anomaly.

  1. Formulating qualitative features using interactive visualization for analysis of multivariate spatiotemporal data

    Science.gov (United States)

    Porter, M.; Hill, M. C.; Pierce, S. A.; Gil, Y.; Pennington, D. D.

    2017-12-01

    DiscoverWater is a web-based visualization tool developed to enable the visual representation of data, and thus, aid scientific and societal understanding of hydrologic systems. Open data sources are coalesced to, for example, illustrate the impacts on streamflow of irrigation withdrawals. Scientists and stakeholders are informed through synchronized time-series data plots that correlate multiple spatiotemporal datasets and an interactive time-evolving map that provides a spatial analytical context. Together, these components elucidate trends so that the user can try to envision the relations between groundwater-surface water interactions, the impacts of pumping on these interactions, and the interplay of climate. Aligning data in this manner has the capacity for interdisciplinary knowledge discovery and motivates dialogue about system processes that we seek to enhance through qualitative features informed through quantitative models. DiscoverWater and its connection is demonstrated using two field cases. First, it is used to visualize data sets from the High Plains aquifer, where reservoir- and groundwater-supported irrigation has affected the Arkansas River in western Kansas. Second, data and model results from Barton Springs segment of the Edwards aquifer in Texas reveal the effects of regional pumping on this important urbanizing aquifer system. Identifying what is interesting about the data and the modeled system in the two different case studies is a step towards moving typically static visualization capabilities to an adaptive framework. Additionally, the dashboard interface incorporates both quantitative and qualitative information about distinctive case studies in a machine-readable form, such that a catalog of qualitative models can capture subject matter expertise alongside associated datasets. As the catalog is expanded to include other case studies, the collection has potential to establish a standard framework able to inform intelligent system

  2. Spatio-temporal intermittency on the sandpile

    International Nuclear Information System (INIS)

    Erzan, A.; Sinha, S.

    1990-08-01

    The self-organized critical state exhibited by a sandpile model is shown to correspond to motion on an attractor characterized by an invariant distribution of the height variable. The largest Lyapunov exponent is equal to zero. The model nonetheless displays intermittent chaos, with a multifractal distribution of local expansion coefficients in history space. Laminar spatio-temporal regions are interrupted by chaotic bursts caused by avalanches. We introduce the concept of local histories in configuration space and show that their expansion parameters also exhibit a multifractal distribution in time and space. (author). 22 refs, 5 figs

  3. Spatiotemporal Change Detection Using Landsat Imagery: the Case Study of Karacabey Flooded Forest, Bursa, Turkey

    Science.gov (United States)

    Akay, A. E.; Gencal, B.; Taş, İ.

    2017-11-01

    This short paper aims to detect spatiotemporal detection of land use/land cover change within Karacabey Flooded Forest region. Change detection analysis applied to Landsat 5 TM images representing July 2000 and a Landsat 8 OLI representing June 2017. Various image processing tools were implemented using ERDAS 9.2, ArcGIS 10.4.1, and ENVI programs to conduct spatiotemporal change detection over these two images such as band selection, corrections, subset, classification, recoding, accuracy assessment, and change detection analysis. Image classification revealed that there are five significant land use/land cover types, including forest, flooded forest, swamp, water, and other lands (i.e. agriculture, sand, roads, settlement, and open areas). The results indicated that there was increase in flooded forest, water, and other lands, while the cover of forest and swamp decreased.

  4. Transient spatiotemporal chaos in the Morris-Lecar neuronal ring network

    Energy Technology Data Exchange (ETDEWEB)

    Keplinger, Keegan, E-mail: keegankeplinger@gmail.com; Wackerbauer, Renate, E-mail: rawackerbauer@alaska.edu [Department of Physics, University of Alaska, Fairbanks, Alaska 99775-5920 (United States)

    2014-03-15

    Transient behavior is thought to play an integral role in brain functionality. Numerical simulations of the firing activity of diffusively coupled, excitable Morris-Lecar neurons reveal transient spatiotemporal chaos in the parameter regime below the saddle-node on invariant circle bifurcation point. The neighborhood of the chaotic saddle is reached through perturbations of the rest state, in which few initially active neurons at an effective spatial distance can initiate spatiotemporal chaos. The system escapes from the neighborhood of the chaotic saddle to either the rest state or to a state of pulse propagation. The lifetime of the chaotic transients is manipulated in a statistical sense through a singular application of a synchronous perturbation to a group of neurons.

  5. Transient spatiotemporal chaos in the Morris-Lecar neuronal ring network.

    Science.gov (United States)

    Keplinger, Keegan; Wackerbauer, Renate

    2014-03-01

    Transient behavior is thought to play an integral role in brain functionality. Numerical simulations of the firing activity of diffusively coupled, excitable Morris-Lecar neurons reveal transient spatiotemporal chaos in the parameter regime below the saddle-node on invariant circle bifurcation point. The neighborhood of the chaotic saddle is reached through perturbations of the rest state, in which few initially active neurons at an effective spatial distance can initiate spatiotemporal chaos. The system escapes from the neighborhood of the chaotic saddle to either the rest state or to a state of pulse propagation. The lifetime of the chaotic transients is manipulated in a statistical sense through a singular application of a synchronous perturbation to a group of neurons.

  6. Spatiotemporal regulation of ATP and Ca2+ dynamics in vertebrate rod and cone ribbon synapses.

    Science.gov (United States)

    Johnson, Jerry E; Perkins, Guy A; Giddabasappa, Anand; Chaney, Shawntay; Xiao, Weimin; White, Andrew D; Brown, Joshua M; Waggoner, Jenna; Ellisman, Mark H; Fox, Donald A

    2007-06-15

    In conventional neurons, Ca2+ enters presynaptic terminals during an action potential and its increased local concentration triggers transient exocytosis. In contrast, vertebrate photoreceptors are nonspiking neurons that maintain sustained depolarization and neurotransmitter release from ribbon synapses in darkness and produce light-dependent graded hyperpolarizing responses. Rods transmit single photon responses with high fidelity, whereas cones are less sensitive and exhibit faster response kinetics. These differences are likely due to variations in presynaptic Ca2+ dynamics. Metabolic coupling and cross-talk between mitochondria, endoplasmic reticulum (ER), plasma membrane Ca2+ ATPase (PMCA), and Na+-Ca2+ exchanger (NCX) coordinately control presynaptic ATP production and Ca2+ dynamics. The goal of our structural and functional studies was to determine the spatiotemporal regulation of ATP and Ca2+ dynamics in rod spherules and cone pedicles. Central retina tissue from C57BL/6 mice was used. Laser scanning confocal microscopy (LSCM) experiments were conducted on fixed-frozen vertical sections. Primary antibodies were selected for their tissue/cellular specificity and ability to recognize single, multiple or all splice variants of selected isoforms. Electron microscopy (EM) and 3-D electron tomography (ET) studies used our standard procedures on thin- and thick-sectioned retinas, respectively. Calibrated fluo-3-Ca2+ imaging experiments of dark- and light-adapted rod and cone terminals in retinal slices were conducted. Confocal microscopy showed that mitochondria, ER, PMCA, and NCX1 exhibited distinct retinal lamination patterns and differential distribution in photoreceptor synapses. Antibodies for three distinct mitochondrial compartments differentially labeled retinal areas with high metabolic demand: rod and cone inner segments, previously undescribed cone juxtanuclear mitochondria and the two plexiform layers. Rod spherule membranes uniformly and intensely

  7. Exploring the spatio-temporal neural basis of face learning

    Science.gov (United States)

    Yang, Ying; Xu, Yang; Jew, Carol A.; Pyles, John A.; Kass, Robert E.; Tarr, Michael J.

    2017-01-01

    Humans are experts at face individuation. Although previous work has identified a network of face-sensitive regions and some of the temporal signatures of face processing, as yet, we do not have a clear understanding of how such face-sensitive regions support learning at different time points. To study the joint spatio-temporal neural basis of face learning, we trained subjects to categorize two groups of novel faces and recorded their neural responses using magnetoencephalography (MEG) throughout learning. A regression analysis of neural responses in face-sensitive regions against behavioral learning curves revealed significant correlations with learning in the majority of the face-sensitive regions in the face network, mostly between 150–250 ms, but also after 300 ms. However, the effect was smaller in nonventral regions (within the superior temporal areas and prefrontal cortex) than that in the ventral regions (within the inferior occipital gyri (IOG), midfusiform gyri (mFUS) and anterior temporal lobes). A multivariate discriminant analysis also revealed that IOG and mFUS, which showed strong correlation effects with learning, exhibited significant discriminability between the two face categories at different time points both between 150–250 ms and after 300 ms. In contrast, the nonventral face-sensitive regions, where correlation effects with learning were smaller, did exhibit some significant discriminability, but mainly after 300 ms. In sum, our findings indicate that early and recurring temporal components arising from ventral face-sensitive regions are critically involved in learning new faces. PMID:28570739

  8. Spatiotemporal mapping of sex differences during attentional processing.

    Science.gov (United States)

    Neuhaus, Andres H; Opgen-Rhein, Carolin; Urbanek, Carsten; Gross, Melanie; Hahn, Eric; Ta, Thi Minh Tam; Koehler, Simone; Dettling, Michael

    2009-09-01

    Functional neuroimaging studies have increasingly aimed at approximating neural substrates of human cognitive sex differences elicited by visuospatial challenge. It has been suggested that females and males use different behaviorally relevant neurocognitive strategies. In females, greater right prefrontal cortex activation has been found in several studies. The spatiotemporal dynamics of neural events associated with these sex differences is still unclear. We studied 22 female and 22 male participants matched for age, education, and nicotine with 29-channel-electroencephalogram recorded under a visual selective attention paradigm, the Attention Network Test. Visual event-related potentials (ERP) were topographically analyzed and neuroelectric sources were estimated. In absence of behavioral differences, ERP analysis revealed a novel frontal-occipital second peak of visual N100 that was significantly increased in females relative to males. Further, in females exclusively, a corresponding central ERP component at around 220 ms was found; here, a strong correlation between stimulus salience and sex difference of the central ERP component amplitude was observed. Subsequent source analysis revealed increased cortical current densities in right rostral prefrontal (BA 10) and occipital cortex (BA 19) in female subjects. This is the first study to report on a tripartite association between sex differences in ERPs, visual stimulus salience, and right prefrontal cortex activation during attentional processing. 2009 Wiley-Liss, Inc.

  9. Spatio-temporal scaling of channels in braided streams.

    Science.gov (United States)

    A.G. Hunt; G.E. Grant; V.K. Gupta

    2006-01-01

    The spatio-temporal scaling relationship for individual channels in braided streams is shown to be identical to the spatio-temporal scaling associated with constant Froude number, e.g., Fr = l. A means to derive this relationship is developed from a new theory of sediment transport. The mechanism by which the Fr = l condition apparently governs the scaling seems to...

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

    Science.gov (United States)

    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…

  11. Simultaneous spatio-temporal focusing for tissue manipulation

    Directory of Open Access Journals (Sweden)

    Squier J.

    2013-11-01

    Full Text Available Simultaneous spatiotemporal focusing (SSTF is applied to lens tissue and compared directly with standard femtosecond micromachining of the tissue at the same numerical aperture. Third harmonic generation imaging is used for spatio-temporal characterization of the processing conditions obtained with both a standard and SSTF focus.

  12. Spatiotemporal Interpolation Methods for Solar Event Trajectories

    Science.gov (United States)

    Filali Boubrahimi, Soukaina; Aydin, Berkay; Schuh, Michael A.; Kempton, Dustin; Angryk, Rafal A.; Ma, Ruizhe

    2018-05-01

    This paper introduces four spatiotemporal interpolation methods that enrich complex, evolving region trajectories that are reported from a variety of ground-based and space-based solar observatories every day. Our interpolation module takes an existing solar event trajectory as its input and generates an enriched trajectory with any number of additional time–geometry pairs created by the most appropriate method. To this end, we designed four different interpolation techniques: MBR-Interpolation (Minimum Bounding Rectangle Interpolation), CP-Interpolation (Complex Polygon Interpolation), FI-Interpolation (Filament Polygon Interpolation), and Areal-Interpolation, which are presented here in detail. These techniques leverage k-means clustering, centroid shape signature representation, dynamic time warping, linear interpolation, and shape buffering to generate the additional polygons of an enriched trajectory. Using ground-truth objects, interpolation effectiveness is evaluated through a variety of measures based on several important characteristics that include spatial distance, area overlap, and shape (boundary) similarity. To our knowledge, this is the first research effort of this kind that attempts to address the broad problem of spatiotemporal interpolation of solar event trajectories. We conclude with a brief outline of future research directions and opportunities for related work in this area.

  13. Spatiotemporal chaos in coupled logistic maps

    International Nuclear Information System (INIS)

    Varella Guedes, Andre; Amorim Savi, Marcelo

    2010-01-01

    The objective of this work is to investigate the spatiotemporal dynamics of coupled logistic maps. These maps are prototypes of high-dimensional dynamical systems and have been used to describe the evolution and pattern formation in different systems. Here, the logistic map lattice is coupled by a power law and, therefore, each map is influenced by other maps in its neighborhood. The Kolmogorov-Sinai entropy density is employed to quantify the complexity of system behavior, permitting a general qualitative understanding of different aspects of system dynamics. Three kinds of boundary conditions are treated and the influence of initial conditions is also of concern. Non-homogeneous maps are investigated, showing interesting aspects of spatiotemporal dynamics. The idea is to analyze the spatial interaction between two qualitative different types of behavior from a grid that is split into two parts. Numerical simulations show what types of conditions present a greater tendency to develop chaotic, periodic and synchronized responses. It should be highlighted that non-homogeneous grids have situations where a chaotic pattern can emerge from two periodic responses and also situations where a periodic pattern can emerge from chaos.

  14. Multiple sclerosis

    International Nuclear Information System (INIS)

    Sadashima, Hiromichi; Kusaka, Hirofumi; Imai, Terukuni; Takahashi, Ryosuke; Matsumoto, Sadayuki; Yamamoto, Toru; Yamasaki, Masahiro; Maya, Kiyomi

    1986-01-01

    Eleven patients with a definite diagnosis of multiple sclerosis were examined in terms of correlations between the clinical features and the results of cranial computed tomography (CT), and magnetic resonance imaging (MRI). Results: In 5 of the 11 patients, both CT and MRI demonstrated lesions consistent with a finding of multiple sclerosis. In 3 patients, only MRI demonstrated lesions. In the remaining 3 patients, neither CT nor MRI revealed any lesion in the brain. All 5 patients who showed abnormal findings on both CT and MRI had clinical signs either of cerebral or brainstem - cerebellar lesions. On the other hand, two of the 3 patients with normal CT and MRI findings had optic-nerve and spinal-cord signs. Therefore, our results suggested relatively good correlations between the clinical features, CT, and MRI. MRI revealed cerebral lesions in two of the four patients with clinical signs of only optic-nerve and spinal-cord lesions. MRI demonstrated sclerotic lesions in 3 of the 6 patients whose plaques were not detected by CT. In conclusion, MRI proved to be more helpful in the demonstration of lesions attributable to chronic multiple sclerosis. (author)

  15. Audio-Visual Speaker Diarization Based on Spatiotemporal Bayesian Fusion.

    Science.gov (United States)

    Gebru, Israel D; Ba, Sileye; Li, Xiaofei; Horaud, Radu

    2018-05-01

    Speaker diarization consists of assigning speech signals to people engaged in a dialogue. An audio-visual spatiotemporal diarization model is proposed. The model is well suited for challenging scenarios that consist of several participants engaged in multi-party interaction while they move around and turn their heads towards the other participants rather than facing the cameras and the microphones. Multiple-person visual tracking is combined with multiple speech-source localization in order to tackle the speech-to-person association problem. The latter is solved within a novel audio-visual fusion method on the following grounds: binaural spectral features are first extracted from a microphone pair, then a supervised audio-visual alignment technique maps these features onto an image, and finally a semi-supervised clustering method assigns binaural spectral features to visible persons. The main advantage of this method over previous work is that it processes in a principled way speech signals uttered simultaneously by multiple persons. The diarization itself is cast into a latent-variable temporal graphical model that infers speaker identities and speech turns, based on the output of an audio-visual association process, executed at each time slice, and on the dynamics of the diarization variable itself. The proposed formulation yields an efficient exact inference procedure. A novel dataset, that contains audio-visual training data as well as a number of scenarios involving several participants engaged in formal and informal dialogue, is introduced. The proposed method is thoroughly tested and benchmarked with respect to several state-of-the art diarization algorithms.

  16. Emergent dynamics of spatio-temporal chaos in a heterogeneous excitable medium.

    Science.gov (United States)

    Bittihn, Philip; Berg, Sebastian; Parlitz, Ulrich; Luther, Stefan

    2017-09-01

    Self-organized activation patterns in excitable media such as spiral waves and spatio-temporal chaos underlie dangerous cardiac arrhythmias. While the interaction of single spiral waves with different types of heterogeneity has been studied extensively, the effect of heterogeneity on fully developed spatio-temporal chaos remains poorly understood. We investigate how the complexity and stability properties of spatio-temporal chaos in the Bär-Eiswirth model of excitable media depend on the heterogeneity of the underlying medium. We employ different measures characterizing the chaoticity of the system and find that the spatial arrangement of multiple discrete lower excitability regions has a strong impact on the complexity of the dynamics. Varying the number, shape, and spatial arrangement of the heterogeneities, we observe strong emergent effects ranging from increases in chaoticity to the complete cessation of chaos, contrasting the expectation from the homogeneous behavior. The implications of our findings for the development and treatment of arrhythmias in the heterogeneous cardiac muscle are discussed.

  17. Selecting a separable parametric spatiotemporal covariance structure for longitudinal imaging data.

    Science.gov (United States)

    George, Brandon; Aban, Inmaculada

    2015-01-15

    Longitudinal imaging studies allow great insight into how the structure and function of a subject's internal anatomy changes over time. Unfortunately, the analysis of longitudinal imaging data is complicated by inherent spatial and temporal correlation: the temporal from the repeated measures and the spatial from the outcomes of interest being observed at multiple points in a patient's body. We propose the use of a linear model with a separable parametric spatiotemporal error structure for the analysis of repeated imaging data. The model makes use of spatial (exponential, spherical, and Matérn) and temporal (compound symmetric, autoregressive-1, Toeplitz, and unstructured) parametric correlation functions. A simulation study, inspired by a longitudinal cardiac imaging study on mitral regurgitation patients, compared different information criteria for selecting a particular separable parametric spatiotemporal correlation structure as well as the effects on types I and II error rates for inference on fixed effects when the specified model is incorrect. Information criteria were found to be highly accurate at choosing between separable parametric spatiotemporal correlation structures. Misspecification of the covariance structure was found to have the ability to inflate the type I error or have an overly conservative test size, which corresponded to decreased power. An example with clinical data is given illustrating how the covariance structure procedure can be performed in practice, as well as how covariance structure choice can change inferences about fixed effects. Copyright © 2014 John Wiley & Sons, Ltd.

  18. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior.

