Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.

PubMed

Ma, Hong-Wu; Zhao, Xue-Ming; Yuan, Ying-Jin; Zeng, An-Ping

2004-08-12

Metabolic networks are organized in a modular, hierarchical manner. Methods for a rational decomposition of the metabolic network into relatively independent functional subsets are essential to better understand the modularity and organization principle of a large-scale, genome-wide network. Network decomposition is also necessary for functional analysis of metabolism by pathway analysis methods that are often hampered by the problem of combinatorial explosion due to the complexity of metabolic network. Decomposition methods proposed in literature are mainly based on the connection degree of metabolites. To obtain a more reasonable decomposition, the global connectivity structure of metabolic networks should be taken into account. In this work, we use a reaction graph representation of a metabolic network for the identification of its global connectivity structure and for decomposition. A bow-tie connectivity structure similar to that previously discovered for metabolite graph is found also to exist in the reaction graph. Based on this bow-tie structure, a new decomposition method is proposed, which uses a distance definition derived from the path length between two reactions. An hierarchical classification tree is first constructed from the distance matrix among the reactions in the giant strong component of the bow-tie structure. These reactions are then grouped into different subsets based on the hierarchical tree. Reactions in the IN and OUT subsets of the bow-tie structure are subsequently placed in the corresponding subsets according to a 'majority rule'. Compared with the decomposition methods proposed in literature, ours is based on combined properties of the global network structure and local reaction connectivity rather than, primarily, on the connection degree of metabolites. The method is applied to decompose the metabolic network of Escherichia coli. Eleven subsets are obtained. More detailed investigations of the subsets show that reactions in the same subset are really functionally related. The rational decomposition of metabolic networks, and subsequent studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level. http://genome.gbf.de/bioinformatics/

Embedding global barrier and collective in torus network with each node combining input from receivers according to class map for output to senders

DOEpatents

Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Heidelberger, Philip; Senger, Robert M; Salapura, Valentina; Steinmacher-Burow, Burkhard; Sugawara, Yutaka; Takken, Todd E

2013-08-27

Embodiments of the invention provide a method, system and computer program product for embedding a global barrier and global interrupt network in a parallel computer system organized as a torus network. The computer system includes a multitude of nodes. In one embodiment, the method comprises taking inputs from a set of receivers of the nodes, dividing the inputs from the receivers into a plurality of classes, combining the inputs of each of the classes to obtain a result, and sending said result to a set of senders of the nodes. Embodiments of the invention provide a method, system and computer program product for embedding a collective network in a parallel computer system organized as a torus network. In one embodiment, the method comprises adding to a torus network a central collective logic to route messages among at least a group of nodes in a tree structure.

Aflatoxin regulations and global pistachio trade: insights from social network analysis.

PubMed

Bui-Klimke, Travis R; Guclu, Hasan; Kensler, Thomas W; Yuan, Jian-Min; Wu, Felicia

2014-01-01

Aflatoxins, carcinogenic toxins produced by Aspergillus fungi, contaminate maize, peanuts, and tree nuts in many regions of the world. Pistachios are the main source of human dietary aflatoxins from tree nuts worldwide. Over 120 countries have regulations for maximum allowable aflatoxin levels in food commodities. We developed social network models to analyze the association between nations' aflatoxin regulations and global trade patterns of pistachios from 1996-2010. The main pistachio producing countries are Iran and the United States (US), which together contribute to nearly 75% of the total global pistachio market. Over this time period, during which many nations developed or changed their aflatoxin regulations in pistachios, global pistachio trade patterns changed; with the US increasingly exporting to countries with stricter aflatoxin standards. The US pistachio crop has had consistently lower levels of aflatoxin than the Iranian crop over this same time period. As similar trading patterns have also been documented in maize, public health may be affected if countries without aflatoxin regulations, or with more relaxed regulations, continually import crops with higher aflatoxin contamination. Unlike the previous studies on maize, this analysis includes a dynamic element, examining how trade patterns change over time with introduction or adjustment of aflatoxin regulations.

Aflatoxin Regulations and Global Pistachio Trade: Insights from Social Network Analysis

PubMed Central

Bui-Klimke, Travis R.; Guclu, Hasan; Kensler, Thomas W.; Yuan, Jian-Min; Wu, Felicia

2014-01-01

Aflatoxins, carcinogenic toxins produced by Aspergillus fungi, contaminate maize, peanuts, and tree nuts in many regions of the world. Pistachios are the main source of human dietary aflatoxins from tree nuts worldwide. Over 120 countries have regulations for maximum allowable aflatoxin levels in food commodities. We developed social network models to analyze the association between nations’ aflatoxin regulations and global trade patterns of pistachios from 1996–2010. The main pistachio producing countries are Iran and the United States (US), which together contribute to nearly 75% of the total global pistachio market. Over this time period, during which many nations developed or changed their aflatoxin regulations in pistachios, global pistachio trade patterns changed; with the US increasingly exporting to countries with stricter aflatoxin standards. The US pistachio crop has had consistently lower levels of aflatoxin than the Iranian crop over this same time period. As similar trading patterns have also been documented in maize, public health may be affected if countries without aflatoxin regulations, or with more relaxed regulations, continually import crops with higher aflatoxin contamination. Unlike the previous studies on maize, this analysis includes a dynamic element, examining how trade patterns change over time with introduction or adjustment of aflatoxin regulations. PMID:24670581

Inferring biome-scale net primary productivity from tree-ring isotopes

NASA Astrophysics Data System (ADS)

Pederson, N.; Levesque, M.; Williams, A. P.; Hobi, M. L.; Smith, W. K.; Andreu-Hayles, L.

2017-12-01

Satellite estimates of vegetation growth (net primary productivity; NPP), tree-ring records, and forest inventories indicate that ongoing climate change and rising atmospheric CO2 concentration are altering productivity and carbon storage of forests worldwide. The impact of global change on the trends of NPP, however, remain unknown because of the lack of long-term high-resolution NPP data. For the first time, we tested if annually resolved carbon (δ13C) and oxygen (δ18O) stable isotopes from the cellulose of tree rings from trees in temperate regions could be used as a tool for inferring NPP across spatiotemporal scales. We compared satellite NPP estimates from the moderate-resolution imaging spectroradiometer sensor (MODIS, product MOD17A) and a newly developed global NPP dataset derived from the Global Inventory Modeling and Mapping Studies (GIMMS) dataset to annually resolved tree-ring width and δ13C and δ18O records from four sites along a hydroclimatic gradient in Eastern and Central United States. We found strong correlations across large geographical regions between satellite-derived NPP and tree-ring isotopes that ranged from -0.40 to -0.91. Notably, tree-ring derived δ18O had the strongest relation to climate. The results were consistent among the studied tree species (Quercus rubra and Liriodendron tulipifera) and along the hydroclimatic conditions of our network. Our study indicates that tree-ring isotopes can potentially be used to reconstruct NPP in time and space. As such, our findings represent an important breakthrough for estimating long-term changes in vegetation productivity at the biome scale.

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

PubMed

Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

2006-06-06

To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.

Classification of epilepsy types through global network analysis of scalp electroencephalograms

NASA Astrophysics Data System (ADS)

Lee, Uncheol; Kim, Seunghwan; Jung, Ki-Young

2006-04-01

Epilepsy is a dynamic disease in which self-organization and emergent structures occur dynamically at multiple levels of neuronal integration. Therefore, the transient relationship within multichannel electroencephalograms (EEGs) is crucial for understanding epileptic processes. In this paper, we show that the global relationship within multichannel EEGs provides us with more useful information in classifying two different epilepsy types than pairwise relationships such as cross correlation. To demonstrate this, we determine the global network structure within channels of the scalp EEG based on the minimum spanning tree method. The topological dissimilarity of the network structures from different types of temporal lobe epilepsy is described in the form of the divergence rate and is computed for 11 patients with left (LTLE) and right temporal lobe epilepsy (RTLE). We find that patients with LTLE and RTLE exhibit different large scale network structures, which emerge at the epoch immediately before the seizure onset, not in the preceding epochs. Our results suggest that patients with the two different epilepsy types display distinct large scale dynamical networks with characteristic epileptic network structures.

Simulated Tree Growth across the Northern Hemisphere and the Seasonality of Climate Signals Encoded within Tree-ring Widths

NASA Astrophysics Data System (ADS)

Li, X.; St George, S.

2013-12-01

Both dendrochronological theory and regional and global networks of tree-ring width measurements indicate that trees can respond to climate variations quite differently from one location to another. To explain these geographical differences at hemispheric scale, we used a process-based model of tree-ring formation (the Vaganov-Shashkin model) to simulate tree growth at over 6000 locations across the Northern Hemisphere. We compared the seasonality and strength of climate signals in the simulated tree-ring records against parallel analysis conducted on a hemispheric network of real tree-ring observations, tested the ability of the model to reproduce behaviors that emerge from large networks of tree-ring widths and used the model outputs to explain why the network exhibits these behaviors. The simulated tree-ring records are consistent with observations with respect to the seasonality and relative strength of the encoded climate signals, and time-related changes in these climate signals can be predicted using the modeled relative growth rate due to temperature or soil moisture. The positive imprint of winter (DJF) precipitation is strongest in simulations from the American Southwest and northern Mexico as well as selected locations in the Mediterranean and central Asia. Summer (JJA) precipitation has higher positive correlations with simulations in the mid-latitudes, but some high-latitude coastal sites exhibit a negative association. The influence of summer temperature is mainly positive at high-latitude or high-altitude sites and negative in the mid-latitudes. The absolute magnitude of climate correlations are generally higher in simulations than in observations, but the pattern and geographical differences remain the same, demonstrating that the model has skill in reproducing tree-ring growth response to climate variability in the Northern Hemisphere. Because the model uses only temperature, precipitation and latitude as input and is not adjusted for species or other biological factors, the fact that the climate response of the simulations largely agrees with the observations may imply that climate, rather than biology, is the main factor that influences large-scale patterns of the climate information recorded by tree rings. Our results also suggest that the Vaganov-Shashkin model could be used to estimate the likely climate response of trees in ';frontier' areas that have not been sampled extensively. Seasonal Climate Correlations of Simulated Tree-ring Records

Arithmetic functions in torus and tree networks

DOEpatents

Bhanot, Gyan; Blumrich, Matthias A.; Chen, Dong; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Steinmacher-Burow, Burkhard D.; Vranas, Pavlos M.

2007-12-25

Methods and systems for performing arithmetic functions. In accordance with a first aspect of the invention, methods and apparatus are provided, working in conjunction of software algorithms and hardware implementation of class network routing, to achieve a very significant reduction in the time required for global arithmetic operation on the torus. Therefore, it leads to greater scalability of applications running on large parallel machines. The invention involves three steps in improving the efficiency and accuracy of global operations: (1) Ensuring, when necessary, that all the nodes do the global operation on the data in the same order and so obtain a unique answer, independent of roundoff error; (2) Using the topology of the torus to minimize the number of hops and the bidirectional capabilities of the network to reduce the number of time steps in the data transfer operation to an absolute minimum; and (3) Using class function routing to reduce latency in the data transfer. With the method of this invention, every single element is injected into the network only once and it will be stored and forwarded without any further software overhead. In accordance with a second aspect of the invention, methods and systems are provided to efficiently implement global arithmetic operations on a network that supports the global combining operations. The latency of doing such global operations are greatly reduced by using these methods.

Topology of the correlation networks among major currencies using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Keskin, Mustafa; Deviren, Bayram; Kocakaplan, Yusuf

2011-02-01

We studied the topology of correlation networks among 34 major currencies using the concept of a minimal spanning tree and hierarchical tree for the full years of 2007-2008 when major economic turbulence occurred. We used the USD (US Dollar) and the TL (Turkish Lira) as numeraires in which the USD was the major currency and the TL was the minor currency. We derived a hierarchical organization and constructed minimal spanning trees (MSTs) and hierarchical trees (HTs) for the full years of 2007, 2008 and for the 2007-2008 period. We performed a technique to associate a value of reliability to the links of MSTs and HTs by using bootstrap replicas of data. We also used the average linkage cluster analysis for obtaining the hierarchical trees in the case of the TL as the numeraire. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial data. We illustrated how the minimal spanning trees and their related hierarchical trees developed over a period of time. From these trees we identified different clusters of currencies according to their proximity and economic ties. The clustered structure of the currencies and the key currency in each cluster were obtained and we found that the clusters matched nicely with the geographical regions of corresponding countries in the world such as Asia or Europe. As expected the key currencies were generally those showing major economic activity.

Optical interconnect for large-scale systems

NASA Astrophysics Data System (ADS)

Dress, William

2013-02-01

This paper presents a switchless, optical interconnect module that serves as a node in a network of identical distribution modules for large-scale systems. Thousands to millions of hosts or endpoints may be interconnected by a network of such modules, avoiding the need for multi-level switches. Several common network topologies are reviewed and their scaling properties assessed. The concept of message-flow routing is discussed in conjunction with the unique properties enabled by the optical distribution module where it is shown how top-down software control (global routing tables, spanning-tree algorithms) may be avoided.

Hierarchical cluster-tendency analysis of the group structure in the foreign exchange market

NASA Astrophysics Data System (ADS)

Wu, Xin-Ye; Zheng, Zhi-Gang

2013-08-01

A hierarchical cluster-tendency (HCT) method in analyzing the group structure of networks of the global foreign exchange (FX) market is proposed by combining the advantages of both the minimal spanning tree (MST) and the hierarchical tree (HT). Fifty currencies of the top 50 World GDP in 2010 according to World Bank's database are chosen as the underlying system. By using the HCT method, all nodes in the FX market network can be "colored" and distinguished. We reveal that the FX networks can be divided into two groups, i.e., the Asia-Pacific group and the Pan-European group. The results given by the hierarchical cluster-tendency method agree well with the formerly observed geographical aggregation behavior in the FX market. Moreover, an oil-resource aggregation phenomenon is discovered by using our method. We find that gold could be a better numeraire for the weekly-frequency FX data.

Roost networks of northern myotis (Myotis septentrionalis) in a managed landscape

USGS Publications Warehouse

Johnson, J.B.; Mark, Ford W.; Edwards, J.W.

2012-01-01

Maternity groups of many bat species conform to fission-fusion models and movements among diurnal roost trees and individual bats belonging to these groups use networks of roost trees. Forest disturbances may alter roost networks and characteristics of roost trees. Therefore, at the Fernow Experimental Forest in West Virginia, we examined roost tree networks of northern myotis (Myotis septentrionalis) in forest stands subjected to prescribed fire and in unmanipulated control treatments in 2008 and 2009. Northern myotis formed social groups whose roost areas and roost tree networks overlapped to some extent. Roost tree networks largely resembled scale-free network models, as 61% had a single central node roost tree. In control treatments, central node roost trees were in early stages of decay and surrounded by greater basal area than other trees within the networks. In prescribed fire treatments, central node roost trees were small in diameter, low in the forest canopy, and surrounded by low basal area compared to other trees in networks. Our results indicate that forest disturbances, including prescribed fire, can affect availability and distribution of roosts within roost tree networks. ?? 2011 Elsevier B.V.

Folding and unfolding phylogenetic trees and networks.

PubMed

Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

2016-12-01

Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

On Tree-Based Phylogenetic Networks.

PubMed

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

The QAP weighted network analysis method and its application in international services trade

NASA Astrophysics Data System (ADS)

Xu, Helian; Cheng, Long

2016-04-01

Based on QAP (Quadratic Assignment Procedure) correlation and complex network theory, this paper puts forward a new method named QAP Weighted Network Analysis Method. The core idea of the method is to analyze influences among relations in a social or economic group by building a QAP weighted network of networks of relations. In the QAP weighted network, a node depicts a relation and an undirect edge exists between any pair of nodes if there is significant correlation between relations. As an application of the QAP weighted network, we study international services trade by using the QAP weighted network, in which nodes depict 10 kinds of services trade relations. After the analysis of international services trade by QAP weighted network, and by using distance indicators, hierarchy tree and minimum spanning tree, the conclusion shows that: Firstly, significant correlation exists in all services trade, and the development of any one service trade will stimulate the other nine. Secondly, as the economic globalization goes deeper, correlations in all services trade have been strengthened continually, and clustering effects exist in those services trade. Thirdly, transportation services trade, computer and information services trade and communication services trade have the most influence and are at the core in all services trade.

Increased water deficit decreases Douglas fir growth throughout western US forests.

PubMed

Restaino, Christina M; Peterson, David L; Littell, Jeremy

2016-08-23

Changes in tree growth rates can affect tree mortality and forest feedbacks to the global carbon cycle. As air temperature increases, evaporative demand also increases, increasing effective drought in forest ecosystems. Using a spatially comprehensive network of Douglas fir (Pseudotsuga menziesii) chronologies from 122 locations that represent distinct climate environments in the western United States, we show that increased temperature decreases growth via vapor pressure deficit (VPD) across all latitudes. Using an ensemble of global circulation models, we project an increase in both the mean VPD associated with the lowest growth extremes and the probability of exceeding these VPD values. As temperature continues to increase in future decades, we can expect deficit-related stress to increase and consequently Douglas fir growth to decrease throughout its US range.

Increased water deficit decreases Douglas fir growth throughout western US forests

USGS Publications Warehouse

Restaino, Christina M; Peterson, David L.; Littell, Jeremy

2016-01-01

Changes in tree growth rates can affect tree mortality and forest feedbacks to the global carbon cycle. As air temperature increases, evaporative demand also increases, increasing effective drought in forest ecosystems. Using a spatially comprehensive network of Douglas-fir (Pseudotsuga menziesii) chronologies from 122 locations that experience distinctly different climate in the western United States, we show that increased temperature decreases growth via vapor pressure deficit (VPD) across all latitudes. Under an ensemble of global circulation models, we project an increase in both the mean VPD associated with the lowest growth extremes and the probability of exceeding these VPD values. As temperature continues to increase in future decades, we can expect deficit-related stress to increase and consequently Douglas-fir growth to decrease throughout its US range.

Increased water deficit decreases Douglas fir growth throughout western US forests

PubMed Central

Restaino, Christina M.; Peterson, David L.; Littell, Jeremy

2016-01-01

Changes in tree growth rates can affect tree mortality and forest feedbacks to the global carbon cycle. As air temperature increases, evaporative demand also increases, increasing effective drought in forest ecosystems. Using a spatially comprehensive network of Douglas fir (Pseudotsuga menziesii) chronologies from 122 locations that represent distinct climate environments in the western United States, we show that increased temperature decreases growth via vapor pressure deficit (VPD) across all latitudes. Using an ensemble of global circulation models, we project an increase in both the mean VPD associated with the lowest growth extremes and the probability of exceeding these VPD values. As temperature continues to increase in future decades, we can expect deficit-related stress to increase and consequently Douglas fir growth to decrease throughout its US range. PMID:27503880

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Sensitivity of proxies on non-linear interactions in the climate system

PubMed Central

Schultz, Johannes A.; Beck, Christoph; Menz, Gunter; Neuwirth, Burkhard; Ohlwein, Christian; Philipp, Andreas

2015-01-01

Recent climate change is affecting the earth system to an unprecedented extent and intensity and has the potential to cause severe ecological and socioeconomic consequences. To understand natural and anthropogenic induced processes, feedbacks, trends, and dynamics in the climate system, it is also essential to consider longer timescales. In this context, annually resolved tree-ring data are often used to reconstruct past temperature or precipitation variability as well as atmospheric or oceanic indices such as the North Atlantic Oscillation (NAO) or the Atlantic Multidecadal Oscillation (AMO). The aim of this study is to assess weather-type sensitivity across the Northern Atlantic region based on two tree-ring width networks. Our results indicate that nonstationarities in superordinate space and time scales of the climate system (here synoptic- to global scale, NAO, AMO) can affect the climate sensitivity of tree-rings in subordinate levels of the system (here meso- to synoptic scale, weather-types). This scale bias effect has the capability to impact even large multiproxy networks and the ability of these networks to provide information about past climate conditions. To avoid scale biases in climate reconstructions, interdependencies between the different scales in the climate system must be considered, especially internal ocean/atmosphere dynamics. PMID:26686001

Rapid self-organised initiation of ad hoc sensor networks close above the percolation threshold

NASA Astrophysics Data System (ADS)

Korsnes, Reinert

2010-07-01

This work shows potentials for rapid self-organisation of sensor networks where nodes collaborate to relay messages to a common data collecting unit (sink node). The study problem is, in the sense of graph theory, to find a shortest path tree spanning a weighted graph. This is a well-studied problem where for example Dijkstra’s algorithm provides a solution for non-negative edge weights. The present contribution shows by simulation examples that simple modifications of known distributed approaches here can provide significant improvements in performance. Phase transition phenomena, which are known to take place in networks close to percolation thresholds, may explain these observations. An initial method, which here serves as reference, assumes the sink node starts organisation of the network (tree) by transmitting a control message advertising its availability for its neighbours. These neighbours then advertise their current cost estimate for routing a message to the sink. A node which in this way receives a message implying an improved route to the sink, advertises its new finding and remembers which neighbouring node the message came from. This activity proceeds until there are no more improvements to advertise to neighbours. The result is a tree network for cost effective transmission of messages to the sink (root). This distributed approach has potential for simple improvements which are of interest when minimisation of storage and communication of network information are a concern. Fast organisation of the network takes place when the number k of connections for each node ( degree) is close above its critical value for global network percolation and at the same time there is a threshold for the nodes to decide to advertise network route updates.

Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)

PubMed Central

Bedford, Trevor; Cobey, Sarah; Beerli, Peter; Pascual, Mercedes

2010-01-01

The global migration patterns of influenza viruses have profound implications for the evolutionary and epidemiological dynamics of the disease. We developed a novel approach to reconstruct the genetic history of human influenza A (H3N2) collected worldwide over 1998 to 2009 and used it to infer the global network of influenza transmission. Consistent with previous models, we find that China and Southeast Asia lie at the center of this global network. However, we also find that strains of influenza circulate outside of Asia for multiple seasons, persisting through dynamic migration between northern and southern regions. The USA acts as the primary hub of temperate transmission and, together with China and Southeast Asia, forms the trunk of influenza's evolutionary tree. These findings suggest that antiviral use outside of China and Southeast Asia may lead to the evolution of long-term local and potentially global antiviral resistance. Our results might also aid the design of surveillance efforts and of vaccines better tailored to different geographic regions. PMID:20523898

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

Automated construction of arterial and venous trees in retinal images.

PubMed

Hu, Qiao; Abràmoff, Michael D; Garvin, Mona K

2015-10-01

While many approaches exist to segment retinal vessels in fundus photographs, only a limited number focus on the construction and disambiguation of arterial and venous trees. Previous approaches are local and/or greedy in nature, making them susceptible to errors or limiting their applicability to large vessels. We propose a more global framework to generate arteriovenous trees in retinal images, given a vessel segmentation. In particular, our approach consists of three stages. The first stage is to generate an overconnected vessel network, named the vessel potential connectivity map (VPCM), consisting of vessel segments and the potential connectivity between them. The second stage is to disambiguate the VPCM into multiple anatomical trees, using a graph-based metaheuristic algorithm. The third stage is to classify these trees into arterial or venous (A/V) trees. We evaluated our approach with a ground truth built based on a public database, showing a pixel-wise classification accuracy of 88.15% using a manual vessel segmentation as input, and 86.11% using an automatic vessel segmentation as input.

iTREE: Long-term variability of tree growth in a changing environment - identifying physiological mechanisms using stable C and O isotopes in tree rings.

NASA Astrophysics Data System (ADS)

Siegwolf, R. T. W.; Buchmann, N.; Frank, D.; Joos, F.; Kahmen, A.; Treydte, K.; Leuenberger, M.; Saurer, M.

2012-04-01

Trees play are a critical role in the carbon cycle - their photosynthetic assimilation is one of the largest terrestrial carbon fluxes and their standing biomass represents the largest carbon pool of the terrestrial biosphere. Understanding how tree physiology and growth respond to long-term environmental change is pivotal to predict the magnitude and direction of the terrestrial carbon sink. iTREE is an interdisciplinary research framework to capitalize on synergies among leading dendroclimatologists, plant physiologists, isotope specialists, and global carbon cycle modelers with the objectives of reducing uncertainties related to tree/forest growth in the context of changing natural environments. Cross-cutting themes in our project are tree rings, stable isotopes, and mechanistic modelling. We will (i) establish a European network of tree-ring based isotope time-series to retrodict interannual to long-term tree physiological changes, (ii) conduct laboratory and field experiments to adapt a mechanistic isotope model to derive plant physiological variables from tree-ring isotopes, (iii) implement this model into a dynamic global vegetation model, and perform subsequent model-data validation exercises to refine model representation of plant physiological processes and (iv) attribute long-term variation in tree growth to plant physiological and environmental drivers, and identify how our refined knowledge revises predictions of the coupled carbon-cycle climate system. We will contribute to i) advanced quantifications of long-term variation in tree growth across Central Europe, ii) novel long-term information on key physiological processes that underlie variations in tree growth, and iii) improved carbon cycle models that can be employed to revise predictions of the coupled carbon-cycle climate system. Hence iTREE will significantly contribute towards a seamless understanding of the responses of terrestrial ecosystems to long-term environmental change, and ultimately help reduce uncertainties of the magnitude and direction of the past and future terrestrial carbon sink.

Macroecology of Australian Tall Eucalypt Forests: Baseline Data from a Continental-Scale Permanent Plot Network

PubMed Central

Wood, Sam W.; Prior, Lynda D.; Stephens, Helen C.; Bowman, David M. J. S.

2015-01-01

Tracking the response of forest ecosystems to climate change demands large (≥1 ha) monitoring plots that are repeatedly measured over long time frames and arranged across macro-ecological gradients. Continental scale networks of permanent forest plots have identified links between climate and carbon fluxes by monitoring trends in tree growth, mortality and recruitment. The relationship between tree growth and climate in Australia has been recently articulated through analysis of data from smaller forest plots, but conclusions were limited by (a) absence of data on recruitment and mortality, (b) exclusion of non-eucalypt species, and (c) lack of knowledge of stand age or disturbance histories. To remedy these gaps we established the Ausplots Forest Monitoring Network: a continental scale network of 48 1 ha permanent plots in highly productive tall eucalypt forests in the mature growth stage. These plots are distributed across cool temperate, Mediterranean, subtropical and tropical climates (mean annual precipitation 850 to 1900 mm per year; mean annual temperature 6 to 21°C). Aboveground carbon stocks (AGC) in these forests are dominated by eucalypts (90% of AGC) whilst non-eucalypts in the understorey dominated species diversity and tree abundance (84% of species; 60% of stems). Aboveground carbon stocks were negatively related to mean annual temperature, with forests at the warm end of the temperature range storing approximately half the amount of carbon as forests at the cool end of the temperature range. This may reflect thermal constraints on tree growth detected through other plot networks and physiological studies. Through common protocols and careful sampling design, the Ausplots Forest Monitoring Network will facilitate the integration of tall eucalypt forests into established global forest monitoring initiatives. In the context of projections of rapidly warming and drying climates in Australia, this plot network will enable detection of links between climate and growth, mortality and carbon dynamics of eucalypt forests. PMID:26368919

Hierarchical structures of correlations networks among Turkey’s exports and imports by currencies

NASA Astrophysics Data System (ADS)

Kocakaplan, Yusuf; Deviren, Bayram; Keskin, Mustafa

2012-12-01

We have examined the hierarchical structures of correlations networks among Turkey’s exports and imports by currencies for the 1996-2010 periods, using the concept of a minimal spanning tree (MST) and hierarchical tree (HT) which depend on the concept of ultrametricity. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial markets. We derived a hierarchical organization and build the MSTs and HTs during the 1996-2001 and 2002-2010 periods. The reason for studying two different sub-periods, namely 1996-2001 and 2002-2010, is that the Euro (EUR) came into use in 2001, and some countries have made their exports and imports with Turkey via the EUR since 2002, and in order to test various time-windows and observe temporal evolution. We have carried out bootstrap analysis to associate a value of the statistical reliability to the links of the MSTs and HTs. We have also used the average linkage cluster analysis (ALCA) to observe the cluster structure more clearly. Moreover, we have obtained the bidimensional minimal spanning tree (BMST) due to economic trade being a bidimensional problem. From the structural topologies of these trees, we have identified different clusters of currencies according to their proximity and economic ties. Our results show that some currencies are more important within the network, due to a tighter connection with other currencies. We have also found that the obtained currencies play a key role for Turkey’s exports and imports and have important implications for the design of portfolio and investment strategies.

Detecting a currency's dominance or dependence using foreign exchange network trees

NASA Astrophysics Data System (ADS)

McDonald, Mark; Suleman, Omer; Williams, Stacy; Howison, Sam; Johnson, Neil F.

2005-10-01

In a system containing a large number of interacting stochastic processes, there will typically be many nonzero correlation coefficients. This makes it difficult to either visualize the system’s interdependencies, or identify its dominant elements. Such a situation arises in foreign exchange (FX), which is the world’s biggest market. Here we develop a network analysis of these correlations using minimum spanning trees (MSTs). We show that not only do the MSTs provide a meaningful representation of the global FX dynamics, but they also enable one to determine momentarily dominant and dependent currencies. We find that information about a country’s geographical ties emerges from the raw exchange-rate data. Most importantly from a trading perspective, we discuss how to infer which currencies are “in play” during a particular period of time.

Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent

PubMed Central

Zhu, Sha; Degnan, James H.

2017-01-01

Abstract Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable—that is whether there could be two distinct networks that lead to the same distribution of gene trees. For cases in which incomplete lineage sorting occurs in addition to hybridization, we demonstrate a new representation of the species network likelihood that expresses the probability distribution of the gene tree topologies as a linear combination of gene tree distributions given a set of species trees. This representation makes it clear that in some cases in which two distinct networks give the same distribution of gene trees when sampling one allele per species, the two networks can be distinguished theoretically when multiple individuals are sampled per species. This result means that network identifiability is not only a function of the trees displayed by the networks but also depends on allele sampling within species. We additionally give an example in which two networks that display exactly the same trees can be distinguished from their gene trees even when there is only one lineage sampled per species. PMID:27780899

Transforming phylogenetic networks: Moving beyond tree space.

PubMed

Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

2016-09-07

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enumeration of spanning trees in planar unclustered networks

NASA Astrophysics Data System (ADS)

Xiao, Yuzhi; Zhao, Haixing; Hu, Guona; Ma, Xiujuan

2014-07-01

Among a variety of subgraphs, spanning trees are one of the most important and fundamental categories. They are relevant to diverse aspects of networks, including reliability, transport, self-organized criticality, loop-erased random walks and so on. In this paper, we introduce a family of modular, self-similar planar networks with zero clustering. Relevant properties of this family are comparable to those networks associated with technological systems having low clustering, like power grids, some electronic circuits, the Internet and some biological systems. So, it is very significant to research on spanning trees of planar networks. However, for a large network, evaluating the relevant determinant is intractable. In this paper, we propose a fairly generic linear algorithm for counting the number of spanning trees of a planar network. Using the algorithm, we derive analytically the exact numbers of spanning trees in planar networks. Our result shows that the computational complexity is O(t) , which is better than that of the matrix tree theorem with O(m2t2) , where t is the number of steps and m is the girth of the planar network. We also obtain the entropy for the spanning trees of a given planar network. We find that the entropy of spanning trees in the studied network is small, which is in sharp contrast to the previous result for planar networks with the same average degree. We also determine an upper bound and a lower bound for the numbers of spanning trees in the family of planar networks by the algorithm. As another application of the algorithm, we give a formula for the number of spanning trees in an outerplanar network with small-world features.

Topological patterns in street networks of self-organized urban settlements

NASA Astrophysics Data System (ADS)

Buhl, J.; Gautrais, J.; Reeves, N.; Solé, R. V.; Valverde, S.; Kuntz, P.; Theraulaz, G.

2006-02-01

Many urban settlements result from a spatially distributed, decentralized building process. Here we analyze the topological patterns of organization of a large collection of such settlements using the approach of complex networks. The global efficiency (based on the inverse of shortest-path lengths), robustness to disconnections and cost (in terms of length) of these graphs is studied and their possible origins analyzed. A wide range of patterns is found, from tree-like settlements (highly vulnerable to random failures) to meshed urban patterns. The latter are shown to be more robust and efficient.

Modeling hormonal control of cambium proliferation.

PubMed

Oles, Vladyslav; Panchenko, Alexander; Smertenko, Andrei

2017-01-01

Rise of atmospheric CO2 is one of the main causes of global warming. Catastrophic climate change can be avoided by reducing emissions and increasing sequestration of CO2. Trees are known to sequester CO2 during photosynthesis, and then store it as wood biomass. Thus, breeding of trees with higher wood yield would mitigate global warming as well as augment production of renewable construction materials, energy, and industrial feedstock. Wood is made of cellulose-rich xylem cells produced through proliferation of a specialized stem cell niche called cambium. Importance of cambium in xylem cells production makes it an ideal target for the tree breeding programs; however our knowledge about control of cambium proliferation remains limited. The morphology and regulation of cambium are different from those of stem cell niches that control axial growth. For this reason, translating the knowledge about axial growth to radial growth has limited use. Furthermore, genetic approaches cannot be easily applied because overlaying tissues conceal cambium from direct observation and complicate identification of mutants. To overcome the paucity of experimental tools in cambium biology, we constructed a Boolean network CARENET (CAmbium REgulation gene NETwork) for modelling cambium activity, which includes the key transcription factors WOX4 and HD-ZIP III as well as their potential regulators. Our simulations predict that: (1) auxin, cytokinin, gibberellin, and brassinosteroids act cooperatively in promoting transcription of WOX4 and HD-ZIP III; (2) auxin and cytokinin pathways negatively regulate each other; (3) hormonal pathways act redundantly in sustaining cambium activity; (4) individual cambium cells can have diverse molecular identities. CARENET can be extended to include components of other signalling pathways and be integrated with models of xylem and phloem differentiation. Such extended models would facilitate breeding trees with higher wood yield.

Tree growth and vegetation activity at the ecosystem-scale in the eastern Mediterranean

NASA Astrophysics Data System (ADS)

Coulthard, Bethany L.; Touchan, Ramzi; Anchukaitis, Kevin J.; Meko, David M.; Sivrikaya, Fatih

2017-08-01

Linking annual tree growth with remotely-sensed terrestrial vegetation indices provides a basis for using tree rings as proxies for ecosystem primary productivity over large spatial and long temporal scales. In contrast with most previous tree ring/remote sensing studies that have focused on temperature-limited boreal and taiga environments, here we compare the normalized difference vegetation index (NDVI) with a network of Pinus brutia tree ring width chronologies collected along ecological gradients in semiarid Cyprus, where both radial tree growth and broader vegetation activity are controlled by drought. We find that the interaction between precipitation, elevation, and land-cover type generate a relationship between radial tree growth and NDVI. While tree ring chronologies at higher-elevation forested sites do not exhibit climate-driven linkages with NDVI, chronologies at lower-elevation dry sites are strongly correlated with NDVI during the winter precipitation season. At lower-elevation sites, land cover is dominated by grasslands and shrublands and tree ring widths operate as a proxy for ecosystem-scale vegetation activity. Tree rings can therefore be used to reconstruct productivity in water-limited grasslands and shrublands, where future drought stress is expected to alter the global carbon cycle, biodiversity, and ecosystem functioning in the 21st century.

Automated construction of arterial and venous trees in retinal images

PubMed Central

Hu, Qiao; Abràmoff, Michael D.; Garvin, Mona K.

2015-01-01

Abstract. While many approaches exist to segment retinal vessels in fundus photographs, only a limited number focus on the construction and disambiguation of arterial and venous trees. Previous approaches are local and/or greedy in nature, making them susceptible to errors or limiting their applicability to large vessels. We propose a more global framework to generate arteriovenous trees in retinal images, given a vessel segmentation. In particular, our approach consists of three stages. The first stage is to generate an overconnected vessel network, named the vessel potential connectivity map (VPCM), consisting of vessel segments and the potential connectivity between them. The second stage is to disambiguate the VPCM into multiple anatomical trees, using a graph-based metaheuristic algorithm. The third stage is to classify these trees into arterial or venous (A/V) trees. We evaluated our approach with a ground truth built based on a public database, showing a pixel-wise classification accuracy of 88.15% using a manual vessel segmentation as input, and 86.11% using an automatic vessel segmentation as input. PMID:26636114

Roost networks of northern myotis (Myotis septentionalis) in a managed landscape

Treesearch

Joshua B. Johnson; W. Mark Ford; John W. Edwards

2012-01-01

Maternity groups of many bat species conform to fission-fusion models and movements among diurnal roost trees and individual bats belonging to these groups use networks of roost trees. Forest disturbances may alter roost networks and characteristics of roost trees. Therefore, at the Fernow Experimental Forest in West Virginia, we examined roost tree networks of...

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

PubMed Central

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-01

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology. PMID:18199838

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks.

PubMed

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-22

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology.

Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global-scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical regions, with 0.74, and 0.61 trillion in boreal and temperate regions, respectively. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming impact of humans across most of the world. Based on our projected tree densities, we estimate that deforestation is currently responsible for removing over 15 billion trees each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Mapping tree density at a global scale

NASA Astrophysics Data System (ADS)

Crowther, T. W.; Glick, H. B.; Covey, K. R.; Bettigole, C.; Maynard, D. S.; Thomas, S. M.; Smith, J. R.; Hintler, G.; Duguid, M. C.; Amatulli, G.; Tuanmu, M.-N.; Jetz, W.; Salas, C.; Stam, C.; Piotto, D.; Tavani, R.; Green, S.; Bruce, G.; Williams, S. J.; Wiser, S. K.; Huber, M. O.; Hengeveld, G. M.; Nabuurs, G.-J.; Tikhonova, E.; Borchardt, P.; Li, C.-F.; Powrie, L. W.; Fischer, M.; Hemp, A.; Homeier, J.; Cho, P.; Vibrans, A. C.; Umunay, P. M.; Piao, S. L.; Rowe, C. W.; Ashton, M. S.; Crane, P. R.; Bradford, M. A.

2015-09-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Mapping tree density at a global scale.

PubMed

Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

2015-09-10

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

On Determining if Tree-based Networks Contain Fixed Trees.

PubMed

Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

2016-05-01

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

Seven Deadliest Network Attacks

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

Prowell, Stacy J; Borkin, Michael; Kraus, Robert

2010-05-01

Do you need to keep up with the latest hacks, attacks, and exploits effecting networks? Then you need "Seven Deadliest Network Attacks". This book pinpoints the most dangerous hacks and exploits specific to networks, laying out the anatomy of these attacks including how to make your system more secure. You will discover the best ways to defend against these vicious hacks with step-by-step instruction and learn techniques to make your computer and network impenetrable. Attacks detailed in this book include: Denial of Service; War Dialing; Penetration 'Testing'; Protocol Tunneling; Spanning Tree Attacks; Man-in-the-Middle; and, Password Replay. Knowledge is power, findmore » out about the most dominant attacks currently waging war on computers and networks globally. Discover the best ways to defend against these vicious attacks; step-by-step instruction shows you how. Institute countermeasures, don't be caught defenseless again, learn techniques to make your computer and network impenetrable.« less

Tree-average distances on certain phylogenetic networks have their weights uniquely determined.

PubMed

Willson, Stephen J

2012-01-01

A phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species in the leaf set, and one seeks to infer properties of the network, possibly including the graph itself. In the case of phylogenetic trees, distances between extant species are frequently used to infer the phylogenetic trees by methods such as neighbor-joining. This paper proposes a tree-average distance for networks more general than trees. The notion requires a weight on each arc measuring the genetic change along the arc. For each displayed tree the distance between two leaves is the sum of the weights along the path joining them. At a hybrid vertex, each character is inherited from one of its parents. We will assume that for each hybrid there is a probability that the inheritance of a character is from a specified parent. Assume that the inheritance events at different hybrids are independent. Then for each displayed tree there will be a probability that the inheritance of a given character follows the tree; this probability may be interpreted as the probability of the tree. The tree-average distance between the leaves is defined to be the expected value of their distance in the displayed trees. For a class of rooted networks that includes rooted trees, it is shown that the weights and the probabilities at each hybrid vertex can be calculated given the network and the tree-average distances between the leaves. Hence these weights and probabilities are uniquely determined. The hypotheses on the networks include that hybrid vertices have indegree exactly 2 and that vertices that are not leaves have a tree-child.

Neural network topology in ADHD; evidence for maturational delay and default-mode network alterations.

PubMed

Janssen, T W P; Hillebrand, A; Gouw, A; Geladé, K; Van Mourik, R; Maras, A; Oosterlaan, J

2017-11-01

Attention-deficit/hyperactivity disorder (ADHD) has been associated with widespread brain abnormalities in white and grey matter, affecting not only local, but global functional networks as well. In this study, we explored these functional networks using source-reconstructed electroencephalography in ADHD and typically developing (TD) children. We expected evidence for maturational delay, with underlying abnormalities in the default mode network. Electroencephalograms were recorded in ADHD (n=42) and TD (n=43) during rest, and functional connectivity (phase lag index) and graph (minimum spanning tree) parameters were derived. Dependent variables were global and local network metrics in theta, alpha and beta bands. We found evidence for a more centralized functional network in ADHD compared to TD children, with decreased diameter in the alpha band (η p 2 =0.06) and increased leaf fraction (η p 2 =0.11 and 0.08) in the alpha and beta bands, with underlying abnormalities in hub regions of the brain, including default mode network. The finding of a more centralized network is in line with maturational delay models of ADHD and should be replicated in longitudinal designs. This study contributes to the literature by combining high temporal and spatial resolution to construct EEG network topology, and associates maturational-delay and default-mode interference hypotheses of ADHD. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Structure and formation of ant transportation networks

PubMed Central

Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

2011-01-01

Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

Graph theory network function in Parkinson's disease assessed with electroencephalography.

PubMed

Utianski, Rene L; Caviness, John N; van Straaten, Elisabeth C W; Beach, Thomas G; Dugger, Brittany N; Shill, Holly A; Driver-Dunckley, Erika D; Sabbagh, Marwan N; Mehta, Shyamal; Adler, Charles H; Hentz, Joseph G

2016-05-01

To determine what differences exist in graph theory network measures derived from electroencephalography (EEG), between Parkinson's disease (PD) patients who are cognitively normal (PD-CN) and matched healthy controls; and between PD-CN and PD dementia (PD-D). EEG recordings were analyzed via graph theory network analysis to quantify changes in global efficiency and local integration. This included minimal spanning tree analysis. T-tests and correlations were used to assess differences between groups and assess the relationship with cognitive performance. Network measures showed increased local integration across all frequency bands between control and PD-CN; in contrast, decreased local integration occurred in PD-D when compared to PD-CN in the alpha1 frequency band. Differences found in PD-MCI mirrored PD-D. Correlations were found between network measures and assessments of global cognitive performance in PD. Our results reveal distinct patterns of band and network measure type alteration and breakdown for PD, as well as with cognitive decline in PD. These patterns suggest specific ways that interaction between cortical areas becomes abnormal and contributes to PD symptoms at various stages. Graph theory analysis by EEG suggests that network alteration and breakdown are robust attributes of PD cortical dysfunction pathophysiology. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Identification of the potential gap areas for the developing green infrastructure in the Urban area using High resolution satellite Imagery

NASA Astrophysics Data System (ADS)

Kanaparthi, M. B.

2017-12-01

In India urban population is growing day by day which is causing air pollution less air quality finally leading to climate change and global warming. To mitigate the effect of the climate change we need to plant more trees in the urban area. The objective of this study is develop a plan to improve the urban Green Infrastructure (GI) to fight against the climate change and global warming. Improving GI is a challenging and difficult task in the urban areas because land unavailability of land, to overcome the problem greenways is a good the solution. Greenway is a linear open space developed along the rivers, canals, roads in the urban areas to form a network of green spaces. Roads are the most common structures in the urban area. The idea is to develop the greenways alongside the road to connecting the different green spaces. Tree crowns will act as culverts to connect the green spaces. This will require the spatial structure of the green space, distribution of trees along the roads and the gap areas along the road where more trees can be planted. This can be achieved with help of high resolution Satellite Imagery and the object extraction techniques. This study was carried in the city Bhimavaram which is located in state Andhra Pradesh. The final outcome of this study is potential gap areas for planting trees in the city.

Tree-Based Unrooted Phylogenetic Networks.

PubMed

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

Architecture of the wood-wide web: Rhizopogon spp. genets link multiple Douglas-fir cohorts.

PubMed

Beiler, Kevin J; Durall, Daniel M; Simard, Suzanne W; Maxwell, Sheri A; Kretzer, Annette M

2010-01-01

*The role of mycorrhizal networks in forest dynamics is poorly understood because of the elusiveness of their spatial structure. We mapped the belowground distribution of the fungi Rhizopogon vesiculosus and Rhizopogon vinicolor and interior Douglas-fir trees (Pseudotsuga menziesii var. glauca) to determine the architecture of a mycorrhizal network in a multi-aged old-growth forest. *Rhizopogon spp. mycorrhizas were collected within a 30 x 30 m plot. Trees and fungal genets were identified using multi-locus microsatellite DNA analysis. Tree genotypes from mycorrhizas were matched to reference trees aboveground. Two trees were considered linked if they shared the same fungal genet(s). *The two Rhizopogon species each formed 13-14 genets, each colonizing up to 19 trees in the plot. Rhizopogon vesiculosus genets were larger, occurred at greater depths, and linked more trees than genets of R. vinicolor. Multiple tree cohorts were linked, with young saplings established within the mycorrhizal network of Douglas-fir veterans. A strong positive relationship was found between tree size and connectivity, resulting in a scale-free network architecture with small-world properties. *This mycorrhizal network architecture suggests an efficient and robust network, where large trees play a foundational role in facilitating conspecific regeneration and stabilizing the ecosystem.

Dynamical analysis of a fractional SIR model with birth and death on heterogeneous complex networks

NASA Astrophysics Data System (ADS)

Huo, Jingjing; Zhao, Hongyong

2016-04-01

In this paper, a fractional SIR model with birth and death rates on heterogeneous complex networks is proposed. Firstly, we obtain a threshold value R0 based on the existence of endemic equilibrium point E∗, which completely determines the dynamics of the model. Secondly, by using Lyapunov function and Kirchhoff's matrix tree theorem, the globally asymptotical stability of the disease-free equilibrium point E0 and the endemic equilibrium point E∗ of the model are investigated. That is, when R0 < 1, the disease-free equilibrium point E0 is globally asymptotically stable and the disease always dies out; when R0 > 1, the disease-free equilibrium point E0 becomes unstable and in the meantime there exists a unique endemic equilibrium point E∗, which is globally asymptotically stable and the disease is uniformly persistent. Finally, the effects of various immunization schemes are studied and compared. Numerical simulations are given to demonstrate the main results.

Missing Rings in Pinus halepensis – The Missing Link to Relate the Tree-Ring Record to Extreme Climatic Events

PubMed Central

Novak, Klemen; de Luis, Martin; Saz, Miguel A.; Longares, Luis A.; Serrano-Notivoli, Roberto; Raventós, Josep; Čufar, Katarina; Gričar, Jožica; Di Filippo, Alfredo; Piovesan, Gianluca; Rathgeber, Cyrille B. K.; Papadopoulos, Andreas; Smith, Kevin T.

2016-01-01

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of a tree ring is largely determined by the rate and duration of cell division by the vascular cambium. In the Mediterranean climate, this division may occur throughout almost the entire year. Alternatively, cell division may cease during relatively cool and dry winters, only to resume in the same calendar year with milder temperatures and increased availability of water. Under particularly adverse conditions, no xylem may be produced in parts of the stem, resulting in a missing ring (MR). A dendrochronological network of Pinus halepensis was used to determine the relationship of MR to ECE. The network consisted of 113 sites, 1,509 trees, 2,593 cores, and 225,428 tree rings throughout the distribution range of the species. A total of 4,150 MR were identified. Binomial logistic regression analysis determined that MR frequency increased with increased cambial age. Spatial analysis indicated that the geographic areas of south-eastern Spain and northern Algeria contained the greatest frequency of MR. Dendroclimatic regression analysis indicated a non-linear relationship of MR to total monthly precipitation and mean temperature. MR are strongly associated with the combination of monthly mean temperature from previous October till current February and total precipitation from previous September till current May. They are likely to occur with total precipitation lower than 50 mm and temperatures higher than 5°C. This conclusion is global and can be applied to every site across the distribution area. Rather than simply being a complication for dendrochronology, MR formation is a fundamental response of trees to adverse environmental conditions. The demonstrated relationship of MR formation to ECE across this dendrochronological network in the Mediterranean basin shows the potential of MR analysis to reconstruct the history of past climatic extremes and to predict future forest dynamics in a changing climate. PMID:27303421

Missing Rings in Pinus halepensis - The Missing Link to Relate the Tree-Ring Record to Extreme Climatic Events.

PubMed

Novak, Klemen; de Luis, Martin; Saz, Miguel A; Longares, Luis A; Serrano-Notivoli, Roberto; Raventós, Josep; Čufar, Katarina; Gričar, Jožica; Di Filippo, Alfredo; Piovesan, Gianluca; Rathgeber, Cyrille B K; Papadopoulos, Andreas; Smith, Kevin T

2016-01-01

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of a tree ring is largely determined by the rate and duration of cell division by the vascular cambium. In the Mediterranean climate, this division may occur throughout almost the entire year. Alternatively, cell division may cease during relatively cool and dry winters, only to resume in the same calendar year with milder temperatures and increased availability of water. Under particularly adverse conditions, no xylem may be produced in parts of the stem, resulting in a missing ring (MR). A dendrochronological network of Pinus halepensis was used to determine the relationship of MR to ECE. The network consisted of 113 sites, 1,509 trees, 2,593 cores, and 225,428 tree rings throughout the distribution range of the species. A total of 4,150 MR were identified. Binomial logistic regression analysis determined that MR frequency increased with increased cambial age. Spatial analysis indicated that the geographic areas of south-eastern Spain and northern Algeria contained the greatest frequency of MR. Dendroclimatic regression analysis indicated a non-linear relationship of MR to total monthly precipitation and mean temperature. MR are strongly associated with the combination of monthly mean temperature from previous October till current February and total precipitation from previous September till current May. They are likely to occur with total precipitation lower than 50 mm and temperatures higher than 5°C. This conclusion is global and can be applied to every site across the distribution area. Rather than simply being a complication for dendrochronology, MR formation is a fundamental response of trees to adverse environmental conditions. The demonstrated relationship of MR formation to ECE across this dendrochronological network in the Mediterranean basin shows the potential of MR analysis to reconstruct the history of past climatic extremes and to predict future forest dynamics in a changing climate.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

PubMed Central

2017-01-01

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com PMID:28407035

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

PubMed

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

A tree-parenchyma coupled model for lung ventilation simulation.

PubMed

Pozin, Nicolas; Montesantos, Spyridon; Katz, Ira; Pichelin, Marine; Vignon-Clementel, Irene; Grandmont, Céline

2017-11-01

In this article, we develop a lung ventilation model. The parenchyma is described as an elastic homogenized media. It is irrigated by a space-filling dyadic resistive pipe network, which represents the tracheobronchial tree. In this model, the tree and the parenchyma are strongly coupled. The tree induces an extra viscous term in the system constitutive relation, which leads, in the finite element framework, to a full matrix. We consider an efficient algorithm that takes advantage of the tree structure to enable a fast matrix-vector product computation. This framework can be used to model both free and mechanically induced respiration, in health and disease. Patient-specific lung geometries acquired from computed tomography scans are considered. Realistic Dirichlet boundary conditions can be deduced from surface registration on computed tomography images. The model is compared to a more classical exit compartment approach. Results illustrate the coupling between the tree and the parenchyma, at global and regional levels, and how conditions for the purely 0D model can be inferred. Different types of boundary conditions are tested, including a nonlinear Robin model of the surrounding lung structures. Copyright © 2017 John Wiley & Sons, Ltd.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change.

PubMed

Anderson-Teixeira, Kristina J; Davies, Stuart J; Bennett, Amy C; Gonzalez-Akre, Erika B; Muller-Landau, Helene C; Wright, S Joseph; Abu Salim, Kamariah; Almeyda Zambrano, Angélica M; Alonso, Alfonso; Baltzer, Jennifer L; Basset, Yves; Bourg, Norman A; Broadbent, Eben N; Brockelman, Warren Y; Bunyavejchewin, Sarayudh; Burslem, David F R P; Butt, Nathalie; Cao, Min; Cardenas, Dairon; Chuyong, George B; Clay, Keith; Cordell, Susan; Dattaraja, Handanakere S; Deng, Xiaobao; Detto, Matteo; Du, Xiaojun; Duque, Alvaro; Erikson, David L; Ewango, Corneille E N; Fischer, Gunter A; Fletcher, Christine; Foster, Robin B; Giardina, Christian P; Gilbert, Gregory S; Gunatilleke, Nimal; Gunatilleke, Savitri; Hao, Zhanqing; Hargrove, William W; Hart, Terese B; Hau, Billy C H; He, Fangliang; Hoffman, Forrest M; Howe, Robert W; Hubbell, Stephen P; Inman-Narahari, Faith M; Jansen, Patrick A; Jiang, Mingxi; Johnson, Daniel J; Kanzaki, Mamoru; Kassim, Abdul Rahman; Kenfack, David; Kibet, Staline; Kinnaird, Margaret F; Korte, Lisa; Kral, Kamil; Kumar, Jitendra; Larson, Andrew J; Li, Yide; Li, Xiankun; Liu, Shirong; Lum, Shawn K Y; Lutz, James A; Ma, Keping; Maddalena, Damian M; Makana, Jean-Remy; Malhi, Yadvinder; Marthews, Toby; Mat Serudin, Rafizah; McMahon, Sean M; McShea, William J; Memiaghe, Hervé R; Mi, Xiangcheng; Mizuno, Takashi; Morecroft, Michael; Myers, Jonathan A; Novotny, Vojtech; de Oliveira, Alexandre A; Ong, Perry S; Orwig, David A; Ostertag, Rebecca; den Ouden, Jan; Parker, Geoffrey G; Phillips, Richard P; Sack, Lawren; Sainge, Moses N; Sang, Weiguo; Sri-Ngernyuang, Kriangsak; Sukumar, Raman; Sun, I-Fang; Sungpalee, Witchaphart; Suresh, Hebbalalu Sathyanarayana; Tan, Sylvester; Thomas, Sean C; Thomas, Duncan W; Thompson, Jill; Turner, Benjamin L; Uriarte, Maria; Valencia, Renato; Vallejo, Marta I; Vicentini, Alberto; Vrška, Tomáš; Wang, Xihua; Wang, Xugao; Weiblen, George; Wolf, Amy; Xu, Han; Yap, Sandra; Zimmerman, Jess

2015-02-01

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25 ha), all stems ≥ 1 cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 °S-61 °N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 °C), changes in precipitation (up to ± 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8 g N m(-2) yr(-1) and 3.1 g S m(-2) yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5 km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change. © 2014 John Wiley & Sons Ltd.

Modeling decay rates of dead wood in a neotropical forest.

PubMed

Hérault, Bruno; Beauchêne, Jacques; Muller, Félix; Wagner, Fabien; Baraloto, Christopher; Blanc, Lilian; Martin, Jean-Michel

2010-09-01

Variation of dead wood decay rates among tropical trees remains one source of uncertainty in global models of the carbon cycle. Taking advantage of a broad forest plot network surveyed for tree mortality over a 23-year period, we measured the remaining fraction of boles from 367 dead trees from 26 neotropical species widely varying in wood density (0.23-1.24 g cm(-3)) and tree circumference at death time (31.5-272.0 cm). We modeled decay rates within a Bayesian framework assuming a first order differential equation to model the decomposition process and tested for the effects of forest management (selective logging vs. unexploited), of mode of death (standing vs. downed) and of topographical levels (bottomlands vs. hillsides vs. hilltops) on wood decay rates. The general decay model predicts the observed remaining fraction of dead wood (R2 = 60%) with only two biological predictors: tree circumference at death time and wood specific density. Neither selective logging nor local topography had a differential effect on wood decay rates. Including the mode of death into the model revealed that standing dead trees decomposed faster than downed dead trees, but the gain of model accuracy remains rather marginal. Overall, these results suggest that the release of carbon from tropical dead trees to the atmosphere can be simply estimated using tree circumference at death time and wood density.

Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

PubMed

Mirzaei, Sajad; Wu, Yufeng

2016-01-01

Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.

Building a high resolution national elevation model from SRTM: The Australian experience

NASA Astrophysics Data System (ADS)

Gallant, J. C.; Read, A.; Dowling, T. I.

2011-12-01

The global SRTM DEM is a valuable global data set that, for many countries including Australia, provides the best basis for a fine resolution national DEM. But the SRTM data suffers from a variety of artefacts and errors that prevent its routine application with familiar terrain analysis tools. The most important of these are stripes, voids, random noise and offsets due to trees. The tree offsets are particularly disruptive in riparian areas where they make rivers appear as ridge lines. This paper describes how a suite of tools was applied to the 1 second SRTM data for Australia to treat each of these artefacts. An FFT-based tool was developed to detect and remove regular striping. Voids were filled using a modification of the delta surface fill method. Offsets due to trees were modelled and removed using a vegetation mask derived from remotely sensed imagery and a statistical estimate of the offset at vegetation patch boundaries. Random noise was removed using an adaptive smoothing method that responds to variations in both local relief and noise magnitude. Finally, mapped channel networks were imposed using a modified version of the ANUDEM software to enforce hydrological connectivity. The resulting products are being distributed by Geoscience Australia and the smoothed and drainage enforced products in particular are suitable for use in routine terrain analysis tasks. With some adaptation, the same processes could be applied to the global SRTM to derive a product that, in combination with an improved ASTER G-DEM, would provide a high quality comprehensive global elevation model suitable for most purposes.

Summer drought reconstruction in northeastern Spain inferred from a tree ring latewood network since 1734

NASA Astrophysics Data System (ADS)

Tejedor, E.; Saz, M. A.; Esper, J.; Cuadrat, J. M.; de Luis, M.

2017-08-01

Drought recurrence in the Mediterranean is regarded as a fundamental factor for socioeconomic development and the resilience of natural systems in context of global change. However, knowledge of past droughts has been hampered by the absence of high-resolution proxies. We present a drought reconstruction for the northeast of the Iberian Peninsula based on a new dendrochronology network considering the Standardized Evapotranspiration Precipitation Index (SPEI). A total of 774 latewood width series from 387 trees of P. sylvestris and P. uncinata was combined in an interregional chronology. The new chronology, calibrated against gridded climate data, reveals a robust relationship with the SPEI representing drought conditions of July and August. We developed a summer drought reconstruction for the period 1734-2013 representative for the northeastern and central Iberian Peninsula. We identified 16 extremely dry and 17 extremely wet summers and four decadal scale dry and wet periods, including 2003-2013 as the driest episode of the reconstruction.

Autumn Algorithm-Computation of Hybridization Networks for Realistic Phylogenetic Trees.

PubMed

Huson, Daniel H; Linz, Simone

2018-01-01

A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and "realistic" trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of "realistic" rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of "autumn trees", a nice framework for the formulation of algorithms based on the mathematics of "maximum acyclic agreement forests". While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.

Changes of hierarchical network in local and world stock market

NASA Astrophysics Data System (ADS)

Patwary, Enayet Ullah; Lee, Jong Youl; Nobi, Ashadun; Kim, Doo Hwan; Lee, Jae Woo

2017-10-01

We consider the cross-correlation coefficients of the daily returns in the local and global stock markets. We generate the minimal spanning tree (MST) using the correlation matrix. We observe that the MSTs change their structure from chain-like networks to star-like networks during periods of market uncertainty. We quantify the measure of the hierarchical network utilizing the value of the hierarchy measured by the hierarchical path. The hierarchy and betweenness centrality characterize the state of the market regarding the impact of crises. During crises, the non-financial company is established as the central node of the MST. However, before the crisis and during stable periods, the financial company is occupying the central node of the MST in the Korean and the U.S. stock markets. The changes in the network structure and the central node are good indicators of an upcoming crisis.

Systemic risk and hierarchical transitions of financial networks

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Lee, Jae Woo

2017-06-01

In this paper, the change in topological hierarchy, which is measured by the minimum spanning tree constructed from the cross-correlations between the stock indices from the S & P 500 for 1998-2012 in a one year moving time window, was used to analyze a financial crisis. The hierarchy increased in all minor crises in the observation time window except for the sharp crisis of 2007-2008 when the global financial crisis occurred. The sudden increase in hierarchy just before the global financial crisis can be used for the early detection of an upcoming crisis. Clearly, the higher the hierarchy, the higher the threats to financial stability. The scaling relations were developed to observe the changes in hierarchy with the network topology. These scaling relations can also identify and quantify the financial crisis periods, and appear to contain the predictive power of an upcoming crisis.