    Science.gov (United States)

    Portugues, Ruben; Feierstein, Claudia E; Engert, Florian; Orger, Michael B

    2014-03-19

    Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate but ordered pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments systematically reveal the functional architecture of neural circuits underlying a sensorimotor behavior in a vertebrate brain. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Multiple myeloma

    International Nuclear Information System (INIS)

    Sohn, Jeong Ick; Ha, Choon Ho; Choi, Karp Shik

    1994-01-01

    Multiple myeloma is a malignant plasma cell tumor that is thought to originate proliferation of a single clone of abnormal plasma cell resulting production of a whole monoclonal paraprotein. The authors experienced a case of multiple myeloma with severe mandibular osteolytic lesions in 46-year-old female. As a result of careful analysis of clinical, radiological, histopathological features, and laboratory findings, we diagnosed it as multiple myeloma, and the following results were obtained. 1. Main clinical symptoms were intermittent dull pain on the mandibular body area, abnormal sensation of lip and pain due to the fracture on the right clavicle. 2. Laboratory findings revealed M-spike, reversed serum albumin-globulin ratio, markedly elevated ESR and hypercalcemia. 3. Radiographically, multiple osteolytic punched-out radiolucencies were evident on the skull, zygoma, jaw bones, ribs, clavicle and upper extremities. Enlarged liver and increased uptakes on the lesional sites in RN scan were also observed. 4. Histopathologically, markedly hypercellular marrow with sheets of plasmoblasts and megakaryocytes were also observed.

  20. Spatiotemporal Stochastic Resonance:Theory and Experiment

    Science.gov (United States)

    Peter, Jung

    1996-03-01

    The amplification of weak periodic signals in bistable or excitable systems via stochastic resonance has been studied intensively over the last years. We are going one step further and ask: Can noise enhance spatiotemporal patterns in excitable media and can this effect be observed in nature? To this end, we are looking at large, two dimensional arrays of coupled excitable elements. Due to the coupling, excitation can propagate through the array in form of nonlinear waves. We observe target waves, rotating spiral waves and other wave forms. If the coupling between the elements is below a critical threshold, any excitational pattern will die out in the absence of noise. Below this threshold, large scale rotating spiral waves - as they are observed above threshold - can be maintained by a proper level of the noise[1]. Furthermore, their geometric features, such as the curvature can be controlled by the homogeneous noise level[2]. If the noise level is too large, break up of spiral waves and collisions with spontaneously nucleated waves yields spiral turbulence. Driving our array with a spatiotemporal pattern, e.g. a rotating spiral wave, we show that for weak coupling the excitational response of the array shows stochastic resonance - an effect we have termed spatiotemporal stochastic resonance. In the last part of the talk I'll make contact with calcium waves, observed in astrocyte cultures and hippocampus slices[3]. A. Cornell-Bell and collaborators[3] have pointed out the role of calcium waves for long-range glial signaling. We demonstrate the similarity of calcium waves with nonlinear waves in noisy excitable media. The noise level in the tissue is characterized by spontaneous activity and can be controlled by applying neuro-transmitter substances[3]. Noise effects in our model are compared with the effect of neuro-transmitters on calcium waves. [1]P. Jung and G. Mayer-Kress, CHAOS 5, 458 (1995). [2]P. Jung and G. Mayer-Kress, Phys. Rev. Lett.62, 2682 (1995). [3

  1. Methodology for Clustering High-Resolution Spatiotemporal Solar Resource Data

    Energy Technology Data Exchange (ETDEWEB)

    Getman, Dan [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lopez, Anthony [National Renewable Energy Lab. (NREL), Golden, CO (United States); Mai, Trieu [National Renewable Energy Lab. (NREL), Golden, CO (United States); Dyson, Mark [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    In this report, we introduce a methodology to achieve multiple levels of spatial resolution reduction of solar resource data, with minimal impact on data variability, for use in energy systems modeling. The selection of an appropriate clustering algorithm, parameter selection including cluster size, methods of temporal data segmentation, and methods of cluster evaluation are explored in the context of a repeatable process. In describing this process, we illustrate the steps in creating a reduced resolution, but still viable, dataset to support energy systems modeling, e.g. capacity expansion or production cost modeling. This process is demonstrated through the use of a solar resource dataset; however, the methods are applicable to other resource data represented through spatiotemporal grids, including wind data. In addition to energy modeling, the techniques demonstrated in this paper can be used in a novel top-down approach to assess renewable resources within many other contexts that leverage variability in resource data but require reduction in spatial resolution to accommodate modeling or computing constraints.

  2. A full time-domain approach to spatio-temporal dynamics of semiconductor lasers. II. Spatio-temporal dynamics

    Science.gov (United States)

    Böhringer, Klaus; Hess, Ortwin

    The spatio-temporal dynamics of novel semiconductor lasers is discussed on the basis of a space- and momentum-dependent full time-domain approach. To this means the space-, time-, and momentum-dependent Full-Time Domain Maxwell Semiconductor Bloch equations, derived and discussed in our preceding paper I [K. Böhringer, O. Hess, A full time-domain approach to spatio-temporal dynamics of semiconductor lasers. I. Theoretical formulation], are solved by direct numerical integration. Focussing on the device physics of novel semiconductor lasers that profit, in particular, from recent advances in nanoscience and nanotechnology, we discuss the examples of photonic band edge surface emitting lasers (PBE-SEL) and semiconductor disc lasers (SDLs). It is demonstrated that photonic crystal effects can be obtained for finite crystal structures, and leading to a significant improvement in laser performance such as reduced lasing thresholds. In SDLs, a modern device concept designed to increase the power output of surface-emitters in combination with near-diffraction-limited beam quality, we explore the complex interplay between the intracavity optical fields and the quantum well gain material in SDL structures. Our simulations reveal the dynamical balance between carrier generation due to pumping into high energy states, momentum relaxation of carriers, and stimulated recombination from states near the band edge. Our full time-domain approach is shown to also be an excellent framework for the modelling of the interaction of high-intensity femtosecond and picosecond pulses with semiconductor nanostructures. It is demonstrated that group velocity dispersion, dynamical gain saturation and fast self-phase modulation (SPM) are the main causes for the induced changes and asymmetries in the amplified pulse shape and spectrum of an ultrashort high-intensity pulse. We attest that the time constants of the intraband scattering processes are critical to gain recovery. Moreover, we present

  3. Spatio-Temporal Patterns of Barmah Forest Virus Disease in Queensland, Australia

    Science.gov (United States)

    Naish, Suchithra; Hu, Wenbiao; Mengersen, Kerrie; Tong, Shilu

    2011-01-01

    Background Barmah Forest virus (BFV) disease is a common and wide-spread mosquito-borne disease in Australia. This study investigated the spatio-temporal patterns of BFV disease in Queensland, Australia using geographical information system (GIS) tools and geostatistical analysis. Methods/Principal Findings We calculated the incidence rates and standardised incidence rates of BFV disease. Moran's I statistic was used to assess the spatial autocorrelation of BFV incidences. Spatial dynamics of BFV disease was examined using semi-variogram analysis. Interpolation techniques were applied to visualise and display the spatial distribution of BFV disease in statistical local areas (SLAs) throughout Queensland. Mapping of BFV disease by SLAs reveals the presence of substantial spatio-temporal variation over time. Statistically significant differences in BFV incidence rates were identified among age groups (χ2 = 7587, df = 7327,pQueensland using GIS and geostatistics. The BFV transmission varied with age and gender, which may be due to exposure rates or behavioural risk factors. There are differences in the spatio-temporal patterns of BFV disease which may be related to local socio-ecological and environmental factors. These research findings may have implications in the BFV disease control and prevention programs in Queensland. PMID:22022430

  4. Cryptanalysis of a spatiotemporal chaotic cryptosystem

    International Nuclear Information System (INIS)

    Rhouma, Rhouma; Belghith, Safya

    2009-01-01

    This paper proposes three different attacks on a recently proposed chaotic cryptosystem in [Li P, Li Z, Halang WA, Chen G. A stream cipher based on a spatiotemporal chaotic system. Chaos, Solitons and Fractals 2007;32:1867-76]. The cryptosystem under study displays weakness in the generation of the keystream. The encryption is made by generating a keystream mixed with blocks generated from the plaintext. The so obtained keystream remains unchanged for every encryption procedure. Moreover, its generation does neither depend on the plaintext nor on the ciphertext, that's to say, the keystream remains unchangeable for every plaintext with the same length. Guessing the keystream leads to guessing the key. This paper presents three possible attacks able to break the whole cryptosystem based on this drawback in generating the keystream.

  5. The Spatiotemporal Dynamics of Digital News Audiences

    DEFF Research Database (Denmark)

    Peters, Chris

    2016-01-01

    of changing the socially-situated affordances of news use. Having sketched these contours, the chapter then highlights analytical challenges for understanding and conceptualizing the new interrelations between digital news content, production, and consumption, grounding this analysis with theoretical insights...... that emphasize the significance of spatiotemporal dynamics. The emphasis here is on the interrelations and mobilities of digital news audiences, based on a recognition of the productive impacts of media use while being careful to note the limitations of a paradigm shift that points solely to the possibilities...... generated by the ubiquitous presence of media in our everyday lives. Aspects of interaction and personalization beget by new media technologies certainly shape the possibilities, practices and power audiences have to choose news wherever, whenever, and however they want. However, this simultaneously...

  6. Spatiotemporal aspects of flood exposure in Switzerland

    Directory of Open Access Journals (Sweden)

    Röthlisberger Veronika

    2016-01-01

    Full Text Available While flood hazard mapping in Switzerland is close to completion, only a limited number of studies have been specifically conducted on exposure and vulnerability. We fill this knowledge gap by conducting a nation-wide study of flood exposure of buildings in Switzerland. Therefore, we generate a country-wide comprehensive and homogenous data set of polygons of residential buildings and their period of construction and overlay these building polygons with compiled and harmonized flood hazard maps provided by the Swiss cantons. In this paper we present first results of spatiotemporal analyses, namely the evolution of exposure from 1919 to 2012. Surprising is the increase in the share of exposure of new constructed buildings since the 1980s which contradicts the indented effects of the Swiss flood risk management strategies and calls for further investigations.

  7. Nonreciprocal Thermal Material by Spatiotemporal Modulation

    Science.gov (United States)

    Torrent, Daniel; Poncelet, Olivier; Batsale, Jean-Chirstophe

    2018-03-01

    The thermal properties of a material with a spatiotemporal modulation, in the form of a traveling wave, in both the thermal conductivity and the specific heat capacity are studied. It is found that these materials behave as materials with an internal convectionlike term that provides them with nonreciprocal properties, in the sense that the heat flux has different properties when it propagates in the same direction or in the opposite one to the modulation of the parameters. An effective medium description is presented which accurately describes the modulated material, and numerical simulations support this description and verify the nonreciprocal properties of the material. It is found that these materials are promising candidates for the design of thermal diodes and other advanced devices for the control of the heat flow at all scales.

  8. Inositol trisphosphate receptor mediated spatiotemporal calcium signalling.

    Science.gov (United States)

    Miyazaki, S

    1995-04-01

    Spatiotemporal Ca2+ signalling in the cytoplasm is currently understood as an excitation phenomenon by analogy with electrical excitation in the plasma membrane. In many cell types, Ca2+ waves and Ca2+ oscillations are mediated by inositol 1,4,5-trisphosphate (IP3) receptor/Ca2+ channels in the endoplasmic reticulum membrane, with positive feedback between cytosolic Ca2+ and IP3-induced Ca2+ release creating a regenerative process. Remarkable advances have been made in the past year in the analysis of subcellular Ca2+ microdomains using confocal microscopy and of Ca2+ influx pathways that are functionally coupled to IP3-induced Ca2+ release. Ca2+ signals can be conveyed into the nucleus and mitochondria. Ca2+ entry from outside the cell allows repetitive Ca2+ release by providing Ca2+ to refill the endoplasmic reticulum stores, thus giving rise to frequency-encoded Ca2+ signals.

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

    Science.gov (United States)

    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

  10. Statistical Approaches for Spatiotemporal Prediction of Low Flows

    Science.gov (United States)

    Fangmann, A.; Haberlandt, U.

    2017-12-01

    An adequate assessment of regional climate change impacts on streamflow requires the integration of various sources of information and modeling approaches. This study proposes simple statistical tools for inclusion into model ensembles, which are fast and straightforward in their application, yet able to yield accurate streamflow predictions in time and space. Target variables for all approaches are annual low flow indices derived from a data set of 51 records of average daily discharge for northwestern Germany. The models require input of climatic data in the form of meteorological drought indices, derived from observed daily climatic variables, averaged over the streamflow gauges' catchments areas. Four different modeling approaches are analyzed. Basis for all pose multiple linear regression models that estimate low flows as a function of a set of meteorological indices and/or physiographic and climatic catchment descriptors. For the first method, individual regression models are fitted at each station, predicting annual low flow values from a set of annual meteorological indices, which are subsequently regionalized using a set of catchment characteristics. The second method combines temporal and spatial prediction within a single panel data regression model, allowing estimation of annual low flow values from input of both annual meteorological indices and catchment descriptors. The third and fourth methods represent non-stationary low flow frequency analyses and require fitting of regional distribution functions. Method three is subject to a spatiotemporal prediction of an index value, method four to estimation of L-moments that adapt the regional frequency distribution to the at-site conditions. The results show that method two outperforms successive prediction in time and space. Method three also shows a high performance in the near future period, but since it relies on a stationary distribution, its application for prediction of far future changes may be

  11. Malaria infection has spatial, temporal, and spatiotemporal heterogeneity in unstable malaria transmission areas in northwest Ethiopia.

    Directory of Open Access Journals (Sweden)

    Kassahun Alemu

    Full Text Available BACKGROUND: Malaria elimination requires successful nationwide control efforts. Detecting the spatiotemporal distribution and mapping high-risk areas are useful to effectively target pockets of malaria endemic regions for interventions. OBJECTIVE: The aim of the study was to identify patterns of malaria distribution by space and time in unstable malaria transmission areas in northwest Ethiopia. METHODS: Data were retrieved from the monthly reports stored in the district malaria offices for the period between 2003 and 2012. Eighteen districts in the highland and fringe malaria areas were included and geo-coded for the purpose of this study. The spatial data were created in ArcGIS10 for each district. The Poisson model was used by applying Kulldorff methods using the SaTScan™ software to analyze the purely temporal, spatial and space-time clusters of malaria at a district levels. RESULTS: The study revealed that malaria case distribution has spatial, temporal, and spatiotemporal heterogeneity in unstable transmission areas. Most likely spatial malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR =197764.1, p<0.001. Significant spatiotemporal malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR=197764.1, p<0.001 between 2003/1/1 and 2012/12/31. A temporal scan statistics identified two high risk periods from 2009/1/1 to 2010/12/31 (LLR=72490.5, p<0.001 and from 2003/1/1 to 2005/12/31 (LLR=26988.7, p<0.001. CONCLUSION: In unstable malaria transmission areas, detecting and considering the spatiotemporal heterogeneity would be useful to strengthen malaria control efforts and ultimately achieve elimination.

  12. Neurogenomic signatures of spatiotemporal memories in time-trained forager honey bees

    Science.gov (United States)

    Naeger, Nicholas L.; Van Nest, Byron N.; Johnson, Jennifer N.; Boyd, Sam D.; Southey, Bruce R.; Rodriguez-Zas, Sandra L.; Moore, Darrell; Robinson, Gene E.

    2011-01-01

    Honey bees can form distinct spatiotemporal memories that allow them to return repeatedly to different food sources at different times of day. Although it is becoming increasingly clear that different behavioral states are associated with different profiles of brain gene expression, it is not known whether this relationship extends to states that are as dynamic and specific as those associated with foraging-related spatiotemporal memories. We tested this hypothesis by training different groups of foragers from the same colony to collect sucrose solution from one of two artificial feeders; each feeder was in a different location and had sucrose available at a different time, either in the morning or afternoon. Bees from both training groups were collected at both the morning and afternoon training times to result in one set of bees that was undergoing stereotypical food anticipatory behavior and another that was inactive for each time of day. Between the two groups with the different spatiotemporal memories, microarray analysis revealed that 1329 genes were differentially expressed in the brains of honey bees. Many of these genes also varied with time of day, time of training or state of food anticipation. Some of these genes are known to be involved in a variety of biological processes, including metabolism and behavior. These results indicate that distinct spatiotemporal foraging memories in honey bees are associated with distinct neurogenomic signatures, and the decomposition of these signatures into sets of genes that are also influenced by time or activity state hints at the modular composition of this complex neurogenomic phenotype. PMID:21346126

  13. Electricity as (Big Data: Metering, spatiotemporal granularity and value

    Directory of Open Access Journals (Sweden)

    Mette Kragh-Furbo

    2018-02-01

    Full Text Available Electricity is hidden within wires and networks only revealing its quantity and flow when metered. The making of its properties into data is therefore particularly important to the relations that are formed around electricity as a produced and managed phenomenon. We propose approaching all metering as a situated activity, a form of quantification work in which data is made and becomes mobile in particular spatial and temporal terms, enabling its entry into data infrastructures and schemes of evaluation and value production. We interrogate the transition from the pre-digital into the making of bigger, more spatiotemporally granular electricity data, through focusing on those actors selling and materialising new metering technologies, data infrastructures and services for larger businesses and public sector organisations in the UK. We examine the claims of truth and visibility that accompany these shifts and their enrolment into management techniques that serve to more precisely apportion responsibility for, and evaluate the status of, particular patterns and instances of electricity use. We argue that whilst through becoming Big Data electricity flow is now able to be known and given identity in significantly new terms, enabling new relations to be formed with the many heterogeneous entities implicated in making and managing energy demand, it is necessary to sustain some ambivalence as to the performative consequences that follow for energy governance. We consider the wider application of our conceptualisation of metering, reflecting on comparisons with the introduction of new metering systems in domestic settings and as part of other infrastructural networks.

  14. A feasibility study: Selection of a personalized radiotherapy fractionation schedule using spatiotemporal optimization

    International Nuclear Information System (INIS)

    Kim, Minsun; Stewart, Robert D.; Phillips, Mark H.

    2015-01-01

    Purpose: To investigate the impact of using spatiotemporal optimization, i.e., intensity-modulated spatial optimization followed by fractionation schedule optimization, to select the patient-specific fractionation schedule that maximizes the tumor biologically equivalent dose (BED) under dose constraints for multiple organs-at-risk (OARs). Methods: Spatiotemporal optimization was applied to a variety of lung tumors in a phantom geometry using a range of tumor sizes and locations. The optimal fractionation schedule for a patient using the linear-quadratic cell survival model depends on the tumor and OAR sensitivity to fraction size (α/β), the effective tumor doubling time (T d ), and the size and location of tumor target relative to one or more OARs (dose distribution). The authors used a spatiotemporal optimization method to identify the optimal number of fractions N that maximizes the 3D tumor BED distribution for 16 lung phantom cases. The selection of the optimal fractionation schedule used equivalent (30-fraction) OAR constraints for the heart (D mean ≤ 45 Gy), lungs (D mean ≤ 20 Gy), cord (D max ≤ 45 Gy), esophagus (D max ≤ 63 Gy), and unspecified tissues (D 05 ≤ 60 Gy). To assess plan quality, the authors compared the minimum, mean, maximum, and D 95 of tumor BED, as well as the equivalent uniform dose (EUD) for optimized plans to conventional intensity-modulated radiation therapy plans prescribing 60 Gy in 30 fractions. A sensitivity analysis was performed to assess the effects of T d (3–100 days), tumor lag-time (T k = 0–10 days), and the size of tumors on optimal fractionation schedule. Results: Using an α/β ratio of 10 Gy, the average values of tumor max, min, mean BED, and D 95 were up to 19%, 21%, 20%, and 19% larger than those from conventional prescription, depending on T d and T k used. Tumor EUD was up to 17% larger than the conventional prescription. For fast proliferating tumors with T d less than 10 days, there was no

  15. A feasibility study: Selection of a personalized radiotherapy fractionation schedule using spatiotemporal optimization

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Minsun, E-mail: mk688@uw.edu; Stewart, Robert D. [Department of Radiation Oncology, University of Washington, Seattle, Washington 98195-6043 (United States); Phillips, Mark H. [Departments of Radiation Oncology and Neurological Surgery, University of Washington, Seattle, Washington 98195-6043 (United States)

    2015-11-15

    Purpose: To investigate the impact of using spatiotemporal optimization, i.e., intensity-modulated spatial optimization followed by fractionation schedule optimization, to select the patient-specific fractionation schedule that maximizes the tumor biologically equivalent dose (BED) under dose constraints for multiple organs-at-risk (OARs). Methods: Spatiotemporal optimization was applied to a variety of lung tumors in a phantom geometry using a range of tumor sizes and locations. The optimal fractionation schedule for a patient using the linear-quadratic cell survival model depends on the tumor and OAR sensitivity to fraction size (α/β), the effective tumor doubling time (T{sub d}), and the size and location of tumor target relative to one or more OARs (dose distribution). The authors used a spatiotemporal optimization method to identify the optimal number of fractions N that maximizes the 3D tumor BED distribution for 16 lung phantom cases. The selection of the optimal fractionation schedule used equivalent (30-fraction) OAR constraints for the heart (D{sub mean} ≤ 45 Gy), lungs (D{sub mean} ≤ 20 Gy), cord (D{sub max} ≤ 45 Gy), esophagus (D{sub max} ≤ 63 Gy), and unspecified tissues (D{sub 05} ≤ 60 Gy). To assess plan quality, the authors compared the minimum, mean, maximum, and D{sub 95} of tumor BED, as well as the equivalent uniform dose (EUD) for optimized plans to conventional intensity-modulated radiation therapy plans prescribing 60 Gy in 30 fractions. A sensitivity analysis was performed to assess the effects of T{sub d} (3–100 days), tumor lag-time (T{sub k} = 0–10 days), and the size of tumors on optimal fractionation schedule. Results: Using an α/β ratio of 10 Gy, the average values of tumor max, min, mean BED, and D{sub 95} were up to 19%, 21%, 20%, and 19% larger than those from conventional prescription, depending on T{sub d} and T{sub k} used. Tumor EUD was up to 17% larger than the conventional prescription. For fast proliferating

  16. Characterizing the Spatio-Temporal Pattern of Land Surface Temperature through Time Series Clustering: Based on the Latent Pattern and Morphology

    Directory of Open Access Journals (Sweden)

    Huimin Liu

    2018-04-01

    Full Text Available Land Surface Temperature (LST is a critical component to understand the impact of urbanization on the urban thermal environment. Previous studies were inclined to apply only one snapshot to analyze the pattern and dynamics of LST without considering the non-stationarity in the temporal domain, or focus on the diurnal, seasonal, and annual pattern analysis of LST which has limited support for the understanding of how LST varies with the advancing of urbanization. This paper presents a workflow to extract the spatio-temporal pattern of LST through time series clustering by focusing on the LST of Wuhan, China, from 2002 to 2017 with a 3-year time interval with 8-day MODerate-resolution Imaging Spectroradiometer (MODIS satellite image products. The Latent pattern of LST (LLST generated by non-parametric Multi-Task Gaussian Process Modeling (MTGP and the Multi-Scale Shape Index (MSSI which characterizes the morphology of LLST are coupled for pattern recognition. Specifically, spatio-temporal patterns are discovered after the extraction of spatial patterns conducted by the incorporation of k -means and the Back-Propagation neural networks (BP-Net. The spatial patterns of the 6 years form a basic understanding about the corresponding temporal variances. For spatio-temporal pattern recognition, LLSTs and MSSIs of the 6 years are regarded as geo-referenced time series. Multiple algorithms including traditional k -means with Euclidean Distance (ED, shape-based k -means with the constrained Dynamic Time Warping ( c DTW distance measure, and the Dynamic Time Warping Barycenter Averaging (DBA centroid computation method ( k - c DBA and k -shape are applied. Ten external indexes are employed to evaluate the performance of the three algorithms and reveal k - c DBA as the optimal time series clustering algorithm for our study. The study area is divided into 17 geographical time series clusters which respectively illustrate heterogeneous temporal dynamics of LST

  17. Somatic mutations, allele loss, and DNA methylation of the Cub and Sushi Multiple Domains 1 (CSMD1 gene reveals association with early age of diagnosis in colorectal cancer patients.

    Directory of Open Access Journals (Sweden)

    Austin Y Shull

    Full Text Available The Cub and Sushi Multiple Domains 1 (CSMD1 gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients.We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A.Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%. The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15:1, a ratio significantly higher than the expected 2:1 ratio (p = 0.014. This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%. Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years than those without somatic mutations (average age, 68 years. The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%, suggesting extensive cytosine methylation predisposing to somatic mutations.Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical

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

    International Nuclear Information System (INIS)

    Astakhov, V.V.; Anishchenko, V.S.; Strelkova, G.I.; Shabunin, A.V.

    1996-01-01

    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 1996 American Institute of Physics

  19. Spatio-temporal patterns of coral recruitment at Vamizi Island ...

    African Journals Online (AJOL)

    Spatio-temporal patterns of coral recruitment at Vamizi Island, Quirimbas Archipelago, Mozambique. ... Spatial and temporal patterns of recruitment of reef corals were assessed for the first time in Mozambique ... AJOL African Journals Online.

  20. The application of a hierarchical Bayesian spatiotemporal model for ...

    Indian Academy of Sciences (India)

    Process (GP) model by using the Gibbs sampling method. The result for ... good indicator of the HBST method. The statistical ... summary and discussion of future works are given .... spatiotemporal package in R language (R core team. 2013).

  1. Annual spatiotemporal migration schedules in three larger insectivorous birds

    DEFF Research Database (Denmark)

    Jacobsen, Lars Bo; Jensen, Niels Odder; Willemoes, Mikkel

    2017-01-01

    Background: Knowledge of spatiotemporal migration patterns is important for our understanding of migration ecology and ultimately conservation of migratory species. We studied the annual migration schedules of European nightjar, a large nocturnal insectivore and compared it with two other larger ...

  2. Spatiotemporal modeling of WNV in mosquitoes in Suffolk County

    Data.gov (United States)

    U.S. Environmental Protection Agency — R code and dataset to produce spatial models. This dataset is associated with the following publication: Meyer, M., S. Campbell, and J. Johnston. Spatiotemporal...

  3. On the genesis of spatio-temporal self-organized structures in plasma devices

    International Nuclear Information System (INIS)

    Talasman, S.J.; Sanduloviciu, M.

    1995-01-01

    The genesis of luminous sharply defined nearly spherical space charges structures formed in an Argon plasma column was experimental investigated. The results reveal spatio-temporal characteristics proper to systems resulting after a self-organization process. Their phenomenology involves electrical charges separation produced by symmetry breaking and spatial separation of the excitation and ionization cross sections functions in a region where electrons are accelerated and, as a result, the appearance of electrostatic forces that, acting as long range correlations, assures, together with dissipative effects, its stability. (Author) 8 Figs., 31 Refs

  4. Reshaping-induced spatiotemporal chaos in driven, damped sine-Gordon systems

    International Nuclear Information System (INIS)

    Chacon, R.

    2007-01-01

    Spatiotemporal chaos arising from the competition between sine-Gordon-breather and kink-antikink-pair solitons by reshaping an ac force is demonstrated. After introducing soliton collective coordinates, Melnikov's method is applied to the resulting effective equation of motion to estimate the parameter-space regions of the ac force where homoclinic bifurcations are induced. The analysis reveals that the chaos-order threshold exhibits sensitivity to small changes in the force shape. Computer simulations of the sine-Gordon system show good agreement with these theoretical predictions

  5. Reshaping-induced spatiotemporal chaos in driven, damped sine-Gordon systems

    Energy Technology Data Exchange (ETDEWEB)

    Chacon, R. [Departamento de Electronica e Ingenieria Electromecanica, Escuela de Ingenierias Industriales, Universidad de Extremadura, E-06071 Badajoz (Spain)]. E-mail: rchacon@unex.es

    2007-03-15

    Spatiotemporal chaos arising from the competition between sine-Gordon-breather and kink-antikink-pair solitons by reshaping an ac force is demonstrated. After introducing soliton collective coordinates, Melnikov's method is applied to the resulting effective equation of motion to estimate the parameter-space regions of the ac force where homoclinic bifurcations are induced. The analysis reveals that the chaos-order threshold exhibits sensitivity to small changes in the force shape. Computer simulations of the sine-Gordon system show good agreement with these theoretical predictions.

  6. Markovian Limit of a Spatio-Temporal Correlated Open Systems

    Science.gov (United States)

    Monnai, T.

    Large fluctuation of Brownian particles is affected by the finiteness of the correlation length of the background noise field. Indeed a Fokker—Planck equation is derived in a Markovian limit of a spatio-temporal short correlated noise. Corresponding kinetic quantities are renormalized due to the spatio-temporal memory. We also investigate the case of open system by connecting a thermostat to the system.

  7. WORLD SPATIOTEMPORAL ANALYTICS AND MAPPING PROJECT (WSTAMP: DISCOVERING, EXPLORING, AND MAPPING SPATIOTEMPORAL PATTERNS ACROSS THE WORLD’S LARGEST OPEN SORUCE DATA SETS

    Directory of Open Access Journals (Sweden)

    R. Stewart

    2015-07-01

    Full Text Available The application of spatiotemporal (ST analytics to integrated data from major sources such as the World Bank, United Nations, and dozens of others holds tremendous potential for shedding new light on the evolution of cultural, health, economic, and geopolitical landscapes on a global level. Realizing this potential first requires an ST data model that addresses challenges in properly merging data from multiple authors, with evolving ontological perspectives, semantical differences, and changing attributes, as well as content that is textual, numeric, categorical, and hierarchical. Equally challenging is the development of analytical and visualization approaches that provide a serious exploration of this integrated data while remaining accessible to practitioners with varied backgrounds. The WSTAMP project at Oak Ridge National Laboratory has yielded two major results in addressing these challenges: 1 development of the WSTAMP database, a significant advance in ST data modeling that integrates 10,000+ attributes covering over 200 nation states spanning over 50 years from over 30 major sources and 2 a novel online ST exploratory and analysis tool providing an array of modern statistical and visualization techniques for analyzing these data temporally, spatially, and spatiotemporally under a standard analytic workflow. We discuss the status of this work and report on major findings.

  8. World Spatiotemporal Analytics and Mapping Project (wstamp): Discovering, Exploring, and Mapping Spatiotemporal Patterns across the World's Largest Open Soruce Data Sets

    Science.gov (United States)

    Stewart, R.; Piburn, J.; Sorokine, A.; Myers, A.; Moehl, J.; White, D.

    2015-07-01

    The application of spatiotemporal (ST) analytics to integrated data from major sources such as the World Bank, United Nations, and dozens of others holds tremendous potential for shedding new light on the evolution of cultural, health, economic, and geopolitical landscapes on a global level. Realizing this potential first requires an ST data model that addresses challenges in properly merging data from multiple authors, with evolving ontological perspectives, semantical differences, and changing attributes, as well as content that is textual, numeric, categorical, and hierarchical. Equally challenging is the development of analytical and visualization approaches that provide a serious exploration of this integrated data while remaining accessible to practitioners with varied backgrounds. The WSTAMP project at Oak Ridge National Laboratory has yielded two major results in addressing these challenges: 1) development of the WSTAMP database, a significant advance in ST data modeling that integrates 10,000+ attributes covering over 200 nation states spanning over 50 years from over 30 major sources and 2) a novel online ST exploratory and analysis tool providing an array of modern statistical and visualization techniques for analyzing these data temporally, spatially, and spatiotemporally under a standard analytic workflow. We discuss the status of this work and report on major findings.

  9. Sex & vision I: Spatio-temporal resolution

    Directory of Open Access Journals (Sweden)

    Abramov Israel

    2012-09-01

    Full Text Available Abstract Background Cerebral cortex has a very large number of testosterone receptors, which could be a basis for sex differences in sensory functions. For example, audition has clear sex differences, which are related to serum testosterone levels. Of all major sensory systems only vision has not been examined for sex differences, which is surprising because occipital lobe (primary visual projection area may have the highest density of testosterone receptors in the cortex. We have examined a basic visual function: spatial and temporal pattern resolution and acuity. Methods We tested large groups of young adults with normal vision. They were screened with a battery of standard tests that examined acuity, color vision, and stereopsis. We sampled the visual system’s contrast-sensitivity function (CSF across the entire spatio-temporal space: 6 spatial frequencies at each of 5 temporal rates. Stimuli were gratings with sinusoidal luminance profiles generated on a special-purpose computer screen; their contrast was also sinusoidally modulated in time. We measured threshold contrasts using a criterion-free (forced-choice, adaptive psychophysical method (QUEST algorithm. Also, each individual’s acuity limit was estimated by fitting his or her data with a model and extrapolating to find the spatial frequency corresponding to 100% contrast. Results At a very low temporal rate, the spatial CSF was the canonical inverted-U; but for higher temporal rates, the maxima of the spatial CSFs shifted: Observers lost sensitivity at high spatial frequencies and gained sensitivity at low frequencies; also, all the maxima of the CSFs shifted by about the same amount in spatial frequency. Main effect: there was a significant (ANOVA sex difference. Across the entire spatio-temporal domain, males were more sensitive, especially at higher spatial frequencies; similarly males had significantly better acuity at all temporal rates. Conclusion As with other sensory systems

  10. Visualization and assessment of spatio-temporal covariance properties

    KAUST Repository

    Huang, Huang

    2017-11-23

    Spatio-temporal covariances are important for describing the spatio-temporal variability of underlying random fields in geostatistical data. For second-order stationary random fields, there exist subclasses of covariance functions that assume a simpler spatio-temporal dependence structure with separability and full symmetry. However, it is challenging to visualize and assess separability and full symmetry from spatio-temporal observations. In this work, we propose a functional data analysis approach that constructs test functions using the cross-covariances from time series observed at each pair of spatial locations. These test functions of temporal lags summarize the properties of separability or symmetry for the given spatial pairs. We use functional boxplots to visualize the functional median and the variability of the test functions, where the extent of departure from zero at all temporal lags indicates the degree of non-separability or asymmetry. We also develop a rank-based nonparametric testing procedure for assessing the significance of the non-separability or asymmetry. Essentially, the proposed methods only require the analysis of temporal covariance functions. Thus, a major advantage over existing approaches is that there is no need to estimate any covariance matrix for selected spatio-temporal lags. The performances of the proposed methods are examined by simulations with various commonly used spatio-temporal covariance models. To illustrate our methods in practical applications, we apply it to real datasets, including weather station data and climate model outputs.

  11. Monitoring urban greenness dynamics using multiple endmember spectral mixture analysis.

    Directory of Open Access Journals (Sweden)

    Muye Gan

    Full Text Available Urban greenness is increasingly recognized as an essential constituent of the urban environment and can provide a range of services and enhance residents' quality of life. Understanding the pattern of urban greenness and exploring its spatiotemporal dynamics would contribute valuable information for urban planning. In this paper, we investigated the pattern of urban greenness in Hangzhou, China, over the past two decades using time series Landsat-5 TM data obtained in 1990, 2002, and 2010. Multiple endmember spectral mixture analysis was used to derive vegetation cover fractions at the subpixel level. An RGB-vegetation fraction model, change intensity analysis and the concentric technique were integrated to reveal the detailed, spatial characteristics and the overall pattern of change in the vegetation cover fraction. Our results demonstrated the ability of multiple endmember spectral mixture analysis to accurately model the vegetation cover fraction in pixels despite the complex spectral confusion of different land cover types. The integration of multiple techniques revealed various changing patterns in urban greenness in this region. The overall vegetation cover has exhibited a drastic decrease over the past two decades, while no significant change occurred in the scenic spots that were studied. Meanwhile, a remarkable recovery of greenness was observed in the existing urban area. The increasing coverage of small green patches has played a vital role in the recovery of urban greenness. These changing patterns were more obvious during the period from 2002 to 2010 than from 1990 to 2002, and they revealed the combined effects of rapid urbanization and greening policies. This work demonstrates the usefulness of time series of vegetation cover fractions for conducting accurate and in-depth studies of the long-term trajectories of urban greenness to obtain meaningful information for sustainable urban development.

  12. Experimental devices for the spatio-temporal characterization of femtosecond high-power laser chains

    International Nuclear Information System (INIS)

    Gallet, Valentin

    2014-01-01

    performed the very first characterization of several TW laser chains. The measurements have revealed the existence of residual space-time couplings leading to a significant decrease of the peak intensity at focus. These results show that it is essential to spatio-temporally characterize high power femtosecond laser chains to obtain the maximum intensity at focus. (author) [fr

  13. Spatiotemporal video deinterlacing using control grid interpolation

    Science.gov (United States)

    Venkatesan, Ragav; Zwart, Christine M.; Frakes, David H.; Li, Baoxin

    2015-03-01

    With the advent of progressive format display and broadcast technologies, video deinterlacing has become an important video-processing technique. Numerous approaches exist in the literature to accomplish deinterlacing. While most earlier methods were simple linear filtering-based approaches, the emergence of faster computing technologies and even dedicated video-processing hardware in display units has allowed higher quality but also more computationally intense deinterlacing algorithms to become practical. Most modern approaches analyze motion and content in video to select different deinterlacing methods for various spatiotemporal regions. We introduce a family of deinterlacers that employs spectral residue to choose between and weight control grid interpolation based spatial and temporal deinterlacing methods. The proposed approaches perform better than the prior state-of-the-art based on peak signal-to-noise ratio, other visual quality metrics, and simple perception-based subjective evaluations conducted by human viewers. We further study the advantages of using soft and hard decision thresholds on the visual performance.