Systemic risk and hierarchical transitions of financial networks.

PubMed

Nobi, Ashadun; Lee, Jae Woo

2017-06-01

In this paper, the change in topological hierarchy, which is measured by the minimum spanning tree constructed from the cross-correlations between the stock indices from the S & P 500 for 1998-2012 in a one year moving time window, was used to analyze a financial crisis. The hierarchy increased in all minor crises in the observation time window except for the sharp crisis of 2007-2008 when the global financial crisis occurred. The sudden increase in hierarchy just before the global financial crisis can be used for the early detection of an upcoming crisis. Clearly, the higher the hierarchy, the higher the threats to financial stability. The scaling relations were developed to observe the changes in hierarchy with the network topology. These scaling relations can also identify and quantify the financial crisis periods, and appear to contain the predictive power of an upcoming crisis.

Estimating tree bole volume using artificial neural network models for four species in Turkey.

PubMed

Ozçelik, Ramazan; Diamantopoulou, Maria J; Brooks, John R; Wiant, Harry V

2010-01-01

Tree bole volumes of 89 Scots pine (Pinus sylvestris L.), 96 Brutian pine (Pinus brutia Ten.), 107 Cilicica fir (Abies cilicica Carr.) and 67 Cedar of Lebanon (Cedrus libani A. Rich.) trees were estimated using Artificial Neural Network (ANN) models. Neural networks offer a number of advantages including the ability to implicitly detect complex nonlinear relationships between input and output variables, which is very helpful in tree volume modeling. Two different neural network architectures were used and produced the Back propagation (BPANN) and the Cascade Correlation (CCANN) Artificial Neural Network models. In addition, tree bole volume estimates were compared to other established tree bole volume estimation techniques including the centroid method, taper equations, and existing standard volume tables. An overview of the features of ANNs and traditional methods is presented and the advantages and limitations of each one of them are discussed. For validation purposes, actual volumes were determined by aggregating the volumes of measured short sections (average 1 meter) of the tree bole using Smalian's formula. The results reported in this research suggest that the selected cascade correlation artificial neural network (CCANN) models are reliable for estimating the tree bole volume of the four examined tree species since they gave unbiased results and were superior to almost all methods in terms of error (%) expressed as the mean of the percentage errors. 2009 Elsevier Ltd. All rights reserved.

78 FR 33457 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing of a Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-04

... Modified by Amendment No. 1 Thereto, Relating to the WisdomTree Global Corporate Bond Fund and the WisdomTree Emerging Markets Corporate Bond Fund May 29, 2013. Pursuant to Section 19(b)(1) of the Securities... relating to the WisdomTree Global Corporate Bond Fund (the ``Global Fund'') and the WisdomTree Emerging...

Evolution of imitation networks in Minority Game model

NASA Astrophysics Data System (ADS)

Lavička, H.; Slanina, F.

2007-03-01

The Minority Game is adapted to study the “imitation dilemma”, i.e. the tradeoff between local benefit and global harm coming from imitation. The agents are placed on a substrate network and are allowed to imitate more successful neighbours. Imitation domains, which are oriented trees, are formed. We investigate size distribution of the domains and in-degree distribution within the trees. We use four types of substrate: one-dimensional chain; Erdös-Rényi graph; Barabási-Albert scale-free graph; Barabási-Albert 'model A' graph. The behaviour of some features of the imitation network strongly depend on the information cost epsilon, which is the percentage of gain the imitators must pay to the imitated. Generally, the system tends to form a few domains of equal size. However, positive epsilon makes the system stay in a long-lasting metastable state with complex structure. The in-degree distribution is found to follow a power law in two cases of those studied: for Erdös-Rényi substrate for any epsilon and for Barabási-Albert scale-free substrate for large enough epsilon. A brief comparison with empirical data is provided.

Global Tree Cover and Biomass Carbon on Agricultural Land: The contribution of agroforestry to global and national carbon budgets.

PubMed

Zomer, Robert J; Neufeldt, Henry; Xu, Jianchu; Ahrends, Antje; Bossio, Deborah; Trabucco, Antonio; van Noordwijk, Meine; Wang, Mingcheng

2016-07-20

Agroforestry systems and tree cover on agricultural land make an important contribution to climate change mitigation, but are not systematically accounted for in either global carbon budgets or national carbon accounting. This paper assesses the role of trees on agricultural land and their significance for carbon sequestration at a global level, along with recent change trends. Remote sensing data show that in 2010, 43% of all agricultural land globally had at least 10% tree cover and that this has increased by 2% over the previous ten years. Combining geographically and bioclimatically stratified Intergovernmental Panel on Climate Change (IPCC) Tier 1 default estimates of carbon storage with this tree cover analysis, we estimated 45.3 PgC on agricultural land globally, with trees contributing >75%. Between 2000 and 2010 tree cover increased by 3.7%, resulting in an increase of >2 PgC (or 4.6%) of biomass carbon. On average, globally, biomass carbon increased from 20.4 to 21.4 tC ha(-1). Regional and country-level variation in stocks and trends were mapped and tabulated globally, and for all countries. Brazil, Indonesia, China and India had the largest increases in biomass carbon stored on agricultural land, while Argentina, Myanmar, and Sierra Leone had the largest decreases.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

PubMed

Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

Alzheimer Classification Using a Minimum Spanning Tree of High-Order Functional Network on fMRI Dataset

PubMed Central

Guo, Hao; Liu, Lei; Chen, Junjie; Xu, Yong; Jie, Xiang

2017-01-01

Functional magnetic resonance imaging (fMRI) is one of the most useful methods to generate functional connectivity networks of the brain. However, conventional network generation methods ignore dynamic changes of functional connectivity between brain regions. Previous studies proposed constructing high-order functional connectivity networks that consider the time-varying characteristics of functional connectivity, and a clustering method was performed to decrease computational cost. However, random selection of the initial clustering centers and the number of clusters negatively affected classification accuracy, and the network lost neurological interpretability. Here we propose a novel method that introduces the minimum spanning tree method to high-order functional connectivity networks. As an unbiased method, the minimum spanning tree simplifies high-order network structure while preserving its core framework. The dynamic characteristics of time series are not lost with this approach, and the neurological interpretation of the network is guaranteed. Simultaneously, we propose a multi-parameter optimization framework that involves extracting discriminative features from the minimum spanning tree high-order functional connectivity networks. Compared with the conventional methods, our resting-state fMRI classification method based on minimum spanning tree high-order functional connectivity networks greatly improved the diagnostic accuracy for Alzheimer's disease. PMID:29249926

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

PubMed

Francis, Andrew; Moulton, Vincent

2018-06-07

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

PubMed

Gambette, Philippe; van Iersel, Leo; Kelk, Steven; Pardi, Fabio; Scornavacca, Celine

2016-09-01

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with one copy in all species can be explained by a given network. In mathematical terms, this is often translated in the following way: is a given phylogenetic tree contained in a given phylogenetic network? Recently this tree containment problem has been widely investigated from a computational perspective, but most studies have only focused on the topology of the phylogenies, ignoring a piece of information that, in the case of phylogenetic trees, is routinely inferred by evolutionary analyses: branch lengths. These measure the amount of change (e.g., nucleotide substitutions) that has occurred along each branch of the phylogeny. Here, we study a number of versions of the tree containment problem that explicitly account for branch lengths. We show that, although length information has the potential to locate more precisely a tree within a network, the problem is computationally hard in its most general form. On a positive note, for a number of special cases of biological relevance, we provide algorithms that solve this problem efficiently. This includes the case of networks of limited complexity, for which it is possible to recover, among the trees contained by the network with the same topology as the input tree, the closest one in terms of branch lengths.

The transmission process: A combinatorial stochastic process for the evolution of transmission trees over networks.

PubMed

Sainudiin, Raazesh; Welch, David

2016-12-07

We derive a combinatorial stochastic process for the evolution of the transmission tree over the infected vertices of a host contact network in a susceptible-infected (SI) model of an epidemic. Models of transmission trees are crucial to understanding the evolution of pathogen populations. We provide an explicit description of the transmission process on the product state space of (rooted planar ranked labelled) binary transmission trees and labelled host contact networks with SI-tags as a discrete-state continuous-time Markov chain. We give the exact probability of any transmission tree when the host contact network is a complete, star or path network - three illustrative examples. We then develop a biparametric Beta-splitting model that directly generates transmission trees with exact probabilities as a function of the model parameters, but without explicitly modelling the underlying contact network, and show that for specific values of the parameters we can recover the exact probabilities for our three example networks through the Markov chain construction that explicitly models the underlying contact network. We use the maximum likelihood estimator (MLE) to consistently infer the two parameters driving the transmission process based on observations of the transmission trees and use the exact MLE to characterize equivalence classes over the space of contact networks with a single initial infection. An exploratory simulation study of the MLEs from transmission trees sampled from three other deterministic and four random families of classical contact networks is conducted to shed light on the relation between the MLEs of these families with some implications for statistical inference along with pointers to further extensions of our models. The insights developed here are also applicable to the simplest models of "meme" evolution in online social media networks through transmission events that can be distilled from observable actions such as "likes", "mentions", "retweets" and "+1s" along with any concomitant comments. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Global Invader Impact Network (GIIN): toward standardized evaluation of the ecological impacts of invasive plants.

PubMed

Barney, Jacob N; Tekiela, Daniel R; Barrios-Garcia, Maria Noelia; Dimarco, Romina D; Hufbauer, Ruth A; Leipzig-Scott, Peter; Nuñez, Martin A; Pauchard, Aníbal; Pyšek, Petr; Vítková, Michaela; Maxwell, Bruce D

2015-07-01

Terrestrial invasive plants are a global problem and are becoming ubiquitous components of most ecosystems. They are implicated in altering disturbance regimes, reducing biodiversity, and changing ecosystem function, sometimes in profound and irreversible ways. However, the ecological impacts of most invasive plants have not been studied experimentally, and most research to date focuses on few types of impacts, which can vary greatly among studies. Thus, our knowledge of existing ecological impacts ascribed to invasive plants is surprisingly limited in both breadth and depth. Our aim was to propose a standard methodology for quantifying baseline ecological impact that, in theory, is scalable to any terrestrial plant invader (e.g., annual grasses to trees) and any invaded system (e.g., grassland to forest). The Global Invader Impact Network (GIIN) is a coordinated distributed experiment composed of an observational and manipulative methodology. The protocol consists of a series of plots located in (1) an invaded area; (2) an adjacent removal treatment within the invaded area; and (3) a spatially separate uninvaded area thought to be similar to pre-invasion conditions of the invaded area. A standardized and inexpensive suite of community, soil, and ecosystem metrics are collected allowing broad comparisons among measurements, populations, and species. The method allows for one-time comparisons and for long-term monitoring enabling one to derive information about change due to invasion over time. Invader removal plots will also allow for quantification of legacy effects and their return rates, which will be monitored for several years. GIIN uses a nested hierarchical scale approach encompassing multiple sites, regions, and continents. Currently, GIIN has network members in six countries, with new members encouraged. To date, study species include representatives of annual and perennial grasses; annual and perennial forbs; shrubs; and trees. The goal of the GIIN framework is to create a standard yet flexible platform for understanding the ecological impacts of invasive plants, allowing both individual and synthetic analyses across a range of taxa and ecosystems. If broadly adopted, this standard approach will offer unique insight into the ecological impacts of invasive plants at local, regional, and global scales.

Global Invader Impact Network (GIIN): toward standardized evaluation of the ecological impacts of invasive plants

PubMed Central

Barney, Jacob N; Tekiela, Daniel R; Barrios-Garcia, Maria Noelia; Dimarco, Romina D; Hufbauer, Ruth A; Leipzig-Scott, Peter; Nuñez, Martin A; Pauchard, Aníbal; Pyšek, Petr; Vítková, Michaela; Maxwell, Bruce D

2015-01-01

Terrestrial invasive plants are a global problem and are becoming ubiquitous components of most ecosystems. They are implicated in altering disturbance regimes, reducing biodiversity, and changing ecosystem function, sometimes in profound and irreversible ways. However, the ecological impacts of most invasive plants have not been studied experimentally, and most research to date focuses on few types of impacts, which can vary greatly among studies. Thus, our knowledge of existing ecological impacts ascribed to invasive plants is surprisingly limited in both breadth and depth. Our aim was to propose a standard methodology for quantifying baseline ecological impact that, in theory, is scalable to any terrestrial plant invader (e.g., annual grasses to trees) and any invaded system (e.g., grassland to forest). The Global Invader Impact Network (GIIN) is a coordinated distributed experiment composed of an observational and manipulative methodology. The protocol consists of a series of plots located in (1) an invaded area; (2) an adjacent removal treatment within the invaded area; and (3) a spatially separate uninvaded area thought to be similar to pre-invasion conditions of the invaded area. A standardized and inexpensive suite of community, soil, and ecosystem metrics are collected allowing broad comparisons among measurements, populations, and species. The method allows for one-time comparisons and for long-term monitoring enabling one to derive information about change due to invasion over time. Invader removal plots will also allow for quantification of legacy effects and their return rates, which will be monitored for several years. GIIN uses a nested hierarchical scale approach encompassing multiple sites, regions, and continents. Currently, GIIN has network members in six countries, with new members encouraged. To date, study species include representatives of annual and perennial grasses; annual and perennial forbs; shrubs; and trees. The goal of the GIIN framework is to create a standard yet flexible platform for understanding the ecological impacts of invasive plants, allowing both individual and synthetic analyses across a range of taxa and ecosystems. If broadly adopted, this standard approach will offer unique insight into the ecological impacts of invasive plants at local, regional, and global scales. PMID:26306173

Global Tree Cover and Biomass Carbon on Agricultural Land: The contribution of agroforestry to global and national carbon budgets

PubMed Central

Zomer, Robert J.; Neufeldt, Henry; Xu, Jianchu; Ahrends, Antje; Bossio, Deborah; Trabucco, Antonio; van Noordwijk, Meine; Wang, Mingcheng

2016-01-01

Agroforestry systems and tree cover on agricultural land make an important contribution to climate change mitigation, but are not systematically accounted for in either global carbon budgets or national carbon accounting. This paper assesses the role of trees on agricultural land and their significance for carbon sequestration at a global level, along with recent change trends. Remote sensing data show that in 2010, 43% of all agricultural land globally had at least 10% tree cover and that this has increased by 2% over the previous ten years. Combining geographically and bioclimatically stratified Intergovernmental Panel on Climate Change (IPCC) Tier 1 default estimates of carbon storage with this tree cover analysis, we estimated 45.3 PgC on agricultural land globally, with trees contributing >75%. Between 2000 and 2010 tree cover increased by 3.7%, resulting in an increase of >2 PgC (or 4.6%) of biomass carbon. On average, globally, biomass carbon increased from 20.4 to 21.4 tC ha−1. Regional and country-level variation in stocks and trends were mapped and tabulated globally, and for all countries. Brazil, Indonesia, China and India had the largest increases in biomass carbon stored on agricultural land, while Argentina, Myanmar, and Sierra Leone had the largest decreases. PMID:27435095

The global extent and determinants of savanna and forest as alternative biome states.

PubMed

Staver, A Carla; Archibald, Sally; Levin, Simon A

2011-10-14

Theoretically, fire-tree cover feedbacks can maintain savanna and forest as alternative stable states. However, the global extent of fire-driven discontinuities in tree cover is unknown, especially accounting for seasonality and soils. We use tree cover, climate, fire, and soils data sets to show that tree cover is globally discontinuous. Climate influences tree cover globally but, at intermediate rainfall (1000 to 2500 millimeters) with mild seasonality (less than 7 months), tree cover is bimodal, and only fire differentiates between savanna and forest. These may be alternative states over large areas, including parts of Amazonia and the Congo. Changes in biome distributions, whether at the cost of savanna (due to fragmentation) or forest (due to climate), will be neither smooth nor easily reversible.

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2012-09-05

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Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Organization and hierarchy of the human functional brain network lead to a chain-like core.

PubMed

Mastrandrea, Rossana; Gabrielli, Andrea; Piras, Fabrizio; Spalletta, Gianfranco; Caldarelli, Guido; Gili, Tommaso

2017-07-07

The brain is a paradigmatic example of a complex system: its functionality emerges as a global property of local mesoscopic and microscopic interactions. Complex network theory allows to elicit the functional architecture of the brain in terms of links (correlations) between nodes (grey matter regions) and to extract information out of the noise. Here we present the analysis of functional magnetic resonance imaging data from forty healthy humans at rest for the investigation of the basal scaffold of the functional brain network organization. We show how brain regions tend to coordinate by forming a highly hierarchical chain-like structure of homogeneously clustered anatomical areas. A maximum spanning tree approach revealed the centrality of the occipital cortex and the peculiar aggregation of cerebellar regions to form a closed core. We also report the hierarchy of network segregation and the level of clusters integration as a function of the connectivity strength between brain regions.

Spectrum of walk matrix for Koch network and its application

NASA Astrophysics Data System (ADS)

Xie, Pinchen; Lin, Yuan; Zhang, Zhongzhi

2015-06-01

Various structural and dynamical properties of a network are encoded in the eigenvalues of walk matrix describing random walks on the network. In this paper, we study the spectra of walk matrix of the Koch network, which displays the prominent scale-free and small-world features. Utilizing the particular architecture of the network, we obtain all the eigenvalues and their corresponding multiplicities. Based on the link between the eigenvalues of walk matrix and random target access time defined as the expected time for a walker going from an arbitrary node to another one selected randomly according to the steady-state distribution, we then derive an explicit solution to the random target access time for random walks on the Koch network. Finally, we corroborate our computation for the eigenvalues by enumerating spanning trees in the Koch network, using the connection governing eigenvalues and spanning trees, where a spanning tree of a network is a subgraph of the network, that is, a tree containing all the nodes.

Transitions from trees to cycles in adaptive flow networks

NASA Astrophysics Data System (ADS)

Martens, Erik A.; Klemm, Konstantin

2017-11-01

Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply. Theoretical and experimental studies have found that real-world transport networks exhibit both tree-like motifs and cycles. When the network is subject to load fluctuations, the presence of cyclic motifs may help to reduce flow fluctuations and, thus, render supply in the network more robust. While previous studies considered network topology via optimization principles, here, we take a dynamical systems approach and study a simple model of a flow network with dynamically adapting weights (conductances). We assume a spatially non-uniform distribution of rapidly fluctuating loads in the sinks and investigate what network configurations are dynamically stable. The network converges to a spatially non-uniform stable configuration composed of both cyclic and tree-like structures. Cyclic structures emerge locally in a transcritical bifurcation as the amplitude of the load fluctuations is increased. The resulting adaptive dynamics thus partitions the network into two distinct regions with cyclic and tree-like structures. The location of the boundary between these two regions is determined by the amplitude of the fluctuations. These findings may explain why natural transport networks display cyclic structures in the micro-vascular regions near terminal nodes, but tree-like features in the regions with larger veins.

Trees and networks before and after Darwin

PubMed Central

2009-01-01

It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, so-called affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were re-introduced in the mid-1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for bacteria and archaea. In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it. Reviewers This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur. PMID:19917100

A Time Tree Medium Access Control for Energy Efficiency and Collision Avoidance in Wireless Sensor Networks

PubMed Central

Lee, Kilhung

2010-01-01

This paper presents a medium access control and scheduling scheme for wireless sensor networks. It uses time trees for sending data from the sensor node to the base station. For an energy efficient operation of the sensor networks in a distributed manner, time trees are built in order to reduce the collision probability and to minimize the total energy required to send data to the base station. A time tree is a data gathering tree where the base station is the root and each sensor node is either a relaying or a leaf node of the tree. Each tree operates in a different time schedule with possibly different activation rates. Through the simulation, the proposed scheme that uses time trees shows better characteristics toward burst traffic than the previous energy and data arrival rate scheme. PMID:22319270

Alternative Path Communication in Wide-Scale Cluster-Tree Wireless Sensor Networks Using Inactive Periods

PubMed Central

Leão, Erico; Montez, Carlos; Moraes, Ricardo; Portugal, Paulo; Vasques, Francisco

2017-01-01

The IEEE 802.15.4/ZigBee cluster-tree topology is a suitable technology to deploy wide-scale Wireless Sensor Networks (WSNs). These networks are usually designed to support convergecast traffic, where all communication paths go through the PAN (Personal Area Network) coordinator. Nevertheless, peer-to-peer communication relationships may be also required for different types of WSN applications. That is the typical case of sensor and actuator networks, where local control loops must be closed using a reduced number of communication hops. The use of communication schemes optimised just for the support of convergecast traffic may result in higher network congestion and in a potentially higher number of communication hops. Within this context, this paper proposes an Alternative-Route Definition (ARounD) communication scheme for WSNs. The underlying idea of ARounD is to setup alternative communication paths between specific source and destination nodes, avoiding congested cluster-tree paths. These alternative paths consider shorter inter-cluster paths, using a set of intermediate nodes to relay messages during their inactive periods in the cluster-tree network. Simulation results show that the ARounD communication scheme can significantly decrease the end-to-end communication delay, when compared to the use of standard cluster-tree communication schemes. Moreover, the ARounD communication scheme is able to reduce the network congestion around the PAN coordinator, enabling the reduction of the number of message drops due to queue overflows in the cluster-tree network. PMID:28481245

Contact Trees: Network Visualization beyond Nodes and Edges

PubMed Central

Sallaberry, Arnaud; Fu, Yang-chih; Ho, Hwai-Chung; Ma, Kwan-Liu

2016-01-01

Node-Link diagrams make it possible to take a quick glance at how nodes (or actors) in a network are connected by edges (or ties). A conventional network diagram of a “contact tree” maps out a root and branches that represent the structure of nodes and edges, often without further specifying leaves or fruits that would have grown from small branches. By furnishing such a network structure with leaves and fruits, we reveal details about “contacts” in our ContactTrees upon which ties and relationships are constructed. Our elegant design employs a bottom-up approach that resembles a recent attempt to understand subjective well-being by means of a series of emotions. Such a bottom-up approach to social-network studies decomposes each tie into a series of interactions or contacts, which can help deepen our understanding of the complexity embedded in a network structure. Unlike previous network visualizations, ContactTrees highlight how relationships form and change based upon interactions among actors, as well as how relationships and networks vary by contact attributes. Based on a botanical tree metaphor, the design is easy to construct and the resulting tree-like visualization can display many properties at both tie and contact levels, thus recapturing a key ingredient missing from conventional techniques of network visualization. We demonstrate ContactTrees using data sets consisting of up to three waves of 3-month contact diaries over the 2004-2012 period, and discuss how this design can be applied to other types of datasets. PMID:26784350

Alternative Path Communication in Wide-Scale Cluster-Tree Wireless Sensor Networks Using Inactive Periods.

PubMed

Leão, Erico; Montez, Carlos; Moraes, Ricardo; Portugal, Paulo; Vasques, Francisco

2017-05-06

The IEEE 802.15.4/ZigBee cluster-tree topology is a suitable technology to deploy wide-scale Wireless Sensor Networks (WSNs). These networks are usually designed to support convergecast traffic, where all communication paths go through the PAN (Personal Area Network) coordinator. Nevertheless, peer-to-peer communication relationships may be also required for different types of WSN applications. That is the typical case of sensor and actuator networks, where local control loops must be closed using a reduced number of communication hops. The use of communication schemes optimised just for the support of convergecast traffic may result in higher network congestion and in a potentially higher number of communication hops. Within this context, this paper proposes an Alternative-Route Definition (ARounD) communication scheme for WSNs. The underlying idea of ARounD is to setup alternative communication paths between specific source and destination nodes, avoiding congested cluster-tree paths. These alternative paths consider shorter inter-cluster paths, using a set of intermediate nodes to relay messages during their inactive periods in the cluster-tree network. Simulation results show that the ARounD communication scheme can significantly decrease the end-to-end communication delay, when compared to the use of standard cluster-tree communication schemes. Moreover, the ARounD communication scheme is able to reduce the network congestion around the PAN coordinator, enabling the reduction of the number of message drops due to queue overflows in the cluster-tree network.

Betweenness centrality in a weighted network

NASA Astrophysics Data System (ADS)

Wang, Huijuan; Hernandez, Javier Martin; van Mieghem, Piet

2008-04-01

When transport in networks follows the shortest paths, the union of all shortest path trees G∪SPT can be regarded as the “transport overlay network.” Overlay networks such as peer-to-peer networks or virtual private networks can be considered as a subgraph of G∪SPT . The traffic through the network is examined by the betweenness Bl of links in the overlay G∪SPT . The strength of disorder can be controlled by, e.g., tuning the extreme value index α of the independent and identically distributed polynomial link weights. In the strong disorder limit (α→0) , all transport flows over a critical backbone, the minimum spanning tree (MST). We investigate the betweenness distributions of wide classes of trees, such as the MST of those well-known network models and of various real-world complex networks. All these trees with different degree distributions (e.g., uniform, exponential, or power law) are found to possess a power law betweenness distribution Pr[Bl=j]˜j-c . The exponent c seems to be positively correlated with the degree variance of the tree and to be insensitive of the size N of a network. In the weak disorder regime, transport in the network traverses many links. We show that a link with smaller link weight tends to carry more traffic. This negative correlation between link weight and betweenness depends on α and the structure of the underlying topology.

Multicasting in Wireless Communications (Ad-Hoc Networks): Comparison against a Tree-Based Approach

NASA Astrophysics Data System (ADS)

Rizos, G. E.; Vasiliadis, D. C.

2007-12-01

We examine on-demand multicasting in ad hoc networks. The Core Assisted Mesh Protocol (CAMP) is a well-known protocol for multicast routing in ad-hoc networks, generalizing the notion of core-based trees employed for internet multicasting into multicast meshes that have much richer connectivity than trees. On the other hand, wireless tree-based multicast routing protocols use much simpler structures for determining route paths, using only parent-child relationships. In this work, we compare the performance of the CAMP protocol against the performance of wireless tree-based multicast routing protocols, in terms of two important factors, namely packet delay and ratio of dropped packets.

Multiscale modeling of the human arterial tree on the TeraGrid.

NASA Astrophysics Data System (ADS)

Karniadakis, Gerorge

2009-03-01

A multiscale model of the human arterial tree will be presented consisting of the macrovascular network (MaN, arteries above 1-2 mm), the mesovascular network (MeN, arterioles above 10 micro-m) and the microvascular network (MiN, capillaries). Coupling conditions between the MaN-MeN-MiN will be discussed and three different methods in modeling each network will be presented. Specific examples will be shown for the intracranial arterial tree for healthy subjects but also for patients with hydrocephalus.

Hierarchical classification with a competitive evolutionary neural tree.

PubMed

Adams, R G.; Butchart, K; Davey, N

1999-04-01

A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species' global distribution: Combining classical population genetics and network analyses.

PubMed

Rodger, Yael S; Greenbaum, Gili; Silver, Micha; Bar-David, Shirli; Winters, Gidon

2018-01-01

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

A precise clock distribution network for MRPC-based experiments

NASA Astrophysics Data System (ADS)

Wang, S.; Cao, P.; Shang, L.; An, Q.

2016-06-01

In high energy physics experiments, the MRPC (Multi-Gap Resistive Plate Chamber) detectors are widely used recently which can provide higher-resolution measurement for particle identification. However, the application of MRPC detectors leads to a series of challenges in electronics design with large number of front-end electronic channels, especially for distributing clock precisely. To deal with these challenges, this paper presents a universal scheme of clock transmission network for MRPC-based experiments with advantages of both precise clock distribution and global command synchronization. For precise clock distributing, the clock network is designed into a tree architecture with two stages: the first one has a point-to-multipoint long range bidirectional distribution with optical channels and the second one has a fan-out structure with copper link inside readout crates. To guarantee the precision of clock frequency or phase, the r-PTP (reduced Precision Time Protocol) and the DDMTD (digital Dual Mixer Time Difference) methods are used for frequency synthesis, phase measurement and adjustment, which is implemented by FPGA (Field Programmable Gate Array) in real-time. In addition, to synchronize global command execution, based upon this clock distribution network, synchronous signals are coded with clock for transmission. With technique of encoding/decoding and clock data recovery, signals such as global triggers or system control commands, can be distributed to all front-end channels synchronously, which greatly simplifies the system design. The experimental results show that both the clock jitter (RMS) and the clock skew can be less than 100 ps.

Improving quantum state transfer efficiency and entanglement distribution in binary tree spin network through incomplete collapsing measurements

NASA Astrophysics Data System (ADS)

Behzadi, Naghi; Ahansaz, Bahram

2018-04-01

We propose a mechanism for quantum state transfer (QST) over a binary tree spin network on the basis of incomplete collapsing measurements. To this aim, we perform initially a weak measurement (WM) on the central qubit of the binary tree network where the state of our concern has been prepared on that qubit. After the time evolution of the whole system, a quantum measurement reversal (QMR) is performed on a chosen target qubit. By taking optimal value for the strength of QMR, it is shown that the QST quality from the sending qubit to any typical target qubit on the binary tree is considerably improved in terms of the WM strength. Also, we show that how high-quality entanglement distribution over the binary tree network is achievable by using this approach.

Depletion of Stem Water of Sclerocarya birrea Agroforestry Tree Precedes Start of Rainy Season in West African Sudanian Zone

NASA Astrophysics Data System (ADS)

Ceperley, Natalie; Mande, Theophile; Parlange, Marc B.

2013-04-01

Understanding water use by agroforestry trees in dry-land ecosystems is essential for improving water management. Agroforestry trees are valued and promoted for many of their ecologic and economic benefits but are often criticized as competing for valuable water resources. In order to understand the seasonal patterns of source water used by agroforestry trees, samples from rain, ground, and surface water were collected weekly in the subcatchment of the Singou watershed that is part of the Volta Basin. Soil and vegetation samples were collected from and under a Sclerocarya birrea agroforstry trees located in this catchment in sealed vials, extracted, and analyzed with a Picarro L2130-i CRDS to obtain both δO18 and δDH fractions. Meteorological measurements were taken with a network of wireless, autonomous stations that communicate through the GSM network (Sensorscope) and two complete eddy-covariance energy balance stations, in addition to intense monitoring of sub-canopy solar radiation, throughfall, stemflow, and soil moisture. Examination of the time series of δO18 concentrations confirm that values in soil and xylem water are coupled, both becoming enriched during the dry season and depleted during the rainy season. Xylem water δO18 levels drops to groundwater δO18 levels in early March when trees access groundwater for leafing out, however soil water does not reach this level until soil moisture increases in mid-June. The relationship between the δDH and δO18 concentrations of water extracted from soil and tree samples do not fall along the global meteoric water line. In order to explore whether this was a seasonally driven, we grouped samples into an "evaporated" group or a "meteoric" group based on the smaller residual to the respective lines. Although more soil samples were found along the m-line during the rainy season than tree samples or dry season soil samples, there was no significant difference in days since rain for any group This suggests that xylem water is always under stress from evapotranspiration and soil water underwent evaporation soon after a rain event. Visual observation of tree confirms conclusion that trees access deep ground water in March and April, before rain begins and before soil is connected to groundwater. Results from the research are being integrated into a local outreach project to improve use of agroforestry.

Node Redeployment Algorithm Based on Stratified Connected Tree for Underwater Sensor Networks

PubMed Central

Liu, Jun; Jiang, Peng; Wu, Feng; Yu, Shanen; Song, Chunyue

2016-01-01

During the underwater sensor networks (UWSNs) operation, node drift with water environment causes network topology changes. Periodic node location examination and adjustment are needed to maintain good network monitoring quality as long as possible. In this paper, a node redeployment algorithm based on stratified connected tree for UWSNs is proposed. At every network adjustment moment, self-examination and adjustment on node locations are performed firstly. If a node is outside the monitored space, it returns to the last location recorded in its memory along straight line. Later, the network topology is stratified into a connected tree that takes the sink node as the root node by broadcasting ready information level by level, which can improve the network connectivity rate. Finally, with synthetically considering network coverage and connectivity rates, and node movement distance, the sink node performs centralized optimization on locations of leaf nodes in the stratified connected tree. Simulation results show that the proposed redeployment algorithm can not only keep the number of nodes in the monitored space as much as possible and maintain good network coverage and connectivity rates during network operation, but also reduce node movement distance during node redeployment and prolong the network lifetime. PMID:28029124

Finding Minimum-Power Broadcast Trees for Wireless Networks

NASA Technical Reports Server (NTRS)

Arabshahi, Payman; Gray, Andrew; Das, Arindam; El-Sharkawi, Mohamed; Marks, Robert, II

2004-01-01

Some algorithms have been devised for use in a method of constructing tree graphs that represent connections among the nodes of a wireless communication network. These algorithms provide for determining the viability of any given candidate connection tree and for generating an initial set of viable trees that can be used in any of a variety of search algorithms (e.g., a genetic algorithm) to find a tree that enables the network to broadcast from a source node to all other nodes while consuming the minimum amount of total power. The method yields solutions better than those of a prior algorithm known as the broadcast incremental power algorithm, albeit at a slightly greater computational cost.

Synchronizing compute node time bases in a parallel computer

DOEpatents

Chen, Dong; Faraj, Daniel A; Gooding, Thomas M; Heidelberger, Philip

2015-01-27

Synchronizing time bases in a parallel computer that includes compute nodes organized for data communications in a tree network, where one compute node is designated as a root, and, for each compute node: calculating data transmission latency from the root to the compute node; configuring a thread as a pulse waiter; initializing a wakeup unit; and performing a local barrier operation; upon each node completing the local barrier operation, entering, by all compute nodes, a global barrier operation; upon all nodes entering the global barrier operation, sending, to all the compute nodes, a pulse signal; and for each compute node upon receiving the pulse signal: waking, by the wakeup unit, the pulse waiter; setting a time base for the compute node equal to the data transmission latency between the root node and the compute node; and exiting the global barrier operation.

Synchronizing compute node time bases in a parallel computer

DOEpatents

Chen, Dong; Faraj, Daniel A; Gooding, Thomas M; Heidelberger, Philip

2014-12-30

Synchronizing time bases in a parallel computer that includes compute nodes organized for data communications in a tree network, where one compute node is designated as a root, and, for each compute node: calculating data transmission latency from the root to the compute node; configuring a thread as a pulse waiter; initializing a wakeup unit; and performing a local barrier operation; upon each node completing the local barrier operation, entering, by all compute nodes, a global barrier operation; upon all nodes entering the global barrier operation, sending, to all the compute nodes, a pulse signal; and for each compute node upon receiving the pulse signal: waking, by the wakeup unit, the pulse waiter; setting a time base for the compute node equal to the data transmission latency between the root node and the compute node; and exiting the global barrier operation.

Tree planting: not a simple solution

Treesearch

Constance I. Millar; William J. Libby

1991-01-01

There's no doubt about it. Planting trees has caught the attention of the American public. In his 1990 State of the Union address, President Bush proposed planting a billion Fees annually for the next ten years. Inspired by the potential for trees to reduce greenhouse gases and mitigate global climate change, tree-planting programs such as Treepeople and Global...

Locating hardware faults in a data communications network of a parallel computer

DOEpatents

Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

2010-01-12

Hardware faults location in a data communications network of a parallel computer. Such a parallel computer includes a plurality of compute nodes and a data communications network that couples the compute nodes for data communications and organizes the compute node as a tree. Locating hardware faults includes identifying a next compute node as a parent node and a root of a parent test tree, identifying for each child compute node of the parent node a child test tree having the child compute node as root, running a same test suite on the parent test tree and each child test tree, and identifying the parent compute node as having a defective link connected from the parent compute node to a child compute node if the test suite fails on the parent test tree and succeeds on all the child test trees.

Analyzing Crisis in Global Financial Indices

NASA Astrophysics Data System (ADS)

Kumar, Sunil; Deo, Nivedita

We apply the Random Matrix Theory and complex network techniques to 20 global financial indices and study the correlation and network properties before and during the financial crisis of 2008 respectively. We find that the largest eigenvalue deviate significantly from the upper bound which shows a strong correlation between financial indices. By using a sliding window of 25 days we find that largest eigenvalue represent the collective information about the correlation between global financial indices and its trend indicate the market conditions. It is confirmed that eigenvectors corresponding to second largest eigenvalue gives useful information about the sector formation in the global financial indices. We find that these clusters are formed on the basis of the geographical location. The correlation network is constructed using threshold method for different values of threshold θ in the range 0 to 0.9, at θ=0.2 the network is fully connected. At θ=0.6, the Americas, Europe and Asia/Pacific form different clusters before the crisis but during the crisis Americas and Europe are strongly linked. If we further increase the threshold to 0.9 we find that European countries France, Germany and UK consistently constitute the most tightly linked markets before and during the crisis. We find that the structure of Minimum Spanning Tree before the crisis is more star like whereas during the crisis it changes to be more chain like. Using the multifractal analysis, we find that Hurst exponents of financial indices increases during the period of crisis as compared to the period before the crisis. The empirical results verify the validity of measures, and this has led to a better understanding of complex financial markets.

Using ROC curves to compare neural networks and logistic regression for modeling individual noncatastrophic tree mortality

Treesearch

Susan L. King

2003-01-01

The performance of two classifiers, logistic regression and neural networks, are compared for modeling noncatastrophic individual tree mortality for 21 species of trees in West Virginia. The output of the classifier is usually a continuous number between 0 and 1. A threshold is selected between 0 and 1 and all of the trees below the threshold are classified as...

An empirical, hierarchical typology of tree species assemblages for assessing forest dynamics under global change scenarios

Treesearch

Jennifer K. Costanza; John W. Coulston; David N. Wear

2017-01-01

The composition of tree species occurring in a forest is important and can be affected by global change drivers such as climate change. To inform assessment and projection of global change impacts at broad extents, we used hierarchical cluster analysis and over 120,000 recent forest inventory plots to empirically define forest tree assemblages across the U.S., and...

Cross Layered Multi-Meshed Tree Scheme for Cognitive Networks

DTIC Science & Technology

2011-06-01

Meshed Tree Routing protocol wireless ad hoc networks ,” Second IEEE International Workshop on Enabling Technologies and Standards for Wireless Mesh ...and Sensor Networks , 2004 43. Chen G.; Stojmenovic I., “Clustering and routing in mobile wireless networks ,” Technical Report TR-99-05, SITE, June...Cross-layer optimization, intra-cluster routing , packet forwarding, inter-cluster routing , mesh network communications,

A 300-year Vietnam hydroclimate and ENSO variability record reconstructed from tree ring δ18O

NASA Astrophysics Data System (ADS)

Sano, Masaki; Xu, Chenxi; Nakatsuka, Takeshi

2012-06-01

A tree ring δ18O chronology is developed for the past 300 years (1705-2004) using 6 cypress trees from northern Vietnam to reconstruct long-term hydroclimatic variations in the summer monsoon season. To the best of our knowledge, this is the first well-replicated tree ringδ18O chronology from Southeast Asia, as well as the longest yet produced. Response analyses reveal that tree ring δ18O is significantly correlated with temperature, precipitation, and the Palmer Drought Severity Index (PDSI) during the period May-October, with highest correlation to the PDSI. Our δ18O chronology accounts for 44% of the PDSI variance, and is in good agreement with a 52-year tree ringδ18O chronology from northern Laos (r = 0.77), indicating that regional hydroclimatic signals are well recorded in the δ18O data. Spatial correlation analyses with global sea surface temperatures suggest that the tropical Pacific plays an important role in modulating hydroclimate over the study region. Further, the δ18O chronology correlates significantly with El Niño-Southern Oscillation (ENSO)-related indices, and is therefore used to reconstruct the annual Multivariate ENSO Index. Because previously published ENSO reconstructions are based mainly on proxy records originating from North America and/or the tropical Pacific, the future development of a tree ringδ18O network from mainland Southeast Asia could lead to an independent and more robust reconstruction of ENSO variability.

Estimation of oxygen isotope in source water of tree-ring cellulose in Indonesia using tree-ring oxygen isotope model

NASA Astrophysics Data System (ADS)

Hisamochi, R.; Watanabe, Y.; Kurita, N.; Sano, M.; Nakatsuka, T.; Matsuo, M.; Yamamoto, H.; Sugiyama, J.; Tsuda, T.; Tagami, T.

2016-12-01

Oxygen isotope composition (δ18O) of tree-ring cellulose has been used as paleoclimate proxy because its origin is atmospheric precipitation. However, interpretation of tree-ring cellulose δ18O is not simple because source water of tree-ring cellulose (the water took up by tree) is not atmospheric precipitation but soil water or ground water in growing season, precisely. In this study, we investigate the relationship between source water of tree-ring cellulose and precipitation in order to improve interpretation of tree-ring cellulose δ18O as paleoclimate proxy. We collected ten teak (Tectona grandis) plantation samples in Java Island, Indonesia. Teak is deciduous tree and grows in rainy season. Samples were cut into annual rings after cellulose extraction. δ18O of individual rings were measured by TCEA-IRMS at the Research Institute of Humanity and Nature. We calculatedδ18O of source water by means of tree-ring oxygen isotope model and then comparedδ18O of source water and that of monthly atmospheric precipitation at Jakarta (GNIP; Global Network of isotopes in Precipitation). Source waterδ18O shows two types of significant correlation withδ18O in atmospheric precipitation. One is positive correlation withδ18O of atmospheric precipitation in previous rainy season. Another is negative correlation with δ18O of atmospheric precipitation in beginning of the growing season. The former indicates that soil water in growing season contains rainfall in previous rainy season and teak mainly takes it up. The latter is difficult to interpret. It may be related to soil moisutre in beginning of growing season.

Node degree distribution in spanning trees

NASA Astrophysics Data System (ADS)

Pozrikidis, C.

2016-03-01

A method is presented for computing the number of spanning trees involving one link or a specified group of links, and excluding another link or a specified group of links, in a network described by a simple graph in terms of derivatives of the spanning-tree generating function defined with respect to the eigenvalues of the Kirchhoff (weighted Laplacian) matrix. The method is applied to deduce the node degree distribution in a complete or randomized set of spanning trees of an arbitrary network. An important feature of the proposed method is that the explicit construction of spanning trees is not required. It is shown that the node degree distribution in the spanning trees of the complete network is described by the binomial distribution. Numerical results are presented for the node degree distribution in square, triangular, and honeycomb lattices.

Increased tree-ring network density reveals more precise estimations of sub-regional hydroclimate variability and climate dynamics in the Midwest, USA

NASA Astrophysics Data System (ADS)

Maxwell, Justin T.; Harley, Grant L.

2017-08-01

Understanding the historic variability in the hydroclimate provides important information on possible extreme dry or wet periods that in turn inform water management plans. Tree rings have long provided historical context of hydroclimate variability of the U.S. However, the tree-ring network used to create these countrywide gridded reconstructions is sparse in certain locations, such as the Midwest. Here, we increase ( n = 20) the spatial resolution of the tree-ring network in southern Indiana and compare a summer (June-August) Palmer Drought Severity Index (PDSI) reconstruction to existing gridded reconstructions of PDSI for this region. We find both droughts and pluvials that were previously unknown that rival the most intense PDSI values during the instrumental period. Additionally, historical drought occurred in Indiana that eclipsed instrumental conditions with regard to severity and duration. During the period 1962-2004 CE, we find that teleconnections of drought conditions through the Atlantic Meridional Overturning Circulation have a strong influence ( r = -0.60, p < 0.01) on secondary tree growth in this region for the late spring-early summer season. These findings highlight the importance of continuing to increase the spatial resolution of the tree-ring network used to infer past climate dynamics to capture the sub-regional spatial variability. Increasing the spatial resolution of the tree-ring network for a given region can better identify sub-regional variability, improve the accuracy of regional tree-ring PDSI reconstructions, and provide better information for climatic teleconnections.

In Forests Globally, Large Trees Suffer Most during Drought

NASA Astrophysics Data System (ADS)

Bennett, A. C.; McDowell, N. G.; Allen, C. D.; Anderson-Teixeira, K. J.

2014-12-01

Globally, drought events are increasing in both frequency and intensity. Spatial and temporal variation in water availability is expected to alter the ecophysiology and structure of forests, with consequent feedbacks to climate change. Extensive tree mortality induced by heat and aridity has been documented across a range of latitudes, and several global vegetation models have simulated widespread forest die-off in the future. The impact of drought on forest structure and function will depend on the differential responses of trees of different sizes. Understanding the size-dependence of drought-induced mortality is necessary to predict local and global impacts. Here we show that in forests worldwide, drought has a greater impact on the growth and mortality of large trees compared to smaller trees. This trend holds true for forests ranging from semiarid woodlands to tropical rainforests. This finding contrasts with what would be expected if deep root access to water were the primary determinant of tree drought response. Rather, the greater drought response of larger trees could be driven by greater inherent vulnerability of large trees to hydraulic stress or by canopy position becoming more of a liability under drought, as exposed crowns face higher evaporative demand. These findings imply that future droughts will have a disproportionate effect on large trees, resulting in a larger feedback to climate change than would occur if all tree size classes were equally affected by drought.

On the quirks of maximum parsimony and likelihood on phylogenetic networks.

PubMed

Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles

2017-03-21

Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relationship of Climatic and Forest Factors to Drought- and Heat-Induced Tree Mortality

PubMed Central

Zhang, Qingyin; Shao, Ming’an; Jia, Xiaoxu; Wei, Xiaorong

2017-01-01

Tree mortality due to warming and drought is a critical aspect of forest ecosystem in responding to climate change. Spatial patterns of tree mortality induced by drought and its influencing factors, however, have yet to be documented at the global scale. We collected observations from 248 sites globally where trees have died due to drought and then assessed the effects of climatic and forest factors on the rate of tree mortality. The global mean annual mortality rate was 5.5%. The rate of tree mortality was significantly and negatively correlated with mean annual precipitation (P < 0.01). Tree mortality was lowest in tropical rainforests with mean annual precipitation >2000 mm and was severe in regions with mean annual precipitation <1000 mm. Mortality rates varied amongst species. The global annual rate of mortality was much higher for gymnosperms (7.1%) than angiosperms (4.8%) but did not differ significantly between evergreen (6.2%) and deciduous (6.1%) species. Stand age and wood density affected the mortality rate. Saplings (4.6%) had a higher mortality rate than mature trees (3.2%), and mortality rates significantly decreased with increasing wood density for all species (P < 0.01). We therefore concluded that the tree mortality around the globe varied with climatic and forest factors. The differences between tree species, wood density, stand density, and stand age should be considered when evaluating tree mortality at a large spatial scale during future climatic extremes. PMID:28095437

Relationship of Climatic and Forest Factors to Drought- and Heat-Induced Tree Mortality.

PubMed

Zhang, Qingyin; Shao, Ming'an; Jia, Xiaoxu; Wei, Xiaorong

2017-01-01

Tree mortality due to warming and drought is a critical aspect of forest ecosystem in responding to climate change. Spatial patterns of tree mortality induced by drought and its influencing factors, however, have yet to be documented at the global scale. We collected observations from 248 sites globally where trees have died due to drought and then assessed the effects of climatic and forest factors on the rate of tree mortality. The global mean annual mortality rate was 5.5%. The rate of tree mortality was significantly and negatively correlated with mean annual precipitation (P < 0.01). Tree mortality was lowest in tropical rainforests with mean annual precipitation >2000 mm and was severe in regions with mean annual precipitation <1000 mm. Mortality rates varied amongst species. The global annual rate of mortality was much higher for gymnosperms (7.1%) than angiosperms (4.8%) but did not differ significantly between evergreen (6.2%) and deciduous (6.1%) species. Stand age and wood density affected the mortality rate. Saplings (4.6%) had a higher mortality rate than mature trees (3.2%), and mortality rates significantly decreased with increasing wood density for all species (P < 0.01). We therefore concluded that the tree mortality around the globe varied with climatic and forest factors. The differences between tree species, wood density, stand density, and stand age should be considered when evaluating tree mortality at a large spatial scale during future climatic extremes.

Mobility based multicast routing in wireless mesh networks

NASA Astrophysics Data System (ADS)

Jain, Sanjeev; Tripathi, Vijay S.; Tiwari, Sudarshan

2013-01-01

There exist two fundamental approaches to multicast routing namely minimum cost trees and shortest path trees. The (MCT's) minimum cost tree is one which connects receiver and sources by providing a minimum number of transmissions (MNTs) the MNTs approach is generally used for energy constraint sensor and mobile ad hoc networks. In this paper we have considered node mobility and try to find out simulation based comparison of the (SPT's) shortest path tree, (MST's) minimum steiner trees and minimum number of transmission trees in wireless mesh networks by using the performance metrics like as an end to end delay, average jitter, throughput and packet delivery ratio, average unicast packet delivery ratio, etc. We have also evaluated multicast performance in the small and large wireless mesh networks. In case of multicast performance in the small networks we have found that when the traffic load is moderate or high the SPTs outperform the MSTs and MNTs in all cases. The SPTs have lowest end to end delay and average jitter in almost all cases. In case of multicast performance in the large network we have seen that the MSTs provide minimum total edge cost and minimum number of transmissions. We have also found that the one drawback of SPTs, when the group size is large and rate of multicast sending is high SPTs causes more packet losses to other flows as MCTs.

A new algorithm to construct phylogenetic networks from trees.

PubMed

Wang, J

2014-03-06

Developing appropriate methods for constructing phylogenetic networks from tree sets is an important problem, and much research is currently being undertaken in this area. BIMLR is an algorithm that constructs phylogenetic networks from tree sets. The algorithm can construct a much simpler network than other available methods. Here, we introduce an improved version of the BIMLR algorithm, QuickCass. QuickCass changes the selection strategy of the labels of leaves below the reticulate nodes, i.e., the nodes with an indegree of at least 2 in BIMLR. We show that QuickCass can construct simpler phylogenetic networks than BIMLR. Furthermore, we show that QuickCass is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary.

From trees to forest: relational complexity network and workload of air traffic controllers.

PubMed

Zhang, Jingyu; Yang, Jiazhong; Wu, Changxu

2015-01-01

In this paper, we propose a relational complexity (RC) network framework based on RC metric and network theory to model controllers' workload in conflict detection and resolution. We suggest that, at the sector level, air traffic showing a centralised network pattern can provide cognitive benefits in visual search and resolution decision which will in turn result in lower workload. We found that the network centralisation index can account for more variance in predicting perceived workload and task completion time in both a static conflict detection task (Study 1) and a dynamic one (Study 2) in addition to other aircraft-level and pair-level factors. This finding suggests that linear combination of aircraft-level or dyad-level information may not be adequate and the global-pattern-based index is necessary. Theoretical and practical implications of using this framework to improve future workload modelling and management are discussed. We propose a RC network framework to model the workload of air traffic controllers. The effect of network centralisation was examined in both a static conflict detection task and a dynamic one. Network centralisation was predictive of perceived workload and task completion time over and above other control variables.

From Google Maps to a fine-grained catalog of street trees

NASA Astrophysics Data System (ADS)

Branson, Steve; Wegner, Jan Dirk; Hall, David; Lang, Nico; Schindler, Konrad; Perona, Pietro

2018-01-01

Up-to-date catalogs of the urban tree population are of importance for municipalities to monitor and improve quality of life in cities. Despite much research on automation of tree mapping, mainly relying on dedicated airborne LiDAR or hyperspectral campaigns, tree detection and species recognition is still mostly done manually in practice. We present a fully automated tree detection and species recognition pipeline that can process thousands of trees within a few hours using publicly available aerial and street view images of Google MapsTM. These data provide rich information from different viewpoints and at different scales from global tree shapes to bark textures. Our work-flow is built around a supervised classification that automatically learns the most discriminative features from thousands of trees and corresponding, publicly available tree inventory data. In addition, we introduce a change tracker that recognizes changes of individual trees at city-scale, which is essential to keep an urban tree inventory up-to-date. The system takes street-level images of the same tree location at two different times and classifies the type of change (e.g., tree has been removed). Drawing on recent advances in computer vision and machine learning, we apply convolutional neural networks (CNN) for all classification tasks. We propose the following pipeline: download all available panoramas and overhead images of an area of interest, detect trees per image and combine multi-view detections in a probabilistic framework, adding prior knowledge; recognize fine-grained species of detected trees. In a later, separate module, track trees over time, detect significant changes and classify the type of change. We believe this is the first work to exploit publicly available image data for city-scale street tree detection, species recognition and change tracking, exhaustively over several square kilometers, respectively many thousands of trees. Experiments in the city of Pasadena, California, USA show that we can detect >70% of the street trees, assign correct species to >80% for 40 different species, and correctly detect and classify changes in >90% of the cases.

Eigenvalues of normalized Laplacian matrices of fractal trees and dendrimers: Analytical results and applications

NASA Astrophysics Data System (ADS)

Julaiti, Alafate; Wu, Bin; Zhang, Zhongzhi

2013-05-01

The eigenvalues of the normalized Laplacian matrix of a network play an important role in its structural and dynamical aspects associated with the network. In this paper, we study the spectra and their applications of normalized Laplacian matrices of a family of fractal trees and dendrimers modeled by Cayley trees, both of which are built in an iterative way. For the fractal trees, we apply the spectral decimation approach to determine analytically all the eigenvalues and their corresponding multiplicities, with the eigenvalues provided by a recursive relation governing the eigenvalues of networks at two successive generations. For Cayley trees, we show that all their eigenvalues can be obtained by computing the roots of several small-degree polynomials defined recursively. By using the relation between normalized Laplacian spectra and eigentime identity, we derive the explicit solution to the eigentime identity for random walks on the two treelike networks, the leading scalings of which follow quite different behaviors. In addition, we corroborate the obtained eigenvalues and their degeneracies through the link between them and the number of spanning trees.

Sapfluxnet: a global database of sap flow measurements to unravel the ecological factors of transpiration regulation in woody plants

NASA Astrophysics Data System (ADS)

Poyatos, Rafael; Martínez-Vilalta, Jordi; Molowny-Horas, Roberto; Steppe, Kathy; Oren, Ram; Katul, Gabriel; Mahecha, Miguel

2016-04-01

Plant transpiration is one of the main components of the global water cycle, it controls land energy balance, determines catchment hydrological responses and exerts strong feedbacks on regional and global climate. At the same time, plant productivity, growth and survival are severely constrained by water availability, which is expected to decline in many areas of the world because of global-change driven increases in drought conditions. While global surveys of drought tolerance traits at the organ level are rapidly increasing our knowledge of the diversity in plant functional strategies to cope with drought stress, a whole-plant perspective of drought vulnerability is still lacking. Sap flow measurements using thermal methods have now been applied to measure seasonal patterns in water use and the response of transpiration to environmental drivers across hundreds of species of woody plants worldwide, covering a wide range of climates, soils and stand structural characteristics. Here, we present the first effort to build a global database of sub-daily, tree-level sap flow (SAPFLUXNET) that will be used to improve our understanding of physiological and structural determinants of plant transpiration and to further investigate the role of vegetation in controlling global water balance. We already have the expression of interest of data contributors representing >115 globally distributed sites, > 185 species and > 700 trees, measured over at least one growing season. However, the potential number of available sites and species is probably much higher given that > 2500 sap flow-related papers have been identified in a Scopus literature search conducted in November 2015. We will give an overview of how data collection, harmonisation and quality control procedures are implemented within the project. We will also discuss potential analytical strategies to synthesize hydroclimatic controls on sap flow into biologically meaningful traits related to whole-plant transpiration regulation and hydraulic status. SAPFLUXNET will lead to the first comprehensive study of the ecological drivers of tree-level transpiration across the globe and will aid to constrain the empirical upscaling between plant traits and ecosystem function. Finally, we anticipate that, once SAPFLUXNET is populated with sufficient observations, it will complement existing ecological networks like FLUXNET and it will also contribute to the evaluation of Earth-system models.

Spread of risk across financial markets: better to invest in the peripheries

NASA Astrophysics Data System (ADS)

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-04-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network.

Spread of risk across financial markets: better to invest in the peripheries

PubMed Central

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-01-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network. PMID:23588852

Modelling of information diffusion on social networks with applications to WeChat

NASA Astrophysics Data System (ADS)

Liu, Liang; Qu, Bo; Chen, Bin; Hanjalic, Alan; Wang, Huijuan

2018-04-01

Traces of user activities recorded in online social networks open new possibilities to systematically understand the information diffusion process on social networks. From the online social network WeChat, we collected a large number of information cascade trees, each of which tells the spreading trajectory of a message/information such as which user creates the information and which users view or forward the information shared by which neighbours. In this work, we propose two heterogeneous non-linear models, one for the topologies of the information cascade trees and the other for the stochastic process of information diffusion on a social network. Both models are validated by the WeChat data in reproducing and explaining key features of cascade trees. Specifically, we apply the Random Recursive Tree (RRT) to model the growth of cascade trees. The RRT model could capture key features, i.e. the average path length and degree variance of a cascade tree in relation to the number of nodes (size) of the tree. Its single identified parameter quantifies the relative depth or broadness of the cascade trees and indicates that information propagates via a star-like broadcasting or viral-like hop by hop spreading. The RRT model explains the appearance of hubs, thus a possibly smaller average path length as the cascade size increases, as observed in WeChat. We further propose the stochastic Susceptible View Forward Removed (SVFR) model to depict the dynamic user behaviour including creating, viewing, forwarding and ignoring a message on a given social network. Beside the average path length and degree variance of the cascade trees in relation to their sizes, the SVFR model could further explain the power-law cascade size distribution in WeChat and unravel that a user with a large number of friends may actually have a smaller probability to read a message (s)he receives due to limited attention.

Global Genome Biodiversity Network: saving a blueprint of the Tree of Life – a botanical perspective

PubMed Central

Seberg, O.; Droege, G.; Barker, K.; Coddington, J. A.; Funk, V.; Gostel, M.; Petersen, G.; Smith, P. P.

2016-01-01

Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies. Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera. PMID:27328683

Observations and analysis of self-similar branching topology in glacier networks

USGS Publications Warehouse

Bahr, D.B.; Peckham, S.D.

1996-01-01

Glaciers, like rivers, have a branching structure which can be characterized by topological trees or networks. Probability distributions of various topological quantities in the networks are shown to satisfy the criterion for self-similarity, a symmetry structure which might be used to simplify future models of glacier dynamics. Two analytical methods of describing river networks, Shreve's random topology model and deterministic self-similar trees, are applied to the six glaciers of south central Alaska studied in this analysis. Self-similar trees capture the topological behavior observed for all of the glaciers, and most of the networks are also reasonably approximated by Shreve's theory. Copyright 1996 by the American Geophysical Union.

Understanding the Scalability of Bayesian Network Inference Using Clique Tree Growth Curves

NASA Technical Reports Server (NTRS)

Mengshoel, Ole J.

2010-01-01

One of the main approaches to performing computation in Bayesian networks (BNs) is clique tree clustering and propagation. The clique tree approach consists of propagation in a clique tree compiled from a Bayesian network, and while it was introduced in the 1980s, there is still a lack of understanding of how clique tree computation time depends on variations in BN size and structure. In this article, we improve this understanding by developing an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN s non-root nodes to the number of root nodes, and (ii) the expected number of moral edges in their moral graphs. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for the total size of each set. For the special case of bipartite BNs, there are two sets and two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, where random bipartite BNs generated using the BPART algorithm are studied, we systematically increase the out-degree of the root nodes in bipartite Bayesian networks, by increasing the number of leaf nodes. Surprisingly, root clique growth is well-approximated by Gompertz growth curves, an S-shaped family of curves that has previously been used to describe growth processes in biology, medicine, and neuroscience. We believe that this research improves the understanding of the scaling behavior of clique tree clustering for a certain class of Bayesian networks; presents an aid for trade-off studies of clique tree clustering using growth curves; and ultimately provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms.

Dynamics of investor spanning trees around dot-com bubble.

PubMed

Ranganathan, Sindhuja; Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles.

Dynamics of investor spanning trees around dot-com bubble

PubMed Central

Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles. PMID:29897973

Satellite assessment of increasing tree cover 1982-2016

NASA Astrophysics Data System (ADS)

Song, X. P.; Hansen, M.

2017-12-01

The Earth's vegetation has undergone dramatic changes as we enter the Anthropocene. Recent studies have quantified global forest cover dynamics and resulting biogeochemical and biophysical impacts to the climate for the post-2000 time period. However, long-term gradual changes in undisturbed forests are less well quantified. We mapped annual tree cover using satellite data and quantified tree cover change during 1982-2016. The dataset was produced by combining optical observations from multiple satellite sensors, including the Advanced Very High Resolution Radiometer, the Moderate Resolution Imaging Spectroradiometer, the Landsat Enhanced Thematic Mapper Plus and various very high spatial resolution sensors. Contrary to current understanding of forest area change, global tree cover increased by 7%. The overall net gain in tree cover is a result of net loss in the tropics overweighed by net gain in the subtropical, temperate and boreal zones. All mountain systems, regardless of climate domain, experienced increases in tree cover. Regional patterns of tree cover gain including eastern United States, eastern Europe and southern China, indicate profound influences of socioeconomic, political or land management changes in shaping long-term environmental change. Results provide the first comprehensive record of global tree cover dynamics over the past four decades and may be used to reduce uncertainties in the quantification of the global carbon cycle.