  14. Spatio-temporal problems of locomotion control

    International Nuclear Information System (INIS)

    Smolyaninov, Vladimir V

    2000-01-01

    The problem of the spatio-temporal construction of legged movements involves structural freedoms due to the multi-link structure of the extremities, kinematic freedoms of the stepping cycle, and interextremity coordination freedoms, whose purposive organization is established by means of appropriate synergies, i.e. additional functional links the brain's control system forms. The main focus of attention in this work is on the kinematic and coordination synergies of the legged movements of humans and animals. The comparative historical analysis of experimental data and modelling metaphors concentrates on obtaining a unified description, whereas the ultimate mathematical metaphor reduces to space-time geometry, with base step synergies as its invariants. Thus, the concept of a synergetic organization for biomechanical movement freedoms is transformed to the geochronometry concept, actually a modification of Minkowskian geometry. To determine the spectrum of possible geochronometries, the consequences of a generalized 'postulate of a constant speed of light' are studied and different models of wave chronometers compared. (reviews of topical problems)

  15. Aspects of second-order analysis of structured inhomogeneous spatio-temporal processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Ghorbani, Mohammad

    2012-01-01

    Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for general inhomogeneous spatio-temporal point processes and for inhomogeneous spatio-temporal Cox processes. Assuming spatio......-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio-temporal Gaussian process. Another...... concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data....

  16. Second-order analysis of structured inhomogeneous spatio-temporal point processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Ghorbani, Mohammad

    Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for first general inhomogeneous spatio-temporal point processes and second inhomogeneous spatio-temporal Cox processes. Assuming...... spatio-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates e.g. to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio......-temporal Gaussian process. Another concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data (the UK 2001 epidemic foot and mouth disease data)....

  17. Spatiotemporal patterns, triggers and anatomies of seismically detected rockfalls

    Directory of Open Access Journals (Sweden)

    M. Dietze

    2017-11-01

    Full Text Available Rockfalls are a ubiquitous geomorphic process and a natural hazard in steep landscapes across the globe. Seismic monitoring can provide precise information on the timing, location and event anatomy of rockfalls, which are parameters that are otherwise hard to constrain. By pairing data from 49 seismically detected rockfalls in the Lauterbrunnen Valley in the Swiss Alps with auxiliary meteorologic and seismic data of potential triggers during autumn 2014 and spring 2015, we are able to (i analyse the evolution of single rockfalls and their common properties, (ii identify spatial changes in activity hotspots (iii and explore temporal activity patterns on different scales ranging from months to minutes to quantify relevant trigger mechanisms. Seismic data allow for the classification of rockfall activity into two distinct phenomenological types. The signals can be used to discern multiple rock mass releases from the same spot, identify rockfalls that trigger further rockfalls and resolve modes of subsequent talus slope activity. In contrast to findings based on discontinuous methods with integration times of several months, rockfall in the monitored limestone cliff is not spatially uniform but shows a systematic downward shift of a rock mass release zone following an exponential law, most likely driven by a continuously lowering water table. Freeze–thaw transitions, approximated at first order from air temperature time series, account for only 5 out of the 49 rockfalls, whereas 19 rockfalls were triggered by rainfall events with a peak lag time of 1 h. Another 17 rockfalls were triggered by diurnal temperature changes and occurred during the coldest hours of the day and during the highest temperature change rates. This study is thus the first to show direct links between proposed rockfall triggers and the spatiotemporal distribution of rockfalls under natural conditions; it extends existing models by providing seismic observations of the

  18. Uncertainty assessment of PM2.5 contamination mapping using spatiotemporal sequential indicator simulations and multi-temporal monitoring data

    Science.gov (United States)

    Yang, Yong; Christakos, George; Huang, Wei; Lin, Chengda; Fu, Peihong; Mei, Yang

    2016-04-01

    Because of the rapid economic growth in China, many regions are subjected to severe particulate matter pollution. Thus, improving the methods of determining the spatiotemporal distribution and uncertainty of air pollution can provide considerable benefits when developing risk assessments and environmental policies. The uncertainty assessment methods currently in use include the sequential indicator simulation (SIS) and indicator kriging techniques. However, these methods cannot be employed to assess multi-temporal data. In this work, a spatiotemporal sequential indicator simulation (STSIS) based on a non-separable spatiotemporal semivariogram model was used to assimilate multi-temporal data in the mapping and uncertainty assessment of PM2.5 distributions in a contaminated atmosphere. PM2.5 concentrations recorded throughout 2014 in Shandong Province, China were used as the experimental dataset. Based on the number of STSIS procedures, we assessed various types of mapping uncertainties, including single-location uncertainties over one day and multiple days and multi-location uncertainties over one day and multiple days. A comparison of the STSIS technique with the SIS technique indicate that a better performance was obtained with the STSIS method.

  19. VAUD: A Visual Analysis Approach for Exploring Spatio-Temporal Urban Data.

    Science.gov (United States)

    Chen, Wei; Huang, Zhaosong; Wu, Feiran; Zhu, Minfeng; Guan, Huihua; Maciejewski, Ross

    2017-10-02

    Urban data is massive, heterogeneous, and spatio-temporal, posing a substantial challenge for visualization and analysis. In this paper, we design and implement a novel visual analytics approach, Visual Analyzer for Urban Data (VAUD), that supports the visualization, querying, and exploration of urban data. Our approach allows for cross-domain correlation from multiple data sources by leveraging spatial-temporal and social inter-connectedness features. Through our approach, the analyst is able to select, filter, aggregate across multiple data sources and extract information that would be hidden to a single data subset. To illustrate the effectiveness of our approach, we provide case studies on a real urban dataset that contains the cyber-, physical-, and socialinformation of 14 million citizens over 22 days.

  20. Spatiotemporal exploratory models for broad-scale survey data.

    Science.gov (United States)

    Fink, Daniel; Hochachka, Wesley M; Zuckerberg, Benjamin; Winkler, David W; Shaby, Ben; Munson, M Arthur; Hooker, Giles; Riedewald, Mirek; Sheldon, Daniel; Kelling, Steve

    2010-12-01

    The distributions of animal populations change and evolve through time. Migratory species exploit different habitats at different times of the year. Biotic and abiotic features that determine where a species lives vary due to natural and anthropogenic factors. This spatiotemporal variation needs to be accounted for in any modeling of species' distributions. In this paper we introduce a semiparametric model that provides a flexible framework for analyzing dynamic patterns of species occurrence and abundance from broad-scale survey data. The spatiotemporal exploratory model (STEM) adds essential spatiotemporal structure to existing techniques for developing species distribution models through a simple parametric structure without requiring a detailed understanding of the underlying dynamic processes. STEMs use a multi-scale strategy to differentiate between local and global-scale spatiotemporal structure. A user-specified species distribution model accounts for spatial and temporal patterning at the local level. These local patterns are then allowed to "scale up" via ensemble averaging to larger scales. This makes STEMs especially well suited for exploring distributional dynamics arising from a variety of processes. Using data from eBird, an online citizen science bird-monitoring project, we demonstrate that monthly changes in distribution of a migratory species, the Tree Swallow (Tachycineta bicolor), can be more accurately described with a STEM than a conventional bagged decision tree model in which spatiotemporal structure has not been imposed. We also demonstrate that there is no loss of model predictive power when a STEM is used to describe a spatiotemporal distribution with very little spatiotemporal variation; the distribution of a nonmigratory species, the Northern Cardinal (Cardinalis cardinalis).

  1. The Spatiotemporal pattern and driving forces of the paddy in the Northeastern China

    Science.gov (United States)

    Du, G.; Li, Q.; Chun, X.

    2017-12-01

    The cropland is the production place that protects the regional food security, and the paddy is the main part of the cropland. Since the 21st century, the China's socio-economy has been grown, the structure of the cropland has significantly changed. The Northeast region has gradually become one of the major commodity grain production bases. Meanwhile, the paddy also has gradually increased year by year. Therefore, it is necessary that analyze the tempo-spatial characteristics and the influencing factors of the northeast in China, and the results provide the basis that reveals the change of cropland structure and its causes.In this study, we use the spatial models of GIS and mathematical statistics methods to analyze the tempo-spatial characteristics and the influencing facts of the paddy in the Northeastern China with the spatial data from 2000 to 2015. In order to fully characterize the spatiotemporal characteristics of the paddy, we choose single land use type dynamic degree and land use extension index to quantitatively describe the change degree and the speed of the regional paddy, and the characteristics are visualized with "3S" means. Meanwhile, the relative change rate and the center of gravity model are chosen to explore the region differences and the distribution of the distribution center of paddy field change in Northeast China. In addition, in order to further reveal the cause of the paddy change, we use the OLS, SAM or SEM models to analyze the main influencing factors of spatiotemporal variation of the paddy field.

  2. Moving mountains with mobiles: Spatiotemporal perspectives on mHealth in Nepal

    Directory of Open Access Journals (Sweden)

    Arul Chib

    2012-03-01

    Full Text Available Community healthcare workers (CHW are an important component of rural healthcare service delivery to remote rural communities in developing countries. The field of mHealth proposes that mobile technologies will have a beneficial impact on rural healthcare development. Current analyses advance the proposition that the utilization of mobile technologies leads to the shifting of space and time (Ling & Campbell, 2009. The current research examined the potential for a sustainable mHealth system for CHW in Achham, Nepal. The community aspect of mobile usage was overlaid with a spatio-temporal lens to examine the information and communication needs and practices of stakeholders within the healthcare infrastructure. Fieldwork was conducted in conjunction with Nyaya Health, at the Bayalpata Hospital, in Accham, Nepal. Qualitative research methods, focus group discussions, and in-depth interviews included 57 respondents. The findings revealed that limited relevance and information-sharing, limited access due to individual ownership and low income, and ineffective training programs were key barriers to the delivery of rural healthcare services. The spatio-temporal perspective, particularly community communicative practices, revealed technological mHealth design solutions to alleviate the problems identified. The potential shifts in power relationships by using mobile technologies and hybrid fixed wireless technologies provide opportunities for further theoretical investigation.

  3. Spatiotemporal dynamics of the spin transition in [Fe (HB(tz)3) 2] single crystals

    Science.gov (United States)

    Ridier, Karl; Rat, Sylvain; Shepherd, Helena J.; Salmon, Lionel; Nicolazzi, William; Molnár, Gábor; Bousseksou, Azzedine

    2017-10-01

    The spatiotemporal dynamics of the spin transition have been thoroughly investigated in single crystals of the mononuclear spin-crossover (SCO) complex [Fe (HB (tz )3)2] (tz = 1 ,2 ,4-triazol-1-yl) by optical microscopy. This compound exhibits an abrupt spin transition centered at 334 K with a narrow thermal hysteresis loop of ˜1 K (first-order transition). Most single crystals of this compound reveal exceptional resilience upon repeated switching (several hundred cycles), which allowed repeatable and quantitative measurements of the spatiotemporal dynamics of the nucleation and growth processes to be carried out. These experiments revealed remarkable properties of the thermally induced spin transition: high stability of the thermal hysteresis loop, unprecedented large velocities of the macroscopic low-spin/high-spin phase boundaries up to 500 µm/s, and no visible dependency on the temperature scan rate. We have also studied the dynamics of the low-spin → high-spin transition induced by a local photothermal excitation generated by a spatially localized (Ø = 2 μ m ) continuous laser beam. Interesting phenomena have been evidenced both in quasistatic and dynamic conditions (e.g., threshold effects and long incubation periods, thermal activation of the phase boundary propagation, stabilization of the crystal in a stationary biphasic state, and thermal cutoff frequency). These measurements demonstrated the importance of thermal effects in the transition dynamics, and they enabled an accurate determination of the thermal properties of the SCO compound in the framework of a simple theoretical model.

  4. Droughts in Amazonia: Spatiotemporal Variability, Teleconnections, and Seasonal Predictions

    Science.gov (United States)

    Lima, Carlos H. R.; AghaKouchak, Amir

    2017-12-01

    Most Amazonia drought studies have focused on rainfall deficits and their impact on river discharges, while the analysis of other important driver variables, such as temperature and soil moisture, has attracted less attention. Here we try to better understand the spatiotemporal dynamics of Amazonia droughts and associated climate teleconnections as characterized by the Palmer Drought Severity Index (PDSI), which integrates information from rainfall deficit, temperature anomalies, and soil moisture capacity. The results reveal that Amazonia droughts are most related to one dominant pattern across the entire region, followed by two seesaw kind of patterns: north-south and east-west. The main two modes are correlated with sea surface temperature (SST) anomalies in the tropical Pacific and Atlantic oceans. The teleconnections associated with global SST are then used to build a seasonal forecast model for PDSI over Amazonia based on predictors obtained from a sparse canonical correlation analysis approach. A unique feature of the presented drought prediction method is using only a few number of predictors to avoid excessive noise in the predictor space. Cross-validated results show correlations between observed and predicted spatial average PDSI up to 0.60 and 0.45 for lead times of 5 and 9 months, respectively. To the best of our knowledge, this is the first study in the region that, based on cross-validation results, leads to appreciable forecast skills for lead times beyond 4 months. This is a step forward in better understanding the dynamics of Amazonia droughts and improving risk assessment and management, through improved drought forecasting.

  5. The timing and spatiotemporal patterning of Neanderthal disappearance.

    Science.gov (United States)

    Higham, Tom; Douka, Katerina; Wood, Rachel; Ramsey, Christopher Bronk; Brock, Fiona; Basell, Laura; Camps, Marta; Arrizabalaga, Alvaro; Baena, Javier; Barroso-Ruíz, Cecillio; Bergman, Christopher; Boitard, Coralie; Boscato, Paolo; Caparrós, Miguel; Conard, Nicholas J; Draily, Christelle; Froment, Alain; Galván, Bertila; Gambassini, Paolo; Garcia-Moreno, Alejandro; Grimaldi, Stefano; Haesaerts, Paul; Holt, Brigitte; Iriarte-Chiapusso, Maria-Jose; Jelinek, Arthur; Jordá Pardo, Jesús F; Maíllo-Fernández, José-Manuel; Marom, Anat; Maroto, Julià; Menéndez, Mario; Metz, Laure; Morin, Eugène; Moroni, Adriana; Negrino, Fabio; Panagopoulou, Eleni; Peresani, Marco; Pirson, Stéphane; de la Rasilla, Marco; Riel-Salvatore, Julien; Ronchitelli, Annamaria; Santamaria, David; Semal, Patrick; Slimak, Ludovic; Soler, Joaquim; Soler, Narcís; Villaluenga, Aritza; Pinhasi, Ron; Jacobi, Roger

    2014-08-21

    The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

  6. Spatiotemporal Variations and Driving Factors of Air Pollution in China.

    Science.gov (United States)

    Zhan, Dongsheng; Kwan, Mei-Po; Zhang, Wenzhong; Wang, Shaojian; Yu, Jianhui

    2017-12-08

    In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP) witness the strongest and most significant positive effects on air pollution ratio.

  7. Spatiotemporal Variations and Driving Factors of Air Pollution in China

    Directory of Open Access Journals (Sweden)

    Dongsheng Zhan

    2017-12-01

    Full Text Available In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP witness the strongest and most significant positive effects on air pollution ratio.

  8. Bridge damage detection using spatiotemporal patterns extracted from dense sensor network

    International Nuclear Information System (INIS)

    Liu, Chao; Sarkar, Soumik; Gong, Yongqiang; Laflamme, Simon; Phares, Brent

    2017-01-01

    The alarmingly degrading state of transportation infrastructures combined with their key societal and economic importance calls for automatic condition assessment methods to facilitate smart management of maintenance and repairs. With the advent of ubiquitous sensing and communication capabilities, scalable data-driven approaches is of great interest, as it can utilize large volume of streaming data without requiring detailed physical models that can be inaccurate and computationally expensive to run. Properly designed, a data-driven methodology could enable fast and automatic evaluation of infrastructures, discovery of causal dependencies among various sub-system dynamic responses, and decision making with uncertainties and lack of labeled data. In this work, a spatiotemporal pattern network (STPN) strategy built on symbolic dynamic filtering (SDF) is proposed to explore spatiotemporal behaviors in a bridge network. Data from strain gauges installed on two bridges are generated using finite element simulation for three types of sensor networks from a density perspective (dense, nominal, sparse). Causal relationships among spatially distributed strain data streams are extracted and analyzed for vehicle identification and detection, and for localization of structural degradation in bridges. Multiple case studies show significant capabilities of the proposed approach in: (i) capturing spatiotemporal features to discover causality between bridges (geographically close), (ii) robustness to noise in data for feature extraction, (iii) detecting and localizing damage via comparison of bridge responses to similar vehicle loads, and (iv) implementing real-time health monitoring and decision making work flow for bridge networks. Also, the results demonstrate increased sensitivity in detecting damages and higher reliability in quantifying the damage level with increase in sensor network density. (paper)

  9. Micro-precise spatiotemporal delivery system embedded in 3D printing for complex tissue regeneration.

    Science.gov (United States)

    Tarafder, Solaiman; Koch, Alia; Jun, Yena; Chou, Conrad; Awadallah, Mary R; Lee, Chang H

    2016-04-25

    Three dimensional (3D) printing has emerged as an efficient tool for tissue engineering and regenerative medicine, given its advantages for constructing custom-designed scaffolds with tunable microstructure/physical properties. Here we developed a micro-precise spatiotemporal delivery system embedded in 3D printed scaffolds. PLGA microspheres (μS) were encapsulated with growth factors (GFs) and then embedded inside PCL microfibers that constitute custom-designed 3D scaffolds. Given the substantial difference in the melting points between PLGA and PCL and their low heat conductivity, μS were able to maintain its original structure while protecting GF's bioactivities. Micro-precise spatial control of multiple GFs was achieved by interchanging dispensing cartridges during a single printing process. Spatially controlled delivery of GFs, with a prolonged release, guided formation of multi-tissue interfaces from bone marrow derived mesenchymal stem/progenitor cells (MSCs). To investigate efficacy of the micro-precise delivery system embedded in 3D printed scaffold, temporomandibular joint (TMJ) disc scaffolds were fabricated with micro-precise spatiotemporal delivery of CTGF and TGFβ3, mimicking native-like multiphase fibrocartilage. In vitro, TMJ disc scaffolds spatially embedded with CTGF/TGFβ3-μS resulted in formation of multiphase fibrocartilaginous tissues from MSCs. In vivo, TMJ disc perforation was performed in rabbits, followed by implantation of CTGF/TGFβ3-μS-embedded scaffolds. After 4 wks, CTGF/TGFβ3-μS embedded scaffolds significantly improved healing of the perforated TMJ disc as compared to the degenerated TMJ disc in the control group with scaffold embedded with empty μS. In addition, CTGF/TGFβ3-μS embedded scaffolds significantly prevented arthritic changes on TMJ condyles. In conclusion, our micro-precise spatiotemporal delivery system embedded in 3D printing may serve as an efficient tool to regenerate complex and inhomogeneous tissues.

  10. Spatio-temporal networks: reachability, centrality and robustness.

    Science.gov (United States)

    Williams, Matthew J; Musolesi, Mirco

    2016-06-01

    Recent advances in spatial and temporal networks have enabled researchers to more-accurately describe many real-world systems such as urban transport networks. In this paper, we study the response of real-world spatio-temporal networks to random error and systematic attack, taking a unified view of their spatial and temporal performance. We propose a model of spatio-temporal paths in time-varying spatially embedded networks which captures the property that, as in many real-world systems, interaction between nodes is non-instantaneous and governed by the space in which they are embedded. Through numerical experiments on three real-world urban transport systems, we study the effect of node failure on a network's topological, temporal and spatial structure. We also demonstrate the broader applicability of this framework to three other classes of network. To identify weaknesses specific to the behaviour of a spatio-temporal system, we introduce centrality measures that evaluate the importance of a node as a structural bridge and its role in supporting spatio-temporally efficient flows through the network. This exposes the complex nature of fragility in a spatio-temporal system, showing that there is a variety of failure modes when a network is subject to systematic attacks.

  11. Live Imaging of Axolotl Digit Regeneration Reveals Spatiotemporal Choreography of Diverse Connective Tissue Progenitor Pools.

    Science.gov (United States)

    Currie, Joshua D; Kawaguchi, Akane; Traspas, Ricardo Moreno; Schuez, Maritta; Chara, Osvaldo; Tanaka, Elly M

    2016-11-21

    Connective tissues-skeleton, dermis, pericytes, fascia-are a key cell source for regenerating the patterned skeleton during axolotl appendage regeneration. This complexity has made it difficult to identify the cells that regenerate skeletal tissue. Inability to identify these cells has impeded a mechanistic understanding of blastema formation. By tracing cells during digit tip regeneration using brainbow transgenic axolotls, we show that cells from each connective tissue compartment have distinct spatial and temporal profiles of proliferation, migration, and differentiation. Chondrocytes proliferate but do not migrate into the regenerate. In contrast, pericytes proliferate, then migrate into the blastema and give rise solely to pericytes. Periskeletal cells and fibroblasts contribute the bulk of digit blastema cells and acquire diverse fates according to successive waves of migration that choreograph their proximal-distal and tissue contributions. We further show that platelet-derived growth factor signaling is a potent inducer of fibroblast migration, which is required to form the blastema. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  12. The Multiple Modernities of Europe

    DEFF Research Database (Denmark)

    Thomassen, Bjørn

    What Europe? Eric Voegelin on the Mediterranean and the Atlantic modernities. The concept ‘multiple modernities’ has during the last decade established itself in social and political theory, not least due to contributions made by Shmul Eisenstadt. The debate on multiple moderntities has served...... to question certain eurocentric assumptions about modernity and has also reignited the question of European particularity in a world historical perspective. This paper will discuss how ‘Europe’ itself can be considered a result of (at least) two different modernities, as proposed by the political theorist......, Eric Voegelin. Eric Voegelin talked of two spatio-temporal specific modernities, the Mediterranean and the Atlantic modernities. In short, for Voegelin the Atlantic modernity with its breakthroughs in the 17th and 18th centuries was a specific figuration that should not be mistaken for ‘modernity...

  13. Spatio-temporal Eigenvector Filtering: Application on Bioenergy Crop Impacts

    Science.gov (United States)

    Wang, M.; Kamarianakis, Y.; Georgescu, M.

    2017-12-01

    A suite of 10-year ensemble-based simulations was conducted to investigate the hydroclimatic impacts due to large-scale deployment of perennial bioenergy crops across the continental United States. Given the large size of the simulated dataset (about 60Tb), traditional hierarchical spatio-temporal statistical modelling cannot be implemented for the evaluation of physics parameterizations and biofuel impacts. In this work, we propose a filtering algorithm that takes into account the spatio-temporal autocorrelation structure of the data while avoiding spatial confounding. This method is used to quantify the robustness of simulated hydroclimatic impacts associated with bioenergy crops to alternative physics parameterizations and observational datasets. Results are evaluated against those obtained from three alternative Bayesian spatio-temporal specifications.

  14. Spiking neural network for recognizing spatiotemporal sequences of spikes

    International Nuclear Information System (INIS)

    Jin, Dezhe Z.

    2004-01-01

    Sensory neurons in many brain areas spike with precise timing to stimuli with temporal structures, and encode temporally complex stimuli into spatiotemporal spikes. How the downstream neurons read out such neural code is an important unsolved problem. In this paper, we describe a decoding scheme using a spiking recurrent neural network. The network consists of excitatory neurons that form a synfire chain, and two globally inhibitory interneurons of different types that provide delayed feedforward and fast feedback inhibition, respectively. The network signals recognition of a specific spatiotemporal sequence when the last excitatory neuron down the synfire chain spikes, which happens if and only if that sequence was present in the input spike stream. The recognition scheme is invariant to variations in the intervals between input spikes within some range. The computation of the network can be mapped into that of a finite state machine. Our network provides a simple way to decode spatiotemporal spikes with diverse types of neurons

  15. Dynamical topology and statistical properties of spatiotemporal chaos.

    Science.gov (United States)

    Zhuang, Quntao; Gao, Xun; Ouyang, Qi; Wang, Hongli

    2012-12-01

    For spatiotemporal chaos described by partial differential equations, there are generally locations where the dynamical variable achieves its local extremum or where the time partial derivative of the variable vanishes instantaneously. To a large extent, the location and movement of these topologically special points determine the qualitative structure of the disordered states. We analyze numerically statistical properties of the topologically special points in one-dimensional spatiotemporal chaos. The probability distribution functions for the number of point, the lifespan, and the distance covered during their lifetime are obtained from numerical simulations. Mathematically, we establish a probabilistic model to describe the dynamics of these topologically special points. In spite of the different definitions in different spatiotemporal chaos, the dynamics of these special points can be described in a uniform approach.

  16. Multiple rare-earth ion environments in amorphous (Gd2O3)0.230(P2O5)0.770 revealed by gadolinium K-edge anomalous X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Jacqueline M.; Cramer, Alisha J.; Shastri, Sarvjit D.; Mukaddem, Karim T.; Newport, Robert J

    2018-04-26

    A Gd K-edge anomalous X-ray scattering (AXS) study is performed on the rare-earth (R) phosphate glass, (Gd2O3)0.230(P2O5)0.770, in order to determine Gd…Gd separations in its local structure. The minimum rare-earth separation is of particular interest given that the optical properties of these glasses can quench when rare-earth ions become too close to each other. To this end, a weak Gd…Gd pairwise correlation is located at 4.2(1) Å which is representative of a meta-phosphate R…R separation. More intense first neighbor Gd…Gd pairwise correlations are found at the larger radial distributions, 4.8(1) Å, 5.1(1) Å and 5.4(1) Å. These reflect a mixed ultra-phosphate and meta-phosphate structural character, respectively. A second neighbor Gd…Gd pairwise correlation lies at 6.6(1) Å which is indicative of meta-phosphate structures. Meta- and ultra-phosphate classifications are made by comparing the R…R separations against those of rare-earth phosphate crystal structures, R(PO3)3 and RP5O14 respectively, or difference pair distribution function (PDF) features determined on similar glasses using difference neutron scattering methods. The local structure of this glass is therefore found to display multiple rare-earth ion environments, presumably because its composition lies between these two stoichiometric formulae. These Gd…Gd separations are well resolved in the PDFs that represent the AXS signal. Indeed, the spatial resolution is so good that it also enables the identification of R…X (X = R, P, O) pairwise correlations up to r ~ 9 Å; their average separations lie at r ~ 7.1(1) Å, 7.6(1) Å 7.9(1) Å, 8.4(1) Å and 8.7(1) Å. This is the first report of a Gd K-edge AXS study on an amorphous material. Its demonstrated ability to characterize the local structure of a glass up to such a long-range of r, heralds exciting prospects for AXS studies on other ternary non-crystalline materials. However, the technical challenge of such an experiment

  17. McMaster Mesonet soil moisture dataset: description and spatio-temporal variability analysis

    Directory of Open Access Journals (Sweden)

    K. C. Kornelsen

    2013-04-01

    Full Text Available This paper introduces and describes the hourly, high-resolution soil moisture dataset continuously recorded by the McMaster Mesonet located in the Hamilton-Halton Watershed in Southern Ontario, Canada. The McMaster Mesonet consists of a network of time domain reflectometer (TDR probes collecting hourly soil moisture data at six depths between 10 cm and 100 cm at nine locations per site, spread across four sites in the 1250 km2 watershed. The sites for the soil moisture arrays are designed to further improve understanding of soil moisture dynamics in a seasonal climate and to capture soil moisture transitions in areas that have different topography, soil and land cover. The McMaster Mesonet soil moisture constitutes a unique database in Canada because of its high spatio-temporal resolution. In order to provide some insight into the dominant processes at the McMaster Mesonet sites, a spatio-temporal and temporal stability analysis were conducted to identify spatio-temporal patterns in the data and to suggest some physical interpretation of soil moisture variability. It was found that the seasonal climate of the Great Lakes Basin causes a transition in soil moisture patterns at seasonal timescales. During winter and early spring months, and at the meadow sites, soil moisture distribution is governed by topographic redistribution, whereas following efflorescence in the spring and summer, soil moisture spatial distribution at the forested site was also controlled by vegetation canopy. Analysis of short-term temporal stability revealed that the relative difference between sites was maintained unless there was significant rainfall (> 20 mm or wet conditions a priori. Following a disturbance in the spatial soil moisture distribution due to wetting, the relative soil moisture pattern re-emerged in 18 to 24 h. Access to the McMaster Mesonet data can be provided by visiting www.hydrology.mcmaster.ca/mesonet.

  18. Exploring Multi-Scale Spatiotemporal Twitter User Mobility Patterns with a Visual-Analytics Approach

    Directory of Open Access Journals (Sweden)

    Junjun Yin

    2016-10-01

    Full Text Available Understanding human mobility patterns is of great importance for urban planning, traffic management, and even marketing campaign. However, the capability of capturing detailed human movements with fine-grained spatial and temporal granularity is still limited. In this study, we extracted high-resolution mobility data from a collection of over 1.3 billion geo-located Twitter messages. Regarding the concerns of infringement on individual privacy, such as the mobile phone call records with restricted access, the dataset is collected from publicly accessible Twitter data streams. In this paper, we employed a visual-analytics approach to studying multi-scale spatiotemporal Twitter user mobility patterns in the contiguous United States during the year 2014. Our approach included a scalable visual-analytics framework to deliver efficiency and scalability in filtering large volume of geo-located tweets, modeling and extracting Twitter user movements, generating space-time user trajectories, and summarizing multi-scale spatiotemporal user mobility patterns. We performed a set of statistical analysis to understand Twitter user mobility patterns across multi-level spatial scales and temporal ranges. In particular, Twitter user mobility patterns measured by the displacements and radius of gyrations of individuals revealed multi-scale or multi-modal Twitter user mobility patterns. By further studying such mobility patterns in different temporal ranges, we identified both consistency and seasonal fluctuations regarding the distance decay effects in the corresponding mobility patterns. At the same time, our approach provides a geo-visualization unit with an interactive 3D virtual globe web mapping interface for exploratory geo-visual analytics of the multi-level spatiotemporal Twitter user movements.

  19. Fast multidimensional ensemble empirical mode decomposition for the analysis of big spatio-temporal datasets.

    Science.gov (United States)

    Wu, Zhaohua; Feng, Jiaxin; Qiao, Fangli; Tan, Zhe-Min

    2016-04-13

    In this big data era, it is more urgent than ever to solve two major issues: (i) fast data transmission methods that can facilitate access to data from non-local sources and (ii) fast and efficient data analysis methods that can reveal the key information from the available data for particular purposes. Although approaches in different fields to address these two questions may differ significantly, the common part must involve data compression techniques and a fast algorithm. This paper introduces the recently developed adaptive and spatio-temporally local analysis method, namely the fast multidimensional ensemble empirical mode decomposition (MEEMD), for the analysis of a large spatio-temporal dataset. The original MEEMD uses ensemble empirical mode decomposition to decompose time series at each spatial grid and then pieces together the temporal-spatial evolution of climate variability and change on naturally separated timescales, which is computationally expensive. By taking advantage of the high efficiency of the expression using principal component analysis/empirical orthogonal function analysis for spatio-temporally coherent data, we design a lossy compression method for climate data to facilitate its non-local transmission. We also explain the basic principles behind the fast MEEMD through decomposing principal components instead of original grid-wise time series to speed up computation of MEEMD. Using a typical climate dataset as an example, we demonstrate that our newly designed methods can (i) compress data with a compression rate of one to two orders; and (ii) speed-up the MEEMD algorithm by one to two orders. © 2016 The Authors.

  20. Multiple Perspectives / Multiple Readings

    Directory of Open Access Journals (Sweden)

    Simon Biggs

    2005-01-01

    Full Text Available People experience things from their own physical point of view. What they see is usually a function of where they are and what physical attitude they adopt relative to the subject. With augmented vision (periscopes, mirrors, remote cameras, etc we are able to see things from places where we are not present. With time-shifting technologies, such as the video recorder, we can also see things from the past; a time and a place we may never have visited.In recent artistic work I have been exploring the implications of digital technology, interactivity and internet connectivity that allow people to not so much space/time-shift their visual experience of things but rather see what happens when everybody is simultaneously able to see what everybody else can see. This is extrapolated through the remote networking of sites that are actual installation spaces; where the physical movements of viewers in the space generate multiple perspectives, linked to other similar sites at remote locations or to other viewers entering the shared data-space through a web based version of the work.This text explores the processes involved in such a practice and reflects on related questions regarding the non-singularity of being and the sense of self as linked to time and place.

  1. a Web-Based Interactive Platform for Co-Clustering Spatio-Temporal Data

    Science.gov (United States)

    Wu, X.; Poorthuis, A.; Zurita-Milla, R.; Kraak, M.-J.

    2017-09-01

    Since current studies on clustering analysis mainly focus on exploring spatial or temporal patterns separately, a co-clustering algorithm is utilized in this study to enable the concurrent analysis of spatio-temporal patterns. To allow users to adopt and adapt the algorithm for their own analysis, it is integrated within the server side of an interactive web-based platform. The client side of the platform, running within any modern browser, is a graphical user interface (GUI) with multiple linked visualizations that facilitates the understanding, exploration and interpretation of the raw dataset and co-clustering results. Users can also upload their own datasets and adjust clustering parameters within the platform. To illustrate the use of this platform, an annual temperature dataset from 28 weather stations over 20 years in the Netherlands is used. After the dataset is loaded, it is visualized in a set of linked visualizations: a geographical map, a timeline and a heatmap. This aids the user in understanding the nature of their dataset and the appropriate selection of co-clustering parameters. Once the dataset is processed by the co-clustering algorithm, the results are visualized in the small multiples, a heatmap and a timeline to provide various views for better understanding and also further interpretation. Since the visualization and analysis are integrated in a seamless platform, the user can explore different sets of co-clustering parameters and instantly view the results in order to do iterative, exploratory data analysis. As such, this interactive web-based platform allows users to analyze spatio-temporal data using the co-clustering method and also helps the understanding of the results using multiple linked visualizations.

  2. Neural avalanches at the critical point between replay and non-replay of spatiotemporal patterns.

    Directory of Open Access Journals (Sweden)

    Silvia Scarpetta

    Full Text Available We model spontaneous cortical activity with a network of coupled spiking units, in which multiple spatio-temporal patterns are stored as dynamical attractors. We introduce an order parameter, which measures the overlap (similarity between the activity of the network and the stored patterns. We find that, depending on the excitability of the network, different working regimes are possible. For high excitability, the dynamical attractors are stable, and a collective activity that replays one of the stored patterns emerges spontaneously, while for low excitability, no replay is induced. Between these two regimes, there is a critical region in which the dynamical attractors are unstable, and intermittent short replays are induced by noise. At the critical spiking threshold, the order parameter goes from zero to one, and its fluctuations are maximized, as expected for a phase transition (and as observed in recent experimental results in the brain. Notably, in this critical region, the avalanche size and duration distributions follow power laws. Critical exponents are consistent with a scaling relationship observed recently in neural avalanches measurements. In conclusion, our simple model suggests that avalanche power laws in cortical spontaneous activity may be the effect of a network at the critical point between the replay and non-replay of spatio-temporal patterns.

  3. Spatio-Temporal Series Remote Sensing Image Prediction Based on Multi-Dictionary Bayesian Fusion

    Directory of Open Access Journals (Sweden)

    Chu He

    2017-11-01

    Full Text Available Contradictions in spatial resolution and temporal coverage emerge from earth observation remote sensing images due to limitations in technology and cost. Therefore, how to combine remote sensing images with low spatial yet high temporal resolution as well as those with high spatial yet low temporal resolution to construct images with both high spatial resolution and high temporal coverage has become an important problem called spatio-temporal fusion problem in both research and practice. A Multi-Dictionary Bayesian Spatio-Temporal Reflectance Fusion Model (MDBFM has been proposed in this paper. First, multiple dictionaries from regions of different classes are trained. Second, a Bayesian framework is constructed to solve the dictionary selection problem. A pixel-dictionary likehood function and a dictionary-dictionary prior function are constructed under the Bayesian framework. Third, remote sensing images before and after the middle moment are combined to predict images at the middle moment. Diverse shapes and textures information is learned from different landscapes in multi-dictionary learning to help dictionaries capture the distinctions between regions. The Bayesian framework makes full use of the priori information while the input image is classified. The experiments with one simulated dataset and two satellite datasets validate that the MDBFM is highly effective in both subjective and objective evaluation indexes. The results of MDBFM show more precise details and have a higher similarity with real images when dealing with both type changes and phenology changes.