Investigation of decadal-scale divergence in tree-ring density chronologies

NASA Astrophysics Data System (ADS)

Vaccaro, A.; Emile-Geay, J.; Anchukaitis, K. J.; Wang, J.

2013-12-01

Tree-ring data from certain forest sites at northern circumpolar latitudes and from some at higher elevation show an anomalous decrease in temperature-sensitivity of tree growth starting in the mid-20th century. This phenomenon, known as the ';divergence problem' (DP), leads to tree-ring reconstructions that underestimate the warming trend exhibited by instrumental measurements over recent decades (e.g. D'Arrigo et al. 2008). In a study conducted in 1998, Briffa et al. discovered a type of divergence wherein latewood density (MXD) chronologies from an early manifestation of the Schweingruber tree-ring dataset showed strong interannual correlation to summer temperature measurements, but increasing divergence between the decadal-scale trends of the tree-rings and temperature records during the second half of the 20th century. This low-frequency divergence suggests that although tree-rings may accurately trace year-to-year changes in temperature, they might not capture longer-term warming trends, making them unsuitable for reconstructions of long-term climate variations. There is reason to believe, however, that the divergence found by Briffa (1998) is at least partly due to detrending or related statistical issues (Esper et al. 2009). Herein, we will investigate the distribution of this decadal-scale ';Briffa-style' divergence to see if it is confined to the earlier chronologies in the Schweingruber dataset or if it is persistent throughout more recent tree-ring data as well. Following the methodology of previous DP investigations (e.g. Briffa et al. 1998), we will draw comparisons between a network of MXD data and instrumental temperature records over an early period (1850-1960) and a recent period (1961-2000) to detect decadal-scale divergence in recent decades. We will apply the Mann et al. 2009 (M09) style of RegEM reconstruction to the M09 dataset, with and without controlling for divergence, and also to a new tree-ring database assembled using strict, objective criteria, including most of the updated Schweingruber network. Other climate field reconstruction (CFR) methods as described by Wang et al. (2013) will be used on our new tree-ring network to check for robustness. The tree-ring data will be independently compared to instrumental temperature series derived from the GHCN-monthly, HadCRUT4, and the M09 infilled HadCRUT3v temperature datasets for cross-validation. Implications for large-scale temperature reconstructions of the Common Era will be discussed. Briffa, K.R., F. H. Schweingruber, P.D. Jones, T.J. Osborn, S.G. Shiyatov, and E.A. Vaganov (1998),Reduced sensitivity of recent tree-growth to temperature at high northern latitudes, Nature, 391, 678-682. D'Arrigo, R., R. Wilson, B. Liepert, and P. Cherubini (2008), On the ';Divergence Problem' in Northern Forests: A review of the tree-ring evidence and possible causes, GAPC, 60, 289-305. Esper, J. and D. Frank (2009), Divergence pitfalls in tree-ring research, Climate Change, 94, 261-266. Mann, M.E., Z. Zhang, M.K. Hughes, R.S. Bradley, S.K. Miller, S. Rutherford, and F. Ni (2009), Proxy-based reconstructions of hemispheric and global surface temperature variations over the past two millennia, PNAS, 105 (36) 13252-13257. Wang, J., J. Emile-Geay, D. Guillot, and J. E. Smerdon (2013), Evaluating climate field reconstruction techniques using improved emulations of real-world conditions. CPD, 9, 3015-3060.

Analysis of the effect of evergreen and deciduous trees on urban nitrogen dioxide levels in the U.S. using land-use regression

NASA Astrophysics Data System (ADS)

Rao, M.; George, L. A.

2012-12-01

Nitrogen dioxide (NO2), an atmospheric pollutant generated primarily by anthropogenic combustion processes, is typically found at higher concentrations in urban areas compared to non-urbanized environments. Elevated NO2 levels have multiple ecosystem effects at different spatial scales. At the local scale, elevated levels affect human health directly and through the formation of secondary pollutants such as ozone and aerosols; at the regional scale secondary pollutants such as nitric acid and organic nitrates have deleterious effects on non-urbanized areas; and, at the global scale, nitrogen oxide emissions significantly alter the natural biogeochemical nitrogen cycle. As cities globally become larger and larger sources of nitrogen oxide emissions, it is important to assess possible mitigation strategies to reduce the impact of emissions locally, regionally and globally. In this study, we build a national land-use regression (LUR) model to compare the impacts of deciduous and evergreen trees on urban NO2 levels in the United States. We use the EPA monitoring network values of NO2 levels for 2006, the 2006 NLCD tree canopy data for deciduous and evergreen canopies, and the US Census Bureau's TIGER shapefiles for roads, railroads, impervious area & population density as proxies for NO2 sources on-road traffic, railroad traffic, off-road and area sources respectively. Our preliminary LUR model corroborates previous LUR studies showing that the presence of trees is associated with reduced urban NO2 levels. Additionally, our model indicates that deciduous and evergreen trees reduce NO2 to different extents, and that the amount of NO2 reduced varies seasonally. The model indicates that every square kilometer of deciduous canopy within a 2km buffer is associated with a reduction in ambient NO2 levels of 0.64 ppb in summer and 0.46ppb in winter. Similarly, every square kilometer of evergreen tree canopy within a 2 km buffer is associated with a reduction in ambient NO2 by 0.53 ppb in summer and 0.84 ppb in winter. Thus, the model indicates that deciduous trees are associated with a 30% smaller reduction in NO2 in winter as compared to summer, while evergreens are associated with a 60% increase in the reduction of NO2 in winter, for every square kilometer of deciduous or evergreen canopy within a 2 km buffer. Leaf- and local canopy-level studies have shown that trees are a sink for urban NO2 through deposition as well as stomatal and cuticular uptake. The winter time versus summer time effects suggest that leaf-level deposition may not be the only uptake mechanism and points to the need for a more holistic analysis of tree and canopy-level deposition for urban air pollution models. Since deposition velocities for NO2 vary by tree species, the reduction may also vary by species. These findings have implications for designing cities to reduce the impact of air pollution.

MERIT DEM: A new high-accuracy global digital elevation model and its merit to global hydrodynamic modeling

NASA Astrophysics Data System (ADS)

Yamazaki, D.; Ikeshima, D.; Neal, J. C.; O'Loughlin, F.; Sampson, C. C.; Kanae, S.; Bates, P. D.

2017-12-01

Digital Elevation Models (DEM) are fundamental data for flood modelling. While precise airborne DEMs are available in developed regions, most parts of the world rely on spaceborne DEMs which include non-negligible height errors. Here we show the most accurate global DEM to date at 90m resolution by eliminating major error components from the SRTM and AW3D DEMs. Using multiple satellite data and multiple filtering techniques, we addressed absolute bias, stripe noise, speckle noise and tree height bias from spaceborne DEMs. After the error removal, significant improvements were found in flat regions where height errors were larger than topography variability, and landscapes features such as river networks and hill-valley structures became clearly represented. We found the topography slope of the previous DEMs was largely distorted in most of world major floodplains (e.g. Ganges, Nile, Niger, Mekong) and swamp forests (e.g. Amazon, Congo, Vasyugan). The developed DEM will largely reduce the uncertainty in both global and regional flood modelling.

Networks and Spanning Trees: The Juxtaposition of Prüfer and Boruvka

ERIC Educational Resources Information Center

Lodder, Jerry

2014-01-01

This paper outlines a method for teaching topics in undergraduate mathematics or computer science via historical curricular modules. The contents of one module, "Networks and Spanning Trees," are discussed from the original work of Arthur Cayley, Heinz Prüfer, and Otakar Boruvka that motivates the enumeration and application of trees in…

Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species.

PubMed

Magrach, Ainhoa; Senior, Rebecca A; Rogers, Andrew; Nurdin, Deddy; Benedick, Suzan; Laurance, William F; Santamaria, Luis; Edwards, David P

2016-03-16

Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the 'health' and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness, and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growing tree species, which could exacerbate the loss of timber value and carbon storage already associated with logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) were more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of 'extinction debt'. © 2016 The Author(s).

Selective logging in tropical forests decreases the robustness of liana–tree interaction networks to the loss of host tree species

PubMed Central

Magrach, Ainhoa; Senior, Rebecca A.; Rogers, Andrew; Nurdin, Deddy; Benedick, Suzan; Laurance, William F.; Santamaria, Luis; Edwards, David P.

2016-01-01

Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the ‘health’ and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness, and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growing tree species, which could exacerbate the loss of timber value and carbon storage already associated with logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana–tree interaction networks if heavily infested trees (i.e. the most connected ones) were more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of ‘extinction debt’. PMID:26936241

At the Crossroads: Does the Configuration of Roadside Vegetation Affect Woodland Bird Communities in Rural Landscapes?

PubMed Central

Hall, Mark; Nimmo, Dale; Bennett, Andrew F.

2016-01-01

In agricultural regions worldwide, linear networks of vegetation such as hedges, fencerows and live fences provide habitat for plant and animal species in heavily modified landscapes. In Australia, networks of remnant native vegetation along roadsides are a distinctive feature of many rural landscapes. Here, we investigated the richness and composition of woodland-dependent bird communities in networks of eucalypt woodland vegetation along roadsides, in an agricultural region in which >80% of native woodland and forest vegetation has been cleared. We stratified sites in a) cross sections and b) linear strips of roadside vegetation, to test the influence on woodland birds of site location and configuration in the linear network (the ‘intersection effect’). We also examined the influence of tree size at the site, the amount of wooded vegetation surrounding the site, and the abundance of an aggressive native species, the noisy miner Manorina melanocephala. Birds were surveyed at 26 pairs of sites (cross section or linear strip) on four occasions. A total of 66 species was recorded, including 35 woodland species. The richness of woodland bird species was influenced by site configuration, with more species present at cross sections, particularly those with larger trees (>30 cm diameter). However, the strongest influence on species richness was the relative abundance of the noisy miner. The richness of woodland birds at sites where noisy miners were abundant was ~20% of that where miners were absent. These results recognise the value of networks of roadside vegetation as habitat for woodland birds in depleted agricultural landscapes; but highlight that this value is not realised for much of this vast vegetation network because of the dominance of the noisy miner. Nevertheless, roadside vegetation is particularly important where the configuration of networks create nodes that facilitate movement. Globally, the protection, conservation and restoration of such linear networks has an important influence on the persistence of biota within human-dominated landscapes. PMID:27183227

At the Crossroads: Does the Configuration of Roadside Vegetation Affect Woodland Bird Communities in Rural Landscapes?

PubMed

Hall, Mark; Nimmo, Dale; Bennett, Andrew F

2016-01-01

In agricultural regions worldwide, linear networks of vegetation such as hedges, fencerows and live fences provide habitat for plant and animal species in heavily modified landscapes. In Australia, networks of remnant native vegetation along roadsides are a distinctive feature of many rural landscapes. Here, we investigated the richness and composition of woodland-dependent bird communities in networks of eucalypt woodland vegetation along roadsides, in an agricultural region in which >80% of native woodland and forest vegetation has been cleared. We stratified sites in a) cross sections and b) linear strips of roadside vegetation, to test the influence on woodland birds of site location and configuration in the linear network (the 'intersection effect'). We also examined the influence of tree size at the site, the amount of wooded vegetation surrounding the site, and the abundance of an aggressive native species, the noisy miner Manorina melanocephala. Birds were surveyed at 26 pairs of sites (cross section or linear strip) on four occasions. A total of 66 species was recorded, including 35 woodland species. The richness of woodland bird species was influenced by site configuration, with more species present at cross sections, particularly those with larger trees (>30 cm diameter). However, the strongest influence on species richness was the relative abundance of the noisy miner. The richness of woodland birds at sites where noisy miners were abundant was ~20% of that where miners were absent. These results recognise the value of networks of roadside vegetation as habitat for woodland birds in depleted agricultural landscapes; but highlight that this value is not realised for much of this vast vegetation network because of the dominance of the noisy miner. Nevertheless, roadside vegetation is particularly important where the configuration of networks create nodes that facilitate movement. Globally, the protection, conservation and restoration of such linear networks has an important influence on the persistence of biota within human-dominated landscapes.

Structure and evolution of a European Parliament via a network and correlation analysis

NASA Astrophysics Data System (ADS)

Puccio, Elena; Pajala, Antti; Piilo, Jyrki; Tumminello, Michele

2016-11-01

We present a study of the network of relationships among elected members of the Finnish parliament, based on a quantitative analysis of initiative co-signatures, and its evolution over 16 years. To understand the structure of the parliament, we constructed a statistically validated network of members, based on the similarity between the patterns of initiatives they signed. We looked for communities within the network and characterized them in terms of members' attributes, such as electoral district and party. To gain insight on the nested structure of communities, we constructed a hierarchical tree of members from the correlation matrix. Afterwards, we studied parliament dynamics yearly, with a focus on correlations within and between parties, by also distinguishing between government and opposition. Finally, we investigated the role played by specific individuals, at a local level. In particular, whether they act as proponents who gather consensus, or as signers. Our results provide a quantitative background to current theories in political science. From a methodological point of view, our network approach has proven able to highlight both local and global features of a complex social system.

Patterns of drought tolerance in major European temperate forest trees: climatic drivers and levels of variability.

PubMed

Zang, Christian; Hartl-Meier, Claudia; Dittmar, Christoph; Rothe, Andreas; Menzel, Annette

2014-12-01

The future performance of native tree species under climate change conditions is frequently discussed, since increasingly severe and more frequent drought events are expected to become a major risk for forest ecosystems. To improve our understanding of the drought tolerance of the three common European temperate forest tree species Norway spruce, silver fir and common beech, we tested the influence of climate and tree-specific traits on the inter and intrasite variability in drought responses of these species. Basal area increment data from a large tree-ring network in Southern Germany and Alpine Austria along a climatic cline from warm-dry to cool-wet conditions were used to calculate indices of tolerance to drought events and their variability at the level of individual trees and populations. General patterns of tolerance indicated a high vulnerability of Norway spruce in comparison to fir and beech and a strong influence of bioclimatic conditions on drought response for all species. On the level of individual trees, low-growth rates prior to drought events, high competitive status and low age favored resilience in growth response to drought. Consequently, drought events led to heterogeneous and variable response patterns in forests stands. These findings may support the idea of deliberately using spontaneous selection and adaption effects as a passive strategy of forest management under climate change conditions, especially a strong directional selection for more tolerant individuals when frequency and intensity of summer droughts will increase in the course of global climate change. © 2014 John Wiley & Sons Ltd.

Seasonality, diaspore traits and the structure of plant-frugivore networks in Neotropical savanna forest

NASA Astrophysics Data System (ADS)

Darosci, Adriano Antonio Brito; Bruna, Emilio M.; Motta-Junior, José Carlos; Ferreira, Cristiane da Silva; Blake, John Gilman; Munhoz, Cássia Beatriz Rodrigues

2017-10-01

Complex frugivory networks are common in heterogeneous environments, but how the structure of those networks varies due to seasonality and other environmental factors remains unclear. For example, seasonal variation in rainfall can influence fruit production and diaspore characteristics, which could alter the quantity and quality of resources available to different animals in the network and, hence, network structure. We investigated how a frugivory network varied seasonally in Brazilian savanna (Cerrado), where there are well-defined dry and wet seasons and fructification mainly during the rainy season for most tree species. We recorded fruit consumption by animals during the dry and wet seasons in two different gallery forests and used these data to test the hypotheses that connectance, links per species and nestedness would be higher in the dry season than rainy season due to low available food in the former that would be consumed by various species of frugivores. Concomitantly, we also measured seed width and lipid content from diaspores of the fruiting trees to determine if these characteristics influenced interaction properties between fruiting trees and frugivores. Among the measured network parameters, connectance, links per species and specialization varied between seasons in one site but not in the other, indicating that seasonal variation in networks is not necessarily consistent over time or space. The number of tree species with small diaspores with high lipid content differed between seasons, and those characteristics were key factors increasing the interaction parameter of fruiting trees. We suggest that network stability between seasons may be related to local frugivore diversity, resource availability, and fruit quality.

TreeMAC: Localized TDMA MAC protocol for real-time high-data-rate sensor networks

USGS Publications Warehouse

Song, W.-Z.; Huang, R.; Shirazi, B.; LaHusen, R.

2009-01-01

Earlier sensor network MAC protocols focus on energy conservation in low-duty cycle applications, while some recent applications involve real-time high-data-rate signals. This motivates us to design an innovative localized TDMA MAC protocol to achieve high throughput and low congestion in data collection sensor networks, besides energy conservation. TreeMAC divides a time cycle into frames and each frame into slots. A parent node determines the children's frame assignment based on their relative bandwidth demand, and each node calculates its own slot assignment based on its hop-count to the sink. This innovative 2-dimensional frame-slot assignment algorithm has the following nice theory properties. First, given any node, at any time slot, there is at most one active sender in its neighborhood (including itself). Second, the packet scheduling with TreeMAC is bufferless, which therefore minimizes the probability of network congestion. Third, the data throughput to the gateway is at least 1/3 of the optimum assuming reliable links. Our experiments on a 24-node testbed show that TreeMAC protocol significantly improves network throughput, fairness, and energy efficiency compared to TinyOS's default CSMA MAC protocol and a recent TDMA MAC protocol Funneling-MAC. Partial results of this paper were published in Song, Huang, Shirazi and Lahusen [W.-Z. Song, R. Huang, B. Shirazi, and R. Lahusen, TreeMAC: Localized TDMA MAC protocol for high-throughput and fairness in sensor networks, in: The 7th Annual IEEE International Conference on Pervasive Computing and Communications, PerCom, March 2009]. Our new contributions include analyses of the performance of TreeMAC from various aspects. We also present more implementation detail and evaluate TreeMAC from other aspects. ?? 2009 Elsevier B.V.

Deriving global parameter estimates for the Noah land surface model using FLUXNET and machine learning

NASA Astrophysics Data System (ADS)

Chaney, Nathaniel W.; Herman, Jonathan D.; Ek, Michael B.; Wood, Eric F.

2016-11-01

With their origins in numerical weather prediction and climate modeling, land surface models aim to accurately partition the surface energy balance. An overlooked challenge in these schemes is the role of model parameter uncertainty, particularly at unmonitored sites. This study provides global parameter estimates for the Noah land surface model using 85 eddy covariance sites in the global FLUXNET network. The at-site parameters are first calibrated using a Latin Hypercube-based ensemble of the most sensitive parameters, determined by the Sobol method, to be the minimum stomatal resistance (rs,min), the Zilitinkevich empirical constant (Czil), and the bare soil evaporation exponent (fxexp). Calibration leads to an increase in the mean Kling-Gupta Efficiency performance metric from 0.54 to 0.71. These calibrated parameter sets are then related to local environmental characteristics using the Extra-Trees machine learning algorithm. The fitted Extra-Trees model is used to map the optimal parameter sets over the globe at a 5 km spatial resolution. The leave-one-out cross validation of the mapped parameters using the Noah land surface model suggests that there is the potential to skillfully relate calibrated model parameter sets to local environmental characteristics. The results demonstrate the potential to use FLUXNET to tune the parameterizations of surface fluxes in land surface models and to provide improved parameter estimates over the globe.

Distributed Events in Sentinel: Design and Implementation of a Global Event Detector

DTIC Science & Technology

1999-01-01

local event detector and a global event detector to detect events. Global event detector in this case plays the role of a message sending/receiving than...significant in this case . The system performance will decrease with increase in the number of applications involved in global event detection. Yet from a...Figure 8: A Global event tree (2) 1. Global composite event is detected at the GED In this case , the whole global composite event tree is sent to the

Tanglegrams for rooted phylogenetic trees and networks

PubMed Central

Scornavacca, Celine; Zickmann, Franziska; Huson, Daniel H.

2011-01-01

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de PMID:21685078

Real-time monitoring and fault locating using amplified spontaneous emission noise reflection for tree-structured Ethernet passive optical networks

NASA Astrophysics Data System (ADS)

Naim, Nani Fadzlina; Ab-Rahman, Mohammad Syuhaimi; Kamaruddin, Nur Hasiba; Bakar, Ahmad Ashrif A.

2013-09-01

Nowadays, optical networks are becoming dense while detecting faulty branches in the tree-structured networks has become problematic. Conventional methods are inconvenient as they require an engineer to visit the failure site to check the optical fiber using an optical time-domain reflectometer. An innovative monitoring technique for tree-structured network topology in Ethernet passive optical networks (EPONs) by using the erbium-doped fiber amplifier to amplify the traffic signal is demonstrated, and in the meantime, a residual amplified spontaneous emission spectrum is used as the input signal to monitor the optical cable from the central office. Fiber Bragg gratings with distinct center wavelengths are employed to reflect the monitoring signals. Faulty branches of the tree-structured EPONs can be identified using a simple and low-cost receiver. We will show that this technique is capable of providing monitoring range up to 32 optical network units using a power meter with a sensitivity of -65 dBm while maintaining the bit error rate of 10-13.

A 280-Year Long Series of Phenological Observations of Cherry Tree Blossoming Dates for Switzerland

NASA Astrophysics Data System (ADS)

Rutishauser, T.; Luterbacher, J.; Wanner, H.

2003-04-01

Phenology is generally described as the timing of life cycle phases or activities of plants and animals in their temporal occurrence throughout the year (Lieth 1974). Recent studies have shown that meteorological and climatological impacts leave their 'fingerprints' across natural systems in general and strongly influence the seasonal activities of single animal and plant species. During the 20th century, phenological observation networks have been established around the world to document and analyze the influence of the globally changing climate to plants and wildlife. This work presents a first attempt of a unique 280-year long series of phenological observations of cherry tree blossoming dates for the Swiss plateau region. In Switzerland, a nation-wide phenological observation network has been established in 1951 currently documenting 69 phenophases of 26 different plant species. A guidebook seeks to increase objectiveness in the network observations. The observations of the blooming of the cherry tree (prunus avium) were chosen to calculate a mean series for the Swiss plateau region with observations from altitudes ranging between 370 and 860 asl. A total number of 737 observations from 21 stations were used. A linear regression was established between the mean blooming date and altitude in order to correct the data to a reference altitude level. Other ecological parameters were unaccounted for. The selected network data series from 1951 to 2000 was combined and prolonged with observations from various sources back to 1721. These include several historical observation series by farmers, clergymen and teachers, data from various stations collected at the newly established Swiss meteorological network from 1864 to 1873 and the single long series of observations from Liestal starting in 1894. The homogenized time series of observations will be compared with reconstructions of late winter temperatures as well as statistical estimations of blooming time based on long instrumental data from Europe. In addition, the series is one of the few historical phenological records to assess past climate and ecological changes. Lieth, H. (1974). Phenology and Seasonality Modeling. Berlin, Heidelberg, New York, Springer.

The BlueGene/L supercomputer

NASA Astrophysics Data System (ADS)

Bhanota, Gyan; Chen, Dong; Gara, Alan; Vranas, Pavlos

2003-05-01

The architecture of the BlueGene/L massively parallel supercomputer is described. Each computing node consists of a single compute ASIC plus 256 MB of external memory. The compute ASIC integrates two 700 MHz PowerPC 440 integer CPU cores, two 2.8 Gflops floating point units, 4 MB of embedded DRAM as cache, a memory controller for external memory, six 1.4 Gbit/s bi-directional ports for a 3-dimensional torus network connection, three 2.8 Gbit/s bi-directional ports for connecting to a global tree network and a Gigabit Ethernet for I/O. 65,536 of such nodes are connected into a 3-d torus with a geometry of 32×32×64. The total peak performance of the system is 360 Teraflops and the total amount of memory is 16 TeraBytes.

A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests

USGS Publications Warehouse

Allen, Craig D.; Macalady, A.K.; Chenchouni, H.; Bachelet, D.; McDowell, N.; Vennetier, Michel; Kitzberger, T.; Rigling, A.; Breshears, D.D.; Hogg, E.H.(T.); Gonzalez, P.; Fensham, R.; Zhang, Z.; Castro, J.; Demidova, N.; Lim, J.-H.; Allard, G.; Running, S.W.; Semerci, A.; Cobb, N.

2010-01-01

Greenhouse gas emissions have significantly altered global climate, and will continue to do so in the future. Increases in the frequency, duration, and/or severity of drought and heat stress associated with climate change could fundamentally alter the composition, structure, and biogeography of forests in many regions. Of particular concern are potential increases in tree mortality associated with climate-induced physiological stress and interactions with other climate-mediated processes such as insect outbreaks and wildfire. Despite this risk, existing projections of tree mortality are based on models that lack functionally realistic mortality mechanisms, and there has been no attempt to track observations of climate-driven tree mortality globally. Here we present the first global assessment of recent tree mortality attributed to drought and heat stress. Although episodic mortality occurs in the absence of climate change, studies compiled here suggest that at least some of the world's forested ecosystems already may be responding to climate change and raise concern that forests may become increasingly vulnerable to higher background tree mortality rates and die-off in response to future warming and drought, even in environments that are not normally considered water-limited. This further suggests risks to ecosystem services, including the loss of sequestered forest carbon and associated atmospheric feedbacks. Our review also identifies key information gaps and scientific uncertainties that currently hinder our ability to predict tree mortality in response to climate change and emphasizes the need for a globally coordinated observation system. Overall, our review reveals the potential for amplified tree mortality due to drought and heat in forests worldwide.

Drought impact on forest carbon dynamics and fluxes in Amazonia.

PubMed

Doughty, Christopher E; Metcalfe, D B; Girardin, C A J; Amézquita, F Farfán; Cabrera, D Galiano; Huasco, W Huaraca; Silva-Espejo, J E; Araujo-Murakami, A; da Costa, M C; Rocha, W; Feldpausch, T R; Mendoza, A L M; da Costa, A C L; Meir, P; Phillips, O L; Malhi, Y

2015-03-05

In 2005 and 2010 the Amazon basin experienced two strong droughts, driven by shifts in the tropical hydrological regime possibly associated with global climate change, as predicted by some global models. Tree mortality increased after the 2005 drought, and regional atmospheric inversion modelling showed basin-wide decreases in CO2 uptake in 2010 compared with 2011 (ref. 5). But the response of tropical forest carbon cycling to these droughts is not fully understood and there has been no detailed multi-site investigation in situ. Here we use several years of data from a network of thirteen 1-ha forest plots spread throughout South America, where each component of net primary production (NPP), autotrophic respiration and heterotrophic respiration is measured separately, to develop a better mechanistic understanding of the impact of the 2010 drought on the Amazon forest. We find that total NPP remained constant throughout the drought. However, towards the end of the drought, autotrophic respiration, especially in roots and stems, declined significantly compared with measurements in 2009 made in the absence of drought, with extended decreases in autotrophic respiration in the three driest plots. In the year after the drought, total NPP remained constant but the allocation of carbon shifted towards canopy NPP and away from fine-root NPP. Both leaf-level and plot-level measurements indicate that severe drought suppresses photosynthesis. Scaling these measurements to the entire Amazon basin with rainfall data, we estimate that drought suppressed Amazon-wide photosynthesis in 2010 by 0.38 petagrams of carbon (0.23-0.53 petagrams of carbon). Overall, we find that during this drought, instead of reducing total NPP, trees prioritized growth by reducing autotrophic respiration that was unrelated to growth. This suggests that trees decrease investment in tissue maintenance and defence, in line with eco-evolutionary theories that trees are competitively disadvantaged in the absence of growth. We propose that weakened maintenance and defence investment may, in turn, cause the increase in post-drought tree mortality observed at our plots.

Using minimal spanning trees to compare the reliability of network topologies

NASA Technical Reports Server (NTRS)

Leister, Karen J.; White, Allan L.; Hayhurst, Kelly J.

1990-01-01

Graph theoretic methods are applied to compute the reliability for several types of networks of moderate size. The graph theory methods used are minimal spanning trees for networks with bi-directional links and the related concept of strongly connected directed graphs for networks with uni-directional links. A comparison is conducted of ring networks and braided networks. The case is covered where just the links fail and the case where both links and nodes fail. Two different failure modes for the links are considered. For one failure mode, the link no longer carries messages. For the other failure mode, the link delivers incorrect messages. There is a description and comparison of link-redundancy versus path-redundancy as methods to achieve reliability. All the computations are carried out by means of a fault tree program.

Hierarchical auto-configuration addressing in mobile ad hoc networks (HAAM)

NASA Astrophysics Data System (ADS)

Ram Srikumar, P.; Sumathy, S.

2017-11-01

Addressing plays a vital role in networking to identify devices uniquely. A device must be assigned with a unique address in order to participate in the data communication in any network. Different protocols defining different types of addressing are proposed in literature. Address auto-configuration is a key requirement for self organizing networks. Existing auto-configuration based addressing protocols require broadcasting probes to all the nodes in the network before assigning a proper address to a new node. This needs further broadcasts to reflect the status of the acquired address in the network. Such methods incur high communication overheads due to repetitive flooding. To address this overhead, a new partially stateful address allocation scheme, namely Hierarchical Auto-configuration Addressing (HAAM) scheme is extended and proposed. Hierarchical addressing basically reduces latency and overhead caused during address configuration. Partially stateful addressing algorithm assigns addresses without the need for flooding and global state awareness, which in turn reduces the communication overhead and space complexity respectively. Nodes are assigned addresses hierarchically to maintain the graph of the network as a spanning tree which helps in effectively avoiding the broadcast storm problem. Proposed algorithm for HAAM handles network splits and merges efficiently in large scale mobile ad hoc networks incurring low communication overheads.

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Fostering Global Citizenship--Tree Planting as a Connective Practice

ERIC Educational Resources Information Center

Haigh, Martin

2016-01-01

Education for Global Citizenship is about living as though the future mattered. This evaluates learner reactions to a tree-planting exercise that invites reflection upon hopes for the world, personal responsibilities and acting locally while thinking globally. Participant hopes concerned: environmental sustainability, peace on earth, then the…

Rearrangement moves on rooted phylogenetic networks

PubMed Central

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2017-01-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network—that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves—named rNNI and rSPR—reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results—separating the contributions of horizontal and vertical moves—we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for practical phylogenetic network reconstruction. PMID:28763439

Optimal fractal tree-like microchannel networks with slip for laminar-flow-modified Murray's law.

PubMed

Jing, Dalei; Song, Shiyu; Pan, Yunlu; Wang, Xiaoming

2018-01-01

The fractal tree-like branched network is an effective channel design structure to reduce the hydraulic resistance as compared with the conventional parallel channel network. In order for a laminar flow to achieve minimum hydraulic resistance, it is believed that the optimal fractal tree-like channel network obeys the well-accepted Murray's law of β m = N -1/3 (β m is the optimal diameter ratio between the daughter channel and the parent channel and N is the branching number at every level), which is obtained under the assumption of no-slip conditions at the channel wall-liquid interface. However, at the microscale, the no-slip condition is not always reasonable; the slip condition should indeed be considered at some solid-liquid interfaces for the optimal design of the fractal tree-like channel network. The present work reinvestigates Murray's law for laminar flow in a fractal tree-like microchannel network considering slip condition. It is found that the slip increases the complexity of the optimal design of the fractal tree-like microchannel network to achieve the minimum hydraulic resistance. The optimal diameter ratio to achieve minimum hydraulic resistance is not only dependent on the branching number, as stated by Murray's law, but also dependent on the slip length, the level number, the length ratio between the daughter channel and the parent channel, and the diameter of the channel. The optimal diameter ratio decreases with the increasing slip length, the increasing level number and the increasing length ratio between the daughter channel and the parent channel, and decreases with decreasing channel diameter. These complicated relations were found to become relaxed and simplified to Murray's law when the ratio between the slip length and the diameter of the channel is small enough.

Inference of Transmission Network Structure from HIV Phylogenetic Trees

DOE PAGES

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan; ...

2017-01-13

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Inference of Transmission Network Structure from HIV Phylogenetic Trees

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

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Development of Gis Tool for the Solution of Minimum Spanning Tree Problem using Prim's Algorithm

NASA Astrophysics Data System (ADS)

Dutta, S.; Patra, D.; Shankar, H.; Alok Verma, P.

2014-11-01

minimum spanning tree (MST) of a connected, undirected and weighted network is a tree of that network consisting of all its nodes and the sum of weights of all its edges is minimum among all such possible spanning trees of the same network. In this study, we have developed a new GIS tool using most commonly known rudimentary algorithm called Prim's algorithm to construct the minimum spanning tree of a connected, undirected and weighted road network. This algorithm is based on the weight (adjacency) matrix of a weighted network and helps to solve complex network MST problem easily, efficiently and effectively. The selection of the appropriate algorithm is very essential otherwise it will be very hard to get an optimal result. In case of Road Transportation Network, it is very essential to find the optimal results by considering all the necessary points based on cost factor (time or distance). This paper is based on solving the Minimum Spanning Tree (MST) problem of a road network by finding it's minimum span by considering all the important network junction point. GIS technology is usually used to solve the network related problems like the optimal path problem, travelling salesman problem, vehicle routing problems, location-allocation problems etc. Therefore, in this study we have developed a customized GIS tool using Python script in ArcGIS software for the solution of MST problem for a Road Transportation Network of Dehradun city by considering distance and time as the impedance (cost) factors. It has a number of advantages like the users do not need a greater knowledge of the subject as the tool is user-friendly and that allows to access information varied and adapted the needs of the users. This GIS tool for MST can be applied for a nationwide plan called Prime Minister Gram Sadak Yojana in India to provide optimal all weather road connectivity to unconnected villages (points). This tool is also useful for constructing highways or railways spanning several cities optimally or connecting all cities with minimum total road length.

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

Development of an Exchange Format for the European Environmental Chemical Data and Information Network (ECDIN).

ERIC Educational Resources Information Center

And Others; Proctor, David, J.

1978-01-01

Uses collection and storage of data in an environmental chemicals data bank to develop an exchange format of hierarchical tree structure between network partners. Rules identify and process the nodes in the tree in such a way that information is neither lost nor degraded upon transfer between network partners. (CWM)

Long-term drought sensitivity of trees in second-growth forests in a humid region

Treesearch

Neil Pederson; Kacie Tackett; Ryan W. McEwan; Stacy Clark; Adrienne Cooper; Glade Brosi; Ray Eaton; R. Drew Stockwell

2012-01-01

Classical field methods of reconstructing drought using tree rings in humid, temperate regions typically target old trees from drought-prone sites. This approach limits investigators to a handful of species and excludes large amounts of data that might be useful, especially for coverage gaps in large-scale networks. By sampling in more “typical” forests, network...

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

PubMed

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

Growing trees in child brains: graph theoretical analysis of electroencephalography-derived minimum spanning tree in 5- and 7-year-old children reflects brain maturation.

PubMed

Boersma, Maria; Smit, Dirk J A; Boomsma, Dorret I; De Geus, Eco J C; Delemarre-van de Waal, Henriette A; Stam, Cornelis J

2013-01-01

The child brain is a small-world network, which is hypothesized to change toward more ordered configurations with development. In graph theoretical studies, comparing network topologies under different conditions remains a critical point. Constructing a minimum spanning tree (MST) might present a solution, since it does not require setting a threshold and uses a fixed number of nodes and edges. In this study, the MST method is introduced to examine developmental changes in functional brain network topology in young children. Resting-state electroencephalography was recorded from 227 children twice at 5 and 7 years of age. Synchronization likelihood (SL) weighted matrices were calculated in three different frequency bands from which MSTs were constructed, which represent constructs of the most important routes for information flow in a network. From these trees, several parameters were calculated to characterize developmental change in network organization. The MST diameter and eccentricity significantly increased, while the leaf number and hierarchy significantly decreased in the alpha band with development. Boys showed significant higher leaf number, betweenness, degree and hierarchy and significant lower SL, diameter, and eccentricity than girls in the theta band. The developmental changes indicate a shift toward more decentralized line-like trees, which supports the previously hypothesized increase toward regularity of brain networks with development. Additionally, girls showed more line-like decentralized configurations, which is consistent with the view that girls are ahead of boys in brain development. MST provides an elegant method sensitive to capture subtle developmental changes in network organization without the bias of network comparison.

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

PubMed Central

Kamneva, Olga K; Rosenberg, Noah A

2017-01-01

Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species. For recent divergences between hybridizing species, when the influence of ILS is sufficiently high, likelihood methods outperform parsimony and consensus methods, which erroneously identify extra hybridizations. The more sophisticated likelihood methods, however, are affected by gene tree errors to a greater extent than are consensus and parsimony. PMID:28469378

The Hierarchy of Brain Networks Is Related to Insulin Growth Factor-1 in a Large, Middle-Aged, Healthy Cohort: An Exploratory Magnetoencephalography Study.

PubMed

Sorrentino, Pierpaolo; Nieboer, Dagmar; Twisk, Jos W R; Stam, Cornelis J; Douw, Linda; Hillebrand, Arjan

2017-06-01

Recently, a large study demonstrated that lower serum levels of insulin growth factor-1 (IGF-1) relate to brain atrophy and to a greater risk for developing Alzheimer's disease in a healthy elderly population. We set out to test if functional brain networks relate to IGF-1 levels in the middle aged. Hence, we studied the association between IGF-1 and magnetoencephalography-based functional network characteristics in a middle-aged population. The functional connections between brain areas were estimated for six frequency bands (delta, theta, alpha1, alpha2, beta, gamma) using the phase lag index. Subsequently, the topology of the frequency-specific functional networks was characterized using the minimum spanning tree. Our results showed that lower levels of serum IGF-1 relate to a globally less integrated functional network in the beta and theta band. The associations remained significant when correcting for gender and systemic effects of IGF-1 that might indirectly affect the brain. The value of this exploratory study is the demonstration that lower levels of IGF-1 are associated with brain network topology in the middle aged.

A P2P Botnet detection scheme based on decision tree and adaptive multilayer neural networks.

PubMed

Alauthaman, Mohammad; Aslam, Nauman; Zhang, Li; Alasem, Rafe; Hossain, M A

2018-01-01

In recent years, Botnets have been adopted as a popular method to carry and spread many malicious codes on the Internet. These malicious codes pave the way to execute many fraudulent activities including spam mail, distributed denial-of-service attacks and click fraud. While many Botnets are set up using centralized communication architecture, the peer-to-peer (P2P) Botnets can adopt a decentralized architecture using an overlay network for exchanging command and control data making their detection even more difficult. This work presents a method of P2P Bot detection based on an adaptive multilayer feed-forward neural network in cooperation with decision trees. A classification and regression tree is applied as a feature selection technique to select relevant features. With these features, a multilayer feed-forward neural network training model is created using a resilient back-propagation learning algorithm. A comparison of feature set selection based on the decision tree, principal component analysis and the ReliefF algorithm indicated that the neural network model with features selection based on decision tree has a better identification accuracy along with lower rates of false positives. The usefulness of the proposed approach is demonstrated by conducting experiments on real network traffic datasets. In these experiments, an average detection rate of 99.08 % with false positive rate of 0.75 % was observed.

A program to compute the soft Robinson-Foulds distance between phylogenetic networks.

PubMed

Lu, Bingxin; Zhang, Louxin; Leong, Hon Wai

2017-03-14

Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.

Connections in wood and foliage

Treesearch

Kevin T. Smith

2009-01-01

Trees are networked systems that capture energy, move massive amounts of water and material, and provide the setting for human society and for the lives of many associated organisms. Tree survival depends on making and breaking the right connections within these networks.

Structural Controllability of Temporal Networks with a Single Switching Controller

PubMed Central

Yao, Peng; Hou, Bao-Yu; Pan, Yu-Jian; Li, Xiang

2017-01-01

Temporal network, whose topology evolves with time, is an important class of complex networks. Temporal trees of a temporal network describe the necessary edges sustaining the network as well as their active time points. By a switching controller which properly selects its location with time, temporal trees are used to improve the controllability of the network. Therefore, more nodes are controlled within the limited time. Several switching strategies to efficiently select the location of the controller are designed, which are verified with synthetic and empirical temporal networks to achieve better control performance. PMID:28107538

78 FR 67427 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing and Immediate Effectiveness of...

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2013-11-12

... Change Proposing to Amend the Rule Governing the Listing and Trading of Shares of the WisdomTree Global... change to the means of achieving the investment objective applicable to the WisdomTree Global Real Return... Rule 8.600 \\4\\ (``Managed Fund Shares'').\\5\\ The Shares are offered by the WisdomTree Trust (``Trust...

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Assessing the stability of tree ranges and influence of disturbance in eastern US forests

Treesearch

C.W. Woodall; K. Zhu; J.A. Westfall; C.M. Oswalt; A.W. D' Amato; B.F. Walters; H.E. Lintz

2013-01-01

Shifts in tree species ranges may occur due to global climate change, which in turn may be exacerbated by natural disturbance events. Within the context of global climate change, developing techniques to monitor tree range dynamics as affected by natural disturbances may enable mitigation/adaptation of projected impacts. Using a forest inventory across the eastern U.S...

Multi-scale structure and topological anomaly detection via a new network statistic: The onion decomposition.

PubMed

Hébert-Dufresne, Laurent; Grochow, Joshua A; Allard, Antoine

2016-08-18

We introduce a network statistic that measures structural properties at the micro-, meso-, and macroscopic scales, while still being easy to compute and interpretable at a glance. Our statistic, the onion spectrum, is based on the onion decomposition, which refines the k-core decomposition, a standard network fingerprinting method. The onion spectrum is exactly as easy to compute as the k-cores: It is based on the stages at which each vertex gets removed from a graph in the standard algorithm for computing the k-cores. Yet, the onion spectrum reveals much more information about a network, and at multiple scales; for example, it can be used to quantify node heterogeneity, degree correlations, centrality, and tree- or lattice-likeness. Furthermore, unlike the k-core decomposition, the combined degree-onion spectrum immediately gives a clear local picture of the network around each node which allows the detection of interesting subgraphs whose topological structure differs from the global network organization. This local description can also be leveraged to easily generate samples from the ensemble of networks with a given joint degree-onion distribution. We demonstrate the utility of the onion spectrum for understanding both static and dynamic properties on several standard graph models and on many real-world networks.

Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure.

PubMed

Lustgarten, Jonathan Lyle; Balasubramanian, Jeya Balaji; Visweswaran, Shyam; Gopalakrishnan, Vanathi

2017-03-01

The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilities to summarize the observed data. We extend a Bayesian Rule Learning (BRL-GSS) algorithm, previously shown to be a significantly better predictor than other classical approaches in this domain. It searches a space of Bayesian networks using a decision tree representation of its parameters with global constraints, and infers a set of IF-THEN rules. The number of parameters and therefore the number of rules are combinatorial to the number of predictor variables in the model. We relax these global constraints to a more generalizable local structure (BRL-LSS). BRL-LSS entails more parsimonious set of rules because it does not have to generate all combinatorial rules. The search space of local structures is much richer than the space of global structures. We design the BRL-LSS with the same worst-case time-complexity as BRL-GSS while exploring a richer and more complex model space. We measure predictive performance using Area Under the ROC curve (AUC) and Accuracy. We measure model parsimony performance by noting the average number of rules and variables needed to describe the observed data. We evaluate the predictive and parsimony performance of BRL-GSS, BRL-LSS and the state-of-the-art C4.5 decision tree algorithm, across 10-fold cross-validation using ten microarray gene-expression diagnostic datasets. In these experiments, we observe that BRL-LSS is similar to BRL-GSS in terms of predictive performance, while generating a much more parsimonious set of rules to explain the same observed data. BRL-LSS also needs fewer variables than C4.5 to explain the data with similar predictive performance. We also conduct a feasibility study to demonstrate the general applicability of our BRL methods on the newer RNA sequencing gene-expression data.

Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area.

PubMed

Greenwood, Sarah; Ruiz-Benito, Paloma; Martínez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D; Fensham, Rod; Laughlin, Daniel C; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J B; Jump, Alistair S

2017-04-01

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees -1  year -1 ) increased 0.46 (95% CI = 0.2-0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future. © 2017 John Wiley & Sons Ltd/CNRS.

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change.

PubMed

Aleman, Julie C; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-30

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa.

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change

NASA Astrophysics Data System (ADS)

Aleman, Julie C.; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-01

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa.

[Statistical prediction methods in violence risk assessment and its application].

PubMed

Liu, Yuan-Yuan; Hu, Jun-Mei; Yang, Min; Li, Xiao-Song

2013-06-01

It is an urgent global problem how to improve the violence risk assessment. As a necessary part of risk assessment, statistical methods have remarkable impacts and effects. In this study, the predicted methods in violence risk assessment from the point of statistics are reviewed. The application of Logistic regression as the sample of multivariate statistical model, decision tree model as the sample of data mining technique, and neural networks model as the sample of artificial intelligence technology are all reviewed. This study provides data in order to contribute the further research of violence risk assessment.

Computing all hybridization networks for multiple binary phylogenetic input trees.

PubMed

Albrecht, Benjamin

2015-07-30

The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

Superframe Duration Allocation Schemes to Improve the Throughput of Cluster-Tree Wireless Sensor Networks

PubMed Central

Leão, Erico; Montez, Carlos; Moraes, Ricardo; Portugal, Paulo; Vasques, Francisco

2017-01-01

The use of Wireless Sensor Network (WSN) technologies is an attractive option to support wide-scale monitoring applications, such as the ones that can be found in precision agriculture, environmental monitoring and industrial automation. The IEEE 802.15.4/ZigBee cluster-tree topology is a suitable topology to build wide-scale WSNs. Despite some of its known advantages, including timing synchronisation and duty-cycle operation, cluster-tree networks may suffer from severe network congestion problems due to the convergecast pattern of its communication traffic. Therefore, the careful adjustment of transmission opportunities (superframe durations) allocated to the cluster-heads is an important research issue. This paper proposes a set of proportional Superframe Duration Allocation (SDA) schemes, based on well-defined protocol and timing models, and on the message load imposed by child nodes (Load-SDA scheme), or by number of descendant nodes (Nodes-SDA scheme) of each cluster-head. The underlying reasoning is to adequately allocate transmission opportunities (superframe durations) and parametrize buffer sizes, in order to improve the network throughput and avoid typical problems, such as: network congestion, high end-to-end communication delays and discarded messages due to buffer overflows. Simulation assessments show how proposed allocation schemes may clearly improve the operation of wide-scale cluster-tree networks. PMID:28134822

Urban warming reduces aboveground carbon storage.

PubMed

Meineke, Emily; Youngsteadt, Elsa; Dunn, Robert R; Frank, Steven D

2016-10-12

A substantial amount of global carbon is stored in mature trees. However, no experiments to date test how warming affects mature tree carbon storage. Using a unique, citywide, factorial experiment, we investigated how warming and insect herbivory affected physiological function and carbon sequestration (carbon stored per year) of mature trees. Urban warming increased herbivorous arthropod abundance on trees, but these herbivores had negligible effects on tree carbon sequestration. Instead, urban warming was associated with an estimated 12% loss of carbon sequestration, in part because photosynthesis was reduced at hotter sites. Ecosystem service assessments that do not consider urban conditions may overestimate urban tree carbon storage. Because urban and global warming are becoming more intense, our results suggest that urban trees will sequester even less carbon in the future. © 2016 The Author(s).

The roosting spatial network of a bird-predator bat.

PubMed

Fortuna, Miguel A; Popa-Lisseanu, Ana G; Ibáñez, Carlos; Bascompte, Jordi

2009-04-01

The use of roosting sites by animal societies is important in conservation biology, animal behavior, and epidemiology. The giant noctule bat (Nyctalus lasiopterus) constitutes fission-fusion societies whose members spread every day in multiple trees for shelter. To assess how the pattern of roosting use determines the potential for information exchange or disease spreading, we applied the framework of complex networks. We found a social and spatial segregation of the population in well-defined modules or compartments, formed by groups of bats sharing the same trees. Inside each module, we revealed an asymmetric use of trees by bats representative of a nested pattern. By applying a simple epidemiological model, we show that there is a strong correlation between network structure and the rate and shape of infection dynamics. This modular structure slows down the spread of diseases and the exchange of information through the entire network. The implication for management is complex, affecting differently the cohesion inside and among colonies and the transmission of parasites and diseases. Network analysis can hence be applied to quantifying the conservation status of individual trees used by species depending on hollows for shelter.

76 FR 27127 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change To List...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-10

... WisdomTree Global Real Return Fund May 5, 2011. Pursuant to Section 19(b)(1) of the Securities Exchange... Exchange proposes to list and trade the shares (``Shares'') of the following series of the WisdomTree Trust (``Trust'') under NYSE Arca Equities Rule 8.600: WisdomTree Global Real Return Fund (``Fund''). The text of...

Multipoint to multipoint routing and wavelength assignment in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Qin, Panke; Wu, Jingru; Li, Xudong; Tang, Yongli

2018-01-01

In multi-point to multi-point (MP2MP) routing and wavelength assignment (RWA) problems, researchers usually assume the optical networks to be a single domain. However, the optical networks develop toward to multi-domain and larger scale in practice. In this context, multi-core shared tree (MST)-based MP2MP RWA are introduced problems including optimal multicast domain sequence selection, core nodes belonging in which domains and so on. In this letter, we focus on MST-based MP2MP RWA problems in multi-domain optical networks, mixed integer linear programming (MILP) formulations to optimally construct MP2MP multicast trees is presented. A heuristic algorithm base on network virtualization and weighted clustering algorithm (NV-WCA) is proposed. Simulation results show that, under different traffic patterns, the proposed algorithm achieves significant improvement on network resources occupation and multicast trees setup latency in contrast with the conventional algorithms which were proposed base on a single domain network environment.

Thermophilization of adult and juvenile tree communities in the northern tropical Andes.

PubMed

Duque, Alvaro; Stevenson, Pablo R; Feeley, Kenneth J

2015-08-25

Climate change is expected to cause shifts in the composition of tropical montane forests towards increased relative abundances of species whose ranges were previously centered at lower, hotter elevations. To investigate this process of "thermophilization," we analyzed patterns of compositional change over the last decade using recensus data from a network of 16 adult and juvenile tree plots in the tropical forests of northern Andes Mountains and adjacent lowlands in northwestern Colombia. Analyses show evidence that tree species composition is strongly linked to temperature and that composition is changing directionally through time, potentially in response to climate change and increasing temperatures. Mean rates of thermophilization [thermal migration rate (TMR), °C ⋅ y(-1)] across all censuses were 0.011 °C ⋅ y(-1) (95% confidence interval = 0.002-0.022 °C ⋅ y(-1)) for adult trees and 0.027 °C ⋅ y(-1) (95% confidence interval = 0.009-0.050 °C ⋅ y(-1)) for juvenile trees. The fact that thermophilization is occurring in both the adult and juvenile trees and at rates consistent with concurrent warming supports the hypothesis that the observed compositional changes are part of a long-term process, such as global warming, and are not a response to any single episodic event. The observed changes in composition were driven primarily by patterns of tree mortality, indicating that the changes in composition are mostly via range retractions, rather than range shifts or expansions. These results all indicate that tropical forests are being strongly affected by climate change and suggest that many species will be at elevated risk for extinction as warming continues.

Climatic Signals in Tree Rings of Heritiera fomes Buch.-Ham. in the Sundarbans, Bangladesh

PubMed Central

Chowdhury, Md. Qumruzzaman; De Ridder, Maaike; Beeckman, Hans

2016-01-01

Mangroves occur along the coastlines throughout the tropics and sub-tropics, supporting a wide variety of resources and services. In order to understand the responses of future climate change on this ecosystem, we need to know how mangrove species have responded to climate changes in the recent past. This study aims at exploring the climatic influences on the radial growth of Heritiera fomes from a local to global scale. A total of 40 stem discs were collected at breast height position from two different zones with contrasting salinity in the Sundarbans, Bangladesh. All specimens showed distinct tree rings and most of the trees (70%) could be visually and statistically crossdated. Successful crossdating enabled the development of two zone-specific chronologies. The mean radial increment was significantly higher at low salinity (eastern) zone compared to higher salinity (western) zone. The two zone-specific chronologies synchronized significantly, allowing for the construction of a regional chronology. The annual and monsoon precipitation mainly influence the tree growth of H. fomes. The growth response to local precipitation is similar in both zones except June and November in the western zone, while the significant influence is lacking. The large-scale climatic drivers such as sea surface temperature (SST) of equatorial Pacific and Indian Ocean as well as the El Niño-Southern Oscillation (ENSO) revealed no teleconnection with tree growth. The tree rings of this species are thus an indicator for monsoon precipitation variations in Bangladesh. The wider distribution of this species from the South to South East Asian coast presents an outstanding opportunity for developing a large-scale tree-ring network of mangroves. PMID:26927229

Thermophilization of adult and juvenile tree communities in the northern tropical Andes

PubMed Central

Duque, Alvaro; Stevenson, Pablo R.; Feeley, Kenneth J.

2015-01-01

Climate change is expected to cause shifts in the composition of tropical montane forests towards increased relative abundances of species whose ranges were previously centered at lower, hotter elevations. To investigate this process of “thermophilization,” we analyzed patterns of compositional change over the last decade using recensus data from a network of 16 adult and juvenile tree plots in the tropical forests of northern Andes Mountains and adjacent lowlands in northwestern Colombia. Analyses show evidence that tree species composition is strongly linked to temperature and that composition is changing directionally through time, potentially in response to climate change and increasing temperatures. Mean rates of thermophilization [thermal migration rate (TMR), °C⋅y−1] across all censuses were 0.011 °C⋅y−1 (95% confidence interval = 0.002–0.022 °C⋅y−1) for adult trees and 0.027 °C⋅y−1 (95% confidence interval = 0.009–0.050 °C⋅y−1) for juvenile trees. The fact that thermophilization is occurring in both the adult and juvenile trees and at rates consistent with concurrent warming supports the hypothesis that the observed compositional changes are part of a long-term process, such as global warming, and are not a response to any single episodic event. The observed changes in composition were driven primarily by patterns of tree mortality, indicating that the changes in composition are mostly via range retractions, rather than range shifts or expansions. These results all indicate that tropical forests are being strongly affected by climate change and suggest that many species will be at elevated risk for extinction as warming continues. PMID:26261350

Stability of synchrony against local intermittent fluctuations in tree-like power grids

NASA Astrophysics Data System (ADS)

Auer, Sabine; Hellmann, Frank; Krause, Marie; Kurths, Jürgen

2017-12-01

90% of all Renewable Energy Power in Germany is installed in tree-like distribution grids. Intermittent power fluctuations from such sources introduce new dynamics into the lower grid layers. At the same time, distributed resources will have to contribute to stabilize the grid against these fluctuations in the future. In this paper, we model a system of distributed resources as oscillators on a tree-like, lossy power grid and its ability to withstand desynchronization from localized intermittent renewable infeed. We find a remarkable interplay of the network structure and the position of the node at which the fluctuations are fed in. An important precondition for our findings is the presence of losses in distribution grids. Then, the most network central node splits the network into branches with different influence on network stability. Troublemakers, i.e., nodes at which fluctuations are especially exciting the grid, tend to be downstream branches with high net power outflow. For low coupling strength, we also find branches of nodes vulnerable to fluctuations anywhere in the network. These network regions can be predicted at high confidence using an eigenvector based network measure taking the turbulent nature of perturbations into account. While we focus here on tree-like networks, the observed effects also appear, albeit less pronounced, for weakly meshed grids. On the other hand, the observed effects disappear for lossless power grids often studied in the complex system literature.

Loss of functional diversity and network modularity in introduced plant–fungal symbioses

PubMed Central

Cooper, Jerry A.; Bufford, Jennifer L.; Hulme, Philip E.; Bates, Scott T.

2017-01-01

The introduction of alien plants into a new range can result in the loss of co-evolved symbiotic organisms, such as mycorrhizal fungi, that are essential for normal plant physiological functions. Prior studies of mycorrhizal associations in alien plants have tended to focus on individual plant species on a case-by-case basis. This approach limits broad scale understanding of functional shifts and changes in interaction network structure that may occur following introduction. Here we use two extensive datasets of plant–fungal interactions derived from fungal sporocarp observations and recorded plant hosts in two island archipelago nations: New Zealand (NZ) and the United Kingdom (UK). We found that the NZ dataset shows a lower functional diversity of fungal hyphal foraging strategies in mycorrhiza of alien when compared with native trees. Across species this resulted in fungal foraging strategies associated with alien trees being much more variable in functional composition compared with native trees, which had a strikingly similar functional composition. The UK data showed no functional difference in fungal associates of alien and native plant genera. Notwithstanding this, both the NZ and UK data showed a substantial difference in interaction network structure of alien trees compared with native trees. In both cases, fungal associates of native trees showed strong modularity, while fungal associates of alien trees generally integrated into a single large module. The results suggest a lower functional diversity (in one dataset) and a simplification of network structure (in both) as a result of introduction, potentially driven by either limited symbiont co-introductions or disruption of habitat as a driver of specificity due to nursery conditions, planting, or plant edaphic-niche expansion. Recognizing these shifts in function and network structure has important implications for plant invasions and facilitation of secondary invasions via shared mutualist populations. PMID:28039116

Ecohydrological and subsurface controls on drought-induced contraction and disconnection of stream networks

NASA Astrophysics Data System (ADS)

Godsey, S.; Kirchner, J. W.; Whiting, J. A.

2016-12-01

Temporary headwater streams - both intermittent and ephemeral waterways - supply water to approximately 1/3 of the US population, and 60% of streams used for drinking water are temporary. Stream ecologists increasingly recognize that a gradient of processes across the drying continuum affect ecosystems at dynamic terrestrial-aquatic interfaces. Understanding the hydrological controls across that gradient of drying may improve management of these sensitive systems. One possible control on surface flows includes transpiration losses from either the riparian zone or the entire watershed. We mapped several stream networks under extreme low flow conditions brought on by severe drought in central Idaho and California in 2015. Compared to previous low-flow stream length estimates, the active drainage network had generally decreased by a very small amount across these sites, perhaps because stored water buffered the precipitation decrease, or because flowing channel heads are fixed by focused groundwater flow emerging at springs. We also examined the apparent sources of water for both riparian and hillslope trees using isotopic techniques. During drought conditions, we hypothesized that riparian trees - but not those far from flowing streams - would be sustained by streamflow recharging riparian aquifers, and thus would transpire water that was isotopically similar to streamflow because little soil water would remain available below the wilting point and stream water would be sustain those trees. We found a more complex pattern, but in most places stream water and water transpired by trees were isotopically distinct regardless of flow intermittency or tree location. We also found that hillslope trees outside of the riparian zone appeared to be using different waters from those used by riparian trees. Finally, we explore subsurface controls on network extent, showing that bedrock characteristics can influence network stability and contraction patterns.

Object based technique for delineating and mapping 15 tree species using VHR WorldView-2 imagery

NASA Astrophysics Data System (ADS)

Mustafa, Yaseen T.; Habeeb, Hindav N.

2014-10-01

Monitoring and analyzing forests and trees are required task to manage and establish a good plan for the forest sustainability. To achieve such a task, information and data collection of the trees are requested. The fastest way and relatively low cost technique is by using satellite remote sensing. In this study, we proposed an approach to identify and map 15 tree species in the Mangish sub-district, Kurdistan Region-Iraq. Image-objects (IOs) were used as the tree species mapping unit. This is achieved using the shadow index, normalized difference vegetation index and texture measurements. Four classification methods (Maximum Likelihood, Mahalanobis Distance, Neural Network, and Spectral Angel Mapper) were used to classify IOs using selected IO features derived from WorldView-2 imagery. Results showed that overall accuracy was increased 5-8% using the Neural Network method compared with other methods with a Kappa coefficient of 69%. This technique gives reasonable results of various tree species classifications by means of applying the Neural Network method with IOs techniques on WorldView-2 imagery.

Causes and consequences of habitat fragmentation in river networks.

PubMed

Fuller, Matthew R; Doyle, Martin W; Strayer, David L

2015-10-01

Increases in river fragmentation globally threaten freshwater biodiversity. Rivers are fragmented by many agents, both natural and anthropogenic. We review the distribution and frequency of these major agents, along with their effects on connectivity and habitat quality. Most fragmentation research has focused on terrestrial habitats, but theories and generalizations developed in terrestrial habitats do not always apply well to river networks. For example, terrestrial habitats are usually conceptualized as two-dimensional, whereas rivers often are conceptualized as one-dimensional or dendritic. In addition, river flow often leads to highly asymmetric effects of barriers on habitat and permeability. New approaches tailored to river networks can be applied to describe the network-wide effects of multiple barriers on both connectivity and habitat quality. The net effects of anthropogenic fragmentation on freshwater biodiversity are likely underestimated, because of time lags in effects and the difficulty of generating a single, simple signal of fragmentation that applies to all aquatic species. We conclude by presenting a decision tree for managing freshwater fragmentation, as well as some research horizons for evaluating fragmented riverscapes. © 2015 New York Academy of Sciences.