  4. Amplitude death and spatiotemporal bifurcations in nonlocally delay-coupled oscillators

    International Nuclear Information System (INIS)

    Guo, Yuxiao; Niu, Ben

    2015-01-01

    Amplitude death and spatiotemporal oscillations are remarkable patterns in coupled systems. We consider a ring of n identical oscillators with distance-dependent couplings and time delay. The amplitude death region is the intersection of three stable regions. Employing the method of multiple scales and normal form theory, the stability and criticality of spatiotemporal oscillations are determined. Around the amplitude death boundary there exist one branch of synchronized oscillations, n − 3 branches of co-existing phase-locked oscillations, n branches of mirror-reflecting oscillations, n branches of standing-wave oscillations, one branch of quasiperiodic oscillations and two branches of co-existing synchronized oscillations. It is proved that amplitude death is robust to small inhomogeneity of couplings, and the stability of synchronized or phase-locked oscillations inherits that of the individual decoupled oscillator. For the arbitrary form of coupling functions, some general results are also obtained for the thermodynamic limit. Finally, two examples are given to support the main results. (paper)

  5. Harbour porpoise distribution can vary at small spatiotemporal scales in energetic habitats

    Science.gov (United States)

    Benjamins, Steven; van Geel, Nienke; Hastie, Gordon; Elliott, Jim; Wilson, Ben

    2017-07-01

    Marine habitat heterogeneity underpins species distribution and can be generated through interactions between physical and biological drivers at multiple spatiotemporal scales. Passive acoustic monitoring (PAM) is used worldwide to study potential impacts of marine industrial activities on cetaceans, but understanding of animals' site use at small spatiotemporal scales (marine renewable energy development (MRED) sites was investigated by deploying dense arrays of C-POD passive acoustic detectors at a wave energy test site (the European Marine Energy Centre [Billia Croo, Orkney]) and by a minor tidal-stream site (Scarba [Inner Hebrides]). Respective arrays consisted of 7 and 11 moorings containing two C-PODs each and were deployed for up to 55 days. Minimum inter-mooring distances varied between 300-600 m. All C-POD data were analysed at a temporal resolution of whole minutes, with each minute classified as 1 or 0 on the basis of presence/absence of porpoise click trains (Porpoise-Positive Minutes/PPMs). Porpoise detection rates were analysed using Generalised Additive Models (GAMs) with Generalised Estimation Equations (GEEs). Although there were many porpoise detections (wave test site: N=3,432; tidal-stream site: N=17,366), daily detection rates varied significantly within both arrays. Within the wave site array (<1 km diameter), average daily detection rates varied from 4.3 to 14.8 PPMs/day. Within the tidal-stream array (<2 km diameter), average daily detection rates varied from 10.3 to 49.7 PPMs/day. GAM-GEE model results for individual moorings within both arrays indicated linkages between porpoise presence and small-scale heterogeneity among different environmental covariates (e.g., tidal phase, time of day). Porpoise detection rates varied considerably but with coherent patterns between moorings only several hundred metres apart and within hours. These patterns presumably have ecological relevance. These results indicate that, in energetically active and

  6. Stochastic resonance based on modulation instability in spatiotemporal chaos.

    Science.gov (United States)

    Han, Jing; Liu, Hongjun; Huang, Nan; Wang, Zhaolu

    2017-04-03

    A novel dynamic of stochastic resonance in spatiotemporal chaos is presented, which is based on modulation instability of perturbed partially coherent wave. The noise immunity of chaos can be reinforced through this effect and used to restore the coherent signal information buried in chaotic perturbation. A theoretical model with fluctuations term is derived from the complex Ginzburg-Landau equation via Wigner transform. It shows that through weakening the nonlinear threshold and triggering energy redistribution, the coherent component dominates the instability damped by incoherent component. The spatiotemporal output showing the properties of stochastic resonance may provide a potential application of signal encryption and restoration.

  7. Spatio-temporal data analytics for wind energy integration

    CERN Document Server

    Yang, Lei; Zhang, Junshan

    2014-01-01

    This SpringerBrief presents spatio-temporal data analytics for wind energy integration using stochastic modeling and optimization methods. It explores techniques for efficiently integrating renewable energy generation into bulk power grids. The operational challenges of wind, and its variability are carefully examined. A spatio-temporal analysis approach enables the authors to develop Markov-chain-based short-term forecasts of wind farm power generation. To deal with the wind ramp dynamics, a support vector machine enhanced Markov model is introduced. The stochastic optimization of economic di

  8. Coexistence of collapse and stable spatiotemporal solitons in multimode fibers

    Science.gov (United States)

    Shtyrina, Olga V.; Fedoruk, Mikhail P.; Kivshar, Yuri S.; Turitsyn, Sergei K.

    2018-01-01

    We analyze spatiotemporal solitons in multimode optical fibers and demonstrate the existence of stable solitons, in a sharp contrast to earlier predictions of collapse of multidimensional solitons in three-dimensional media. We discuss the coexistence of blow-up solutions and collapse stabilization by a low-dimensional external potential in graded-index media, and also predict the existence of stable higher-order nonlinear waves such as dipole-mode spatiotemporal solitons. To support the main conclusions of our numerical studies we employ a variational approach and derive analytically the stability criterion for input powers for the collapse stabilization.

  9. Replication Strategy for Spatiotemporal Data Based on Distributed Caching System.

    Science.gov (United States)

    Xiong, Lian; Yang, Liu; Tao, Yang; Xu, Juan; Zhao, Lun

    2018-01-14

    The replica strategy in distributed cache can effectively reduce user access delay and improve system performance. However, developing a replica strategy suitable for varied application scenarios is still quite challenging, owing to differences in user access behavior and preferences. In this paper, a replication strategy for spatiotemporal data (RSSD) based on a distributed caching system is proposed. By taking advantage of the spatiotemporal locality and correlation of user access, RSSD mines high popularity and associated files from historical user access information, and then generates replicas and selects appropriate cache node for placement. Experimental results show that the RSSD algorithm is simple and efficient, and succeeds in significantly reducing user access delay.

  10. Artificial neural network does better spatiotemporal compressive sampling

    Science.gov (United States)

    Lee, Soo-Young; Hsu, Charles; Szu, Harold

    2012-06-01

    Spatiotemporal sparseness is generated naturally by human visual system based on artificial neural network modeling of associative memory. Sparseness means nothing more and nothing less than the compressive sensing achieves merely the information concentration. To concentrate the information, one uses the spatial correlation or spatial FFT or DWT or the best of all adaptive wavelet transform (cf. NUS, Shen Shawei). However, higher dimensional spatiotemporal information concentration, the mathematics can not do as flexible as a living human sensory system. The reason is obviously for survival reasons. The rest of the story is given in the paper.

  11. Tensor analysis methods for activity characterization in spatiotemporal data

    Energy Technology Data Exchange (ETDEWEB)

    Haass, Michael Joseph; Van Benthem, Mark Hilary; Ochoa, Edward M

    2014-03-01

    Tensor (multiway array) factorization and decomposition offers unique advantages for activity characterization in spatio-temporal datasets because these methods are compatible with sparse matrices and maintain multiway structure that is otherwise lost in collapsing for regular matrix factorization. This report describes our research as part of the PANTHER LDRD Grand Challenge to develop a foundational basis of mathematical techniques and visualizations that enable unsophisticated users (e.g. users who are not steeped in the mathematical details of matrix algebra and mulitway computations) to discover hidden patterns in large spatiotemporal data sets.

  12. Pattern control and suppression of spatiotemporal chaos using geometrical resonance

    International Nuclear Information System (INIS)

    Gonzalez, J.A.; Bellorin, A.; Reyes, L.I.; Vasquez, C.; Guerrero, L.E.

    2004-01-01

    We generalize the concept of geometrical resonance to perturbed sine-Gordon, Nonlinear Schroedinger, phi (cursive,open) Greek 4 , and Complex Ginzburg-Landau equations. Using this theory we can control different dynamical patterns. For instance, we can stabilize breathers and oscillatory patterns of large amplitudes successfully avoiding chaos. On the other hand, this method can be used to suppress spatiotemporal chaos and turbulence in systems where these phenomena are already present. This method can be generalized to even more general spatiotemporal systems. A short report of some of our results has been published in [Europhys. Lett. 64 (2003) 743

  13. Replication Strategy for Spatiotemporal Data Based on Distributed Caching System

    Science.gov (United States)

    Xiong, Lian; Tao, Yang; Xu, Juan; Zhao, Lun

    2018-01-01

    The replica strategy in distributed cache can effectively reduce user access delay and improve system performance. However, developing a replica strategy suitable for varied application scenarios is still quite challenging, owing to differences in user access behavior and preferences. In this paper, a replication strategy for spatiotemporal data (RSSD) based on a distributed caching system is proposed. By taking advantage of the spatiotemporal locality and correlation of user access, RSSD mines high popularity and associated files from historical user access information, and then generates replicas and selects appropriate cache node for placement. Experimental results show that the RSSD algorithm is simple and efficient, and succeeds in significantly reducing user access delay. PMID:29342897

  14. Spatio-Temporal Data Mining for Location-Based Services

    DEFF Research Database (Denmark)

    Gidofalvi, Gyozo

    . The objectives of the presented thesis are three-fold. First, to extend popular data mining methods to the spatio-temporal domain. Second, to demonstrate the usefulness of the extended methods and the derived knowledge in promising LBS examples. Finally, to eliminate privacy concerns in connection with spatio......-temporal data mining by devising systems for privacy-preserving location data collection and mining.......Location-Based Services (LBS) are continuously gaining popularity. Innovative LBSes integrate knowledge about the users into the service. Such knowledge can be derived by analyzing the location data of users. Such data contain two unique dimensions, space and time, which need to be analyzed...

  15. Spatio-temporal databases complex motion pattern queries

    CERN Document Server

    Vieira, Marcos R

    2013-01-01

    This brief presents several new query processing techniques, called complex motion pattern queries, specifically designed for very large spatio-temporal databases of moving objects. The brief begins with the definition of flexible pattern queries, which are powerful because of the integration of variables and motion patterns. This is followed by a summary of the expressive power of patterns and flexibility of pattern queries. The brief then present the Spatio-Temporal Pattern System (STPS) and density-based pattern queries. STPS databases contain millions of records with information about mobi

  16. Routes to spatiotemporal chaos in Kerr optical frequency combs.

    Science.gov (United States)

    Coillet, Aurélien; Chembo, Yanne K

    2014-03-01

    We investigate the various routes to spatiotemporal chaos in Kerr optical frequency combs, obtained through pumping an ultra-high Q-factor whispering-gallery mode resonator with a continuous-wave laser. The Lugiato-Lefever model is used to build bifurcation diagrams with regards to the parameters that are externally controllable, namely, the frequency and the power of the pumping laser. We show that the spatiotemporal chaos emerging from Turing patterns and solitons display distinctive dynamical features. Experimental spectra of chaotic Kerr combs are also presented for both cases, in excellent agreement with theoretical spectra.

  17. Size-dependent diffusion promotes the emergence of spatiotemporal patterns

    DEFF Research Database (Denmark)

    Zhang, Lai; Thygesen, Uffe Høgsbro; Banerjee, Malay

    2014-01-01

    intraspecific physiological variations at the individual level. Here we explore the impacts of size variation within species resulting from individual ontogeny, on the emergence of spatiotemporal patterns in a fully size-structured population model. We found that size dependency of animal's diffusivity greatly......, we found that the single-generation cycle is more likely to drive spatiotemporal patterns compared to predator-prey cycles, meaning that the mechanism of Hopf bifurcation might be more common than hitherto appreciated since the former cycle is more widespread than the latter in case of interacting...

  18. Spatiotemporal variability in carbon exchange fluxes across the Sahel

    DEFF Research Database (Denmark)

    Tagesson, Håkan Torbern; Fensholt, Rasmus; Cappelaere, Bernard

    2016-01-01

    for semi-arid ecosystems. We have synthesized data on the land-atmosphere exchange of CO2 measured with the eddy covariance technique from the six existing sites across the Sahel, one of the largest semi-arid regions in the world. The overall aim of the study is to analyse and quantify the spatiotemporal...... variability in these fluxes and to analyse to which degree spatiotemporal variation can be explained by hydrological, climatic, edaphic and vegetation variables. All ecosystems were C sinks (average ± total error -162 ± 48 g C m-2 y-1), but were smaller when strongly impacted by anthropogenic influences...

  19. Spatio-temporal modeling of nonlinear distributed parameter systems

    CERN Document Server

    Li, Han-Xiong

    2011-01-01

    The purpose of this volume is to provide a brief review of the previous work on model reduction and identifi cation of distributed parameter systems (DPS), and develop new spatio-temporal models and their relevant identifi cation approaches. In this book, a systematic overview and classifi cation on the modeling of DPS is presented fi rst, which includes model reduction, parameter estimation and system identifi cation. Next, a class of block-oriented nonlinear systems in traditional lumped parameter systems (LPS) is extended to DPS, which results in the spatio-temporal Wiener and Hammerstein s

  20. Mobile technologies and the spatiotemporal configurations of institutional practice

    DEFF Research Database (Denmark)

    Shklovski, Irina; Troshynski, Emily; Dourish, Paul

    2015-01-01

    are specifically concerned with what happens to institutional roles, power relationships, and decision-making processes when a particular type of information—that of spatiotemporal location of people—is made into a technologically tradable object through the use of location-based systems. We examine...... in which broad adoption of location-based and mobile technologies has the capacity to radically reconfigure the spatiotemporal arrangement of institutional processes. The presence of digital location traces creates new forms of institutional accountability, facilitates a shift in the understood relation...... between location and action, and necessitates new models of interpretation and sense making in practice....

  1. Estimating the state of large spatio-temporally chaotic systems

    International Nuclear Information System (INIS)

    Ott, E.; Hunt, B.R.; Szunyogh, I.; Zimin, A.V.; Kostelich, E.J.; Corazza, M.; Kalnay, E.; Patil, D.J.; Yorke, J.A.

    2004-01-01

    We consider the estimation of the state of a large spatio-temporally chaotic system from noisy observations and knowledge of a system model. Standard state estimation techniques using the Kalman filter approach are not computationally feasible for systems with very many effective degrees of freedom. We present and test a new technique (called a Local Ensemble Kalman Filter), generally applicable to large spatio-temporally chaotic systems for which correlations between system variables evaluated at different points become small at large separation between the points

  2. Spatiotemporal characteristics of physiological gastroesophageal reflux

    NARCIS (Netherlands)

    Weusten, B. L.; Akkermans, L. M.; vanBerge-Henegouwen, G. P.; Smout, A. J.

    1994-01-01

    Recent technological developments have made it possible to measure intraluminal pH simultaneously at multiple sites using one single small-caliber catheter. The aim of this study was to investigate the dynamics of physiological gastroesophageal reflux in eight ambulatory healthy volunteers (age

  3. Molecular epidemiology and spatiotemporal analysis of hospital-acquired Acinetobacter baumannii infection in a tertiary care hospital in southern Thailand.

    Science.gov (United States)

    Chusri, S; Chongsuvivatwong, V; Rivera, J I; Silpapojakul, K; Singkhamanan, K; McNeil, E; Doi, Y

    2017-01-01

    Acinetobacter baumannii is a major hospital-acquired pathogen in Thailand that has a negative effect on patient survival. The nature of its transmission is poorly understood. To investigate the genotypic and spatiotemporal pattern of A. baumannii infection at a hospital in Thailand. The medical records of patients infected with A. baumannii at an 800-bed tertiary care hospital in southern Thailand between January 2010 and December 2011 were reviewed retrospectively. A. baumannii was identified at the genomospecies level. Carbapenemase genes were identified among carbapenem-resistant isolates associated with A. baumannii infection. A spatiotemporal analysis was performed by admission ward, time of infection and pulsed-field gel electrophoresis (PFGE) groups of A. baumannii. Nine PFGE groups were identified among the 197 A. baumannii infections. All A. baumannii isolates were assigned to International Clonal Lineage II. bla OXA-23 was the most prevalent carbapenemase gene. Outbreaks were observed mainly in respiratory and intensive care units. The association between PFGE group and hospital unit was significant. Spatiotemporal analysis identified 20 clusters of single PFGE group infections. Approximately half of the clusters involved multiple hospital units simultaneously. A. baumannii transmitted both within and between hospital wards. Better understanding and control of the transmission of A. baumannii are needed. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  4. Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China

    Directory of Open Access Journals (Sweden)

    Chunxiang Cao

    2016-01-01

    Full Text Available Severe acute respiratory syndrome (SARS is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases.

  5. Multi-perspective analysis and spatiotemporal mapping of air pollution monitoring data.

    Science.gov (United States)

    Kolovos, Alexander; Skupin, André; Jerrett, Michael; Christakos, George

    2010-09-01

    Space-time data analysis and assimilation techniques in atmospheric sciences typically consider input from monitoring measurements. The input is often processed in a manner that acknowledges characteristics of the measurements (e.g., underlying patterns, fluctuation features) under conditions of uncertainty; it also leads to the derivation of secondary information that serves study-oriented goals, and provides input to space-time prediction techniques. We present a novel approach that blends a rigorous space-time prediction model (Bayesian maximum entropy, BME) with a cognitively informed visualization of high-dimensional data (spatialization). The combined BME and spatialization approach (BME-S) is used to study monthly averaged NO2 and mean annual SO4 measurements in California over the 15-year period 1988-2002. Using the original scattered measurements of these two pollutants BME generates spatiotemporal predictions on a regular grid across the state. Subsequently, the prediction network undergoes the spatialization transformation into a lower-dimensional geometric representation, aimed at revealing patterns and relationships that exist within the input data. The proposed BME-S provides a powerful spatiotemporal framework to study a variety of air pollution data sources.

  6. Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China.

    Science.gov (United States)

    Cao, Chunxiang; Chen, Wei; Zheng, Sheng; Zhao, Jian; Wang, Jinfeng; Cao, Wuchun

    2016-01-01

    Severe acute respiratory syndrome (SARS) is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases.

  7. Spatio-temporal epidemiology of the cholera outbreak in Papua New Guinea, 2009-2011.

    Science.gov (United States)

    Horwood, Paul F; Karl, Stephan; Mueller, Ivo; Jonduo, Marinjho H; Pavlin, Boris I; Dagina, Rosheila; Ropa, Berry; Bieb, Sibauk; Rosewell, Alexander; Umezaki, Masahiro; Siba, Peter M; Greenhill, Andrew R

    2014-08-20

    Cholera continues to be a devastating disease in many developing countries where inadequate safe water supply and poor sanitation facilitate spread. From July 2009 until late 2011 Papua New Guinea experienced the first outbreak of cholera recorded in the country, resulting in >15,500 cases and >500 deaths. Using the national cholera database, we analysed the spatio-temporal distribution and clustering of the Papua New Guinea cholera outbreak. The Kulldorff space-time permutation scan statistic, contained in the software package SatScan v9.2 was used to describe the first 8 weeks of the outbreak in Morobe Province before cholera cases spread throughout other regions of the country. Data were aggregated at the provincial level to describe the spread of the disease to other affected provinces. Spatio-temporal and cluster analyses revealed that the outbreak was characterized by three distinct phases punctuated by explosive propagation of cases when the outbreak spread to a new region. The lack of road networks across most of Papua New Guinea is likely to have had a major influence on the slow spread of the disease during this outbreak. Identification of high risk areas and the likely mode of spread can guide government health authorities to formulate public health strategies to mitigate the spread of the disease through education campaigns, vaccination, increased surveillance in targeted areas and interventions to improve water, sanitation and hygiene.

  8. Exploring Spatiotemporal Patterns of Long-Distance Taxi Rides in Shanghai

    Directory of Open Access Journals (Sweden)

    Hangbin Wu

    2017-11-01

    Full Text Available Floating Car Data (FCD has been analyzed for various purposes in past years. However, limited research about the behaviors of taking long-distance taxi rides has been made available. In this paper, we used data from over 12,000 taxis during a six-month period in Shanghai to analyze the spatiotemporal patterns of long-distance taxi trips. We investigated these spatiotemporal patterns by comparing them with metro usage in Shanghai, in order to determine the extent and how the suburban trains divert the passenger flow from taxis. The results identified 12 pick-up and six drop-off hotspots in Shanghai. Overall, the pick-up locations were relatively more concentrated than the drop-off locations. Temporal patterns were also revealed. Passengers on long-distance taxi rides were observed to avoid the rush hours on the street as their first priority and tried to avoid the inconvenience of interchanges on the metro lines as their second priority.