Reconstructing targetable pathways in lung cancer by integrating diverse omics data

PubMed Central

Balbin, O. Alejandro; Prensner, John R.; Sahu, Anirban; Yocum, Anastasia; Shankar, Sunita; Malik, Rohit; Fermin, Damian; Dhanasekaran, Saravana M.; Chandler, Benjamin; Thomas, Dafydd; Beer, David G.; Cao, Xuhong; Nesvizhskii, Alexey I.; Chinnaiyan, Arul M.

2014-01-01

Global ‘multi-omics’ profiling of cancer cells harbours the potential for characterizing the signaling networks associated with specific oncogenes. Here we profile the transcriptome, proteome and phosphoproteome in a panel of non-small cell lung cancer (NSCLC) cell lines in order to reconstruct targetable networks associated with KRAS dependency. We develop a two-step bioinformatics strategy addressing the challenge of integrating these disparate data sets. We first define an ‘abundance-score’ combining transcript, protein and phospho-protein abundances to nominate differentially abundant proteins and then use the Prize Collecting Steiner Tree algorithm to identify functional sub-networks. We identify three modules centered on KRAS and MET, LCK and PAK1 and b-Catenin. We validate activation of these proteins in KRAS-dependent (KRAS-Dep) cells and perform functional studies defining LCK as a critical gene for cell proliferation in KRAS-Dep but not KRAS-independent NSCLCs. These results suggest that LCK is a potential druggable target protein in KRAS-Dep lung cancers. PMID:24135919

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

PubMed

Yin, Weiwei; Garimalla, Swetha; Moreno, Alberto; Galinski, Mary R; Styczynski, Mark P

2015-08-28

There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). However, complex animal model systems typically have significant limitations on cohort sizes, number of samples, and the ability to perform follow-up and validation experiments. These constraints are particularly problematic for many current network learning approaches, which require large numbers of samples and may predict many more regulatory relationships than actually exist. Here, we test the idea that by leveraging the accuracy and efficiency of classifiers, we can construct high-quality networks that capture important interactions between variables in datasets with few samples. We start from a previously-developed tree-like Bayesian classifier and generalize its network learning approach to allow for arbitrary depth and complexity of tree-like networks. Using four diverse sample networks, we demonstrate that this approach performs consistently better at low sample sizes than the Sparse Candidate Algorithm, a representative approach for comparison because it is known to generate Bayesian networks with high positive predictive value. We develop and demonstrate a resampling-based approach to enable the identification of a viable root for the learned tree-like network, important for cases where the root of a network is not known a priori. We also develop and demonstrate an integrated resampling-based approach to the reduction of variable space for the learning of the network. Finally, we demonstrate the utility of this approach via the analysis of a transcriptional dataset of a malaria challenge in a non-human primate model system, Macaca mulatta, suggesting the potential to capture indicators of the earliest stages of cellular differentiation during leukopoiesis. We demonstrate that by starting from effective and efficient approaches for creating classifiers, we can identify interesting tree-like network structures with significant ability to capture the relationships in the training data. This approach represents a promising strategy for inferring networks with high positive predictive value under the constraint of small numbers of samples, meeting a need that will only continue to grow as more high-throughput studies are applied to complex model systems.

Revealing the ISO/IEC 9126-1 Clique Tree for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2007-01-01

Previous research has shown that acyclic dependency models, if they exist, can be extracted from software quality standards and that these models can be used to assess software safety and product quality. In the case of commercial off-the-shelf (COTS) software, the extracted dependency model can be used in a probabilistic Bayesian network context for COTS software evaluation. Furthermore, while experts typically employ Bayesian networks to encode domain knowledge, secondary structures (clique trees) from Bayesian network graphs can be used to determine the probabilistic distribution of any software variable (attribute) using any clique that contains that variable. Secondary structures, therefore, provide insight into the fundamental nature of graphical networks. This paper will apply secondary structure calculations to reveal the clique tree of the acyclic dependency model extracted from the ISO/IEC 9126-1 software quality standard. Suggestions will be provided to describe how the clique tree may be exploited to aid efficient transformation of an evaluation model.

Algorithm for protecting light-trees in survivable mesh wavelength-division-multiplexing networks

NASA Astrophysics Data System (ADS)

Luo, Hongbin; Li, Lemin; Yu, Hongfang

2006-12-01

Wavelength-division-multiplexing (WDM) technology is expected to facilitate bandwidth-intensive multicast applications such as high-definition television. A single fiber cut in a WDM mesh network, however, can disrupt the dissemination of information to several destinations on a light-tree based multicast session. Thus it is imperative to protect multicast sessions by reserving redundant resources. We propose a novel and efficient algorithm for protecting light-trees in survivable WDM mesh networks. The algorithm is called segment-based protection with sister node first (SSNF), whose basic idea is to protect a light-tree using a set of backup segments with a higher priority to protect the segments from a branch point to its children (sister nodes). The SSNF algorithm differs from the segment protection scheme proposed in the literature in how the segments are identified and protected. Our objective is to minimize the network resources used for protecting each primary light-tree such that the blocking probability can be minimized. To verify the effectiveness of the SSNF algorithm, we conduct extensive simulation experiments. The simulation results demonstrate that the SSNF algorithm outperforms existing algorithms for the same problem.

Inferring Phylogenetic Networks Using PhyloNet.

PubMed

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Determination of incoming solar radiation in major tree species in Turkey.

PubMed

Yilmaz, Osman Yalcin; Sevgi, Orhan; Koc, Ayhan

2012-07-01

Light requirements and spatial distribution of major forest tree species in Turkey hasn't been analyzed yet. Continuous surface solar radiation data, especially at mountainous-forested areas, are needed to put forward this relationship between forest tree species and solar radiation. To achieve this, GIS-based modeling of solar radiation is one of the methods used in rangelands to estimate continuous surface solar radiation. Therefore, mean monthly and annual total global solar radiation maps of whole Turkey were computed spatially using GRASS GIS software "r.sun" model under clear-sky (cloudless) conditions. 147498 pure forest stand point-based data were used in the study for calculating mean global solar radiation values of all the major forest tree species of Turkey. Beech had the lowest annual mean total global solar radiation value of 1654.87 kWh m(-2), whereas juniper had the highest value of 1928.89 kWh m(-2). The rank order of tree species according to the mean monthly and annual total global solar radiation values, using a confidence level of p < 0.05, was as follows: Beech < Spruce < Fir species < Oak species < Scotch pine < Red pine < Cedar < Juniper. The monthly and annual solar radiation values of sites and light requirements of forest trees ranked similarly.

Disparate effects of global-change drivers on mountain conifer forests: warming-induced growth enhancement in young trees vs. CO2 fertilization in old trees from wet sites.

PubMed

Camarero, J Julio; Gazol, Antonio; Galván, Juan Diego; Sangüesa-Barreda, Gabriel; Gutiérrez, Emilia

2015-02-01

Theory predicts that the postindustrial rise in the concentration of CO2 in the atmosphere (c(a)) should enhance tree growth either through a direct fertilization effect or indirectly by improving water use efficiency in dry areas. However, this hypothesis has received little support in cold-limited and subalpine forests where positive growth responses to either rising ca or warmer temperatures are still under debate. In this study, we address this issue by analyzing an extensive dendrochronological network of high-elevation Pinus uncinata forests in Spain (28 sites, 544 trees) encompassing the whole biogeographical extent of the species. We determine if the basal area increment (BAI) trends are linked to climate warming and increased c(a) by focusing on region- and age-dependent responses. The largest improvement in BAI over the past six centuries occurred during the last 150 years affecting young trees and being driven by recent warming. Indeed, most studied regions and age classes presented BAI patterns mainly controlled by temperature trends, while growing-season precipitation was only relevant in the driest sites. Growth enhancement was linked to rising ca in mature (151-300 year-old trees) and old-mature trees (301-450 year-old trees) from the wettest sites only. This finding implies that any potential fertilization effect of elevated c(a) on forest growth is contingent on tree features that vary with ontogeny and it depends on site conditions (for instance water availability). Furthermore, we found widespread growth decline in drought-prone sites probably indicating that the rise in ca did not compensate for the reduction in water availability. Thus, warming-triggered drought stress may become a more important direct driver of growth than rising ca in similar subalpine forests. We argue that broad approaches in biogeographical and temporal terms are required to adequately evaluate any effect of rising c(a) on forest growth. © 2014 John Wiley & Sons Ltd.

Automated method for identification and artery-venous classification of vessel trees in retinal vessel networks.

PubMed

Joshi, Vinayak S; Reinhardt, Joseph M; Garvin, Mona K; Abramoff, Michael D

2014-01-01

The separation of the retinal vessel network into distinct arterial and venous vessel trees is of high interest. We propose an automated method for identification and separation of retinal vessel trees in a retinal color image by converting a vessel segmentation image into a vessel segment map and identifying the individual vessel trees by graph search. Orientation, width, and intensity of each vessel segment are utilized to find the optimal graph of vessel segments. The separated vessel trees are labeled as primary vessel or branches. We utilize the separated vessel trees for arterial-venous (AV) classification, based on the color properties of the vessels in each tree graph. We applied our approach to a dataset of 50 fundus images from 50 subjects. The proposed method resulted in an accuracy of 91.44% correctly classified vessel pixels as either artery or vein. The accuracy of correctly classified major vessel segments was 96.42%.

Global forest sector modeling: application to some impacts of climate change

Treesearch

Joseph Buongiorno

2016-01-01

This paper explored the potential long-term effects of a warming climate on the global wood sector, based on Way and Oren's synthesis (Tree Physiology 30,669-688) indicating positive responses of tree growth to higher temperature in boreal and temperative climates, and negative responses in the topics. Changes in forest productivity were introduced in the Global...

Globalization and the Christian Idea of a University (or, the Lexus, the Olive Tree, and Higher Education)

ERIC Educational Resources Information Center

Adrian, William

2007-01-01

Thomas Friedman uses the Lexus and the olive tree as symbols to describe the characteristics and challenges of globalization. They can also be used to describe the issues facing the new "global" university. The Lexus is an appropriate symbol of the American university whose material success has been unrivaled and whose dominant values have…

Diverse growth trends and climate responses across Eurasia’s boreal forest

NASA Astrophysics Data System (ADS)

Hellmann, Lena; Agafonov, Leonid; Charpentier Ljungqvist, Fredrik; Churakova (Sidorova, Olga; Düthorn, Elisabeth; Esper, Jan; Hülsmann, Lisa; Kirdyanov, Alexander V.; Moiseev, Pavel; Myglan, Vladimir S.; Nikolaev, Anatoly N.; Reinig, Frederick; Schweingruber, Fritz H.; Solomina, Olga; Tegel, Willy; Büntgen, Ulf

2016-07-01

The area covered by boreal forests accounts for ˜16% of the global and 22% of the Northern Hemisphere landmass. Changes in the productivity and functioning of this circumpolar biome not only have strong effects on species composition and diversity at regional to larger scales, but also on the Earth’s carbon cycle. Although temporal inconsistency in the response of tree growth to temperature has been reported from some locations at the higher northern latitudes, a systematic dendroecological network assessment is still missing for most of the boreal zone. Here, we analyze the geographical patterns of changes in summer temperature and precipitation across northern Eurasia >60 °N since 1951 AD, as well as the growth trends and climate responses of 445 Pinus, Larix and Picea ring width chronologies in the same area and period. In contrast to widespread summer warming, fluctuations in precipitation and tree growth are spatially more diverse and overall less distinct. Although the influence of summer temperature on ring formation is increasing with latitude and distinct moisture effects are restricted to a few southern locations, growth sensitivity to June-July temperature variability is only significant at 16.6% of all sites (p ≤ 0.01). By revealing complex climate constraints on the productivity of Eurasia’s northern forests, our results question the a priori suitability of boreal tree-ring width chronologies for reconstructing summer temperatures. This study further emphasizes regional climate differences and their role on the dynamics of boreal ecosystems, and also underlines the importance of free data access to facilitate the compilation and evaluation of massively replicated and updated dendroecological networks.

Evolving optimised decision rules for intrusion detection using particle swarm paradigm

NASA Astrophysics Data System (ADS)

Sivatha Sindhu, Siva S.; Geetha, S.; Kannan, A.

2012-12-01

The aim of this article is to construct a practical intrusion detection system (IDS) that properly analyses the statistics of network traffic pattern and classify them as normal or anomalous class. The objective of this article is to prove that the choice of effective network traffic features and a proficient machine-learning paradigm enhances the detection accuracy of IDS. In this article, a rule-based approach with a family of six decision tree classifiers, namely Decision Stump, C4.5, Naive Baye's Tree, Random Forest, Random Tree and Representative Tree model to perform the detection of anomalous network pattern is introduced. In particular, the proposed swarm optimisation-based approach selects instances that compose training set and optimised decision tree operate over this trained set producing classification rules with improved coverage, classification capability and generalisation ability. Experiment with the Knowledge Discovery and Data mining (KDD) data set which have information on traffic pattern, during normal and intrusive behaviour shows that the proposed algorithm produces optimised decision rules and outperforms other machine-learning algorithm.

Understanding the Scalability of Bayesian Network Inference using Clique Tree Growth Curves

NASA Technical Reports Server (NTRS)

Mengshoel, Ole Jakob

2009-01-01

Bayesian networks (BNs) are used to represent and efficiently compute with multi-variate probability distributions in a wide range of disciplines. One of the main approaches to perform computation in BNs is clique tree clustering and propagation. In this approach, BN computation consists of propagation in a clique tree compiled from a Bayesian network. There is a lack of understanding of how clique tree computation time, and BN computation time in more general, depends on variations in BN size and structure. On the one hand, complexity results tell us that many interesting BN queries are NP-hard or worse to answer, and it is not hard to find application BNs where the clique tree approach in practice cannot be used. On the other hand, it is well-known that tree-structured BNs can be used to answer probabilistic queries in polynomial time. In this article, we develop an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN's non-root nodes to the number of root nodes, or (ii) the expected number of moral edges in their moral graphs. Our approach is based on combining analytical and experimental results. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for each set. For the special case of bipartite BNs, we consequently have two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, we systematically increase the degree of the root nodes in bipartite Bayesian networks, and find that root clique growth is well-approximated by Gompertz growth curves. It is believed that this research improves the understanding of the scaling behavior of clique tree clustering, provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms, and presents an aid for analytical trade-off studies of clique tree clustering using growth curves.

Life on the Edge - Improved Forest Cover Mapping in Mixed-Use Tropical Regions

NASA Astrophysics Data System (ADS)

Anderson, C.; Mendenhall, C. D.; Daily, G.

2016-12-01

Tropical ecosystems and biodiversity are experiencing rapid change, primarily due to conversion of forest habitat to agriculture. Protected areas, while effective for conservation, only manage 15% of terrestrial area, whereas approximately 58% is privately owned. To incentivize private forest management and slow the loss of biodiversity, payments for ecosystem services (PES) programs were established in Costa Rica that pay landowners who maintain trees on their property. While this program is effective in improving livelihoods and preventing forest conversion, it is only managing payments to landowners on 1% of eligible, non-protected forested land.A major bottleneck for this program is access to accurate, national-scale tree cover maps. While the remote sensing community has made great progress in global-scale tree cover mapping, these maps are not sufficient to guide investments for PES programs. The major limitations of current global-scale tree-cover maps are that they a) do not distinguish between forest and agriculture and b) overestimate tree cover in mixed land-use areas (e.g. Global Forest Change overestimates by 20% on average in this region). This is especially problematic in biodiversity-rich Costa Rica, where small patches of forest intermix with agricultural production, and where the conservation value of tree-cover is high. To address this problem, we are developing a new forest cover mapping method that a) performs a least-squares spectral mixture analysis (SMA) using repeat Landsat imagery and canopy radiative transfer modeling: b) combines Landsat data, SMA results, and radar backscatter data using multi-sensor fusion techniques and: c) trains tree-cover classification models using high resolution data sets along a land use-intensity gradient. Our method predicted tree cover with 85% accuracy when compared to a fine-scale map of tree cover in a tropical, agricultural landscape, whereas the next-best method, the Global Forest Change map, predicted tree cover with 72% accuracy. Next steps will aim to test, improve, and apply this method globally to guide investments in nature in agricultural landscapes where forest stewardship will sustain biodiversity.

Nonlinear multiplicative dendritic integration in neuron and network models

PubMed Central

Zhang, Danke; Li, Yuanqing; Rasch, Malte J.; Wu, Si

2013-01-01

Neurons receive inputs from thousands of synapses distributed across dendritic trees of complex morphology. It is known that dendritic integration of excitatory and inhibitory synapses can be highly non-linear in reality and can heavily depend on the exact location and spatial arrangement of inhibitory and excitatory synapses on the dendrite. Despite this known fact, most neuron models used in artificial neural networks today still only describe the voltage potential of a single somatic compartment and assume a simple linear summation of all individual synaptic inputs. We here suggest a new biophysical motivated derivation of a single compartment model that integrates the non-linear effects of shunting inhibition, where an inhibitory input on the route of an excitatory input to the soma cancels or “shunts” the excitatory potential. In particular, our integration of non-linear dendritic processing into the neuron model follows a simple multiplicative rule, suggested recently by experiments, and allows for strict mathematical treatment of network effects. Using our new formulation, we further devised a spiking network model where inhibitory neurons act as global shunting gates, and show that the network exhibits persistent activity in a low firing regime. PMID:23658543

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change

PubMed Central

Aleman, Julie C.; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-01

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa. PMID:28134259

Self-constructed tree-shape high thermal conductivity nanosilver networks in epoxy.

PubMed

Pashayi, Kamyar; Fard, Hafez Raeisi; Lai, Fengyuan; Iruvanti, Sushumna; Plawsky, Joel; Borca-Tasciuc, Theodorian

2014-04-21

We report the formation of high aspect ratio nanoscale tree-shape silver networks in epoxy, at low temperatures (<150 °C) and atmospheric pressures, that are correlated to a ∼200 fold enhancement of thermal conductivity (κ) of the nanocomposite compared to the polymer matrix. The networks form through a three-step process comprising of self-assembly by diffusion limited aggregation of polyvinylpyrrolidone (PVP) coated nanoparticles, removal of PVP coating from the surface, and sintering of silver nanoparticles in high aspect ratio networked structures. Controlling self-assembly and sintering by carefully designed multistep temperature and time processing leads to κ of our silver nanocomposites that are up to 300% of the present state of the art polymer nanocomposites at similar volume fractions. Our investigation of the κ enhancements enabled by tree-shaped network nanocomposites provides a basis for the development of new polymer nanocomposites for thermal transport and storage applications.

A Depth-Adjustment Deployment Algorithm Based on Two-Dimensional Convex Hull and Spanning Tree for Underwater Wireless Sensor Networks.

PubMed

Jiang, Peng; Liu, Shuai; Liu, Jun; Wu, Feng; Zhang, Le

2016-07-14

Most of the existing node depth-adjustment deployment algorithms for underwater wireless sensor networks (UWSNs) just consider how to optimize network coverage and connectivity rate. However, these literatures don't discuss full network connectivity, while optimization of network energy efficiency and network reliability are vital topics for UWSN deployment. Therefore, in this study, a depth-adjustment deployment algorithm based on two-dimensional (2D) convex hull and spanning tree (NDACS) for UWSNs is proposed. First, the proposed algorithm uses the geometric characteristics of a 2D convex hull and empty circle to find the optimal location of a sleep node and activate it, minimizes the network coverage overlaps of the 2D plane, and then increases the coverage rate until the first layer coverage threshold is reached. Second, the sink node acts as a root node of all active nodes on the 2D convex hull and then forms a small spanning tree gradually. Finally, the depth-adjustment strategy based on time marker is used to achieve the three-dimensional overall network deployment. Compared with existing depth-adjustment deployment algorithms, the simulation results show that the NDACS algorithm can maintain full network connectivity with high network coverage rate, as well as improved network average node degree, thus increasing network reliability.

A Depth-Adjustment Deployment Algorithm Based on Two-Dimensional Convex Hull and Spanning Tree for Underwater Wireless Sensor Networks

PubMed Central

Jiang, Peng; Liu, Shuai; Liu, Jun; Wu, Feng; Zhang, Le

2016-01-01

Most of the existing node depth-adjustment deployment algorithms for underwater wireless sensor networks (UWSNs) just consider how to optimize network coverage and connectivity rate. However, these literatures don’t discuss full network connectivity, while optimization of network energy efficiency and network reliability are vital topics for UWSN deployment. Therefore, in this study, a depth-adjustment deployment algorithm based on two-dimensional (2D) convex hull and spanning tree (NDACS) for UWSNs is proposed. First, the proposed algorithm uses the geometric characteristics of a 2D convex hull and empty circle to find the optimal location of a sleep node and activate it, minimizes the network coverage overlaps of the 2D plane, and then increases the coverage rate until the first layer coverage threshold is reached. Second, the sink node acts as a root node of all active nodes on the 2D convex hull and then forms a small spanning tree gradually. Finally, the depth-adjustment strategy based on time marker is used to achieve the three-dimensional overall network deployment. Compared with existing depth-adjustment deployment algorithms, the simulation results show that the NDACS algorithm can maintain full network connectivity with high network coverage rate, as well as improved network average node degree, thus increasing network reliability. PMID:27428970

Unique growth strategy in the Earth's first trees revealed in silicified fossil trunks from China.

PubMed

Xu, Hong-He; Berry, Christopher M; Stein, William E; Wang, Yi; Tang, Peng; Fu, Qiang

2017-11-07

Cladoxylopsida included the earliest large trees that formed critical components of globally transformative pioneering forest ecosystems in the Mid- and early Late Devonian (ca. 393-372 Ma). Well-known cladoxylopsid fossils include the up to ∼1-m-diameter sandstone casts known as Eospermatopteris from Middle Devonian strata of New York State. Cladoxylopsid trunk structure comprised a more-or-less distinct cylinder of numerous separate cauline xylem strands connected internally with a network of medullary xylem strands and, near the base, externally with downward-growing roots, all embedded within parenchyma. However, the means by which this complex vascular system was able to grow to a large diameter is unknown. We demonstrate-based on exceptional, up to ∼70-cm-diameter silicified fossil trunks with extensive preservation of cellular anatomy from the early Late Devonian (Frasnian, ca. 374 Ma) of Xinjiang, China-that trunk expansion is associated with a cylindrical zone of diffuse secondary growth within ground and cortical parenchyma and with production of a large amount of wood containing both rays and growth increments concentrically around individual xylem strands by normal cambia. The xylem system accommodates expansion by tearing of individual strand interconnections during secondary development. This mode of growth seems indeterminate, capable of producing trees of large size and, despite some unique features, invites comparison with secondary development in some living monocots. Understanding the structure and growth of cladoxylopsids informs analysis of canopy competition within early forests with the potential to drive global processes. Published under the PNAS license.

Relay-based information broadcast in complex networks

NASA Astrophysics Data System (ADS)

Fan, Zhongyan; Han, Zeyu; Tang, Wallace K. S.; Lin, Dong

2018-04-01

Information broadcast (IB) is a critical process in complex network, usually accomplished by flooding mechanism. Although flooding is simple and no prior topological information is required, it consumes a lot of transmission overhead. Another extreme is the tree-based broadcast (TB), for which information is disseminated via a spanning tree. It achieves the minimal transmission overhead but the maintenance of spanning tree for every node is an obvious obstacle for implementation. Motivated by the success of scale-free network models for real-world networks, in this paper, we investigate the issues in IB by considering an alternative solution in-between these two extremes. A novel relay-based broadcast (RB) mechanism is proposed by employing a subset of nodes as relays. Information is firstly forwarded to one of these relays and then re-disseminated to others through the spanning tree whose root is the relay. This mechanism provides a trade-off solution between flooding and TB. On one hand, it saves up a lot of transmission overhead as compared to flooding; on the other hand, it costs much less resource for maintenance than TB as only a few spanning trees are needed. Based on two major criteria, namely the transmission overhead and the convergence time, the effectiveness of RB is confirmed. The impacts of relay assignment and network structures on performance are also studied in this work.

Getting a better picture of microbial evolution en route to a network of genomes.

PubMed

Dagan, Tal; Martin, William

2009-08-12

Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution.

Tree tensor network approach to simulating Shor's algorithm

NASA Astrophysics Data System (ADS)

Dumitrescu, Eugene

2017-12-01

Constructively simulating quantum systems furthers our understanding of qualitative and quantitative features which may be analytically intractable. In this paper, we directly simulate and explore the entanglement structure present in the paradigmatic example for exponential quantum speedups: Shor's algorithm. To perform our simulation, we construct a dynamic tree tensor network which manifestly captures two salient circuit features for modular exponentiation. These are the natural two-register bipartition and the invariance of entanglement with respect to permutations of the top-register qubits. Our construction help identify the entanglement entropy properties, which we summarize by a scaling relation. Further, the tree network is efficiently projected onto a matrix product state from which we efficiently execute the quantum Fourier transform. Future simulation of quantum information states with tensor networks exploiting circuit symmetries is discussed.

An improved spanning tree approach for the reliability analysis of supply chain collaborative network

NASA Astrophysics Data System (ADS)

Lam, C. Y.; Ip, W. H.

2012-11-01

A higher degree of reliability in the collaborative network can increase the competitiveness and performance of an entire supply chain. As supply chain networks grow more complex, the consequences of unreliable behaviour become increasingly severe in terms of cost, effort and time. Moreover, it is computationally difficult to calculate the network reliability of a Non-deterministic Polynomial-time hard (NP-hard) all-terminal network using state enumeration, as this may require a huge number of iterations for topology optimisation. Therefore, this paper proposes an alternative approach of an improved spanning tree for reliability analysis to help effectively evaluate and analyse the reliability of collaborative networks in supply chains and reduce the comparative computational complexity of algorithms. Set theory is employed to evaluate and model the all-terminal reliability of the improved spanning tree algorithm and present a case study of a supply chain used in lamp production to illustrate the application of the proposed approach.

Causal Networks with Selectively Influenced Components

DTIC Science & Technology

2012-02-29

influences a different vertex. If so, the form of a processing tree accounting for the data can determined. Prior to the work on the grant, processing...their order. Processing trees were found to account well for data in the literature on immediate ordered recall and on effects of sleep and...ordered in the network) or concurrent (unordered). Ordinarily for a given data set, if one directed acyclic network can account for the data

Very short-term reactive forecasting of the solar ultraviolet index using an extreme learning machine integrated with the solar zenith angle.

PubMed

Deo, Ravinesh C; Downs, Nathan; Parisi, Alfio V; Adamowski, Jan F; Quilty, John M

2017-05-01

Exposure to erythemally-effective solar ultraviolet radiation (UVR) that contributes to malignant keratinocyte cancers and associated health-risk is best mitigated through innovative decision-support systems, with global solar UV index (UVI) forecast necessary to inform real-time sun-protection behaviour recommendations. It follows that the UVI forecasting models are useful tools for such decision-making. In this study, a model for computationally-efficient data-driven forecasting of diffuse and global very short-term reactive (VSTR) (10-min lead-time) UVI, enhanced by drawing on the solar zenith angle (θ s ) data, was developed using an extreme learning machine (ELM) algorithm. An ELM algorithm typically serves to address complex and ill-defined forecasting problems. UV spectroradiometer situated in Toowoomba, Australia measured daily cycles (0500-1700h) of UVI over the austral summer period. After trialling activations functions based on sine, hard limit, logarithmic and tangent sigmoid and triangular and radial basis networks for best results, an optimal ELM architecture utilising logarithmic sigmoid equation in hidden layer, with lagged combinations of θ s as the predictor data was developed. ELM's performance was evaluated using statistical metrics: correlation coefficient (r), Willmott's Index (WI), Nash-Sutcliffe efficiency coefficient (E NS ), root mean square error (RMSE), and mean absolute error (MAE) between observed and forecasted UVI. Using these metrics, the ELM model's performance was compared to that of existing methods: multivariate adaptive regression spline (MARS), M5 Model Tree, and a semi-empirical (Pro6UV) clear sky model. Based on RMSE and MAE values, the ELM model (0.255, 0.346, respectively) outperformed the MARS (0.310, 0.438) and M5 Model Tree (0.346, 0.466) models. Concurring with these metrics, the Willmott's Index for the ELM, MARS and M5 Model Tree models were 0.966, 0.942 and 0.934, respectively. About 57% of the ELM model's absolute errors were small in magnitude (±0.25), whereas the MARS and M5 Model Tree models generated 53% and 48% of such errors, respectively, indicating the latter models' errors to be distributed in larger magnitude error range. In terms of peak global UVI forecasting, with half the level of error, the ELM model outperformed MARS and M5 Model Tree. A comparison of the magnitude of hourly-cumulated errors of 10-min lead time forecasts for diffuse and global UVI highlighted ELM model's greater accuracy compared to MARS, M5 Model Tree or Pro6UV models. This confirmed the versatility of an ELM model drawing on θ s data for VSTR forecasting of UVI at near real-time horizon. When applied to the goal of enhancing expert systems, ELM-based accurate forecasts capable of reacting quickly to measured conditions can enhance real-time exposure advice for the public, mitigating the potential for solar UV-exposure-related disease. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Long-term growth decline in Toona ciliata in a moist tropical forest in Bangladesh: Impact of global warming

NASA Astrophysics Data System (ADS)

Rahman, Mizanur; Islam, Rofiqul; Islam, Mahmuda

2017-04-01

Tropical forests are carbon rich ecosystems and small changes in tropical forest tree growth substantially influence the global carbon cycle. Forest monitoring studies report inconsistent growth changes in tropical forest trees over the past decades. Most of the studies highlighted changes in the forest level carbon gain, neglecting the species-specific growth changes which ultimately determine community-level responses. Tree-ring analysis can provide historical data on species-specific tree growth with annual resolution. Such studies are inadequate in Bangladesh, which is one of the most climate sensitive regions in the tropics. In this study, we investigated long-term growth rates of Toona ciliata in a moist tropical forest of Bangladesh by using tree-ring analysis. We sampled 50 trees of varying size, obtained increment cores from these trees and measured tree-ring width. Analyses of growth patterns revealed size-dependent growth increments. After correcting for the effect of tree size on tree growth (ontogenetic changes) by two different methods we found declining growth rates in T. ciliata from 1960 to 2013. Standardized ring-width index (RWI) was strongly negatively correlated with annual mean and maximum temperatures suggesting that rising temperature might cause the observed growth decline in T. ciliata. Assuming that global temperatures will rise at the current rate, the observed growth decline is assumed to continue. The analysis of stable carbon and oxygen isotopes may reveal more insight on the physiological response of this species to future climatic changes.

Global Genome Biodiversity Network: saving a blueprint of the Tree of Life - a botanical perspective.

PubMed

Seberg, O; Droege, G; Barker, K; Coddington, J A; Funk, V; Gostel, M; Petersen, G; Smith, P P

2016-09-01

Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on 'harvesting' the Tree of Life for vascular plant taxa to enable genome-level studies. While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company.

BGCI’s Rrole in co-ordinating a botanic garden-centred global system for the conservation of all tree diversity

Treesearch

Paul Smith

2017-01-01

It is estimated that there are at least 60,000 tree species globally and that more than 20 percent of them are threatened with extinction. This threatened tree diversity will have a critical impact for solving some of this century’s major challenges in the areas of energy, water scarcity, human health, food security, climate change and habitat degradation. Botanic...

Reconstructing missing daily precipitation data using regression trees and artificial neural networks

USDA-ARS?s Scientific Manuscript database

Incomplete meteorological data has been a problem in environmental modeling studies. The objective of this work was to develop a technique to reconstruct missing daily precipitation data in the central part of Chesapeake Bay Watershed using regression trees (RT) and artificial neural networks (ANN)....

MINER: exploratory analysis of gene interaction networks by machine learning from expression data.

PubMed

Kadupitige, Sidath Randeni; Leung, Kin Chun; Sellmeier, Julia; Sivieng, Jane; Catchpoole, Daniel R; Bain, Michael E; Gaëta, Bruno A

2009-12-03

The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "one-shot" reconstruction of the whole network with no intervention from the user, or offer only simple correlation analysis to infer gene dependencies. We have developed MINER (Microarray Interactive Network Exploration and Representation), an application that combines multivariate non-linear tree learning of individual gene regulatory dependencies, visualisation of these dependencies as both trees and networks, and representation of known biological relationships based on common Gene Ontology annotations. MINER allows biologists to explore the dependencies influencing the expression of individual genes in a gene expression data set in the form of decision, model or regression trees, using their domain knowledge to guide the exploration and formulate hypotheses. Multiple trees can then be summarised in the form of a gene network diagram. MINER is being adopted by several of our collaborators and has already led to the discovery of a new significant regulatory relationship with subsequent experimental validation. Unlike most gene regulatory network inference methods, MINER allows the user to start from genes of interest and build the network gene-by-gene, incorporating domain expertise in the process. This approach has been used successfully with RNA microarray data but is applicable to other quantitative data produced by high-throughput technologies such as proteomics and "next generation" DNA sequencing.

Reconstructions of Columbia River streamflow from tree-ring chronologies in the Pacific Northwest, USA

USGS Publications Warehouse

Littell, Jeremy; Pederson, Gregory T.; Gray, Stephen T.; Tjoelker, Michael; Hamlet, Alan F.; Woodhouse, Connie A.

2016-01-01

We developed Columbia River streamflow reconstructions using a network of existing, new, and updated tree-ring records sensitive to the main climatic factors governing discharge. Reconstruction quality is enhanced by incorporating tree-ring chronologies where high snowpack limits growth, which better represent the contribution of cool-season precipitation to flow than chronologies from trees positively sensitive to hydroclimate alone. The best performing reconstruction (back to 1609 CE) explains 59% of the historical variability and the longest reconstruction (back to 1502 CE) explains 52% of the variability. Droughts similar to the high-intensity, long-duration low flows observed during the 1920s and 1940s are rare, but occurred in the early 1500s and 1630s-1640s. The lowest Columbia flow events appear to be reflected in chronologies both positively and negatively related to streamflow, implying low snowpack and possibly low warm-season precipitation. High flows of magnitudes observed in the instrumental record appear to have been relatively common, and high flows from the 1680s to 1740s exceeded the magnitude and duration of observed wet periods in the late-19th and 20th Century. Comparisons between the Columbia River reconstructions and future projections of streamflow derived from global climate and hydrologic models show the potential for increased hydrologic variability, which could present challenges for managing water in the face of competing demands

Annual global tree cover estimated by fusing optical and SAR satellite observations

NASA Astrophysics Data System (ADS)

Feng, M.; Sexton, J. O.; Channan, S.; Townshend, J. R.

2017-12-01

Tree cover defined structurally as the proportional, vertically projected area of vegetation (including leaves, stems, branches, etc.) of woody plants above a given height affects terrestrial energy and water exchanges, photosynthesis and transpiration, net primary production, and carbon and nutrient fluxes. Tree cover provides a measurable attribute upon which forest cover may be defined. Changes in tree cover over time can be used to monitor and retrieve site-specific histories of forest disturbance, succession, and degradation. Measurements of Earth's tree cover have been produced at regional, national, and global extents. However, most representations are static, and those for which multiple time periods have been produced are neither intended nor adequate for consistent, long-term monitoring. Moreover, although a substantial proportion of change has been shown to occur at resolutions below 250 m, existing long-term, Landsat-resolution datasets are either produced as static layers or with annual, five- or ten-year temporal resolution. We have developed an algorithms to retrieve seamless and consistent, sub-hectare resolution estimates of tree-canopy from optical and radar satellite data sources (e.g., Landsat, Sentinel-2, and ALOS-PALSAR). Our approach to estimation enables assimilation of multiple data sources and produces estimates of both cover and its uncertainty at the scale of pixels. It has generated the world's first Landsat-based percent tree cover dataset in 2013. Our previous algorithms are being adapted to produce prototype percent-tree and water-cover layers globally in 2000, 2005, and 2010—as well as annually over North and South America from 2010 to 2015—from passive-optical (Landsat and Sentinel-2) and SAR measurements. Generating a global, annual dataset is beyond the scope of this support; however, North and South America represent all of the world's major biomes and so offer the complete global range of environmental sources of error and uncertainty.

Upper air teleconnections to Ob River flows and tree rings

NASA Astrophysics Data System (ADS)

Meko, David; Panyushkina, Irina; Agafonov, Leonid

2015-04-01

The Ob River, one of the world's greatest rivers, with a catchment basin about the size of Western Europe, contributes 12% or more of the annual freshwater inflow to the Arctic Ocean. The input of heat and fresh water is important to the global climate system through effects on sea ice, salinity, and the thermohaline circulation of the ocean. As part of a tree-ring project to obtain multi-century long information on variability of Ob River flows, a network of 18 sites of Pinus, Larix, Populus and Salix has been collected along the Ob in the summers of 2013 and 2014. Analysis of collections processed so far indicates a significant relationship of tree-growth to river discharge. Moderation of the floodplain air temperature regime by flooding appears to be an important driver of the tree-ring response. In unraveling the relationship of tree-growth to river flows, it is important to identify atmospheric circulation features directly linked to observed time series variations of flow and tree growth. In this study we examine statistical links between primary teleconnection modes of Northern Hemisphere upper-air (500 mb) circulation, Ob River flow, and tree-ring chronologies. Annual discharge at the mouth of the Ob River is found to be significantly positively related to the phase of the East Atlantic (EA) pattern, the second prominent mode of low-frequency variability over the North Atlantic. The EA pattern, consisting of a north-south dipole of pressure-anomaly centers spanning the North Atlantic from east to west, is associated with a low-pressure anomaly centered over the Ob River Basin, and with a pattern of positive precipitation anomaly of the same region. The positive correlation of discharge and EA is consistent with these know patterns, and is contrasted with generally negative (though smaller) correlations between EA and tree-ring chronologies. The signs of correlations are consistent with a conceptual model of river influence on tree growth through air temperature. Future work aims at combining the tree-ring samples from living trees and remnant wood to reconstruction to quantitiative reconstruction of annual flow over the past millennium.

Climate Warming Threatens Semi-arid Forests in Inner Asia

NASA Astrophysics Data System (ADS)

WU, X.; Liu, H.; Qi, Z.; Li, X.

2014-12-01

A line of evidences reveal an increasing tree growth decline and tree mortality mainly attributable to climate warming and the warming-mediated changes in drought and other processes (such as fire and insect dynamics) in many parts of world tropical, temperate and boreal forests. However, the growth responses to climate change of the widely distributed semi-arid forests are unclear. Here, we synthetically investigate the tree growth patterns during past decades and its interannual response to climate variations in Inner Asia combining the ground truth field survey and samplings, remote sensing observations and climate data. We identified a pervasive tree growth decline since mid-1990s in semi-arid forests in Inner Asia. The widely observed tree growth decline is dominantly attributable to warming-induced water stress during pre- and early growing season. Tree growth of semi-arid forests in Inner Asia is particularly susceptible to spring warming and has been suffering a prolonged growth limitation in recent decades due to spring warming-mediated water conditions. Additionally, we identified a much slower growth rate in younger trees and a lack of tree regeneration in these semi-arid forests. The widely observed forest growth reduction and lack of tree regeneration over semi-arid forests in Inner Asia could predictably exert great effects on forest structure, regionally/globally biophysical and biochemical processes and the feedbacks between biosphere and atmosphere. Notably, further increases in forest stress and tree mortality could be reasonably expected, especially in context of the increase frequency and severity of high temperature and heat waves and changes in forest disturbances, potentially driving the eventual regional loss of current semi-arid forests. Given the potential risks of climate induced forest dieback, increased management attention to adaptation options for enhancing forest resistance and resilience to projected climate stress can be expected. However, the functionally realistic mechanisms beneath the pervasively climate-induced forest decline/dieback still remain unclear. Network-based long-term surveys and experiment studies are urgently needed for further understandings regarding the responses of forest/tree growth to climate warming/variations.

Routing Algorithm based on Minimum Spanning Tree and Minimum Cost Flow for Hybrid Wireless-optical Broadband Access Network

NASA Astrophysics Data System (ADS)

Le, Zichun; Suo, Kaihua; Fu, Minglei; Jiang, Ling; Dong, Wen

2012-03-01

In order to minimize the average end to end delay for data transporting in hybrid wireless optical broadband access network, a novel routing algorithm named MSTMCF (minimum spanning tree and minimum cost flow) is devised. The routing problem is described as a minimum spanning tree and minimum cost flow model and corresponding algorithm procedures are given. To verify the effectiveness of MSTMCF algorithm, extensively simulations based on OWNS have been done under different types of traffic source.

Global accumulation of tree-crops and its competition with forest loss and food security in Southeast Asia

NASA Astrophysics Data System (ADS)

Shigematsu, A.; Mizoue, N.; Yoshida, S.

2011-12-01

Tree-crops, which are the plants holding trunks for several decades and supply products in a form of fruits or resin, such as oil palm and natural rubber, comprises 5% of crop land of the world in 2008. While the expansion has been a major driver of forest loss and food security, a research on the process and proportion of tree-crops on global scale has been lacking. We examined the regional and temporal difference on the expansion process of the top five abundant tree-crops of the world while linking the trend of crop areas (for food production) and forest areas between 1960s and 2000s. We adopted FAOSTAT database and focused on globally abundant top-five tree crops (oil palm, rubber, coconuts, coffee, cocoa). Globally, notable proportional change of these five tree-crops on total crop lands was observed in Asia from 1.8% in 1961 to 5.2% in 2008. Regionally, it was Southeast Asia that exhibited the growth in the ratio of these five tree-crops on overall crop lands for the last half a century; from only one-tenth in 1961 to as much as one-fourth in 2008. While oil palm plantations are established in southern part of Southeast Asia, rubber plantations are being established in expense of traditional agricultural fields in northern Southeast Asia. We identified the tree-crops expansion has been increased in expense of agricultural areas (production for food) in Thailand from 1961 to 2008 (r = -0.828, P < 0.0001) and Myanmar from 1961 to 1989 (r = -0.741, P < 0.0001). The impacts of ongoing tree-crops expansion on food and wood security of the region need to be carefully monitored in terms of biodiversity, carbon storage, the local climate and the hydrological cycle. We proposed the suggestion the necessity of a new framework of protecting agricultural land from the expansion of tree-crops, especially oil palm and rubber.

Evaluating the responses of forest ecosystems to climate change and CO2 using dynamic global vegetation models.

PubMed

Song, Xiang; Zeng, Xiaodong

2017-02-01

The climate has important influences on the distribution and structure of forest ecosystems, which may lead to vital feedback to climate change. However, much of the existing work focuses on the changes in carbon fluxes or water cycles due to climate change and/or atmospheric CO 2 , and few studies have considered how and to what extent climate change and CO 2 influence the ecosystem structure (e.g., fractional coverage change) and the changes in the responses of ecosystems with different characteristics. In this work, two dynamic global vegetation models (DGVMs): IAP-DGVM coupled with CLM3 and CLM4-CNDV, were used to investigate the response of the forest ecosystem structure to changes in climate (temperature and precipitation) and CO 2 concentration. In the temperature sensitivity tests, warming reduced the global area-averaged ecosystem gross primary production in the two models, which decreased global forest area. Furthermore, the changes in tree fractional coverage (Δ F tree ; %) from the two models were sensitive to the regional temperature and ecosystem structure, i.e., the mean annual temperature (MAT; °C) largely determined whether Δ F tree was positive or negative, while the tree fractional coverage ( F tree ; %) played a decisive role in the amplitude of Δ F tree around the globe, and the dependence was more remarkable in IAP-DGVM. In cases with precipitation change, F tree had a uniformly positive relationship with precipitation, especially in the transition zones of forests (30% <  F tree  < 60%) for IAP-DGVM and in semiarid and arid regions for CLM4-CNDV. Moreover, Δ F tree had a stronger dependence on F tree than on the mean annual precipitation (MAP; mm/year). It was also demonstrated that both models captured the fertilization effects of the CO 2 concentration.

The sweet side of global change-dynamic responses of non-structural carbohydrates to drought, elevated CO2 and nitrogen fertilization in tree species.

PubMed

Li, Weibin; Hartmann, Henrik; Adams, Henry D; Zhang, Hongxia; Jin, Changjie; Zhao, Chuanyan; Guan, Dexin; Wang, Anzhi; Yuan, Fenghui; Wu, Jiabing

2018-06-11

Non-structural carbohydrates (NSC) play a central role in plant functioning as energy carriers and building blocks for primary and secondary metabolism. Many studies have investigated how environmental and anthropogenic changes, like increasingly frequent and severe drought episodes, elevated CO2 and atmospheric nitrogen (N) deposition, influence NSC concentrations in individual trees. However, this wealth of data has not been analyzed yet to identify general trends using a common statistical framework. A thorough understanding of tree responses to global change is required for making realistic predictions of vegetation dynamics. Here we compiled data from 57 experimental studies on 71 tree species and conducted a meta-analysis to evaluate general responses of stored soluble sugars, starch and total NSC (soluble sugars + starch) concentrations in different tree organs (foliage, above-ground wood and roots) to drought, elevated CO2 and N deposition. We found that drought significantly decreased total NSC in roots (-17.3%), but not in foliage and above-ground woody tissues (bole, branch, stem and/or twig). Elevated CO2 significantly increased total NSC in foliage (+26.2%) and roots (+12.8%), but not in above-ground wood. By contrast, total NSC significantly decreased in roots (-17.9%), increased in above-ground wood (+6.1%), but was unaffected in foliage from N fertilization. In addition, the response of NSC to three global change drivers was strongly affected by tree taxonomic type, leaf habit, tree age and treatment intensity. Our results pave the way for a better understanding of general tree function responses to drought, elevated CO2 and N fertilization. The existing data also reveal that more long-term studies on mature trees that allow testing interactions between these factors are urgently needed to provide a basis for forecasting tree responses to environmental change at the global scale.

Use of Bayesian event trees in semi-quantitative volcano eruption forecasting and hazard analysis

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

Use of Bayesian event trees to forecast eruptive activity during volcano crises is an increasingly common practice for the USGS-USAID Volcano Disaster Assistance Program (VDAP) in collaboration with foreign counterparts. This semi-quantitative approach combines conceptual models of volcanic processes with current monitoring data and patterns of occurrence to reach consensus probabilities. This approach allows a response team to draw upon global datasets, local observations, and expert judgment, where the relative influence of these data depends upon the availability and quality of monitoring data and the degree to which the volcanic history is known. The construction of such event trees additionally relies upon existence and use of relevant global databases and documented past periods of unrest. Because relevant global databases may be underpopulated or nonexistent, uncertainty in probability estimations may be large. Our 'hybrid' approach of combining local and global monitoring data and expert judgment facilitates discussion and constructive debate between disciplines: including seismology, gas geochemistry, geodesy, petrology, physical volcanology and technology/engineering, where difference in opinion between response team members contributes to definition of the uncertainty in the probability estimations. In collaboration with foreign colleagues, we have created event trees for numerous areas experiencing volcanic unrest. Event trees are created for a specified time frame and are updated, revised, or replaced as the crisis proceeds. Creation of an initial tree is often prompted by a change in monitoring data, such that rapid assessment of probability is needed. These trees are intended as a vehicle for discussion and a way to document relevant data and models, where the target audience is the scientists themselves. However, the probabilities derived through the event-tree analysis can also be used to help inform communications with emergency managers and the public. VDAP trees evaluate probabilities of: magmatic intrusion, likelihood of eruption, magnitude of eruption, and types of associated hazardous events and their extents. In a few cases, trees have been extended to also assess and communicate vulnerability and relative risk.

Activity classification using realistic data from wearable sensors.

PubMed

Pärkkä, Juha; Ermes, Miikka; Korpipää, Panu; Mäntyjärvi, Jani; Peltola, Johannes; Korhonen, Ilkka

2006-01-01

Automatic classification of everyday activities can be used for promotion of health-enhancing physical activities and a healthier lifestyle. In this paper, methods used for classification of everyday activities like walking, running, and cycling are described. The aim of the study was to find out how to recognize activities, which sensors are useful and what kind of signal processing and classification is required. A large and realistic data library of sensor data was collected. Sixteen test persons took part in the data collection, resulting in approximately 31 h of annotated, 35-channel data recorded in an everyday environment. The test persons carried a set of wearable sensors while performing several activities during the 2-h measurement session. Classification results of three classifiers are shown: custom decision tree, automatically generated decision tree, and artificial neural network. The classification accuracies using leave-one-subject-out cross validation range from 58 to 97% for custom decision tree classifier, from 56 to 97% for automatically generated decision tree, and from 22 to 96% for artificial neural network. Total classification accuracy is 82 % for custom decision tree classifier, 86% for automatically generated decision tree, and 82% for artificial neural network.

Global Tree Range Shifts Under Forecasts from Two Alternative GCMs Using Two Future Scenarios

NASA Astrophysics Data System (ADS)

Hargrove, W. W.; Kumar, J.; Potter, K. M.; Hoffman, F. M.

2013-12-01

Global shifts in the environmentally suitable ranges of 215 tree species were predicted under forecasts from two GCMs (the Parallel Climate Model (PCM), and the Hadley Model), each under two IPCC future climatic scenarios (A1 and B1), each at two future dates (2050 and 2100). The analysis considers all global land surface at a resolution of 4 km2. A statistical multivariate clustering procedure was used to quantitatively delineate 30 thousand environmentally homogeneous ecoregions across present and 8 potential future global locations at once, using global maps of 17 environmental characteristics describing temperature, precipitation, soils, topography and solar insolation. Presence of each tree species on Forest Inventory Analysis (FIA) plots and in Global Biodiversity Information Facility (GBIF) samples was used to select a subset of suitable ecoregions from the full set of 30 thousand. Once identified, this suitable subset of ecoregions was compared to the known current range of the tree species under present conditions. Predicted present ranges correspond well with current understanding for all but a few of the 215 tree species. The subset of suitable ecoregions for each tree species can then be tracked into the future to determine whether the suitable home range for this species remains the same, moves, grows, shrinks, or disappears under each model/scenario combination. Occurrence and growth performance measurements for various tree species across the U.S. are limited to FIA plots. We present a new, general-purpose empirical imputation method which associates sparse measurements of dependent variables with particular multivariate clustered combinations of the independent variables, and then estimates values for unmeasured clusters, based on directional proximity in multidimensional data space, at both the cluster and map-cell levels of resolution. Using Associative Clustering, we scaled up the FIA point measurements into contonuous maps that show the expected growth and suitability for individual tree species across the continental US. Maps were generated for each tree species showing the Minimum Required Movement (MRM) straight-line distance from each currently suitable location to the geographically nearest "lifeboat" location having suitable conditions in the future. Locations that are the closest "lifeboats" for many MRM propagules originating from wide surrounding areas may constitute high-priority preservation targets as a refugium against climatic change.

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.

PubMed

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters' approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

Toward an optimal design principle in symmetric and asymmetric tree flow networks.

PubMed

Miguel, Antonio F

2016-01-21

Fluid flow in tree-shaped networks plays an important role in both natural and engineered systems. This paper focuses on laminar flows of Newtonian and non-Newtonian power law fluids in symmetric and asymmetric bifurcating trees. Based on the constructal law, we predict the tree-shaped architecture that provides greater access to the flow subjected to the total network volume constraint. The relationships between the sizes of parent and daughter tubes are presented both for symmetric and asymmetric branching tubes. We also approach the wall-shear stresses and the flow resistance in terms of first tube size, degree of asymmetry between daughter branches, and rheological behavior of the fluid. The influence of tubes obstructing the fluid flow is also accounted for. The predictions obtained by our theory-driven approach find clear support in the findings of previous experimental studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Human impacts drive a global topographic signature in tree cover.

PubMed

Sandel, Brody; Svenning, Jens-Christian

2013-01-01

The Anthropocene is a geological epoch marked by major human influences on processes in the atmosphere, biosphere, hydrosphere and geosphere. One of the most dramatic features of the Anthropocene is the massive alteration of the Earth's vegetation, including forests. Here we investigate the role of topography in shaping human impacts on tree cover from local to global scales. We show that human impacts have resulted in a global tendency for tree cover to be constrained to sloped terrain and losses to be concentrated on flat terrain. This effect increases in strength with increasing human pressure and is most pronounced in countries with rapidly growing economies, limited human population stress and highly effective governments. These patterns likely reflect the relative inaccessibility of sloped topography and have important implications for conservation and modelling of future tree cover.

Disrupted Brain Functional Organization in Epilepsy Revealed by Graph Theory Analysis.

PubMed

Song, Jie; Nair, Veena A; Gaggl, Wolfgang; Prabhakaran, Vivek

2015-06-01

The human brain is a complex and dynamic system that can be modeled as a large-scale brain network to better understand the reorganizational changes secondary to epilepsy. In this study, we developed a brain functional network model using graph theory methods applied to resting-state fMRI data acquired from a group of epilepsy patients and age- and gender-matched healthy controls. A brain functional network model was constructed based on resting-state functional connectivity. A minimum spanning tree combined with proportional thresholding approach was used to obtain sparse connectivity matrices for each subject, which formed the basis of brain networks. We examined the brain reorganizational changes in epilepsy thoroughly at the level of the whole brain, the functional network, and individual brain regions. At the whole-brain level, local efficiency was significantly decreased in epilepsy patients compared with the healthy controls. However, global efficiency was significantly increased in epilepsy due to increased number of functional connections between networks (although weakly connected). At the functional network level, there were significant proportions of newly formed connections between the default mode network and other networks and between the subcortical network and other networks. There was a significant proportion of decreasing connections between the cingulo-opercular task control network and other networks. Individual brain regions from different functional networks, however, showed a distinct pattern of reorganizational changes in epilepsy. These findings suggest that epilepsy alters brain efficiency in a consistent pattern at the whole-brain level, yet alters brain functional networks and individual brain regions differently.

Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area

USGS Publications Warehouse

Greenwood, Sarah; Ruiz-Benito, Paloma; Martinez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D.; Fensham, Rod; Laughlin, Daniel C.; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J. B.; Jump, Alistair S.

2017-01-01

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees−1 year−1) increased 0.46 (95% CI = 0.2–0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future.

Model-Based Design of Tree WSNs for Decentralized Detection.

PubMed

Tantawy, Ashraf; Koutsoukos, Xenofon; Biswas, Gautam

2015-08-20

The classical decentralized detection problem of finding the optimal decision rules at the sensor and fusion center, as well as variants that introduce physical channel impairments have been studied extensively in the literature. The deployment of WSNs in decentralized detection applications brings new challenges to the field. Protocols for different communication layers have to be co-designed to optimize the detection performance. In this paper, we consider the communication network design problem for a tree WSN. We pursue a system-level approach where a complete model for the system is developed that captures the interactions between different layers, as well as different sensor quality measures. For network optimization, we propose a hierarchical optimization algorithm that lends itself to the tree structure, requiring only local network information. The proposed design approach shows superior performance over several contentionless and contention-based network design approaches.

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

PubMed

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.

Graphical models for optimal power flow

DOE PAGES

Dvijotham, Krishnamurthy; Chertkov, Michael; Van Hentenryck, Pascal; ...

2016-09-13

Optimal power flow (OPF) is the central optimization problem in electric power grids. Although solved routinely in the course of power grid operations, it is known to be strongly NP-hard in general, and weakly NP-hard over tree networks. In this paper, we formulate the optimal power flow problem over tree networks as an inference problem over a tree-structured graphical model where the nodal variables are low-dimensional vectors. We adapt the standard dynamic programming algorithm for inference over a tree-structured graphical model to the OPF problem. Combining this with an interval discretization of the nodal variables, we develop an approximation algorithmmore » for the OPF problem. Further, we use techniques from constraint programming (CP) to perform interval computations and adaptive bound propagation to obtain practically efficient algorithms. Compared to previous algorithms that solve OPF with optimality guarantees using convex relaxations, our approach is able to work for arbitrary tree-structured distribution networks and handle mixed-integer optimization problems. Further, it can be implemented in a distributed message-passing fashion that is scalable and is suitable for “smart grid” applications like control of distributed energy resources. In conclusion, numerical evaluations on several benchmark networks show that practical OPF problems can be solved effectively using this approach.« less

Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs

NASA Astrophysics Data System (ADS)

Biazzo, Indaco; Braunstein, Alfredo; Zecchina, Riccardo

2012-08-01

We study the behavior of an algorithm derived from the cavity method for the prize-collecting steiner tree (PCST) problem on graphs. The algorithm is based on the zero temperature limit of the cavity equations and as such is formally simple (a fixed point equation resolved by iteration) and distributed (parallelizable). We provide a detailed comparison with state-of-the-art algorithms on a wide range of existing benchmarks, networks, and random graphs. Specifically, we consider an enhanced derivative of the Goemans-Williamson heuristics and the dhea solver, a branch and cut integer linear programming based approach. The comparison shows that the cavity algorithm outperforms the two algorithms in most large instances both in running time and quality of the solution. Finally we prove a few optimality properties of the solutions provided by our algorithm, including optimality under the two postprocessing procedures defined in the Goemans-Williamson derivative and global optimality in some limit cases.

An overview of natural hazard impacts to railways and urban transportation systems

NASA Astrophysics Data System (ADS)

Bíl, Michal; Nezval, Vojtěch; Bílová, Martina; Andrášik, Richard; Kubeček, Jan

2017-04-01

We present an overview and two case studies of natural hazard impacts on rail transportation systems in the Czech Republic. Flooding, landsliding, heavy snowfall, windstorms and glaze (black ice) are the most common natural processes which occur in this region. Whereas flooding and landsliding usually cause direct damage to the transportation infrastructure, other hazards predominantly cause indirect losses. Railway and urban tramline networks are almost fully dependent on electricity which is provided by a system of overhead lines (electric lines above the tracks). These lines are extremely susceptible to formation of glaze which blocks conduction of electric current. A December 2014 glaze event caused significant indirect losses in the largest Czech cities and railways due to the above-mentioned process. Details of this event will be provided during the presentation. Windstorms usually cause tree falls which can affect overhead lines and physically block railway tracks. Approximately 30 % of the Czech railway network is closer than 50 m from the nearest forest. This presents significant potential for transport interruption due to falling trees. Complicated legal relations among the owners of the plots of land along railways, the environment (full-grown trees and related habitat), and the railway administrator are behind many traffic interruptions due to falling trees. We have registered 2040 tree falls between 2012 and 2015 on the railway network. A model of the fallen tree hazard was created for the entire Czech railway network. Both above-mentioned case studies provide illustrative examples of the increased fragility of the modern transportation systems which fully rely on electricity. Natural processes with a low destructive power are thereby able to cause network wide service cut-offs.

Support-vector-machine tree-based domain knowledge learning toward automated sports video classification

NASA Astrophysics Data System (ADS)

Xiao, Guoqiang; Jiang, Yang; Song, Gang; Jiang, Jianmin

2010-12-01

We propose a support-vector-machine (SVM) tree to hierarchically learn from domain knowledge represented by low-level features toward automatic classification of sports videos. The proposed SVM tree adopts a binary tree structure to exploit the nature of SVM's binary classification, where each internal node is a single SVM learning unit, and each external node represents the classified output type. Such a SVM tree presents a number of advantages, which include: 1. low computing cost; 2. integrated learning and classification while preserving individual SVM's learning strength; and 3. flexibility in both structure and learning modules, where different numbers of nodes and features can be added to address specific learning requirements, and various learning models can be added as individual nodes, such as neural networks, AdaBoost, hidden Markov models, dynamic Bayesian networks, etc. Experiments support that the proposed SVM tree achieves good performances in sports video classifications.

A pseudoproxy assessment of data assimilation for reconstructing the atmosphere-ocean dynamics of hydroclimate extremes

NASA Astrophysics Data System (ADS)

Steiger, Nathan J.; Smerdon, Jason E.

2017-10-01

Because of the relatively brief observational record, the climate dynamics that drive multiyear to centennial hydroclimate variability are not adequately characterized and understood. Paleoclimate reconstructions based on data assimilation (DA) optimally fuse paleoclimate proxies with the dynamical constraints of climate models, thus providing a coherent dynamical picture of the past. DA is therefore an important new tool for elucidating the mechanisms of hydroclimate variability over the last several millennia. But DA has so far remained untested for global hydroclimate reconstructions. Here we explore whether or not DA can be used to skillfully reconstruct global hydroclimate variability along with the driving climate dynamics. Through a set of idealized pseudoproxy experiments, we find that an established DA reconstruction approach can in principle be used to reconstruct hydroclimate at both annual and seasonal timescales. We find that the skill of such reconstructions is generally highest near the proxy sites. This set of reconstruction experiments is specifically designed to estimate a realistic upper bound for the skill of this DA approach. Importantly, this experimental framework allows us to see where and for what variables the reconstruction approach may never achieve high skill. In particular for tree rings, we find that hydroclimate reconstructions depend critically on moisture-sensitive trees, while temperature reconstructions depend critically on temperature-sensitive trees. Real-world DA-based reconstructions will therefore likely require a spatial mixture of temperature- and moisture-sensitive trees to reconstruct both temperature and hydroclimate variables. Additionally, we illustrate how DA can be used to elucidate the dynamical mechanisms of drought with two examples: tropical drivers of multiyear droughts in the North American Southwest and in equatorial East Africa. This work thus provides a foundation for future DA-based hydroclimate reconstructions using real-proxy networks while also highlighting the utility of this important tool for hydroclimate research.

VESGEN Software for Mapping and Quantification of Vascular Regulators

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, Patricia A.; Vickerman, Mary B.; Keith, Patricia A.

2012-01-01

VESsel GENeration (VESGEN) Analysis is an automated software that maps and quantifies effects of vascular regulators on vascular morphology by analyzing important vessel parameters. Quantification parameters include vessel diameter, length, branch points, density, and fractal dimension. For vascular trees, measurements are reported as dependent functions of vessel branching generation. VESGEN maps and quantifies vascular morphological events according to fractal-based vascular branching generation. It also relies on careful imaging of branching and networked vascular form. It was developed as a plug-in for ImageJ (National Institutes of Health, USA). VESGEN uses image-processing concepts of 8-neighbor pixel connectivity, skeleton, and distance map to analyze 2D, black-and-white (binary) images of vascular trees, networks, and tree-network composites. VESGEN maps typically 5 to 12 (or more) generations of vascular branching, starting from a single parent vessel. These generations are tracked and measured for critical vascular parameters that include vessel diameter, length, density and number, and tortuosity per branching generation. The effects of vascular therapeutics and regulators on vascular morphology and branching tested in human clinical or laboratory animal experimental studies are quantified by comparing vascular parameters with control groups. VESGEN provides a user interface to both guide and allow control over the users vascular analysis process. An option is provided to select a morphological tissue type of vascular trees, network or tree-network composites, which determines the general collections of algorithms, intermediate images, and output images and measurements that will be produced.

Development of hybrid genetic-algorithm-based neural networks using regression trees for modeling air quality inside a public transportation bus.

PubMed

Kadiyala, Akhil; Kaur, Devinder; Kumar, Ashok

2013-02-01

The present study developed a novel approach to modeling indoor air quality (IAQ) of a public transportation bus by the development of hybrid genetic-algorithm-based neural networks (also known as evolutionary neural networks) with input variables optimized from using the regression trees, referred as the GART approach. This study validated the applicability of the GART modeling approach in solving complex nonlinear systems by accurately predicting the monitored contaminants of carbon dioxide (CO2), carbon monoxide (CO), nitric oxide (NO), sulfur dioxide (SO2), 0.3-0.4 microm sized particle numbers, 0.4-0.5 microm sized particle numbers, particulate matter (PM) concentrations less than 1.0 microm (PM10), and PM concentrations less than 2.5 microm (PM2.5) inside a public transportation bus operating on 20% grade biodiesel in Toledo, OH. First, the important variables affecting each monitored in-bus contaminant were determined using regression trees. Second, the analysis of variance was used as a complimentary sensitivity analysis to the regression tree results to determine a subset of statistically significant variables affecting each monitored in-bus contaminant. Finally, the identified subsets of statistically significant variables were used as inputs to develop three artificial neural network (ANN) models. The models developed were regression tree-based back-propagation network (BPN-RT), regression tree-based radial basis function network (RBFN-RT), and GART models. Performance measures were used to validate the predictive capacity of the developed IAQ models. The results from this approach were compared with the results obtained from using a theoretical approach and a generalized practicable approach to modeling IAQ that included the consideration of additional independent variables when developing the aforementioned ANN models. The hybrid GART models were able to capture majority of the variance in the monitored in-bus contaminants. The genetic-algorithm-based neural network IAQ models outperformed the traditional ANN methods of the back-propagation and the radial basis function networks. The novelty of this research is the development of a novel approach to modeling vehicular indoor air quality by integration of the advanced methods of genetic algorithms, regression trees, and the analysis of variance for the monitored in-vehicle gaseous and particulate matter contaminants, and comparing the results obtained from using the developed approach with conventional artificial intelligence techniques of back propagation networks and radial basis function networks. This study validated the newly developed approach using holdout and threefold cross-validation methods. These results are of great interest to scientists, researchers, and the public in understanding the various aspects of modeling an indoor microenvironment. This methodology can easily be extended to other fields of study also.

Visualization of time-varying natural tree data

Treesearch

S. Brasch; L. Linsen; E.G. McPherson

2007-01-01

Given a set of global (natural) tree parameters measured for many specimens of different ages for a range of species, we have developed a tool that visualizes these parameters over time. The parameters include measures of tree dimensions like heights, diameters, and crown shape, and measures of costs and benefits for growing the tree. We visualize the tree dimensions...

Zero Pearson coefficient for strongly correlated growing trees

NASA Astrophysics Data System (ADS)

Dorogovtsev, S. N.; Ferreira, A. L.; Goltsev, A. V.; Mendes, J. F. F.

2010-03-01

We obtained Pearson’s coefficient of strongly correlated recursive networks growing by preferential attachment of every new vertex by m edges. We found that the Pearson coefficient is exactly zero in the infinite network limit for the recursive trees (m=1) . If the number of connections of new vertices exceeds one (m>1) , then the Pearson coefficient in the infinite networks equals zero only when the degree distribution exponent γ does not exceed 4. We calculated the Pearson coefficient for finite networks and observed a slow power-law-like approach to an infinite network limit. Our findings indicate that Pearson’s coefficient strongly depends on size and details of networks, which makes this characteristic virtually useless for quantitative comparison of different networks.

Zero Pearson coefficient for strongly correlated growing trees.

PubMed

Dorogovtsev, S N; Ferreira, A L; Goltsev, A V; Mendes, J F F

2010-03-01

We obtained Pearson's coefficient of strongly correlated recursive networks growing by preferential attachment of every new vertex by m edges. We found that the Pearson coefficient is exactly zero in the infinite network limit for the recursive trees (m=1). If the number of connections of new vertices exceeds one (m>1), then the Pearson coefficient in the infinite networks equals zero only when the degree distribution exponent gamma does not exceed 4. We calculated the Pearson coefficient for finite networks and observed a slow power-law-like approach to an infinite network limit. Our findings indicate that Pearson's coefficient strongly depends on size and details of networks, which makes this characteristic virtually useless for quantitative comparison of different networks.

The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

NASA Astrophysics Data System (ADS)

Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

2017-12-01

Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

A spatially explicit approach to the study of socio-demographic inequality in the spatial distribution of trees across Boston neighborhoods.

PubMed

Duncan, Dustin T; Kawachi, Ichiro; Kum, Susan; Aldstadt, Jared; Piras, Gianfranco; Matthews, Stephen A; Arbia, Giuseppe; Castro, Marcia C; White, Kellee; Williams, David R

2014-04-01

The racial/ethnic and income composition of neighborhoods often influences local amenities, including the potential spatial distribution of trees, which are important for population health and community wellbeing, particularly in urban areas. This ecological study used spatial analytical methods to assess the relationship between neighborhood socio-demographic characteristics (i.e. minority racial/ethnic composition and poverty) and tree density at the census tact level in Boston, Massachusetts (US). We examined spatial autocorrelation with the Global Moran's I for all study variables and in the ordinary least squares (OLS) regression residuals as well as computed Spearman correlations non-adjusted and adjusted for spatial autocorrelation between socio-demographic characteristics and tree density. Next, we fit traditional regressions (i.e. OLS regression models) and spatial regressions (i.e. spatial simultaneous autoregressive models), as appropriate. We found significant positive spatial autocorrelation for all neighborhood socio-demographic characteristics (Global Moran's I range from 0.24 to 0.86, all P =0.001), for tree density (Global Moran's I =0.452, P =0.001), and in the OLS regression residuals (Global Moran's I range from 0.32 to 0.38, all P <0.001). Therefore, we fit the spatial simultaneous autoregressive models. There was a negative correlation between neighborhood percent non-Hispanic Black and tree density (r S =-0.19; conventional P -value=0.016; spatially adjusted P -value=0.299) as well as a negative correlation between predominantly non-Hispanic Black (over 60% Black) neighborhoods and tree density (r S =-0.18; conventional P -value=0.019; spatially adjusted P -value=0.180). While the conventional OLS regression model found a marginally significant inverse relationship between Black neighborhoods and tree density, we found no statistically significant relationship between neighborhood socio-demographic composition and tree density in the spatial regression models. Methodologically, our study suggests the need to take into account spatial autocorrelation as findings/conclusions can change when the spatial autocorrelation is ignored. Substantively, our findings suggest no need for policy intervention vis-à-vis trees in Boston, though we hasten to add that replication studies, and more nuanced data on tree quality, age and diversity are needed.

Loops in hierarchical channel networks

NASA Astrophysics Data System (ADS)

Katifori, Eleni; Magnasco, Marcelo

2012-02-01

Nature provides us with many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated and natural graphs extracted from digitized images of dicotyledonous leaves and animal vasculature. We calculate various metrics on the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

Trophic level, successional age and trait matching determine specialization of deadwood-based interaction networks of saproxylic beetles

PubMed Central

Gossner, Martin M.; Grass, Ingo; Arnstadt, Tobias; Hofrichter, Martin; Floren, Andreas; Linsenmair, Karl Eduard; Weisser, Wolfgang W.; Steffan-Dewenter, Ingolf

2017-01-01

The specialization of ecological networks provides important insights into possible consequences of biodiversity loss for ecosystem functioning. However, mostly mutualistic and antagonistic interactions of living organisms have been studied, whereas detritivore networks and their successional changes are largely unexplored. We studied the interactions of saproxylic (deadwood-dependent) beetles with their dead host trees. In a large-scale experiment, 764 logs of 13 tree species were exposed to analyse network structure of three trophic groups of saproxylic beetles over 3 successional years. We found remarkably high specialization of deadwood-feeding xylophages and lower specialization of fungivorous and predatory species. During deadwood succession, community composition, network specialization and network robustness changed differently for the functional groups. To reveal potential drivers of network specialization, we linked species' functional traits to their network roles, and tested for trait matching between plant (i.e. chemical compounds) and beetle (i.e. body size) traits. We found that both plant and animal traits are major drivers of species specialization, and that trait matching can be more important in explaining interactions than neutral processes reflecting species abundance distributions. High network specialization in the early successional stage and decreasing network robustness during succession indicate vulnerability of detritivore networks to reduced tree species diversity and beetle extinctions, with unknown consequences for wood decomposition and nutrient cycling. PMID:28469020

Woody-plant ecosystems under climate change and air pollution-response consistencies across zonobiomes?

PubMed

Matyssek, R; Kozovits, A R; Wieser, G; King, J; Rennenberg, H

2017-06-01

Forests store the largest terrestrial pools of carbon (C), helping to stabilize the global climate system, yet are threatened by climate change (CC) and associated air pollution (AP, highlighting ozone (O3) and nitrogen oxides (NOx)). We adopt the perspective that CC-AP drivers and physiological impacts are universal, resulting in consistent stress responses of forest ecosystems across zonobiomes. Evidence supporting this viewpoint is presented from the literature on ecosystem gross/net primary productivity and water cycling. Responses to CC-AP are compared across evergreen/deciduous foliage types, discussing implications of nutrition and resource turnover at tree and ecosystem scales. The availability of data is extremely uneven across zonobiomes, yet unifying patterns of ecosystem response are discernable. Ecosystem warming results in trade-offs between respiration and biomass production, affecting high elevation forests more than in the lowland tropics and low-elevation temperate zone. Resilience to drought is modulated by tree size and species richness. Elevated O3 tends to counteract stimulation by elevated carbon dioxide (CO2). Biotic stress and genomic structure ultimately determine ecosystem responsiveness. Aggrading early- rather than mature late-successional communities respond to CO2 enhancement, whereas O3 affects North American and Eurasian tree species consistently under free-air fumigation. Insect herbivory is exacerbated by CC-AP in biome-specific ways. Rhizosphere responses reflect similar stand-level nutritional dynamics across zonobiomes, but are modulated by differences in tree-soil nutrient cycling between deciduous and evergreen systems, and natural versus anthropogenic nitrogen (N) oversupply. The hypothesis of consistency of forest responses to interacting CC-AP is supported by currently available data, establishing the precedent for a global network of long-term coordinated research sites across zonobiomes to simultaneously advance both bottom-up (e.g., mechanistic) and top-down (systems-level) understanding. This global, synthetic approach is needed because high biological plasticity and physiographic variation across individual ecosystems currently limit development of predictive models of forest responses to CC-AP. Integrated research on C and nutrient cycling, O3-vegetation interactions and water relations must target mechanisms' ecosystem responsiveness. Worldwide case studies must be subject to biostatistical exploration to elucidate overarching response patterns and synthesize the resulting empirical data through advanced modelling, in order to provide regionally coherent, yet globally integrated information in support of internationally coordinated decision-making and policy development. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Anthropogenic nitrogen deposition alters growth responses of European beech (Fagus sylvativa L.) to climate change.

PubMed

Hess, Carsten; Niemeyer, Thomas; Fichtner, Andreas; Jansen, Kirstin; Kunz, Matthias; Maneke, Moritz; von Wehrden, Henrik; Quante, Markus; Walmsley, David; von Oheimb, Goddert; Härdtle, Werner

2018-02-01

Global change affects the functioning of forest ecosystems and the services they provide, but little is known about the interactive effects of co-occurring global change drivers on important functions such as tree growth and vitality. In the present study we quantified the interactive (i.e. synergistic or antagonistic) effects of atmospheric nitrogen (N) deposition and climatic variables (temperature, precipitation) on tree growth (in terms of tree-ring width, TRW), taking forest ecosystems with European beech (Fagus sylvatica L.) as an example. We hypothesised that (i) N deposition and climatic variables can evoke non-additive responses of the radial increment of beech trees, and (ii) N loads have the potential to strengthen the trees' sensitivity to climate change. In young stands, we found a synergistic positive effect of N deposition and annual mean temperature on TRW, possibly linked to the alleviation of an N shortage in young stands. In mature stands, however, high N deposition significantly increased the trees' sensitivity to increasing annual mean temperatures (antagonistic effect on TRW), possibly due to increased fine root dieback, decreasing mycorrhizal colonization or shifts in biomass allocation patterns (aboveground vs. belowground). Accordingly, N deposition and climatic variables caused both synergistic and antagonistic effects on the radial increment of beech trees, depending on tree age and stand characteristics. Hence, the nature of interactions could mediate the long-term effects of global change drivers (including N deposition) on forest carbon sequestration. In conclusion, our findings illustrate that interaction processes between climatic variables and N deposition are complex and have the potential to impair growth and performance of European beech. This in turn emphasises the importance of multiple-factor studies to foster an integrated understanding and models aiming at improved projections of tree growth responses to co-occurring drivers of global change. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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...

Disassortativity of random critical branching trees

NASA Astrophysics Data System (ADS)

Kim, J. S.; Kahng, B.; Kim, D.

2009-06-01

Random critical branching trees (CBTs) are generated by the multiplicative branching process, where the branching number is determined stochastically, independent of the degree of their ancestor. Here we show analytically that despite this stochastic independence, there exists the degree-degree correlation (DDC) in the CBT and it is disassortative. Moreover, the skeletons of fractal networks, the maximum spanning trees formed by the edge betweenness centrality, behave similarly to the CBT in the DDC. This analytic solution and observation support the argument that the fractal scaling in complex networks originates from the disassortativity in the DDC.

Model-Based Design of Tree WSNs for Decentralized Detection †

PubMed Central

Tantawy, Ashraf; Koutsoukos, Xenofon; Biswas, Gautam

2015-01-01

The classical decentralized detection problem of finding the optimal decision rules at the sensor and fusion center, as well as variants that introduce physical channel impairments have been studied extensively in the literature. The deployment of WSNs in decentralized detection applications brings new challenges to the field. Protocols for different communication layers have to be co-designed to optimize the detection performance. In this paper, we consider the communication network design problem for a tree WSN. We pursue a system-level approach where a complete model for the system is developed that captures the interactions between different layers, as well as different sensor quality measures. For network optimization, we propose a hierarchical optimization algorithm that lends itself to the tree structure, requiring only local network information. The proposed design approach shows superior performance over several contentionless and contention-based network design approaches. PMID:26307989

Inferring Epidemic Contact Structure from Phylogenetic Trees

PubMed Central

Leventhal, Gabriel E.; Kouyos, Roger; Stadler, Tanja; von Wyl, Viktor; Yerly, Sabine; Böni, Jürg; Cellerai, Cristina; Klimkait, Thomas; Günthard, Huldrych F.; Bonhoeffer, Sebastian

2012-01-01

Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology. However, detailed knowledge of the exact contact structure underlying real epidemics is limited. Here we address the question whether the structure of the contact network leaves a detectable genetic fingerprint in the pathogen population. To this end we compare phylogenies generated by disease outbreaks in simulated populations with different types of contact networks. We find that the shape of these phylogenies strongly depends on contact structure. In particular, measures of tree imbalance allow us to quantify to what extent the contact structure underlying an epidemic deviates from a null model contact network and illustrate this in the case of random mixing. Using a phylogeny from the Swiss HIV epidemic, we show that this epidemic has a significantly more unbalanced tree than would be expected from random mixing. PMID:22412361

Multi-agent based control of large-scale complex systems employing distributed dynamic inference engine

NASA Astrophysics Data System (ADS)

Zhang, Daili

Increasing societal demand for automation has led to considerable efforts to control large-scale complex systems, especially in the area of autonomous intelligent control methods. The control system of a large-scale complex system needs to satisfy four system level requirements: robustness, flexibility, reusability, and scalability. Corresponding to the four system level requirements, there arise four major challenges. First, it is difficult to get accurate and complete information. Second, the system may be physically highly distributed. Third, the system evolves very quickly. Fourth, emergent global behaviors of the system can be caused by small disturbances at the component level. The Multi-Agent Based Control (MABC) method as an implementation of distributed intelligent control has been the focus of research since the 1970s, in an effort to solve the above-mentioned problems in controlling large-scale complex systems. However, to the author's best knowledge, all MABC systems for large-scale complex systems with significant uncertainties are problem-specific and thus difficult to extend to other domains or larger systems. This situation is partly due to the control architecture of multiple agents being determined by agent to agent coupling and interaction mechanisms. Therefore, the research objective of this dissertation is to develop a comprehensive, generalized framework for the control system design of general large-scale complex systems with significant uncertainties, with the focus on distributed control architecture design and distributed inference engine design. A Hybrid Multi-Agent Based Control (HyMABC) architecture is proposed by combining hierarchical control architecture and module control architecture with logical replication rings. First, it decomposes a complex system hierarchically; second, it combines the components in the same level as a module, and then designs common interfaces for all of the components in the same module; third, replications are made for critical agents and are organized into logical rings. This architecture maintains clear guidelines for complexity decomposition and also increases the robustness of the whole system. Multiple Sectioned Dynamic Bayesian Networks (MSDBNs) as a distributed dynamic probabilistic inference engine, can be embedded into the control architecture to handle uncertainties of general large-scale complex systems. MSDBNs decomposes a large knowledge-based system into many agents. Each agent holds its partial perspective of a large problem domain by representing its knowledge as a Dynamic Bayesian Network (DBN). Each agent accesses local evidence from its corresponding local sensors and communicates with other agents through finite message passing. If the distributed agents can be organized into a tree structure, satisfying the running intersection property and d-sep set requirements, globally consistent inferences are achievable in a distributed way. By using different frequencies for local DBN agent belief updating and global system belief updating, it balances the communication cost with the global consistency of inferences. In this dissertation, a fully factorized Boyen-Koller (BK) approximation algorithm is used for local DBN agent belief updating, and the static Junction Forest Linkage Tree (JFLT) algorithm is used for global system belief updating. MSDBNs assume a static structure and a stable communication network for the whole system. However, for a real system, sub-Bayesian networks as nodes could be lost, and the communication network could be shut down due to partial damage in the system. Therefore, on-line and automatic MSDBNs structure formation is necessary for making robust state estimations and increasing survivability of the whole system. A Distributed Spanning Tree Optimization (DSTO) algorithm, a Distributed D-Sep Set Satisfaction (DDSSS) algorithm, and a Distributed Running Intersection Satisfaction (DRIS) algorithm are proposed in this dissertation. Combining these three distributed algorithms and a Distributed Belief Propagation (DBP) algorithm in MSDBNs makes state estimations robust to partial damage in the whole system. Combining the distributed control architecture design and the distributed inference engine design leads to a process of control system design for a general large-scale complex system. As applications of the proposed methodology, the control system design of a simplified ship chilled water system and a notional ship chilled water system have been demonstrated step by step. Simulation results not only show that the proposed methodology gives a clear guideline for control system design for general large-scale complex systems with dynamic and uncertain environment, but also indicate that the combination of MSDBNs and HyMABC can provide excellent performance for controlling general large-scale complex systems.

TreePlus: interactive exploration of networks with enhanced tree layouts.

PubMed

Lee, Bongshin; Parr, Cynthia S; Plaisant, Catherine; Bederson, Benjamin B; Veksler, Vladislav D; Gray, Wayne D; Kotfila, Christopher

2006-01-01

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus.

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

NASA Astrophysics Data System (ADS)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

Harnessing Electrostatic Forces to Grow Bio-inspired Hierarchical Vascular Networks

NASA Astrophysics Data System (ADS)

Behler, Kristopher; Melrose, Zachary; Schott, Andrew; Wetzel, Eric

2012-02-01

Vascular networks provide a system for fluid distribution. Artificial vascular materials with enhanced properties are currently being developed that could ultimately be integrated into systems reliant upon fluid transport while retaining their structural properties. An uninterrupted and controllable supply of liquid is optimal for many applications such as continual self-healing materials, in-situ delivery of index matched fluids, thermal management and drug delivery systems could benefit from a bio-inspired vascular approach that combines complex network geometries with minimal processing parameters. Two such approaches to induce vascular networks are electrohydrodynamic viscous fingering (EHVF) and electrical treeing (ET). EHVF is a phenomenon that occurs when a low viscosity liquid is forced through a high viscosity fluid or matrix, resulting in branches due to capillary and viscous forces in the high viscosity material. By applying voltages of 0 -- 60 kV, finger diameter is reduced. ET is the result of partial discharges in a dielectric material. In the vicinity of a small diameter electrode, the local electric field is greater than the global dielectric strength, causing a localized, step-wise, breakdown to occur forming a highly branched interconnected structure. ET is a viable method to produce networks on a smaller, micron, scale than the products of the EHVF method.

Networks of channels for self-healing composite materials

NASA Astrophysics Data System (ADS)

Bejan, A.; Lorente, S.; Wang, K.-M.

2006-08-01

This is a fundamental study of how to vascularize a self-healing composite material so that healing fluid reaches all the crack sites that may occur randomly through the material. The network of channels is built into the material and is filled with pressurized healing fluid. When a crack forms, the pressure drops at the crack site and fluid flows from the network into the crack. The objective is to discover the network configuration that is capable of delivering fluid to all the cracks the fastest. The crack site dimension and the total volume of the channels are fixed. It is argued that the network must be configured as a grid and not as a tree. Two classes of grids are considered and optimized: (i) grids with one channel diameter and regular polygonal loops (square, triangle, hexagon) and (ii) grids with two channel sizes. The best architecture of type (i) is the grid with triangular loops. The best architecture of type (ii) has a particular (optimal) ratio of diameters that departs from 1 as the crack length scale becomes smaller than the global scale of the vascularized structure from which the crack draws its healing fluid. The optimization of the ratio of channel diameters cuts in half the time of fluid delivery to the crack.

Can Network Linkage Effects Determine Return? Evidence from Chinese Stock Market

PubMed Central

Qiao, Haishu; Xia, Yue; Li, Ying

2016-01-01

This study used the dynamic conditional correlations (DCC) method to identify the linkage effects of Chinese stock market, and further detected the influence of network linkage effects on magnitude of security returns across different industries. Applying two physics-derived techniques, the minimum spanning tree and the hierarchical tree, we analyzed the stock interdependence within the network of the China Securities Index (CSI) industry index basket. We observed that that obvious linkage effects existed among stock networks. CII and CCE, CAG and ITH as well as COU, CHA and REI were confirmed as the core nodes in the three different networks respectively. We also investigated the stability of linkage effects by estimating the mean correlations and mean distances, as well as the normalized tree length of these indices. In addition, using the GMM model approach, we found inter-node influence within the stock network had a pronounced effect on stock returns. Our results generally suggested that there appeared to be greater clustering effect among the indexes belonging to related industrial sectors than those of diverse sectors, and network comovement was significantly affected by impactive financial events in the reality. Besides, stocks that were more central within the network of stock market usually had higher returns for compensation because they endured greater exposure to correlation risk. PMID:27257816

Can Network Linkage Effects Determine Return? Evidence from Chinese Stock Market.

PubMed

Qiao, Haishu; Xia, Yue; Li, Ying

2016-01-01

This study used the dynamic conditional correlations (DCC) method to identify the linkage effects of Chinese stock market, and further detected the influence of network linkage effects on magnitude of security returns across different industries. Applying two physics-derived techniques, the minimum spanning tree and the hierarchical tree, we analyzed the stock interdependence within the network of the China Securities Index (CSI) industry index basket. We observed that that obvious linkage effects existed among stock networks. CII and CCE, CAG and ITH as well as COU, CHA and REI were confirmed as the core nodes in the three different networks respectively. We also investigated the stability of linkage effects by estimating the mean correlations and mean distances, as well as the normalized tree length of these indices. In addition, using the GMM model approach, we found inter-node influence within the stock network had a pronounced effect on stock returns. Our results generally suggested that there appeared to be greater clustering effect among the indexes belonging to related industrial sectors than those of diverse sectors, and network comovement was significantly affected by impactive financial events in the reality. Besides, stocks that were more central within the network of stock market usually had higher returns for compensation because they endured greater exposure to correlation risk.

On implementation of DCTCP on three-tier and fat-tree data center network topologies.

PubMed

Zafar, Saima; Bashir, Abeer; Chaudhry, Shafique Ahmad

2016-01-01

A data center is a facility for housing computational and storage systems interconnected through a communication network called data center network (DCN). Due to a tremendous growth in the computational power, storage capacity and the number of inter-connected servers, the DCN faces challenges concerning efficiency, reliability and scalability. Although transmission control protocol (TCP) is a time-tested transport protocol in the Internet, DCN challenges such as inadequate buffer space in switches and bandwidth limitations have prompted the researchers to propose techniques to improve TCP performance or design new transport protocols for DCN. Data center TCP (DCTCP) emerge as one of the most promising solutions in this domain which employs the explicit congestion notification feature of TCP to enhance the TCP congestion control algorithm. While DCTCP has been analyzed for two-tier tree-based DCN topology for traffic between servers in the same rack which is common in cloud applications, it remains oblivious to the traffic patterns common in university and private enterprise networks which traverse the complete network interconnect spanning upper tier layers. We also recognize that DCTCP performance cannot remain unaffected by the underlying DCN architecture hence there is a need to test and compare DCTCP performance when implemented over diverse DCN architectures. Some of the most notable DCN architectures are the legacy three-tier, fat-tree, BCube, DCell, VL2, and CamCube. In this research, we simulate the two switch-centric DCN architectures; the widely deployed legacy three-tier architecture and the promising fat-tree architecture using network simulator and analyze the performance of DCTCP in terms of throughput and delay for realistic traffic patterns. We also examine how DCTCP prevents incast and outcast congestion when realistic DCN traffic patterns are employed in above mentioned topologies. Our results show that the underlying DCN architecture significantly impacts DCTCP performance. We find that DCTCP gives optimal performance in fat-tree topology and is most suitable for large networks.

Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata*

PubMed Central

Pascual, Jesús; Cañal, María Jesús; Escandón, Mónica; Meijón, Mónica; Weckwerth, Wolfram

2017-01-01

Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine. PMID:28096192

A roadmap for global synthesis of the plant tree of life.

PubMed

Eiserhardt, Wolf L; Antonelli, Alexandre; Bennett, Dominic J; Botigué, Laura R; Burleigh, J Gordon; Dodsworth, Steven; Enquist, Brian J; Forest, Félix; Kim, Jan T; Kozlov, Alexey M; Leitch, Ilia J; Maitner, Brian S; Mirarab, Siavash; Piel, William H; Pérez-Escobar, Oscar A; Pokorny, Lisa; Rahbek, Carsten; Sandel, Brody; Smith, Stephen A; Stamatakis, Alexandros; Vos, Rutger A; Warnow, Tandy; Baker, William J

2018-03-01

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis. © 2018 Botanical Society of America.

The application of data mining techniques to oral cancer prognosis.

PubMed

Tseng, Wan-Ting; Chiang, Wei-Fan; Liu, Shyun-Yeu; Roan, Jinsheng; Lin, Chun-Nan

2015-05-01

This study adopted an integrated procedure that combines the clustering and classification features of data mining technology to determine the differences between the symptoms shown in past cases where patients died from or survived oral cancer. Two data mining tools, namely decision tree and artificial neural network, were used to analyze the historical cases of oral cancer, and their performance was compared with that of logistic regression, the popular statistical analysis tool. Both decision tree and artificial neural network models showed superiority to the traditional statistical model. However, as to clinician, the trees created by the decision tree models are relatively easier to interpret compared to that of the artificial neural network models. Cluster analysis also discovers that those stage 4 patients whose also possess the following four characteristics are having an extremely low survival rate: pN is N2b, level of RLNM is level I-III, AJCC-T is T4, and cells mutate situation (G) is moderate.

Optimization of matrix tablets controlled drug release using Elman dynamic neural networks and decision trees.

PubMed

Petrović, Jelena; Ibrić, Svetlana; Betz, Gabriele; Đurić, Zorica

2012-05-30

The main objective of the study was to develop artificial intelligence methods for optimization of drug release from matrix tablets regardless of the matrix type. Static and dynamic artificial neural networks of the same topology were developed to model dissolution profiles of different matrix tablets types (hydrophilic/lipid) using formulation composition, compression force used for tableting and tablets porosity and tensile strength as input data. Potential application of decision trees in discovering knowledge from experimental data was also investigated. Polyethylene oxide polymer and glyceryl palmitostearate were used as matrix forming materials for hydrophilic and lipid matrix tablets, respectively whereas selected model drugs were diclofenac sodium and caffeine. Matrix tablets were prepared by direct compression method and tested for in vitro dissolution profiles. Optimization of static and dynamic neural networks used for modeling of drug release was performed using Monte Carlo simulations or genetic algorithms optimizer. Decision trees were constructed following discretization of data. Calculated difference (f(1)) and similarity (f(2)) factors for predicted and experimentally obtained dissolution profiles of test matrix tablets formulations indicate that Elman dynamic neural networks as well as decision trees are capable of accurate predictions of both hydrophilic and lipid matrix tablets dissolution profiles. Elman neural networks were compared to most frequently used static network, Multi-layered perceptron, and superiority of Elman networks have been demonstrated. Developed methods allow simple, yet very precise way of drug release predictions for both hydrophilic and lipid matrix tablets having controlled drug release. Copyright © 2012 Elsevier B.V. All rights reserved.

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees

Treesearch

Lijun Liu; Vladimir Filkov; Andrew Groover

2013-01-01

The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary...

A Global Perspective on Warmer Droughts as a Key Driver of Forest Disturbances and Tree Mortality (Invited)

NASA Astrophysics Data System (ADS)

Allen, C. D.

2013-12-01

Recent global warming, in concert with episodic droughts, is causing elevated levels of both chronic and acute forest water stress across large regions. Such increases in water stress affect forest dynamics in multiple ways, including by amplifying the incidence and severity of many significant forest disturbances, particularly drought-induced tree mortality, wildfire, and outbreaks of damaging insects and diseases. Emerging global-scale patterns of drought-related forest die-off are presented, including a newly updated map overview of documented drought- and heat-induced tree mortality events from around the world, demonstrating the vulnerability of all major forest types to forest drought stress, even in typically wet environments. Comparative patterns of drought stress and associated forest disturbances are reviewed for several regions (southwestern Australia, Inner Asia, western North America, Mediterranean Basin), including interactions among climate and various disturbance processes. From the Southwest USA, research is presented that derives a tree-ring-based Forest Drought Stress Index (FDSI) for the most regionally-widespread conifer species (Pinus edulis, Pinus ponderosa, and Pseudotsuga menziesii), demonstrating recent escalation of FDSI to extreme levels relative to the past 1000 years, due to both drought and especially warming. This new work further highlights strong correlations between drought stress and amplified forest disturbances (fire, bark beetle outbreaks), and projects that by CE 2050 anticipated regional warming will cause mean FDSI values to reach historically unprecedented levels that may exceed thresholds for the survival of current tree species in large portions of their current range in the Southwest. Similar patterns of recent climate-amplified forest disturbance risk are apparent from a variety of relatively dry regions across this planet, and given climate projections for substantially warmer temperatures and greater drought stress for many areas globally, the growing water-stress risks to forest health in such regions are becoming clearer. However, the effects of drought stress on forest dynamics are ameliorated through diverse compensatory and resilience-enhancing mechanisms and processes which operate at scales ranging from intracellular tree physiologies and individual tree developmental and morphological adjustments to species population-level demographic and genetic responses to forest stand-level structural and compositional responses up to landscape-scale tree host-insect pest outbreak dynamics and forest-climate ecohydrological feedbacks. In addition, significant uncertainties exist regarding how various other global atmospheric changes (e.g., CO2 enrichment, increased N deposition, and elevated surface-level ozone) will interact with the world's diverse spectrum of tree species to also affect global forest dynamics. Research efforts to address such core scientific uncertainties associated with modeling drought-induced tree mortality and resultant forest dynamics will be discussed.

Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth.

PubMed

Liu, Jinwen; Hai, Guanghui; Wang, Chong; Cao, Shenquan; Xu, Wenjing; Jia, Zhigang; Yang, Chuanping; Wang, Jack P; Dai, Shaojun; Cheng, Yuxiang

2015-08-03

Wood is derived from the secondary growth of tree stems. In this study, we investigated the global changes of protein abundance in Populus early stems using a proteomic approach. Morphological and histochemical analyses revealed three typical stages during Populus early stems, which were the primary growth stage, the transition stage from primary to secondary growth and the secondary growth stage. A total of 231 spots were differentially abundant during various growth stages of Populus early stems. During Populus early stem lignifications, 87 differential spots continuously increased, while 49 spots continuously decreased. These two categories encompass 58.9% of all differential spots, which suggests significant molecular changes from primary to secondary growth. Among 231 spots, 165 unique proteins were identified using LC-ESI-Q-TOF-MS, which were classified into 14 biological function groups. The proteomic characteristics indicated that carbohydrate metabolism, oxido-reduction, protein degradation and secondary cell wall metabolism were the dominantly occurring biochemical processes during Populus early stem development. This study helps in elucidating biochemical processes and identifies potential wood formation-related proteins during tree early stem development. It is a comprehensive proteomic investigation on tree early stem development that, for the first time, reveals the overall molecular networks that occur during Populus early stem lignifications. Copyright © 2015. Published by Elsevier B.V.

Climate Change Increases Drought Stress of Juniper Trees in the Mountains of Central Asia

PubMed Central

Seim, Andrea; Omurova, Gulzar; Azisov, Erlan; Musuraliev, Kanaat; Aliev, Kumar; Tulyaganov, Timur; Nikolyai, Lyutsian; Botman, Evgeniy; Helle, Gerd; Dorado Liñan, Isabel; Jivcov, Sandra; Linderholm, Hans W.

2016-01-01

Assessments of climate change impacts on forests and their vitality are essential for semi-arid environments such as Central Asia, where the mountain regions belong to the globally important biodiversity hotspots. Alterations in species distribution or drought-induced tree mortality might not only result in a loss of biodiversity but also in a loss of other ecosystem services. Here, we evaluate spatial trends and patterns of the growth-climate relationship in a tree-ring network comprising 33 juniper sites from the northern Pamir-Alay and Tien Shan mountain ranges in eastern Uzbekistan and across Kyrgyzstan for the common period 1935–2011. Junipers growing at lower elevations are sensitive to summer drought, which has increased in intensity during the studied period. At higher elevations, juniper growth, previously favored by warm summer temperatures, has in the recent few decades become negatively affected by increasing summer aridity. Moreover, response shifts are observed during all seasons. Rising temperatures and alterations in precipitation patterns during the past eight decades can account for the observed increase in drought stress of junipers at all altitudes. The implications of our findings are vital for the application of adequate long-term measures of ecosystem conservation, but also for paleo-climatic approaches and coupled climate-vegetation model simulations for Central Asia. PMID:27100092

Estimating global distribution of boreal, temperate, and tropical tree plant functional types using clustering techniques

NASA Astrophysics Data System (ADS)

Wang, Audrey; Price, David T.

2007-03-01

A simple integrated algorithm was developed to relate global climatology to distributions of tree plant functional types (PFT). Multivariate cluster analysis was performed to analyze the statistical homogeneity of the climate space occupied by individual tree PFTs. Forested regions identified from the satellite-based GLC2000 classification were separated into tropical, temperate, and boreal sub-PFTs for use in the Canadian Terrestrial Ecosystem Model (CTEM). Global data sets of monthly minimum temperature, growing degree days, an index of climatic moisture, and estimated PFT cover fractions were then used as variables in the cluster analysis. The statistical results for individual PFT clusters were found consistent with other global-scale classifications of dominant vegetation. As an improvement of the quantification of the climatic limitations on PFT distributions, the results also demonstrated overlapping of PFT cluster boundaries that reflected vegetation transitions, for example, between tropical and temperate biomes. The resulting global database should provide a better basis for simulating the interaction of climate change and terrestrial ecosystem dynamics using global vegetation models.

A Hierarchical Analysis of Tree Growth and Environmental Drivers Across Eastern US Temperate Forests

NASA Astrophysics Data System (ADS)

Mantooth, J.; Dietze, M.

2014-12-01

Improving predictions of how forests in the eastern United States will respond to future global change requires a better understanding of the drivers of variability in tree growth rates. Current inventory data lack the temporal resolution to characterize interannual variability, while existing growth records lack the extent required to assess spatial scales of variability. Therefore, we established a network of forest inventory plots across ten sites across the eastern US, and measured growth in adult trees using increment cores. Sites were chosen to maximize climate space explored, while within sites, plots were spread across primary environmental gradients to explore landscape-level variability in growth. Using the annual growth record available from tree cores, we explored the responses of trees to multiple environmental covariates over multiple spatial and temporal scales. We hypothesized that within and across sites growth rates vary among species, and that intraspecific growth rates increase with temperature along a species' range. We also hypothesized that trees show synchrony in growth responses to landscape-scale climatic changes. Initial analyses of growth increments indicate that across sites, trees with intermediate shade tolerance, e.g. Red Oak (Quercus rubra), tend to have the highest growth rates. At the site level, there is evidence for synchrony in response to large-scale climatic events (e.g. prolonged drought and above average temperatures). However, growth responses to climate at the landscape scale have yet to be detected. Our current analysis utilizes hierarchical Bayesian state-space modeling to focus on growth responses of adult trees to environmental covariates at multiple spatial and temporal scales. This predictive model of tree growth currently incorporates observed effects at the individual, plot, site, and landscape scale. Current analysis using this model shows a potential slowing of growth in the past decade for two sites in the northeastern US (Harvard Forest and Bartlett Experimental Forest), however more work is required to determine the robustness of this trend. Finally, these observations are being incorporated into ecosystem models using the Brown Dog informatics tools and the Predictive Ecosystem Analyzer (PEcAn) data assimilation workflow.

Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

PubMed Central

Chase, Mark W.; Kim, Joo-Hwan

2013-01-01

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses. PMID:23544071

 A global evaluation of forest interior area dynamics using tree cover data from 2000 to 2012

Treesearch

Kurt Riitters; James Wickham; Jennifer K. Costanza; Peter Vogt

2016-01-01

Context Published maps of global tree cover derived from Landsat data have indicated substantial changes in forest area from 2000 to 2012. The changes can be arranged in different patterns, with different consequences for forest fragmentation. Thus, the changes in forest area do not necessarily equate to changes in...

FVS and global Warming: A prospectus for future development

Treesearch

Nicholas L. Crookston; Gerald E. Rehfeldt; Dennis E. Ferguson; Marcus Warwell

2008-01-01

Climate change-global warming and changes in precipitation-will cause changes in tree growth rates, mortality rates, the distribution of tree species, competition, and species interactions. An implicit assumption in FVS is that site quality will remain the same as it was during the time period observations used to calibrate the component models were made and that the...

Climate-induced tree mortality: Earth system consequences

USGS Publications Warehouse

Adams, Henry D.; Macalady, Alison K.; Breshears, David D.; Allen, Craig D.; Stephenson, Nathan L.; Saleska, Scott; Huxman, Travis E.; McDowell, Nathan G.

2010-01-01

One of the greatest uncertainties in global environmental change is predicting changes in feedbacks between the biosphere and the Earth system. Terrestrial ecosystems and, in particular, forests exert strong controls on the global carbon cycle and influence regional hydrology and climatology directly through water and surface energy budgets [Bonan, 2008; Chapin et al., 2008].According to new research, tree mortality associated with elevated temperatures and drought has the potential to rapidly alter forest ecosystems, potentially affecting feedbacks to the Earth system [Allen et al., 2010]. Several lines of recent research demonstrate how tree mortality rates in forests may be sensitive to climate change—particularly warming and drying. This emerging consequence of global change has important effects on Earth system processes (Figure 1).

Spatial Pattern of Standing Timber Value across the Brazilian Amazon

PubMed Central

Ahmed, Sadia E.; Ewers, Robert M.

2012-01-01

The Amazon is a globally important system, providing a host of ecosystem services from climate regulation to food sources. It is also home to a quarter of all global diversity. Large swathes of forest are removed each year, and many models have attempted to predict the spatial patterns of this forest loss. The spatial patterns of deforestation are determined largely by the patterns of roads that open access to frontier areas and expansion of the road network in the Amazon is largely determined by profit seeking logging activities. Here we present predictions for the spatial distribution of standing value of timber across the Amazon. We show that the patterns of timber value reflect large-scale ecological gradients, determining the spatial distribution of functional traits of trees which are, in turn, correlated with timber values. We expect that understanding the spatial patterns of timber value across the Amazon will aid predictions of logging movements and thus predictions of potential future road developments. These predictions in turn will be of great use in estimating the spatial patterns of deforestation in this globally important biome. PMID:22590520

Tropical Tree Trait Diversity Enhances Forest Biomass Resilience in a Dynamic Global Vegetation Model

NASA Astrophysics Data System (ADS)

Sakschewski, B.; Kirsten, T.; von Bloh, W.; Poorter, L.; Pena-Claros, M.; Boit, A.

2016-12-01

Functional diversity of ecosystems has been found to increase ecosystem functions and therefore enhance ecosystem resilience against environmental stressors. However, global carbon-cycle and biosphere models still classify the global vegetation into a relatively small number of distinct plant functional types (PFT) with constant features over space and time. Therefore, those models might underestimate the resilience and adaptive capacity of natural vegetation under climate change by ignoring positive effects that functional diversity might bring about. We diversified a set a of selected tree traits in a dynamic global vegetation model (LPJmL). In the new subversion, called LPJmL-FIT, Amazon region biomass stocks and forest structure appear significantly more resilient against climate change. Enhanced tree trait diversity enables the simulated rainforests to adjust to new environmental conditions via ecological sorting. These results may stimulate a new debate on the value of biodiversity for climate change mitigation.

Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms

NASA Astrophysics Data System (ADS)

Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho

The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.

Towards a hybrid energy efficient multi-tree-based optimized routing protocol for wireless networks.

PubMed

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-12-13

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm.

Towards a Hybrid Energy Efficient Multi-Tree-Based Optimized Routing Protocol for Wireless Networks

PubMed Central

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-01-01

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm. PMID:23443398

Walking tree heuristics for biological string alignment, gene location, and phylogenies

NASA Astrophysics Data System (ADS)

Cull, P.; Holloway, J. L.; Cavener, J. D.

1999-03-01

Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. We propose a family of heuristics called walking trees to align biologically reasonable strings. Both edit-distance and walking tree methods can locate specific genes within a large string when the genes' sequences are given. When we attempt to match whole strings, the walking tree matches most genes, while the edit-distance method fails. We also give examples in which the walking tree matches substrings even if they have been moved or inverted. The edit-distance method was not designed to handle these problems. We include an example in which the walking tree "discovered" a gene. Calculating scores for whole genome matches gives a method for approximating evolutionary distance. We show two evolutionary trees for the picornaviruses which were computed by the walking tree heuristic. Both of these trees show great similarity to previously constructed trees. The point of this demonstration is that WHOLE genomes can be matched and distances calculated. The first tree was created on a Sequent parallel computer and demonstrates that the walking tree heuristic can be efficiently parallelized. The second tree was created using a network of work stations and demonstrates that there is suffient parallelism in the phylogenetic tree calculation that the sequential walking tree can be used effectively on a network.

Delay-induced cluster patterns in coupled Cayley tree networks

NASA Astrophysics Data System (ADS)

Singh, A.; Jalan, S.

2013-07-01

We study effects of delay in diffusively coupled logistic maps on the Cayley tree networks. We find that smaller coupling values exhibit sensitiveness to value of delay, and lead to different cluster patterns of self-organized and driven types. Whereas larger coupling strengths exhibit robustness against change in delay values, and lead to stable driven clusters comprising nodes from last generation of the Cayley tree. Furthermore, introduction of delay exhibits suppression as well as enhancement of synchronization depending upon coupling strength values. To the end we discuss the importance of results to understand conflicts and cooperations observed in family business.

A global reference database from very high resolution commercial satellite data and methodology for application to Landsat derived 30 m continuous field tree cover data

USGS Publications Warehouse

Pengra, Bruce; Long, Jordan; Dahal, Devendra; Stehman, Stephen V.; Loveland, Thomas R.

2015-01-01

The methodology for selection, creation, and application of a global remote sensing validation dataset using high resolution commercial satellite data is presented. High resolution data are obtained for a stratified random sample of 500 primary sampling units (5 km  ×  5 km sample blocks), where the stratification based on Köppen climate classes is used to distribute the sample globally among biomes. The high resolution data are classified to categorical land cover maps using an analyst mediated classification workflow. Our initial application of these data is to evaluate a global 30 m Landsat-derived, continuous field tree cover product. For this application, the categorical reference classification produced at 2 m resolution is converted to percent tree cover per 30 m pixel (secondary sampling unit)for comparison to Landsat-derived estimates of tree cover. We provide example results (based on a subsample of 25 sample blocks in South America) illustrating basic analyses of agreement that can be produced from these reference data. Commercial high resolution data availability and data quality are shown to provide a viable means of validating continuous field tree cover. When completed, the reference classifications for the full sample of 500 blocks will be released for public use.

A spatially explicit approach to the study of socio-demographic inequality in the spatial distribution of trees across Boston neighborhoods

PubMed Central

Duncan, Dustin T.; Kawachi, Ichiro; Kum, Susan; Aldstadt, Jared; Piras, Gianfranco; Matthews, Stephen A.; Arbia, Giuseppe; Castro, Marcia C.; White, Kellee; Williams, David R.

2017-01-01

The racial/ethnic and income composition of neighborhoods often influences local amenities, including the potential spatial distribution of trees, which are important for population health and community wellbeing, particularly in urban areas. This ecological study used spatial analytical methods to assess the relationship between neighborhood socio-demographic characteristics (i.e. minority racial/ethnic composition and poverty) and tree density at the census tact level in Boston, Massachusetts (US). We examined spatial autocorrelation with the Global Moran’s I for all study variables and in the ordinary least squares (OLS) regression residuals as well as computed Spearman correlations non-adjusted and adjusted for spatial autocorrelation between socio-demographic characteristics and tree density. Next, we fit traditional regressions (i.e. OLS regression models) and spatial regressions (i.e. spatial simultaneous autoregressive models), as appropriate. We found significant positive spatial autocorrelation for all neighborhood socio-demographic characteristics (Global Moran’s I range from 0.24 to 0.86, all P=0.001), for tree density (Global Moran’s I=0.452, P=0.001), and in the OLS regression residuals (Global Moran’s I range from 0.32 to 0.38, all P<0.001). Therefore, we fit the spatial simultaneous autoregressive models. There was a negative correlation between neighborhood percent non-Hispanic Black and tree density (rS=−0.19; conventional P-value=0.016; spatially adjusted P-value=0.299) as well as a negative correlation between predominantly non-Hispanic Black (over 60% Black) neighborhoods and tree density (rS=−0.18; conventional P-value=0.019; spatially adjusted P-value=0.180). While the conventional OLS regression model found a marginally significant inverse relationship between Black neighborhoods and tree density, we found no statistically significant relationship between neighborhood socio-demographic composition and tree density in the spatial regression models. Methodologically, our study suggests the need to take into account spatial autocorrelation as findings/conclusions can change when the spatial autocorrelation is ignored. Substantively, our findings suggest no need for policy intervention vis-à-vis trees in Boston, though we hasten to add that replication studies, and more nuanced data on tree quality, age and diversity are needed. PMID:29354668

Performance of a distributed superscalar storage server

NASA Technical Reports Server (NTRS)

Finestead, Arlan; Yeager, Nancy

1993-01-01

The RS/6000 performed well in our test environment. The potential exists for the RS/6000 to act as a departmental server for a small number of users, rather than as a high speed archival server. Multiple UniTree Disk Server's utilizing one UniTree Disk Server's utilizing one UniTree Name Server could be developed that would allow for a cost effective archival system. Our performance tests were clearly limited by the network bandwidth. The performance gathered by the LibUnix testing shows that UniTree is capable of exceeding ethernet speeds on an RS/6000 Model 550. The performance of FTP might be significantly faster if asked to perform across a higher bandwidth network. The UniTree Name Server also showed signs of being a potential bottleneck. UniTree sites that would require a high ratio of file creations and deletions to reads and writes would run into this bottleneck. It is possible to improve the UniTree Name Server performance by bypassing the UniTree LibUnix Library altogether and communicating directly with the UniTree Name Server and optimizing creations. Although testing was performed in a less than ideal environment, hopefully the performance statistics stated in this paper will give end-users a realistic idea as to what performance they can expect in this type of setup.

Vegetation Continuous Fields--Transitioning from MODIS to VIIRS

NASA Astrophysics Data System (ADS)

DiMiceli, C.; Townshend, J. R.; Sohlberg, R. A.; Kim, D. H.; Kelly, M.

2015-12-01

Measurements of fractional vegetation cover are critical for accurate and consistent monitoring of global deforestation rates. They also provide important parameters for land surface, climate and carbon models and vital background data for research into fire, hydrological and ecosystem processes. MODIS Vegetation Continuous Fields (VCF) products provide four complementary layers of fractional cover: tree cover, non-tree vegetation, bare ground, and surface water. MODIS VCF products are currently produced globally and annually at 250m resolution for 2000 to the present. Additionally, annual VCF products at 1/20° resolution derived from AVHRR and MODIS Long-Term Data Records are in development to provide Earth System Data Records of fractional vegetation cover for 1982 to the present. In order to provide continuity of these valuable products, we are extending the VCF algorithms to create Suomi NPP/VIIRS VCF products. This presentation will highlight the first VIIRS fractional cover product: global percent tree cover at 1 km resolution. To create this product, phenological and physiological metrics were derived from each complete year of VIIRS 8-day surface reflectance products. A supervised regression tree method was applied to the metrics, using training derived from Landsat data supplemented by high-resolution data from Ikonos, RapidEye and QuickBird. The regression tree model was then applied globally to produce fractional tree cover. In our presentation we will detail our methods for creating the VIIRS VCF product. We will compare the new VIIRS VCF product to our current MODIS VCF products and demonstrate continuity between instruments. Finally, we will outline future VIIRS VCF development plans.

USSR Report: Machine Tools and Metalworking Equipment.

DTIC Science & Technology

1986-01-23

between satellite stop and the camshaft of the programer unit. The line has 23 positions including 12 automatic ones. Specification of line Number...technological, processes, automated research, etc.) are as follows.: a monochannel based on a shared trunk line, ring, star and tree (polychannel...line or ring networks based on decentralized control of data exchange between subscribers are very robust. A tree -form network has star structure

Estimating the global conservation status of more than 15,000 Amazonian tree species.

PubMed

Ter Steege, Hans; Pitman, Nigel C A; Killeen, Timothy J; Laurance, William F; Peres, Carlos A; Guevara, Juan Ernesto; Salomão, Rafael P; Castilho, Carolina V; Amaral, Iêda Leão; de Almeida Matos, Francisca Dionízia; de Souza Coelho, Luiz; Magnusson, William E; Phillips, Oliver L; de Andrade Lima Filho, Diogenes; de Jesus Veiga Carim, Marcelo; Irume, Mariana Victória; Martins, Maria Pires; Molino, Jean-François; Sabatier, Daniel; Wittmann, Florian; López, Dairon Cárdenas; da Silva Guimarães, José Renan; Mendoza, Abel Monteagudo; Vargas, Percy Núñez; Manzatto, Angelo Gilberto; Reis, Neidiane Farias Costa; Terborgh, John; Casula, Katia Regina; Montero, Juan Carlos; Feldpausch, Ted R; Honorio Coronado, Euridice N; Montoya, Alvaro Javier Duque; Zartman, Charles Eugene; Mostacedo, Bonifacio; Vasquez, Rodolfo; Assis, Rafael L; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Camargo, José Luís; Laurance, Susan G W; Nascimento, Henrique Eduardo Mendonça; Marimon, Beatriz S; Marimon, Ben-Hur; Costa, Flávia; Targhetta, Natalia; Vieira, Ima Célia Guimarães; Brienen, Roel; Castellanos, Hernán; Duivenvoorden, Joost F; Mogollón, Hugo F; Piedade, Maria Teresa Fernandez; Aymard C, Gerardo A; Comiskey, James A; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Diaz, Pablo Roberto Stevenson; Vincentini, Alberto; Emilio, Thaise; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Alonso, Alfonso; Dallmeier, Francisco; Ferreira, Leandro Valle; Neill, David; Araujo-Murakami, Alejandro; Arroyo, Luzmila; Carvalho, Fernanda Antunes; Souza, Fernanda Coelho; do Amaral, Dário Dantas; Gribel, Rogerio; Luize, Bruno Garcia; Pansonato, Marcelo Petrati; Venticinque, Eduardo; Fine, Paul; Toledo, Marisol; Baraloto, Chris; Cerón, Carlos; Engel, Julien; Henkel, Terry W; Jimenez, Eliana M; Maas, Paul; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Revilla, Juan David Cardenas; Silveira, Marcos; Stropp, Juliana; Thomas-Caesar, Raquel; Baker, Tim R; Daly, Doug; Paredes, Marcos Ríos; da Silva, Naara Ferreira; Fuentes, Alfredo; Jørgensen, Peter Møller; Schöngart, Jochen; Silman, Miles R; Arboleda, Nicolás Castaño; Cintra, Bruno Barçante Ladvocat; Valverde, Fernando Cornejo; Di Fiore, Anthony; Phillips, Juan Fernando; van Andel, Tinde R; von Hildebrand, Patricio; Barbosa, Edelcilio Marques; de Matos Bonates, Luiz Carlos; de Castro, Deborah; de Sousa Farias, Emanuelle; Gonzales, Therany; Guillaumet, Jean-Louis; Hoffman, Bruce; Malhi, Yadvinder; de Andrade Miranda, Ires Paula; Prieto, Adriana; Rudas, Agustín; Ruschell, Ademir R; Silva, Natalino; Vela, César I A; Vos, Vincent A; Zent, Eglée L; Zent, Stanford; Cano, Angela; Nascimento, Marcelo Trindade; Oliveira, Alexandre A; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Sierra, Rodrigo; Tirado, Milton; Medina, Maria Natalia Umaña; van der Heijden, Geertje; Torre, Emilio Vilanova; Vriesendorp, Corine; Wang, Ophelia; Young, Kenneth R; Baider, Claudia; Balslev, Henrik; de Castro, Natalia; Farfan-Rios, William; Ferreira, Cid; Mendoza, Casimiro; Mesones, Italo; Torres-Lezama, Armando; Giraldo, Ligia Estela Urrego; Villarroel, Daniel; Zagt, Roderick; Alexiades, Miguel N; Garcia-Cabrera, Karina; Hernandez, Lionel; Huamantupa-Chuquimaco, Isau; Milliken, William; Cuenca, Walter Palacios; Pansini, Susamar; Pauletto, Daniela; Arevalo, Freddy Ramirez; Sampaio, Adeilza Felipe; Valderrama Sandoval, Elvis H; Gamarra, Luis Valenzuela

2015-11-01

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world's >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

Estimating the global conservation status of more than 15,000 Amazonian tree species

PubMed Central

ter Steege, Hans; Pitman, Nigel C. A.; Killeen, Timothy J.; Laurance, William F.; Peres, Carlos A.; Guevara, Juan Ernesto; Salomão, Rafael P.; Castilho, Carolina V.; Amaral, Iêda Leão; de Almeida Matos, Francisca Dionízia; de Souza Coelho, Luiz; Magnusson, William E.; Phillips, Oliver L.; de Andrade Lima Filho, Diogenes; de Jesus Veiga Carim, Marcelo; Irume, Mariana Victória; Martins, Maria Pires; Molino, Jean-François; Sabatier, Daniel; Wittmann, Florian; López, Dairon Cárdenas; da Silva Guimarães, José Renan; Mendoza, Abel Monteagudo; Vargas, Percy Núñez; Manzatto, Angelo Gilberto; Reis, Neidiane Farias Costa; Terborgh, John; Casula, Katia Regina; Montero, Juan Carlos; Feldpausch, Ted R.; Honorio Coronado, Euridice N.; Montoya, Alvaro Javier Duque; Zartman, Charles Eugene; Mostacedo, Bonifacio; Vasquez, Rodolfo; Assis, Rafael L.; Medeiros, Marcelo Brilhante; Simon, Marcelo Fragomeni; Andrade, Ana; Camargo, José Luís; Laurance, Susan G. W.; Nascimento, Henrique Eduardo Mendonça; Marimon, Beatriz S.; Marimon, Ben-Hur; Costa, Flávia; Targhetta, Natalia; Vieira, Ima Célia Guimarães; Brienen, Roel; Castellanos, Hernán; Duivenvoorden, Joost F.; Mogollón, Hugo F.; Piedade, Maria Teresa Fernandez; Aymard C., Gerardo A.; Comiskey, James A.; Damasco, Gabriel; Dávila, Nállarett; García-Villacorta, Roosevelt; Diaz, Pablo Roberto Stevenson; Vincentini, Alberto; Emilio, Thaise; Levis, Carolina; Schietti, Juliana; Souza, Priscila; Alonso, Alfonso; Dallmeier, Francisco; Ferreira, Leandro Valle; Neill, David; Araujo-Murakami, Alejandro; Arroyo, Luzmila; Carvalho, Fernanda Antunes; Souza, Fernanda Coelho; do Amaral, Dário Dantas; Gribel, Rogerio; Luize, Bruno Garcia; Pansonato, Marcelo Petrati; Venticinque, Eduardo; Fine, Paul; Toledo, Marisol; Baraloto, Chris; Cerón, Carlos; Engel, Julien; Henkel, Terry W.; Jimenez, Eliana M.; Maas, Paul; Mora, Maria Cristina Peñuela; Petronelli, Pascal; Revilla, Juan David Cardenas; Silveira, Marcos; Stropp, Juliana; Thomas-Caesar, Raquel; Baker, Tim R.; Daly, Doug; Paredes, Marcos Ríos; da Silva, Naara Ferreira; Fuentes, Alfredo; Jørgensen, Peter Møller; Schöngart, Jochen; Silman, Miles R.; Arboleda, Nicolás Castaño; Cintra, Bruno Barçante Ladvocat; Valverde, Fernando Cornejo; Di Fiore, Anthony; Phillips, Juan Fernando; van Andel, Tinde R.; von Hildebrand, Patricio; Barbosa, Edelcilio Marques; de Matos Bonates, Luiz Carlos; de Castro, Deborah; de Sousa Farias, Emanuelle; Gonzales, Therany; Guillaumet, Jean-Louis; Hoffman, Bruce; Malhi, Yadvinder; de Andrade Miranda, Ires Paula; Prieto, Adriana; Rudas, Agustín; Ruschell, Ademir R.; Silva, Natalino; Vela, César I. A.; Vos, Vincent A.; Zent, Eglée L.; Zent, Stanford; Cano, Angela; Nascimento, Marcelo Trindade; Oliveira, Alexandre A.; Ramirez-Angulo, Hirma; Ramos, José Ferreira; Sierra, Rodrigo; Tirado, Milton; Medina, Maria Natalia Umaña; van der Heijden, Geertje; Torre, Emilio Vilanova; Vriesendorp, Corine; Wang, Ophelia; Young, Kenneth R.; Baider, Claudia; Balslev, Henrik; de Castro, Natalia; Farfan-Rios, William; Ferreira, Cid; Mendoza, Casimiro; Mesones, Italo; Torres-Lezama, Armando; Giraldo, Ligia Estela Urrego; Villarroel, Daniel; Zagt, Roderick; Alexiades, Miguel N.; Garcia-Cabrera, Karina; Hernandez, Lionel; Huamantupa-Chuquimaco, Isau; Milliken, William; Cuenca, Walter Palacios; Pansini, Susamar; Pauletto, Daniela; Arevalo, Freddy Ramirez; Sampaio, Adeilza Felipe; Valderrama Sandoval, Elvis H.; Gamarra, Luis Valenzuela

2015-01-01

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world’s >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century. PMID:26702442

Forest health in a changing world: Effects of globalization and climate change on forest insect and pathogen impacts

Treesearch

T. D. Ramsfield; Barbara Bentz; M. Faccoli; H. Jactel; E. G. Brockerhoff

2016-01-01

Forests and trees throughout the world are increasingly affected by factors related to global change. Expanding international trade has facilitated invasions of numerous insects and pathogens into new regions. Many of these invasions have caused substantial forest damage, economic impacts and losses of ecosystem goods and services provided by trees. Climate...