  9. World Spatiotemporal Analytics and Mapping Project (WSTAMP): Discovering, Exploring, and Mapping Spatiotemporal Patterns across the World s Largest Open Source Geographic Data Sets

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Robert N [ORNL; Piburn, Jesse O [ORNL; Sorokine, Alexandre [ORNL; Myers, Aaron T [ORNL; White, Devin A [ORNL

    2015-01-01

    The application of spatiotemporal (ST) analytics to integrated data from major sources such as the World Bank, United Nations, and dozens of others holds tremendous potential for shedding new light on the evolution of cultural, health, economic, and geopolitical landscapes on a global level. Realizing this potential first requires an ST data model that addresses challenges in properly merging data from multiple authors, with evolving ontological perspectives, semantical differences, and changing attributes, as well as content that is textual, numeric, categorical, and hierarchical. Equally challenging is the development of analytical and visualization approaches that provide a serious exploration of this integrated data while remaining accessible to practitioners with varied backgrounds. The WSTAMP project at Oak Ridge National Laboratory has yielded two major results in addressing these challenges: 1) development of the WSTAMP database, a significant advance in ST data modeling that integrates 10,000+ attributes covering over 200 nation states spanning over 50 years from over 30 major sources and 2) a novel online ST exploratory and analysis tool providing an array of modern statistical and visualization techniques for analyzing these data temporally, spatially, and spatiotemporally under a standard analytic workflow. We discuss the status of this work and report on major findings. Acknowledgment Prepared by Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6285, managed by UT-Battelle, LLC for the U. S. Department of Energy under contract no. DEAC05-00OR22725. Copyright This manuscript has been authored by employees of UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the U.S. Department of Energy. Accordingly, the United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or

  10. Spatiotemporal variability of marine renewable energy resources in Norway

    NARCIS (Netherlands)

    Varlas, George; Christakos, Konstantinos; Cheliotis, Ioannis; Papadopoulos, A.; Steeneveld, G.J.

    2017-01-01

    Marine Renewable Energy (MRE) resources such as wind and wave energy depend on the complex behaviour of weather and climatic conditions which determine the development of MRE technologies, energy grid, supply and prices. This study investigates the spatiotemporal variability of MRE resources along

  11. Spatiotemporal distribution patterns of forest fires in northern Mexico

    Science.gov (United States)

    Gustavo Pérez-Verdin; M. A. Márquez-Linares; A. Cortes-Ortiz; M. Salmerón-Macias

    2013-01-01

    Using the 2000-2011 CONAFOR databases, a spatiotemporal analysis of the occurrence of forest fires in Durango, one of the most affected States in Mexico, was conducted. The Moran's index was used to determine a spatial distribution pattern; also, an analysis of seasonal and temporal autocorrelation of the data collected was completed. The geographically weighted...

  12. Large scale stochastic spatio-temporal modelling with PCRaster

    NARCIS (Netherlands)

    Karssenberg, D.J.; Drost, N.; Schmitz, O.; Jong, K. de; Bierkens, M.F.P.

    2013-01-01

    PCRaster is a software framework for building spatio-temporal models of land surface processes (http://www.pcraster.eu). Building blocks of models are spatial operations on raster maps, including a large suite of operations for water and sediment routing. These operations are available to model

  13. Spatiotemporal dynamics of cortical representations during and after stimulus presentation

    NARCIS (Netherlands)

    Nieuwenhuijzen, M.E. van de; Borne, E.W.P. van den; Jensen, O.; Gerven, M.A.J. van

    2016-01-01

    Visual perception is a spatiotemporally complex process. In this study, we investigated cortical dynamics during and after stimulus presentation. We observed that visual category information related to the difference between faces and objects became apparent in the occipital lobe after 63 ms. Within

  14. ELASTIC CLOUD COMPUTING ARCHITECTURE AND SYSTEM FOR HETEROGENEOUS SPATIOTEMPORAL COMPUTING

    Directory of Open Access Journals (Sweden)

    X. Shi

    2017-10-01

    Full Text Available Spatiotemporal computation implements a variety of different algorithms. When big data are involved, desktop computer or standalone application may not be able to complete the computation task due to limited memory and computing power. Now that a variety of hardware accelerators and computing platforms are available to improve the performance of geocomputation, different algorithms may have different behavior on different computing infrastructure and platforms. Some are perfect for implementation on a cluster of graphics processing units (GPUs, while GPUs may not be useful on certain kind of spatiotemporal computation. This is the same situation in utilizing a cluster of Intel's many-integrated-core (MIC or Xeon Phi, as well as Hadoop or Spark platforms, to handle big spatiotemporal data. Furthermore, considering the energy efficiency requirement in general computation, Field Programmable Gate Array (FPGA may be a better solution for better energy efficiency when the performance of computation could be similar or better than GPUs and MICs. It is expected that an elastic cloud computing architecture and system that integrates all of GPUs, MICs, and FPGAs could be developed and deployed to support spatiotemporal computing over heterogeneous data types and computational problems.

  15. Elastic Cloud Computing Architecture and System for Heterogeneous Spatiotemporal Computing

    Science.gov (United States)

    Shi, X.

    2017-10-01

    Spatiotemporal computation implements a variety of different algorithms. When big data are involved, desktop computer or standalone application may not be able to complete the computation task due to limited memory and computing power. Now that a variety of hardware accelerators and computing platforms are available to improve the performance of geocomputation, different algorithms may have different behavior on different computing infrastructure and platforms. Some are perfect for implementation on a cluster of graphics processing units (GPUs), while GPUs may not be useful on certain kind of spatiotemporal computation. This is the same situation in utilizing a cluster of Intel's many-integrated-core (MIC) or Xeon Phi, as well as Hadoop or Spark platforms, to handle big spatiotemporal data. Furthermore, considering the energy efficiency requirement in general computation, Field Programmable Gate Array (FPGA) may be a better solution for better energy efficiency when the performance of computation could be similar or better than GPUs and MICs. It is expected that an elastic cloud computing architecture and system that integrates all of GPUs, MICs, and FPGAs could be developed and deployed to support spatiotemporal computing over heterogeneous data types and computational problems.

  16. Spatiotemporal radiotherapy planning using a global optimization approach

    Science.gov (United States)

    Adibi, Ali; Salari, Ehsan

    2018-02-01

    This paper aims at quantifying the extent of potential therapeutic gain, measured using biologically effective dose (BED), that can be achieved by altering the radiation dose distribution over treatment sessions in fractionated radiotherapy. To that end, a spatiotemporally integrated planning approach is developed, where the spatial and temporal dose modulations are optimized simultaneously. The concept of equivalent uniform BED (EUBED) is used to quantify and compare the clinical quality of spatiotemporally heterogeneous dose distributions in target and critical structures. This gives rise to a large-scale non-convex treatment-plan optimization problem, which is solved using global optimization techniques. The proposed spatiotemporal planning approach is tested on two stylized cancer cases resembling two different tumor sites and sensitivity analysis is performed for radio-biological and EUBED parameters. Numerical results validate that spatiotemporal plans are capable of delivering a larger BED to the target volume without increasing the BED in critical structures compared to conventional time-invariant plans. In particular, this additional gain is attributed to the irradiation of different regions of the target volume at different treatment sessions. Additionally, the trade-off between the potential therapeutic gain and the number of distinct dose distributions is quantified, which suggests a diminishing marginal gain as the number of dose distributions increases.

  17. Gaze control during interceptive actions with different spatiotemporal demands.

    NARCIS (Netherlands)

    Navia, J.A.; Dicks, M.S.; van der Kamp, J; Ruiz, L.

    It is widely accepted that the sources of information used to guide interceptive actions depend on conflicting spatiotemporal task demands. However, there is a paucity of evidence that shows how information pick-up during interceptive actions is adapted to such conflicting constraints. The present

  18. Pain Recognition using Spatiotemporal Oriented Energy of Facial Muscles

    DEFF Research Database (Denmark)

    Irani, Ramin; Nasrollahi, Kamal; Moeslund, Thomas B.

    2015-01-01

    Pain is a critical sign in many medical situations and its automatic detection and recognition using computer vision techniques is of great importance. Utilizes this fact that pain is a spatiotemporal process, the proposed system in this paper employs steerable and separable filters to measures e...

  19. Spatio-temporal point process filtering methods with an application

    Czech Academy of Sciences Publication Activity Database

    Frcalová, B.; Beneš, V.; Klement, Daniel

    2010-01-01

    Roč. 21, 3-4 (2010), s. 240-252 ISSN 1180-4009 R&D Projects: GA AV ČR(CZ) IAA101120604 Institutional research plan: CEZ:AV0Z50110509 Keywords : cox point process * filtering * spatio-temporal modelling * spike Subject RIV: BA - General Mathematics Impact factor: 0.750, year: 2010

  20. Spatio-temporal analysis of Salmonella surveillance data in Thailand

    DEFF Research Database (Denmark)

    Coutinho Calado Domingues, Ana Rita; Vieira, Antonio; Hendriksen, Rene S.

    2014-01-01

    This study evaluates the usefulness of spatio-temporal statistical tools to detect outbreaks using routine surveillance data where limited epidemiological information is available. A dataset from 2002 to 2007 containing information regarding date, origin, source and serotype of 29 586 Salmonella ...

  1. On spatio-temporal Lévy based Cox processes

    DEFF Research Database (Denmark)

    Prokesova, Michaela; Hellmund, Gunnar; Jensen, Eva Bjørn Vedel

    2006-01-01

    The paper discusses a new class of models for spatio-temporal Cox point processes. In these models, the driving field is defined by means of an integral of a weight function with respect to a Lévy basis. The relations to other Cox process models studied previously are discussed and formulas for t...

  2. Spatiotemporal Coupling of the Tongue in Amyotrophic Lateral Sclerosis

    Science.gov (United States)

    Kuruvilla, Mili S.; Green, Jordan R.; Yunusova, Yana; Hanford, Kathy

    2012-01-01

    Purpose: The primary aim of the investigation was to identify deficits in spatiotemporal coupling between tongue regions in amyotrophic lateral sclerosis (ALS). The relations between disease-related changes in tongue movement patterns and speech intelligibility were also determined. Methods: The authors recorded word productions from 11…

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

    Directory of Open Access Journals (Sweden)

    Zhiqiang Tian

    2013-03-01

    Full Text Available 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.

  4. Spatio-temporal joins on symbolic indoor tracking data

    DEFF Research Database (Denmark)

    Lu, Hua; Yang, Bin; Jensen, Christian S.

    2011-01-01

    and studies probabilistic, spatio-temporal joins on historical indoor tracking data. Two meaningful types of join are defined. They return object pairs that satisfy spatial join predicates either at a time point or during a time interval. The predicates considered include “same X,” where X is a semantic...

  5. Mode locking and spatiotemporal chaos in periodically driven Gunn diodes

    DEFF Research Database (Denmark)

    Mosekilde, Erik; Feldberg, Rasmus; Knudsen, Carsten

    1990-01-01

    oscillation entrains with the external signal. This produces a devil’s staircase of frequency-locked solutions. At higher microwave amplitudes, period doubling and other forms of mode-converting bifurcations can be seen. In this interval the diode also exhibits spatiotemporal chaos. At still higher microwave...

  6. Spatiotemporal Diffusive Evolution and Fractal Structure of Ground Motion

    Science.gov (United States)

    Suwada, Tsuyoshi

    2018-02-01

    The spatiotemporal diffusive evolution and fractal structure of ground motion have been investigated at the in-ground tunnel of the KEK B-Factory (KEKB) injector linear accelerator (linac). The slow dynamic fluctuating displacements of the tunnel floor are measured in real time with a new remote-controllable sensing system based on a laser-based alignment system. Based on spatiotemporal analyses with linear-regression models, which were applied in both the time and frequency domains to time-series data recorded over a period of approximately 8 months, both coherent and stochastic components in the displacements of the tunnel floor were clearly observed along the entire length of the linac. In particular, it was clearly observed that the stochastic components exhibited characteristic spatiotemporal diffusive evolution with the fractal structure and fractional dimension. This report describes in detail the experimental techniques and analyses of the spatiotemporal diffusive evolution of ground motion observed at the in-ground tunnel of the injector linac using a real-time remote-controllable sensing system.

  7. Synchronization of spatiotemporal chaotic systems by feedback control

    International Nuclear Information System (INIS)

    Lai, Y.; Grebogi, C.

    1994-01-01

    We demonstrate that two identical spatiotemporal chaotic systems can be synchronized by (1) linking one or a few of their dynamical variables, and (2) applying a small feedback control to one of the systems. Numerical examples using the diffusively coupled logistic map lattice are given. The effect of noise and the limitation of the technique are discussed

  8. Spatiotemporal synchronization of drift waves in a magnetron sputtering plasma

    Czech Academy of Sciences Publication Activity Database

    Martines, E.; Zuin, M.; Cavazzana, R.; Adámek, Jiří; Antoni, V.; Serianni, G.; Spolaore, M.; Vianello, N.

    2014-01-01

    Roč. 21, č. 10 (2014), s. 102309-102309 ISSN 1070-664X Institutional support: RVO:61389021 Keywords : Drift waves * Magnetron sputtering plasma * Spatiotemporal synchronization Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 2.142, year: 2014 http://dx.doi.org/10.1063/1.4898693

  9. Multiple sclerosis

    Science.gov (United States)

    ... indwelling catheter Osteoporosis or thinning of the bones Pressure sores Side effects of medicines used to treat the ... Daily bowel care program Multiple sclerosis - discharge Preventing pressure ulcers Swallowing problems Images Multiple sclerosis MRI of the ...

  10. GISpark: A Geospatial Distributed Computing Platform for Spatiotemporal Big Data

    Science.gov (United States)

    Wang, S.; Zhong, E.; Wang, E.; Zhong, Y.; Cai, W.; Li, S.; Gao, S.

    2016-12-01

    Geospatial data are growing exponentially because of the proliferation of cost effective and ubiquitous positioning technologies such as global remote-sensing satellites and location-based devices. Analyzing large amounts of geospatial data can provide great value for both industrial and scientific applications. Data- and compute- intensive characteristics inherent in geospatial big data increasingly pose great challenges to technologies of data storing, computing and analyzing. Such challenges require a scalable and efficient architecture that can store, query, analyze, and visualize large-scale spatiotemporal data. Therefore, we developed GISpark - a geospatial distributed computing platform for processing large-scale vector, raster and stream data. GISpark is constructed based on the latest virtualized computing infrastructures and distributed computing architecture. OpenStack and Docker are used to build multi-user hosting cloud computing infrastructure for GISpark. The virtual storage systems such as HDFS, Ceph, MongoDB are combined and adopted for spatiotemporal data storage management. Spark-based algorithm framework is developed for efficient parallel computing. Within this framework, SuperMap GIScript and various open-source GIS libraries can be integrated into GISpark. GISpark can also integrated with scientific computing environment (e.g., Anaconda), interactive computing web applications (e.g., Jupyter notebook), and machine learning tools (e.g., TensorFlow/Orange). The associated geospatial facilities of GISpark in conjunction with the scientific computing environment, exploratory spatial data analysis tools, temporal data management and analysis systems make up a powerful geospatial computing tool. GISpark not only provides spatiotemporal big data processing capacity in the geospatial field, but also provides spatiotemporal computational model and advanced geospatial visualization tools that deals with other domains related with spatial property. We

  11. Evaluating the disparity of female breast cancer mortality among racial groups - a spatiotemporal analysis

    Directory of Open Access Journals (Sweden)

    Jacobson Holly

    2004-02-01

    Full Text Available Abstract Background The literature suggests that the distribution of female breast cancer mortality demonstrates spatial concentration. There remains a lack of studies on how the mortality burden may impact racial groups across space and over time. The present study evaluated the geographic variations in breast cancer mortality in Texas females according to three predominant racial groups (non-Hispanic White, Black, and Hispanic females over a twelve-year period. It sought to clarify whether the spatiotemporal trend might place an uneven burden on particular racial groups, and whether the excess trend has persisted into the current decade. Methods The Spatial Scan Statistic was employed to examine the geographic excess of breast cancer mortality by race in Texas counties between 1990 and 2001. The statistic was conducted with a scan window of a maximum of 90% of the study period and a spatial cluster size of 50% of the population at risk. The next scan was conducted with a purely spatial option to verify whether the excess mortality persisted further. Spatial queries were performed to locate the regions of excess mortality affecting multiple racial groups. Results The first scan identified 4 regions with breast cancer mortality excess in both non-Hispanic White and Hispanic female populations. The most likely excess mortality with a relative risk of 1.12 (p = 0.001 occurred between 1990 and 1996 for non-Hispanic Whites, including 42 Texas counties along Gulf Coast and Central Texas. For Hispanics, West Texas with a relative risk of 1.18 was the most probable region of excess mortality (p = 0.001. Results of the second scan were identical to the first. This suggested that the excess mortality might not persist to the present decade. Spatial queries found that 3 counties in Southeast and 9 counties in Central Texas had excess mortality involving multiple racial groups. Conclusion Spatiotemporal variations in breast cancer mortality affected racial

  12. A Mixed Land Cover Spatio-temporal Data Model Based on Object-oriented and Snapshot

    Directory of Open Access Journals (Sweden)

    LI Yinchao

    2016-07-01

    Full Text Available Spatio-temporal data model (STDM is one of the hot topics in the domains of spatio-temporal database and data analysis. There is a common view that a universal STDM is always of high complexity due to the various situation of spatio-temporal data. In this article, a mixed STDM is proposed based on object-oriented and snapshot models for modelling and analyzing landcover change (LCC. This model uses the object-oriented STDM to describe the spatio-temporal processes of land cover patches and organize their spatial and attributive properties. In the meantime, it uses the snapshot STDM to present the spatio-temporal distribution of LCC on the whole via snapshot images. The two types of models are spatially and temporally combined into a mixed version. In addition to presenting the spatio-temporal events themselves, this model could express the transformation events between different classes of spatio-temporal objects. It can be used to create database for historical data of LCC, do spatio-temporal statistics, simulation and data mining with the data. In this article, the LCC data in Heilongjiang province is used for case study to validate spatio-temporal data management and analysis abilities of mixed STDM, including creating database, spatio-temporal query, global evolution analysis and patches spatio-temporal process expression.

  13. MULTIPLE OBJECTS

    Directory of Open Access Journals (Sweden)

    A. A. Bosov

    2015-04-01

    Full Text Available Purpose. The development of complicated techniques of production and management processes, information systems, computer science, applied objects of systems theory and others requires improvement of mathematical methods, new approaches for researches of application systems. And the variety and diversity of subject systems makes necessary the development of a model that generalizes the classical sets and their development – sets of sets. Multiple objects unlike sets are constructed by multiple structures and represented by the structure and content. The aim of the work is the analysis of multiple structures, generating multiple objects, the further development of operations on these objects in application systems. Methodology. To achieve the objectives of the researches, the structure of multiple objects represents as constructive trio, consisting of media, signatures and axiomatic. Multiple object is determined by the structure and content, as well as represented by hybrid superposition, composed of sets, multi-sets, ordered sets (lists and heterogeneous sets (sequences, corteges. Findings. In this paper we study the properties and characteristics of the components of hybrid multiple objects of complex systems, proposed assessments of their complexity, shown the rules of internal and external operations on objects of implementation. We introduce the relation of arbitrary order over multiple objects, we define the description of functions and display on objects of multiple structures. Originality.In this paper we consider the development of multiple structures, generating multiple objects.Practical value. The transition from the abstract to the subject of multiple structures requires the transformation of the system and multiple objects. Transformation involves three successive stages: specification (binding to the domain, interpretation (multiple sites and particularization (goals. The proposed describe systems approach based on hybrid sets

  14. Live cell CRISPR-imaging in plants reveals dynamic telomere movements

    KAUST Repository

    Dreissig, Steven

    2017-05-16

    Elucidating the spatio-temporal organization of the genome inside the nucleus is imperative to understand the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies which reveal genomic information and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial CRISPR-Cas9 system. By fusing eGFP/mRuby2 to the catalytically inactive version of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm within 30 minutes during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for imaging of multiple genomic loci in live plants cells. CRISPR-imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells.