Plant diversity increases with the strength of negative density dependence at the global scale

Treesearch

Joseph A. LaManna; Scott A. Mangan; Alfonso Alonso; Norman A. Bourg; Warren Y. Brockelman; Sarayudh Bunyavejchewin; Li-Wan Chang; Jyh-Min Chiang; George B. Chuyong; Keith Clay; Richard Condit; Susan Cordell; Stuart J. Davies; Tucker J. Furniss; Christian P. Giardina; I. A. U. Nimal Gunatilleke; C. V. Savitri Gunatilleke; Fangliang He; Robert W. Howe; Stephen P. Hubbell; Chang-Fu Hsieh; Faith M. Inman-Narahari; David Janík; Daniel J. Johnson; David Kenfack; Lisa Korte; Kamil Král; Andrew J. Larson; James A. Lutz; Sean M. McMahon; William J. McShea; Hervé R. Memiaghe; Anuttara Nathalang; Vojtech Novotny; Perry S. Ong; David A. Orwig; Rebecca Ostertag; Geoffrey G. Parker; Richard P. Phillips; Lawren Sack; I-Fang Sun; J. Sebastián Tello; Duncan W. Thomas; Benjamin L. Turner; Dilys M. Vela Díaz; Tomáš Vrška; George D. Weiblen; Amy Wolf; Sandra Yap; Jonathan A. Myers

2017-01-01

Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only...

Tree die-off in response to global change-type drought: Mortality insights from a decade of plant water potential measurements

USGS Publications Warehouse

Breshears, D.D.; Myers, O.B.; Meyer, Clifton W.; Barnes, F.J.; Zou, C.B.; Allen, Craig D.; McDowell, N.G.; Pockman, W. T.

2009-01-01

Global climate change is projected to produce warmer, longer, and more frequent droughts, referred to here as “global change-type droughts”, which have the potential to trigger widespread tree die-off. However, drought-induced tree mortality cannot be predicted with confidence, because long-term field observations of plant water stress prior to, and culminating in, mortality are rare, precluding the development and testing of mechanisms. Here, we document plant water stress in two widely distributed, co-occurring species, piñon pine (Pinus edulis) and juniper (Juniperus monosperma), over more than a decade, leading up to regional-scale die-off of piñon pine trees in response to global change-related drought. Piñon leaf water potentials remained substantially below their zero carbon assimilation point for at least 10 months prior to dying, in contrast to those of juniper, which rarely dropped below their zero-assimilation point. These data suggest that piñon mortality was driven by protracted water stress, leading to carbon starvation and associated increases in susceptibility to other disturbances (eg bark beetles), a finding that should help to improve predictions of mortality during drought.

Compensatory responses in plant-herbivore interactions: Impacts of insects on leaf water relations

NASA Astrophysics Data System (ADS)

Peschiutta, María L.; Bucci, Sandra J.; Scholz, Fabián G.; Goldstein, Guillermo

2016-05-01

Herbivore damage to leaves has been typically evaluated in terms of fractions of area removed; however morpho-physiological changes in the remaining tissues can occur in response to removal. We assessed the effects of partial removal of the leaf mesophyll by Caliroa cerasi (Hymenoptera) on leaf hydraulic conductance (Kleaf), vascular architecture, water relations and leaf size of three Prunus avium cultivars. The insect feeds on the leaf mesophyll leaving the vein network intact (skeletonization). Within each cultivar there were trees without infestations and trees chronically infested, at least over the last three years. Leaf size of intact leaves tended to be similar during leaf expansion before herbivore attack occurs across infested and non-infested trees. However, after herbivore attack and when the leaves were fully expanded, damaged leaves were smaller than leaves from non-infested trees. Damaged area varied between 21 and 31% depending on cultivar. The non-disruption of the vascular system together with either vein density or capacitance increased in damaged leaves resulted in similar Kleaf and stomatal conductance in infested and non-infested trees. Non-stomatal water loss from repeated leaf damage led to lower leaf water potentials in two of the infested cultivars. Lower leaf osmotic potentials and vulnerability to loss of Kleaf were observed in infested plants. Our results show that skeletonization resulted in compensatory changes in terms of water relations and hydraulics traits and in cultivar-specific physiological changes in phylogenetic related P. avium. Our findings indicate that detrimental effects of herbivory on the photosynthetic surface are counterbalanced by changes providing higher drought resistance, which has adaptive significance in ecosystems where water availability is low and furthermore where global climate changes would decrease soil water availability in the future even further.

Newer classification and regression tree techniques: Bagging and Random Forests for ecological prediction

Treesearch

Anantha M. Prasad; Louis R. Iverson; Andy Liaw; Andy Liaw

2006-01-01

We evaluated four statistical models - Regression Tree Analysis (RTA), Bagging Trees (BT), Random Forests (RF), and Multivariate Adaptive Regression Splines (MARS) - for predictive vegetation mapping under current and future climate scenarios according to the Canadian Climate Centre global circulation model.

Topological Filtering of Dynamic Functional Brain Networks Unfolds Informative Chronnectomics: A Novel Data-Driven Thresholding Scheme Based on Orthogonal Minimal Spanning Trees (OMSTs)

PubMed Central

Dimitriadis, Stavros I.; Salis, Christos; Tarnanas, Ioannis; Linden, David E.

2017-01-01

The human brain is a large-scale system of functionally connected brain regions. This system can be modeled as a network, or graph, by dividing the brain into a set of regions, or “nodes,” and quantifying the strength of the connections between nodes, or “edges,” as the temporal correlation in their patterns of activity. Network analysis, a part of graph theory, provides a set of summary statistics that can be used to describe complex brain networks in a meaningful way. The large-scale organization of the brain has features of complex networks that can be quantified using network measures from graph theory. The adaptation of both bivariate (mutual information) and multivariate (Granger causality) connectivity estimators to quantify the synchronization between multichannel recordings yields a fully connected, weighted, (a)symmetric functional connectivity graph (FCG), representing the associations among all brain areas. The aforementioned procedure leads to an extremely dense network of tens up to a few hundreds of weights. Therefore, this FCG must be filtered out so that the “true” connectivity pattern can emerge. Here, we compared a large number of well-known topological thresholding techniques with the novel proposed data-driven scheme based on orthogonal minimal spanning trees (OMSTs). OMSTs filter brain connectivity networks based on the optimization between the global efficiency of the network and the cost preserving its wiring. We demonstrated the proposed method in a large EEG database (N = 101 subjects) with eyes-open (EO) and eyes-closed (EC) tasks by adopting a time-varying approach with the main goal to extract features that can totally distinguish each subject from the rest of the set. Additionally, the reliability of the proposed scheme was estimated in a second case study of fMRI resting-state activity with multiple scans. Our results demonstrated clearly that the proposed thresholding scheme outperformed a large list of thresholding schemes based on the recognition accuracy of each subject compared to the rest of the cohort (EEG). Additionally, the reliability of the network metrics based on the fMRI static networks was improved based on the proposed topological filtering scheme. Overall, the proposed algorithm could be used across neuroimaging and multimodal studies as a common computationally efficient standardized tool for a great number of neuroscientists and physicists working on numerous of projects. PMID:28491032

Artificial Neural Networks for Processing Graphs with Application to Image Understanding: A Survey

NASA Astrophysics Data System (ADS)

Bianchini, Monica; Scarselli, Franco

In graphical pattern recognition, each data is represented as an arrangement of elements, that encodes both the properties of each element and the relations among them. Hence, patterns are modelled as labelled graphs where, in general, labels can be attached to both nodes and edges. Artificial neural networks able to process graphs are a powerful tool for addressing a great variety of real-world problems, where the information is naturally organized in entities and relationships among entities and, in fact, they have been widely used in computer vision, f.i. in logo recognition, in similarity retrieval, and for object detection. In this chapter, we propose a survey of neural network models able to process structured information, with a particular focus on those architectures tailored to address image understanding applications. Starting from the original recursive model (RNNs), we subsequently present different ways to represent images - by trees, forests of trees, multiresolution trees, directed acyclic graphs with labelled edges, general graphs - and, correspondingly, neural network architectures appropriate to process such structures.

Recapitulating phylogenies using k-mers: from trees to networks.

PubMed

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

A recursive method for calculating the total number of spanning trees and its applications in self-similar small-world scale-free network models

NASA Astrophysics Data System (ADS)

Ma, Fei; Su, Jing; Yao, Bing

2018-05-01

The problem of determining and calculating the number of spanning trees of any finite graph (model) is a great challenge, and has been studied in various fields, such as discrete applied mathematics, theoretical computer science, physics, chemistry and the like. In this paper, firstly, thank to lots of real-life systems and artificial networks built by all kinds of functions and combinations among some simpler and smaller elements (components), we discuss some helpful network-operation, including link-operation and merge-operation, to design more realistic and complicated network models. Secondly, we present a method for computing the total number of spanning trees. As an accessible example, we apply this method to space of trees and cycles respectively, and our results suggest that it is indeed a better one for such models. In order to reflect more widely practical applications and potentially theoretical significance, we study the enumerating method in some existing scale-free network models. On the other hand, we set up a class of new models displaying scale-free feature, that is to say, following P(k) k-γ, where γ is the degree exponent. Based on detailed calculation, the degree exponent γ of our deterministic scale-free models satisfies γ > 3. In the rest of our discussions, we not only calculate analytically the solutions of average path length, which indicates our models have small-world property being prevailing in amounts of complex systems, but also derive the number of spanning trees by means of the recursive method described in this paper, which clarifies our method is convenient to research these models.

Tropical forests and global change: filling knowledge gaps.

PubMed

Zuidema, Pieter A; Baker, Patrick J; Groenendijk, Peter; Schippers, Peter; van der Sleen, Peter; Vlam, Mart; Sterck, Frank

2013-08-01

Tropical forests will experience major changes in environmental conditions this century. Understanding their responses to such changes is crucial to predicting global carbon cycling. Important knowledge gaps exist: the causes of recent changes in tropical forest dynamics remain unclear and the responses of entire tropical trees to environmental changes are poorly understood. In this Opinion article, we argue that filling these knowledge gaps requires a new research strategy, one that focuses on trees instead of leaves or communities, on long-term instead of short-term changes, and on understanding mechanisms instead of documenting changes. We propose the use of tree-ring analyses, stable-isotope analyses, manipulative field experiments, and well-validated simulation models to improve predictions of forest responses to global change. Copyright © 2013 Elsevier Ltd. All rights reserved.

Investigation of an artificial intelligence technology--Model trees. Novel applications for an immediate release tablet formulation database.

PubMed

Shao, Q; Rowe, R C; York, P

2007-06-01

This study has investigated an artificial intelligence technology - model trees - as a modelling tool applied to an immediate release tablet formulation database. The modelling performance was compared with artificial neural networks that have been well established and widely applied in the pharmaceutical product formulation fields. The predictability of generated models was validated on unseen data and judged by correlation coefficient R(2). Output from the model tree analyses produced multivariate linear equations which predicted tablet tensile strength, disintegration time, and drug dissolution profiles of similar quality to neural network models. However, additional and valuable knowledge hidden in the formulation database was extracted from these equations. It is concluded that, as a transparent technology, model trees are useful tools to formulators.

The contribution of respiration in tree-stems to the Dole Effect

NASA Astrophysics Data System (ADS)

Angert, A.; Muhr, J.; Negron Juarez, R.; Alegria Muñoz, W.; Kraemer, G.; Ramirez Santillan, J.; Chambers, J. Q.; Trumbore, S. E.

2012-01-01

Understanding the variability and the current value of the Dole Effect, which has been used to infer past changes in biospheric productivity, requires accurate information on the discrimination associated with respiratory oxygen consumption in each of the biosphere components. Respiration in tree stems is an important component of the land carbon cycle. Here we measured, for the first time, the discrimination associated with tree stem oxygen uptake. The measurements included tropical forest trees, which are major contributors to the global fluxes of carbon and oxygen. We found discrimination in the range of 12.6-21.5 ‰, indicating both diffusion limitation, resulting in O2 discrimination values below 20 ‰, and alternative oxidase respiration, which resulted in discrimination values greater than 20 ‰. Discrimination varied seasonally, between and within tree species. Calculations based on these results show that variability in woody plants discrimination can result in significant variations in the global Dole Effect.

The contribution of respiration in tree stems to the Dole Effect

NASA Astrophysics Data System (ADS)

Angert, A.; Muhr, J.; Negron Juarez, R.; Alegria Muñoz, W.; Kraemer, G.; Ramirez Santillan, J.; Chambers, J. Q.; Trumbore, S. E.

2012-10-01

Understanding the variability and the current value of the Dole Effect, which has been used to infer past changes in biospheric productivity, requires accurate information on the isotopic discrimination associated with respiratory oxygen consumption in each of the biosphere components. Respiration in tree stems is an important component of the land carbon cycle. Here we measured, for the first time, the discrimination associated with tree stem oxygen uptake. The measurements included tropical forest trees, which are major contributors to the global fluxes of carbon and oxygen. We found discrimination in the range of 12.6-21.5‰, indicating both diffusion limitation, resulting in O2 discrimination values below 20‰, and alternative oxidase respiration, which resulted in discrimination values greater than 20‰. Discrimination varied seasonally, between and within tree species. Calculations based on these results show that variability in woody plants discrimination can result in significant variations in the global Dole Effect.

GLOBAL WARMING MITIGATION POTENTIAL OF THREE TREE PLANTATION SCENARIIOS

EPA Science Inventory

The report gives results of an analysis of three alternative uses of forests in the U.S. to reduce atmospheric carbon dioxide (CO2)concentrations: (1) planting trees with no harvesting, (2) traditional forestry, and (3) short-rotation intensive culture of trees for biomass. ncrea...

A dynamical model for bark beetle outbreaks

Treesearch

Vlastimil Krivan; Mark Lewis; Barbara J. Bentz; Sharon Bewick; Suzanne M. Lenhart; Andrew Liebhold

2016-01-01

Tree-killing bark beetles are major disturbance agents affecting coniferous forest ecosystems. The role of environmental conditions on driving beetle outbreaks is becoming increasingly important as global climatic change alters environmental factors, such as drought stress, that, in turn, govern tree resistance. Furthermore, dynamics between beetles and trees...

A Skilful Marine Sclerochronological Network Based Reconstruction of North Atlantic Subpolar Gyre Dynamics

NASA Astrophysics Data System (ADS)

Reynolds, D.; Hall, I. R.; Slater, S. M.; Scourse, J. D.; Wanamaker, A. D.; Halloran, P. R.; Garry, F. K.

2017-12-01

Spatial network analyses of precisely dated, and annually resolved, tree-ring proxy records have facilitated robust reconstructions of past atmospheric climate variability and the associated mechanisms and forcings that drive it. In contrast, a lack of similarly dated marine archives has constrained the use of such techniques in the marine realm, despite the potential for developing a more robust understanding of the role basin scale ocean dynamics play in the global climate system. Here we show that a spatial network of marine molluscan sclerochronological oxygen isotope (δ18Oshell) series spanning the North Atlantic region provides a skilful reconstruction of basin scale North Atlantic sea surface temperatures (SSTs). Our analyses demonstrate that the composite marine series (referred to as δ18Oproxy_PC1) is significantly sensitive to inter-annual variability in North Atlantic SSTs (R=-0.61 P<0.01) and surface air temperatures (SATs; R=-0.67, P<0.01) over the 20th century. Subpolar gyre (SPG) SSTs dominates variability in the δ18Oproxy_PC1 series at sub-centennial frequencies (R=-0.51, P<0.01). Comparison of the δ18Oproxy_PC1 series against variability in the strength of the European Slope Current and maximum North Atlantic meridional overturning circulation derived from numeric climate models (CMIP5), indicates that variability in the SPG region, associated with the strength of the surface currents of the North Atlantic, are playing a significant role in shaping the multi-decadal scale SST variability over the industrial era. These analyses demonstrate that spatial networks developed from sclerochronological archives can provide powerful baseline archives of past ocean variability that can facilitate the development of a quantitative understanding for the role the oceans play in the global climate systems and constraining uncertainties in numeric climate models.

Noise enhances information transfer in hierarchical networks.

PubMed

Czaplicka, Agnieszka; Holyst, Janusz A; Sloot, Peter M A

2013-01-01

We study the influence of noise on information transmission in the form of packages shipped between nodes of hierarchical networks. Numerical simulations are performed for artificial tree networks, scale-free Ravasz-Barabási networks as well for a real network formed by email addresses of former Enron employees. Two types of noise are considered. One is related to packet dynamics and is responsible for a random part of packets paths. The second one originates from random changes in initial network topology. We find that the information transfer can be enhanced by the noise. The system possesses optimal performance when both kinds of noise are tuned to specific values, this corresponds to the Stochastic Resonance phenomenon. There is a non-trivial synergy present for both noisy components. We found also that hierarchical networks built of nodes of various degrees are more efficient in information transfer than trees with a fixed branching factor.

Noise enhances information transfer in hierarchical networks

PubMed Central

Czaplicka, Agnieszka; Holyst, Janusz A.; Sloot, Peter M. A.

2013-01-01

We study the influence of noise on information transmission in the form of packages shipped between nodes of hierarchical networks. Numerical simulations are performed for artificial tree networks, scale-free Ravasz-Barabási networks as well for a real network formed by email addresses of former Enron employees. Two types of noise are considered. One is related to packet dynamics and is responsible for a random part of packets paths. The second one originates from random changes in initial network topology. We find that the information transfer can be enhanced by the noise. The system possesses optimal performance when both kinds of noise are tuned to specific values, this corresponds to the Stochastic Resonance phenomenon. There is a non-trivial synergy present for both noisy components. We found also that hierarchical networks built of nodes of various degrees are more efficient in information transfer than trees with a fixed branching factor. PMID:23390574

Tree growth-climate relationships in a forest-plot network on Mediterranean mountains.

PubMed

Fyllas, Nikolaos M; Christopoulou, Anastasia; Galanidis, Alexandros; Michelaki, Chrysanthi Z; Dimitrakopoulos, Panayiotis G; Fulé, Peter Z; Arianoutsou, Margarita

2017-11-15

In this study we analysed a novel tree-growth dataset, inferred from annual ring-width measurements, of 7 forest tree species from 12 mountain regions in Greece, in order to identify tree growth - climate relationships. The tree species of interest were: Abies cephalonica, Abies borisii-regis, Picea abies, Pinus nigra, Pinus sylvestris, Fagus sylvatica and Quercus frainetto growing across a gradient of climate conditions with mean annual temperature ranging from 5.7 to 12.6°C and total annual precipitation from 500 to 950mm. In total, 344 tree cores (one per tree) were analysed across a network of 20 study sites. We found that water availability during the summer period (May-August) was a strong predictor of interannual variation in tree growth for all study species. Across species and sites, annual tree growth was positively related to summer season precipitation (P SP ). The responsiveness of annual growth to P SP was tightly related to species and site specific measurements of instantaneous photosynthetic water use efficiency (WUE), suggesting that the growth of species with efficient water use is more responsive to variations in precipitation during the dry months of the year. Our findings support the importance of water availability for the growth of mountainous Mediterranean tree species and highlight that future reductions in precipitation are likely to lead to reduced tree-growth under climate change conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Applying and Individual-Based Model to Simultaneously Evaluate Net Ecosystem Production and Tree Diameter Increment

NASA Astrophysics Data System (ADS)

Fang, F. J.

2017-12-01

Reconciling observations at fundamentally different scales is central in understanding the global carbon cycle. This study investigates a model-based melding of forest inventory data, remote-sensing data and micrometeorological-station data ("flux towers" estimating forest heat, CO2 and H2O fluxes). The individual tree-based model FORCCHN was used to evaluate the tree DBH increment and forest carbon fluxes. These are the first simultaneous simulations of the forest carbon budgets from flux towers and individual-tree growth estimates of forest carbon budgets using the continuous forest inventory data — under circumstances in which both predictions can be tested. Along with the global implications of such findings, this also improves the capacity for forest sustainable management and the comprehensive understanding of forest ecosystems. In forest ecology, diameter at breast height (DBH) of a tree significantly determines an individual tree's cross-sectional sapwood area, its biomass and carbon storage. Evaluation the annual DBH increment (ΔDBH) of an individual tree is central to understanding tree growth and forest ecology. Ecosystem Carbon flux is a consequence of key ecosystem processes in the forest-ecosystem carbon cycle, Gross and Net Primary Production (GPP and NPP, respectively) and Net Ecosystem Respiration (NEP). All of these closely relate with tree DBH changes and tree death. Despite advances in evaluating forest carbon fluxes with flux towers and forest inventories for individual tree ΔDBH, few current ecological models can simultaneously quantify and predict the tree ΔDBH and forest carbon flux.

Rate of tree carbon accumulation increases continuously with tree size.

PubMed

Stephenson, N L; Das, A J; Condit, R; Russo, S E; Baker, P J; Beckman, N G; Coomes, D A; Lines, E R; Morris, W K; Rüger, N; Alvarez, E; Blundo, C; Bunyavejchewin, S; Chuyong, G; Davies, S J; Duque, A; Ewango, C N; Flores, O; Franklin, J F; Grau, H R; Hao, Z; Harmon, M E; Hubbell, S P; Kenfack, D; Lin, Y; Makana, J-R; Malizia, A; Malizia, L R; Pabst, R J; Pongpattananurak, N; Su, S-H; Sun, I-F; Tan, S; Thomas, D; van Mantgem, P J; Wang, X; Wiser, S K; Zavala, M A

2014-03-06

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

Efficient threshold for volumetric segmentation

NASA Astrophysics Data System (ADS)

Burdescu, Dumitru D.; Brezovan, Marius; Stanescu, Liana; Stoica Spahiu, Cosmin; Ebanca, Daniel

2015-07-01

Image segmentation plays a crucial role in effective understanding of digital images. However, the research on the existence of general purpose segmentation algorithm that suits for variety of applications is still very much active. Among the many approaches in performing image segmentation, graph based approach is gaining popularity primarily due to its ability in reflecting global image properties. Volumetric image segmentation can simply result an image partition composed by relevant regions, but the most fundamental challenge in segmentation algorithm is to precisely define the volumetric extent of some object, which may be represented by the union of multiple regions. The aim in this paper is to present a new method to detect visual objects from color volumetric images and efficient threshold. We present a unified framework for volumetric image segmentation and contour extraction that uses a virtual tree-hexagonal structure defined on the set of the image voxels. The advantage of using a virtual tree-hexagonal network superposed over the initial image voxels is that it reduces the execution time and the memory space used, without losing the initial resolution of the image.

Metro-access integrated network based on optical OFDMA with dynamic sub-carrier allocation and power distribution.

PubMed

Zhang, Chongfu; Zhang, Qiongli; Chen, Chen; Jiang, Ning; Liu, Deming; Qiu, Kun; Liu, Shuang; Wu, Baojian

2013-01-28

We propose and demonstrate a novel optical orthogonal frequency-division multiple access (OFDMA)-based metro-access integrated network with dynamic resource allocation. It consists of a single fiber OFDMA ring and many single fiber OFDMA trees, which transparently integrates metropolitan area networks with optical access networks. The single fiber OFDMA ring connects the core network and the central nodes (CNs), the CNs are on demand reconfigurable and use multiple orthogonal sub-carriers to realize parallel data transmission and dynamic resource allocation, meanwhile, they can also implement flexible power distribution. The remote nodes (RNs) distributed in the user side are connected by the single fiber OFDMA trees with the corresponding CN. The obtained results indicate that our proposed metro-access integrated network is feasible and the power distribution is agile.

LDFT-based watermarking resilient to local desynchronization attacks.

PubMed

Tian, Huawei; Zhao, Yao; Ni, Rongrong; Qin, Lunming; Li, Xuelong

2013-12-01

Up to now, a watermarking scheme that is robust against desynchronization attacks (DAs) is still a grand challenge. Most image watermarking resynchronization schemes in literature can survive individual global DAs (e.g., rotation, scaling, translation, and other affine transforms), but few are resilient to challenging cropping and local DAs. The main reason is that robust features for watermark synchronization are only globally invariable rather than locally invariable. In this paper, we present a blind image watermarking resynchronization scheme against local transform attacks. First, we propose a new feature transform named local daisy feature transform (LDFT), which is not only globally but also locally invariable. Then, the binary space partitioning (BSP) tree is used to partition the geometrically invariant LDFT space. In the BSP tree, the location of each pixel is fixed under global transform, local transform, and cropping. Lastly, the watermarking sequence is embedded bit by bit into each leaf node of the BSP tree by using the logarithmic quantization index modulation watermarking embedding method. Simulation results show that the proposed watermarking scheme can survive numerous kinds of distortions, including common image-processing attacks, local and global DAs, and noninvertible cropping.

Effects of contact network structure on epidemic transmission trees: implications for data required to estimate network structure.

PubMed

Carnegie, Nicole Bohme

2018-01-30

Understanding the dynamics of disease spread is key to developing effective interventions to control or prevent an epidemic. The structure of the network of contacts over which the disease spreads has been shown to have a strong influence on the outcome of the epidemic, but an open question remains as to whether it is possible to estimate contact network features from data collected in an epidemic. The approach taken in this paper is to examine the distributions of epidemic outcomes arising from epidemics on networks with particular structural features to assess whether that structure could be measured from epidemic data and what other constraints might be needed to make the problem identifiable. To this end, we vary the network size, mean degree, and transmissibility of the pathogen, as well as the network feature of interest: clustering, degree assortativity, or attribute-based preferential mixing. We record several standard measures of the size and spread of the epidemic, as well as measures that describe the shape of the transmission tree in order to ascertain whether there are detectable signals in the final data from the outbreak. The results suggest that there is potential to estimate contact network features from transmission trees or pure epidemic data, particularly for diseases with high transmissibility or for which the relevant contact network is of low mean degree. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Simulating phenological shifts in French temperate forests under two climatic change scenarios and four driving global circulation models

NASA Astrophysics Data System (ADS)

Lebourgeois, François; Pierrat, Jean-Claude; Perez, Vincent; Piedallu, Christian; Cecchini, Sébastien; Ulrich, Erwin

2010-09-01

After modeling the large-scale climate response patterns of leaf unfolding, leaf coloring and growing season length of evergreen and deciduous French temperate trees, we predicted the effects of eight future climate scenarios on phenological events. We used the ground observations from 103 temperate forests (10 species and 3,708 trees) from the French Renecofor Network and for the period 1997-2006. We applied RandomForest algorithms to predict phenological events from climatic and ecological variables. With the resulting models, we drew maps of phenological events throughout France under present climate and under two climatic change scenarios (A2, B2) and four global circulation models (HadCM3, CGCM2, CSIRO2 and PCM). We compared current observations and predicted values for the periods 2041-2070 and 2071-2100. On average, spring development of oaks precedes that of beech, which precedes that of conifers. Annual cycles in budburst and leaf coloring are highly correlated with January, March-April and October-November weather conditions through temperature, global solar radiation or potential evapotranspiration depending on species. At the end of the twenty-first century, each model predicts earlier budburst (mean: 7 days) and later leaf coloring (mean: 13 days) leading to an average increase in the growing season of about 20 days (for oaks and beech stands). The A2-HadCM3 hypothesis leads to an increase of up to 30 days in many areas. As a consequence of higher predicted warming during autumn than during winter or spring, shifts in leaf coloring dates appear greater than trends in leaf unfolding. At a regional scale, highly differing climatic response patterns were observed.

Simulating phenological shifts in French temperate forests under two climatic change scenarios and four driving global circulation models.

PubMed

Lebourgeois, François; Pierrat, Jean-Claude; Perez, Vincent; Piedallu, Christian; Cecchini, Sébastien; Ulrich, Erwin

2010-09-01

After modeling the large-scale climate response patterns of leaf unfolding, leaf coloring and growing season length of evergreen and deciduous French temperate trees, we predicted the effects of eight future climate scenarios on phenological events. We used the ground observations from 103 temperate forests (10 species and 3,708 trees) from the French Renecofor Network and for the period 1997-2006. We applied RandomForest algorithms to predict phenological events from climatic and ecological variables. With the resulting models, we drew maps of phenological events throughout France under present climate and under two climatic change scenarios (A2, B2) and four global circulation models (HadCM3, CGCM2, CSIRO2 and PCM). We compared current observations and predicted values for the periods 2041-2070 and 2071-2100. On average, spring development of oaks precedes that of beech, which precedes that of conifers. Annual cycles in budburst and leaf coloring are highly correlated with January, March-April and October-November weather conditions through temperature, global solar radiation or potential evapotranspiration depending on species. At the end of the twenty-first century, each model predicts earlier budburst (mean: 7 days) and later leaf coloring (mean: 13 days) leading to an average increase in the growing season of about 20 days (for oaks and beech stands). The A2-HadCM3 hypothesis leads to an increase of up to 30 days in many areas. As a consequence of higher predicted warming during autumn than during winter or spring, shifts in leaf coloring dates appear greater than trends in leaf unfolding. At a regional scale, highly differing climatic response patterns were observed.

Forest structure in low-diversity tropical forests: a study of Hawaiian wet and dry forests.

PubMed

Ostertag, Rebecca; Inman-Narahari, Faith; Cordell, Susan; Giardina, Christian P; Sack, Lawren

2014-01-01

The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai'i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai'i forests were characterized by low species richness and very high relative dominance. The two Hawai'i forests were floristically distinct, yet similar in species richness (15 vs. 21 species) and stem density (3078 vs. 3486/ha). While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5->50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai'i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15-1182 species), six-fold variation in mean annual rainfall (835-5272 mm yr(-1)) and 1.8-fold variation in mean annual temperature (16.0-28.4°C). Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological theory for links among species diversity, environmental variation and ecosystem function.

Forest Structure in Low-Diversity Tropical Forests: A Study of Hawaiian Wet and Dry Forests

PubMed Central

Ostertag, Rebecca; Inman-Narahari, Faith; Cordell, Susan; Giardina, Christian P.; Sack, Lawren

2014-01-01

The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai‘i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai‘i forests were characterized by low species richness and very high relative dominance. The two Hawai‘i forests were floristically distinct, yet similar in species richness (15 vs. 21 species) and stem density (3078 vs. 3486/ha). While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5–>50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai‘i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15–1182 species), six-fold variation in mean annual rainfall (835–5272 mm yr−1) and 1.8-fold variation in mean annual temperature (16.0–28.4°C). Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological theory for links among species diversity, environmental variation and ecosystem function. PMID:25162731

GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

NASA Astrophysics Data System (ADS)

Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the distributed operation, reduplication operation transfer operation of spatial index in the grid environment. The design of GSHR-Tree has ensured the performance of the load balance in the parallel computation. This tree structure is fit for the parallel process of the spatial information in the distributed network environments. Instead of spatial object's recursive comparison where original R tree has been used, the algorithm builds the spatial index by applying binary code operation in which computer runs more efficiently, and extended dynamic hash code for bit comparison. In GSHR-Tree, a new server is assigned to the network whenever a split of a full node is required. We describe a more flexible allocation protocol which copes with a temporary shortage of storage resources. It uses a distributed balanced binary spatial tree that scales with insertions to potentially any number of storage servers through splits of the overloaded ones. The application manipulates the GSHR-Tree structure from a node in the grid environment. The node addresses the tree through its image that the splits can make outdated. This may generate addressing errors, solved by the forwarding among the servers. In this paper, a spatial index data distribution algorithm that limits the number of servers has been proposed. We improve the storage utilization at the cost of additional messages. The structure of GSHR-Tree is believed that the scheme of this grid spatial index should fit the needs of new applications using endlessly larger sets of spatial data. Our proposal constitutes a flexible storage allocation method for a distributed spatial index. The insertion policy can be tuned dynamically to cope with periods of storage shortage. In such cases storage balancing should be favored for better space utilization, at the price of extra message exchanges between servers. This structure makes a compromise in the updating of the duplicated index and the transformation of the spatial index data. Meeting the needs of the grid computing, GSHRTree has a flexible structure in order to satisfy new needs in the future. The GSHR-Tree provides the R-tree capabilities for large spatial datasets stored over interconnected servers. The analysis, including the experiments, confirmed the efficiency of our design choices. The scheme should fit the needs of new applications of spatial data, using endlessly larger datasets. Using the system response time of the parallel processing of spatial scope query algorithm as the performance evaluation factor, According to the result of the simulated the experiments, GSHR-Tree is performed to prove the reasonable design and the high performance of the indexing structure that the paper presented.

Tree Amigos.

ERIC Educational Resources Information Center

Center for Environmental Study, Grand Rapids, MI.

Tree Amigos is a special cross-cultural program that uses trees as a common bond to bring the people of the Americas together in unique partnerships to preserve and protect the shared global environment. It is a tangible program that embodies the philosophy that individuals, acting together, can make a difference. This resource book contains…

Trait Acclimation Mitigates Mortality Risks of Tropical Canopy Trees under Global Warming.

PubMed

Sterck, Frank; Anten, Niels P R; Schieving, Feike; Zuidema, Pieter A

2016-01-01

There is a heated debate about the effect of global change on tropical forests. Many scientists predict large-scale tree mortality while others point to mitigating roles of CO2 fertilization and - the notoriously unknown - physiological trait acclimation of trees. In this opinion article we provided a first quantification of the potential of trait acclimation to mitigate the negative effects of warming on tropical canopy tree growth and survival. We applied a physiological tree growth model that incorporates trait acclimation through an optimization approach. Our model estimated the maximum effect of acclimation when trees optimize traits that are strongly plastic on a week to annual time scale (leaf photosynthetic capacity, total leaf area, stem sapwood area) to maximize carbon gain. We simulated tree carbon gain for temperatures (25-35°C) and ambient CO2 concentrations (390-800 ppm) predicted for the 21st century. Full trait acclimation increased simulated carbon gain by up to 10-20% and the maximum tolerated temperature by up to 2°C, thus reducing risks of tree death under predicted warming. Functional trait acclimation may thus increase the resilience of tropical trees to warming, but cannot prevent tree death during extremely hot and dry years at current CO2 levels. We call for incorporating trait acclimation in field and experimental studies of plant functional traits, and in models that predict responses of tropical forests to climate change.

Development of a Global Wetland Sustainability Index for comprehensive land use planning

NASA Astrophysics Data System (ADS)

Schleupner, C.; Schneider, U. A.; Havlik, P.; Stacke, T.

2012-04-01

Allocation of nature reserves for conservation of ecosystem functions and services is a multi-dimensional task. Conservation programs act from local to regional or national scales, and some efforts involve entire continents. Globally, several international environmental agreements have been established which include conservation issues. Examples are the Convention on Biological Diversity, the Convention on Migratory Species of Wild Animals, the UN Framework Convention on Climate Change, and the Ramsar Convention on Wetlands. A common aim of most initiatives is the protection and restoration of valuable natural sites by providing a functional network of sites. The planning of protected habitat networks to safeguard global biodiversity requires substantial knowledge on exposure, services, and functions of ecosystems. Further, the complex spatial relationships between humans and the environment under consideration of costs and land use competition have to be determined. Often such analyses are hindered by lack of data. We developed a global index that ranks sites for wetland protection according to its wetland quantity, wetland quality and pressure upon the wetland sites. Each of the three parts is based on several spatial-ecological datasets that contain important information for the adequate assessment of spatial economic and ecologic interdependencies. Applying cluster analyses and ecological decision trees the data are combined and results are translated to the final index and expressed per simulation unit for integration into the Global Biomass Optimization Model GLOBIOM. This global recursive dynamic partial equilibrium model integrates the agricultural, bio energy and forestry sectors with the aim to provide policy analyses on global issues concerning land use competition between the major land-based production sectors. Results not only show the most vulnerable wetland areas to nature loss and the most valuable wetland areas for biodiversity protection under certain land use scenarios. Moreover, costs of protection are estimated and the results give recommendations for action by illustrating wetland conservation areas in need for conservation. Often wetlands provide numerous ecosystem services to society, such as water retention, flood control, water purification, to name only a few. The sustainable conservation of wetland sites, especially in highly human dominated landscapes, is therefore an important global but still underestimated objective.

Expanding the network of crossdated tree-ring chronologies for Sequoia sempervirens

Treesearch

Allyson L. Carroll; Stephen C. Sillett; Ethan J. Coonen; Benjamin G. Iberle

2017-01-01

Crossdated tree-ring chronologies for the Arcata Community Forest (ACF) and Muir Woods National Monument (Muir Woods) expand the spatial coverage of dated coast redwood (Sequoia sempervirens (D. Don) Endl.) series. Crossdating relies on the common pattern of ring-width variation among tree populations, and dated chronologies have many applications...

Crown dynamics and wood production of Douglas-fir trees in an old-growth forest

Treesearch

H. Roaki Ishii; Stephen C. Sillett; Allyson L. Carroll

2017-01-01

Large trees are the most prominent structural features of old-growth forests, which are considered to be globally important carbon sinks. Because of their large size, estimates of biomass and growth of large trees are often based on ground-level measurements (e.g., diameter at breast height, DBH) and little is known about growth dynamics within the crown. As trees...

Precipitation thresholds and drought-induced tree die-off: Insights from patterns of Pinus edulis mortality along an environmental stress gradient

Treesearch

Michael J. Clifford; Patrick D. Royer; Neil S. Cobb; David D. Breshears; Paulette L. Ford

2013-01-01

Recent regional tree die-off events appear to have been triggered by a combination of drought and heat - referred to as 'global-change-type drought'. To complement experiments focused on resolving mechanisms of drought-induced tree mortality, an evaluation of how patterns of tree die-off relate to highly spatially variable precipitation is needed....

Teaching Structured Design of Network Algorithms in Enhanced Versions of SQL

ERIC Educational Resources Information Center

de Brock, Bert

2004-01-01

From time to time developers of (database) applications will encounter, explicitly or implicitly, structures such as trees, graphs, and networks. Such applications can, for instance, relate to bills of material, organization charts, networks of (rail)roads, networks of conduit pipes (e.g., plumbing, electricity), telecom networks, and data…

Experimental basin studies—an international and historical perspective of forest impacts

NASA Astrophysics Data System (ADS)

Whitehead, P. G.; Robinson, M.

1993-05-01

The long tradition of catchment studies in hydrology results from the need to understand the water balance operating in basins, the processes controlling water movements and the impacts of land-use change on water quantity and quality. The interactions between physical, chemical and biological behaviour have become an increasingly dominant theme in recent years, and this has been boosted by global environmental problems such as acid rain and climatic change. After a historical summary of catchment studies, a brief review is given of some of the most influential experiments and their underlying objectives and results, concentrating on those concerned with one land-use change in particular — to/from forestry. In interpreting the effects of a change in forest cover, it is necessary also to consider impacts of the associated site disturbance, including possible soil compaction and road construction as a result of logging and any artificial drainage before tree planting. The recent tendency to link basin studies into networks is discussed, with examples of currently active networks.

Contribution made by biomarkers of status to an FP6 Network of Excellence, EURopean micronutrient RECommendations Aligned (EURRECA).

PubMed

Fairweather-Tait, Susan J

2011-08-01

Dietary reference values for micronutrients vary considerably among countries, and harmonization is needed to facilitate nutrition policy and public health strategies at the European and global levels. The EURopean micronutrient RECommendations Aligned (EURRECA) Network of Excellence is developing generic instruments for systematically deriving and updating micronutrient reference values and dietary recommendations. These include best practice guidelines, interlinked web pages, online databases, and decision trees. Journal supplements have been published on micronutrient intakes and status, and an ongoing activity of EURRECA is the completion of systematic reviews on associations between intakes, status, and various health outcomes for priority micronutrients (ie, iron, zinc, folate, vitamin B-12, and iodine), which were selected by using a triage technique. Future activities include meta-analyses to identify dose-response relations and the variability, factorial estimates of requirements, bioavailability from whole diets, effects of genotype, and modeling techniques for addressing dietary recommendations for combinations of nutrients with common health endpoints.

An effective fractal-tree closure model for simulating blood flow in large arterial networks.

PubMed

Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em

2015-06-01

The aim of the present work is to address the closure problem for hemodynamic simulations by developing a flexible and effective model that accurately distributes flow in the downstream vasculature and can stably provide a physiological pressure outflow boundary condition. To achieve this goal, we model blood flow in the sub-pixel vasculature by using a non-linear 1D model in self-similar networks of compliant arteries that mimic the structure and hierarchy of vessels in the meso-vascular regime (radii [Formula: see text]). We introduce a variable vessel length-to-radius ratio for small arteries and arterioles, while also addressing non-Newtonian blood rheology and arterial wall viscoelasticity effects in small arteries and arterioles. This methodology aims to overcome substantial cut-off radius sensitivities, typically arising in structured tree and linearized impedance models. The proposed model is not sensitive to outflow boundary conditions applied at the end points of the fractal network, and thus does not require calibration of resistance/capacitance parameters typically required for outflow conditions. The proposed model convergences to a periodic state in two cardiac cycles even when started from zero-flow initial conditions. The resulting fractal-trees typically consist of thousands to millions of arteries, posing the need for efficient parallel algorithms. To this end, we have scaled up a Discontinuous Galerkin solver that utilizes the MPI/OpenMP hybrid programming paradigm to thousands of computer cores, and can simulate blood flow in networks of millions of arterial segments at the rate of one cycle per 5 min. The proposed model has been extensively tested on a large and complex cranial network with 50 parent, patient-specific arteries and 21 outlets to which fractal trees where attached, resulting to a network of up to 4,392,484 vessels in total, and a detailed network of the arm with 276 parent arteries and 103 outlets (a total of 702,188 vessels after attaching the fractal trees), returning physiological flow and pressure wave predictions without requiring any parameter estimation or calibration procedures. We present a novel methodology to overcome substantial cut-off radius sensitivities.

An efective fractal-tree closure model for simulating blood flow in large arterial networks

PubMed Central

Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em.

2014-01-01

The aim of the present work is to address the closure problem for hemodynamic simulations by developing a exible and effective model that accurately distributes flow in the downstream vasculature and can stably provide a physiological pressure out flow boundary condition. To achieve this goal, we model blood flow in the sub-pixel vasculature by using a non-linear 1D model in self-similar networks of compliant arteries that mimic the structure and hierarchy of vessels in the meso-vascular regime (radii 500 μm – 10 μm). We introduce a variable vessel length-to-radius ratio for small arteries and arterioles, while also addressing non-Newtonian blood rheology and arterial wall viscoelasticity effects in small arteries and arterioles. This methodology aims to overcome substantial cut-off radius sensitivities, typically arising in structured tree and linearized impedance models. The proposed model is not sensitive to out flow boundary conditions applied at the end points of the fractal network, and thus does not require calibration of resistance/capacitance parameters typically required for out flow conditions. The proposed model convergences to a periodic state in two cardiac cycles even when started from zero-flow initial conditions. The resulting fractal-trees typically consist of thousands to millions of arteries, posing the need for efficient parallel algorithms. To this end, we have scaled up a Discontinuous Galerkin solver that utilizes the MPI/OpenMP hybrid programming paradigm to thousands of computer cores, and can simulate blood flow in networks of millions of arterial segments at the rate of one cycle per 5 minutes. The proposed model has been extensively tested on a large and complex cranial network with 50 parent, patient-specific arteries and 21 outlets to which fractal trees where attached, resulting to a network of up to 4,392,484 vessels in total, and a detailed network of the arm with 276 parent arteries and 103 outlets (a total of 702,188 vessels after attaching the fractal trees), returning physiological flow and pressure wave predictions without requiring any parameter estimation or calibration procedures. We present a novel methodology to overcome substantial cut-off radius sensitivities PMID:25510364

Rate of tree carbon accumulation increases continuously with tree size

USGS Publications Warehouse

Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

2014-01-01

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

Spatially-explicit models of global tree density.

PubMed

Glick, Henry B; Bettigole, Charlie; Maynard, Daniel S; Covey, Kristofer R; Smith, Jeffrey R; Crowther, Thomas W

2016-08-16

Remote sensing and geographic analysis of woody vegetation provide means of evaluating the distribution of natural resources, patterns of biodiversity and ecosystem structure, and socio-economic drivers of resource utilization. While these methods bring geographic datasets with global coverage into our day-to-day analytic spheres, many of the studies that rely on these strategies do not capitalize on the extensive collection of existing field data. We present the methods and maps associated with the first spatially-explicit models of global tree density, which relied on over 420,000 forest inventory field plots from around the world. This research is the result of a collaborative effort engaging over 20 scientists and institutions, and capitalizes on an array of analytical strategies. Our spatial data products offer precise estimates of the number of trees at global and biome scales, but should not be used for local-level estimation. At larger scales, these datasets can contribute valuable insight into resource management, ecological modelling efforts, and the quantification of ecosystem services.

Global marine protected areas do not secure the evolutionary history of tropical corals and fishes

PubMed Central

Mouillot, D.; Parravicini, V.; Bellwood, D. R.; Leprieur, F.; Huang, D.; Cowman, P. F.; Albouy, C.; Hughes, T. P.; Thuiller, W.; Guilhaumon, F.

2016-01-01

Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7% of scleractinian coral species and 21.7% of labrid fish species reach the minimum protection target of 10% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7% of the Tree of Life for corals, and 17.6% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs. PMID:26756609

Distributed Contour Trees

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

Morozov, Dmitriy; Weber, Gunther H.

2014-03-31

Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di erent problems that rely on contour trees can be solved in parallel with minimal communication.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change.

PubMed

Ashraf, M Irfan; Meng, Fan-Rui; Bourque, Charles P-A; MacLean, David A

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm(2) 5-year(-1) and volume: 0.0008 m(3) 5-year(-1)). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm(2) 5-year(-1) and 0.0393 m(3) 5-year(-1) in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change

PubMed Central

Ashraf, M. Irfan; Meng, Fan-Rui; Bourque, Charles P.-A.; MacLean, David A.

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm2 5-year-1 and volume: 0.0008 m3 5-year-1). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm2 5-year-1 and 0.0393 m3 5-year-1 in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling. PMID:26173081

Climatic Change over the 'Third Pole' from Long Tree-Ring Records

NASA Astrophysics Data System (ADS)

Cook, E.

2011-12-01

Climatic change over the Greater Himalayas and Tibetan Plateau, the 'Third Pole' of the world, is of great concern now as the Earth continues to warm at an alarming rate. While future climatic change over this region and its resulting impacts on humanity and the environment are difficult to predict with much certainty, knowing how climate has varied in the past can provide both an improved understanding of the range of variability and change that could occur in the future and the necessary context for assessing recent observed climatic change there. For this purpose, one of the best natural archives of past climate information available for study of the Third Pole environment is the changing pattern of annual ring widths found in long tree-ring chronologies. The forests of the Third Pole support many long-lived tree species, with some having life spans in excess of 1,000 years. This natural resource is steadily dwindling now due to continuing deforestation caused by human activity, but there is still enough remaining forest cover to produce a detailed network of long tree-ring chronologies for study of climate variability and change covering the past several centuries. The tree-ring records provide a mix of climate information, including that related to both temperature and precipitation. Examples of long drought-sensitive tree-ring records from the more arid parts of the Karakoram and Tibetan Plateau will be presented, along with records that primarily reflect changing temperatures in moister environments such as in Bhutan. Together they provide a glimpse of how climate of the Third Pole has changed over the past several centuries, the range of natural variability that could occur in the future independent of changes caused by greenhouse warming, and how changes during the latter part of the 20th century period of rapid global warming compare to the past.

Quantifying loopy network architectures.

PubMed

Katifori, Eleni; Magnasco, Marcelo O

2012-01-01

Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of approaches have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes) from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

Motion planning for autonomous vehicle based on radial basis function neural network in unstructured environment.

PubMed

Chen, Jiajia; Zhao, Pan; Liang, Huawei; Mei, Tao

2014-09-18

The autonomous vehicle is an automated system equipped with features like environment perception, decision-making, motion planning, and control and execution technology. Navigating in an unstructured and complex environment is a huge challenge for autonomous vehicles, due to the irregular shape of road, the requirement of real-time planning, and the nonholonomic constraints of vehicle. This paper presents a motion planning method, based on the Radial Basis Function (RBF) neural network, to guide the autonomous vehicle in unstructured environments. The proposed algorithm extracts the drivable region from the perception grid map based on the global path, which is available in the road network. The sample points are randomly selected in the drivable region, and a gradient descent method is used to train the RBF network. The parameters of the motion-planning algorithm are verified through the simulation and experiment. It is observed that the proposed approach produces a flexible, smooth, and safe path that can fit any road shape. The method is implemented on autonomous vehicle and verified against many outdoor scenes; furthermore, a comparison of proposed method with the existing well-known Rapidly-exploring Random Tree (RRT) method is presented. The experimental results show that the proposed method is highly effective in planning the vehicle path and offers better motion quality.

Integron associated mobile genes: Just a collection of plug in apps or essential components of cell network hardware?

PubMed

Labbate, Maurizio; Boucher, Yan; Luu, Ivan; Chowdhury, Piklu Roy; Stokes, H W

2012-01-01

Lateral gene transfer (LGT) impacts on the evolution of prokaryotes in both the short and long-term. The short-term impacts of mobilized genes are a concern to humans since LGT explains the global rise of multi drug resistant pathogens seen in the past 70 years. However, LGT has been a feature of prokaryotes from the earliest days of their existence and the concept of a bifurcating tree of life is not entirely applicable to prokaryotes since most genes in extant prokaryotic genomes have probably been acquired from other lineages. Successful transfer and maintenance of a gene in a new host is understandable if it acts independently of cell networks and confers an advantage. Antibiotic resistance provides an example of this whereby a gene can be advantageous in virtually any cell across broad species backgrounds. In a longer evolutionary context however laterally transferred genes can be assimilated into even essential cell networks. How this happens is not well understood and we discuss recent work that identifies a mobile gene, unique to a cell lineage, which is detrimental to the cell when lost. We also present some additional data and believe our emerging model will be helpful in understanding how mobile genes integrate into cell networks.

Motion Planning for Autonomous Vehicle Based on Radial Basis Function Neural Network in Unstructured Environment

PubMed Central

Chen, Jiajia; Zhao, Pan; Liang, Huawei; Mei, Tao

2014-01-01

The autonomous vehicle is an automated system equipped with features like environment perception, decision-making, motion planning, and control and execution technology. Navigating in an unstructured and complex environment is a huge challenge for autonomous vehicles, due to the irregular shape of road, the requirement of real-time planning, and the nonholonomic constraints of vehicle. This paper presents a motion planning method, based on the Radial Basis Function (RBF) neural network, to guide the autonomous vehicle in unstructured environments. The proposed algorithm extracts the drivable region from the perception grid map based on the global path, which is available in the road network. The sample points are randomly selected in the drivable region, and a gradient descent method is used to train the RBF network. The parameters of the motion-planning algorithm are verified through the simulation and experiment. It is observed that the proposed approach produces a flexible, smooth, and safe path that can fit any road shape. The method is implemented on autonomous vehicle and verified against many outdoor scenes; furthermore, a comparison of proposed method with the existing well-known Rapidly-exploring Random Tree (RRT) method is presented. The experimental results show that the proposed method is highly effective in planning the vehicle path and offers better motion quality. PMID:25237902

Living Trees are a Major Source of Methane in the Temperate Forest

NASA Astrophysics Data System (ADS)

Covey, Kristofer

2017-04-01

Globally, forests sequester about 1.1 ± 0.8 Pg C yr-1, an ecosystem service worth hundreds of billions of dollars annually. Following the COP21 meeting in Paris, an international consensus emerged: The protection and expansion of forests worldwide is a necessary component of climate mitigation strategies to limit warming to less than 2°C. The physiological processes governing sequestration of CO2 in living trees are well studied and the resulting pattern in global forest carbon sequestration is clear. The role living trees play in the production and emission of methane (CH4) remains unclear, despite the fact it has the potential to offset climate benefits of forest CO2 sequestration. A known but largely unexplored pathway of forest CH4 production involves microbial-based methanogenesis in the wood of living trees. In the first regional-scale study of tree trunk gas composition, we examine the ubiquity and potential source strength of this pathway. Trunk methane concentrations were as high as 67.4% by volume (375,000-times atmospheric), with the highest concentrations found in older angiosperms (18,293 μLṡL-1 ± 3,096). Bark flux chambers from 23 living trees show emissions under field conditions, and large static chambers demonstrate high rates of production in felled Acer rubrum trunk sections. Diffusion flux modeling of trunk concentrations suggests wood-based microflora could produce a global CH4 efflux of 26 Tg CH4 yr-1. Applying these fluxes to provide a spatially explicit map of trunk-based CH4 flux, we estimate the potential relationship between carbon sequestration rates and CH4 emission by forest trees in Eastern North America. Methane emissions from the trunk-based methanogenic pathway could reduce the average climate mitigation value of these temperate forests by 10-30%. We highlight the need to improve earth systems models to account for the full complexity of forest climate interactions and provide a data layer useful in reducing large uncertainty in global methane budgets.

The P-Mesh: A Commodity-based Scalable Network Architecture for Clusters

NASA Technical Reports Server (NTRS)

Nitzberg, Bill; Kuszmaul, Chris; Stockdale, Ian; Becker, Jeff; Jiang, John; Wong, Parkson; Tweten, David (Technical Monitor)

1998-01-01

We designed a new network architecture, the P-Mesh which combines the scalability and fault resilience of a torus with the performance of a switch. We compare the scalability, performance, and cost of the hub, switch, torus, tree, and P-Mesh architectures. The latter three are capable of scaling to thousands of nodes, however, the torus has severe performance limitations with that many processors. The tree and P-Mesh have similar latency, bandwidth, and bisection bandwidth, but the P-Mesh outperforms the switch architecture (a lower bound for tree performance) on 16-node NAB Parallel Benchmark tests by up to 23%, and costs 40% less. Further, the P-Mesh has better fault resilience characteristics. The P-Mesh architecture trades increased management overhead for lower cost, and is a good bridging technology while the price of tree uplinks is expensive.

A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks.

PubMed

Park, HoSung; Kim, Beom-Su; Kim, Kyong Hoon; Shah, Babar; Kim, Ki-Il

2017-11-09

Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new ( m , k )-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the ( m , k )-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured ( m , k )-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption.

Tree Tensor Network State with Variable Tensor Order: An Efficient Multireference Method for Strongly Correlated Systems

PubMed Central

2015-01-01

We study the tree-tensor-network-state (TTNS) method with variable tensor orders for quantum chemistry. TTNS is a variational method to efficiently approximate complete active space (CAS) configuration interaction (CI) wave functions in a tensor product form. TTNS can be considered as a higher order generalization of the matrix product state (MPS) method. The MPS wave function is formulated as products of matrices in a multiparticle basis spanning a truncated Hilbert space of the original CAS-CI problem. These matrices belong to active orbitals organized in a one-dimensional array, while tensors in TTNS are defined upon a tree-like arrangement of the same orbitals. The tree-structure is advantageous since the distance between two arbitrary orbitals in the tree scales only logarithmically with the number of orbitals N, whereas the scaling is linear in the MPS array. It is found to be beneficial from the computational costs point of view to keep strongly correlated orbitals in close vicinity in both arrangements; therefore, the TTNS ansatz is better suited for multireference problems with numerous highly correlated orbitals. To exploit the advantages of TTNS a novel algorithm is designed to optimize the tree tensor network topology based on quantum information theory and entanglement. The superior performance of the TTNS method is illustrated on the ionic-neutral avoided crossing of LiF. It is also shown that the avoided crossing of LiF can be localized using only ground state properties, namely one-orbital entanglement. PMID:25844072

Architecture of an Antagonistic Tree/Fungus Network: The Asymmetric Influence of Past Evolutionary History

PubMed Central

Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

2008-01-01

Background Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Methology/Principal Findings Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Conclusion/Significance Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes. PMID:18320058

Climate Controls on Tree Growth in the Western Mediterranean

NASA Technical Reports Server (NTRS)

Touchan, Ramzi; Anchukaitis, Kevin J.; Meko, David M.; Kerchouche, Dalila; Slimani, Said; Ilmen, Rachid; Hasnaoui, Fouad; Guibal, Frederic; Canarerim Hesys Hykui; Sanchez-Salguero, Raul;

TreeMAC: Localized TDMA MAC protocol for real-time high-data-rate sensor networks

USGS Publications Warehouse

Song, W.-Z.; Huang, R.; Shirazi, B.; Husent, R.L.

2009-01-01

Earlier sensor network MAC protocols focus on energy conservation in low-duty cycle applications, while some recent applications involve real-time high-data-rate signals. This motivates us to design an innovative localized TDMA MAC protocol to achieve high throughput and low congestion in data collection sensor networks, besides energy conservation. TreeMAC divides a time cycle into frames and frame into slots. Parent determines children's frame assigmnent based on their relative bandwidth demand, and each node calculates its own slot assignment based on its hop-count to the sink. This innovative 2-dimensional frame-slot assignment algorithm has the following nice theory properties. Firstly, given any node, at any time slot, there is at most one active sender in its neighborhood (includ ing itself). Secondly, the packet scheduling with TreelMAC is bufferless, which therefore minimizes the probability of network congestion. Thirdly, the data throughput to gateway is at least 1/3 of the optimum assuming reliable links. Our experiments on a 24 node test bed demonstrate that TreeMAC protocol significantly improves network throughput and energy efficiency, by comparing to the TinyOS's default CSMA MAC protocol and a recent TDMA MAC protocol Funneling-MAC[8]. ?? 2009 IEEE.

Artificial Intelligence Procedures for Tree Taper Estimation within a Complex Vegetation Mosaic in Brazil

PubMed Central

Nunes, Matheus Henrique

2016-01-01

Tree stem form in native tropical forests is very irregular, posing a challenge to establishing taper equations that can accurately predict the diameter at any height along the stem and subsequently merchantable volume. Artificial intelligence approaches can be useful techniques in minimizing estimation errors within complex variations of vegetation. We evaluated the performance of Random Forest® regression tree and Artificial Neural Network procedures in modelling stem taper. Diameters and volume outside bark were compared to a traditional taper-based equation across a tropical Brazilian savanna, a seasonal semi-deciduous forest and a rainforest. Neural network models were found to be more accurate than the traditional taper equation. Random forest showed trends in the residuals from the diameter prediction and provided the least precise and accurate estimations for all forest types. This study provides insights into the superiority of a neural network, which provided advantages regarding the handling of local effects. PMID:27187074

Locating hardware faults in a parallel computer

DOEpatents

Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

2010-04-13

Locating hardware faults in a parallel computer, including defining within a tree network of the parallel computer two or more sets of non-overlapping test levels of compute nodes of the network that together include all the data communications links of the network, each non-overlapping test level comprising two or more adjacent tiers of the tree; defining test cells within each non-overlapping test level, each test cell comprising a subtree of the tree including a subtree root compute node and all descendant compute nodes of the subtree root compute node within a non-overlapping test level; performing, separately on each set of non-overlapping test levels, an uplink test on all test cells in a set of non-overlapping test levels; and performing, separately from the uplink tests and separately on each set of non-overlapping test levels, a downlink test on all test cells in a set of non-overlapping test levels.

Artificial Intelligence Procedures for Tree Taper Estimation within a Complex Vegetation Mosaic in Brazil.

PubMed

Nunes, Matheus Henrique; Görgens, Eric Bastos

2016-01-01

Tree stem form in native tropical forests is very irregular, posing a challenge to establishing taper equations that can accurately predict the diameter at any height along the stem and subsequently merchantable volume. Artificial intelligence approaches can be useful techniques in minimizing estimation errors within complex variations of vegetation. We evaluated the performance of Random Forest® regression tree and Artificial Neural Network procedures in modelling stem taper. Diameters and volume outside bark were compared to a traditional taper-based equation across a tropical Brazilian savanna, a seasonal semi-deciduous forest and a rainforest. Neural network models were found to be more accurate than the traditional taper equation. Random forest showed trends in the residuals from the diameter prediction and provided the least precise and accurate estimations for all forest types. This study provides insights into the superiority of a neural network, which provided advantages regarding the handling of local effects.

Optimal Stomatal Behaviour Around the World: Synthesis of a Global Stomatal Conductance Database and Scaling from Leaf to Ecosystem

NASA Astrophysics Data System (ADS)

Lin, Y. S.; Medlyn, B. E.; Duursma, R.; Prentice, I. C.; Wang, H.

2014-12-01

Stomatal conductance (gs) is a key land surface attribute as it links transpiration, the dominant component of global land evapotranspiration and a key element of the global water cycle, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of gs in predictions of global water and carbon cycles, a global scale database and an associated globally applicable model of gs that allow predictions of stomatal behaviour are lacking. We present a unique database of globally distributed gs obtained in the field for a wide range of plant functional types (PFTs) and biomes. We employed a model of optimal stomatal conductance to assess differences in stomatal behaviour, and estimated the model slope coefficient, g1, which is directly related to the marginal carbon cost of water, for each dataset. We found that g1 varies considerably among PFTs, with evergreen savanna trees having the largest g1 (least conservative water use), followed by C3 grasses and crops, angiosperm trees, gymnosperm trees, and C4 grasses. Amongst angiosperm trees, species with higher wood density had a higher marginal carbon cost of water, as predicted by the theory underpinning the optimal stomatal model. There was an interactive effect between temperature and moisture availability on g1: for wet environments, g1 was largest in high temperature environments, indicated by high mean annual temperature during the period when temperature above 0oC (Tm), but it did not vary with Tm across dry environments. We examine whether these differences in leaf-scale behaviour are reflected in ecosystem-scale differences in water-use efficiency. These findings provide a robust theoretical framework for understanding and predicting the behaviour of stomatal conductance across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of productivity and ecohydrological processes in a future changing climate.

Tree Density and Species Decline in the African Sahel Attributable to Climate

NASA Technical Reports Server (NTRS)

Gonzalez, Patrick; Tucker, Compton J.; Sy, H.

2012-01-01

Increased aridity and human population have reduced tree cover in parts of the African Sahel and degraded resources for local people. Yet, tree cover trends and the relative importance of climate and population remain unresolved. From field measurements, aerial photos, and Ikonos satellite images, we detected significant 1954-2002 tree density declines in the western Sahel of 18 +/- 14% (P = 0.014, n = 204) and 17 +/- 13% (P = 0.0009, n = 187). From field observations, we detected a significant 1960-2000 species richness decline of 21 +/- 11% (P = 0.0028, n = 14) across the Sahel and a southward shift of the Sahel, Sudan, and Guinea zones. Multivariate analyses of climate, soil, and population showed that temperature most significantly (P < 0.001) explained tree cover changes. Multivariate and bivariate tests and field observations indicated the dominance of temperature and precipitation, supporting attribution of tree cover changes to climate variability. Climate change forcing of Sahel climate variability, particularly the significant (P < 0.05) 1901-2002 temperature increases and precipitation decreases in the research areas, connects Sahel tree cover changes to global climate change. This suggests roles for global action and local adaptation to address ecological change in the Sahel.

Predicting Tree Mortality Die-off Events Associated with Hotter Drought and Assessing Their Global Consequences via Ecoclimate Teleconnections.

NASA Astrophysics Data System (ADS)

Breshears, D. D.; Allen, C. D.; McDowell, N. G.; Adams, H. D.; Barnes, M.; Barron-Gafford, G.; Bradford, J. B.; Cobb, N.; Field, J. P.; Froend, R.; Fontaine, J. B.; Garcia, E.; Hardy, G. E. S. J.; Huxman, T. E.; Kala, J.; Lague, M. M.; Martinez-Yrizar, A.; Matusick, G.; Minor, D. M.; Moore, D. J.; Ng, M.; Ruthrof, K. X.; Saleska, S. R.; Stark, S. C.; Swann, A. L. S.; Villegas, J. C.; Williams, A. P.; Zou, C.

2017-12-01

Evidence that tree mortality is increasingly likely occur in extensive die-off events across the terrestrial biosphere continues to mount. The consequences of such extensive mortality events are potentially profound, not only for the locations where die-off events occur, but also for other locations that could be impacted via ecoclimate teleconnections, whereby the land surface changes associated with die-off in one location could alter atmospheric circulation patterns and affect vegetation elsewhere. Here, we (1) recap the background of tree mortality as an emerging environmental issue, (2) highlight recent advances that could help us improve predictions of the vulnerability to tree mortality, including the underlying importance of hydraulic failure, the potential to develop climatic envelopes specific to tree mortality events, and consideration of the role of heat waves; and (3) initial bounding simulations that indicate the potential for tree die-off events in different locations to alter ecoclimate teleconnections. As we move toward globally coordinated carbon accounting and management, the high vulnerability to tree die-off events and the potential for such events to affect vegetation elsewhere will both need to be accounted for.

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

PubMed Central

Marcussen, Thomas; Heier, Lise; Brysting, Anne K.; Oxelman, Bengt; Jakobsen, Kjetill S.

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage—between 67% and 88%—of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. PMID:25281848

Airway reopening through catastrophic events in a hierarchical network

PubMed Central

Baudoin, Michael; Song, Yu; Manneville, Paul; Baroud, Charles N.

2013-01-01

When you reach with your straw for the final drops of a milkshake, the liquid forms a train of plugs that flow slowly initially because of the high viscosity. They then suddenly rupture and are replaced with a rapid airflow with the characteristic slurping sound. Trains of liquid plugs also are observed in complex geometries, such as porous media during petroleum extraction, in microfluidic two-phase flows, or in flows in the pulmonary airway tree under pathological conditions. The dynamics of rupture events in these geometries play the dominant role in the spatial distribution of the flow and in determining how much of the medium remains occluded. Here we show that the flow of a train of plugs in a straight channel is always unstable to breaking through a cascade of ruptures. Collective effects considerably modify the rupture dynamics of plug trains: Interactions among nearest neighbors take place through the wetting films and slow down the cascade, whereas global interactions, through the total resistance to flow of the train, accelerate the dynamics after each plug rupture. In a branching tree of microchannels, similar cascades occur along paths that connect the input to a particular output. This divides the initial tree into several independent subnetworks, which then evolve independently of one another. The spatiotemporal distribution of the cascades is random, owing to strong sensitivity to the plug divisions at the bifurcations. PMID:23277557

Long tree-ring chronologies provide evidence of recent tree growth decrease in a Central African tropical forest.

PubMed

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla-Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2.

Long Tree-Ring Chronologies Provide Evidence of Recent Tree Growth Decrease in a Central African Tropical Forest

PubMed Central

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla- Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2. PMID:25806946

Investigation of major international and Turkish companies via hierarchical methods and bootstrap approach

NASA Astrophysics Data System (ADS)

Kantar, E.; Deviren, B.; Keskin, M.

2011-11-01

We present a study, within the scope of econophysics, of the hierarchical structure of 98 among the largest international companies including 18 among the largest Turkish companies, namely Banks, Automobile, Software-hardware, Telecommunication Services, Energy and the Oil-Gas sectors, viewed as a network of interacting companies. We analyze the daily time series data of the Boerse-Frankfurt and Istanbul Stock Exchange. We examine the topological properties among the companies over the period 2006-2010 by using the concept of hierarchical structure methods (the minimal spanning tree (MST) and the hierarchical tree (HT)). The period is divided into three subperiods, namely 2006-2007, 2008 which was the year of global economic crisis, and 2009-2010, in order to test various time-windows and observe temporal evolution. We carry out bootstrap analyses to associate the value of statistical reliability to the links of the MSTs and HTs. We also use average linkage clustering analysis (ALCA) in order to better observe the cluster structure. From these studies, we find that the interactions among the Banks/Energy sectors and the other sectors were reduced after the global economic crisis; hence the effects of the Banks and Energy sectors on the correlations of all companies were decreased. Telecommunication Services were also greatly affected by the crisis. We also observed that the Automobile and Banks sectors, including Turkish companies as well as some companies from the USA, Japan and Germany were strongly correlated with each other in all periods.

Optimal tree-stem bucking of northeastern species of China

Treesearch

Jingxin Wang; Chris B. LeDoux; Joseph McNeel

2004-01-01

An application of optimal tree-stem bucking to the northeastern tree species of China is reported. The bucking procedures used in this region are summarized, which are the basic guidelines for the optimal bucking design. The directed graph approach was adopted to generate the bucking patterns by using the network analysis labeling algorithm. A computer-based bucking...

The k-d Tree: A Hierarchical Model for Human Cognition.

ERIC Educational Resources Information Center

Vandendorpe, Mary M.

This paper discusses a model of information storage and retrieval, the k-d tree (Bentley, 1975), a binary, hierarchical tree with multiple associate terms, which has been explored in computer research, and it is suggested that this model could be useful for describing human cognition. Included are two models of human long-term memory--networks and…

Rapid Calculation of Max-Min Fair Rates for Multi-Commodity Flows in Fat-Tree Networks

DOE PAGES

Mollah, Md Atiqul; Yuan, Xin; Pakin, Scott; ...

2017-08-29

Max-min fairness is often used in the performance modeling of interconnection networks. Existing methods to compute max-min fair rates for multi-commodity flows have high complexity and are computationally infeasible for large networks. In this paper, we show that by considering topological features, this problem can be solved efficiently for the fat-tree topology that is widely used in data centers and high performance compute clusters. Several efficient new algorithms are developed for this problem, including a parallel algorithm that can take advantage of multi-core and shared-memory architectures. Using these algorithms, we demonstrate that it is possible to find the max-min fairmore » rate allocation for multi-commodity flows in fat-tree networks that support tens of thousands of nodes. We evaluate the run-time performance of the proposed algorithms and show improvement in orders of magnitude over the previously best known method. Finally, we further demonstrate a new application of max-min fair rate allocation that is only computationally feasible using our new algorithms.« less

Rapid Calculation of Max-Min Fair Rates for Multi-Commodity Flows in Fat-Tree Networks

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

Mollah, Md Atiqul; Yuan, Xin; Pakin, Scott

Max-min fairness is often used in the performance modeling of interconnection networks. Existing methods to compute max-min fair rates for multi-commodity flows have high complexity and are computationally infeasible for large networks. In this paper, we show that by considering topological features, this problem can be solved efficiently for the fat-tree topology that is widely used in data centers and high performance compute clusters. Several efficient new algorithms are developed for this problem, including a parallel algorithm that can take advantage of multi-core and shared-memory architectures. Using these algorithms, we demonstrate that it is possible to find the max-min fairmore » rate allocation for multi-commodity flows in fat-tree networks that support tens of thousands of nodes. We evaluate the run-time performance of the proposed algorithms and show improvement in orders of magnitude over the previously best known method. Finally, we further demonstrate a new application of max-min fair rate allocation that is only computationally feasible using our new algorithms.« less

Global, long-term Earth Science Data Records of forest cover, change, and fragmentation from Landsat: the Global Forest Cover Change Project

NASA Astrophysics Data System (ADS)

Sexton, J.; Huang, C.; Channan, S.; Feng, M.; Song, X.; Kim, D.; Song, D.; Vermote, E.; Masek, J.; Townshend, J. R.

2013-12-01

Monitoring, analysis, and management of forests require measurements of forest cover that are both spatio-temporally consistent and resolved globally at sub-hectare resolution. The Global Forest Cover Change project, a cooperation between the University of Maryland Global Land Cover Facility and NASA Goddard Space Flight Center, is providing the first long-term, sub-hectare, globally consistent data records of forest cover, change, and fragmentation in circa-1975, -1990, -2000, and -2005 epochs. These data are derived from the Global Land Survey collection of Landsat images in the respective epochs, atmospherically corrected to surface reflectance in 1990, 2000, and 2005 using the Landsat Ecosystem Disturbance Adaptive Processing System (LEDAPS) implementation of the 6S radiative transfer algorithm, with ancillary information from MODIS Land products, ASTER Global Digital Elevation Model (GDEM), and climatological data layers. Forest cover and change were estimated by a novel continuous-field approach, which produced for the 2000 and 2005 epochs the world's first global, 30-m resolution database of tree cover. Surface reflectance estimates were validated against coincident MODIS measurements, the results of which have been corroborated by subsequent, independent validations against measurements from AERONET sites. Uncertainties in tree- and forest-cover values were estimated in each pixel as a compounding of within-sample uncertainty and accuracy relative to a sample of independent measurements from small-footprint lidar. Accuracy of forest cover and change estimates was further validated relative to expert-interpreted high-resolution imagery, from which unbiased estimates of forest cover and change have been produced at national and eco-regional scales. These first-of-kind Earth Science Data Records--surface reflectance in 1990, 2000, and 2005 and forest cover, change, and fragmentation in and between 1975, 1990, 2000, and 2005--are hosted at native, Landsat resolution for free public access at the Global Land Cover Facility website (www.landcover.org). Global mosaic of circa-2000, Landsat-based estimates of tree cover. Gaps due to clouds and/or snow in each scene were filled first with Landsat-based data from overlapping paths, and the remaining gaps were filled with data from the MODIS VCF Tree Cover layer in 2000.

Detecting trends in tree growth: not so simple.

PubMed

Bowman, David M J S; Brienen, Roel J W; Gloor, Emanuel; Phillips, Oliver L; Prior, Lynda D

2013-01-01

Tree biomass influences biogeochemical cycles, climate, and biodiversity across local to global scales. Understanding the environmental control of tree biomass demands consideration of the drivers of individual tree growth over their lifespan. This can be achieved by studies of tree growth in permanent sample plots (prospective studies) and tree ring analyses (retrospective studies). However, identification of growth trends and attribution of their drivers demands statistical control of the axiomatic co-variation of tree size and age, and avoiding sampling biases at the stand, forest, and regional scales. Tracking and predicting the effects of environmental change on tree biomass requires well-designed studies that address the issues that we have reviewed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Efficient Orchestration of Data Centers Via Comprehensive and Application Aware Trade Off Exploration

DTIC Science & Technology

2016-12-01

proposes to save power by concentrating traffic over a small subset of links. data center architecture [12], as depicted in Figure 1.1. The fat-tree... architecture is a physical network topology commonly used in data networks representing a hier- archical multi-rooted tree consisting of four levels...milliseconds) is an order of magnitude faster than the GASO variants (tens of seconds). 3.4.3 LAW for Architectures of Different Dimensions In this section

Authenticated IGMP for Controlling Access to Multicast Distribution Tree

NASA Astrophysics Data System (ADS)

Park, Chang-Seop; Kang, Hyun-Sun

A receiver access control scheme is proposed to protect the multicast distribution tree from DoS attack induced by unauthorized use of IGMP, by extending the security-related functionality of IGMP. Based on a specific network and business model adopted for commercial deployment of IP multicast applications, a key management scheme is also presented for bootstrapping the proposed access control as well as accounting and billing for CP (Content Provider), NSP (Network Service Provider), and group members.

Impacts of short-term heatwaves on sun-induced chlorophyll fluorescence(SiF) in temperate tree species

NASA Astrophysics Data System (ADS)

Wang, F.; Gu, L.; Guha, A.; Han, J.; Warren, J.

2017-12-01

The current projections for global climate change forecast an increase in the intensity and frequency of extreme climatic events, such as droughts and short-term heat waves. Understanding the effects of short-term heat wave on photosynthesis process is of critical importance to predict global impacts of extreme weather event on vegetation. The diurnal and seasonal characteristics of SIF emitted from natural vegetation, e.g., forest and crop, have been studied at the ecosystem-scale, regional-scale and global-scale. However, the detailed response of SIF from different plant species under extremely weather event, especially short-term heat wave, have not been reported. The purpose of this study was to study the response of solar-induced chlorophyll fluorescence, gas exchange and continuous fluorescence at leaf scale for different temperate tree species. The short-term heatwave experiment was conducted using plant growth chamber (CMP6050, Conviron Inc., Canada). We developed an advanced spectral fitting method to obtain the plant SIF in the plant growth chamber. We compared SIF variation among different wavelength and chlorophyll difference among four temperate tree species. The diurnal variation of SIF signals at leaf-scales for temperate tree species are different under heat stress. The SIF response at leaf-scales and their difference for four temperate tree species are different during a cycle of short-term heatwave stress. We infer that SIF be used as a measure of heat tolerance for temperate tree species.

Trait Acclimation Mitigates Mortality Risks of Tropical Canopy Trees under Global Warming

PubMed Central

Sterck, Frank; Anten, Niels P. R.; Schieving, Feike; Zuidema, Pieter A.

2016-01-01

There is a heated debate about the effect of global change on tropical forests. Many scientists predict large-scale tree mortality while others point to mitigating roles of CO2 fertilization and – the notoriously unknown – physiological trait acclimation of trees. In this opinion article we provided a first quantification of the potential of trait acclimation to mitigate the negative effects of warming on tropical canopy tree growth and survival. We applied a physiological tree growth model that incorporates trait acclimation through an optimization approach. Our model estimated the maximum effect of acclimation when trees optimize traits that are strongly plastic on a week to annual time scale (leaf photosynthetic capacity, total leaf area, stem sapwood area) to maximize carbon gain. We simulated tree carbon gain for temperatures (25–35°C) and ambient CO2 concentrations (390–800 ppm) predicted for the 21st century. Full trait acclimation increased simulated carbon gain by up to 10–20% and the maximum tolerated temperature by up to 2°C, thus reducing risks of tree death under predicted warming. Functional trait acclimation may thus increase the resilience of tropical trees to warming, but cannot prevent tree death during extremely hot and dry years at current CO2 levels. We call for incorporating trait acclimation in field and experimental studies of plant functional traits, and in models that predict responses of tropical forests to climate change. PMID:27242814

Network structure impacts global commodity trade growth and resilience.

PubMed

Kharrazi, Ali; Rovenskaya, Elena; Fath, Brian D

2017-01-01

Global commodity trade networks are critical to our collective sustainable development. Their increasing interconnectedness pose two practical questions: (i) Do the current network configurations support their further growth? (ii) How resilient are these networks to economic shocks? We analyze the data of global commodity trade flows from 1996 to 2012 to evaluate the relationship between structural properties of the global commodity trade networks and (a) their dynamic growth, as well as (b) the resilience of their growth with respect to the 2009 global economic shock. Specifically, we explore the role of network efficiency and redundancy using the information theory-based network flow analysis. We find that, while network efficiency is positively correlated with growth, highly efficient systems appear to be less resilient, losing more and gaining less growth following an economic shock. While all examined networks are rather redundant, we find that network redundancy does not hinder their growth. Moreover, systems exhibiting higher levels of redundancy lose less and gain more growth following an economic shock. We suggest that a strategy to support making global trade networks more efficient via, e.g., preferential trade agreements and higher specialization, can promote their further growth; while a strategy to increase the global trade networks' redundancy via e.g., more abundant free-trade agreements, can improve their resilience to global economic shocks.

Region effects influence local tree species diversity.

PubMed

Ricklefs, Robert E; He, Fangliang

2016-01-19

Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species.

Emerging Chagas disease: trophic network and cycle of transmission of Trypanosoma cruzi from palm trees in the Amazon.

PubMed Central

Teixeira, A. R.; Monteiro, P. S.; Rebelo, J. M.; Argañaraz, E. R.; Vieira, D.; Lauria-Pires, L.; Nascimento, R.; Vexenat, C. A.; Silva, A. R.; Ault, S. K.; Costa, J. M.

2001-01-01

A trophic network involving molds, invertebrates, and vertebrates, ancestrally adapted to the palm tree (Attalaea phalerata) microhabitat, maintains enzootic Trypanosoma cruzi infections in the Amazonian county Paço do Lumiar, state of Maranhão, Brazil. We assessed seropositivity for T. cruzi infections in the human population of the county, searched in palm trees for the triatomines that harbor these infections, and gathered demographic, environmental, and socioeconomic data. Rhodnius pictipes and R. neglectus in palm-tree frond clefts or in houses were infected with T. cruzi (57% and 41%, respectively). Human blood was found in 6.8% of R. pictipes in houses, and 9 of 10 wild Didelphis marsupialis had virulent T. cruzi infections. Increasing human population density, rain forest deforestation, and human predation of local fauna are risk factors for human T. cruzi infections. PMID:11266300

A decomposition theory for phylogenetic networks and incompatible characters.

PubMed

Gusfield, Dan; Bansal, Vikas; Bafna, Vineet; Song, Yun S

2007-12-01

Phylogenetic networks are models of evolution that go beyond trees, incorporating non-tree-like biological events such as recombination (or more generally reticulation), which occur either in a single species (meiotic recombination) or between species (reticulation due to lateral gene transfer and hybrid speciation). The central algorithmic problems are to reconstruct a plausible history of mutations and non-tree-like events, or to determine the minimum number of such events needed to derive a given set of binary sequences, allowing one mutation per site. Meiotic recombination, reticulation and recurrent mutation can cause conflict or incompatibility between pairs of sites (or characters) of the input. Previously, we used "conflict graphs" and "incompatibility graphs" to compute lower bounds on the minimum number of recombination nodes needed, and to efficiently solve constrained cases of the minimization problem. Those results exposed the structural and algorithmic importance of the non-trivial connected components of those two graphs. In this paper, we more fully develop the structural importance of non-trivial connected components of the incompatibility and conflict graphs, proving a general decomposition theorem (Gusfield and Bansal, 2005) for phylogenetic networks. The decomposition theorem depends only on the incompatibilities in the input sequences, and hence applies to many types of phylogenetic networks, and to any biological phenomena that causes pairwise incompatibilities. More generally, the proof of the decomposition theorem exposes a maximal embedded tree structure that exists in the network when the sequences cannot be derived on a perfect phylogenetic tree. This extends the theory of perfect phylogeny in a natural and important way. The proof is constructive and leads to a polynomial-time algorithm to find the unique underlying maximal tree structure. We next examine and fully solve the major open question from Gusfield and Bansal (2005): Is it true that for every input there must be a fully decomposed phylogenetic network that minimizes the number of recombination nodes used, over all phylogenetic networks for the input. We previously conjectured that the answer is yes. In this paper, we show that the answer in is no, both for the case that only single-crossover recombination is allowed, and also for the case that unbounded multiple-crossover recombination is allowed. The latter case also resolves a conjecture recently stated in (Huson and Klopper, 2007) in the context of reticulation networks. Although the conjecture from Gusfield and Bansal (2005) is disproved in general, we show that the answer to the conjecture is yes in several natural special cases, and establish necessary combinatorial structure that counterexamples to the conjecture must possess. We also show that counterexamples to the conjecture are rare (for the case of single-crossover recombination) in simulated data.

An information-based network approach for protein classification

PubMed Central

Wan, Xiaogeng; Zhao, Xin; Yau, Stephen S. T.

2017-01-01

Protein classification is one of the critical problems in bioinformatics. Early studies used geometric distances and polygenetic-tree to classify proteins. These methods use binary trees to present protein classification. In this paper, we propose a new protein classification method, whereby theories of information and networks are used to classify the multivariate relationships of proteins. In this study, protein universe is modeled as an undirected network, where proteins are classified according to their connections. Our method is unsupervised, multivariate, and alignment-free. It can be applied to the classification of both protein sequences and structures. Nine examples are used to demonstrate the efficiency of our new method. PMID:28350835

Logistic growth for the Nuzi cuneiform tablets: Analyzing family networks in ancient Mesopotamia

NASA Astrophysics Data System (ADS)

Ueda, Sumie; Makino, Kumi; Itoh, Yoshiaki; Tsuchiya, Takashi

2015-03-01

We reconstruct the published year of each cuneiform tablet of the Nuzi society in ancient Mesopotamia. The tablets are on land transaction, marriage, loan, slavery contracts, etc. The number of tablets seems to increase by logistic growth. It may show the dynamics of concentration of lands or other properties into few powerful families in a period of about sixty years and most of them are in about thirty years. We reconstruct family trees and social networks of Nuzi and estimate the published years of cuneiform tablets consistently with the trees and networks, formulating least squares problems with linear inequality constraints.

Neural-tree call admission controller for ATM networks

NASA Astrophysics Data System (ADS)

Rughooputh, Harry C. S.

1999-03-01

Asynchronous Transfer Mode (ATM) has been recommended by ITU-T as the transport method for broadband integrated services digital networks. In high-speed ATM networks different types of multimedia traffic streams with widely varying traffic characteristics and Quality of Service (QoS) are asynchronously multiplexed on transmission links and switched without window flow control as found in X.25. In such an environment, a traffic control scheme is required to manage the required QoS of each class individually. To meet the QoS requirements, Bandwidth Allocation and Call Admission Control (CAC) in ATM networks must be able to adapt gracefully to the dynamic behavior of traffic and the time-varying nature of the network condition. In this paper, a Neural Network approach for CAC is proposed. The call admission problem is addressed by designing controllers based on Neural Tree Networks. Simulations reveal that the proposed scheme is not only simple but it also offers faster response than conventional neural/neuro-fuzzy controllers.

Classifying dysmorphic syndromes by using artificial neural network based hierarchical decision tree.

PubMed

Özdemir, Merve Erkınay; Telatar, Ziya; Eroğul, Osman; Tunca, Yusuf

2018-05-01

Dysmorphic syndromes have different facial malformations. These malformations are significant to an early diagnosis of dysmorphic syndromes and contain distinctive information for face recognition. In this study we define the certain features of each syndrome by considering facial malformations and classify Fragile X, Hurler, Prader Willi, Down, Wolf Hirschhorn syndromes and healthy groups automatically. The reference points are marked on the face images and ratios between the points' distances are taken into consideration as features. We suggest a neural network based hierarchical decision tree structure in order to classify the syndrome types. We also implement k-nearest neighbor (k-NN) and artificial neural network (ANN) classifiers to compare classification accuracy with our hierarchical decision tree. The classification accuracy is 50, 73 and 86.7% with k-NN, ANN and hierarchical decision tree methods, respectively. Then, the same images are shown to a clinical expert who achieve a recognition rate of 46.7%. We develop an efficient system to recognize different syndrome types automatically in a simple, non-invasive imaging data, which is independent from the patient's age, sex and race at high accuracy. The promising results indicate that our method can be used for pre-diagnosis of the dysmorphic syndromes by clinical experts.

A combined NLP-differential evolution algorithm approach for the optimization of looped water distribution systems

NASA Astrophysics Data System (ADS)

Zheng, Feifei; Simpson, Angus R.; Zecchin, Aaron C.

2011-08-01

This paper proposes a novel optimization approach for the least cost design of looped water distribution systems (WDSs). Three distinct steps are involved in the proposed optimization approach. In the first step, the shortest-distance tree within the looped network is identified using the Dijkstra graph theory algorithm, for which an extension is proposed to find the shortest-distance tree for multisource WDSs. In the second step, a nonlinear programming (NLP) solver is employed to optimize the pipe diameters for the shortest-distance tree (chords of the shortest-distance tree are allocated the minimum allowable pipe sizes). Finally, in the third step, the original looped water network is optimized using a differential evolution (DE) algorithm seeded with diameters in the proximity of the continuous pipe sizes obtained in step two. As such, the proposed optimization approach combines the traditional deterministic optimization technique of NLP with the emerging evolutionary algorithm DE via the proposed network decomposition. The proposed methodology has been tested on four looped WDSs with the number of decision variables ranging from 21 to 454. Results obtained show the proposed approach is able to find optimal solutions with significantly less computational effort than other optimization techniques.

Hide and go seek with temperature signals of Northeastern US Tree Species

NASA Astrophysics Data System (ADS)

Alexander, M. R.; Pederson, N.; Bishop, D. A.; Pearl, J. K.; Anchukaitis, K. J.

2017-12-01

Improving reconstructions of past climate is vital in providing long-term context for regional climate change. There have been only two published reconstructions of past temperatures in the northeastern U.S. (NEUS) since the 1980s, one based on Picea rubens, and one out in 2017 based upon Chamaecyparis thyoides (Atlantic white cedar; AWC). Because increased species diversity generally improves dendrohydroclimatic reconstructions and both Picea rubens and AWC have limitations as paleoproxies due to land-use and air pollution, we conducted a series of tests to ask, "Does species diversity improve reconstructions of temperature history in the northeastern United States?" The first two tests were performed on AWC and then a network of AWC and Picea rubens. Subsequent tests added groups of species or genera from a network of 230 tree-ring chronologies beginning with those having the strongest relation between warming temperatures and increased growth. PC1 of the AWC test represented 40% of the variance and showed a significant positive relation with winter temperature (r = 0.38). As additional species were included, the "winter temperature PC" accounted for less of the overall variance, ranging from 26% of the variance in test 2 to 5% by test 5. AWC is swamped by the hydroclimatic signal that dominates our network. Populations of species such as Fagus grandifolia, Fraxinus nigra, Juniperus virginiana, Liriodendron tulipifera, Pinus rigida, and Pinus strobus from our network loaded strongest with AWC on the winter temperature PC. Including multiple species accounted for almost 20% more variance in the winter temperature record than AWC alone. Although drought is a dominating influence of tree growth in this region, our results suggest that winter temperatures are recorded within NEUS tree rings. Increasing the species diversity of tree proxies has the potential for improving reconstruction of paleotemperatures in regions lacking latitudinal or altitudinal tree lines, such as those found in the NEUS.

Banking on the future: progress, challenges and opportunities for the genetic conservation of forest trees

Treesearch

Kevin M. Potter; Robert M. Jetton; Andrew Bower; Douglass F. Jacobs; Gary Man; Valerie D. Hipkins; Murphy Westwood

2017-01-01

Genetic diversity provides the essential basis for the adaptation and resilience of tree species to environmental stress and change. The genetic conservation of tree species is an urgent global necessity as forest conversion and fragmentation continue apace, damaging insects and pathogens are transported between continents, and climate change alters local habitat...

Potential redistribution of tree species habitat under five climate change scenarios in the eastern US

Treesearch

Louis R. Iverson; Anantha M. Prasad; Anantha M. Prasad

2002-01-01

Global climate change could have profound effects on the Earth's biota, including large redistributions of tree species and forest types. We used DISTRIB, a deterministic regression tree analysis model, to examine environmental drivers related to current forest-species distributions and then model potential suitable habitat under five climate change scenarios...

Hydraulic redistribution of water from Pinus ponderosa trees to seedlings: evidence for an ectomycorrhizal pathway.

Treesearch

Jeffrey M. Warren; J. Renee Brooks; Frederick C. Meinzer; Joyce L. Eberhart

2008-01-01

Although there is strong evidence for hydraulic redistribution (HR) of soil water by trees, it is not known if common myconhizal networks (CMN) can facilitate HR from mature trees to seedlings under field conditions. Ponderosa pine (Pinus ponderosa) seedlings were planted into root-excluding 61-micron mesh barrier chambers buried in an old-growth...

Evidential Networks for Fault Tree Analysis with Imprecise Knowledge

NASA Astrophysics Data System (ADS)

Yang, Jianping; Huang, Hong-Zhong; Liu, Yu; Li, Yan-Feng

2012-06-01

Fault tree analysis (FTA), as one of the powerful tools in reliability engineering, has been widely used to enhance system quality attributes. In most fault tree analyses, precise values are adopted to represent the probabilities of occurrence of those events. Due to the lack of sufficient data or imprecision of existing data at the early stage of product design, it is often difficult to accurately estimate the failure rates of individual events or the probabilities of occurrence of the events. Therefore, such imprecision and uncertainty need to be taken into account in reliability analysis. In this paper, the evidential networks (EN) are employed to quantify and propagate the aforementioned uncertainty and imprecision in fault tree analysis. The detailed conversion processes of some logic gates to EN are described in fault tree (FT). The figures of the logic gates and the converted equivalent EN, together with the associated truth tables and the conditional belief mass tables, are also presented in this work. The new epistemic importance is proposed to describe the effect of ignorance degree of event. The fault tree of an aircraft engine damaged by oil filter plugs is presented to demonstrate the proposed method.

Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.

PubMed

Baraff, Aaron J; McCormick, Tyler H; Raftery, Adrian E

2016-12-20

Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

PubMed

Beauregard-Racine, Julie; Bicep, Cédric; Schliep, Klaus; Lopez, Philippe; Lapointe, François-Joseph; Bapteste, Eric

2011-07-20

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches. We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.

Access to mycorrhizal networks and roots of trees: importance for seedling survival and resource transfer.

PubMed

Teste, François P; Simard, Suzanne W; Durall, Daniel M; Guy, Robert D; Jones, Melanie D; Schoonmaker, Amanda L

2009-10-01

Mycorrhizal networks (MNs) are fungal hyphae that connect roots of at least two plants. It has been suggested that these networks are ecologically relevant because they may facilitate interplant resource transfer and improve regeneration dynamics. This study investigated the effects of MNs on seedling survival, growth and physiological responses, interplant resource (carbon and nitrogen) transfer, and ectomycorrhizal (EM) fungal colonization of seedlings by trees in dry interior Douglas-fir (Pseudotsuga menziesii var. glauca) forests. On a large, recently harvested site that retained some older trees, we established 160 isolated plots containing pairs of older Douglas-fir "donor" trees and either manually sown seed or planted Douglas-fir "receiver" seedlings. Seed- and greenhouse-grown seedlings were sown and planted into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, 250-microm pores, or without mesh). Older trees were pulse labeled with carbon (13CO2) and nitrogen (15NH4(15)NO3) to quantify resource transfer. After two years, seedlings grown from seed in the field had the greatest survival and received the greatest amounts of transferred carbon (0.0063% of donor photo-assimilates) and nitrogen (0.0018%) where they were grown without mesh; however, planted seedlings were not affected by access to tree roots and hyphae. Size of "donor" trees was inversely related to the amount of carbon transferred to seedlings. The potential for MNs to form was high (based on high similarity of EM communities between hosts), and MN-mediated colonization appeared only to be important for seedlings grown from seed in the field. These results demonstrate that MNs and mycorrhizal roots of trees may be ecologically important for natural regeneration in dry forests, but it is still uncertain whether resource transfer is an important mechanism underlying seedling establishment.

A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks

PubMed Central

Park, HoSung; Kim, Beom-Su; Kim, Kyong Hoon; Shah, Babar; Kim, Ki-Il

2017-01-01

Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new (m, k)-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the (m, k)-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured (m, k)-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption. PMID:29120404

Advancing biodiversity-ecosystem functioning science using high-density tree-based experiments over functional diversity gradients.

PubMed

Tobner, Cornelia M; Paquette, Alain; Reich, Peter B; Gravel, Dominique; Messier, Christian

2014-03-01

Increasing concern about loss of biodiversity and its effects on ecosystem functioning has triggered a series of manipulative experiments worldwide, which have demonstrated a general trend for ecosystem functioning to increase with diversity. General mechanisms proposed to explain diversity effects include complementary resource use and invoke a key role for species' functional traits. The actual mechanisms by which complementary resource use occurs remain, however, poorly understood, as well as whether they apply to tree-dominated ecosystems. Here we present an experimental approach offering multiple innovative aspects to the field of biodiversity-ecosystem functioning (BEF) research. The International Diversity Experiment Network with Trees (IDENT) allows research to be conducted at several hierarchical levels within individuals, neighborhoods, and communities. The network investigates questions related to intraspecific trait variation, complementarity, and environmental stress. The goal of IDENT is to identify some of the mechanisms through which individuals and species interact to promote coexistence and the complementary use of resources. IDENT includes several implemented and planned sites in North America and Europe, and uses a replicated design of high-density tree plots of fixed species-richness levels varying in functional diversity (FD). The design reduces the space and time needed for trees to interact allowing a thorough set of mixtures varying over different diversity gradients (specific, functional, phylogenetic) and environmental conditions (e.g., water stress) to be tested in the field. The intention of this paper is to share the experience in designing FD-focused BEF experiments with trees, to favor collaborations and expand the network to different conditions.

Time and Energy Efficient Relay Transmission for Multi-Hop Wireless Sensor Networks.

PubMed

Kim, Jin-Woo; Barrado, José Ramón Ramos; Jeon, Dong-Keun

2016-06-27

The IEEE 802.15.4 standard is widely recognized as one of the most successful enabling technologies for short range low rate wireless communications and it is used in IoT applications. It covers all the details related to the MAC and PHY layers of the IoT protocol stack. Due to the nature of IoT, the wireless sensor networks are autonomously self-organized networks without infrastructure support. One of the issues in IoT is the network scalability. To address this issue, it is necessary to support the multi-hop topology. The IEEE 802.15.4 network can support a star, peer-to-peer, or cluster-tree topology. One of the IEEE 802.15.4 topologies suited for the high predictability of performance guarantees and energy efficient behavior is a cluster-tree topology where sensor nodes can switch off their transceivers and go into a sleep state to save energy. However, the IEEE 802.15.4 cluster-tree topology may not be able to provide sufficient bandwidth for the increased traffic load and the additional information may not be delivered successfully. The common drawback of the existing approaches is that they do not address the poor bandwidth utilization problem in IEEE 802.15.4 cluster-tree networks, so it is difficult to increase the network performance. Therefore, to solve this problem in this paper we study a relay transmission protocol based on the standard protocol in the IEEE 802.15.4 MAC. In the proposed scheme, the coordinators can relay data frames to their parent devices or their children devices without contention and can provide bandwidth for the increased traffic load or the number of devices. We also evaluate the performance of the proposed scheme through simulation. The simulation results demonstrate that the proposed scheme can improve the reliability, the end-to-end delay, and the energy consumption.

Time and Energy Efficient Relay Transmission for Multi-Hop Wireless Sensor Networks

PubMed Central

Kim, Jin-Woo; Barrado, José Ramón Ramos; Jeon, Dong-Keun

2016-01-01

The IEEE 802.15.4 standard is widely recognized as one of the most successful enabling technologies for short range low rate wireless communications and it is used in IoT applications. It covers all the details related to the MAC and PHY layers of the IoT protocol stack. Due to the nature of IoT, the wireless sensor networks are autonomously self-organized networks without infrastructure support. One of the issues in IoT is the network scalability. To address this issue, it is necessary to support the multi-hop topology. The IEEE 802.15.4 network can support a star, peer-to-peer, or cluster-tree topology. One of the IEEE 802.15.4 topologies suited for the high predictability of performance guarantees and energy efficient behavior is a cluster-tree topology where sensor nodes can switch off their transceivers and go into a sleep state to save energy. However, the IEEE 802.15.4 cluster-tree topology may not be able to provide sufficient bandwidth for the increased traffic load and the additional information may not be delivered successfully. The common drawback of the existing approaches is that they do not address the poor bandwidth utilization problem in IEEE 802.15.4 cluster-tree networks, so it is difficult to increase the network performance. Therefore, to solve this problem in this paper we study a relay transmission protocol based on the standard protocol in the IEEE 802.15.4 MAC. In the proposed scheme, the coordinators can relay data frames to their parent devices or their children devices without contention and can provide bandwidth for the increased traffic load or the number of devices. We also evaluate the performance of the proposed scheme through simulation. The simulation results demonstrate that the proposed scheme can improve the reliability, the end-to-end delay, and the energy consumption. PMID:27355952

Transport through a network of capillaries from ultrametric diffusion equation with quadratic nonlinearity

NASA Astrophysics Data System (ADS)

Oleschko, K.; Khrennikov, A.

2017-10-01

This paper is about a novel mathematical framework to model transport (of, e.g., fluid or gas) through networks of capillaries. This framework takes into account the tree structure of the networks of capillaries. (Roughly speaking, we use the tree-like system of coordinates.) As is well known, tree-geometry can be topologically described as the geometry of an ultrametric space, i.e., a metric space in which the metric satisfies the strong triangle inequality: in each triangle, the third side is less than or equal to the maximum of two other sides. Thus transport (e.g., of oil or emulsion of oil and water in porous media, or blood and air in biological organisms) through networks of capillaries can be mathematically modelled as ultrametric diffusion. Such modelling was performed in a series of recently published papers of the authors. However, the process of transport through capillaries can be only approximately described by the linear diffusion, because the concentration of, e.g., oil droplets, in a capillary can essentially modify the dynamics. Therefore nonlinear dynamical equations provide a more adequate model of transport in a network of capillaries. We consider a nonlinear ultrametric diffusion equation with quadratic nonlinearity - to model transport in such a network. Here, as in the linear case, we apply the theory of ultrametric wavelets. The paper also contains a simple introduction to theory of ultrametric spaces and analysis on them.

Network structure impacts global commodity trade growth and resilience

PubMed Central

Rovenskaya, Elena; Fath, Brian D.

2017-01-01

Global commodity trade networks are critical to our collective sustainable development. Their increasing interconnectedness pose two practical questions: (i) Do the current network configurations support their further growth? (ii) How resilient are these networks to economic shocks? We analyze the data of global commodity trade flows from 1996 to 2012 to evaluate the relationship between structural properties of the global commodity trade networks and (a) their dynamic growth, as well as (b) the resilience of their growth with respect to the 2009 global economic shock. Specifically, we explore the role of network efficiency and redundancy using the information theory-based network flow analysis. We find that, while network efficiency is positively correlated with growth, highly efficient systems appear to be less resilient, losing more and gaining less growth following an economic shock. While all examined networks are rather redundant, we find that network redundancy does not hinder their growth. Moreover, systems exhibiting higher levels of redundancy lose less and gain more growth following an economic shock. We suggest that a strategy to support making global trade networks more efficient via, e.g., preferential trade agreements and higher specialization, can promote their further growth; while a strategy to increase the global trade networks’ redundancy via e.g., more abundant free-trade agreements, can improve their resilience to global economic shocks. PMID:28207790

Drought-associated tree mortality: Global patterns and insights from tree-ring studies in the southwestern U.S.A

NASA Astrophysics Data System (ADS)

Macalady, Alison Kelly

Forests play an important role in the earth system, regulating climate, maintaining biodiversity, and provisioning human communities with water, food and fuel. Interactions between climate and forest dynamics are not well constrained, and high uncertainty characterizes projections of global warming impacts on forests and associated ecosystem services. Recently observed tree mortality and forest die-off forewarn an acceleration of forest change with rising temperature and increased drought. However, the processes leading to tree death during drought are poorly understood, limiting our ability to anticipate future forest dynamics. The objective of this dissertation was to improve understanding of drought-associated tree mortality through literature synthesis and tree-ring studies on trees that survived and died during droughts in the southwestern USA. Specifically, this dissertation 1) documented global tree mortality patterns and identified emerging trends and research gaps; 2) quantified relationships between growth, climate, competition and mortality of pinon pine during droughts in New Mexico; 3) investigated tree defense anatomy as a potentially key element in pinon avoidance of death; and, 4) characterized the climate sensitivity of pinon resin ducts in order to gain insight into potential trends in tree defenses with climate variability and change. There has been an increase in studies reporting tree mortality linked to drought, heat, and the associated activity of insects and pathogens. Cases span the forested continents and occurred in water, light and temperature-limited forests. We hypothesized that increased tree mortality may be an emerging global phenomenon related to rising temperatures and drought (Appendix A). Recent radial growth was 53% higher on average in pinon that survived versus died during two episodes of drought-associated mortality, and statistical models of mortality risk based on average growth, growth variability, and abrupt growth changes correctly classified the status of ˜70% of trees. Climate responses and competitive interactions partly explained growth differences between dying and surviving trees, with muted response to wet/cool conditions and enhanced sensitivity to competition from congeners linked to growth patterns associated with death. Discrimination and validation of models of mortality risk varied widely across sites and drought events, indicating shifting growth-mortality relationships and differences in mortality processes across space and time (Appendix B). Pre-formed defense anatomy is strongly associated with pinon survivorship over a range of sites and stand conditions. Models of mortality risk that account for both growth and resin duct attributes had ≈10 19 more support than models that contained only growth. The greatest improvement in classification was among trees from the 2000s drought, suggesting an enhanced role for tree defense allocation and/or bark beetle activity during recent warm versus historic cool drought. Accounting for defense characteristics and growth-defense allocation is likely to be important for improving representation of drought-associated mortality (Appendix C). Pinon resin duct chronologies contain climate responses that are coherent and distinct from those of radial growth. Growth responds positively and strongly to previous fall and current winter precipitation, and negatively to late spring and early summer temperature. A relatively equal positive resin duct response to winter precipitation and positive response to mid-to-late summer drought suggests that changes in climate will affect tree defense anatomy in complex ways, with the outcome determined by seasonal changes in precipitation and temperature (Appendix D).

Tree Resin Composition, Collection Behavior and Selective Filters Shape Chemical Profiles of Tropical Bees (Apidae: Meliponini)

PubMed Central

Leonhardt, Sara D.; Schmitt, Thomas; Blüthgen, Nico

2011-01-01

The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental source for terpenes that serve as appeasement allomones and protection against predators when accumulated on the bees' body surfaces. To unravel the origin of the bees' complex chemical profiles, we investigated resin collection and the processing of resin-derived terpenes. We therefore analyzed chemical networks of tree resins, foraging networks of resin collecting bees, and their acquired chemical networks. We revealed that 113 terpenes in nests of six bee species and 83 on their body surfaces comprised a subset of the 1,117 compounds found in resins from seven tree species. Sesquiterpenes were the most variable class of terpenes. Albeit widely present in tree resins, they were only found on the body surface of some species, but entirely lacking in others. Moreover, whereas the nest profile of Tetragonula melanocephala contained sesquiterpenes, its surface profile did not. Stingless bees showed a generalized collecting behavior among resin sources, and only a hitherto undescribed species-specific “filtering” of resin-derived terpenes can explain the variation in chemical profiles of nests and body surfaces from different species. The tight relationship between bees and tree resins of a large variety of species elucidates why the bees' surfaces contain a much higher chemodiversity than other hymenopterans. PMID:21858119

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change.

PubMed

Schueler, Silvio; Falk, Wolfgang; Koskela, Jarkko; Lefèvre, François; Bozzano, Michele; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C

2014-05-01

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33-65 % of conservation units, mostly located in southern Europe, will be at the limit or outside the species' current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%. The highest average decrease in favourabilities throughout the network can be expected for coniferous trees although they are mainly occurring within units in mountainous landscapes for which we estimated lower velocities of change. Generally, the species-specific estimates of favourabilities showed only low correlations to the velocity of climate change in individual units, indicating that both vulnerability measures should be considered for climate risk analysis. The variation in favourabilities among target species within the same conservation units is expected to increase with climate change and will likely require a prioritization among co-occurring species. The present results suggest that there is a strong need to intensify monitoring efforts and to develop additional conservation measures for populations in the most vulnerable units. Also, our results call for continued transnational actions for genetic conservation of European forest trees, including the establishment of dynamic conservation populations outside the current species distribution ranges within European assisted migration schemes. © 2013 John Wiley & Sons Ltd.

Burned and buried by the Siberian traps: tree trunks in volcaniclastics and lavas

NASA Astrophysics Data System (ADS)

Polozov, Alexander G.; Planke, Sverre; Svensen, Henrik H.; Jerram, Dougal A.; Looy, Cindy

2017-04-01

Major Phanerozoic mass extinctions could be explained by intense volcanic activity related to the formation of Large Igneous Provinces (LIPs). The Siberian Traps LIP possibly caused the most severe mass extinction on the Earth, the end-Permian extinction. This event is documented by global data showing the extinction of floral and faunal species and by stable isotope excursions. Information about the direct impact of the Siberian Traps on the local flora and fauna is scarce. By our knowledge, no detailed description has been done on the faith of trees in Siberia. However, the story of Late Permian giant trees like Cordaites and wood ferns, could shed light on the impact of the onset of the LIP magmatism and the related mass extinction. For the first time we describe that Late Permian tree trunks were buried in volcaniclastic deposits and at the footwall contact of the oldest lava flows of the Siberian Traps, and despite that this phenomenon is known by local geologists it is not well described in the literature. Tree trunks in volcaniclastic deposits were compressed during consolidation of the volcaniclastic material originated from pyroclastic density currents from nearby volcanic centers. Tree petrification is presented by quartz with minor sulphides, zeolite, calcite and sulphates. Tree trunks at the footwall contact of the lava flows have a better preserved year rings structure and late permineralization presented by calcite with minor quartz and sulphides. Our results demonstrate that intensive magmatic activity related with LIP formation affects land vegetation at various grades. Lavas have had a local violent impact, but burned and buried tree trunks have a better preserved structure reflecting single dominated permineralization processes than the tree trunks buried by pyroclastics that have covered extensive areas and followed by trees compression and later multistage permineralization. In a global context, such type of volcanic activity has a variable influence on vegetation realms. Lava flows have had a harsh impact on land flora locally, but in some cases was favorable for preservation of tree remnants. Volcaniclastic deposits covered a wide area, but tree trunks were deformed due to compaction of the pyroclastic rocks. Late water circulation is reflected in multistage permineralization phenomena. Further ash expansion and settling could have a global impact and accelerate the mass extinction.

Zigbee networking technology and its application in Lamost optical fiber positioning and control system

NASA Astrophysics Data System (ADS)

Jin, Yi; Zhai, Chao; Gu, Yonggang; Zhou, Zengxiang; Gai, Xiaofeng

2010-07-01

4,000 fiber positioning units need to be positioned precisely in LAMOST(Large Sky Area Multi-object Optical Spectroscopic Telescope) optical fiber positioning & control system, and every fiber positioning unit needs two stepper motors for its driven, so 8,000 stepper motors need to be controlled in the entire system. Wireless communication mode is adopted to save the installing space on the back of the focal panel, and can save more than 95% external wires compared to the traditional cable control mode. This paper studies how to use the ZigBee technology to group these 8000 nodes, explores the pros and cons of star network and tree network in order to search the stars quickly and efficiently. ZigBee technology is a short distance, low-complexity, low power, low data rate, low-cost two-way wireless communication technology based on the IEEE 802.15.4 protocol. It based on standard Open Systems Interconnection (OSI): The 802.15.4 standard specifies the lower protocol layers-the physical layer (PHY), and the media access control (MAC). ZigBee Alliance defined on this basis, the rest layers such as the network layer and application layer, and is responsible for high-level applications, testing and marketing. The network layer used here, based on ad hoc network protocols, includes the following functions: construction and maintenance of the topological structure, nomenclature and associated businesses which involves addressing, routing and security and a self-organizing-self-maintenance functions which will minimize consumer spending and maintenance costs. In this paper, freescale's 802.15.4 protocol was used to configure the network layer. A star network and a tree network topology is realized, which can build network, maintenance network and create a routing function automatically. A concise tree network address allocate algorithm is present to assign the network ID automatically.

Collective network for computer structures

DOEpatents

Blumrich, Matthias A; Coteus, Paul W; Chen, Dong; Gara, Alan; Giampapa, Mark E; Heidelberger, Philip; Hoenicke, Dirk; Takken, Todd E; Steinmacher-Burow, Burkhard D; Vranas, Pavlos M

2014-01-07

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to the needs of a processing algorithm.

Collective network for computer structures

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Coteus, Paul W [Yorktown Heights, NY; Chen, Dong [Croton On Hudson, NY; Gara, Alan [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Takken, Todd E [Brewster, NY; Steinmacher-Burow, Burkhard D [Wernau, DE; Vranas, Pavlos M [Bedford Hills, NY

2011-08-16

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices ate included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network and class structures. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to needs of a processing algorithm.

Research in Presistent Simulation: Development of the Persistent ModSim Object-Oriented Programming Language

DTIC Science & Technology

1993-07-01

version tree is formed that permits users to go back to any previous version. There are methods for traversing the version tree of a particular...workspace. Workspace objects are linked (or nested) hierarchically into a workspace tree . Applications can set the access privileges to parts of this...workspace tree to control access (and hence change). There must be a default global workspace. Workspace objects are then allocated within the context

System Analysis by Mapping a Fault-tree into a Bayesian-network

NASA Astrophysics Data System (ADS)

Sheng, B.; Deng, C.; Wang, Y. H.; Tang, L. H.

2018-05-01

In view of the limitations of fault tree analysis in reliability assessment, Bayesian Network (BN) has been studied as an alternative technology. After a brief introduction to the method for mapping a Fault Tree (FT) into an equivalent BN, equations used to calculate the structure importance degree, the probability importance degree and the critical importance degree are presented. Furthermore, the correctness of these equations is proved mathematically. Combining with an aircraft landing gear’s FT, an equivalent BN is developed and analysed. The results show that richer and more accurate information have been achieved through the BN method than the FT, which demonstrates that the BN is a superior technique in both reliability assessment and fault diagnosis.

Base structure consisting of an endothelialized vascular-tree network and hepatocytes for whole liver engineering.

PubMed

Shirakigawa, Nana; Takei, Takayuki; Ijima, Hiroyuki

2013-12-01

Reconstructed liver has been desired as a liver substitute for transplantation. However, reconstruction of a whole liver has not been achieved because construction of a vascular network at an organ scale is very difficult. We focused on decellularized liver (DC-liver) as an artificial scaffold for the construction of a hierarchical vascular network. In this study, we obtained DC-liver and the tubular network structure in which both portal vein and hepatic vein systems remained intact. Furthermore, endothelialization of the tubular structure in DC-liver was achieved, which prevented blood leakage from the tubular structure. In addition, hepatocytes suspended in a collagen sol were injected from the surroundings using a syringe as a suitable procedure for liver cell inoculation. In summary, we developed a base structure consisting of an endothelialized vascular-tree network and hepatocytes for whole liver engineering. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Simulation of Drought-induced Tree Mortality Using a New Individual and Hydraulic Trait-based Model (S-TEDy)

NASA Astrophysics Data System (ADS)

Sinha, T.; Gangodagamage, C.; Ale, S.; Frazier, A. G.; Giambelluca, T. W.; Kumagai, T.; Nakai, T.; Sato, H.

2017-12-01

Drought-related tree mortality at a regional scale causes drastic shifts in carbon and water cycling in Southeast Asian tropical rainforests, where severe droughts are projected to occur more frequently, especially under El Niño conditions. To provide a useful tool for projecting the tropical rainforest dynamics under climate change conditions, we developed the Spatially Explicit Individual-Based (SEIB) Dynamic Global Vegetation Model (DGVM) applicable to simulating mechanistic tree mortality induced by the climatic impacts via individual-tree-scale ecophysiology such as hydraulic failure and carbon starvation. In this study, we present the new model, SEIB-originated Terrestrial Ecosystem Dynamics (S-TEDy) model, and the computation results were compared with observations collected at a field site in a Bornean tropical rainforest. Furthermore, after validating the model's performance, numerical experiments addressing a future of the tropical rainforest were conducted using some global climate model (GCM) simulation outputs.

Bioinformatics in proteomics: application, terminology, and pitfalls.

PubMed

Wiemer, Jan C; Prokudin, Alexander

2004-01-01

Bioinformatics applies data mining, i.e., modern computer-based statistics, to biomedical data. It leverages on machine learning approaches, such as artificial neural networks, decision trees and clustering algorithms, and is ideally suited for handling huge data amounts. In this article, we review the analysis of mass spectrometry data in proteomics, starting with common pre-processing steps and using single decision trees and decision tree ensembles for classification. Special emphasis is put on the pitfall of overfitting, i.e., of generating too complex single decision trees. Finally, we discuss the pros and cons of the two different decision tree usages.

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

PubMed

Marcussen, Thomas; Heier, Lise; Brysting, Anne K; Oxelman, Bengt; Jakobsen, Kjetill S

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the "correct" network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ("ghost subgenome lineages") significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage-between 67% and 88%-of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

SVM-based tree-type neural networks as a critic in adaptive critic designs for control.

PubMed

Deb, Alok Kanti; Jayadeva; Gopal, Madan; Chandra, Suresh

2007-07-01

In this paper, we use the approach of adaptive critic design (ACD) for control, specifically, the action-dependent heuristic dynamic programming (ADHDP) method. A least squares support vector machine (SVM) regressor has been used for generating the control actions, while an SVM-based tree-type neural network (NN) is used as the critic. After a failure occurs, the critic and action are retrained in tandem using the failure data. Failure data is binary classification data, where the number of failure states are very few as compared to the number of no-failure states. The difficulty of conventional multilayer feedforward NNs in learning this type of classification data has been overcome by using the SVM-based tree-type NN, which due to its feature to add neurons to learn misclassified data, has the capability to learn any binary classification data without a priori choice of the number of neurons or the structure of the network. The capability of the trained controller to handle unforeseen situations is demonstrated.

Augmenting computer networks

NASA Technical Reports Server (NTRS)

Bokhari, S. H.; Raza, A. D.

1984-01-01

Three methods of augmenting computer networks by adding at most one link per processor are discussed: (1) A tree of N nodes may be augmented such that the resulting graph has diameter no greater than 4log sub 2((N+2)/3)-2. Thi O(N(3)) algorithm can be applied to any spanning tree of a connected graph to reduce the diameter of that graph to O(log N); (2) Given a binary tree T and a chain C of N nodes each, C may be augmented to produce C so that T is a subgraph of C. This algorithm is O(N) and may be used to produce augmented chains or rings that have diameter no greater than 2log sub 2((N+2)/3) and are planar; (3) Any rectangular two-dimensional 4 (8) nearest neighbor array of size N = 2(k) may be augmented so that it can emulate a single step shuffle-exchange network of size N/2 in 3(t) time steps.

Climatic, landform, microtopographic, and overstory canopy controls of tree invasion in a subalpine meadow landscape, Oregon Cascades, USA

Treesearch

Harold S.J. Zald; Thomas A. Spies; Manuela Huso; Demetrios Gatziolis

2012-01-01

Tree invasions have been documented throughout Northern Hemisphere high elevation meadows, as well as globally in many grass and forb-dominated ecosystems. Tree invasions are often associated with large-scale changes in climate or disturbance regimes, but are fundamentally driven by regeneration processes influenced by interactions between climatic, topographic, and...

Failure to migrate: lack of tree range expansion in response to climate change

Treesearch

Kai Zhu; Christopher W. Woodall; James S. Clark

2012-01-01

Tree species are expected to track warming climate by shifting their ranges to higher latitudes or elevations, but current evidence of latitudinal range shifts for suites of species is largely indirect. In response to global warming, offspring of trees are predicted to have ranges extend beyond adults at leading edges and the opposite relationship at trailing edges....

Projections of forest contributions to global carbon cycles

Treesearch

Michael E. Goerndt; Stephen R. Shifley; Patrick D. Miles; Dave Wear; Francisco X. Aguilar

2016-01-01

Forests cover 42 percent of the Northern United States, and collectively they store 13 billion tons of carbon in live trees (29 percent), roots (6 percent), forest floor (9 percent), dead trees (6 percent), and soils (50 percent). About half the biomass of a live tree (dry weight basis) is sequestered carbon (Woodall et al. 2011) - not the largest but the most dynamic...

Urban forest biomass estimates: is it important to use allometric relationships developed specifically for urban trees? 

Treesearch

M.R. McHale; I.C. Burke; M.A. Lefsky; P.J. Peper; E.G. McPherson

2009-01-01

Many studies have analyzed the benefits, costs, and carbon storage capacity associated with urban trees. These studies have been limited by a lack of research on urban tree biomass, such that estimates of carbon storage in urban systems have relied upon allometric relationships developed in traditional forests. As urbanization increases globally, it is becoming...

A new global 1-km dataset of percentage tree cover derived from remote sensing

USGS Publications Warehouse

DeFries, R.S.; Hansen, M.C.; Townshend, J.R.G.; Janetos, A.C.; Loveland, Thomas R.

2000-01-01

Accurate assessment of the spatial extent of forest cover is a crucial requirement for quantifying the sources and sinks of carbon from the terrestrial biosphere. In the more immediate context of the United Nations Framework Convention on Climate Change, implementation of the Kyoto Protocol calls for estimates of carbon stocks for a baseline year as well as for subsequent years. Data sources from country level statistics and other ground-based information are based on varying definitions of 'forest' and are consequently problematic for obtaining spatially and temporally consistent carbon stock estimates. By combining two datasets previously derived from the Advanced Very High Resolution Radiometer (AVHRR) at 1 km spatial resolution, we have generated a prototype global map depicting percentage tree cover and associated proportions of trees with different leaf longevity (evergreen and deciduous) and leaf type (broadleaf and needleleaf). The product is intended for use in terrestrial carbon cycle models, in conjunction with other spatial datasets such as climate and soil type, to obtain more consistent and reliable estimates of carbon stocks. The percentage tree cover dataset is available through the Global Land Cover Facility at the University of Maryland at http://glcf.umiacs.umd.edu.