  15. Spatiotemporal psychopathology I: No rest for the brain's resting state activity in depression? Spatiotemporal psychopathology of depressive symptoms.

    Science.gov (United States)

    Northoff, Georg

    2016-01-15

    Despite intense neurobiological investigation in psychiatric disorders like major depressive disorder (MDD), the basic disturbance that underlies the psychopathological symptoms of MDD remains, nevertheless, unclear. Neuroimaging has focused mainly on the brain's extrinsic activity, specifically task-evoked or stimulus-induced activity, as related to the various sensorimotor, affective, cognitive, and social functions. Recently, the focus has shifted to the brain's intrinsic activity, otherwise known as its resting state activity. While various abnormalities have been observed during this activity, their meaning and significance for depression, along with its various psychopathological symptoms, are yet to be defined. Based on findings in healthy brain resting state activity and its particular spatial and temporal structure - defined in a functional and physiological sense rather than anatomical and structural - I claim that the various depressive symptoms are spatiotemporal disturbances of the resting state activity and its spatiotemporal structure. This is supported by recent findings that link ruminations and increased self-focus in depression to abnormal spatial organization of resting state activity. Analogously, affective and cognitive symptoms like anhedonia, suicidal ideation, and thought disorder can be traced to an increased focus on the past, increased past-focus as basic temporal disturbance o the resting state. Based on these findings, I conclude that the various depressive symptoms must be conceived as spatiotemporal disturbances of the brain's resting state's activity and its spatiotemporal structure. Importantly, this entails a new form of psychopathology, "Spatiotemporal Psychopathology" that directly links the brain and psyche, therefore having major diagnostic and therapeutic implications for clinical practice. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. The spatio-temporal Development of Copenhagen's bicycle infrastructure 1912-2013

    DEFF Research Database (Denmark)

    Carstensen, Trine Agervig; Olafsson, Anton Stahl; Bech, Nynne Marie

    2015-01-01

    Cycling plays an important role in low-carbon transitions. Around the globe, cities are constructing bicycle infrastructure. The city of Copenhagen has a bicycle-friendly infrastructure celebrated for its fine-meshed network. This study documents the spatio-temporal development of Copenhagen......’s bicycle infrastructure and explores how the development corresponds to other processes of urban transformation. The study builds on historical maps of bicycle infrastructure that are digitised into geographical information, which allows for a comprehensive analysis of the formation of the network....... In search for identifying drivers, the study analyses the city’s spatial growth pattern, migration pattern, development of road network and changes in the transport culture. Analyses reveal that the bicycle infrastructure expanded at a relatively constant pace during distinct periods of urban transformation...

  17. Effective and efficient analysis of spatio-temporal data

    Science.gov (United States)

    Zhang, Zhongnan

    Spatio-temporal data mining, i.e., mining knowledge from large amount of spatio-temporal data, is a highly demanding field because huge amounts of spatio-temporal data have been collected in various applications, ranging from remote sensing, to geographical information systems (GIS), computer cartography, environmental assessment and planning, etc. The collection data far exceeded human's ability to analyze which make it crucial to develop analysis tools. Recent studies on data mining have extended to the scope of data mining from relational and transactional datasets to spatial and temporal datasets. Among the various forms of spatio-temporal data, remote sensing images play an important role, due to the growing wide-spreading of outer space satellites. In this dissertation, we proposed two approaches to analyze the remote sensing data. The first one is about applying association rules mining onto images processing. Each image was divided into a number of image blocks. We built a spatial relationship for these blocks during the dividing process. This made a large number of images into a spatio-temporal dataset since each image was shot in time-series. The second one implemented co-occurrence patterns discovery from these images. The generated patterns represent subsets of spatial features that are located together in space and time. A weather analysis is composed of individual analysis of several meteorological variables. These variables include temperature, pressure, dew point, wind, clouds, visibility and so on. Local-scale models provide detailed analysis and forecasts of meteorological phenomena ranging from a few kilometers to about 100 kilometers in size. When some of above meteorological variables have some special change tendency, some kind of severe weather will happen in most cases. Using the discovery of association rules, we found that some special meteorological variables' changing has tight relation with some severe weather situation that will happen

  18. A Flexible High-Performance Photoimaging Device Based on Bioinspired Hierarchical Multiple-Patterned Plasmonic Nanostructures.

    Science.gov (United States)

    Lee, Yoon Ho; Lee, Tae Kyung; Kim, Hongki; Song, Inho; Lee, Jiwon; Kang, Saewon; Ko, Hyunhyub; Kwak, Sang Kyu; Oh, Joon Hak

    2018-03-01

    In insect eyes, ommatidia with hierarchical structured cornea play a critical role in amplifying and transferring visual signals to the brain through optic nerves, enabling the perception of various visual signals. Here, inspired by the structure and functions of insect ommatidia, a flexible photoimaging device is reported that can simultaneously detect and record incoming photonic signals by vertically stacking an organic photodiode and resistive memory device. A single-layered, hierarchical multiple-patterned back reflector that can exhibit various plasmonic effects is incorporated into the organic photodiode. The multiple-patterned flexible organic photodiodes exhibit greatly enhanced photoresponsivity due to the increased light absorption in comparison with the flat systems. Moreover, the flexible photoimaging device shows a well-resolved spatiotemporal mapping of optical signals with excellent operational and mechanical stabilities at low driving voltages below half of the flat systems. Theoretical calculation and scanning near-field optical microscopy analyses clearly reveal that multiple-patterned electrodes have much stronger surface plasmon coupling than flat and single-patterned systems. The developed methodology provides a versatile and effective route for realizing high-performance optoelectronic and photonic systems. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Spatiotemporal analysis of land use and land cover change in the Brazilian Amazon.

    Science.gov (United States)

    Lu, Dengsheng; Li, Guiying; Moran, Emilio; Hetrick, Scott

    2013-01-01

    This paper provides a comparative analysis of land use and land cover (LULC) changes among three study areas with different biophysical environments in the Brazilian Amazon at multiple scales, from per-pixel, polygon, census sector, to study area. Landsat images acquired in the years of 1990/1991, 1999/2000, and 2008/2010 were used to examine LULC change trajectories with the post-classification comparison approach. A classification system composed of six classes - forest, savanna, other-vegetation (secondary succession and plantations), agro-pasture, impervious surface, and water, was designed for this study. A hierarchical-based classification method was used to classify Landsat images into thematic maps. This research shows different spatiotemporal change patterns, composition and rates among the three study areas and indicates the importance of analyzing LULC change at multiple scales. The LULC change analysis over time for entire study areas provides an overall picture of change trends, but detailed change trajectories and their spatial distributions can be better examined at a per-pixel scale. The LULC change at the polygon scale provides the information of the changes in patch sizes over time, while the LULC change at census sector scale gives new insights on how human-induced activities (e.g., urban expansion, roads, and land use history) affect LULC change patterns and rates. This research indicates the necessity to implement change detection at multiple scales for better understanding the mechanisms of LULC change patterns and rates.

  20. The influence of the interactions between anthropogenic activities and multiple ecological factors on land surface temperatures of urban forests

    Science.gov (United States)

    Ren, Y.

    2017-12-01

    Context Land surface temperatures (LSTs) spatio-temporal distribution pattern of urban forests are influenced by many ecological factors; the identification of interaction between these factors can improve simulations and predictions of spatial patterns of urban cold islands. This quantitative research requires an integrated method that combines multiple sources data with spatial statistical analysis. Objectives The purpose of this study was to clarify urban forest LST influence interaction between anthropogenic activities and multiple ecological factors using cluster analysis of hot and cold spots and Geogdetector model. We introduced the hypothesis that anthropogenic activity interacts with certain ecological factors, and their combination influences urban forests LST. We also assumed that spatio-temporal distributions of urban forest LST should be similar to those of ecological factors and can be represented quantitatively. Methods We used Jinjiang as a representative city in China as a case study. Population density was employed to represent anthropogenic activity. We built up a multi-source data (forest inventory, digital elevation models (DEM), population, and remote sensing imagery) on a unified urban scale to support urban forest LST influence interaction research. Through a combination of spatial statistical analysis results, multi-source spatial data, and Geogdetector model, the interaction mechanisms of urban forest LST were revealed. Results Although different ecological factors have different influences on forest LST, in two periods with different hot spots and cold spots, the patch area and dominant tree species were the main factors contributing to LST clustering in urban forests. The interaction between anthropogenic activity and multiple ecological factors increased LST in urban forest stands, linearly and nonlinearly. Strong interactions between elevation and dominant species were generally observed and were prevalent in either hot or cold spots

  1. Approximate spatio-temporal top-k publish/subscribe

    KAUST Repository

    Chen, Lisi; Shang, Shuo

    2018-01-01

    Location-based publish/subscribe plays a significant role in mobile information disseminations. In this light, we propose and study a novel problem of processing location-based top-k subscriptions over spatio-temporal data streams. We define a new type of approximate location-based top-k subscription, Approximate Temporal Spatial-Keyword Top-k (ATSK) Subscription, that continuously feeds users with relevant spatio-temporal messages by considering textual similarity, spatial proximity, and information freshness. Different from existing location-based top-k subscriptions, Approximate Temporal Spatial-Keyword Top-k (ATSK) Subscription can automatically adjust the triggering condition by taking the triggering score of other subscriptions into account. The group filtering efficacy can be substantially improved by sacrificing the publishing result quality with a bounded guarantee. We conduct extensive experiments on two real datasets to demonstrate the performance of the developed solutions.

  2. Spatiotemporal Characteristics for the Depth from Luminance Contrast

    Directory of Open Access Journals (Sweden)

    Kazuya Matsubara

    2011-05-01

    Full Text Available Images with higher luminance contrast tend to be perceived closer in depth. To investigate a spatiotemporal characteristic of this effect, we evaluated subjective depth of a test stimulus with various spatial and temporal frequencies. For the purpose, the depth of a reference stimulus was matched to that of the test stimulus by changing the binocular disparity. The results showed that the test stimulus was perceived closer with higher luminance contrast for all conditions. Contrast efficiency was obtained from the contrast that provided the subjective depth for each spatiotemporal frequency. The shape of the contrast efficiency function was spatially low-pass and temporally band-pass. This characteristic is different from the one measure for a detection task. This suggests that only subset of contrast signals are used for depth from contrast.

  3. Against Laplacian Reduction of Newtonian Mass to Spatiotemporal Quantities

    Science.gov (United States)

    Martens, Niels C. M.

    2018-03-01

    Laplace wondered about the minimal choice of initial variables and parameters corresponding to a well-posed initial value problem. Discussions of Laplace's problem in the literature have focused on choosing between spatiotemporal variables relative to absolute space (i.e. substantivalism) or merely relative to other material bodies (i.e. relationalism) and between absolute masses (i.e. absolutism) or merely mass ratios (i.e. comparativism). This paper extends these discussions of Laplace's problem, in the context of Newtonian Gravity, by asking whether mass needs to be included in the initial state at all, or whether a purely spatiotemporal initial state suffices. It is argued that mass indeed needs to be included; removing mass from the initial state drastically reduces the predictive and explanatory power of Newtonian Gravity.

  4. Spatial and spatio-temporal bayesian models with R - INLA

    CERN Document Server

    Blangiardo, Marta

    2015-01-01

    Dedication iiiPreface ix1 Introduction 11.1 Why spatial and spatio-temporal statistics? 11.2 Why do we use Bayesian methods for modelling spatial and spatio-temporal structures? 21.3 Why INLA? 31.4 Datasets 32 Introduction to 212.1 The language 212.2 objects 222.3 Data and session management 342.4 Packages 352.5 Programming in 362.6 Basic statistical analysis with 393 Introduction to Bayesian Methods 533.1 Bayesian Philosophy 533.2 Basic Probability Elements 573.3 Bayes Theorem 623.4 Prior and Posterior Distributions 643.5 Working with the Posterior Distribution 663.6 Choosing the Prior Distr

  5. Approximate spatio-temporal top-k publish/subscribe

    KAUST Repository

    Chen, Lisi

    2018-04-26

    Location-based publish/subscribe plays a significant role in mobile information disseminations. In this light, we propose and study a novel problem of processing location-based top-k subscriptions over spatio-temporal data streams. We define a new type of approximate location-based top-k subscription, Approximate Temporal Spatial-Keyword Top-k (ATSK) Subscription, that continuously feeds users with relevant spatio-temporal messages by considering textual similarity, spatial proximity, and information freshness. Different from existing location-based top-k subscriptions, Approximate Temporal Spatial-Keyword Top-k (ATSK) Subscription can automatically adjust the triggering condition by taking the triggering score of other subscriptions into account. The group filtering efficacy can be substantially improved by sacrificing the publishing result quality with a bounded guarantee. We conduct extensive experiments on two real datasets to demonstrate the performance of the developed solutions.

  6. Using Covariant Lyapunov Vectors to Understand Spatiotemporal Chaos in Fluids

    Science.gov (United States)

    Paul, Mark; Xu, Mu; Barbish, Johnathon; Mukherjee, Saikat

    2017-11-01

    The spatiotemporal chaos of fluids present many difficult and fascinating challenges. Recent progress in computing covariant Lyapunov vectors for a variety of model systems has made it possible to probe fundamental ideas from dynamical systems theory including the degree of hyperbolicity, the fractal dimension, the dimension of the inertial manifold, and the decomposition of the dynamics into a finite number of physical modes and spurious modes. We are interested in building upon insights such as these for fluid systems. We first demonstrate the power of covariant Lyapunov vectors using a system of maps on a lattice with a nonlinear coupling. We then compute the covariant Lyapunov vectors for chaotic Rayleigh-Bénard convection for experimentally accessible conditions. We show that chaotic convection is non-hyperbolic and we quantify the spatiotemporal features of the spectrum of covariant Lyapunov vectors. NSF DMS-1622299 and DARPA/DSO Models, Dynamics, and Learning (MoDyL).

  7. Precursor of transition to turbulence: spatiotemporal wave front.

    Science.gov (United States)

    Bhaumik, S; Sengupta, T K

    2014-04-01

    To understand transition to turbulence via 3D disturbance growth, we report here results obtained from the solution of Navier-Stokes equation (NSE) to reproduce experimental results obtained by minimizing background disturbances and imposing deterministic excitation inside the shear layer. A similar approach was adopted in Sengupta and Bhaumik [Phys. Rev. Lett. 107, 154501 (2011)], where a route of transition from receptivity to fully developed turbulent stage was explained for 2D flow in terms of the spatio-temporal wave-front (STWF). The STWF was identified as the unit process of 2D turbulence creation for low amplitude wall excitation. Theoretical prediction of STWF for boundary layer was established earlier in Sengupta, Rao, and Venkatasubbaiah [Phys. Rev. Lett. 96, 224504 (2006)] from the Orr-Sommerfeld equation as due to spatiotemporal instability. Here, the same unit process of the STWF during transition is shown to be present for 3D disturbance field from the solution of governing NSE.

  8. Spatiotemporal Scaling Effect on Rainfall Network Design Using Entropy

    Directory of Open Access Journals (Sweden)

    Chiang Wei

    2014-08-01

    Full Text Available Because of high variation in mountainous areas, rainfall data at different spatiotemporal scales may yield potential uncertainty for network design. However, few studies focus on the scaling effect on both the spatial and the temporal scale. By calculating the maximum joint entropy of hourly typhoon events, monthly, six dry and wet months and annual rainfall between 1992 and 2012 for 1-, 3-, and 5-km grids, the relocated candidate rain gauges in the National Taiwan University Experimental Forest of Central Taiwan are prioritized. The results show: (1 the network exhibits different locations for first prioritized candidate rain gauges for different spatiotemporal scales; (2 the effect of spatial scales is insignificant compared to temporal scales; and (3 a smaller number and a lower percentage of required stations (PRS reach stable joint entropy for a long duration at finer spatial scale. Prioritized candidate rain gauges provide key reference points for adjusting the network to capture more accurate information and minimize redundancy.

  9. A Spatio-Temporal Analysis of Mitochondrial DNA Haplogroup I

    Directory of Open Access Journals (Sweden)

    Revesz Peter Z.

    2016-01-01

    Full Text Available The recent recovery of ancient DNA from a growing number of human samples shows that mitochondrial DNA haplogroup I was introduced to Europe after the end of the Last Glacial Maximum. This paper provides a spatio-temporal analysis of the various subhaplogroups of mitochondrial DNA I. The study suggests that haplogroup I diversified into haplogroups I1, I2’3, I4 and I5 at specific regions in Eurasia and then spread southward to Crete and Egypt.

  10. Spatio-temporal reasoning and decision support tools

    OpenAIRE

    Renso, Chiara; Wachowicz, Monica

    2014-01-01

    Currently, mobility data is revolutionizing the traditional fields of spatio-temporal reasoning and decision making analysis, not only to scale-up to the large and growing data volumes, but also to address complex questions related to change, trends, duration, and evolution. In mobility data, space and time are inextricably linked, since humans, robots and systems that dynamically act, and interact within social networks, are embedded in space, and any change is often the result of actions an...

  11. Characteristics and Applications of Spatiotemporally Focused Femtosecond Laser Pulses

    Directory of Open Access Journals (Sweden)

    Chenrui Jing

    2016-12-01

    Full Text Available Simultaneous spatial and temporal focusing (SSTF of femtosecond laser pulses gives rise to strong suppression of nonlinear self-focusing during the propagation of the femtosecond laser beam. In this paper, we begin with an introduction of the principle of SSTF, followed by a review of our recent experimental results on the characterization and application of the spatiotemporally focused pulses for femtosecond laser micromachining. Finally, we summarize all of the results and give a future perspective of this technique.

  12. Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks

    Science.gov (United States)

    Pyle, Ryan; Rosenbaum, Robert

    2017-01-01

    Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.

  13. Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks.

    Science.gov (United States)

    Pyle, Ryan; Rosenbaum, Robert

    2017-01-06

    Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.

  14. A simple spatiotemporal chaotic Lotka-Volterra model

    International Nuclear Information System (INIS)

    Sprott, J.C.; Wildenberg, J.C.; Azizi, Yousef

    2005-01-01

    A mathematically simple example of a high-dimensional (many-species) Lotka-Volterra model that exhibits spatiotemporal chaos in one spatial dimension is described. The model consists of a closed ring of identical agents, each competing for fixed finite resources with two of its four nearest neighbors. The model is prototypical of more complicated models in its quasiperiodic route to chaos (including attracting 3-tori), bifurcations, spontaneous symmetry breaking, and spatial pattern formation

  15. Multiple sclerosis