Challenges to estimating tree height via LiDAR in closed-canopy forest: a parable from western Oregon

Treesearch

Demetrios Gatziolis; Jeremy S. Fried; Vicente S. Monleon

2010-01-01

We examine the accuracy of tree height estimates obtained via light detection and ranging (LiDAR) in a temperate rainforest characterized by complex terrain, steep slopes, and high canopy cover. The evaluation was based on precise top and base locations for > 1,000 trees in 45 plots distributed across three forest types, a dense network of ground elevation...

Water availability drives gas exchange and growth of trees in northeastern US, not elevated CO2 and reduced acid deposition.

PubMed

Levesque, Mathieu; Andreu-Hayles, Laia; Pederson, Neil

2017-04-10

Dynamic global vegetation models (DGVM) exhibit high uncertainty about how climate change, elevated atmospheric CO 2 (atm. CO 2 ) concentration, and atmospheric pollutants will impact carbon sequestration in forested ecosystems. Although the individual roles of these environmental factors on tree growth are understood, analyses examining their simultaneous effects are lacking. We used tree-ring isotopic data and structural equation modeling to examine the concurrent and interacting effects of water availability, atm. CO 2 concentration, and SO 4 and nitrogen deposition on two broadleaf tree species in a temperate mesic forest in the northeastern US. Water availability was the strongest driver of gas exchange and tree growth. Wetter conditions since the 1980s have enhanced stomatal conductance, photosynthetic assimilation rates and, to a lesser extent, tree radial growth. Increased water availability seemingly overrides responses to reduced acid deposition, CO 2 fertilization, and nitrogen deposition. Our results indicate that water availability as a driver of ecosystem productivity in mesic temperate forests is not adequately represented in DGVMs, while CO 2 fertilization is likely overrepresented. This study emphasizes the importance to simultaneously consider interacting climatic and biogeochemical drivers when assessing forest responses to global environmental changes.

Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions.

PubMed

Sundaram, Mekala; Willoughby, Janna R; Lichti, Nathanael I; Steele, Michael A; Swihart, Robert K

2015-01-01

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27-73%), and combined effects of seed traits and phylogeny of hardwood trees (5-55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 "global" axes of traits that were phylogenetically autocorrelated at the family and genus level and a third "local" axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30-76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.

Belowground carbon trade among tall trees in a temperate forest.

PubMed

Klein, Tamir; Siegwolf, Rolf T W; Körner, Christian

2016-04-15

Forest trees compete for light and soil resources, but photoassimilates, once produced in the foliage, are not considered to be exchanged between individuals. Applying stable carbon isotope labeling at the canopy scale, we show that carbon assimilated by 40-meter-tall spruce is traded over to neighboring beech, larch, and pine via overlapping root spheres. Isotope mixing signals indicate that the interspecific, bidirectional transfer, assisted by common ectomycorrhiza networks, accounted for 40% of the fine root carbon (about 280 kilograms per hectare per year tree-to-tree transfer). Although competition for resources is commonly considered as the dominant tree-to-tree interaction in forests, trees may interact in more complex ways, including substantial carbon exchange. Copyright © 2016, American Association for the Advancement of Science.

Semiautomated landscape feature extraction and modeling

NASA Astrophysics Data System (ADS)

Wasilewski, Anthony A.; Faust, Nickolas L.; Ribarsky, William

2001-08-01

We have developed a semi-automated procedure for generating correctly located 3D tree objects form overhead imagery. Cross-platform software partitions arbitrarily large, geocorrected and geolocated imagery into management sub- images. The user manually selected tree areas from one or more of these sub-images. Tree group blobs are then narrowed to lines using a special thinning algorithm which retains the topology of the blobs, and also stores the thickness of the parent blob. Maxima along these thinned tree grous are found, and used as individual tree locations within the tree group. Magnitudes of the local maxima are used to scale the radii of the tree objects. Grossly overlapping trees are culled based on a comparison of tree-tree distance to combined radii. Tree color is randomly selected based on the distribution of sample tree pixels, and height is estimated form tree radius. The final tree objects are then inserted into a terrain database which can be navigated by VGIS, a high-resolution global terrain visualization system developed at Georgia Tech.

Leaf and stem economics spectra drive diversity of functional plant traits in a dynamic global vegetation model.

PubMed

Sakschewski, Boris; von Bloh, Werner; Boit, Alice; Rammig, Anja; Kattge, Jens; Poorter, Lourens; Peñuelas, Josep; Thonicke, Kirsten

2015-01-22

Functional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant parameters. Here, we develop an individual- and trait-based version of the DGVM LPJmL (Lund-Potsdam-Jena managed Land) called LPJmL- flexible individual traits (LPJmL-FIT) with flexible individual traits) which we apply to generate plant trait maps for the Amazon basin. LPJmL-FIT incorporates empirical ranges of five traits of tropical trees extracted from the TRY global plant trait database, namely specific leaf area (SLA), leaf longevity (LL), leaf nitrogen content (N area ), the maximum carboxylation rate of Rubisco per leaf area (vcmaxarea), and wood density (WD). To scale the individual growth performance of trees, the leaf traits are linked by trade-offs based on the leaf economics spectrum, whereas wood density is linked to tree mortality. No preselection of growth strategies is taking place, because individuals with unique trait combinations are uniformly distributed at tree establishment. We validate the modeled trait distributions by empirical trait data and the modeled biomass by a remote sensing product along a climatic gradient. Including trait variability and trade-offs successfully predicts natural trait distributions and achieves a more realistic representation of functional diversity at the local to regional scale. As sites of high climatic variability, the fringes of the Amazon promote trait divergence and the coexistence of multiple tree growth strategies, while lower plant trait diversity is found in the species-rich center of the region with relatively low climatic variability. LPJmL-FIT enables to test hypotheses on the effects of functional biodiversity on ecosystem functioning and to apply the DGVM to current challenges in ecosystem management from local to global scales, that is, deforestation and climate change effects. © 2015 John Wiley & Sons Ltd.

The spring and autumn phenophases of the broadleaves trees indicate the extension of growing season in the boreal forest environment

NASA Astrophysics Data System (ADS)

Kubin, Eero; Poikolainen, Jarmo; Karhu, Jouni; Tolvanen, Anne

2014-05-01

The long-term historical data since 1752 shows an advancement in the timing of flowering by five days per century in Prunus padus. The onset of flowering in Sorbus aucuparia has become correspondingly earlier in Finland at the rate of three days per century. The results of the Finnish National Phenological Network fit well in the historical data. The Finnish National Phenological Network was established in 1996 in collaboration with research institutes and universities. The phenomena being studied by trained observers using a standardized manner are flowering and flushing of trees, yellowing and shedding of leaves, height growth and flowering of conifers, flowering of Vaccinium vitis-idaea and Vaccinium myrtillus and the ripening of berries. The monitoring covers eight tree species: Betula pubescens, Betula pendula, Pinus silvestris, Picea abies, Populus tremula, Juniperus communis, Prunus padus and Sorbus aucuparia. The observations are made repeatedly of the same tree individuals at least twice per week. The real time results are visible in the form of animations and charts (http://www.metla.fi/metinfo/fenologia/index-en.htm). The green wave from south to north and yellowishing from north to south will be presented in the conference. The onset of downy birch leaves occurred in northernmost Lapland about a month later compared with southern Finland and began to turn yellow already at the beginning of September. The onset and progress of growth are primarily dependeing on air temperature. The results of the network confirm that spring phenophases have especially in northern Finland advanced with respect to climatic conditions. For autumn phenopases we found in several sites delaying trend, but not as strong as in spring phenopases. Downy birch, Betula pubescens, has been found to leaf on average when the effective temperature sum has reached 54 dd. in the southern part of the country, but in the north only 38 dd. is needed. The less temperature sum requirement within the boreal zone in the north compared with south is not reported earlier. In the north less temperature sum was also needed for the flowering of bird cherry. Phenological monitoring by using field observations is nowadays more important than ever especially in arctic and boreal regions, where spring temperatures are elevated. Compilation and documentation of observations on plant phenophases play a key role in working out the rate of global climate change. There occurs however great variation of phenophases between the years and sites causing uncertainty for the use of data. The observation term of the Finnish National Phenological Network, seventeen years, starts to be long enough for recent responses, but it is still too short to tell whether the advancement of spring or delaying autumn is a constant phenomenon or a consequence of normal climatic variability. The timing of especially autumn phenophases and onset of leafing with respect to temperature sum will be discussed in the conference.

APHiD: Hierarchical Task Placement to Enable a Tapered Fat Tree Topology for Lower Power and Cost in HPC Networks

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

Michelogiannakis, George; Ibrahim, Khaled Z.; Shalf, John

The power and procurement cost of bandwidth in system-wide networks has forced a steady drop in the byte/flop ratio. This trend of computation becoming faster relative to the network is expected to hold. In this paper, we explore how cost-oriented task placement enables reducing the cost of system-wide networks by enabling high performance even on tapered topologies where more bandwidth is provisioned at lower levels. We describe APHiD, an efficient hierarchical placement algorithm that uses new techniques to improve the quality of heuristic solutions and reduces the demand on high-level, expensive bandwidth in hierarchical topologies. We apply APHiD to amore » tapered fat-tree, demonstrating that APHiD maintains application scalability even for severely tapered network configurations. Using simulation, we show that for tapered networks APHiD improves performance by more than 50% over random placement and even 15% in some cases over costlier, state-of-the-art placement algorithms.« less

A novel survivable architecture for hybrid WDM/TDM passive optical networks

NASA Astrophysics Data System (ADS)

Qiu, Yang; Chan, Chun-Kit

2014-02-01

A novel tree-ring survivable architecture, which consists of an organization of a wavelength-division-multiplexing (WDM) tree from optical line terminal (OLT) to remote nodes (RNs) and a time division multiplexing (TDM) ring in each RN, is proposed for hybrid WDM/TDM passive optical networks. By utilizing the cyclic property of arrayed waveguide gratings (AWGs) and the single-ring topology among a group of optical network units (ONUs) in the remote node, not only the feeder and distribution fibers, but also any fiber failures in the RN rings are protected simultaneously. Five-Gbit/s transmissions under both normal working and protection modes were experimentally demonstrated and a traffic restoration time was successfully measured.

Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?

PubMed Central

Czégel, Dániel; Palla, Gergely

2015-01-01

Signs of hierarchy are prevalent in a wide range of systems in nature and society. One of the key problems is quantifying the importance of hierarchical organisation in the structure of the network representing the interactions or connections between the fundamental units of the studied system. Although a number of notable methods are already available, their vast majority is treating all directed acyclic graphs as already maximally hierarchical. Here we propose a hierarchy measure based on random walks on the network. The novelty of our approach is that directed trees corresponding to multi level pyramidal structures obtain higher hierarchy scores compared to directed chains and directed stars. Furthermore, in the thermodynamic limit the hierarchy measure of regular trees is converging to a well defined limit depending only on the branching number. When applied to real networks, our method is computationally very effective, as the result can be evaluated with arbitrary precision by subsequent multiplications of the transition matrix describing the random walk process. In addition, the tests on real world networks provided very intuitive results, e.g., the trophic levels obtained from our approach on a food web were highly consistent with former results from ecology. PMID:26657012

Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?

NASA Astrophysics Data System (ADS)

Czégel, Dániel; Palla, Gergely

2015-12-01

Signs of hierarchy are prevalent in a wide range of systems in nature and society. One of the key problems is quantifying the importance of hierarchical organisation in the structure of the network representing the interactions or connections between the fundamental units of the studied system. Although a number of notable methods are already available, their vast majority is treating all directed acyclic graphs as already maximally hierarchical. Here we propose a hierarchy measure based on random walks on the network. The novelty of our approach is that directed trees corresponding to multi level pyramidal structures obtain higher hierarchy scores compared to directed chains and directed stars. Furthermore, in the thermodynamic limit the hierarchy measure of regular trees is converging to a well defined limit depending only on the branching number. When applied to real networks, our method is computationally very effective, as the result can be evaluated with arbitrary precision by subsequent multiplications of the transition matrix describing the random walk process. In addition, the tests on real world networks provided very intuitive results, e.g., the trophic levels obtained from our approach on a food web were highly consistent with former results from ecology.

Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?

PubMed

Czégel, Dániel; Palla, Gergely

2015-12-10

Signs of hierarchy are prevalent in a wide range of systems in nature and society. One of the key problems is quantifying the importance of hierarchical organisation in the structure of the network representing the interactions or connections between the fundamental units of the studied system. Although a number of notable methods are already available, their vast majority is treating all directed acyclic graphs as already maximally hierarchical. Here we propose a hierarchy measure based on random walks on the network. The novelty of our approach is that directed trees corresponding to multi level pyramidal structures obtain higher hierarchy scores compared to directed chains and directed stars. Furthermore, in the thermodynamic limit the hierarchy measure of regular trees is converging to a well defined limit depending only on the branching number. When applied to real networks, our method is computationally very effective, as the result can be evaluated with arbitrary precision by subsequent multiplications of the transition matrix describing the random walk process. In addition, the tests on real world networks provided very intuitive results, e.g., the trophic levels obtained from our approach on a food web were highly consistent with former results from ecology.

Combining multiple isotopes and metagenomic to delineate the role of tree canopy nitrification in European forests along nitrogen deposition and climate gradients

NASA Astrophysics Data System (ADS)

Guerrieri, R.; Avila, A.; Barceló, A.; Elustondo, D.; Hellstein, S.; Magnani, F.; Mattana, S.; Matteucci, G.; Merilä, P.; Michalski, G. M.; Nicolas, M.; Vanguelova, E.; Verstraeten, A.; Waldner, P.; Watanabe, M.; Penuelas, J.; Mencuccini, M.

2017-12-01

Forest canopies influence our climate through carbon, water and energy exchanges with the atmosphere. However, less investigated is whether and how tree canopies change the chemical composition of precipitation, with important implications on forest nutrient cycling. Recently, we provided for the first time isotopic evidence that biological nitrification in tree canopies was responsible for significant changes in the amount of nitrate from rainfall to throughfall across two UK forests at high nitrogen (N) deposition [1]. This finding strongly suggested that bacteria and/or Archaea species of the phyllosphere are responsible for transforming atmospheric N before it reaches the soil. Despite microbial epiphytes representing an important component of tree canopies, attention has been mostly directed to their role as pathogens, while we still do not know whether and how they affect nutrient cycling. Our study aims to 1) characterize microbial communities harboured in tree canopies for two of the most dominant species in Europe (Fagus sylvatica L. and Pinus sylvestris L.) using metagenomic techniques, 2) quantify the functional genes related to nitrification but also to denitrification and N fixation, and 3) estimate the contribution of NO3 derived from biological canopy nitrification vs. atmospheric NO3 input by using δ15N, δ18O and δ17O of NO3in forest water. We considered i) twelve sites included in the EU ICP long term intensive forest monitoring network, chosen along a climate and nitrogen deposition gradient, spanning from Fennoscandia to the Mediterranean and ii) a manipulation experiment where N mist treatments were carried out either to the soil or over tree canopies. We will present preliminary results regarding microbial diversity in the phyllosphere, water (rainfall and throughfall) and soil samples over the gradient. Furthermore, we will report differences between the two investigated tree species for the phyllosphere core microbiome in terms of relative abundance of bacterial and Archaea classes and those species related to N cycling. Finally we will assess whether there are differences among tree species and sites in the number of functional genes related to N cycling and how they are related to the N deposition and/or climate. [1] Guerrieri et al. 2015 Global Change and Biology 21 (12): 4613-4626.

Edge-to-Stem Variability in Wet-Canopy Evaporation From an Urban Tree Row

NASA Astrophysics Data System (ADS)

Van Stan, John T.; Norman, Zachary; Meghoo, Adrian; Friesen, Jan; Hildebrandt, Anke; Côté, Jean-François; Underwood, S. Jeffrey; Maldonado, Gustavo

2017-11-01

Evaporation from wet-canopy (E_C) and stem (E_S) surfaces during rainfall represents a significant portion of municipal-to-global scale hydrologic cycles. For urban ecosystems, E_C and E_S dynamics play valuable roles in stormwater management. Despite this, canopy-interception loss studies typically ignore crown-scale variability in E_C and assume (with few indirect data) that E_S is generally {<}2% of total wet-canopy evaporation. We test these common assumptions for the first time with a spatially-distributed network of in-canopy meteorological monitoring and 45 surface temperature sensors in an urban Pinus elliottii tree row to estimate E_C and E_S under the assumption that crown surfaces behave as "wet bulbs". From December 2015 through July 2016, 33 saturated crown periods (195 h of 5-min observations) were isolated from storms for determination of 5-min evaporation rates ranging from negligible to 0.67 mm h^{-1}. Mean E_S (0.10 mm h^{-1}) was significantly lower (p < 0.01) than mean E_C (0.16 mm h^{-1}). But, E_S values often equalled E_C and, when scaled to trunk area using terrestrial lidar, accounted for 8-13% (inter-quartile range) of total wet-crown evaporation (E_S+E_C scaled to surface area). E_S contributions to total wet-crown evaporation maximized at 33%, showing a general underestimate (by 2-17 times) of this quantity in the literature. Moreover, results suggest wet-crown evaporation from urban tree rows can be adequately estimated by simply assuming saturated tree surfaces behave as wet bulbs, avoiding problematic assumptions associated with other physically-based methods.

Shallow landsliding, root reinforcement, and the spatial distribution of trees in the Oregon Coast Range

USGS Publications Warehouse

Roering, J.J.; Schmidt, K.M.; Stock, J.D.; Dietrich, W.E.; Montgomery, D.R.

2003-01-01

The influence of root reinforcement on shallow landsliding has been well established through mechanistic and empirical studies, yet few studies have examined how local vegetative patterns influence slope stability. Because root networks spread outward from trees, the species, size, and spacing of trees should influence the spatial distribution of root strength. We documented the distribution and characteristics of trees adjacent to 32 shallow landslides that occurred during 1996 in the Oregon Coast Range. Although broadly classified as a conifer-dominated forest, we observed sparse coniferous and abundant hardwood trees near landslide scars in an industrial forest (Mapleton) that experienced widespread burning in the 19th century. In industrial forests that were burned, selectively harvested, and not replanted (Elliott State Forest), swordfern was ubiquitous near landslides, and we observed similar numbers of live conifer and hardwood trees proximal to landslide scarps. We demonstrate that root strength quantified in landslide scarps and soil pits correlates with a geometry-based index of root network contribution derived from mapping the size, species, condition, and spacing of local trees, indicating that root strength can be predicted by mapping the distribution and characteristics of trees on potentially unstable slopes. In our study sites, landslides tend to occur in areas of reduced root strength, suggesting that to make site-specific predictions of landslide occurrence slope stability analyses must account for the diversity and distribution of vegetation in potentially unstable terrain.

Natural migration rates of trees: Global terrestrial carbon cycle implications. Book chapter

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

Solomon, A.M.

The paper discusses the forest-ecological processes which constrain the rate of response by forests to rapid future environmental change. It establishes a minimum response time by natural tree populations which invade alien landscapes and reach the status of a mature, closed canopy forest when maximum carbon storage is realized. It considers rare long-distance and frequent short-distance seed transport, seedling and tree establishment, sequential tree and stand maturation, and spread between newly established colonies.

Isoscapes of tree-ring carbon-13 perform like meteorological networks in predicting regional precipitation patterns

NASA Astrophysics Data System (ADS)

del Castillo, Jorge; Aguilera, Mònica; Voltas, Jordi; Ferrio, Juan Pedro

2013-03-01

isotopes in tree rings provide climatic information with annual resolution dating back for centuries or even millennia. However, deriving spatially explicit climate models from isotope networks remains challenging. Here we propose a methodology to model regional precipitation from carbon isotope discrimination (Δ13C) in tree rings by (1) building regional spatial models of Δ13C (isoscapes) and (2) deriving precipitation maps from Δ13C-isoscapes, taking advantage of the response of Δ13C to precipitation in seasonally dry climates. As a case study, we modeled the spatial distribution of mean annual precipitation (MAP) in the northeastern Iberian Peninsula, a region with complex topography and climate (MAP = 303-1086 mm). We compiled wood Δ13C data for two Mediterranean species that exhibit complementary responses to seasonal precipitation (Pinus halepensis Mill., N = 38; Quercus ilex L.; N = 44; pooling period: 1975-2008). By combining multiple regression and geostatistical interpolation, we generated one Δ13 C-isoscape for each species. A spatial model of MAP was then built as the sum of two complementary maps of seasonal precipitation, each one derived from the corresponding Δ13C-isoscape (September-November from Q. ilex; December-August from P. halepensis). Our approach showed a predictive power for MAP (RMSE = 84 mm) nearly identical to that obtained by interpolating data directly from a similarly dense network of meteorological stations (RMSE = 80-83 mm, N = 65), being only outperformed when using a much denser meteorological network (RMSE = 56-57 mm, N = 340). This method offers new avenues for modeling spatial variability of past precipitation, exploiting the large amount of information currently available from tree-ring networks.

Node Deployment Algorithm Based on Connected Tree for Underwater Sensor Networks

PubMed Central

Jiang, Peng; Wang, Xingmin; Jiang, Lurong

2015-01-01

Designing an efficient deployment method to guarantee optimal monitoring quality is one of the key topics in underwater sensor networks. At present, a realistic approach of deployment involves adjusting the depths of nodes in water. One of the typical algorithms used in such process is the self-deployment depth adjustment algorithm (SDDA). This algorithm mainly focuses on maximizing network coverage by constantly adjusting node depths to reduce coverage overlaps between two neighboring nodes, and thus, achieves good performance. However, the connectivity performance of SDDA is irresolute. In this paper, we propose a depth adjustment algorithm based on connected tree (CTDA). In CTDA, the sink node is used as the first root node to start building a connected tree. Finally, the network can be organized as a forest to maintain network connectivity. Coverage overlaps between the parent node and the child node are then reduced within each sub-tree to optimize coverage. The hierarchical strategy is used to adjust the distance between the parent node and the child node to reduce node movement. Furthermore, the silent mode is adopted to reduce communication cost. Simulations show that compared with SDDA, CTDA can achieve high connectivity with various communication ranges and different numbers of nodes. Moreover, it can realize coverage as high as that of SDDA with various sensing ranges and numbers of nodes but with less energy consumption. Simulations under sparse environments show that the connectivity and energy consumption performances of CTDA are considerably better than those of SDDA. Meanwhile, the connectivity and coverage performances of CTDA are close to those depth adjustment algorithms base on connected dominating set (CDA), which is an algorithm similar to CTDA. However, the energy consumption of CTDA is less than that of CDA, particularly in sparse underwater environments. PMID:26184209

Dynamic conservation of forest genetic resources in 33 European countries.

PubMed

Lefèvre, François; Koskela, Jarkko; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C; Schüler, Silvio; Bozzano, Michele; Alizoti, Paraskevi; Bakys, Remigijus; Baldwin, Cathleen; Ballian, Dalibor; Black-Samuelsson, Sanna; Bednarova, Dagmar; Bordács, Sándor; Collin, Eric; de Cuyper, Bart; de Vries, Sven M G; Eysteinsson, Thröstur; Frýdl, Josef; Haverkamp, Michaela; Ivankovic, Mladen; Konrad, Heino; Koziol, Czesław; Maaten, Tiit; Notivol Paino, Eduardo; Oztürk, Hikmet; Pandeva, Ivanova Denitsa; Parnuta, Gheorghe; Pilipovič, Andrej; Postolache, Dragos; Ryan, Cathal; Steffenrem, Arne; Varela, Maria Carolina; Vessella, Federico; Volosyanchuk, Roman T; Westergren, Marjana; Wolter, Frank; Yrjänä, Leena; Zariŋa, Inga

2013-04-01

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan-European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species-oriented strategy in which national conservation networks are specifically designed for key target species and a site-oriented strategy in which multiple-target units include so-called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however, <2% of the conserved populations seem to be at risk of extinction. On the basis of our results, we recommend combining species-oriented and site-oriented strategies. © 2012 Society for Conservation Biology.

Combining Passive Microwave and Optical Data to Estimate Snow Water Equivalent in Afghanistan's Hindu Kush

NASA Astrophysics Data System (ADS)

Dozier, J.; Bair, N.; Calfa, A. A.; Skalka, C.; Tolle, K.; Bongard, J.

2015-12-01

The task is to estimate spatiotemporally distributed estimates of snow water equivalent (SWE) in snow-dominated mountain environments, including those that lack on-the-ground measurements such as the Hindu Kush range in Afghanistan. During the snow season, we can use two measurements: (1) passive microwave estimates of SWE, which generally underestimate in the mountains; (2) fractional snow-covered area from MODIS. Once the snow has melted, we can reconstruct the accumulated SWE back to the last significant snowfall by calculating the energy used in melt. The reconstructed SWE values provide a training set for predictions from the passive microwave SWE and snow-covered area. We examine several machine learning methods—regression-boosted decision trees, bagged trees, neural networks, and genetic programming—to estimate SWE. All methods work reasonably well, with R2 values greater than 0.8. Predictors built with multiple years of data reduce the bias that usually appears if we predict one year from just one other year's training set. Genetic programming tends to produce results that additionally provide physical insight. Adding precipitation estimates from the Global Precipitation Measurements mission is in progress.

The algebra of the general Markov model on phylogenetic trees and networks.

PubMed

Sumner, J G; Holland, B R; Jarvis, P D

2012-04-01

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the “splitting” operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.

Tree proximity, soil pathways and common mycorrhizal networks: their influence on the utilization of redistributed water by understory seedlings.

PubMed

Schoonmaker, Amanda L; Teste, François P; Simard, Suzanne W; Guy, Robert D

2007-12-01

Hydraulic redistribution (HR) is a process by which water moves through plant roots from moist to dry soils. An experiment was conducted to quantify the influence of common mycorrhizal networks (CMNs) and proximity to mature HR-source trees on the water relations of surrounding seedlings. Douglas-fir (Pseudotsuga menziesii var glauca (Mirb.) Franco) seedlings were planted at four distances (0.5, 1, 2.5, and 5 m) from six mature Douglas-fir trees, either directly into soil (soil plus CMN pathway) or inside 0.5 microm mesh bags (soil-only pathway). Deuterated water was used to irrigate soil beside mature trees in order to identify different HR water pathways to surrounding seedlings. This was followed by measurements of seedling deuterium enrichment, seedling water potential, soil water potential, gravimetric soil water content, and tree root density surrounding the seedlings. There was no significantly detectable difference in the quantity of HR water transferred to seedlings having access to soil and CMN pathways or soil-only pathways of water movement. Water from the irrigation plot contributed up to 1.4% of the water of Douglas-fir seedlings. Based on the assumption that the only pathway through which seedlings could access irrigation water was through the mature trees, we estimate that as much as 21.6% of the seedling water was supplied by the nearby tree. Seedling water potential was not significantly affected either by proximity to mature trees or pathway, suggesting HR may have compensated for increasing tree competitive effects with proximity. It is also possible that the lack of difference was due to a relatively moist summer. Our results suggest that residual mature trees are potentially important for hydraulic redistribution to regenerating seedlings in harvested dry interior Douglas-fir forests.

Atmospheric pollution in an urban environment by tree bark biomonitoring--part I: trace element analysis.

PubMed

Guéguen, Florence; Stille, Peter; Lahd Geagea, Majdi; Boutin, René

2012-03-01

Tree bark has been shown to be a useful biomonitor of past air quality because it accumulates atmospheric particulate matter (PM) in its outermost structure. Trace element concentrations of tree bark of more than 73 trees allow to elucidate the impact of past atmospheric pollution on the urban environment of the cities of Strasbourg and Kehl in the Rhine Valley. Compared to the upper continental crust (UCC) tree barks are strongly enriched in Mn, Ni, Cu, Zn, Cd and Pb. To assess the degree of pollution of the different sites in the cities, a geoaccumulation index I(geo) was applied. Global pollution by V, Ni, Cr, Sb, Sn and Pb was observed in barks sampled close to traffic axes. Cr, Mo, Cd pollution principally occurred in the industrial area. A total geoaccumulation index I(GEO-tot) was defined; it is based on the total of the investigated elements and allows to evaluate the global pollution of the studied environment by assembling the I(geo) indices on a pollution map. Copyright © 2011 Elsevier Ltd. All rights reserved.

Adversarial search by evolutionary computation.

PubMed

Hong, T P; Huang, K Y; Lin, W Y

2001-01-01

In this paper, we consider the problem of finding good next moves in two-player games. Traditional search algorithms, such as minimax and alpha-beta pruning, suffer great temporal and spatial expansion when exploring deeply into search trees to find better next moves. The evolution of genetic algorithms with the ability to find global or near global optima in limited time seems promising, but they are inept at finding compound optima, such as the minimax in a game-search tree. We thus propose a new genetic algorithm-based approach that can find a good next move by reserving the board evaluation values of new offspring in a partial game-search tree. Experiments show that solution accuracy and search speed are greatly improved by our algorithm.

State Support: A Prerequisite for Global Health Network Effectiveness Comment on "Four Challenges that Global Health Networks Face".

PubMed

Marten, Robert; Smith, Richard D

2017-07-24

Shiffman recently summarized lessons for network effectiveness from an impressive collection of case-studies. However, in common with most global health governance analysis in recent years, Shiffman underplays the important role of states in these global networks. As the body which decides and signs international agreements, often provides the resourcing, and is responsible for implementing initiatives all contributing to the prioritization of certain issues over others, state recognition and support is a prerequisite to enabling and determining global health networks' success. The role of states deserves greater attention, analysis and consideration. We reflect upon the underappreciated role of the state within the current discourse on global health. We present the tobacco case study to illustrate the decisive role of states in determining progress for global health networks, and highlight how states use a legitimacy loop to gain legitimacy from and provide legitimacy to global health networks. Moving forward in assessing global health networks' effectiveness, further investigating state support as a determinant of success will be critical. Understanding how global health networks and states interact and evolve to shape and support their respective interests should be a focus for future research. © 2018 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Random walks with long-range steps generated by functions of Laplacian matrices

NASA Astrophysics Data System (ADS)

Riascos, A. P.; Michelitsch, T. M.; Collet, B. A.; Nowakowski, A. F.; Nicolleau, F. C. G. A.

2018-04-01

In this paper, we explore different Markovian random walk strategies on networks with transition probabilities between nodes defined in terms of functions of the Laplacian matrix. We generalize random walk strategies with local information in the Laplacian matrix, that describes the connections of a network, to a dynamic determined by functions of this matrix. The resulting processes are non-local allowing transitions of the random walker from one node to nodes beyond its nearest neighbors. We find that only two types of Laplacian functions are admissible with distinct behaviors for long-range steps in the infinite network limit: type (i) functions generate Brownian motions, type (ii) functions Lévy flights. For this asymptotic long-range step behavior only the lowest non-vanishing order of the Laplacian function is relevant, namely first order for type (i), and fractional order for type (ii) functions. In the first part, we discuss spectral properties of the Laplacian matrix and a series of relations that are maintained by a particular type of functions that allow to define random walks on any type of undirected connected networks. Once described general properties, we explore characteristics of random walk strategies that emerge from particular cases with functions defined in terms of exponentials, logarithms and powers of the Laplacian as well as relations of these dynamics with non-local strategies like Lévy flights and fractional transport. Finally, we analyze the global capacity of these random walk strategies to explore networks like lattices and trees and different types of random and complex networks.

Correlation and network analysis of global financial indices

NASA Astrophysics Data System (ADS)

Kumar, Sunil; Deo, Nivedita

2012-08-01

Random matrix theory (RMT) and network methods are applied to investigate the correlation and network properties of 20 financial indices. The results are compared before and during the financial crisis of 2008. In the RMT method, the components of eigenvectors corresponding to the second largest eigenvalue form two clusters of indices in the positive and negative directions. The components of these two clusters switch in opposite directions during the crisis. The network analysis uses the Fruchterman-Reingold layout to find clusters in the network of indices at different thresholds. At a threshold of 0.6, before the crisis, financial indices corresponding to the Americas, Europe, and Asia-Pacific form separate clusters. On the other hand, during the crisis at the same threshold, the American and European indices combine together to form a strongly linked cluster while the Asia-Pacific indices form a separate weakly linked cluster. If the value of the threshold is further increased to 0.9 then the European indices (France, Germany, and the United Kingdom) are found to be the most tightly linked indices. The structure of the minimum spanning tree of financial indices is more starlike before the crisis and it changes to become more chainlike during the crisis. The average linkage hierarchical clustering algorithm is used to find a clearer cluster structure in the network of financial indices. The cophenetic correlation coefficients are calculated and found to increase significantly, which indicates that the hierarchy increases during the financial crisis. These results show that there is substantial change in the structure of the organization of financial indices during a financial crisis.

Correlation and network analysis of global financial indices.

PubMed

Kumar, Sunil; Deo, Nivedita

2012-08-01

Random matrix theory (RMT) and network methods are applied to investigate the correlation and network properties of 20 financial indices. The results are compared before and during the financial crisis of 2008. In the RMT method, the components of eigenvectors corresponding to the second largest eigenvalue form two clusters of indices in the positive and negative directions. The components of these two clusters switch in opposite directions during the crisis. The network analysis uses the Fruchterman-Reingold layout to find clusters in the network of indices at different thresholds. At a threshold of 0.6, before the crisis, financial indices corresponding to the Americas, Europe, and Asia-Pacific form separate clusters. On the other hand, during the crisis at the same threshold, the American and European indices combine together to form a strongly linked cluster while the Asia-Pacific indices form a separate weakly linked cluster. If the value of the threshold is further increased to 0.9 then the European indices (France, Germany, and the United Kingdom) are found to be the most tightly linked indices. The structure of the minimum spanning tree of financial indices is more starlike before the crisis and it changes to become more chainlike during the crisis. The average linkage hierarchical clustering algorithm is used to find a clearer cluster structure in the network of financial indices. The cophenetic correlation coefficients are calculated and found to increase significantly, which indicates that the hierarchy increases during the financial crisis. These results show that there is substantial change in the structure of the organization of financial indices during a financial crisis.

Routing Topologies of Wireless Sensor Networks for Health Monitoring of a Cultural Heritage Site.

PubMed

Aparicio, Sofía; Martínez-Garrido, María I; Ranz, Javier; Fort, Rafael; Izquierdo, Miguel Ángel G

2016-10-19

This paper provides a performance evaluation of tree and mesh routing topologies of wireless sensor networks (WSNs) in a cultural heritage site. The historical site selected was San Juan Bautista church in Talamanca de Jarama (Madrid, Spain). We report the preliminary analysis required to study the effects of heating in this historical location using WSNs to monitor the temperature and humidity conditions during periods of weeks. To test which routing topology was better for this kind of application, the WSNs were first deployed on the upper floor of the CAEND institute in Arganda del Rey simulating the church deployment, but in the former scenario there was no direct line of sight between the WSN elements. Two parameters were selected to evaluate the performance of the routing topologies of WSNs: the percentage of received messages and the lifetime of the wireless sensor network. To analyze in more detail which topology gave the best performance, other communication parameters were also measured. The tree topology used was the collection tree protocol and the mesh topology was the XMESH provided by MEMSIC (Andover, MA, USA). For the scenarios presented in this paper, it can be concluded that the tree topology lost fewer messages than the mesh topology.

Application of Fault Tree Analysis and Fuzzy Neural Networks to Fault Diagnosis in the Internet of Things (IoT) for Aquaculture.

PubMed

Chen, Yingyi; Zhen, Zhumi; Yu, Huihui; Xu, Jing

2017-01-14

In the Internet of Things (IoT) equipment used for aquaculture is often deployed in outdoor ponds located in remote areas. Faults occur frequently in these tough environments and the staff generally lack professional knowledge and pay a low degree of attention in these areas. Once faults happen, expert personnel must carry out maintenance outdoors. Therefore, this study presents an intelligent method for fault diagnosis based on fault tree analysis and a fuzzy neural network. In the proposed method, first, the fault tree presents a logic structure of fault symptoms and faults. Second, rules extracted from the fault trees avoid duplicate and redundancy. Third, the fuzzy neural network is applied to train the relationship mapping between fault symptoms and faults. In the aquaculture IoT, one fault can cause various fault symptoms, and one symptom can be caused by a variety of faults. Four fault relationships are obtained. Results show that one symptom-to-one fault, two symptoms-to-two faults, and two symptoms-to-one fault relationships can be rapidly diagnosed with high precision, while one symptom-to-two faults patterns perform not so well, but are still worth researching. This model implements diagnosis for most kinds of faults in the aquaculture IoT.

Application of Fault Tree Analysis and Fuzzy Neural Networks to Fault Diagnosis in the Internet of Things (IoT) for Aquaculture

PubMed Central

Chen, Yingyi; Zhen, Zhumi; Yu, Huihui; Xu, Jing

2017-01-01

In the Internet of Things (IoT) equipment used for aquaculture is often deployed in outdoor ponds located in remote areas. Faults occur frequently in these tough environments and the staff generally lack professional knowledge and pay a low degree of attention in these areas. Once faults happen, expert personnel must carry out maintenance outdoors. Therefore, this study presents an intelligent method for fault diagnosis based on fault tree analysis and a fuzzy neural network. In the proposed method, first, the fault tree presents a logic structure of fault symptoms and faults. Second, rules extracted from the fault trees avoid duplicate and redundancy. Third, the fuzzy neural network is applied to train the relationship mapping between fault symptoms and faults. In the aquaculture IoT, one fault can cause various fault symptoms, and one symptom can be caused by a variety of faults. Four fault relationships are obtained. Results show that one symptom-to-one fault, two symptoms-to-two faults, and two symptoms-to-one fault relationships can be rapidly diagnosed with high precision, while one symptom-to-two faults patterns perform not so well, but are still worth researching. This model implements diagnosis for most kinds of faults in the aquaculture IoT. PMID:28098822

A Wireless Sensor Network for Growth Environment Measurement and Multi-Band Optical Sensing to Diagnose Tree Vigor

PubMed Central

Kameoka, Shinichi; Isoda, Shuhei; Hashimoto, Atsushi; Ito, Ryoei; Miyamoto, Satoru; Wada, Genki; Watanabe, Naoki; Yamakami, Takashi; Suzuki, Ken; Kameoka, Takaharu

2017-01-01

We have tried to develop the guidance system for farmers to cultivate using various phenological indices. As the sensing part of this system, we deployed a new Wireless Sensor Network (WSN). This system uses the 920 MHz radio wave based on the Wireless Smart Utility Network that enables long-range wireless communication. In addition, the data acquired by the WSN were standardized for the advanced web service interoperability. By using these standardized data, we can create a web service that offers various kinds of phenological indices as secondary information to the farmers in the field. We have also established the field management system using thermal image, fluorescent and X-ray fluorescent methods, which enable the nondestructive, chemical-free, simple, and rapid measurement of fruits or trees. We can get the information about the transpiration of plants through a thermal image. The fluorescence sensor gives us information, such as nitrate balance index (NBI), that shows the nitrate balance inside the leaf, chlorophyll content, flavonol content and anthocyanin content. These methods allow one to quickly check the health of trees and find ways to improve the tree vigor of weak ones. Furthermore, the fluorescent x-ray sensor has the possibility to quantify the loss of minerals necessary for fruit growth. PMID:28448452

A Wireless Sensor Network for Growth Environment Measurement and Multi-Band Optical Sensing to Diagnose Tree Vigor.

PubMed

Kameoka, Shinichi; Isoda, Shuhei; Hashimoto, Atsushi; Ito, Ryoei; Miyamoto, Satoru; Wada, Genki; Watanabe, Naoki; Yamakami, Takashi; Suzuki, Ken; Kameoka, Takaharu

2017-04-27

We have tried to develop the guidance system for farmers to cultivate using various phenological indices. As the sensing part of this system, we deployed a new Wireless Sensor Network (WSN). This system uses the 920 MHz radio wave based on the Wireless Smart Utility Network that enables long-range wireless communication. In addition, the data acquired by the WSN were standardized for the advanced web service interoperability. By using these standardized data, we can create a web service that offers various kinds of phenological indices as secondary information to the farmers in the field. We have also established the field management system using thermal image, fluorescent and X-ray fluorescent methods, which enable the nondestructive, chemical-free, simple, and rapid measurement of fruits or trees. We can get the information about the transpiration of plants through a thermal image. The fluorescence sensor gives us information, such as nitrate balance index (NBI), that shows the nitrate balance inside the leaf, chlorophyll content, flavonol content and anthocyanin content. These methods allow one to quickly check the health of trees and find ways to improve the tree vigor of weak ones. Furthermore, the fluorescent x-ray sensor has the possibility to quantify the loss of minerals necessary for fruit growth.

International global network of fiducial stations: Scientific and implementation issues

NASA Astrophysics Data System (ADS)

1991-11-01

In this report, an ad hoc panel of the National Research Council's Committee on Geodesy, Board of Earth Sciences and Resources (1) evaluates the scientific importance of a global network of fiducial sites, monitored very precisely, using a combination of surface- and space-geodetic techniques; (2) examines strategies for implementing and operating such a network; and (3) assesses whether such a network would provide a suitable global infrastructure for geodetic and other geophysical systems of the next century. The panel concludes that a global network of fiducial sites would be a valuable tool for addressing global change issues and play a critical role in providing a reference frame for scientific Earth missions. The panel suggests that existing global networks be integrated and anticipates that such a network would grow from about 30 to the ultimate size of about 200 fiducial sites. It is noted that such a global network will provide a long-term infrastructure for geodetic and geophysical studies. The panel expects that these fiducial sites would evolve into terrestrial observatories or laboratories that would permit more comprehensive studies of the Earth than those now possible.

International global network of fiducial stations: Scientific and implementation issues

NASA Technical Reports Server (NTRS)

1991-01-01

In this report, an ad hoc panel of the National Research Council's Committee on Geodesy, Board of Earth Sciences and Resources (1) evaluates the scientific importance of a global network of fiducial sites, monitored very precisely, using a combination of surface- and space-geodetic techniques; (2) examines strategies for implementing and operating such a network; and (3) assesses whether such a network would provide a suitable global infrastructure for geodetic and other geophysical systems of the next century. The panel concludes that a global network of fiducial sites would be a valuable tool for addressing global change issues and play a critical role in providing a reference frame for scientific Earth missions. The panel suggests that existing global networks be integrated and anticipates that such a network would grow from about 30 to the ultimate size of about 200 fiducial sites. It is noted that such a global network will provide a long-term infrastructure for geodetic and geophysical studies. The panel expects that these fiducial sites would evolve into terrestrial observatories or laboratories that would permit more comprehensive studies of the Earth than those now possible.

Spatio-temporal patterns of tree establishment are indicative of biotic interactions during early invasion of a montane meadow

Treesearch

J.M. Rice; C.B. Halpern; J.A. Antos; J.A. Jones

2012-01-01

Tree invasions of grasslands are occurring globally, with profound consequences for ecosystem structure and function. We explore the spatio-temporal dynamics of tree invasion of a montane meadow in the Cascade Mountains of Oregon, where meadow loss is a conservation concern. We examine the early stages of invasion, where extrinsic and intrinsic processes can be clearly...

Using inventory data to determine the impact of drought on tree mortality

Treesearch

Greg C. Liknes; Christopher W. Woodall; Charles H. Perry

2012-01-01

Drought has been the subject of numerous recent studies that hint at an acceleration of tree mortality due to climate change. In particular, a recent global survey of tree mortality events implicates drought as the cause of quaking aspen mortality in Minnesota, USA in 2007. In this study, data from the Forest Inventory and Analysis program of the USDA Forest Service...

Criterion 5: Maintenance of forest contributions to global carbon cycles

Treesearch

Stephen R. Shifley; Francisco X. Aguilar; Nianfu Song; Susan I. Stewart; David J. Nowak; Dale D. Gormanson; W. Keith Moser; Sherri Wormstead; Eric J. Greenfield

2012-01-01

Northern forests cover more than 42 percent of the region and are enormous reservoirs of carbon. Through photosynthesis, live trees emit oxygen in exchange for carbon dioxide they pull from the atmosphere. As a tree grows it stores carbon in wood above and below ground, and sequestered carbon comprises about half of its dry weight. Dead trees and down logs are also...

Climate-driven tree mortality: insights from the pinon pine die-off in the United States

Treesearch

Jeffrey A. Hicke; Melanie J. B. Zeppel

2013-01-01

The global climate is changing, and a range of negative effects on plants has already been observed and will likely continue into the future. One of the most apparent consequences of climate change is widespread tree mortality (Fig. 1). Extensive tree die-offs resulting from recent climate change have been documented across a range of forest types on all forested...

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

NASA Technical Reports Server (NTRS)

Ganguly, Sangram; Kalia, Subodh; Li, Shuang; Michaelis, Andrew; Nemani, Ramakrishna R.; Saatchi, Sassan A

2017-01-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above ground biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

λ-augmented tree for robust data collection in Advanced Metering Infrastructure

DOE PAGES

Kamto, Joseph; Qian, Lijun; Li, Wei; ...

2016-01-01

In this study, tree multicast configuration of smart meters (SMs) can maintain the connectivity and meet the latency requirements for the Advanced Metering Infrastructure (AMI). However, such topology is extremely weak as any single failure suffices to break its connectivity. On the other hand, the impact of a SM node failure can be more or less significant: a noncut SM node will have a limited local impact compared to a cut SM node that will break the network connectivity. In this work, we design a highly connected tree with a set of backup links to minimize the weakness of treemore » topology of SMs. A topology repair scheme is proposed to address the impact of a SM node failure on the connectivity of the augmented tree network. It relies on a loop detection scheme to define the criticality of a SM node and specifically targets cut SM node by selecting backup parent SM to cover its children. Detailed algorithms to create such AMI tree and related theoretical and complexity analysis are provided with insightful simulation results: sufficient redundancy is provided to alleviate data loss at the cost of signaling overhead. It is however observed that biconnected tree provides the best compromise between the two entities.« less

λ-augmented tree for robust data collection in Advanced Metering Infrastructure

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

Kamto, Joseph; Qian, Lijun; Li, Wei

In this study, tree multicast configuration of smart meters (SMs) can maintain the connectivity and meet the latency requirements for the Advanced Metering Infrastructure (AMI). However, such topology is extremely weak as any single failure suffices to break its connectivity. On the other hand, the impact of a SM node failure can be more or less significant: a noncut SM node will have a limited local impact compared to a cut SM node that will break the network connectivity. In this work, we design a highly connected tree with a set of backup links to minimize the weakness of treemore » topology of SMs. A topology repair scheme is proposed to address the impact of a SM node failure on the connectivity of the augmented tree network. It relies on a loop detection scheme to define the criticality of a SM node and specifically targets cut SM node by selecting backup parent SM to cover its children. Detailed algorithms to create such AMI tree and related theoretical and complexity analysis are provided with insightful simulation results: sufficient redundancy is provided to alleviate data loss at the cost of signaling overhead. It is however observed that biconnected tree provides the best compromise between the two entities.« less

Lidar-based individual tree species classification using convolutional neural network

NASA Astrophysics Data System (ADS)

Mizoguchi, Tomohiro; Ishii, Akira; Nakamura, Hiroyuki; Inoue, Tsuyoshi; Takamatsu, Hisashi

2017-06-01

Terrestrial lidar is commonly used for detailed documentation in the field of forest inventory investigation. Recent improvements of point cloud processing techniques enabled efficient and precise computation of an individual tree shape parameters, such as breast-height diameter, height, and volume. However, tree species are manually specified by skilled workers to date. Previous works for automatic tree species classification mainly focused on aerial or satellite images, and few works have been reported for classification techniques using ground-based sensor data. Several candidate sensors can be considered for classification, such as RGB or multi/hyper spectral cameras. Above all candidates, we use terrestrial lidar because it can obtain high resolution point cloud in the dark forest. We selected bark texture for the classification criteria, since they clearly represent unique characteristics of each tree and do not change their appearance under seasonable variation and aged deterioration. In this paper, we propose a new method for automatic individual tree species classification based on terrestrial lidar using Convolutional Neural Network (CNN). The key component is the creation step of a depth image which well describe the characteristics of each species from a point cloud. We focus on Japanese cedar and cypress which cover the large part of domestic forest. Our experimental results demonstrate the effectiveness of our proposed method.

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

NASA Astrophysics Data System (ADS)

Ganguly, S.; Kalia, S.; Li, S.; Michaelis, A.; Nemani, R. R.; Saatchi, S.

2017-12-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above gound biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition/ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree/non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial/satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

A Tree Based Self-routing Scheme for Mobility Support in Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Kim, Young-Duk; Yang, Yeon-Mo; Kang, Won-Seok; Kim, Jin-Wook; An, Jinung

Recently, WSNs (Wireless Sensor Networks) with mobile robot is a growing technology that offer efficient communication services for anytime and anywhere applications. However, the tiny sensor node has very limited network resources due to its low battery power, low data rate, node mobility, and channel interference constraint between neighbors. Thus, in this paper, we proposed a tree based self-routing protocol for autonomous mobile robots based on beacon mode and implemented in real test-bed environments. The proposed scheme offers beacon based real-time scheduling for reliable association process between parent and child nodes. In addition, it supports smooth handover procedure by reducing flooding overhead of control packets. Throughout the performance evaluation by using a real test-bed system and simulation, we illustrate that our proposed scheme demonstrates promising performance for wireless sensor networks with mobile robots.

Dynamic segment shared protection for multicast traffic in meshed wavelength-division-multiplexing optical networks

NASA Astrophysics Data System (ADS)

Liao, Luhua; Li, Lemin; Wang, Sheng

2006-12-01

We investigate the protection approach for dynamic multicast traffic under shared risk link group (SRLG) constraints in meshed wavelength-division-multiplexing optical networks. We present a shared protection algorithm called dynamic segment shared protection for multicast traffic (DSSPM), which can dynamically adjust the link cost according to the current network state and can establish a primary light-tree as well as corresponding SRLG-disjoint backup segments for a dependable multicast connection. A backup segment can efficiently share the wavelength capacity of its working tree and the common resources of other backup segments based on SRLG-disjoint constraints. The simulation results show that DSSPM not only can protect the multicast sessions against a single-SRLG breakdown, but can make better use of the wavelength resources and also lower the network blocking probability.

Focus-based filtering + clustering technique for power-law networks with small world phenomenon

NASA Astrophysics Data System (ADS)

Boutin, François; Thièvre, Jérôme; Hascoët, Mountaz

2006-01-01

Realistic interaction networks usually present two main properties: a power-law degree distribution and a small world behavior. Few nodes are linked to many nodes and adjacent nodes are likely to share common neighbors. Moreover, graph structure usually presents a dense core that is difficult to explore with classical filtering and clustering techniques. In this paper, we propose a new filtering technique accounting for a user-focus. This technique extracts a tree-like graph with also power-law degree distribution and small world behavior. Resulting structure is easily drawn with classical force-directed drawing algorithms. It is also quickly clustered and displayed into a multi-level silhouette tree (MuSi-Tree) from any user-focus. We built a new graph filtering + clustering + drawing API and report a case study.

River landscapes and optimal channel networks.

PubMed

Balister, Paul; Balogh, József; Bertuzzo, Enrico; Bollobás, Béla; Caldarelli, Guido; Maritan, Amos; Mastrandrea, Rossana; Morris, Robert; Rinaldo, Andrea

2018-06-26

We study tree structures termed optimal channel networks (OCNs) that minimize the total gravitational energy loss in the system, an exact property of steady-state landscape configurations that prove dynamically accessible and strikingly similar to natural forms. Here, we show that every OCN is a so-called natural river tree, in the sense that there exists a height function such that the flow directions are always directed along steepest descent. We also study the natural river trees in an arbitrary graph in terms of forbidden substructures, which we call k-path obstacles, and OCNs on a d-dimensional lattice, improving earlier results by determining the minimum energy up to a constant factor for every [Formula: see text] Results extend our capabilities in environmental statistical mechanics. Copyright © 2018 the Author(s). Published by PNAS.

A Simulator for the Respiratory Tree in Healthy Subjects Derived from Continued Fractions Expansions

NASA Astrophysics Data System (ADS)

Muntean, Ionuţ; Ionescu, Clara; Naşcu, Ioan

2009-04-01

Taking into account the self-similar recurrent geometrical structure of the human respiratory tree, the total respiratory impedance can be represented using an electrical equivalent of a ladder network model. In this paper, the parameters of the respiratory tree are employed in simulation, based on clinical insight and morphology. Once the transfer function of the total input impedance model is calculated, it is further interpreted in its continued fraction expansion form. The purpose is to compare the ladder network structure with the continuous fraction expansion form of the impedance. The results are supporting the theory of fractional-order impedance appearance (also known as constant-phase behaviour) and help understanding the mathematical and morphological basis for constructing a physiology-based simulator of the human lungs.

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

PubMed Central

Mooers, Arne Ø.; Caccone, Adalgisa; Russello, Michael A.

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization. PMID:27635324

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation.

PubMed

Jensen, Evelyn L; Mooers, Arne Ø; Caccone, Adalgisa; Russello, Michael A

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.

A Mixtures-of-Trees Framework for Multi-Label Classification

PubMed Central

Hong, Charmgil; Batal, Iyad; Hauskrecht, Milos

2015-01-01

We propose a new probabilistic approach for multi-label classification that aims to represent the class posterior distribution P(Y|X). Our approach uses a mixture of tree-structured Bayesian networks, which can leverage the computational advantages of conditional tree-structured models and the abilities of mixtures to compensate for tree-structured restrictions. We develop algorithms for learning the model from data and for performing multi-label predictions using the learned model. Experiments on multiple datasets demonstrate that our approach outperforms several state-of-the-art multi-label classification methods. PMID:25927011

The Promise of Global Networks. 1999 Annual Review.

ERIC Educational Resources Information Center

Institute for Information Studies, Queenstown, MD.

This collection of commissioned papers provides a variety of perspectives on the impact of global information networks. The following articles are included: "The Promise of Global Networks: An Introduction" (Jorge Reina Schement); "Architecture and Expectations: Networks of the World--Unite!" (Marjory S. Blumenthal); "The…

The distribution of grasslands, savannas and forests in Africa: a new look at the relationships between vegetation, fire and climate at continental scale

NASA Astrophysics Data System (ADS)

D'Onofrio, Donatella; von Hardenberg, Jost; Baudena, Mara

2017-04-01

Savannas occupy about a fifth of the global land surface and store approximately 15% of the terrestrial carbon. They also encompass about 85% of the global land area burnt annually. Along an increasing rainfall gradient, they are the intermediate biome between grassland and forest. Undergoing and predicted increasing temperature and CO2 concentration, modified precipitation regimes, as well as increasing land-use intensity, are expected to induce important shifts in savanna structure and in the distribution of grasslands, savannas and forests. Owing to the large extent and productivity of savanna biomes, these changes could have larger impacts on the global biogeochemical cycle and precipitation than for any other biome, thus influencing the vegetation-climate system. The dynamics of these biomes has been long studied, and the current theory postulates that while arid savannas are observed because of tree-water limitation, and competition with grasses, in mesic conditions savannas persist because a grass-fire feedback exists, which can maintain them as an alternatively stable state to closed forests. This feedback is reinforced by the different responses of savanna and forest tree type. In this context, despite their relevance, grasses and tree types have been studied mostly in small scale ecological studies, while continental analyses focused on total tree cover only. Here we analyze a recent MODIS product including explicitly the non-tree vegetation cover, allowing us to illustrate for the first time at continental scale the importance of grass cover and of tree-fire responses in determining the emergence of the different biomes. We analyze the relationships of woody and herbaceous cover with fire return time (all from MODIS satellite observations), rainfall annual average and seasonality (from TRMM satellite measurements), and we include tree phenology information, based on the ESA Global Land Cover map, also used to exclude areas with large anthropogenic land use. From this analysis we distinctively observe that tropical vegetation dynamics changes along a rainfall gradient more markedly than previously observed, in particular identifying three zones: (i) a dry region, where grasses are dominant and water-limited, and fires are rare; (ii) an intermediate rainfall range, where savanna with grass dominance is the predominant biome, maintained by frequent fires and rainfall seasonality; and (iii) a more humid area, where both savannas and forests can occur, as determined by the grass-fire feedback and the occurrence of different types of trees. The analysis of these important ecological processes can also be applied to the evaluation of Dynamic Global Vegetation Models, that currently have particular difficulties in simulating tropical vegetation.

Machine-Learning Classifier for Patients with Major Depressive Disorder: Multifeature Approach Based on a High-Order Minimum Spanning Tree Functional Brain Network.

PubMed

Guo, Hao; Qin, Mengna; Chen, Junjie; Xu, Yong; Xiang, Jie

2017-01-01

High-order functional connectivity networks are rich in time information that can reflect dynamic changes in functional connectivity between brain regions. Accordingly, such networks are widely used to classify brain diseases. However, traditional methods for processing high-order functional connectivity networks generally include the clustering method, which reduces data dimensionality. As a result, such networks cannot be effectively interpreted in the context of neurology. Additionally, due to the large scale of high-order functional connectivity networks, it can be computationally very expensive to use complex network or graph theory to calculate certain topological properties. Here, we propose a novel method of generating a high-order minimum spanning tree functional connectivity network. This method increases the neurological significance of the high-order functional connectivity network, reduces network computing consumption, and produces a network scale that is conducive to subsequent network analysis. To ensure the quality of the topological information in the network structure, we used frequent subgraph mining technology to capture the discriminative subnetworks as features and combined this with quantifiable local network features. Then we applied a multikernel learning technique to the corresponding selected features to obtain the final classification results. We evaluated our proposed method using a data set containing 38 patients with major depressive disorder and 28 healthy controls. The experimental results showed a classification accuracy of up to 97.54%.

Machine-Learning Classifier for Patients with Major Depressive Disorder: Multifeature Approach Based on a High-Order Minimum Spanning Tree Functional Brain Network

PubMed Central

Qin, Mengna; Chen, Junjie; Xu, Yong; Xiang, Jie

2017-01-01

High-order functional connectivity networks are rich in time information that can reflect dynamic changes in functional connectivity between brain regions. Accordingly, such networks are widely used to classify brain diseases. However, traditional methods for processing high-order functional connectivity networks generally include the clustering method, which reduces data dimensionality. As a result, such networks cannot be effectively interpreted in the context of neurology. Additionally, due to the large scale of high-order functional connectivity networks, it can be computationally very expensive to use complex network or graph theory to calculate certain topological properties. Here, we propose a novel method of generating a high-order minimum spanning tree functional connectivity network. This method increases the neurological significance of the high-order functional connectivity network, reduces network computing consumption, and produces a network scale that is conducive to subsequent network analysis. To ensure the quality of the topological information in the network structure, we used frequent subgraph mining technology to capture the discriminative subnetworks as features and combined this with quantifiable local network features. Then we applied a multikernel learning technique to the corresponding selected features to obtain the final classification results. We evaluated our proposed method using a data set containing 38 patients with major depressive disorder and 28 healthy controls. The experimental results showed a classification accuracy of up to 97.54%. PMID:29387141

Evaluation of NASA's Carbon Monitoring System (CMS) Flux Pilot: Terrestrial CO2 Fluxes

NASA Astrophysics Data System (ADS)

Fisher, J. B.; Polhamus, A.; Bowman, K. W.; Collatz, G. J.; Potter, C. S.; Lee, M.; Liu, J.; Jung, M.; Reichstein, M.

2011-12-01

NASA's Carbon Monitoring System (CMS) flux pilot project combines NASA's Earth System models in land, ocean and atmosphere to track surface CO2 fluxes. The system is constrained by atmospheric measurements of XCO2 from the Japanese GOSAT satellite, giving a "big picture" view of total CO2 in Earth's atmosphere. Combining two land models (CASA-Ames and CASA-GFED), two ocean models (ECCO2 and NOBM) and two atmospheric chemistry and inversion models (GEOS-5 and GEOS-Chem), the system brings together the stand-alone component models of the Earth System, all of which are run diagnostically constrained by a multitude of other remotely sensed data. Here, we evaluate the biospheric land surface CO2 fluxes (i.e., net ecosystem exchange, NEE) as estimated from the atmospheric flux inversion. We compare against the prior bottom-up estimates (e.g., the CASA models) as well. Our evaluation dataset is the independently derived global wall-to-wall MPI-BGC product, which uses a machine learning algorithm and model tree ensemble to "scale-up" a network of in situ CO2 flux measurements from 253 globally-distributed sites in the FLUXNET network. The measurements are based on the eddy covariance method, which uses observations of co-varying fluxes of CO2 (and water and energy) from instruments on towers extending above ecosystem canopies; the towers integrate fluxes over large spatial areas (~1 km2). We present global maps of CO2 fluxes and differences between products, summaries of fluxes by TRANSCOM region, country, latitude, and biome type, and assess the time series, including timing of minimum and maximum fluxes. This evaluation shows both where the CMS is performing well, and where improvements should be directed in further work.